diff --git a/data/covid/preprints-summary.csv b/data/covid/preprints-summary.csv index 45414697..36f8f359 100644 --- a/data/covid/preprints-summary.csv +++ b/data/covid/preprints-summary.csv @@ -1,49 +1,49 @@ -microbiology,biochemistry,pediatrics,orthopedics,ophthalmology,obstetrics and gynecology,surgery,health systems and quality improvement,pharmacology and therapeutics,health informatics,scientific communication and education,biophysics,occupational and environmental health,intensive care and critical care medicine,oncology,geriatric medicine,allergy and immunology,emergency medicine,psychiatry and clinical psychology,radiology and imaging,hiv aids,respiratory medicine,pathology,systems biology,genomics,infectious diseases,public and global health,primary care research,health economics,epidemiology,molecular biology,health policy,month,neurology,Total,dentistry and oral medicine,evolutionary biology,dermatology,bioinformatics,immunology,genetic and genomic medicine,cardiovascular medicine -,,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,Jan-24,,1,,,,,,, -,,,,,,,,,,,,1,,,,,,,,,,,,,,1,,2,4,,,Dec-23,1,10,,,,,,,1 -,,,,,,,,,,,,,,1,,,,,,,,,,,1,,,,2,,,Nov-23,,4,,,,,,, -,,,,,,,,,1,,,,,,,,,,,,1,,,,1,,,,1,,,Oct-23,,5,,,,,1,, -,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,,,,Sep-23,,1,,,,,,, -,,,,,,,,,,,,1,,,,,,,,,,,,,,1,1,,4,,,Aug-23,,7,,,,,,, -,,,,,,,2,,,,,,,,,,,,,,,,,,,1,,,3,,,Jul-23,,7,,,,,,1, -,,,1,,,,,,1,1,,1,,,,,,,,,,,,,2,,,,1,,,Jun-23,,7,,,,,,, -,,,,,,,,,,,,,,,,,,,,,1,,,,1,1,,,2,,,May-23,,6,,,,,1,, -,,,,,,,,,,,,,,,,,,,,,,,,,1,2,,,,,,Apr-23,,3,,,,,,, -,,,,,,,,,,,,1,,,,,,1,,,,,,,3,2,,,2,,,Mar-23,,9,,,,,,, -,,,,,,,,,,,,,,,,,,,,,1,,,,,2,,,4,,,Feb-23,1,8,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,1,,,,5,,,Jan-23,,6,,,,,,, -,,,,,,,,,,,,,,,,,,,,,2,1,,,4,1,,,3,,1,Dec-22,,12,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,4,,,,,,,Nov-22,,4,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,2,2,,,1,,,Oct-22,,6,,,,,,,1 -1,,1,,,,,,,,,,2,,,,,,,,,1,,,,2,1,,,1,,,Sep-22,,9,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,3,3,,,4,,,Aug-22,,10,,,,,,, -,,1,,,,,,,1,,,,,,,,,,,,,,,,3,,,,2,,,Jul-22,,8,,,,,1,, -,,,,,,,,,1,,,,,,,,,5,,,,,,,4,1,,,6,,,Jun-22,,18,,,,,,1, -1,,,,,,,1,,,,,,,,,,,2,,,,,,,5,1,1,1,2,,,May-22,,14,,,,,,, -1,,,,,,,2,,,,,1,,,,,,,,,1,,,,3,1,,1,5,,,Apr-22,,16,,,,,,,1 -,,,,,,,,,,,,,,,,,,1,,,1,,,,4,,1,,9,,,Mar-22,,17,,1,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,4,1,,,6,,,Feb-22,1,12,,,,,,, -,,,,,,,,,2,,,1,,,,,,,,,,,,,3,1,,,5,,,Jan-22,,14,,,,,1,,1 -,,1,,,,,,,,,,,,,,,,,,,,,,,8,,1,,10,,,Dec-21,1,22,,,,,,,1 -,,,,,,,2,,,,1,,1,,,,,1,,,,,,1,4,3,1,,9,,,Nov-21,1,24,,,,,,, -,,1,,,,,,,,,,,,,1,,,2,,,,,,,3,,,,4,,,Oct-21,,11,,,,,,, -,,,,,,,,1,1,,,,1,,,,,,,,,,,,4,2,,,6,,,Sep-21,,16,,,,,,,1 -,,,,,,,,,1,,,1,1,,,,,,,,1,,,,3,3,,,2,,,Aug-21,,13,,,,,,,1 -,,1,,,,,,,,,,,1,,,,1,,,,2,,,,12,4,,,3,,,Jul-21,,25,,,,,,1, -,,1,,,,,1,,1,,,1,1,,,1,,1,,,,,,,7,4,1,,6,,,Jun-21,1,27,,,,,1,, -,,,,,,,,,,,,,,,,,,1,,,,,,,7,1,,,11,,,May-21,,22,,,1,,,1, -1,,,,,,,1,,1,,,2,,,,1,,1,,,,,,,7,1,1,,3,,,Apr-21,,19,,,,,,, -,1,1,,,,1,,,2,,,,,,2,,,1,1,,,,,,17,5,,,5,,,Mar-21,1,38,,,,,,1, -,,,,,,1,1,,1,,,,,,,,,,,,,,,,9,1,,1,9,,,Feb-21,,23,,,,,,, -,,,,,,,1,,,,,,1,,1,,,1,,,,,,,8,3,1,,4,,1,Jan-21,,22,1,,,,,, -1,,,,,,,1,,3,,,,,,,,,2,,,,,,2,4,3,1,,4,,,Dec-20,,23,,,,,,,2 -,,,,,,,,,1,,,,,,,,,,,,,,,,12,5,,,5,,1,Nov-20,,26,,,,1,1,, -,,,,,,,,,1,,,,1,1,1,,,3,,,,,1,,12,,1,,6,,1,Oct-20,,30,,,,1,1,, -1,,,,,,,,,1,,,,1,,,,2,2,,1,,,,,8,3,1,,6,,,Sep-20,,26,,,,,,, -,,,,,1,,1,,,,,1,,,,,2,,,,,,,,12,2,,,6,1,,Aug-20,,27,,,,,,1, -,,,,,,,,,,,,,1,,,,,1,,,1,,,1,8,4,,,10,,,Jul-20,,28,,,,,1,,1 -,,,,1,,,1,,1,,,,3,1,1,,,4,,,1,,,,10,3,,,7,,1,Jun-20,,36,,,,1,1,, -,,,,,,,,,1,,,1,1,1,1,,,,,,1,,,,10,8,,1,8,,,May-20,,36,,,,1,,,2 -,,,,,,,1,,,,,,,,,,,,,,,,,1,7,1,,,7,,,Apr-20,,19,,,,,,2, -,,,,,,,,,,,,,,,,,,,,,,,,,1,3,,,4,,,Mar-20,,8,,,,,,, -,,,,,,,,,,,,,,,,,,,,,,,,,,2,,,4,,,Feb-20,,6,,,,,,, +dermatology,genomics,immunology,health systems and quality improvement,evolutionary biology,obstetrics and gynecology,month,pediatrics,biophysics,molecular biology,radiology and imaging,health economics,primary care research,pharmacology and therapeutics,intensive care and critical care medicine,scientific communication and education,psychiatry and clinical psychology,infectious diseases,surgery,genetic and genomic medicine,microbiology,ophthalmology,pathology,respiratory medicine,orthopedics,neurology,biochemistry,occupational and environmental health,allergy and immunology,epidemiology,emergency medicine,bioinformatics,hiv aids,oncology,geriatric medicine,cardiovascular medicine,systems biology,health policy,health informatics,public and global health,Total,dentistry and oral medicine +,,,,,,Jan-24,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,1,1, +,,,,,,Dec-23,,,,,2,,,,,,,,,,,,,,1,,1,,4,,,,,,1,,,,1,10, +,,,,,,Nov-23,,,,,,,,,,,1,,,,,,,,,,,,2,,,,1,,,,,,,4, +,,1,,,,Oct-23,,,,,,,,,,,1,,,,,,1,,,,,,1,,,,,,,,,1,,5, +,,,,,,Sep-23,,,,,,,,,,,1,,,,,,,,,,,,,,,,,,,,,,,1, +,,,,,,Aug-23,,,,,,1,,,,,,,,,,,,,,,1,,4,,,,,,,,,,1,7, +,,,2,,,Jul-23,,,,,,,,,,,,,1,,,,,,,,,,3,,,,,,,,,,1,7, +,,,,,,Jun-23,,,,,,,,,1,,2,,,,,,,1,,,1,,1,,,,,,,,,1,,7, +,,1,,,,May-23,,,,,,,,,,,1,,,,,,1,,,,,,2,,,,,,,,,,1,6, +,,,,,,Apr-23,,,,,,,,,,,1,,,,,,,,,,,,,,,,,,,,,,2,3, +,,,,,,Mar-23,,,,,,,,,,1,3,,,,,,,,,,1,,2,,,,,,,,,,2,9, +,,,,,,Feb-23,,,,,,,,,,,,,,,,,1,,1,,,,4,,,,,,,,,,2,8, +,,,,,,Jan-23,,,,,,,,,,,1,,,,,,,,,,,,5,,,,,,,,,,,6, +,,,,,,Dec-22,,,,,,,,,,,4,,,,,1,2,,,,,,3,,,,,,,,1,,1,12, +,,,,,,Nov-22,,,,,,,,,,,4,,,,,,,,,,,,,,,,,,,,,,,4, +,,,,,,Oct-22,,,,,,,,,,,2,,,,,,,,,,,,1,,,,,,1,,,,2,6, +,,,,,,Sep-22,1,,,,,,,,,,2,,,1,,,1,,,,2,,1,,,,,,,,,,1,9, +,,,,,,Aug-22,,,,,,,,,,,3,,,,,,,,,,,,4,,,,,,,,,,3,10, +,,1,,,,Jul-22,1,,,,,,,,,,3,,,,,,,,,,,,2,,,,,,,,,1,,8, +,,,,,,Jun-22,,,,,,,,,,5,4,,1,,,,,,,,,,6,,,,,,,,,1,1,18, +,,,,,,May-22,,,,,1,1,,,,2,5,,,1,,,,,,,,,2,,,,,,,,,,1,13, +,,,2,,,Apr-22,,,,,1,,,,,,3,,,,,,1,,,,1,,5,,,,,,1,,,,1,15, +,,,,1,,Mar-22,,,,,,1,,,,1,5,,,,,,1,,,,,,8,,,,,,,,,,,17, +,,,,,,Feb-22,,,,,,,,,,,4,,,,,,,,1,,,,6,,,,,,,,,,1,12, +,,1,,,,Jan-22,,,,,,,,,,,3,,,,,,,,,,,,5,,,,,,1,,,2,1,13, +,,,,,,Dec-21,1,,,,,1,,,,,8,,,1,,,,,1,,,,10,,,,,,1,,,,1,24, +,1,,2,,,Nov-21,,1,,,,1,,1,,1,4,,,,,,,,1,,,,8,,,,,,,,,,3,23, +,,,,,,Oct-21,1,,,,,,,,,2,3,,,,,,,,,,,,3,,,,,1,,,,,,10, +,,,,,,Sep-21,,,,,,,1,1,,,5,,,,,,,,,,,,6,,,,,,1,,,1,2,17, +,,,,,,Aug-21,,,,,,,,1,,,3,,,,,,1,,,,1,,2,,,,,,1,,,1,3,13, +,,,,,,Jul-21,1,,,,,,,1,,,12,,1,,,,2,,,,,,3,1,,,1,,,,,,4,26, +,,1,1,,,Jun-21,1,,,,,1,,1,,1,6,,,,,,,,1,,1,1,7,,,,,,,,,1,4,27, +1,,,,,,May-21,,,,,,,,,,1,6,,1,,,,,,,,,,11,,,,,,,,,1,1,22, +,,,1,,,Apr-21,,,,,,1,,,,1,7,,,1,,,,,,,1,,4,,,,,,,,,1,1,18, +,,,,,,Mar-21,1,,,1,,,,,,1,17,1,1,,,,,,1,1,,,6,,,,,2,,,,2,5,39, +,,,1,,,Feb-21,,,,,1,,,,,,8,1,,,,,,,,,,,9,,,,,,1,,,1,1,23, +,,1,1,,,Jan-21,,,,,,1,,1,,1,8,,,,,,,,,,,,4,,,,,1,,,1,,3,23,1 +,1,,1,,,Dec-20,,,,,,1,,,,2,4,,,1,,,,,,,,,4,,,,,,2,,,3,3,22, +,,1,,,,Nov-20,,,,,,,,,,,13,,,,,,,,,,,,6,,,,,,,,1,1,5,27, +,,1,,,,Oct-20,,,,,,1,,1,,3,11,,,,,,,,,,,,6,,1,,1,1,,1,1,1,,29, +,,,,,,Sep-20,,,,,,1,,1,,2,8,,,1,,,,,,,,,6,2,,1,,,,,,1,3,26, +,,,1,,1,Aug-20,,,1,,,,,,,,12,,1,,,,,,,,1,,6,2,,,,,,,,,2,27, +,1,1,,,,Jul-20,,,,,,,,1,,1,8,,,,,,1,,,,,,10,,,,,,1,,,,4,28, +,,1,1,,,Jun-20,,,,,,,,3,,3,10,,,,1,,1,,,,,,7,,1,,1,1,1,,1,1,2,35, +,,,,,,May-20,,,,,1,,,1,,,10,,,,,,1,,,,1,,8,,1,,1,1,2,,,1,9,37, +,1,,1,,,Apr-20,,,,,,,,,,,7,,2,,,,,,,,,,7,,,,,,,,,,1,19, +,,,,,,Mar-20,,,,,,,,,,,1,,,,,,,,,,,,4,,,,,,,,,,3,8, +,,,,,,Feb-20,,,,,,,,,,,1,,,,,,,,,,,,4,,,,,,,,,,2,7, diff --git a/data/covid/preprints.csv b/data/covid/preprints.csv index b5935ab8..243806f4 100644 --- a/data/covid/preprints.csv +++ b/data/covid/preprints.csv @@ -1260,13 +1260,6 @@ FindingsVaccination programmes with early start dates incur the most health bene InterpretationAfrican countries with large proportions of their populations unvaccinated by late 2021 may find vaccination programmes less cost-effective than they could have been earlier in 2021. Lower vaccine purchasing costs and/or the emergence of new variants may improve cost-effectiveness. FundingBill and Melinda Gates Foundation, World Health Organization, National Institute of Health Research (UK), Health Data Research (UK)",health economics,fuzzy,100,100 -medRxiv,10.1101/2022.05.06.22274658,2022-05-07,https://medrxiv.org/cgi/content/short/2022.05.06.22274658,"STIMULATE-ICP-CAREINEQUAL - Defining usual care and examining inequalities in Long Covid support: protocol for a mixed-methods study (part of STIMULATE-ICP: Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways).",Mel Ramasawmy; Yi Mu; Donna Clutterbuck; Marija Pantelic; Gregory Y.H. Lip; Christina Van der Feltz-Cornelis; Dan Wootton; Nefyn H Williams; Hugh Montgomery; Rita Mallinson Cookson; Emily Attree; Mark Gabbay; Melissa J Heightman; Nisreen A Alwan; Amitava Banerjee; Paula Lorgelly; - STIMULATE-ICP consortium,"Institute of Health Informatics, University College London; Institute of Health Informatics, University College London; School of Primary Care, Population Sciences and Medical Education, University of Southampton; Brighton and Sussex Medical School, University of Sussex; Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, United Kingdom; and Department of Clinical; Department of Health Sciences, HYMS, University of York, and Institute of Health Informatics, University College London; Institute of Infection Veterinary and Ecological Sciences, University of Liverpool; Department of Primary Care and Mental Health, University of Liverpool; Centre for Human Health and Performance, Department of Medicine, University College London; PPIE Representative; PPIE Representative; Department of Primary Care and Mental Health, University of Liverpool; University College London Hospitals NHS Trust; School of Primary Care, Population Sciences and Medical Education, University of Southampton; NIHR Southampton Biomedical Research Centre, University of Southam; Institute of Health Informatics, University College London; School of Population Health and Department of Economics, University of Auckland; ","IntroductionIndividuals with Long Covid represent a new and growing patient population. In England, fewer than 90 Long Covid clinics deliver assessment and treatment informed by NICE guidelines. However, a paucity of clinical trials or longitudinal cohort studies means that the epidemiology, clinical trajectory, healthcare utilisation and effectiveness of current Long Covid care are poorly documented, and that neither evidence-based treatments nor rehabilitation strategies exist. In addition, and in part due to pre-pandemic health inequalities, access to referral and care varies, and patient experience of the Long Covid care pathways can be poor. - -In a mixed methods study, we therefore aim to: (1) describe the usual healthcare, outcomes and resource utilisation of individuals with Long Covid; (2) assess the extent of inequalities in access to Long Covid care, and specifically to understand Long Covid patients experiences of stigma and discrimination. - -Methods and analysisA mixed methods study will address our aims. Qualitative data collection from patients and health professionals will be achieved through surveys, interviews and focus group discussions, to understand their experience and document the function of clinics. A patient cohort study will provide an understanding of outcomes and costs of care. Accessible data will be further analysed to understand the nature of Long Covid, and the care received. - -Ethics and disseminationEthical approval was obtained from South Central - Berkshire Research Ethics Committee (reference 303958). The dissemination plan will be decided by the patient and public involvement and engagement (PPIE) group members and study Co-Is, but will target 1) policy makers, and those responsible for commissioning and delivering Long Covid services, 2) patients and the public, and 3) academics.",health systems and quality improvement,fuzzy,100,100 medRxiv,10.1101/2022.05.05.22273234,2022-05-07,https://medrxiv.org/cgi/content/short/2022.05.05.22273234,Changes in English medication safety indicators throughout the COVID-19 pandemic: a federated analysis of 57 million patients' primary care records in situ using OpenSAFELY,Louis Fisher; Lisa E M Hopcroft; Sarah Rodgers; James Barrett; Kerry Oliver; Anthony J Avery; Dai Evans; Helen Curtis; Richard Croker; Orla Macdonald; Jessica Morley; Amir Mehrkar; Seb Bacon; Simon Davy; Iain Dillingham; David Evans; George Hickman; Peter Inglesby; Caroline E Morton; Becky Smith; Tom Ward; William Hulme; Amelia Green; Jon Massey; Alex J Walker; Chris Bates; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Paul Griffiths; Aaron Fowles; Nasreen Parkes; Ben Goldacre; Brian MacKenna,"Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; Centre for Academic Primary Care, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG","ObjectiveTo describe the impact of the COVID-19 pandemic on safe prescribing, using the PINCER prescribing indicators; to implement complex prescribing indicators at national scale using GP data. DesignPopulation based cohort study, with the approval of NHS England using the OpenSAFELY platform. @@ -1352,7 +1345,6 @@ C_LI",health economics,fuzzy,100,100 medRxiv,10.1101/2022.04.22.22274176,2022-04-22,https://medrxiv.org/cgi/content/short/2022.04.22.22274176,Association between household composition and severe COVID-19 outcomes in older people by ethnicity: an observational cohort study using the OpenSAFELY platform,Kevin Wing; Daniel J Grint; Rohini Mathur; Hamish Gibbs; George Hickman; Emily Nightingale; Anna Schultze; Harriet Forbes; Vahe Nafilyan; Krishnan Bhaskaran; Elizabeth Williamson; Thomas House; Lorenzo Pellis; Emily Herrett; Nileesa Gautam; Helen J Curtis; Christopher T. Rentsch; Angel Wong; Brian MacKenna; Amir Mehrkar; Seb Bacon; Ian J Douglas; Stephen Evans; Laurie Tomlinson; Ben Goldacre; Rosalind M Eggo,"London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Trop. Med.; University of Bristol; Office for National Statistics; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Manchester; The University of Manchester; London School of Hygiene & Tropical Medicine; Aetion Inc; University of Oxford; US Department of Veterans Affairs, London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Oxford; London School of Hygiene & Tropical Medicine","Ethnic differences in the risk of severe COVID-19 may be linked to household composition. We quantified the association between household composition and risk of severe COVID-19 by ethnicity for older individuals. With the approval of NHS England, we analysed ethnic differences in the association between household composition and severe COVID-19 in people aged 67 or over in England. We defined households by number of generations living together, and used multivariable Cox regression stratified by location and wave of the pandemic and accounted for age, sex, comorbidities, smoking, obesity, housing density and deprivation. We included 2 692 223 people over 67 years in wave 1 (01/02/2020-31/08/2020) and 2 731 427 in wave 2 (01/09/2020-31/01/2021). Multigenerational living was associated with increased risk of severe COVID-19 for White and South Asian older people in both waves (e.g. wave 2, 67+ living with 3 other generations vs 67+ year olds only: White HR 1{middle dot}61 95% CI 1{middle dot}38-1{middle dot}87, South Asian HR 1{middle dot}76 95% CI 1{middle dot}48-2{middle dot}10), with a trend for increased risks of severe COVID-19 with increasing generations in wave 2. Multigenerational living was associated with severe COVID-19 in older adults. Older South Asian people are over-represented within multigenerational households in England, especially in the most deprived settings. The number of generations in a household, number of occupants, ethnicity and deprivation status are important considerations in the continued roll-out of COVID-19 vaccination and targeting of interventions for future pandemics. FundingThis research was funded in part, by the Wellcome Trust. For the purpose of open access, the author has applied a CC-BY public copyright licence to any Author Accepted Manuscript version arising from this submission.",epidemiology,fuzzy,100,100 -bioRxiv,10.1101/2022.04.20.488895,2022-04-20,https://biorxiv.org/cgi/content/short/2022.04.20.488895,Emergence of new subgenomic mRNAs in SARS-CoV-2,Harriet V Mears; George R Young; Theo Sanderson; Ruth Harvey; Margaret Crawford; Daniel M Snell; Ashley S Fowler; Saira Hussain; Jerome Nicod; Edward Emmott; Katja Finsterbusch; Jakub Luptak; Emma Wall; Bryan Williams; Sonia Gandhi; Charles Swanton; David LV Bauer,"RNA Virus Replication Laboratory, The Francis Crick Institute, London, UK; RNA Virus Replication Laboratory & Bioinformatics and Biostatistics STP, The Francis Crick Institute, London, UK; Malaria Biochemistry Laboratory, The Francis Crick Institute, London, UK; Worldwide Influenza Centre, The Francis Crick Institute, London, UK; Advanced Sequencing Facility, The Francis Crick Institute, London, UK; Advanced Sequencing Facility, The Francis Crick Institute, London, UK; Advanced Sequencing Facility, The Francis Crick Institute, London, UK; RNA Virus Replication Laboratory, The Francis Crick Institute, London, UK; Advanced Sequencing Facility, The Francis Crick Institute, London, UK; Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems Molecular & Integrative Biology, University of Liverpool, Liver; Immunoregulation Laboratory, The Francis Crick Institute, London, UK; MRC Laboratory of Molecular Biology, Cambridge, UK; Crick/UCLH Legacy Study, The Francis Crick Institute, London, UK; and National Institute for Health Research (NIHR) University College London Hospitals (UCLH) B; University College London; and National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre, London, UK; Neurodegeneration Biology Laboratory, The Francis Crick Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; RNA Virus Replication Laboratory, The Francis Crick Institute, London, UK","Two mutations occurred in SARS-CoV-2 early during the COVID-19 pandemic that have come to define circulating virus lineages1: first a change in the spike protein (D614G) that defines the B.1 lineage and second, a double substitution in the nucleocapsid protein (R203K, G204R) that defines the B.1.1 lineage, which has subsequently given rise to three Variants of Concern: Alpha, Gamma and Omicron. While the latter mutations appear unremarkable at the protein level, there are dramatic implications at the nucleotide level: the GGG[->]AAC substitution generates a new Transcription Regulatory Sequence (TRS) motif, driving SARS-CoV-2 to express a novel subgenomic mRNA (sgmRNA) encoding a truncated C-terminal portion of nucleocapsid (N.iORF3), which is an inhibitor of type I interferon production. We find that N.iORF3 also emerged independently within the Iota variant, and further show that additional TRS motifs have convergently evolved to express novel sgmRNAs; notably upstream of Spike within the nsp16 coding region of ORF1b, which is expressed during human infection. Our findings demonstrate that SARS-CoV-2 is undergoing evolutionary changes at the functional RNA level in addition to the amino acid level, reminiscent of eukaryotic evolution. Greater attention to this aspect in the assessment of emerging strains of SARS-CoV-2 is warranted.",microbiology,fuzzy,100,100 medRxiv,10.1101/2022.04.14.22273903,2022-04-20,https://medrxiv.org/cgi/content/short/2022.04.14.22273903,Effects of COVID-19 in Care Homes - A Mixed Methods Review,C Heneghan; M Dietrich; J Brassey; T Jefferson,The University of Oxford; Collateral Global; Trip Database Ltd; The University of Oxford,"IntroductionThe report provides an up-to-date review of the global effects of the COVID-19 pandemic in care homes. We used a mixed methods approach to assess care home mortality by country, how the deaths compared with previous periods, and how excess deaths may be explained. We retrieved national datasets for 25 countries on mortality, 17 cohort studies assessing deaths compared to a previous period, and 16 cohort studies reporting interventions or factors associated with excess mortality. The COVID-19 pandemic disproportionately impacted those living in care homes at the highest risk for severe outcomes. However, the pandemic only highlighted and exacerbated a long-running problem: underfunding, poor structural layout, undertraining, under-skilling, under-equipping, and finally, lack of humanity in dealing with the most vulnerable members of society. @@ -1449,23 +1441,13 @@ TRIAL REGISTRATIONClinicalTrials.gov no. NCT04579640 SUMMARY BOXO_ST_ABSWhat is already known on this topic?C_ST_ABSVitamin D metabolites support innate immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory pathogens. Sub-optimal vitamin D status (25-hydroxyvitamin D <75 nmol/L) associates with increased susceptibility to all-cause acute respiratory infections (ARI) and coronavirus disease 2019 (COVID-19). Phase 3 randomised controlled trials of vitamin D to prevent COVID-19 have not yet reported. What this study addsThis phase 3 randomised controlled trial, including 6200 participants, shows that implementation of a population-level test-and-treat approach to oral vitamin D replacement at a dose of 800 IU or 3200 IU per day did not reduce risk of all-cause ARI or COVID-19 among adults with a high baseline prevalence of sub-optimal vitamin D status.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2022.03.22.22272775,2022-03-23,https://medrxiv.org/cgi/content/short/2022.03.22.22272775,Risk of death following SARS-CoV-2 infection or COVID-19 vaccination in young people in England: a self-controlled case series study,Vahe Nafilyan; Charlotte Bermingham; Isobel L Ward; Jasper Morgan; Francesco Zaccardi; Kamlesh Khunti; Julie Stanborough; Amitava Banerjee,"Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Real World Evidence Unit, Diabetes Research Centre, University of Leicester; Real World Evidence Unit, Diabetes Research Centre, University of Leicester; Office for National Statistics; Institute of Health Informatics, University College London","ObjectivesTo assess whether there is a change in the incidence of cardiac and all-cause death in young people following COVID-19 vaccination or SARS-CoV-2 infection in unvaccinated individuals. - -DesignSelf-controlled case series. - -SettingNational, linked electronic health record data in England. - -Study populationIndividuals aged 12-29 who had received at least one dose of COVID-19 vaccination and died between 8 December 2020 and 2 February 2022 and registered by 16 February 2022 within 12 weeks of COVID-19 vaccination; Individuals aged 12-29 who died within 12 weeks of testing positive for SARS-CoV-2. - -Main outcome measuresCardiac and all-cause deaths occurring within 12 weeks of vaccination or SARS-CoV-2 infection. +medRxiv,10.1101/2022.03.23.22272804,2022-03-23,https://medrxiv.org/cgi/content/short/2022.03.23.22272804,Waning effectiveness of BNT162b2 and ChAdOx1 COVID-19 vaccines over six months since second dose: a cohort study using linked electronic health records,Elsie MF Horne; William J Hulme; Ruth H Keogh; Tom M Palmer; Elizabeth J Williamson; Edward PK Parker; Amelia Green; Venexia Walker; Alex J Walker; Helen Curtis; Louis Fisher; Brian MacKenna; Richard Croker; Lisa Hopcroft; Robin Y Park; Jon Massey; Jessica Morely; Amir Mehrkar; Sebastian Bacon; David Evans; Peter Inglesby; Caroline E Morton; George Hickman; Simon Davy; Tom Ward; Iain Dillingham; Ben Goldacre; Miguel A Hernan; Jonathan AC Sterne,University of Bristol; Univeristy of Oxford; London School of Hygiene and Tropical Medicine; University of Bristol; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Univeristy of Oxford; University of Bristol; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Harvard University; University of Bristol,"BackgroundThe rate at which COVID-19 vaccine effectiveness wanes over time is crucial for vaccination policies, but is incompletely understood with conflicting results from different studies. -ResultsCompared to the baseline period, there was no evidence of a change in the incidence of cardiac death in the six weeks after vaccination, whether for each of weeks 1 to 6 or the whole six-week period. There was a decrease in the risk of all-cause death in the first week after vaccination and no change in each of weeks 2 to 6 after vaccination or whole six-week period after vaccination. Subgroup analyses by sex, age, vaccine type, and last dose also showed no change in the risk of death in the first six weeks after vaccination. There was a large increase in the incidence of cardiac and all-cause death in the overall risk period after SARS-CoV-2 infection among the unvaccinated. +MethodsThis cohort study, using the OpenSAFELY-TPP database and approved by NHS England, included individuals without prior SARS-CoV-2 infection assigned to vaccines priority groups 2-12 defined by the UK Joint Committee on Vaccination and Immunisation. We compared individuals who had received two doses of BNT162b2 or ChAdOx1 with unvaccinated individuals during six 4-week comparison periods, separately for subgroups aged 65+ years; 16-64 years and clinically vulnerable; 40-64 years and 18-39 years. We used Cox regression, stratified by first dose eligibility and geographical region and controlled for calendar time, to estimate adjusted hazard ratios (aHRs) comparing vaccinated with unvaccinated individuals, and quantified waning vaccine effectiveness as ratios of aHRs per-4-week period. The outcomes were COVID-19 hospitalisation, COVID-19 death, positive SARS-CoV-2 test, and non-COVID-19 death. -ConclusionThere is no evidence of an association between COVID-19 vaccination and an increased risk of death in young people. By contrast, SARS-CoV-2 infection was associated with substantially higher risk of cardiac related death and all-cause death. +FindingsThe BNT162b2, ChAdOx1 and unvaccinated groups comprised 1,773,970, 2,961,011 and 2,433,988 individuals, respectively. Waning of vaccine effectiveness was similar across outcomes and vaccine brands: e.g. in the 65+ years subgroup ratios of aHRs versus unvaccinated for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test ranged from 1.23 (95% CI 1.15-1.32) to 1.27 (1.20-1.34) for BNT162b2 and 1.16 (0.98-1.37) to 1.20 (1.14-1.27) for ChAdOx1. Despite waning, rates of COVID-19 hospitalisation and COVID-19 death were substantially lower among vaccinated individuals compared to unvaccinated individuals up to 26 weeks after second dose, with estimated aHRs <0.20 (>80% vaccine effectiveness) for BNT162b2, and <0.26 (>74%) for ChAdOx1. By weeks 23-26, rates of SARS-CoV-2 infection in fully vaccinated individuals were similar to or higher than those in unvaccinated individuals: aHRs ranged from 0.85 (0.78-0.92) to 1.53 (1.07-2.18) for BNT162b2, and 1.21 (1.13-1.30) to 1.99 (1.94-2.05) for ChAdOx1. -What is already known on this topicSeveral studies have highlighted the association between COVID-19 vaccination and the risk of myocarditis, myopericarditis, and other cardiac problems, especially in young people, but associated risk of mortality is unclear. Since younger people have lower risk of COVID-19 hospitalisation and mortality, the mortality risk associated with vaccination is potentially more important to them in balancing the risk and benefit of vaccination. - -What this study addsAlthough there is a risk of myocarditis or myopericarditis with COVID-19, there is no evidence of increased risk of cardiac or all-cause mortality following COVID-19 vaccination in young people aged 12 to 29. Given the increased risk of mortality following SARS-CoV-2 infection in this group, the risk-benefit analysis favours COVID-19 vaccination for this age group.",epidemiology,fuzzy,100,100 +InterpretationThe rate at which estimated vaccine effectiveness waned was strikingly consistent for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test, and similar across subgroups defined by age and clinical vulnerability. If sustained to outcomes of infection with the Omicron variant and to booster vaccination, these findings will facilitate scheduling of booster vaccination doses.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.03.18.22272607,2022-03-21,https://medrxiv.org/cgi/content/short/2022.03.18.22272607,"Multi-organ impairment and Long COVID: a 1-year prospective, longitudinal cohort study",Andrea Dennis; Daniel J Cuthbertson; Dan Wootton; Michael Crooks; Mark Gabbay; Nicole Eichert; Sofia Mouchti; Michele Pansini; Adriana Roca-Fernandez; Helena Thomaides-Brears; Matt Kelly; Matthew Robson; Lyth Hishmeh; Emily Attree; Melissa J Heightman; Rajarshi Banerjee; Amitava Banerjee,Perspectum Ltd; University of Liverpool; University of Liverpool; University of Hull; University of Liverpool; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Diagnostics; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Long COVID SoS; UKDoctors#Longcovid; UCLH; Perspectum Ltd; University College London,"ImportanceMulti-organ impairment associated with Long COVID is a significant burden to individuals, populations and health systems, presenting challenges for diagnosis and care provision. Standardised assessment across multiple organs over time is lacking, particularly in non-hospitalised individuals. ObjectiveTo determine the prevalence of organ impairment in Long COVID patients at 6 and at 12 months after initial symptoms and to explore links to clinical presentation. @@ -1723,19 +1705,6 @@ DiscussionApproximately 4 in 5 participants with prior PCR-confirmed infection w FundingThe research costs for the study have been supported by the MRC Grant Ref: MC_PC 19070 awarded to UCL on 30 March 2020 and MRC Grant Ref: MR/V028375/1 awarded on 17 August 2020. The study also received $15,000 of Facebook advertising credit to support a pilot social media recruitment campaign on 18th August 2020. The study also received funding from the UK Government Department of Health and Social Cares Vaccine Evaluation Programme to provide monthly Thriva antibody tests to adult participants. This study was supported by the Wellcome Trust through a Wellcome Clinical Research Career Development Fellowship to RA [206602].",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.02.01.22270235,2022-02-02,https://medrxiv.org/cgi/content/short/2022.02.01.22270235,Hospitalisation for COVID-19 predicts long lasting cerebrovascular impairment: A prospective observational cohort study,Kamen A Tsvetanov; Lennart R B Spindler; Emmanuel A Stamatakis; Virginia FJ Newcombe; Victoria C Lupson; Doris A Chatfield; Anne E Manktelow; Joanne G Outtrim; Anne Elmer; Nathalie Kingston; John R Bradley; Edward T Bullmore; James B Rowe; David K Menon; - the Cambridge NeuroCOVID Group; - the NIHR COVID-19 BioResource; - the Cambridge NIHR Clinical Research Facility; - the CITIID-NIHR BioResource COVID-19 collaboration,"Department of Clinilcal Neurosciences, University of Cambridge, Cambridge, UK; Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.; Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University Cambridge, Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University Cambridge, Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University Cambridge, Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University Cambridge, Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University Cambridge, Cambridge, UK.; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK.; Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.; Department of Psychiatry, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.; Medical Research Council Cognition and Brain Sciences Unit, Department of Psychiatry, Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University Cambridge, Cambridge, UK.; -; -; -; -","Human coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has multiple neurological consequences, but its long-term effect on brain health is still uncertain. The cerebrovascular consequences of COVID-19 may also affect brain health. Here we assess cerebrovascular health in 45 hospitalised patients using the resting state fluctuation amplitudes (RSFA) from functional magnetic resonance imaging, in relation to disease severity and in contrast with 42 controls. Widespread changes in frontoparietal RSFA were related to the severity of the acute COVID-19 episode, as indexed by COVID-19 WHO Progression Scale, inflammatory and coagulatory biomarkers. This relationship was not explained by chronic cardiorespiratory dysfunction, age, or sex. Exploratory analysis suggests that the level of cerebrovascular dysfunction is associated with cognitive, mental, and physical health at follow-up. The principal findings were consistent across univariate and multivariate approaches. The results indicate chronic cerebrovascular impairment following severe acute COVID-19, with the potential for long-term consequences on cognitive function and mental wellbeing.",neurology,fuzzy,100,100 medRxiv,10.1101/2022.01.31.22269194,2022-02-01,https://medrxiv.org/cgi/content/short/2022.01.31.22269194,"An outbreak of SARS-CoV-2 in a public-facing office in England, 2021",Barry Atkinson; Karin van Veldhoven; Ian Nicholls; Matthew Coldwell; Adam Clarke; Gillian Frost; Christina J Atchison; Amber I Raja; Allan M Bennett; Derek Morgan; Neil Pearce; Tony Fletcher; Elizabeth B Brickley; Yiqun Chen,UK Health Security Agency; London School of Hygiene & Tropical Medicine; UK Health Security Agency; Health and Safety Executive; Health and Safety Executive; Health and Safety Executive; UK Health Security Agency; London School of Hygiene & Tropical Medicine; UK Health Security Agency; Health and Safety Executive; London School of Hygiene & Tropical Medicine; UK Health Security Agency; London School of Hygiene & Tropical Medicine; Health and Safety Executive,"Between August-September 2021, an outbreak of SARS-CoV-2, with an attack rate of 55% (22/40 workers), occurred in a public-facing office in England. To identify workplace and worker-related risk factors, a comprehensive investigation involving surface sampling, environmental assessment, molecular and serological testing, and worker questionnaires was performed in September - October 2021. The results affirm the utility of surface sampling to identify SARS-CoV-2 control deficiencies and the importance of evolving, site-specific risk assessments with layered COVID-19 mitigation strategies.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2022.01.28.22270013,2022-01-29,https://medrxiv.org/cgi/content/short/2022.01.28.22270013,Agility and sustainability: A qualitative evaluation of COVID-19 Non-pharmaceutical Interventions (NPIs) in the UK logistics sector,Hua Wei; Sarah A Daniels; Carl A Whitfield; Yang Han; David W Denning; Ian Hall; Martyn Regan; Arpana Verma; Martie J van Tongeren,The University of Manchester; The University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester,"BackgroundThe emergence of SARS-CoV-2 triggered a chain of public health responses that radically changed our way of living and working. Non-healthcare sectors, such as the logistics sector, play a key role in such responses. This research aims to qualitatively evaluate the non-pharmaceutical interventions (NPIs) implemented in the UK logistics sector during the COVID-19 pandemic. - -MethodsWe conducted nine semi-structured interviews in July-August 2020 and May-June 2021. In total 11 interviewees represented six companies occupying a range of positions in the UKs logistics sector, including takeaway food delivery, large and small goods delivery and home appliance installation, and logistics technology providers. Inductive thematic analysis was completed using NVivo12 to generate emerging themes and subthemes. Themes/subthemes relevant to interventions were mapped deductively onto an adapted Hierarchy of Control (HoC) framework, focusing on delivery workers. Themes/subthemes relevant to the process of implementation were analyzed to understand the barriers and facilitators of rapid responses. - -ResultsHoC analysis suggests the sector has implemented a wide range of risk mitigation measures, with each company developing their own portfolio of measures. Contact-free delivery was the most commonly implemented measure and perceived effective. In addition, a broad range of measures were implemented, including social distancing, internal contact tracing, communication and collaboration with other key stakeholders of the sector. Process evaluation identified facilitators of rapid responses including capacity to develop interventions internally, localized government support, overwhelming external mandates, effective communication, leadership support and financial support for self-isolation, while barriers included unclear government guidance, shortage of testing capacity and supply, high costs and diversified language and cultural backgrounds. Main sustainability issues included compliance fatigue, and the possible mental health impacts of a prolonged rapid response. - -ConclusionsThis research identified drivers and obstacles of rapid implementation of NPIs in response to a respiratory infection pandemic. Existing implementation process models do not consider speed to respond and the absence or lack of guidance in emergency situations such as the COVID-19. We recommend the development of a rapid response model to inform the design of effective and sustainable infection prevention and control policies and to focus future research priorities. - -Contributions to the fieldO_LIThe study offered important insights into the process of the UK logistics sectors response to the COVID-19 pandemic. -C_LIO_LIThe Hierarchy of Control (HoC) framework was adapted for the evaluation of a collection of non-pharmaceutical interventions (NPIs) implemented in a non-healthcare sector. -C_LIO_LIThematic analysis of qualitative data generated themes that were relevant to the process of rapid implementation of NPIs during a public health emergency. -C_LIO_LIBarriers, facilitators and sustainability issues of the sectors rapid response to the COVID-19 pandemic have been highlighted to inform future research on implementation strategies. -C_LI",occupational and environmental health,fuzzy,100,100 medRxiv,10.1101/2022.01.26.22269901,2022-01-28,https://medrxiv.org/cgi/content/short/2022.01.26.22269901,The impact of the COVID-19 pandemic on health service utilisation following self-harm: a systematic review,Sarah Steeg; Ann John; David Gunnell; Nav Kapur; Dana Dekel; Lena Schmidt; Duleeka Kniipe; Ella Arensman; Keith Hawton; Julian PT Higgins; Emily Eyles; Catherine Macleod-Hall; Luke A McGuinness; Roger T Webb,University of Manchester; Swansea University; University of Bristol; University of Manchester; University of Swansea; University of Bristol; University of Bristol; University College Cork; University of Oxford; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Manchester,"BackgroundEvidence on the impacts of the pandemic on healthcare presentations for self-harm has accumulated rapidly. However, existing reviews do not include studies published beyond 2020. AimsTo systematically review evidence on health services utilisation for self-harm during the COVID-19 pandemic. @@ -1874,6 +1843,7 @@ MethodTrial emulation was conducted by pooling results from six cohorts whose re ResultsAcross six cohorts, there were a total of 21,283 participants who were eligible and vaccinated with either ChAdOx1 (n = 13,813) or BNT162b2 (n = 7,470) with a median follow-up time of 266 days (IQR: 235 - 282). By November 12th 2021, 750 (5.4%) adults who had ChAdOx1 as their vaccine experienced a SARS-CoV-2 infection, compared to 296 (4.0%) who had BNT162b2. We found that people who received ChAdOx1 vaccinations had 10.54 per 1000 people higher cumulative incidence for SARS-CoV-2 infection compared to BNT162b2 for infections during a maximum of 315 days of follow-up. When adjusted for age at vaccination, sex, minority ethnic status, index of multiple deprivation, and clinical vulnerability status, we found a pooled adjusted hazard ratio of 1.35 [HR: 1.35, 95%CI: 1.15 - 1.58], demonstrating a 35% increase in SARS-CoV-2 infections in people who received ChAdOx1 compared to BNT162b2. DiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",epidemiology,fuzzy,100,100 +bioRxiv,10.1101/2021.12.17.473248,2021-12-21,https://biorxiv.org/cgi/content/short/2021.12.17.473248,"SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion",Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta,"University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge","The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.",microbiology,fuzzy,100,100 medRxiv,10.1101/2021.12.20.21268098,2021-12-21,https://medrxiv.org/cgi/content/short/2021.12.20.21268098,"Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol",Shamil Haroon; Krishnarajah Nirantharakumar; Sarah Hughes; Anuradhaa Subramanian; Olalekan Lee Aiyegbusi; Elin Haf Davies; Puja Myles; Tim Williams; Grace Turner; Joht Singh Chandan; Christel McMullan; Janet Lord; David Wraith; Kirsty McGee; Alastair Denniston; Tom Taverner; Louise Jackson; Elizabeth Sapey; Georgios Gkoutos; Krishna Gokhale; Edward Leggett; Clare Iles; Christopher Frost; Gary McNamara; Amy Bamford; Tom Marshall; Dawit Zemedikun; Gary Price; Steven Marwaha; Nikita Simms-Williams; Kirsty Brown; Anita Walker; Karen Jones; Karen Matthews; Jennifer Camaradou; Michael Saint-Cricq; Sumita Kumar; Yvonne Alder; David Stanton; Lisa Agyen; Megan Baber; Hannah Blaize; Melanie Calvert,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University ofBirmingham; University of Birmingham; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; Aparito; Aparito; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; N/A; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; University ofBirmingham,"IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies. Methods and analysisA cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink (CPRD) and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability, and patient reported outcome measures. Data will be collected monthly for one year. @@ -1958,6 +1928,13 @@ Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe systematically s Added value of this studyIn a diverse population of adults post-hospital admission with COVID-19, our large UK prospective multi-centre study reports several novel findings: the minority felt fully recovered at one year with minimal recovery from five months across any health domain; female sex and obesity are associated with being less likely to feel fully recovered at one year; several inflammatory mediators were increased in individuals with the most severe physical, mental health, and cognitive impairments compared to individuals with milder ongoing impairments. Implications of all the available evidenceBoth pharmacological and non-pharmacological interventions are urgently needed to improve the ongoing burden following hospitalisation for COVID-19 both for individuals and healthcare systems; our findings support the use of a precision medicine approach with potential treatable traits of systemic inflammation and obesity.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.12.13.21267368,2021-12-15,https://medrxiv.org/cgi/content/short/2021.12.13.21267368,Acute COVID-19 severity and 16-month mental morbidity trajectories in patient populations of six nations,Ingibjorg Magnusdottir; Aniko Lovik; Anna Bara Unnarsdottir; Daniel L. McCartney; Helga Ask; Kadri Koiv; Lea Arregui Nordahl Christoffersen; Sverre Urnes Johnson; Andrew M McIntosh; Anna K. Kahler; Archie Campbell; Arna Hauksdottir; Chloe Fawns-Ritchie; Christian Erikstrup; Dorte Helenius; Drew Altschul; Edda Bjork Thordardottir; Elias Eythorsson; Emma M. Frans; Gunnar Tomasson; Harpa Lind Jonsdottir; Harpa Runarsdottir; Henrik Hjalgrim; Hronn Hardardottir; Juan Gonzalez-Hijon; Karina Banasik; Khoa Manh Dinh; Li Lu; Lili Milani; Lill Trogstad; Maria Didriksen; Omid V. Ebrahimi; Patrick F. Sullivan; Per Minor Magnus; Qing Shen; Ragnar Nesvag; Reedik Magi; Runolfur Palsson; Sisse Rye Ostrowski; Thomas Werge; Asle Hoffart; David J. Porteous; Fang Fang; Johanna Jakobsdottir; Kelli Lehto; Ole A. Andreassen; Ole B.V. Pedersen; Thor Aspelund; Unnur Anna Valdimarsdottir,"Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Division of Psychiatry, University of Edinburgh, Edinburgh, UK; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Edinburgh, Edinburgh, UK; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Faculty of Psychology, University of Iceland School of Health Sciences, Reykjavik, Iceland; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Danish Cancer Society Research Center, Copenhagen, Denmark; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA; Centre of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway.; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Clinical Immunology, Zealand University Hospital, Denmark; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland","BACKGROUNDThe aim of this multinational study was to assess the development of adverse mental health symptoms among individuals diagnosed with COVID-19 in the general population by acute infection severity up to 16 months after diagnosis. + +METHODSParticipants consisted of 247 249 individuals from seven cohorts across six countries (Denmark, Estonia, Iceland, Norway, Scotland, and Sweden) recruited from April 2020 through August 2021. We used multivariable Poisson regression to contrast symptom-prevalence of depression, anxiety, COVID-19 related distress, and poor sleep quality among individuals with and without a diagnosis of COVID-19 at entry to respective cohorts by time (0-16 months) from diagnosis. We also applied generalised estimating equations (GEE) analysis to test differences in repeated measures of mental health symptoms before and after COVID-19 diagnosis among individuals ever diagnosed with COVID-19 over time. + +FINDINGSA total of 9979 individuals (4%) were diagnosed with COVID-19 during the study period and presented overall with a higher symptom burden of depression (prevalence ratio [PR] 1{middle dot}18, 95% confidence interval [95% CI] 1{middle dot}03-1{middle dot}36) and poorer sleep quality (1{middle dot}13, 1{middle dot}03-1{middle dot}24) but not with higher levels of symptoms of anxiety or COVID-19 related distress compared with individuals without a COVID-19 diagnosis. While the prevalence of depression and COVID-19 related distress attenuated with time, the trajectories varied significantly by COVID-19 acute infection severity. Individuals diagnosed with COVID-19 but never bedridden due to their illness were consistently at lower risks of depression and anxiety (PR 0{middle dot}83, 95% CI 0{middle dot}75-0{middle dot}91 and 0{middle dot}77, 0{middle dot}63-0{middle dot}94, respectively), while patients bedridden for more than 7 days were persistently at higher risks of symptoms of depression and anxiety (PR 1{middle dot}61, 95% CI 1{middle dot}27-2{middle dot}05 and 1{middle dot}43, 1{middle dot}26-1{middle dot}63, respectively) throughout the 16-month study period. + +CONCLUSIONAcute infection severity is a key determinant of long-term mental morbidity among COVID-19 patients.",public and global health,fuzzy,100,92 medRxiv,10.1101/2021.12.14.21267460,2021-12-15,https://medrxiv.org/cgi/content/short/2021.12.14.21267460,Differential Risk of SARS-CoV-2 Infection by Occupation: Evidence from the Virus Watch prospective cohort study in England and Wales,Sarah Beale; Susan J Hoskins; Thomas Edward Byrne; Erica Wing Lam Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan MD Navaratnam; Vincent Nguyen; Parth Patel; Alexei Yavlinsky; Anne Johnson; Martie Van Tongeren; Robert W Aldridge; Andrew Hayward,University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University of Manchester; University College London; University College London,"BackgroundWorkers differ in their risk of SARS-CoV-2 infection according to their occupation, but the direct contribution of occupation to this relationship is unclear. This study aimed to investigate how infection risk differed across occupational groups in England and Wales up to April 2022, after adjustment for potential confounding and stratification by pandemic phase. MethodsData from 15,190 employed/self-employed participants in the Virus Watch prospective cohort study were used to generate risk ratios for virologically- or serologically-confirmed SARS-CoV-2 infection using robust Poisson regression, adjusting for socio-demographic and health-related factors and non-work public activities. We calculated attributable fractions (AF) amongst the exposed for belonging to each occupational group based on adjusted risk ratios (aRR). @@ -2067,27 +2044,13 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSTo identify existin Added value of this studyUsing data from one of the largest UK citizen science epidemiological initiatives, we describe and compare illness (symptom duration, burden, profile, risk of long illness, and hospital attendance) in symptomatic community-based adults presenting when either the Alpha or Delta variant was the predominant circulating strain of SARS-CoV-2 in the UK. We assess evidence of transmission, reinfection, and vaccine effectiveness. Our data show that the seven most common symptoms with Delta infection were the same as with Alpha infection. Risks of illness duration [≥]7 days and [≥]28 days, and of requiring hospital care, were not increased. In line with previous research, we found increased transmissibility of Delta vs. previous variants; and no evidence of increased re-infection rates. Our data support high vaccine efficacy of BNT162b2 and ChAdOx1 nCoV-19 formulations against Delta variant infection. Overall, our study adds quantitative information regarding meaningful clinical differences in COVID-19 due to Delta vs. other variants. Implications of all the available evidenceOur observational data confirm that COVID-19 disease in UK in adults is generally comparable to infection with the Alpha variant, including in elderly individuals. Our data contribute to epidemiological surveillance from the wider UK population and may capture information from COVID-19 presentation within the community that might be missed in healthcare-based surveillance. Our data may be useful in informing healthcare service planning, vaccination policies, and measures for social protection.",epidemiology,fuzzy,94,100 -medRxiv,10.1101/2021.11.22.21266512,2021-11-24,https://medrxiv.org/cgi/content/short/2021.11.22.21266512,Association of COVID-19 with arterial and venous vascular diseases: a population-wide cohort study of 48 million adults in England and Wales,Rochelle Knight; Venexia Walker; Samantha Ip; Jennifer A Cooper; Thomas Bolton; Spencer Keene; Rachel Denholm; Ashley Akbari; Hoda Abbasizanjani; Fatemeh Torabi; Efosa Omigie; Sam Hollings; Teri-Louise North; Renin Toms; Emanuele Di Angelantonio; Spiros Denaxas; Johan H Thygesen; Christopher Tomlinson; Ben Bray; Craig J Smith; Mark Barber; George Davey Smith; Nishi Chaturvedi; Cathie Sudlow; William N Whiteley; Angela Wood; Jonathan A C Sterne; - CVD-COVID-UK/COVID-IMPACT consortium; - Longitudinal Health and Wellbeing COVID-19 National Core Study,University of Bristol; University of Bristol; University of Cambridge; University of Bristol; University of Cambridge; University of Cambridge; University of Bristol; Swansea University; Swansea University; Swansea University; NHS Digital; NHS Digital; University of Bristol; University of Bristol; University of Cambridge; University College London; University College London; University College London; Kings College London; University of Manchester; Glasgow Caledonian University; University of Bristol; University College London; Health Data Research UK; University of Edinburgh; University of Cambridge; University of Bristol; ; ,"ImportanceThe long-term effects of COVID-19 on the incidence of vascular diseases are unclear. - -ObjectiveTo quantify the association between time since diagnosis of COVID-19 and vascular disease, overall and by age, sex, ethnicity, and pre-existing disease. - -DesignCohort study based on population-wide linked electronic health records, with follow up from January 1st to December 7th 2020. - -Setting and participantsAdults registered with an NHS general practice in England or Wales and alive on January 1st 2020. +medRxiv,10.1101/2021.11.22.21266692,2021-11-24,https://medrxiv.org/cgi/content/short/2021.11.22.21266692,Serological responses to COVID-19 booster vaccine in England,Georgina Ireland; Heather Whitaker; Shamez N Ladhani; Frances Baawuah; Vani Subbarao; Ezra Linley; Lenesha Warrener; Michelle O'Brien; Corrine Whillock; Paul Moss; Mary E Ramsay; Gayatri Amirthalingam; Kevin E Brown,"UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; Brondesbury Medical Centre, Kilburn, London, United Kingdom; UK Health Security Agency; University of Birmingham; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency","IntroductionThere are limited data on immune responses after COVID-19 vaccine boosters in individuals receiving primary immunisation with BNT162b2 (Pfizer-BioNTech) or AZD1222 (AstraZeneca). -ExposuresTime since diagnosis of COVID-19 (categorised as 0-6 days, 1-2 weeks, 3-4, 5-8, 9-12, 13-26 and 27-49 weeks since diagnosis), with and without hospitalisation within 28 days of diagnosis. +MethodsA prospective, cohort study to assess SARS-CoV-2 antibody responses before and after booster vaccination with BNT162b2 in adults receiving either (i) two BNT162b2 doses <30 days apart (BNT162b2-control), (ii) two BNT162b2 doses [≥]30 days apart (BNT162b2-extended) or (iii) two AZD1222 doses [≥]30 days apart (AZD1222-extended) in London, England. SARS-CoV-2 spike protein antibody geometric mean titres (GMTs) before and 2-4 weeks after booster were compared. -Main outcomes and measuresPrimary outcomes were arterial thromboses (mainly acute myocardial infarction and ischaemic stroke) and venous thromboembolic events (VTE, mainly pulmonary embolism and lower limb deep vein thrombosis). We also studied other vascular events (transient ischaemic attack, haemorrhagic stroke, heart failure and angina). Hazard ratios were adjusted for demographic characteristics, previous disease diagnoses, comorbidities and medications. +ResultsOf 750 participants, 626 provided serum samples for up to 38 weeks after their second vaccine dose. Antibody GMTs peaked at 2-4 weeks after the second dose, before declining by 68% at 36-38 weeks after dose 2 for BNT162b2-control participants, 85% at 24-29 weeks for BNT162b2-extended participants and 78% at 24-29 weeks for AZD1222-extended participants. Antibody GMTs was highest in BNT162b2-extended participants (942 [95%CI, 797-1113]) than AZD1222-extended (183 [124-268]) participants at 24-29 weeks or BNT162b2-control participants at 36-38 weeks (208; 95%CI, 150-289). At 2-4 weeks after booster, GMTs were significantly higher than after primary vaccination in all three groups: 18,104 (95%CI, 13,911-23,560; n=47) in BNT162b2-control (76.3-fold), 13,980 (11,902-16,421; n=118) in BNT162b2-extended (15.9-fold) and 10,799 (8,510-13,704; n=43) in AZD1222-extended (57.2-fold) participants. BNT162b2-control participants (median:262 days) had a longer interval between primary and booster doses than BNT162b2-extended or AZD1222-extended (both median:186 days) participants. -ResultsAmong 48 million adults, 130,930 were and 1,315,471 were not hospitalised within 28 days of COVID-19. In England, there were 259,742 first arterial thromboses and 60,066 first VTE during 41.6 million person-years follow-up. Adjusted hazard ratios (aHRs) for first arterial thrombosis compared with no COVID-19 declined rapidly from 21.7 (95% CI 21.0-22.4) to 3.87 (3.58-4.19) in weeks 1 and 2 after COVID-19, 2.80 (2.61-3.01) during weeks 3-4 then to 1.34 (1.21-1.48) during weeks 27-49. aHRs for first VTE declined from 33.2 (31.3-35.2) and 8.52 (7.59-9.58) in weeks 1 and 2 to 7.95 (7.28-8.68) and 4.26 (3.86-4.69) during weeks 3-4 and 5-8, then 2.20 (1.99-2.44) and 1.80 (1.50-2.17) during weeks 13-26 and 27-49 respectively. aHRs were higher, for longer after diagnosis, after hospitalised than non-hospitalised COVID-19. aHRs were also higher among people of Black and Asian than White ethnicity and among people without than with a previous event. Across the whole population estimated increases in risk of arterial thromboses and VTEs were 2.5% and 0.6% respectively 49 weeks after COVID-19, corresponding to 7,197 and 3,517 additional events respectively after 1.4 million COVID-19 diagnoses. - -Conclusions and RelevanceHigh rates of vascular disease early after COVID-19 diagnosis decline more rapidly for arterial thromboses than VTEs but rates remain elevated up to 49 weeks after COVID_19. These results support continued policies to avoid COVID-19 infection with effective COVID-19 vaccines and use of secondary preventive agents in high-risk patients. - -Key pointsO_ST_ABSQuestionC_ST_ABSIs COVID-19 associated with higher long-term incidence of vascular diseases? - -FindingsIn this cohort study of 48 million adults in England and Wales, COVID-19 was associated with higher incidence, that declined with time since diagnosis, of both arterial thromboses [week 1: adjusted HR [aHR] 21.7 (95% CI 21.0-22.4) weeks 27-49: aHR 1.34 (1.21-1.48)] and venous thromboembolism [week 1: aHR 33.2 (31.3-35.2), weeks 27-49 1.80 (1.50-2.17)]. aHRs were higher, for longer, after hospitalised than non-hospitalised COVID-19. The estimated excess number of arterial thromboses and venous thromboembolisms was 10,500. - -MeaningAvoidance of COVID-19 infection through vaccination, and use of secondary preventive agents after infection in high-risk patients, may reduce post-COVID-19 acute vascular diseases.",infectious diseases,fuzzy,100,100 +ConclusionsWe observed rapid serological responses to boosting with BNT162b2, irrespective of vaccine type or schedule used for primary immunisation, with higher post-booster responses with longer interval between primary immunisation and boosting. Boosters will not only provide additional protection for those at highest risk of severe COVID-19 but also prevent infection and, therefore, interrupt transmission, thereby reducing infections rates in the population. Ongoing surveillance will be important for monitoring the duration of protection after the booster.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.11.23.21266574,2021-11-24,https://medrxiv.org/cgi/content/short/2021.11.23.21266574,"Reinfection with SARS-CoV-2: outcome, risk factors and vaccine efficacy in a Scottish cohort",Paul M McKeigue; David McAllister; Chris Robertson; Diane Stockton; Helen Colhoun,University of Edinburgh; University of Glasgow; University of Strathclyde; Public Health Scotland; University of Edinburgh,"BackgroundThe objective of this study was to investigate how protection against COVID-19 conferred by previous infection is modified by vaccination. MethodsIn a cohort of all 152655 individuals in Scotland alive at 90 days after a positive test for SARS-CoV-2 (confirmed by cycle threshold < 30, or two tests) followed till 22 September 2021, rate ratios for reinfection were estimated with calendar time or tests as timescale. @@ -2169,13 +2132,6 @@ ConclusionAmong hypoxic but not critically patients with COVID-19 in hospital, a What is already known on this topicProne positioning is considered standard of care for mechanically ventilated patients who have severe acute respiratory distress syndrome. Recent data suggest prone positioning is beneficial for patients with COVID-19 who are requiring high flow oxygen. It is unknown of prone positioning is beneficial for patients not on high flow oxygen. What this study addsProne positioning is generally not well tolerated and innovative approaches are needed to improve adherence. Clinical and physiologic outcomes were not improved with prone positioning among hypoxic but not critically ill patients hospitalized with COVID-19.",intensive care and critical care medicine,fuzzy,96,100 -medRxiv,10.1101/2021.11.08.21265380,2021-11-08,https://medrxiv.org/cgi/content/short/2021.11.08.21265380,Describing the population experiencing COVID-19 vaccine breakthrough following second vaccination in England: A cohort study from OpenSAFELY,Amelia CA Green; Helen J Curtis; William J Hulme; Elizabeth J Williamson; Helen I McDonald; Krishnan Bhaskaran; Christopher T Rentsch; Anna Schultze; Brian MacKenna; Viyaasan Mahalingasivam; Laurie Tomlinson; Alex J Walker; Louis Fisher; Jon Massey; Colm D Andrews; Lisa E M Hopcroft; Caroline E Morton; Richard Croker; Jessica Morley; Amir Mehrkar; Sebastian CJ Bacon; David Evans; Peter Inglesby; George Hickman; Tom Ward; Simon Davy; Rohini Mathur; John Tazare; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; Christopher Bates; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Ian J Douglas; Stephen JW Evans; Liam Smeeth; Ben Goldacre,University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Bristol; TPP; TPP; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundWhile the vaccines against COVID-19 are considered to be highly effective, COVID-19 vaccine breakthrough is likely and a small number of people will still fall ill, be hospitalised, or die from COVID-19, despite being fully vaccinated. With the continued increase in numbers of positive SARS-CoV-2 tests, describing the characters of individuals who have experienced a COVID-19 vaccine breakthrough could be hugely important in helping to determine who may be at greatest risk. - -MethodWith the approval of NHS England we conducted a retrospective cohort study using routine clinical data from the OpenSAFELY TPP database of fully vaccinated individuals, linked to secondary care and death registry data, and described the characteristics of those experiencing a COVID-19 vaccine breakthrough. - -ResultsAs of 01st November 2021, a total of 15,436,455 individuals were identified as being fully vaccinated against COVID-19, with a median follow-up time of 149 days (IQR: 107-179). From within this population, a total of 577245 (<4%) individuals reported a positive SARS-CoV-2 test. For every 1000 years of patient follow-up time, the corresponding incidence rate was 98.02 (95% CI 97.9-98.15). There were 16,120 COVID-19-related hospital admissions, 1,100 COVID-19 critical care admission patients and 3,925 COVID-19-related deaths; corresponding incidence rates of 2.72 (95% C 2.7-2.74), 0.19 (95% C 0.18-0.19) and 0.66 (95% C 0.65-0.67), respectively. When broken down by the initial priority group, higher rates of hospitalisation and death were seen in those in care homes and those over 80 years of age. Comorbidities with the highest rates of breakthrough COVID-19 included chronic kidney disease, dialysis, transplant, haematological malignancy, and immunocompromised. - -ConclusionThe majority of COVID-19 vaccine breakthrough cases in England were mild with relatively few fully vaccinated individuals being hospitalised or dying as a result. However, some concerning differences in rates of breakthrough cases were identified in several clinical and demographic groups. While it is important to note that these findings are simply descriptive and cannot be used to answer why certain groups have higher rates of COVID-19 breakthrough than others, the emergence of the Omicron variant of COVID-19 coupled with the continued increase in numbers of positive SARS-CoV-2 tests are concerning. As numbers of fully vaccinated individuals increases and follow-up time lengthens, so too will the number of COVID-19 breakthrough cases. Additional analyses, aimed at identifying individuals at higher risk, are therefore required.",epidemiology,fuzzy,100,100 bioRxiv,10.1101/2021.11.05.467529,2021-11-08,https://biorxiv.org/cgi/content/short/2021.11.05.467529,Structural basis of main proteases of coronavirus bound to drug candidate PF-07321332,Jian Li; Cheng Lin; Xuelan Zhou; Fanglin Zhong; Pei Zeng; Haihai Jiang; Yang Yang; Peter McCormick; Yang Fu; Jin Zhang,"College of Pharmaceutical Sciences, Gannan Medical University, Ganzhou 341000, China.; School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.; Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen 518118, China.; Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou 341000, China.; Jiangxi Jmerry Biopharmaceutical Co., Ltd, Ganzhou 341000, China.; School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.; Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen 518118, China.; William Harvey Research Institute, Queen Mary University of London; School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China 518055; School of Basic Medical Sciences, Nanchang University, Nanchang 330031, China.","The high mutation rate of COVID-19 and the prevalence of multiple variants strongly support the need for pharmacological options to complement vaccine strategies. One region that appears highly conserved among different genus of coronaviruses is the substrate binding site of the main protease (Mpro or 3CLpro), making it an attractive target for the development of broad-spectrum drugs for multiple coronaviruses. PF-07321332 developed by Pfizer is the first orally administered inhibitor targeting the main protease of SARS-CoV-2, which also has shown potency against other coronaviruses. Here we report three crystal structures of main protease of SARS-CoV-2, SARS-CoV and MERS-CoV bound to the inhibitor PF-07321332. The structures reveal a ligand-binding site that is conserved among SARS-CoV-2, SARS-CoV and MERS-CoV, providing insights into the mechanism of inhibition of viral replication. The long and narrow cavity in the cleft between domains I and II of main protease harbors multiple inhibitor binding sites, where PF-07321332 occupies subsites S1, S2 and S4 and appears more restricted compared with other inhibitors. A detailed analysis of these structures illuminated key structural determinants essential for inhibition and elucidated the binding mode of action of main proteases from different coronaviruses. Given the importance of main protease for the treatment of SARS-CoV-2 infection, insights derived from this study should accelerate the design of safer and more effective antivirals.",biophysics,fuzzy,100,100 medRxiv,10.1101/2021.11.04.21265918,2021-11-05,https://medrxiv.org/cgi/content/short/2021.11.04.21265918,Longitudinal Changes of Cardiac and Aortic Imaging Phenotypes Following COVID-19 in the UK Biobank Cohort,Wenjia Bai; Betty Raman; Steffen E Peterson; Stefan Neubauer; Zahra Raisi-Estabragh; Nay Aung; Nicholas C Harvey; Naomi Allen; Rory Collins; Paul M Matthews,"Department of Brain Sciences, Imperial College London and British Heart Foundation Centre for Research Excellence, Imperial College London, London, UK; University of Oxford; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford and British Heart Foundation; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London; MRC Lifecourse Epidemiology Centre, University of Southampton and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital; Nuffield Department of Population Health, University of Oxford, Oxford, UK and UK Biobank, Stockport, UK; Nuffield Department of Population Health, University of Oxford, Oxford, UK and UK Biobank, Stockport, UK; Imperial College, London","Case studies conducted after recovery from acute infection with SARS-CoV-2 have frequently identified abnormalities on CMR imaging, suggesting the possibility that SARS-CoV-2 infection commonly leads to cardiac pathology. However, these observations have not been able to distinguish between associations that reflect pre-existing cardiac abnormalities (that might confer a greater likelihood of more severe infection) from those that arise as consequences of infection. To address this question, UK Biobank volunteers (n=1285; 54.5% women; mean age at baseline, 59.8 years old; 96.3% white) who attended an imaging assessment including cardiac magnetic resonance (CMR) before the start of the COVID-19 pandemic were invited to attend a second imaging assessment in 2021. Cases with evidence of previous SARS-CoV-2 infection were identified through linkage to PCR-testing or other medical records, or a positive antibody lateral flow test; n=640 in data available on 22 Sep 2021) and were matched to controls with no evidence of previous infection (n=645). The majority of these infections were milder and did not involve hospitalisation. Measures of cardiac and aortic structure and function were derived from the CMR images obtained on the cases before and after SARS-CoV-2 infection from images for the controls obtained over the same time interval using a previously validated, automated algorithm. Cases and controls had similar cardiac and aortic imaging phenotypes at their first imaging assessment. Changes between CMR imaging measures in cases before and after infection were not significantly different from those in the matched control group. Additional adjustment for comorbidities made no material difference to the results. While these results are preliminary and limited to imaging metrics derived from automated analyses, they do not suggest clinically significant persistent cardiac pathology in the UK Biobank population after generally milder (non-hospitalised) SARS-CoV-2 infection.",neurology,fuzzy,100,100 medRxiv,10.1101/2021.11.02.21265767,2021-11-03,https://medrxiv.org/cgi/content/short/2021.11.02.21265767,Determinants of pre-vaccination antibody responses to SARS-CoV-2: a population-based longitudinal study (COVIDENCE UK),Mohammad Talaei; Sian Faustini; Hayley Holt; David A. Jolliffe; Giulia Vivaldi; Matthew Greenig; Natalia Perdek; Sheena Maltby; Carola M Bigogno; Jane Symons; Gwyneth A. Davies; Ronan A. Lyons; Christopher J Griffiths; Frank Kee; Aziz Sheikh; Alex G. Richter; Seif O. Shaheen; Adrian R Martineau,Queen Mary University of London; University of Birmingham; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; Swansea University Medical School; Swansea University Medical School; Queen Mary University of London; Queens University Belfast; University of Edinburgh; University of Birminghan; Queen Mary University of London; Queen Mary University of London,"BackgroundProspective population-based studies investigating multiple determinants of pre-vaccination antibody responses to SARS-CoV-2 are lacking. @@ -2245,21 +2201,6 @@ MethodsIn the REal-time Assessment of Community Transmission-1 (REACT-1) study, ResultsWe observed stable or rising prevalence (with an R of 1.03 (0.94, 1.14) overall) during round 14 with a weighted prevalence of 0.83% (0.76%, 0.89%). The highest weighted prevalence was found in children aged 5 to 12 years at 2.32% (1.96%, 2.73%) and 13 to 17 years at 2.55% (2.11%, 3.08%). All positive virus samples analysed correspond to the Delta variant or sub-lineages of Delta with one instance of the E484K escape mutation detected. The epidemic was growing in those aged 17 years and under with an R of 1.18 (1.03, 1.34), but decreasing in those aged 18 to 54 years with an R of 0.81 (0.68, 0.97). For all participants and all vaccines combined, at ages 18 to 64 years, vaccine effectiveness against infection (rounds 13 and 14 combined) was estimated to be 62.8% (49.3%, 72.7%) after two doses compared to unvaccinated people when adjusted for round, age, sex, index of multiple deprivation, region and ethnicity; the adjusted estimate was 44.8% (22.5%, 60.7%) for AstraZeneca and 71.3% (56.6%, 81.0%) for Pfizer-BioNTech, and for all vaccines combined it was 66.4% (49.6%, 77.6%) against symptomatic infection (one or more of 26 surveyed symptoms in month prior). Across rounds 13 and 14, at ages 18 years and over, weighted prevalence of swab-positivity was 0.55% (0.50%, 0.61%) for those who received their second dose 3-6 months before their swab compared to 0.35% (0.31%, 0.40%) for those whose second dose was within 3 months of their swab, while weighted prevalence among unvaccinated individuals was1.76% (1.60%, 1.95%). In round 14, age group, region, key worker status, and household size jointly contributed to the risk of higher prevalence of swab-positivity. DiscussionIn September 2021 infections were increasing exponentially in the 5-to-17-year age group coinciding with the start of the autumn school term in England. Relatively few schoolchildren aged 5 to 17 years have been vaccinated in the UK though single doses are now being offered to those aged 12 years and over. In adults, the higher prevalence of swab-positivity following two doses of vaccine from 3 to 6 months compared to within 3 months of second dose supports the use of a booster vaccine. It is important that the vaccination programme maintains high coverage and reaches children and unvaccinated or partially vaccinated adults to reduce transmission and associated disruptions to work and education.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.10.13.21264937,2021-10-18,https://medrxiv.org/cgi/content/short/2021.10.13.21264937,Comparative effectiveness of ChAdOx1 versus BNT162b2 COVID-19 vaccines in Health and Social Care workers in England: a cohort study using OpenSAFELY,William J Hulme; Elizabeth J Williamson; Amelia CA Green; Krishnan Bhaskaran; Helen I McDonald; Christopher T Rentsch; Anna Schultze; John Tazare; Helen J Curtis; Alex J Walker; Laurie Tomlinson; Tom M Palmer; Elsie Horne; Brian MacKenna; Caroline E Morton; Amir Mehrkar; Louis Fisher; Sebastian CJ Bacon; David Evans; Peter Inglesby; George Hickman; Simon Davy; Tom Ward; Richard Croker; Rosalind M Eggo; Angel YS Wong; Rohini Mathur; Kevin Wing; Harriet Forbes; Daniel J Grint; Ian J Douglas; Stephen JW Evans; Liam Smeeth; Christopher Bates; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Jonathan AC Sterne; Miguel A Hernan; Ben Goldacre,"The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; London School of Hygiene and Tropical Medicine, London, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; London School of Hygiene and Tropical Medicine, London, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; TPP, Horsforth, Leeds, UK; TPP, Horsforth, Leeds, UK; TPP, Horsforth, Leeds, UK; TPP, Horsforth, Leeds, UK; TPP, Horsforth, Leeds, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Bristol, Biomedical Research Centre, Bristol, UK; CAUSALab, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Departments of Epidemiology and Biostatistics, Harvard T.H. Chan School of Public Health, ; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK","ObjectivesTo compare the effectiveness of the BNT162b2 mRNA (Pfizer-BioNTech) and the ChAdOx1 (Oxford-AstraZeneca) COVID-19 vaccines against infection and COVID-19 disease in health and social care workers. - -DesignCohort study, emulating a comparative effectiveness trial. - -SettingLinked primary care, hospital, and COVID-19 surveillance records available within the OpenSAFELY-TPP research platform. - -Participants317,341 health and social care workers vaccinated between 4 January and 28 February 2021, registered with a GP practice using the TPP SystmOne clinical information system in England, and not clinically extremely vulnerable. - -InterventionsVaccination with either BNT162b2 or ChAdOx1 administered as part of the national COVID-19 vaccine roll-out. - -Main outcome measuresRecorded SARS-CoV-2 positive test, or COVID-19 related Accident and Emergency attendance or hospital admission occurring within 20 weeks of vaccination. - -ResultsThe cumulative incidence of each outcome was similar for both vaccines during the first 20 weeks post-vaccination. The cumulative incidence of recorded SARS-CoV-2 infection 6 weeks after vaccination with BNT162b2 was 19.2 per 1000 people (95%CI 18.6 to 19.7) and with ChAdOx1 was 18.9 (95%CI 17.6 to 20.3), representing a difference of -0.24 per 1000 people (95%CI -1.71 to 1.22). The difference in the cumulative incidence per 1000 people of COVID-19 accident and emergency attendance at 6 weeks was 0.01 per 1000 people (95%CI -0.27 to 0.28). For COVID-19 hospital admission, this difference was 0.03 per 1000 people (95%CI -0.22 to 0.27). - -ConclusionsIn this cohort of healthcare workers where we would not anticipate vaccine type to be related to health status, we found no substantial differences in the incidence of SARS-CoV-2 infection or COVID-19 disease up to 20 weeks after vaccination. Incidence dropped sharply after 3-4 weeks and there were very few COVID-19 hospital attendance and admission events after this period. This is in line with expected onset of vaccine-induced immunity, and suggests strong protection against COVID-19 disease for both vaccines.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.10.13.21264956,2021-10-16,https://medrxiv.org/cgi/content/short/2021.10.13.21264956,Changes in paediatric respiratory infections at a UK teaching hospital 2016-2021; impact of the SARS-CoV-2 pandemic.,Sheila F Lumley; Nicholas Richens; Emily Lees; Jack Cregan; Elizabeth Kalimeris; Sarah Oakley; Marcus Morgan; Shelley Segal; Moya Dawson; Ann Sarah F Walker; David W Eyre; Derrick W Crook; Sally Beer; Alex Novak; Nicole Stoesser; Philippa C Matthews,University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hosptials NHS Foundation Trust; University of Oxford; University of Oxford; NIHR Oxford Biomedical Research Centre; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford,"ObjectiveTo describe the impact of the SARS-CoV-2 pandemic on the incidence of paediatric viral respiratory tract infection in Oxfordshire, UK. MethodsData on paediatric Emergency Department (ED) attendances (0-15 years inclusive), respiratory virus testing, vital signs and mortality at Oxford University Hospitals were summarised using descriptive statistics. @@ -2389,6 +2330,7 @@ Methods and findingsWe performed a rapid systematic review, searching Medline, E 49 observational studies (15 peer-reviewed papers and 34 preprints) reported primary outcomes for eight drug groups hypothesised to be deleterious. Meta-analysis showed that acute inpatient corticosteroid use was associated with increased mortality (OR 2.22, 95% CI 1.26-3.90), however this result appeared to have been biased by confounding via indication. One subgroup analysis indicated an association between immunosuppressant use and susceptibility to COVID-19 among case control and cross-sectional studies (OR 1.29, 95% CI 1.19-1.40) but this was not found with cohort studies (OR 1.11, 95% CI 0.86-1.43). Studies which adjusted for multiple confounders showed that people taking angiotensin-converting-enzyme inhibitors (ACEIs) or angiotensin-II-receptor blockers (ARBs) required a lower level of care (OR 0.85, 95% CI 0.74-0.98). Furthermore, studies which combined these two drug groups in their analysis demonstrated an association with a lower mortality (OR 0.68, 95% CI 0.55-0.85). ConclusionsWe found minimal high quality or consistent evidence that any drug groups increase susceptibility, severity or mortality in COVID-19. Converse to initial hypotheses, we found some evidence that regular use of ACEIs and ARBs prior to infection may be effective in reducing the level of care required, such as requiring intensive care, in patients with COVID-19.",pharmacology and therapeutics,fuzzy,100,100 +medRxiv,10.1101/2021.09.13.21263487,2021-09-16,https://medrxiv.org/cgi/content/short/2021.09.13.21263487,SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population,Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.09.13.21262360,2021-09-16,https://medrxiv.org/cgi/content/short/2021.09.13.21262360,Efficacy of two doses of COVID-19 vaccine against severe COVID-19 in those with risk conditions and residual risk to the clinically extremely vulnerable: the REACT-SCOT case-control study,Paul M McKeigue; David McAllister; Chris Robertson; Sharon J Hutchinson; Stuart McGurnaghan; Diane Stockton; Helen M Colhoun,University of Edinburgh; University of Glasgow; University of Strathclyde; Glasgow Caledonian University; University of Edinburgh; Public Health Scotland; University of Edinburgh,"ObjectivesTo determine whether COVID-19 efficacy varies with clinical risk category and to investigate risk factors for severe COVID-19 in those who have received two doses of vaccine. DesignMatched case-control study (REACT-SCOT). @@ -2640,6 +2582,13 @@ QuestionDoes the association between BMI and COVID-19 mortality vary by ethnicit FindingsIn this study of 12.6 million adults, BMI was associated with COVID-19 in all ethnicities, but with stronger associations in ethnic minority populations such that the risk of COVID-19 mortality for a BMI of 40 kg/m2 in white ethnicities was observed at a BMI of 30.1 kg/m2, 27.0 kg/m2, and 32.2 kg/m2 in black, South Asian and other ethnicities, respectively. MeaningBMI is a stronger risk factor for COVID-19 mortality in ethnic minorities. Obesity management is therefore a priority in these populations.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.07.20.21260558,2021-07-22,https://medrxiv.org/cgi/content/short/2021.07.20.21260558,Intentions to participate in cervical and colorectal cancer screening during the COVID-19 pandemic: a mixed-methods study,Rebecca Wilson; Harriet Quinn-Scoggins; Yvonne Moriarty; Jacqueline Hughes; Mark Goddard; Rebecca Cannings-John; Victoria Whitelock; Katriina L Whitaker; Detelina Grozeva; Julia Townson; Kirstie Osborne; Stephanie Smits; Michael Robling; Julie Hepburn; Graham Moore; Ardiana Gjini; Kate Brain; Jo Waller,"Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cancer Research UK; University of Surrey; Cardiff University; Cardiff University; Cancer Research UK; Cardiff University; Cardiff University; Public Involvement Community, Health and Care Research Wales; Cardiff University; Public Health Wales; Cardiff University; Kings College London","Worldwide, cancer screening faced significant disruption in 2020 due to the COVID-19 pandemic. If this has led to changes in public attitudes towards screening and reduced intention to participate, there is a risk of long-term adverse impact on cancer outcomes. In this study, we examined previous participation and future intentions to take part in cervical and colorectal cancer (CRC) screening following the first national lockdown in the UK. + +Overall, 7543 adults were recruited to a cross-sectional online survey in August-September 2020. Logistic regression analyses were used to identify correlates of strong screening intentions among 2,319 participants eligible for cervical screening and 2,502 eligible for home-based CRC screening. Qualitative interviews were conducted with a sub-sample of 30 participants. Verbatim transcripts were analysed thematically. + +Of those eligible, 74% of survey participants intended to attend cervical screening and 84% intended to complete home-based CRC screening when next invited. Thirty percent and 19% of the cervical and CRC samples respectively said they were less likely to attend a cancer screening appointment now than before the pandemic. Previous non-participation was the strongest predictor of low intentions for cervical (aOR 26.31, 95% CI: 17.61-39.30) and CRC (aOR 67.68, 95% CI: 33.91-135.06) screening. Interview participants expressed concerns about visiting healthcare settings but were keen to participate when screening programmes resumed. + +Intentions to participate in future screening were high and strongly associated with previous engagement in both programmes. As screening services recover, it will be important to monitor participation and to ensure people feel safe to attend.",oncology,fuzzy,100,98 medRxiv,10.1101/2021.07.19.21260782,2021-07-22,https://medrxiv.org/cgi/content/short/2021.07.19.21260782,Does COVID-19 vaccination improve mental health? A difference-in-difference analysis of the UnderstandingCoronavirus in America study,Jonathan Koltai; Julia Raifman; Jacob Bor; Martin McKee; David Stuckler,University of New Hampshire; Boston University; Boston University; London School of Hygiene and Tropical Medicine; Bocconi University,"BackgroundMental health problems increased during the COVID-19 pandemic. Knowledge that one is less at risk after being vaccinated may alleviate distress, but this hypothesis remains unexplored. Here we test whether psychological distress declined in those vaccinated against COVID-19 in the US and whether changes in perceived risk mediated any association. MethodsA nationally-representative cohort of U.S. adults (N=5,792) in the Understanding America Study were interviewed every two weeks from March 2020 to June 2021 (28 waves). Difference-in-difference regression tested whether getting vaccinated reduced distress (PHQ-4 scores), with mediation analysis used to identify potential mechanisms, including perceived risks of infection, hospitalization, and death. @@ -2836,13 +2785,6 @@ MethodParticipants were recruited into Virus Watch starting in June 2020. Weekly ResultsWe analysed the daily travel distance of 228 vaccinated adults. Between 157 days prior to vaccination until the day before vaccination, the median daily travel distance travelled was 8.9km (IQR: 3.50km, 24.17km). Between the day of vaccination and 100 days after vaccination, the median daily travel distance travelled was 10.30km (IQR: 4.11, 27.53km). Between 157 days prior to vaccination and the vaccination date, there was a daily median decrease in mobility of 40m (95%CI: -51m, -31m, p-value <0.001) per day. After the removal of outlier data, and between the vaccination date and 99 days after vaccination, there was a median daily increase in movement of 45.0m (95%CI: 25m, 65m, p-value = <0.001). Restricting the analysis to the 3rd national lockdown (4th of January 2021 to the 5th of April 2021), we found a median daily movement increase of 9m (95%CI: -25m, 45m, p = 0.57) in the 30 days prior to vaccination and the vaccination date, and a median daily movement increase of 10m (95%CI: -60m, 94m, p-value = 0.69) in the 30 days after vaccination. ConclusionsOur study demonstrates the feasibility of collecting high volume geolocation data as part of research projects, and the utility of these for understanding public health issues. Our results are consistent with both an increase and decrease in movement after vaccination and suggest that, amongst Virus Watch participants, any changes in movement distances post-vaccination are small.",public and global health,fuzzy,100,100 -medRxiv,10.1101/2021.06.21.21259104,2021-06-28,https://medrxiv.org/cgi/content/short/2021.06.21.21259104,Models of COVID-19 vaccine prioritisation: a systematic literature search and narrative review,Nuru Saadi; Y-Ling Chi; Srobana Ghosh; Rosalind M Eggo; Ciara McCarthy; Matthew Quaife; Jeanette Dawa; Mark Jit; Anna Vassall,"London School of Hygiene and Tropical Medicine; International Decision Support Inititative, Center for Global Health and Development; International Decision Support Inititative, Center for Global Health and Development; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine; Washington State University - Global Health Program, Nairobi, Kenya. Center for Epidemiological Modelling and Analysis, University of Nairobi, Nairobi, Kenya; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine","BackgroundHow best to prioritise COVID-19 vaccination within and between countries has been a public health and an ethical challenge for decision-makers globally. We systematically reviewed epidemiological and economic modelling evidence on population priority groups to minimise COVID-19 mortality, transmission and morbidity outcomes. - -MethodsWe searched the National Institute of Health iSearch COVID-19 Portfolio (a database of peer-reviewed and pre-print articles), Econlit, the Centre for Economic Policy Research and the National Bureau of Economic Research for mathematical modelling studies evaluating the impact of prioritising COVID-19 vaccination to population target groups. We narratively synthesised the main study conclusions on prioritisation and the conditions under which the conclusions changed. - -FindingsThe search identified 1820 studies. 36 studies met the inclusion criteria and were narratively synthesised. 83% of studies described outcomes in high-income countries. We found that for countries seeking to minimise deaths, prioritising vaccination of senior adults was the optimal strategy and for countries seeking to minimise cases the young were prioritised. There were several exceptions to the main conclusion, notably reductions in deaths could be increased, if groups at high risk of both transmission and death could be further identified. Findings were also sensitive to the level of vaccine coverage. - -InterpretationThe evidence supports WHO SAGE recommendations on COVID-19 vaccine prioritisation. There is however an evidence gap on optimal prioritisation for low- and middle-income countries, studies that included an economic evaluation, and studies that explore prioritisation strategies if the aim is to reduce overall health burden including morbidity.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.06.24.21259107,2021-06-28,https://medrxiv.org/cgi/content/short/2021.06.24.21259107,SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men,Oliver Stirrup; Florencia A.T. Boshier; Cristina Venturini; Jose Guerra-Assuncao; Adela Alcolea-Medina; Angela H. Becket; Themoula Charalampous; Ana da Silva Filipe; Sharon Glaysher; Tabassum Khan; Raghavendran Kulasegara-Shylini; Beatrix Kele; Irene M. Monahan; Guy Mollett; Matthew Parker; Emanuela Pelosi; Paul Randell; Sunando Roy; Joshua F. Taylor; Sophie J. Weller; Eleri Wilson-Davies; Phillip Wade; Rachel Williams; - COG-UK HOCI Variant Substudy consortium; - The COVID-19 Genomics UK (COG-UK) consortium; Andrew J. Copas; Teresa Cutino-Moguel; Nick Freemantle; Andrew C. Hayward; Alison Holmes; Joseph Hughes; Tabitha W. Mahungu; Gaia Nebbia; David G. Partridge; Cassie F. Pope; James R. Price; Samuel C. Robson; Kordo Saeed; Thushan I. de Silva; Luke B. Snell; Emma C. Thomson; Adam A. Witney; Judith Breuer,"Institute for Global Health, University College London, London, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Centre for Clinical Infection and Diagnostics Research, Kings College London; Centre for Enzyme Innovation, University of Portsmouth, Portsmouth, UK, PO1 2DT; Centre for Clinical Infection and Diagnostics Research, Kings College London; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Portsmouth Hospitals University NHS Trust, Queen Alexandra Hospital, Portsmouth, UK, PO6 3LY; Division of Infection, The Royal London Hospital, Barts Health; Division of Infection, The Royal London Hospital, Barts Health; Division of Infection, The Royal London Hospital, Barts Health; Institute for Infection and Immunity, St Georges University of London, Cranmer Terrace, London, SW17 0RE; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK; Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK; Department of Infection and Immunity, North West London Pathology, London, UK; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; Department of Microbiology, South West London Pathology, Jenner Wing, St. Georges Hospital, Blackshaw Road, London, SW17 0QT; Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom; Southampton Specialist Virology Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield; Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom; -; -; Institute for Global Health, University College London, London, UK; Division of Infection, The Royal London Hospital, Barts Health; Institute for Clinical Trials and Methodology, University College London; Institute of Epidemiology and Health Care, UCL; Department of Infectious Disease, Faculty of Medicine, Imperial College London; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom; Department of Infectious Diseases, Guys and St Thomas Hospital NHS Foundation Trust, London; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield; Institute for Infection and Immunity, St Georges University of London; Imperial College Healthcare NHS Trust, London, UK; Centre for Enzyme Innovation, University of Portsmouth; Microbiology Innovation and Research Unit (MIRU), Department of Microbiology, University Hospital Southampton NHS Foundation Trust, Tremona Road, Southampton, U; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield; Department of Infectious Diseases, Guys and St Thomas Hospital NHS Foundation Trust, London; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; Institute for Infection and Immunity, St Georges University of London, Cranmer Terrace, London, SW17 0RE; Department of Infection, Immunity and Inflammation, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom","BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage B.1.1.7 has been associated with an increased rate of transmission and disease severity among subjects testing positive in the community. Its impact on hospitalised patients is less well documented. MethodsWe collected viral sequences and clinical data of patients admitted with SARS-CoV-2 and hospital-onset COVID-19 infections (HOCIs), sampled 16/11/2020 - 10/01/2021, from eight hospitals participating in the COG-UK-HOCI study. Associations between the variant and the outcomes of all-cause mortality and intensive therapy unit (ITU) admission were evaluated using mixed effects Cox models adjusted by age, sex, comorbidities, care home residence, pregnancy and ethnicity. @@ -2941,6 +2883,15 @@ Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed Added value of this studyImmune interference and safety are always a concern when two vaccines are administered at the same time. This is the first study to demonstrate the safety and immunogenicity profile and clinical vaccine efficacy of a COVID-19 vaccine when co-administered with a seasonal influenza vaccine. Implications of all the available evidenceThis study provides much needed information to help guide national immunisation policy decision making on the critical issue of concomitant use of COVID-19 vaccines with influenza vaccines.",allergy and immunology,fuzzy,95,100 +medRxiv,10.1101/2021.06.08.21258533,2021-06-12,https://medrxiv.org/cgi/content/short/2021.06.08.21258533,The impact of co-circulating pathogens on SARS-CoV-2/COVID-19 surveillance. How concurrent epidemics may decrease true SARS-CoV-2 percent positivity.,Aleksandra Kovacevic; Rosalind M Eggo; Marc Baguelin; Matthieu Domenech de Cellès; Lulla Opatowski,Institut Pasteur; London School of Hygiene & Tropical Medicine; Imperial College London; Max Planck Institute for Infection Biology; Univ Versailles Saint Quentin / Institut Pasteur / Inserm,"BackgroundCirculation of non-SARS-CoV-2 respiratory viruses during the COVID-19 pandemic may alter quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures. Here, we assess the impact of an increased circulation of other respiratory viruses on the monitoring of positivity rates of SARS-CoV-2 and interpretation of surveillance data. + +MethodsUsing a multi-pathogen Susceptible-Exposed-Infectious-Recovered (SEIR) transmission model formalizing co-circulation of SARS-CoV-2 and another respiratory we assess how an outbreak of secondary virus may inflate the number of SARS-CoV-2 tests and affect the interpretation of COVID-19 surveillance data. Using simulation, we assess to what extent the use of multiplex PCR tests on a subsample of symptomatic individuals can support correction of the observed SARS-CoV-2 percent positive during other virus outbreaks and improve surveillance quality. + +ResultsModel simulations demonstrated that a non-SARS-CoV-2 epidemic creates an artificial decrease in the observed percent positivity of SARS-CoV-2, with stronger effect during the growth phase, until the peak is reached. We estimate that performing one multiplex test for every 1,000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percent positive. + +ConclusionsThis study highlights that co-circulating respiratory viruses can disrupt SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance. + +SummaryCOVID-19 surveillance indicators may be impacted by increased co-circulation of other respiratory viruses delaying control measure implementation. Continued surveillance through multiplex PCR testing in a subsample of the symptomatic population may play a role in fixing this problem.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.06.08.21258546,2021-06-12,https://medrxiv.org/cgi/content/short/2021.06.08.21258546,Inequalities in healthcare disruptions during the Covid-19 pandemic: Evidence from 12 UK population-based longitudinal studies,Jane Maddock; Sam Parsons; Giorgio Di Gessa; Michael J Green; Ellen J Thompson; Anna J Stevenson; Alex S.F. Kwong; Eoin McElroy; Gillian Santorelli; Richard J Silverwood; Gabriella Captur; Nish Chaturvedi; Claire J Steves; Andrew Steptoe; Praveetha Patalay; George B Ploubidis; Srinivasa Vittal Katikireddi,University College London; University College London; University College London; University of Glasgow; King's College London; University of Edinburgh; University of Bristol; University of Leicester; Bradford Institute for Health Research; University College London; University College London; University College London; King's College London; University College London; University College London; University College London; University of Glasgow,"BackgroundHealth systems worldwide have faced major disruptions due to COVID-19 which could exacerbate health inequalities. The UK National Health Service (NHS) provides free healthcare and prioritises equity of delivery, but the pandemic may be hindering the achievement of these goals. We investigated associations between multiple social characteristics (sex, age, occupational social class, education and ethnicity) and self-reported healthcare disruptions in over 65,000 participants across twelve UK longitudinal studies. MethodsParticipants reported disruptions from March 2020 up to late January 2021. Associations between social characteristics and three types of self-reported healthcare disruption (medication access, procedures, appointments) and a composite of any of these were assessed in logistic regression models, adjusting for age, sex and ethnicity where relevant. Random-effects meta-analysis was conducted to obtain pooled estimates. @@ -3010,9 +2961,6 @@ Research in contextO_ST_ABSPrevious evidenceC_ST_ABSLong COVID and post-COVID sy Added value of this studyFor the first time, we report the baseline characteristics, investigation and outcomes of initial assessment of all eligible patients in a dedicated multi-professional post-COVID service, including 547 post-hospitalisation, 566 non-hospitalised and 212 patients discharged from emergency department. Despite relatively low comorbidity and risk factor burden in non-hospitalised patients, we show that both non-hospitalised and hospitalised patients presenting with persistent symptoms after SARS-CoV2 infection have high rates of functional impairment, specialist referral and rehabilitation, even 6-12 months after the acute infection. These real-world data will inform models of care during and beyond the pandemic. Implications of all the available evidenceThe significant, long-lasting health and social consequences of SARS-CoV-2 infection are not confined to those who required hospitalisation. As with other long-term conditions, care of patients experiencing Long COVID or specific end-organ effects require consistent, integrated, patient-centred approaches to investigation and management. At public health and policy level, burden of post-COVID morbidity demands renewed focus on effective infection suppression for all age groups.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.05.27.21257032,2021-05-31,https://medrxiv.org/cgi/content/short/2021.05.27.21257032,How immunity from and interaction with seasonal coronaviruses can shape SARS-CoV-2 epidemiology,Naomi R Waterlow; Edwin Van Leeuwen; Nicholas G Davies; - CMMID COVID-19 working group; Stefan Flasche; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; Public Health England; London School of Hygiene and Tropical Medicine; ; LSHTM; London School of Hygiene & Tropical Medicine,"We hypothesised that cross-protection from seasonal epidemics of human coronaviruses (HCoVs) could have affected SARS-CoV-2 transmission, including generating reduced susceptibility in children. To determine what the pre-pandemic distribution of immunity to HCoVs was, we fitted a mathematical model to 6 years of seasonal coronavirus surveillance data from England and Wales. We estimated a duration of immunity to seasonal HCoVs of 7.3 years (95%CI 6.8 - 7.9) and show that, while cross-protection between HCoV and SARS-CoV-2 may contribute to the age distribution, it is insufficient to explain the age pattern of SARS-CoV-2 infections in the first wave of the pandemic in England and Wales. Projections from our model illustrate how different strengths of cross-protection between circulating coronaviruses could determine the frequency and magnitude of SARS-CoV-2 epidemics over the coming decade, as well as the potential impact of cross-protection on future seasonal coronavirus transmission. - -Significance statementCross-protection from seasonal epidemics of human coronaviruses (HCoVs) has been hypothesised to contribute to the relative sparing of children during the early phase of the pandemic. Testing this relies on understanding the pre-pandemic age-distribution of recent HCoV infections, but little is known about their dynamics. Using England and Wales as a case study, we use a transmission model to estimate the duration of immunity to seasonal coronaviruses, and show how cross-protection could have affected the age distribution of susceptibility during the first wave, and alter SARS-CoV-2 transmission patterns over the coming decade.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.05.22.21257633,2021-05-26,https://medrxiv.org/cgi/content/short/2021.05.22.21257633,Genomic reconstruction of the SARS-CoV-2 epidemic across England from September 2020 to May 2021,Harald S. Vohringer; Theo Sanderson; Matthew Sinnott; Nicola De Maio; Thuy Nguyen; Richard Goater; Frank Schwach; Ian Harrison; Joel Hellewell; Cristina Ariani; Sonia Goncalves; David Jackson; Ian Johnston; Alexander W. Jung; Callum Saint; John Sillitoe; Maria Suciu; Nick Goldman; Jasmina Panovska-Griffiths; - The Wellcome Sanger Institute Covid-19 Surveillance Team; - The COVID-19 Genomics UK (COG-UK) Consortium; Ewan Birney; Erik Volz; Sebastian Funk; Dominic Kwiatkowski; Meera Chand; Inigo Martincorena; Jeffrey C. Barrett; Moritz Gerstung,"European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Current address: Joint Biosecurity Center JBC; Wellcome Sanger Institute, Hinxton, UK; The Francis Crick Institute, London, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE; Public Health England PHE; London School of Hygiene & Tropical Medicine, London, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Joint Biosecurity Center JBC, Big Data Institute, University of Oxford, UK; ; ; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; Imperial College, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Wellcome Sanger Institute, Hinxton, UK; Public Health England PHE; Wellcome Sanger Institute, Hinxton, UK; Wellcome Sanger Institute, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute EMBL-EBI, Hinxton, UK; German Cancer Research Centre dkfz, Heidelberg, Germany","The evolution of the SARS-CoV-2 pandemic continuously produces new variants, which warrant timely epidemiological characterisation. Here we use the dense genomic surveillance generated by the COVID-19 Genomics UK Consortium to reconstruct the dynamics of 71 different lineages in each of 315 English local authorities between September 2020 and June 2021. This analysis reveals a series of sub-epidemics that peaked in the early autumn of 2020, followed by a jump in transmissibility of the B.1.1.7/Alpha lineage. Alpha grew when other lineages declined during the second national lockdown and regionally tiered restrictions between November and December 2020. A third more stringent national lockdown suppressed Alpha and eliminated nearly all other lineages in early 2021. However, a series of variants (mostly containing the spike E484K mutation) defied these trends and persisted at moderately increasing proportions. Accounting for sustained introductions, however, indicates that their transmissibility is unlikely to have exceeded that of Alpha. Finally, B.1.617.2/Delta was repeatedly introduced to England and grew rapidly in the early summer of 2021, constituting approximately 98% of sampled SARS-CoV-2 genomes on June 26.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.05.24.21257738,2021-05-26,https://medrxiv.org/cgi/content/short/2021.05.24.21257738,"Post-vaccination SARS-CoV-2 infection: risk factors and illness profile in a prospective, observational community-based case-control study",Michela Antonelli; Rose S Penfold; Jordi Merino; Carole H Sudre; Erika Molteni; Sarah Berry; Liane S Canas; Mark S Graham; Kerstin Klaser; Marc Modat; Benjamin Murray; Eric Kerfoot; Liyuan Chen; Jie Deng; Marc F Österdahl; Nathan J Cheetham; David Alden Drew; Long Alden Nguyen; Joan Capdeila; Christina Hu; Somesh Selvachandran; Lorenzo Polidori; Anna May; Jonathan Wolf; Andrew T Chan; Alexander Hammers; Emma Duncan; Timothy Spector; Sebastien Ourselin; Claire J Steves,"King's College London; King's College London; Department of Medicine, Harvard Medical School, Boston, MA, USA; Centre for Medical Image Computing, University College London, London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; King's College London; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, UK; Massachusetts General Hospital; Massachusetts General Hospital and Harvard Medical School; Zoe Global, London, UK; Zoe Global, London, UK; Zoe Global, London, UK; Lorenzo Polidori; Zoe Global, London, UK; Zoe Global, London, UK; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, UK; King's College London; School of Biomedical Engineering & Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, King's College London, UK","BackgroundCOVID-19 vaccines show excellent efficacy in clinical trials and real-world data, but some people still contract SARS-CoV-2 despite vaccination. This study sought to identify risk factors associated with SARS-CoV-2 infection post-vaccination and describe characteristics of post-vaccination illness. @@ -3029,9 +2977,6 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSTo identify existin Added value of this studyThis is the first observational study investigating characteristics of and factors associated with SARS-CoV-2 infection after COVID-19 vaccination. We found that vaccinated individuals with frailty had higher rates of infection after vaccination than those without. Adverse determinants of health such as increased social deprivation, obesity, or a less healthy diet were associated with higher likelihood of infection after vaccination. In comparison with unvaccinated individuals, those with post-vaccination infection had fewer symptoms of COVID-19, and more were entirely asymptomatic. Fewer vaccinated individuals experienced five or more symptoms, required hospitalisation, and, in the older adult group, fewer had prolonged illness duration (symptoms lasting longer than 28 days). Implications of all the available evidenceSome individuals still contract COVID-19 after vaccination and our data suggest that frail older adults and those living in more deprived areas are at higher risk. However, in most individuals illness appears less severe, with reduced need for hospitalisation and lower risk of prolonged illness duration. Our results are relevant for health policy post-vaccination and highlight the need to prioritise those most at risk, whilst also emphasising the balance between the importance of personal protective measures versus adverse effects from ongoing social restrictions. Strategies such as timely prioritisation of booster vaccination and optimised infection control could be considered for at-risk groups. Research is also needed on how to enhance the immune response to vaccination in those at higher risk.",epidemiology,fuzzy,94,100 -medRxiv,10.1101/2021.05.25.21257505,2021-05-25,https://medrxiv.org/cgi/content/short/2021.05.25.21257505,Plitidepsin has a positive therapeutic index in adult patients with COVID-19 requiring hospitalization.,Jose F. Varona; Pedro Landete; Jose A Lopez-Martin; Vicente Estrada; Roger Paredes; Pablo Guisado-Vasco; Lucia Fernandez de Orueta; Miguel Torralba; Jesus Fortun; Roberto Vates; Jose Barberan; Bonaventura Clotet; Julio Ancochea; Daniel Carnevali; Noemi Cabello; Lourdes Porras; Paloma Gijon; Alfonso Monereo; Daniel Abad; Sonia Zuñiga; Isabel Sola; Jordi Rodon; Nuria Izquierdo-Useros; Salvador Fudio; Maria Jose Pontes; Beatriz de Rivas; Patricia Giron de Velasco; Belen Sopesen; Antonio Nieto; Javier Gomez; Pablo Aviles; Rubin Lubomirov; Kris M White; Romel Rosales; Soner Yildiz; Ann-Kathrin Reuschl; Lucy G. Thorne; Clare Jolly; Greg J. Towers; Lorena Zuliani-Alvarez; Mehdi Bouhaddou; Kirsten Obernier; Luis Enjuanes; Jose M Fernandez-Sousa; - Plitidepsin COVID Study Group; Nevan J Krogan; Jose M. Jimeno; Adolfo Garcia-Sastre,"Departamento de Medicina Interna, Hospital Universitario HM Monteprincipe, HM Hospitales, Madrid, Spain. Facultad de Medicina, Universidad San Pablo-CEU, Madrid; Hospital Universitario de La Princesa. Madrid, Spain. Universidad Autonoma de Madrid, Madrid, Spain.; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain.; Hospital Clinico San Carlos, Madrid, Spain. Universidad Complutense de Madrid, Madrid, Spain.; IrsiCaixa AIDS Research Institute; Internal Medicine Department, Hospital Universitario Quironsalud, Madrid, Spain. Universidad Europea, Madrid, Spain.; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain. European University of Madrid, Madrid, Spain.; Internal Medicine, Guadalajara University Hospital, Guadalajara, Spain. University of Alcala, Madrid, Spain.; Hospital Universitario Ramon y Cajal, Madrid, Spain.; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain.; Hospital Universitario HM Monteprincipe, Madrid, Spain. Facultad de Medicina San Pablo CEU, Madrid, Spain.; Head of Infectious Diseases Department, Director of the Research Lab, IrsiCaixa, Barcelone, Spain. Professor of the UAB and the UVIC-UCC, Barcelone, Spain.; Hospital Universitario La Princesa, Madrid, Spain. Centro de Investigacion en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII; Hospital Universitario Quironsalud, Madrid, Spain Universidad Europea, Madrid, Spain.; Infectious Diseases Department, San Carlos University Hospital. Madrid Spain.; Internal Medicine, Hospital General de Ciudad Real, Ciudad Real, Spain.; Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Marañon, Instituto de Investigacion Sanitaria Gregorio Marañon; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain. European University of Madrid, Madrid, Spain.; Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNBCSIC), Madrid, Spain.; Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNBCSIC), Madrid, Spain.; IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, Bellaterra, Spain; IrsiCaixa AIDS Research Institute, 08916, Badalona, Spain. Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, 08916, Badalona, Spain.; PharmaMar - Clinical Pharmacology Unit. Colmenar Viejo, Madrid, Spain; PharmaMar - Medical Affairs Unit. Colmenar Viejo. Madrid, Spain.; PharmaMar - Medical Affairs Unit. Colmenar Viejo, Madrid, Spain.; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain.; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain. Sylentis, S.A.U., Tres Cantos, Madrid, Spain. Biocross, S.L., Valladolid, Spain.; PharmaMar - Statistics Unit. Colmenar Viejo, Madrid, Spain.; PharmaMar - Statistics Unit. Colmenar Viejo, Madrid, Spain.; PharmaMar - Preclinical Unit. Colmenar Viejo, Madrid, Spain; PharmaMar - Clinical Pharmacology Unit. Colmenar Viejo, Madrid, Spain; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom.; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom.; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom.; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G; Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain.; PharmaMar, S.A., Colmenar Viejo, Madrid, Spain.; ; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. ; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain.; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ","Plitidepsin is a marine-derived cyclic-peptide that inhibits SARS-CoV-2 replication at low nanomolar concentrations by the targeting of host protein eEF1A (eukaryotic translation-elongation-factor-1A). We evaluated a model of intervention with plitidepsin in hospitalized COVID-19 adult patients where three doses were assessed (1.5, 2 and 2.5 mg/day for 3 days, as a 90-minute intravenous infusion) in 45 patients (15 per dose-cohort). Treatment was well tolerated, with only two Grade 3 treatment-related adverse events observed (hypersensitivity and diarrhea). The discharge rates by Days 8 and 15 were 56.8% and 81.8%, respectively, with data sustaining dose-effect. A mean 4.2 log10 viral load reduction was attained by Day 15. Improvement in inflammation markers was also noted in a seemingly dose-dependent manner. These results suggest that plitidepsin impacts the outcome of patients with COVID-19. - -One-Sentence SummaryPlitidepsin, an inhibitor of SARS-Cov-2 in vitro, is safe and positively influences the outcome of patients hospitalized with COVID-19.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.05.18.21257396,2021-05-23,https://medrxiv.org/cgi/content/short/2021.05.18.21257396,A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program,Anurag Verma; Noah L. Tsao; Lauren O. Thomann; Yuk-Lam Ho; Sudha K. Iyengar; Shiuh-Wen Luoh; Rotonya Carr; Dana C. Crawford; Jimmy T. Efird; Giulio Genovese; Adriana Hung; Kerry L. Ivey; Michael G. Levin; Julie Lynch; Pradeep Natarajan; Saiju Pyarajan; Alexander Bick; Lauren Costa; Giulio Genovese; Richard Hauger; Ravi Madduri; Gita A. Pathak; Renato Polimanti; Benjamin F. Voight; Marijana Vujkovic; Maryam Zekavat; Hongyu Zhao; Marylyn Ritchie; Kyong-Mi Chang; Kelly Cho; Juan P Casas; Philip S Tsao; J. Michael Gaziano; Christopher O?Donnell; Scott M. Damrauer; Katherine P. Liao,"Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi; VA Boston Healthcare System, Boston, Massachusetts, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Departments of Population and Quantitative Health Sciences, Ophthalmology and Visual Sciences and Genetics and Genome Sciences, Case Western Reserve University,; VA Portland Health Care System, Portland OR, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph; Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA; Cooperative Studies Program Epidemiology Center, Health Services Research and Development, DVAHCS (Duke University Affiliate), Durham, North Carolina, USA.; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.; Tennessee Valley Healthcare System (Nashville VA) , Nashville, Tennessee, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah, USA.; Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, USA.; VA Boston Healthcare System, Boston, Massachusetts, USA;Harvard Medical School, Boston, Massachusetts, USA; VA Boston Healthcare System, Boston, Massachusetts, USA;Vanderbilt University, Nashville, Tennessee, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.; Department of Psychiatry, University of California, San Diego, La Jolla, CA; Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, ; University of Chicago Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois, USA;Data Science and Learning Division, Arg; Department of Psychiatry, Yale School of Medicine, Connecticut, USA; Department of Psychiatry, Yale School of Medicine, Connecticut, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Ph; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Ph; VA Boston Healthcare System, Boston, Massachusetts, USA; VA Connecticut Healthcare System, West Haven, CT, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; VA Palo Alto Health Care System, Palo Alto, California, USA; Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, USA; VA Boston Healthcare System, Boston, Massachusetts, USA; Corporal Michael Crescenz VA Medical Center, Philadelphia, Philadelphia, USA;Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Phi; VA Boston Healthcare System, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Brigham and Women's Hospital, Boston, Massachusetts","The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n=35) or hospitalization (n=42) due to severe COVID-19 using genome-wide association summary from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828= 53 and nrs505922=59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p=1.32 x 10-199), and thrombosis ORrs505922 1.33, p=2.2 x10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p=4.12 x 10-191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p=2.26x 10-12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p=6.48 x10-23, lupus OR 0.84, p=3.97 x 10-06. PheWAS stratified by genetic ancestry demonstrated differences in genotype-phenotype associations across ancestry. LMNA (rs581342) associated with neutropenia OR 1.29 p=4.1 x 10-13 among Veterans of African ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.",genetic and genomic medicine,fuzzy,91,92 medRxiv,10.1101/2021.05.13.21257161,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.13.21257161,"Occupation, Work-Related Contact, and SARS-CoV-2 Anti-Nucleocapsid Serological Status: Findings from the Virus Watch prospective cohort study",Sarah Beale; Parth Patel; Alison Rodger; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan MD Navaratnam; Vincent Nguyen; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative,University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ,"BackgroundWorkers differ in their risk of acquiring SARS-CoV-2 infection according to their occupation; however, few studies have been able to control for multiple confounders or investigate the work-related factors that drive differences in occupational risk. Using data from the Virus Watch community cohort study in England and Wales, we set out to estimate the total effect of occupation on SARS-CoV-2 serological status, whether this is mediated by frequency of close contact within the workplace, and how exposure to poorly ventilated workplaces varied across occupations. @@ -3047,6 +2992,15 @@ MethodsVirus Watch is a large community cohort with prospective daily recording FindingsWe included results from 8213 swabbed illnesses, 944 of which tested positive for SARS-CoV-2. All symptoms were more common in test positive than test negative illnesses and symptoms were also more severe and of longer duration. Common symptoms such as cough, headache, fatigue, muscle aches, and loss of appetite occurred early in the course of illness but were also very common in test-negative illnesses. In contrast, high temperature and loss of or altered sense of smell or taste were less frequently identified in swab positive illnesses but were markedly more common than in swab negative illnesses. The current UK definition had a sensitivity and specificity of 81% and 47% respectively for symptomatic COVID-19 compared to 93% and 26% for the broader definition. On average, cases met the broader case definition 0.3 days earlier than the current definition. 1.7-fold more illnesses met the broader definition than the current case definition. InterpretationCOVID-19 is difficult to distinguish from other respiratory infections and common ailments on the basis of symptoms. Broadening the list of symptoms used to encourage engagement with TTI could moderately increase the number of infections identified and shorten delays to isolation, but with a large increase in the number of tests needed and the number of unwell individuals and contacts who are advised to self-isolate whilst awaiting results, and subsequently test negative for SARS-CoV-2.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.05.18.21257267,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.18.21257267,"Colchicine in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial",Peter W Horby; Mark Campbell; Enti Spata; Jonathan R Emberson; Natalie Staplin; Guilherme Pessoa-Amorim; Leon Peto; Martin Wiselka; Laura Wiffen; Simon Tiberi; Ben Caplin; Caroline Wroe; Christopher Green; Paul Hine; Benjamin Prudon; Tina George; Andrew Wight; J Kenneth Baillie; Buddha Basnyat; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Faust; Raph L Hamers; Thomas Jaki; Edmund Juszczak; Katie Jeffery; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray,"Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and International Severe Acute Res; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and Nuffield Department of Populat; Department of Infectious Diseases, University Hospital Leicester, Leicester, United Kingdom; Portsmouth Hospitals University NHS Foundation Trust, Portsmouth, United Kingdom; Department of Infection, Barts Health NHS Trust, London, United Kingdom; Department of Renal Medicine, University College London, London, United Kingdom and Royal Free London NHS Trust, London, United Kingdom; James Cook University Hospital, Middlesbrough, United Kingdom; University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom; Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom; North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom; Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom; Wirral University Teaching Hospital NHS Foundation Trust, Birkenhead, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Oxford University Clinical Research Unit -Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Course Sciences, King?s College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia and Faculty of Medicine, University of Indonesia, Jakarta, Indonesia and Centre for Tropical Medicine ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom and MRC Biostatistics Unit, University of Cambridge, Cambridge, United; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom and Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Notting; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un","BackgroundColchicine has been proposed as a treatment for COVID-19 on the basis of its anti-inflammatory actions. + +MethodsIn this randomised, controlled, open-label trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care alone or usual standard of care plus colchicine twice daily for 10 days or until discharge (or one of the other treatment arms) using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). + +FindingsBetween 27 November 2020 and 4 March 2021, 5610 patients were randomly allocated to receive colchicine and 5730 patients to receive usual care alone. Overall, 1173 (21%) patients allocated to colchicine and 1190 (21%) patients allocated to usual care died within 28 days (rate ratio 1.01; 95% confidence interval [CI] 0.93-1.10; p=0.77). Consistent results were seen in all pre-specified subgroups of patients. There was no significant difference in duration of hospitalisation (median 10 days vs. 10 days) or the proportion of patients discharged from hospital alive within 28 days (70% vs. 70%; rate ratio 0.98; 95% CI 0.94-1.03; p=0.44). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (25% vs. 25%; risk ratio 1.02; 95% CI 0.96-1.09; p=0.47). + +InterpretationIn adults hospitalised with COVID-19, colchicine was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death. + +FundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056). Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.05.17.21256818,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.17.21256818,Local prevalence of transmissible SARS-CoV-2 infection : an integrative causal model for debiasing fine-scale targeted testing data,George Nicholson; Brieuc CL Lehmann; Tullia Padellini; Koen B Pouwels; Radka Jersakova; James Lomax; Ruairidh E King; Ann-Marie Mallon; Peter J Diggle; Sylvia Richardson; Marta Blangiardo; Chris Holmes,University of Oxford; University of Oxford; Imperial College London; University of Oxford; The Alan Turing Institute; The Alan Turing Institute; MRC Harwell Institute; MRC Harwell Institute; Lancaster University; MRC Biostatistics Unit; Imperial College London; University of Oxford,"Targeted surveillance testing schemes for SARS-CoV-2 focus on certain subsets of the population, such as individuals experiencing one or more of a prescribed list of symptoms. These schemes have routinely been used to monitor the spread of SARS-CoV-2 in countries across the world. The number of positive tests in a given region can provide local insights into important epidemiological parameters, such as prevalence and effective reproduction number. Moreover, targeted testing data has been used inform the deployment of localised non-pharmaceutical interventions. However, surveillance schemes typically suffer from ascertainment bias; the individuals who are tested are not necessarily representative of the wider population of interest. Here, we show that data from randomised testing schemes, such as the REACT study in the UK, can be used to debias fine-scale targeted testing data in order to provide accurate localised estimates of the number of infectious individuals. We develop a novel, integrative causal framework that explicitly models the process underlying the selection of individuals for targeted testing. The output from our model can readily be incorporated into longitudinal analyses to provide local estimates of the reproduction number. We apply our model to characterise the size of the infectious population in England between June 2020 and January 2021. Our local estimates of the effective reproduction number are predictive of future changes in positive case numbers. We also capture local increases in both prevalence and effective reproductive number in the South East from November 2020 to December 2020, reflecting the spread of the Kent variant. Our results illustrate the complementary roles of randomised and targeted testing schemes. Preparations for future epidemics should ensure the rapid deployment of both types of schemes to accurately monitor the spread of emerging and ongoing infectious diseases.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.05.15.21257017,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.15.21257017,Extended interval BNT162b2 vaccination enhances peak antibody generation in older people,Helen M Parry; Rachel Bruton; Christine Stephens; Kevin Brown; Gayatri Amirthalingam; Bassam Hallis; Ashley Otter; Jianmin Zuo; Paul Moss,"University of Birmingham, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; National infection Service, Public Health England, Colindale, London NW9 5EQ, UK; National infection Service, Public Health England, Colindale, London NW9 5EQ, UK; National infection Service, Public Health England, Porton Down, Salisbury, SP4 OJG, UK; National infection Service, Public Health England, Porton Down, Salisbury, SP4 OJG, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK; Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham. B15 2TT, UK","ObjectivesTo assess the relative immunogenicity of standard or extended interval BNT162b2 vaccination. @@ -3168,6 +3122,9 @@ MethodsThe Virus Watch study is a household community cohort of acute respirator ResultsThe proportion of participants with a positive SARS-CoV-2 PCR result was highest in the overcrowded group (6.6%; 73/1,102) and lowest in the under-occupied group (2.9%; 682/23,219). In a mixed effects logistic regression model that included age, sex, ethnicity, household income and geographical region, we found strong evidence of an increased odds of having a positive PCR SARS-CoV-2 antigen result (Odds Ratio 3.72; 95% CI: 1.92, 7.13; p-value < 0.001) and increased odds of having a positive SARS-CoV-2 antibody result in individuals living in overcrowded houses (2.96; 95% CI: 1.13, 7.74; p-value =0.027) compared to people living in under-occupied houses. The proportion of variation at the household level was 9.91% and 9.97% in the PCR and antibody models respectively. DiscussionPublic health interventions to prevent and stop the spread of SARS-CoV-2 should consider the much greater risk of infection for people living in overcrowded households and pay greater attention to reducing household transmission. There is an urgent need to better recognise housing as a leading determinant of health in the context of a pandemic and beyond.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.05.05.21256668,2021-05-09,https://medrxiv.org/cgi/content/short/2021.05.05.21256668,COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland,Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz,The University of Edinburgh; The University of Edinburgh; The University of Edinburgh,"The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively. + +Clinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.",health informatics,fuzzy,100,100 medRxiv,10.1101/2021.05.05.21256649,2021-05-08,https://medrxiv.org/cgi/content/short/2021.05.05.21256649,Illness duration and symptom profile in a large cohort of symptomatic UK school-aged children tested for SARS-CoV-2,Erika Molteni; Carole Helene Sudre; Liane Santos Canas; Sunil S Bhopal; Robert C Hughes; Michela S Antonelli; Benjamin Murray; Kerstin Klaser; Eric Kerfoot; Liyuan Chen; Jie Deng; Christina Hu; Somesh Selvachandran; Kenneth Read; Joan Capdevila Pujol; Alexander Hammers; Timothy Spector; Sebastien Ourselin; Claire J Steves; Marc Modat; Michael Absoud; Emma L Duncan,King's College London; University College London; King's College London; King's College London; Newcastle University; London School of Hygiene & Tropical Medicine; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; ZOE Global Ltd; Zoe Global Ltd; ZOE Global Ltd; Zoe Global Ltd; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Evelina Hospital London; King's College London,"BackgroundIn children, SARS-CoV-2 is usually asymptomatic or causes a mild illness of short duration. Persistent illness has been reported; however, its prevalence and characteristics are unclear. We aimed to determine illness duration and characteristics in symptomatic UK school-aged children tested for SARS-CoV-2 using data from the COVID Symptom Study, the largest UK citizen participatory epidemiological study to date. MethodsData from 258,790 children aged 5-17 years were reported by an adult proxy between 24 March 2020 and 22 February 2021. Illness duration and symptom profiles were analysed for all children testing positive for SARS-CoV-2 for whom illness duration could be determined, considered overall and within younger (5-11 years) and older (12-17 years) groups. Data from symptomatic children testing negative for SARS-CoV-2, matched 1:1 for age, gender, and week of testing, were also assessed. @@ -3217,6 +3174,13 @@ What this study addsO_LIIn 70,464 people with atrial fibrillation, at the thresh C_LIO_LIThis might be explained by OACs preventing severe COVID-19 outcomes, or more cautious behaviours and environmental factors reducing the risk of SARS-CoV-2 infection in those taking OACs. C_LIO_LIIn 372,746 people with non-valvular atrial fibrillation, there was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin compared with DOACs. C_LI",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.04.26.21255732,2021-04-28,https://medrxiv.org/cgi/content/short/2021.04.26.21255732,Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales,Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative,"University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ","BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation. + +MethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period. + +ResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods. + +ConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.04.24.21255968,2021-04-27,https://medrxiv.org/cgi/content/short/2021.04.24.21255968,MORTALITY OF CARE HOME RESIDENTS AND COMMUNITY-DWELLING CONTROLS DURING THE COVID-19 PANDEMIC IN 2020: MATCHED COHORT STUDY,Martin C Gulliford; A Toby Prevost; Andrew Clegg; Emma C Rezel-Potts,King's College London; King's College London; University of Leeds; King's College London,"ObjectiveTo estimate mortality of care home (CH) residents, and matched community-dwelling controls, during the Covid-19 pandemic from primary care electronic health records. DesignMatched cohort study @@ -3277,7 +3241,6 @@ ResultsOdds of new SARS-CoV-2 infection were reduced 65% (95% CI 60 to 70%; P<0. ConclusionVaccination with a single dose of Oxford-AstraZeneca or Pfizer-BioNTech vaccines, or two doses of Pfizer-BioNTech, significantly reduced new SARS-CoV-2 infections in this large community surveillance study. Greater reductions in symptomatic infections and/or infections with a higher viral burden are reflected in reduced rates of hospitalisations/deaths, but highlight the potential for limited ongoing transmission from asymptomatic infections in vaccinated individuals. RegistrationThe study is registered with the ISRCTN Registry, ISRCTN21086382.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.04.12.21255275,2021-04-19,https://medrxiv.org/cgi/content/short/2021.04.12.21255275,Children develop strong and sustained cross-reactive immune responses against spike protein following SARS-CoV-2 infection,Alexander C Dowell; Megan S. Butler; Elizabeth Jinks; Gokhan Tut; Tara Lancaster; Panagiota Sylla; Jusnara Begum; Rachel Bruton; Hayden Pearce; Kriti Verma; Nicola Logan; Grace Tyson; Eliska Spalkova; Sandra Margielewska-Davies; Graham S. Taylor; Eleni Syrimi; Frances Baawuah; Joanne Beckmann; Ifeanyichukwu Okike; Shazaad Ahmad; Joanna Garstang; Andrew Brent; Bernadette Brent; Georgina Ireland; Felicity Aiano; Zahin Amin-Chowdhury; Samuel Jones; Ray Borrow; Ezra Linley; Rafaq Azad; John Wright; Dagmar Waiblinger; Chris Davis; Emma C Thomson; Massimo Palmarini; Brian James Willett; Wendy S Barclay; John Poh; Vanessa Saliba; Gayatri Amirthalingam; Kevin Brown; Mary Ramsay; Jianmin Zuo; Paul Moss; Shamez Ladhani,"Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; University of Birmingham; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; University of Birmingham; MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61-1QH, UK; MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61-1QH, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; East London NHS Foundation Trust, 9 Allie Street, London E1 8DE, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK 4. University Hospitals of Derby and Burton NHS Foundation Trust, Uttoxeter New Road, Derby; Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9WL, UK; Birmingham Community Healthcare NHS Trust, Holt Street, Aston B7 4BN, UK; Oxford University Hospitals NHS Foundation Trust, Old Road, Oxford OX3 7HE University of Oxford, Wellington Square, Oxford OX1 2JD, UK; Oxford University Hospitals NHS Foundation Trust, Old Road, Oxford OX3 7HE; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, Manchester Royal Infirmary, Manchester, United Kingdom; Public Health England, Manchester Royal Infirmary, Manchester, United Kingdom; Bradford Teaching Hospitals NHS Foundation Trust; Bradford Teaching Hospitals NHS Foundation Trust; Bradford Teaching Hospitals NHS Foundation Trust; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; Imperial College, London; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK","SARS-CoV-2 infection is generally mild or asymptomatic in children but the biological basis for this is unclear. We studied the profile of antibody and cellular immunity in children aged 3-11 years in comparison with adults. Antibody responses against spike and receptor binding domain (RBD) were high in children and seroconversion boosted antibody responses against seasonal Beta-coronaviruses through cross-recognition of the S2 domain. Seroneutralisation assays against alpha, beta and delta SARS-CoV-2 variants demonstrated comparable neutralising activity between children and adults. T cell responses against spike were >2-fold higher in children compared to adults and displayed a TH1 cytokine profile. SARS-CoV-2 spike-specific T cells were also detected in many seronegative children, revealing pre-existing responses that were cross-reactive with seasonal Alpha and Beta-coronaviruses. Importantly, all children retained high antibody titres and cellular responses at 6 months after infection whilst relative antibody waning was seen in adults. Spike-specific responses in children also remained broadly stable beyond 12 months. Children thus distinctly generate robust, cross-reactive and sustained immune responses after SARS-CoV-2 infection with focussed specificity against spike protein. These observations demonstrate novel features of SARS-CoV-2-specific immune responses in children and may provide insight into their relative clinical protection. Furthermore, this information will help to guide the introduction of vaccination regimens in the paediatric population.",allergy and immunology,fuzzy,100,100 medRxiv,10.1101/2021.04.08.21255100,2021-04-15,https://medrxiv.org/cgi/content/short/2021.04.08.21255100,REACT-1 round 10 report: Level prevalence of SARS-CoV-2 swab-positivity in England during third national lockdown in March 2021,Steven Riley; Oliver Eales; David Haw; Caroline E. Walters; Haowei Wang; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","BackgroundIn England, hospitalisations and deaths due to SARS-CoV-2 have been falling consistently since January 2021 during the third national lockdown of the COVID-19 pandemic. The first significant relaxation of that lockdown occurred on 8 March when schools reopened. MethodsThe REal-time Assessment of Community Transmission-1 (REACT-1) study augments routine surveillance data for England by measuring swab-positivity for SARS-CoV-2 in the community. The current round, round 10, collected swabs from 11 to 30 March 2021 and is compared here to round 9, in which swabs were collected from 4 to 23 February 2021. @@ -3329,27 +3292,6 @@ ConclusionsThis study provides further evidence that a single dose of either the In those declining vaccination higher rates were seen in those living in the most deprived areas and in Black and Black British groups. There was no definitive evidence to suggest COVID-19 was transmitted as a result of vaccination hubs during vaccine the administration roll-out in NWL, and the risk of contracting COVID-19 and/or becoming hospitalised after vaccination has been demonstrated to be very low in the vaccinated population.",health informatics,fuzzy,100,100 -medRxiv,10.1101/2021.04.08.21255128,2021-04-10,https://medrxiv.org/cgi/content/short/2021.04.08.21255128,Changing patterns of sickness absence among healthcare workers in England during the COVID-19 pandemic.,Rhiannon Edge; Diana A van der Plaat; Vaughan Parsons; David Coggon; Martie J van Tongeren; Rupert Muiry; Ira Madan; Paul Cullinan,"Lancaster University; National Heart and Lung Institute (NHLI), Imperial College London; Guys and St Thomas NHS Foundation Trust; MRC Lifecourse Epidemiology Unit, University of Southampton; Centre for Occupational and Environmental Health, University of Manchester; Guys and St Thomas NHS Foundation Trust; Guy's and St Thomas' NHS Foundation Trust; National Heart and Lung Institute (NHLI), Imperial College London","ObjectiveTo explore impacts of the COVID-19 pandemic on patterns of sickness absence among staff employed by the National Health Service (NHS) in England. - -MethodsWe analysed prospectively collected, pseudonymised data on 959,356 employees who were continuously employed by NHS trusts during 1 January 2019 to 31 July 2020, comparing the frequency of new sickness absence in 2020 with that at corresponding times in 2019. - -ResultsAfter exclusion of episodes directly related to COVID-19, the overall incidence of sickness absence during the initial 10 weeks of the pandemic (March-May 2020) was more than 20% lower than in corresponding weeks of 2019, but trends for specific categories of illness varied. Marked increases were observed for asthma (122%), infectious diseases (283%) and mental illness (42.3%), while reductions were apparent for gastrointestinal problems (48.4%), genitourinary/gynaecological disorders (33.8%), eye problems (42.7%), injury and fracture (27.7%), back problems (19.6%), other musculoskeletal disorders (29.3%), disorders of ear, nose and throat (32.7%), cough/flu (24.5%) and cancer (24.1%). A doubling of new absences for pregnancy-related disorders during 18 May to 19 July of 2020 was limited to women with earlier COVID-19 sickness absence. - -ConclusionsVarious factors will have contributed to the large and divergent changes that were observed. The findings add to concerns regarding delays in diagnosis and treatment of cancers, and support a need to plan for a large backlog of treatment for many other diseases. Further research should explore the rise in absence for pregnancy-related disorders among women with earlier COVID-19 sickness absence. - -O_TEXTBOX1. What is already known about this subject? - -Historically, rates of sickness absence among the NHS workforce in England have been relatively high but stable. Reports of a marked increase during the first wave of the COVID-19 pandemic have not distinguished between different categories of underlying illness. - -2. What are the new findings? - -During the first wave of COVID-19, incidence of sickness-absence changed markedly when compared to the previous year, with major increases for some categories of illness, and large declines for many others, including cancer. - -3. How might this impact on policy or clinical practice in the foreseeable future? - -The findings support a need to plan for effects from delayed diagnosis and treatment of cancer, and to manage a large backlog of treatment for many other diseases. - -C_TEXTBOX",occupational and environmental health,fuzzy,100,100 medRxiv,10.1101/2021.04.07.21255072,2021-04-09,https://medrxiv.org/cgi/content/short/2021.04.07.21255072,Behavioural responses to Covid-19 health certification: A rapid review,John Drury; Guanlan Mao; Ann John; Atiya Kamal; James Rubin; Clifford Stott; Tushna Vandrevala; Theresa Marteau,University of Sussex; University of Sussex; Swansea University; Birmingham City University; King's College London; Keele University; Kingston University; University of Cambridge,"BackgroundCovid-status certification - certificates for those who test negative for the SARS-CoV-2 virus, test positive for antibodies, or who have been vaccinated against SARS-CoV-2 - has been proposed to enable safer access to a range of activities. Realising these benefits will depend in part upon the behavioural and social impacts of certification. The aim of this rapid review was to describe public attitudes towards certification, and its possible impact on uptake of testing and vaccination, protective behaviours, and crime. MethodA search was undertaken in peer-reviewed databases, pre-print databases, and the grey literature, from 2000 to December 2020. Studies were included if they measured attitudes towards or behavioural consequences of health certificates based on one of three indices of Covid-19 status: test-negative result for current infectiousness, test-positive for antibodies conferring natural immunity, or vaccination(s) conferring immunity. @@ -3550,6 +3492,7 @@ Added value of this studyThrough prospective collection of symptom and test repo Implications of all the available evidenceDespite the UK having a simple set of symptom-based testing criteria, with tests made freely available through nationalised healthcare, a quarter of individuals with qualifying symptoms do not get tested. Our findings suggest testing uptake may be limited by individuals not acting on mild or transient symptoms, not recognising the testing criteria, and not knowing where to get tested. Improved messaging may help address this testing gap, with opportunities to target individuals of older age or fewer years of education. Messaging may prove even more valuable in countries with more fragmented testing infrastructure or more nuanced testing criteria, where knowledge barriers are likely to be greater.",public and global health,fuzzy,94,100 bioRxiv,10.1101/2021.03.14.435295,2021-03-16,https://biorxiv.org/cgi/content/short/2021.03.14.435295,3D genomic capture of regulatory immuno-genetic profiles in COVID-19 patients for prognosis of severe COVID disease outcome,Ewan Hunter; Christina Koutsothanasi; Adam Wilson; Francisco Coroado Santos; Matthew Salter; Ryan Powell; Ann Dring; Paulina Brajer; Benedict Egan; Jurjen Westra; Aroul Ramadass; William Messner; Amanda Brunton; Zoe Lyski; Rama Vancheeswaran; Andrew Barlow; Dmitri Pchejetski; Alexandre Akoulitchev,"Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oxford BioDynamics Plc, Oxford UK; Oregon Health & Science University, Portland, OR; Oregon Health & Science University, Portland, OR; Oregon Health & Science University, Portland, OR; West Hertfordshire NHS Trust, Watford, UK; West Hertfordshire NHS Trust, Watford, UK; Norwich Medical School, University of East Anglia; Oxford BioDynamics Plc, Oxford UK","Human infection with the SARS-CoV-2 virus leads to coronavirus disease (COVID-19). A striking characteristic of COVID-19 infection in humans is the highly variable host response and the diverse clinical outcomes, ranging from clinically asymptomatic to severe immune reactions leading to hospitalization and death. Here we used a 3D genomic approach to analyse blood samples at the time of COVID diagnosis, from a global cohort of 80 COVID-19 patients, with different degrees of clinical disease outcomes. Using 3D whole genome EpiSwitch(R) arrays to generate over 1 million data points per patient, we identified a distinct and measurable set of differences in genomic organization at immune-related loci that demonstrated prognostic power at baseline to stratify patients with mild forms of illness and those with severe forms that required hospitalization and intensive care unit (ICU) support. Further analysis revealed both well established and new COVID-related dysregulated pathways and loci, including innate and adaptive immunity; ACE2; olfactory, G{beta}{psi}, Ca2+ and nitric oxide (NO) signalling; prostaglandin E2 (PGE2), the acute inflammatory cytokine CCL3, and the T-cell derived chemotactic cytokine CCL5. We identified potential therapeutic agents for mitigation of severe disease outcome, with several already being tested independently, including mTOR inhibitors (rapamycin and tacrolimus) and general immunosuppressants (dexamethasone and hydrocortisone). Machine learning algorithms based on established EpiSwitch(R) methodology further identified a subset of 3D genomic changes that could be used as prognostic molecular biomarker leads for the development of a COVID-19 disease severity test.",biochemistry,fuzzy,92,100 medRxiv,10.1101/2021.03.09.21253012,2021-03-15,https://medrxiv.org/cgi/content/short/2021.03.09.21253012,The local and systemic response to SARS-CoV-2 infection in children and adults,Masahiro Yoshida; Kaylee B Worlock; Ni Huang; Rik GH Lindeboom; Colin R Butler; Natsuhiko Kumasaka; Cecilia Dominguez Conde; Lira Mamanova; Liam Bolt; Laura Richardson; Krzysztof Polanski; Elo Madissoon; Josephine L Barnes; Jessica Allen-Hyttinen; Eliz Kilich; Brendan C Jones; Angus de Wilton; Anna Wilbrey-Clark; Waradon Sungnak; Jan Patrick Prett; Elena Prigmore; Henry Yung; Puja Mehta; Aarash Saleh; Anita Saigal; Vivian Chu; Jonathan M Cohen; Clare Cane; Aikaterini Iordanidou; Soichi Shibuya; Ann-Kathrin Reuschl; A. Christine Argento; Richard G Wunderink; Sean B Smith; Taylor A Poor; Catherine A Gao; Jane E Dematte; - NU SCRIPT Study Investigators; Gary Reynolds; Muzlifah Haniffa; Georgina S Bowyer; Matthew Coates; Menna R Clatworthy; Fernando J Calero-Nieto; Berthold Gottgens; Neil J Sebire; Clare Jolly; Paolo de Coppi; Claire M Smith; Alexander V Misharin; Sam M Janes; Sarah A Teichmann; Marko Z Nikolic; Kerstin B Meyer,"UCL Respiratory, Division of Medicine, University College London, London, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; UCL Great Ormond Street Institute of Child Health, London, UK; Wellcome Trust Sanger Institute; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; UCL Great Ormond Street Institute of Child Health, London, UK; University College London Hospital Trust; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute; Wellcome Sanger Institute, Cambridge, UK; Wellcome Sanger Institute, Cambridge, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; Royal Free Hospital, London, UK; Royal Free Hospital, London, UK; Royal Free Hospital, London, UK; University College London Hospitals NHS Foundation Trust, London, UK; Royal Free Hospital, London, UK; Royal Free Hospital, London, UK; UCL Great Ormond Street Institute of Child Health, London, UK; Division of Infection and Immunity, University College London, London, UK; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; Northwestern University Feinberg School of Medicine; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; Division of Pulmonary and Critical Care Medicine, Northwestern University, Feinberg School of Medicine, Chicago, USA; ; Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK; Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK; Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; University of Cambridge, Department of Medicine; University of Cambride, Department of Medicine; Wellcome Trust & MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge UK; Wellcome Trust & MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Cambridge UK; NIHR Great Ormond Street BRC and Institute of Child Health, London, UK; Division of Infection and Immunity, University College London, UK; UCL Great Ormond Street Institute of Child Health, London, UK; UCL Great Ormond Street Institute of Child Health, London, UK; Northwestern University; UCL Respiratory, Division of Medicine, University College London, London, UK; Wellcome Sanger Institute, Cambridge, UK; UCL Respiratory, Division of Medicine, University College London, London, UK; Wellcome Sanger Institute, Cambridge, UK","While a substantial proportion of adults infected with SARS-CoV-2 progress to develop severe disease, children rarely manifest respiratory complications. Therefore, understanding differences in the local and systemic response to SARS-CoV-2 infection between children and adults may provide important clues about the pathogenesis of SARS-CoV-2 infection. To address this, we first generated a healthy reference multi-omics single cell data set from children (n=30) in whom we have profiled triple matched samples: nasal and tracheal brushings and PBMCs, where we track the developmental changes for 42 airway and 31 blood cell populations from infancy, through childhood to adolescence. This has revealed the presence of naive B and T lymphocytes in neonates and infants with a unique gene expression signature bearing hallmarks of innate immunity. We then contrast the healthy reference with equivalent data from severe paediatric and adult COVID-19 patients (total n=27), from the same three types of samples: upper and lower airways and blood. We found striking differences: children with COVID-19 as opposed to adults had a higher proportion of innate lymphoid and non-clonally expanded naive T cells in peripheral blood, and a limited interferon-response signature. In the airway epithelium, we found the highest viral load in goblet and ciliated cells and describe a novel inflammatory epithelial cell population. These cells represent a transitional regenerative state between secretory and ciliated cells; they were found in healthy children and were enriched in paediatric and adult COVID-19 patients. Epithelial cells display an antiviral and neutrophil-recruiting gene signature that is weaker in severe paediatric versus adult COVID-19. Our matched blood and airway samples allowed us to study the spatial dynamics of infection. Lastly, we provide a user-friendly interface for this data1 as a highly granular reference for the study of immune responses in airways and blood in children.",pediatrics,fuzzy,100,100 +medRxiv,10.1101/2021.03.12.21253484,2021-03-13,https://medrxiv.org/cgi/content/short/2021.03.12.21253484,Limits of lockdown: characterising essential contacts during strict physical distancing,Amy C Thomas; Leon Danon; Hannah Christensen; Kate Northstone; Daniel Smith; Emily J Nixon; Adam Trickey; Gibran Hemani; Sarah Sauchelli; Adam Finn; Nicholas J Timpson; Ellen Brooks-Pollock,"University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; NIHR Bristol Biomedical Research Centre, University of Bristol; University of Bristol; University of Bristol; University of Bristol","COVID-19 has exposed health inequalities within countries and globally. The fundamental determining factor behind an individuals risk of infection is the number of social contacts they make. In many countries, physical distancing measures have been implemented to control transmission of SARS-CoV-2, reducing social contacts to a minimum. Characterising unavoidable social contacts is key for understanding the inequalities behind differential risks and planning vaccination programmes. We utilised an existing English longitudinal birth cohort, which is broadly representative of the wider population (n=6807), to explore social contact patterns and behaviours when strict physical distancing measures were in place during the UKs first lockdown in March-May 2020. Essential workers, specifically those in healthcare, had 4.5 times as many contacts as non-essential workers [incident rate ratio = 4.42 (CI95%: 3.88-5.04)], whilst essential workers in other sectors, mainly teaching and the police force had three times as many contacts [IRR = 2.84 (2.58-3.13)]. The number of individuals in a household, which is conflated by number of children, increases essential social contacts by 40%. Self-isolation effectively reduces numbers of contacts outside of the home, but not entirely. Together, these findings will aid the interpretation of epidemiological data and impact the design of effective SARS-CoV-2 control strategies, such as vaccination, testing and contact tracing.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.03.10.21253173,2021-03-12,https://medrxiv.org/cgi/content/short/2021.03.10.21253173,"High household transmission of SARS-CoV-2 in the United States: living density, viral load, and disproportionate impact on communities of color",Carla Cerami; Tyler Rapp; Feng-Chang Lin; Kathleen Tompkins; Christopher Basham; Meredith Smith Muller; Maureen Whittelsey; Haoming Zhang; Srijana Bhattarai Chhetri; Judy Smith; Christy Litel; Kelly Lin; Mehal Churiwal; Salman Khan; Faith Claman; Rebecca Rubinstein; Katie Mollan; David Wohl; Lakshmanane Premkumar; Jonathan J. Juliano; Jessica T Lin,"MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; University of North Carolina School of Medicine; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA; Institute of Global Health and Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC USA","BackgroundFew prospective studies of SARS-CoV-2 transmission within households have been reported from the United States, where COVID-19 cases are the highest in the world and the pandemic has had disproportionate impact on communities of color. Methods and FindingsThis is a prospective observational study. Between April-October 2020, the UNC CO-HOST study enrolled 102 COVID-positive persons and 213 of their household members across the Piedmont region of North Carolina, including 45% who identified as Hispanic/Latinx or non-white. Households were enrolled a median of 6 days from onset of symptoms in the index case. Secondary cases within the household were detected either by PCR of a nasopharyngeal (NP) swab on study day 1 and weekly nasal swabs (days 7, 14, 21) thereafter, or based on seroconversion by day 28. After excluding household contacts exposed at the same time as the index case, the secondary attack rate (SAR) among susceptible household contacts was 60% (106/176, 95% CI 53%-67%). The majority of secondary cases were already infected at study enrollment (73/106), while 33 were observed during study follow-up. Despite the potential for continuous exposure and sequential transmission over time, 93% (84/90, 95% CI 86%-97%) of PCR-positive secondary cases were detected within 14 days of symptom onset in the index case, while 83% were detected within 10 days. Index cases with high NP viral load (>10^6 viral copies/ul) at enrollment were more likely to transmit virus to household contacts during the study (OR 4.9, 95% CI 1.3-18 p=0.02). Furthermore, NP viral load was correlated within families (ICC=0.44, 95% CI 0.26-0.60), meaning persons in the same household were more likely to have similar viral loads, suggesting an inoculum effect. High household living density was associated with a higher risk of secondary household transmission (OR 5.8, 95% CI 1.3-55) for households with >3 persons occupying <6 rooms (SAR=91%, 95% CI 71-98%). Index cases who self-identified as Hispanic/Latinx or non-white were more likely to experience a high living density and transmit virus to a household member, translating into an SAR in minority households of 70%, versus 52% in white households (p=0.05). @@ -3732,21 +3675,6 @@ MethodsWe performed a cohort study among U.S. and U.K. participants in the smart ResultsIn the U.S. (n=87,388), compared to White non-Hispanic participants, the multivariable ORs of vaccine hesitancy were 3.15 (95% CI: 2.86 to 3.47) for Black participants, 1.42 (1.28 to 1.58) for Hispanic participants, 1.34 (1.18 to 1.52) for Asian participants, and 2.02 (1.70 to 2.39) for participants reporting more than one race/other. In the U.K. (n=1,254,294), racial and ethnic minorities had similarly elevated hesitancy: compared to White participants, their corresponding ORs were 2.84 (95% CI: 2.69 to 2.99) for Black participants, 1.66 (1.57 to 1.76) for South Asian participants, 1.84 (1.70 to 1.98) for Middle East/East Asian participants, and 1.48 (1.39 to 1.57) for participants reporting more than one race/other. Among U.S. participants, the OR of vaccine receipt was 0.71 (0.64 to 0.79) for Black participants, a disparity that persisted among individuals who specifically endorsed a willingness to obtain a vaccine. In contrast, disparities in uptake were not observed in the U.K. ConclusionsCOVID-19 vaccine hesitancy was greater among racial and ethnic minorities, and Black participants living in the U.S. were less likely to receive a vaccine than White participants. Lower uptake among Black participants in the U.S. during the initial vaccine rollout is attributable to both hesitancy and disparities in access.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.02.23.21251975,2021-02-25,https://medrxiv.org/cgi/content/short/2021.02.23.21251975,The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH): Protocol for a prospective longitudinal cohort study of healthcare and ancillary workers in UK healthcare settings,Katherine Woolf; Carl Melbourne; Luke Bryant; Anna Louise Guyatt; Ian Christopher McManus; Amit Gupta; Robert C Free; Laura Nellums; Sue Carr; Catherine John; Christopher A Martin; Louise V Wain; Laura J Gray; Claire Garwood; Vishant Modhwadia; Keith Abrams; Martin D Tobin; Kamlesh Khunti; Manish Pareek; - UK-REACH Study Collaborative Group,"University College London; University of Leicester; University of Leicester; University of Leicester; University College London; University Hospitals Oxford NHS Foundation Trust; University of Leicester; University of Nottingham; General Medical Council, University Hospitals Leicester NHS Trust; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of York; University of Leicester; University of Leicester; University of Leicester; ","IntroductionThe COVID-19 pandemic has resulted in significant morbidity and mortality, and has devastated economies in many countries. Amongst the groups identified as being at increased risk from COVID-19 are healthcare workers (HCWs) and ethnic minority groups. Emerging evidence suggests HCWs from ethnic minority groups are at increased risk of adverse COVID-19-related physical and mental health outcomes. To date there has been no large-scale analysis of these risks in UK healthcare workers or ancillary workers in healthcare settings, stratified by ethnicity or occupation type, and adjusted for potential confounders. This paper reports the protocol for a prospective longitudinal questionnaire study of UK HCWs, as part of the UK-REACH programme (The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers). - -Methods and analysisA baseline questionnaire with follow-up questionnaires at 4 and 8 months will be administered to a national cohort of UK healthcare workers and ancillary workers in healthcare settings, and those registered with UK healthcare regulators. With consent, data will be linked to health records, and participants followed up for 25 years. - -Univariate associations between ethnicity and primary outcome measures (clinical COVID-19 outcomes, and physical and mental health) and key confounders/explanatory variables will be tested, followed by multivariable analyses to test for associations between ethnicity and key outcomes adjusted for the confounder/explanatory variables, with interactions included as appropriate. Using follow-up data, multilevel models will be used to model changes over time by ethnic group, facilitating understanding of absolute and relative risks in different ethnic groups, and generalisability of findings. - -Ethics and disseminationThe study is approved by Health Research Authority (reference 20/HRA/4718), and carries minimal risk to participants. We aim to manage the small risk of participant distress due to being asked questions on sensitive topics by clearly indicating on the participant information sheet that the questionnaire covers sensitive topics and that participants are under no obligation to answer these, or indeed any other, questions, and by providing links to support organisations. Results will be disseminated with reports to Government and papers uploaded to pre-print servers and submitted to peer reviewed journals. - -Registration detailsTrial ID: ISRCTN11811602 - -STRENGTHS AND LIMITATIONS OF THIS STUDYO_LINational, UK-wide, study, aiming to capture variety of healthcare worker job roles including ancillary workers in healthcare settings. -C_LIO_LILongitudinal study including three waves of questionnaire data collection, and linkage to administrative data over 25 years, with consent. -C_LIO_LIUnique support from all major UK healthcare worker regulators, relevant healthcare worker organisations, and a Professional Expert Panel to increase participant uptake and the validity of findings. -C_LIO_LIPotential for self-selection bias and low response rates, and the use of electronic invitations and online data collection makes it harder to reach ancillary workers without regular access to work email addresses. -C_LI",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.24.21252338,2021-02-25,https://medrxiv.org/cgi/content/short/2021.02.24.21252338,"Health impact and cost-effectiveness of COVID-19 vaccination in Sindh Province, Pakistan",Carl Andrew Pearson; Fiammetta Bozzani; Simon R Procter; Nicholas G Davies; Maryam Huda; Henning Tarp Jensen; Marcus Keogh-Brown; Muhammad Khalid; Sedona Sweeney; Sergio Torres-Rueda; - CHiL COVID-19 Working Group; - CMMID COVID-19 Working Group; Rosalind M Eggo; Anna Vassall; Mark Jit,"London School of Hygiene & Tropical Medicine; Centre for Health Economics in London, London School of Hygiene & Tropical Medicine; Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene & Tropical Medicine; Centre for Health Economics in London, London School of ; Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene & Tropical Medicine; Aga Khan University Hospital; Centre for Health Economics in London, London School of Hygiene & Tropical Medicine; Centre for Health Economics in London, London School of Hygiene & Tropical Medicine; Ministry of National Health Services Regulations & Coordination, Pakistan; Centre for Health Economics in London, London School of Hygiene & Tropical Medicine; Centre for Health Economics in London, London School of Hygiene & Tropical Medicine; Centre for Health Economics in London, London School of Hygiene & Tropical Medicine; Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene & Tropical Medicine; Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene & Tropical Medicine; Centre for Health Economics in London, London School of Hygiene & Tropical Medicine; Centre for Mathematical Modelling of Infectious Disease, London School of Hygiene & Tropical Medicine; Centre for Health Economics in London, London School of ","BackgroundMultiple COVID-19 vaccines appear to be safe and efficacious, but only high-income countries have the resources to procure sufficient vaccine doses for most of their eligible populations. The World Health Organization has published guidelines for vaccine prioritisation, but most vaccine impact projections have focused on high-income countries, and few incorporate economic considerations. To address this evidence gap, we projected the health and economic impact of different vaccination scenarios in Sindh province, Pakistan (population: 48 million). Methods and FindingsWe fitted a compartmental transmission model to COVID-19 cases and deaths in Sindh from 30 April to 15 September 2020. We then projected cases, deaths, and hospitalization outcomes over 10 years under different vaccine scenarios. Finally, we combined these projections with a detailed economic model to estimate incremental costs (from healthcare and partial societal perspectives), disability adjusted life years (DALYs), and incremental cost-effectiveness ratio (ICER) for each scenario. @@ -3908,6 +3836,13 @@ ResultsWave 2 patients were younger, more ethnically diverse, had less co-morbid ConclusionPrior to new SARS-CoV-2 variants, outcomes for hospitalised patients with COVID-19 were improving but with similar intensive care needs.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.03.21251054,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.03.21251054,Age-related heterogeneity in Neutralising antibody responses to SARS-CoV-2 following BNT162b2 vaccination,Dami Collier; Isabella Ferreira; Rawlings Datir; Prasanti Kotagiri; Eleanor Lim; Bo Meng; - The CITIID-NIHR Bioresource COVID-19 Collaboration; Anne Elmer; Nathalie Kingston; Barbara Graves; Barbara Graves; Kenneth GC Smith; John Bradley; Paul Lyons; Lourdes Ceron-Gutierrez; Gabriela Barcenas-Morales; Michelle Linterman; Laura McCoy; Rainer Doffinger; Mark Wills; Ravindra K Gupta,UCL; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; -; Cambridge; NIHR; NIHR; Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Babraham Institute; UCL; University of Cambridge; University of Cambridge; University of Cambridge,"Two dose mRNA vaccination provides excellent protection against SARS-CoV-2. However, there are few data on vaccine efficacy in elderly individuals above the age of 801. Additionally, new variants of concern (VOC) with reduced sensitivity to neutralising antibodies have raised fears for vulnerable groups. Here we assessed humoral and cellular immune responses following vaccination with mRNA vaccine BNT162b22 in elderly participants prospectively recruited from the community and younger health care workers. Median age was 72 years and 51% were females amongst 140 participants. Neutralising antibody responses after the first vaccine dose diminished with increasing age, with a marked drop in participants over 80 years old. Sera from participants below and above 80 showed significantly lower neutralisation potency against B.1.1.7, B.1.351 and P.1. variants of concern as compared to wild type. Those over 80 were more likely to lack any neutralisation against VOC compared to younger participants following first dose. The adjusted odds ratio for inadequate neutralisation activity against the B.1.1.7, P.1 and B.1.351 variant in the older versus younger age group was 4.3 (95% CI 2.0-9.3, p<0.001), 6.7 (95% CI 1.7-26.3, p=0.008) and 1.7 (95% CI 0.5-5.7, p=0.41). Binding IgG and IgA antibodies were lower in the elderly, as was the frequency of SARS-CoV-2 Spike specific B-memory cells. We observed a trend towards lower somatic hypermutation in participants with suboptimal neutralisation, and elderly participants demonstrated clear reduction in class switched somatic hypermutation, driven by the IgA1/2 isotype. SARS-CoV-2 Spike specific T-cell IFN{gamma} and IL-2 responses fell with increasing age, and both cytokines were secreted primarily by CD4 T cells. We conclude that the elderly are a high risk population that warrant specific measures in order to mitigate against vaccine failure, particularly where variants of concern are circulating.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.02.02.21251043,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.02.21251043,COVID-19 infection and subsequent thromboembolism: A self-controlled case series analysis of a population cohort,Frederick Ho; Kenneth Man; Mark Toshner; Colin Church; Carlos Celis-Morales; Ian Wong; Colin Berry; Naveed Sattar; Jill Pell,University of Glasgow; UCL; University of Cambridge; NHS Greater Glasgow and Clyde; University of Glasgow; UCL; University of Glasgow; University of Glasgow; University of Glasgow,"ObjectiveAn unexpectedly large number of people infected with Covid-19 had experienced a thrombotic event. This study aims to assess the associations between Covid-19 infection and thromboembolism including myocardial infarction (MI), ischaemic stroke, deep-vein thrombosis (DVT), and pulmonary embolism (PE). + +Patients and MethodsA self-controlled case-series study was conducted covering the whole of Scotlands general population. The study population comprised individuals with confirmed (positive test) Covid-19 and at least one thromboembolic event between March 2018 and October 2020. Their incidence rates during the risk interval (5 days before to 56 days after the positive test) and the control interval (the remaining periods) were compared intra-personally. + +ResultsAcross Scotland, 1,449 individuals tested positive for Covid-19 and experienced a thromboembolic event. The risk of thromboembolism was significantly elevated over the whole risk period but highest in the 7 days following the positive test (IRR 12.01, 95% CI 9.91-14.56) in all included individuals. The association was also present in individuals not originally hospitalised for Covid-19 (IRR 4.07, 95% CI 2.83-5.85). Risk of MI, stroke, PE and DVT were all significantly higher in the week following a positive test. The risk of PE and DVT was particularly high and remained significantly elevated even 56 days following the test. + +ConclusionConfirmed Covid-19 infection was associated with early elevations in risk with MI, ischaemic stroke, and substantially stronger and prolonged elevations with DVT and PE both in hospital and community settings. Clinicians should consider thromboembolism, especially PE, among people with Covid-19 in the community.",cardiovascular medicine,fuzzy,100,100 medRxiv,10.1101/2021.02.03.21251004,2021-02-05,https://medrxiv.org/cgi/content/short/2021.02.03.21251004,Ethnic differences in COVID-19 mortality during the first two waves of the Coronavirus Pandemic: a nationwide cohort study of 29 million adults in England,Vahe Nafilyan; Nazrul Islam; Rohini Mathur; Daniel Ayoubkhani; Amitava Banerjee; Myer Glickman; Ben Humberstone; Ian DIamond; Kamlesh Khunti,"Office for National Statistics; Nuffield Department of Population Health, Big Data Institute, University of Oxford; London School of Hygiene and Tropical Medicine; Office for National Statistics; University College London; Office for National Statistics; Office for National Statistics; Office for National Statistics; Diabetes Research Centre, University of Leicester","BackgroundEthnic minorities have experienced disproportionate COVID-19 mortality rates in the UK and many other countries. We compared the differences in the risk of COVID-19 related death between ethnic groups in the first and second waves the of COVID-19 pandemic in England. We also investigated whether the factors explaining differences in COVID-19 death between ethnic groups changed between the two waves. MethodsUsing data from the Office for National Statistics Public Health Data Asset on individuals aged 30-100 years living in private households, we conducted an observational cohort study to examine differences in the risk of death involving COVID-19 between ethnic groups in the first wave (from 24th January 2020 until 31st August 2020) and second wave (from 1st September to 28th December 2020). We estimated age-standardised mortality rates (ASMR) in the two waves stratified by ethnic groups and sex. We also estimated hazard ratios (HRs) for ethnic-minority groups compared with the White British population, adjusted for geographical factors, socio-demographic characteristics, and pre-pandemic health conditions. @@ -4079,6 +4014,7 @@ RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSPublic policy measu Added value of this studyCommissioned by the Chief Medical Officer for England, we validated the novel clinical risk prediction model (QCovid) to identify risks of short-term severe outcomes due to COVID-19. We used national linked datasets from general practice, death registry and hospital episode data for a population-representative sample of over 34 million adults. The risk models have excellent discrimination in men and women (Harrells C statistic>0.9) and are well calibrated. QCovid represents a new, evidence-based opportunity for population risk-stratification. Implications of all the available evidenceQCovid has the potential to support public health policy, from enabling shared decision making between clinicians and patients in relation to health and work risks, to targeted recruitment for clinical trials, and prioritisation of vaccination, for example.",public and global health,fuzzy,100,100 +bioRxiv,10.1101/2021.01.25.428136,2021-01-25,https://biorxiv.org/cgi/content/short/2021.01.25.428136,mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge,Michelle Meyer; Yuan Wang; Darin Edwards; Gregory R Smith; Aliza B Rubenstein; Palaniappan Ramanathan; Chad E Mire; Colette Pietzsch; Xi Chen; Yongchao Ge; Wan Sze Cheng; Carole Henry; Angela Woods; LingZhi Ma; Guillaume B. E. Stewart-Jones; Kevin W Bock; Minai Mahnaz; Bianca M Nagata; Sivakumar Periasamy; Pei-Yong Shi; Barney S Graham; Ian N Moore; Irene Ramos; Olga G. Troyanskaya; Elena Zaslavsky; Andrea Carfi; Stuart C Sealfon; Alexander Bukreyev,"University of Texas Medical Branch; Princeton University; Moderna Inc; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch; University of Texas Medical Branch; University of Texas Medical Branch; Flatiron Institute, Simons Foundation; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; Moderna Inc; Moderna Inc; Moderna Inc; Moderna Inc; National Institute of Health; National Institutes of Health; National Institutes of Health; University of Texas Medical Branch; University of Texas Medical Branch; National Institutes of Health; National Institutes of Health; Icahn School of Medicine at Mount Sinai; Princeton University; Icahn School of Medicine at Mount Sinai; Moderna Inc; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch at Galveston","The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.",immunology,fuzzy,96,94 medRxiv,10.1101/2021.01.21.20240887,2021-01-22,https://medrxiv.org/cgi/content/short/2021.01.21.20240887,"The psychosocial impact of the COVID-19 pandemic on 4,378 UK healthcare workers and ancillary staff: initial baseline data from a cohort study collected during the first wave of the pandemic.",Danielle Lamb; Sam Gnanapragasam; Neil Greenberg; Rupa Bhundia; Ewan Carr; Matthew Hotopf; Reza Razavi; Rosalind Raine; Sean Cross; Amy Dewar; Mary Docherty; Sarah Dorrington; Stephani Hatch; Charlotte Wilson-Jones; Daniel Leightley; Ira Madan; Sally Marlow; Isabel McMullen; Anne Marie Rafferty; Martin Parsons; Catherine Polling; Danai Serfioti; Helen Gaunt; Peter Aitken; Joanna Morris-Bone; Chloe Simela; Veronica French; Rachel Harris; Sharon A.M. Stevelink; Simon Wessely,"Department of Applied Health Research, UCL, 1-19 Torrington Place, London, WC1E 7HB; South London and Maudsley NHS Foundation Trust, London, UK; Health Protection Research Unit, King's College London, Weston Education Centre, 10 Cutcombe Road, London, SE5 9RJ; Department of Psychological Medicine, King's College London, London, UK.; Department of Biostatistics and Health Informatics, King's College London, London, UK; National Institute of Health Research Biomedical Research Centre at the South London and Maudsley NHS Foundation Trust.; 1 Lambeth Palace Rd, South Bank, London, SE1 7EU; Dept of Applied Health Research, UCL; Department of Psychological Medicine, King's College Hospital. Denmark Hill. SE5 9RS; Guy's and St Thomas' NHS Foundation Trust; Department of Psychological Medicine, King's College Hospital. Denmark Hill. SE5 9RS; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; King's Centre for Military Health Research, Department of Psychological Medicine, King's College London, London, UK. AND Department of Psychological Medicine, K; Guy's and St Thomas' NHS Foundation Trust, London; Institute of Psychiatry, Psychology and Neuroscience, King's College London; Department of Psychological Medicine, King's College Hospital, South London and Maudsley NHS Foundation Trust; Adult Nursing, King's College London; Mental Health Liaison Team, King's College Hospital; Institute of Psychiatry, Psychology and Neuroscience, King's College London; King's Centre for Military Health Research, King's College London, Room 307, Weston Education Centre, 10 Cutcombe Road, London SE5 9RJ; University Hospital of Leciester NHS Trust. Groby Road Leciester LE4 9QP; Devon Partnership NHS Trust, Trust HQ, R&D, Dryden Road, Exeter, Devon, EX2 5AF; Avon & Wiltshire Mental Health Partnership NHS Trust, R&D, Fromeside, Blackberry Hill Hospital, Bristol, BS16 1EG; Guy's and St Thomas' NHS Foundation Trust, London; Nottinghamshire Healthcare NHS Foundation Trust; Cornwall Partnership Foundation NHS Trust/ Research and Innovation Team; King's Centre for Military Health Research, Department of Psychological Medicine, King's College London, London, UK. AND Department of Psychological Medicine, K; Department of Psychological Medicine, King's College London, Weston Education, Denmark Hill, London, SE5 9JR","ObjectivesThis study reports preliminary findings on the prevalence of, and factors associated with, mental health and wellbeing outcomes of healthcare workers during the early months (April-June) of the COVID-19 pandemic in the UK. MethodsPreliminary cross-sectional data were analysed from a cohort study (n=4,378). Clinical and non-clinical staff of three London-based NHS Trusts (UK), including acute and mental health Trusts, took part in an online baseline survey. The primary outcome measure used is the presence of probable common mental disorders (CMDs), measured by the General Health Questionnaire (GHQ-12). Secondary outcomes are probable anxiety (GAD-7), depression (PHQ-9), Post-Traumatic Stress Disorder (PTSD) (PCL-6), suicidal ideation (CIS-R), and alcohol use (AUDIT). Moral injury is measured using the Moray Injury Event Scale (MIES). @@ -4220,7 +4156,6 @@ Added value of this studyTranslating current knowledge and uncertainty of vaccin Implications of all the available evidenceVaccination is likely to provide substantial individual protection to those receiving two doses, but the degree of protection to the wider population is still uncertain. While substantial immunisation of the most vulnerable groups will allow for some relaxation of controls, this must be done gradually to prevent large scale public health consequences.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.12.30.20248603,2021-01-01,https://medrxiv.org/cgi/content/short/2020.12.30.20248603,SARS-CoV-2 positivity in asymptomatic-screened dental patients,David I Conway; Shauna Culshaw; Maura Edwards; Claire Clark; Chris Watling; Chris Robertson; Raymond Braid; Emma O'Keefe; Niall McGoldrick; Jacky Burns; Stacey Provan; Harper VanSteenhouse; Jodie Hay; Rory Gunson; - Dental COVID-19 Surveillance Survey Group,University of Glasgow and Public Health Scotland; University of Glasgow; NHS Ayrshire and Arran; Public Health Scotland; Public Health Scotland; Strathclyde University and Public Health Scotland; Public Health Scotland; NHS Fife; NHS Fife; NHS Fife; NHS Greater Glasgow & Clyde; BioClavis Ltd; University of Glasgow; NHS Greater Glasgow & Clyde; ,"Enhanced community surveillance is a key pillar of the public health response to COVID-19. Asymptomatic carriage of SARS-CoV-2 is a potentially significant source of transmission, yet remains relatively poorly understood. Disruption of dental services continues with significantly reduced capacity. Ongoing precautions include pre- and/or at appointment COVID-19 symptom screening and use of enhanced personal protective equipment (PPE). This study aimed to investigate SARS-CoV-2 infection in dental patients to inform community surveillance and improve understanding of risks in the dental setting. Thirty-one dental care centres across Scotland invited asymptomatic screened patients over 5-years-old to participate. Following verbal consent and completion of sociodemographic and symptom history questionnaire, trained dental teams took a combined oropharyngeal and nasal swab sample using standardised VTM-containing testkits. Samples were processed by the Lighthouse Lab and patients informed of their results by SMS/e-mail with appropriate self-isolation guidance in the event of a positive test. Over a 13-week period (from 3August to 31October2020) n=4,032 patients, largely representative of the population, were tested. Of these n=22 (0.5%; 95%CI 0.5%, 0.8%) tested positive for SARS-CoV-2. The positivity rate increased over the period, commensurate with uptick in community prevalence identified across all national testing monitoring data streams. All positive cases were successfully followed up by the national contact tracing program. To the best of our knowledge this is the first report of a COVID-19 testing survey in asymptomatic-screened patients presenting in a dental setting. The positivity rate in this patient group reflects the underlying prevalence in community at the time. These data are a salient reminder, particularly when community infection levels are rising, of the importance of appropriate ongoing Infection Prevention Control and PPE vigilance, which is relevant as healthcare team fatigue increases as the pandemic continues. Dental settings are a valuable location for public health surveillance.",dentistry and oral medicine,fuzzy,100,100 medRxiv,10.1101/2020.12.24.20248822,2020-12-26,https://medrxiv.org/cgi/content/short/2020.12.24.20248822,Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England,Nicholas G Davies; Sam Abbott; Rosanna C. Barnard; Christopher I. Jarvis; Adam J. Kucharski; James D Munday; Carl A. B. Pearson; Timothy Russell; Damien Tully; Alex D. Washburne; Tom Wenseleers; Amy Gimma; William Waites; Kerry L. M. Wong; Kevin van Zandvoort; Justin D. Silverman; - CMMID COVID-19 Working Group; - The COVID-19 Genomics UK (COG-UK) Consortium; Karla Diaz-Ordaz; Ruth H Keogh; Rosalind M Eggo; Sebastian Funk; Mark Jit; Katherine E. Atkins; W. John Edmunds,"London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Selva Analytics LLC; KU Leuven; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; College of Information Science and Technology, Pennsylvania State University; ; ; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine","A novel SARS-CoV-2 variant, VOC 202012/01 (lineage B.1.1.7), emerged in southeast England in November 2020 and is rapidly spreading towards fixation. Using a variety of statistical and dynamic modelling approaches, we estimate that this variant has a 43-90% (range of 95% credible intervals 38-130%) higher reproduction number than preexisting variants. A fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases. Without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine roll-out, COVID-19 hospitalisations and deaths across England in 2021 will exceed those in 2020. Concerningly, VOC 202012/01 has spread globally and exhibits a similar transmission increase (59-74%) in Denmark, Switzerland, and the United States.",epidemiology,fuzzy,100,100 -bioRxiv,10.1101/2020.12.23.424229,2020-12-25,https://biorxiv.org/cgi/content/short/2020.12.23.424229,Patterns of within-host genetic diversity in SARS-CoV-2,Gerry Tonkin-Hill; Inigo Martincorena; Roberto Amato; Andrew R J Lawson; Moritz Gerstung; Ian Johnston; David K Jackson; Naomi R Park; Stefanie V Lensing; Michael A Quail; Sónia Gonçalves; Cristina Ariani; Michael Spencer Chapman; William L Hamilton; Luke W Meredith; Grant Hall; Aminu S Jahun; Yasmin Chaudhry; Myra Hosmillo; Malte L Pinckert; Iliana Georgana; Anna Yakovleva; Laura G Caller; Sarah L Caddy; Theresa Feltwell; Fahad A Khokhar; Charlotte J Houldcroft; Martin D Curran; Surendra Parmar; - The COVID-19 Genomics UK (COG-UK) Consortium; Alex Alderton; Rachel Nelson; Ewan Harrison; John Sillitoe; Stephen D Bentley; Jeffrey C Barrett; M. Estee Torok; Ian G Goodfellow; Cordelia Langford; Dominic Kwiatkowski; - Wellcome Sanger Institute COVID-19 Surveillance Team,"Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge and The Francis Crick Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge and Cambridge Institute of Therapeutic Immunology and Infectious Disease; Department of Medicine, University of Cambridge; Public Health England; Public Health England; COG-UK; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute and European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute and Oxford University; ","Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1,181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within and between host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.",genomics,fuzzy,100,100 medRxiv,10.1101/2020.12.21.20248607,2020-12-22,https://medrxiv.org/cgi/content/short/2020.12.21.20248607,Time use and social mixing during and around festive periods: Potential changes in the age distribution of COVID-19 cases from increased intergenerational interactions,Edwin van Leeuwen; Frank G. Sandmann; Rosalind M. Eggo; - PHE Joint modelling group; Peter J. White,Public Health England; Public Health England; London School of Hygiene &Tropical Medicine; London School of Hygiene & Tropical Medicine; ; Public Health England; Imperial College London,"RationaleAmid the ongoing coronavirus disease 2019 (COVID-19) pandemic in which many countries have adopted physical distancing measures, tiered restrictions, and episodic ""lockdowns,"" the impact of potentially increased social mixing during festive holidays on the age distribution of new COVID-19 cases remains unclear. ObjectiveWe aimed to gain insights into possible changes in the age distribution of COVID-19 cases in the UK after temporarily increased intergenerational interactions in late December 2020. @@ -4428,6 +4363,7 @@ C_LIO_LIOptimal symptom combinations maximise case capture considering available C_LIO_LIImplications for COVID-19 vaccine efficacy trials and wider public health C_LI",health informatics,fuzzy,100,100 medRxiv,10.1101/2020.11.19.20234120,2020-11-23,https://medrxiv.org/cgi/content/short/2020.11.19.20234120,Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19,Liam Gaziano; Claudia Giambartolomei; Alexandre C Pereira; Anna Gaulton; Daniel C Posner; Sonja A Swanson; Yuk Lam Ho; Sudha K Iyengar; Nicole M Kosik; Marijana Vujkovic; David R Gagnon; A Patricia Bento; Pedro Beltrao; Inigo Barrio Hernandez; Lars Ronnblom; Niklas Hagberg; Christian Lundtoft; Claudia Langenberg; Maik Pietzner; Dennis Valentine; Elias Allara; Praveen Surendran; Stephen Burgess; Jing Hua Zhao; James E Peters; Bram P Prins; John Danesh; Poornima Devineni; Yunling Shi; Kristine E Lynch; Scott L DuVall; Helene Garcon; Lauren Thomann; Jin J Zhou; Bryan R Gorman; Jennifer E Huffman; Christopher J O'Donnell; Philip S Tsao; Jean C Beckham; Saiju Pyarajan; Sumitra Muralidhar; Grant D Huang; Rachel Ramoni; Adriana M Hung; Kyong-Mi Chang; Yan V Sun; Jacob Joseph; Andrew R Leach; Todd L Edwards; Kelly Cho; J Michael Gaziano; Adam S Butterworth; Juan P Casas,"VA Boston Healthcare System, University of Cambridge; Instituto Italiano di Tecnologia, University of California Los Angeles; University of Sao Paulo, Harvard University; European Molecular Biology Laboratory, European Bioinformatics Institute; VA Boston Healthcare System; Erasmus Medical Center; VA Boston Healthcare System; Case Western Reserve University and Louis Stoke Cleveland VAMC; VA Boston Healthcare System; The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine; Boston University, VA Boston Healthcare System; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; Uppsala University; Uppsala University; Uppsala University; Charite University Medicine Berlin, Universityof Cambridge; Universityof Cambridge; University College London; University of Cambridge; Wellcome Genome Campus and University of Cambridge; University of Cambridge; University of Cambridge; Imperial College London; Wellcome Genome Campus and University of Cambridge; University of Cambridge; VA Boston Healthcare System; VA Boston Healthcare System; VA Salt Lake City Health Care System, University of Utah; VA Salt Lake City Health Care System, University of Utah; VA Boston Healthcare System; VA Boston Healthcare System; University of Arizona, Phoenix VA Health Care System; VA Boston Healthcare System; VA Boston Healthcare System; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Palo Alto Health Care System, Stanford University School of Medicine; Durham VA Medical Center, Duke University School of Medicine; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs, Vanderbilt University; The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania; Atlanta VA Health Care System, Emory University Rollins School of Public Health; VA Boston Healthcare System and Brigham & Women's Hospital; European Molecular Biology Laboratory, European Bioinformatics Institute; Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; University of Cambridge, Wellcome Genome Campus and University of Cambridge; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School","Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.11.19.20234849,2020-11-22,https://medrxiv.org/cgi/content/short/2020.11.19.20234849,Community factors and excess mortality in first wave of the COVID-19 pandemic.,Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.11.18.20233932,2020-11-20,https://medrxiv.org/cgi/content/short/2020.11.18.20233932,REACT-1 round 6 updated report: high prevalence of SARS-CoV-2 swab positivity with reduced rate of growth in England at the start of November 2020,Steven Riley; Kylie E. C. Ainslie; Oliver Eales; Caroline E. Walters; Haowei Wang; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","BackgroundEngland is now in the midst of its second wave of the COVID-19 pandemic. Multiple regions of the country are at high infection prevalence and all areas experienced rapid recent growth of the epidemic during October 2020. MethodsREACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positivity in England designed to monitor the spread of the epidemic and thus increase situational awareness. Round 6 of REACT-1 commenced swab-collection on 16th October. A prior interim report included data from 16th to 25th October for 85,971 participants. Here, we report data for the entire round on 160,175 participants with swab results obtained up to 2nd November 2020. @@ -4442,6 +4378,13 @@ MethodsWe use a data-driven approach to parameterise an individual-based network ResultsThe progress of the epidemic can be significantly hindered by instructing a significant proportion of the workforce to work from home. Furthermore, if required to be present at the workplace, asynchronous work patterns can help to reduce infections when compared with scenarios where all workers work on the same days, particularly for longer working weeks. When assessing COVID-secure workplace measures, we found that smaller work teams and a greater reduction in transmission risk reduced the probability of large, prolonged outbreaks. Finally, following isolation guidance and engaging with contact tracing without other measures is an effective tool to curb transmission, but is highly sensitive to adherence levels. ConclusionsIn the absence of sufficient adherence to non-pharmaceutical interventions, our results indicate a high likelihood of SARS-CoV-2 spreading widely throughout a worker population. Given the heterogeneity of demographic attributes across worker roles, in addition to the individual nature of controls such as contact tracing, we demonstrate the utility of a network model approach to investigate workplace-targeted intervention strategies and the role of test, trace and isolation in tackling disease spread.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2020.11.18.20225029,2020-11-20,https://medrxiv.org/cgi/content/short/2020.11.18.20225029,The Invasive Respiratory Infection Surveillance (IRIS) Initiative reveals significant reductions in invasive bacterial infections during the COVID-19 pandemic,Angela B Brueggemann; Melissa J Jansen van Rensburg; David Shaw; Noel D McCarthy; Keith A Jolley; Martin CJ Maiden; Mark PG van der Linden,University of Oxford; University of Oxford; University of Oxford; University of Warwick; University of Oxford; University of Oxford; University Hospital RWTH Aachen,"BackgroundStreptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis are leading causes of invasive diseases including bacteraemic pneumonia and meningitis, and of secondary infections post-viral respiratory disease. They are typically transmitted via respiratory droplets. We investigated rates of invasive disease due to these pathogens during the early phase of the COVID-19 pandemic. + +MethodsLaboratories in 26 countries across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae and N meningitidis from 1 January 2018 to 31 May 2020. Weekly cases in 2020 vs 2018-2019 were compared. Streptococcus agalactiae data were collected from nine laboratories for comparison to a non-respiratory pathogen. The stringency of COVID-19 containment measures was quantified by the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed by Google COVID-19 Community Mobility Reports. Interrupted time series modelling quantified changes in rates of invasive disease in 2020 relative to when containment measures were imposed. + +FindingsAll countries experienced a significant, sustained reduction in invasive diseases due to S pneumoniae, H influenzae and N meningitidis, but not S agalactiae, in early 2020, which coincided with the introduction of COVID-19 containment measures in each country. Similar impacts were observed across most countries despite differing stringency in COVID-19 control policies. There was no evidence of a specific effect due to enforced school closures. + +InterpretationThe introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of these bacterial respiratory pathogens, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.11.18.20234369,2020-11-19,https://medrxiv.org/cgi/content/short/2020.11.18.20234369,Antibodies to SARS-CoV-2 are associated with protection against reinfection,Sheila F Lumley; Nicole E Stoesser; Philippa C Matthews; Alison Howarth; Stephanie B Hatch; Brian D Marsden; Stuart Cox; Tim James; Fiona Warren; Liam J Peck; Thomas G Ritter; Zoe de Toledo; Laura Warren; David Axten; Richard J Cornall; E Yvonne Jones; David I Stuart; Gavin Screaton; Daniel Ebner; Sarah Hoosdally; Meera Chand; - Oxford University Hospitals Staff Testing Group; Derrick W Crook; Christopher P Conlon; Koen B Pouwels; A Sarah Walker; Tim EA Peto; Susan Hopkins; Tim M Walker; Katie Jeffery; David W Eyre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Public Health England; ; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Public Health England; University of Oxford; University of Oxford; University of Oxford,"BackgroundIt is critical to understand whether infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) protects from subsequent reinfection. MethodsWe investigated the incidence of SARS-CoV-2 PCR-positive results in seropositive and seronegative healthcare workers (HCWs) attending asymptomatic and symptomatic staff testing at Oxford University Hospitals, UK. Baseline antibody status was determined using anti-spike and/or anti-nucleocapsid IgG assays and staff followed for up to 30 weeks. We used Poisson regression to estimate the relative incidence of PCR-positive results and new symptomatic infection by antibody status, accounting for age, gender and changes in incidence over time. @@ -4506,7 +4449,6 @@ How might this impact on clinical practice or future developments?O_LIVariable s C_LI",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.11.06.20227108,2020-11-07,https://medrxiv.org/cgi/content/short/2020.11.06.20227108,Primary school staff reflections on school closures due to COVID-19 and recommendations for the future: a national qualitative survey,Emily Marchant; Charlotte Todd; Michaela James; Tom Crick; Russell Dwyer; Sinead Brophy,Swansea University; Swansea University; Swansea University; Swansea University; St Thomas Community Primary School; Swansea University,"School closures due to the COVID-19 global pandemic are likely to have a range of negative consequences spanning the domains of child development, education and health, in addition to the widening of inequalities and inequities. Research is required to improve understanding of the impact of school closures on the education, health and wellbeing of pupils and school staff, the challenges posed during reopening and importantly to identify how countries can return to in-school education and to inform policy. This qualitative study aimed to reflect on the perspectives and experiences of primary school staff (pupils aged 3-11) in Wales regarding school closures and the initial reopening of schools and to identify recommendations for the future. A total of 208 school staff completed a national online survey through the HAPPEN primary school network, consisting of questions about school closures (March to June 2020), the phased reopening of schools (June to July 2020) and a return to full-time education. Thematic analysis of survey responses highlighted that primary school staff perceive that gaps in learning, health and wellbeing have increased and inequalities have widened during school closures. Findings from this study identified five recommendations; (i) prioritise the health and wellbeing of pupils and staff; (ii) focus on enabling parental engagement and support; (iii) improve digital competence amongst pupils, teachers and parents; (iv) consider opportunities for smaller class sizes and additional staffing; and (v) improve the mechanism of communication between schools and families, and between government and schools.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.11.05.20223289,2020-11-06,https://medrxiv.org/cgi/content/short/2020.11.05.20223289,Longitudinal proteomic profiling of high-risk patients with COVID-19 reveals markers of severity and predictors of fatal disease,Jack Gisby; Candice L Clarke; Nicholas Medjeral-Thomas; Talat H Malik; Artemis Papadaki; Paige M Mortimer; Norzawani B Buang; Shanice Lewis; Marie Pereira; Frederic Toulza; Ester Fagnano; Marie-Anne Mawhin; Emma E Dutton; Lunnathaya Tapeng; Arianne C Richard; Paul Kirk; Jacques Behmoaras; Eleanor Sandhu; Stephen P McAdoo; Maria F Prendecki; Matthew C Pickering; Marina Botto; Michelle Willicombe; David C Thomas; James E. Peters,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; University of Cambridge; MRC Biostatistics Unit University of Cambridge; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"End-stage kidney disease (ESKD) patients are at high risk of severe COVID-19. We measured 436 circulating proteins in serial blood samples from hospitalised and non-hospitalised ESKD patients with COVID-19 (n=256 samples from 55 patients). Comparison to 51 non-infected patients revealed 221 differentially expressed proteins, with consistent results in a separate subcohort of 46 COVID-19 patients. 203 proteins were associated with clinical severity, including IL6, markers of monocyte recruitment (e.g. CCL2, CCL7), neutrophil activation (e.g. proteinase-3) and epithelial injury (e.g. KRT19). Machine learning identified predictors of severity including IL18BP, CTSD, GDF15, and KRT19. Survival analysis with joint models revealed 69 predictors of death. Longitudinal modelling with linear mixed models uncovered 32 proteins displaying different temporal profiles in severe versus non-severe disease, including integrins and adhesion molecules. These data implicate epithelial damage, innate immune activation, and leucocyte-endothelial interactions in the pathology of severe COVID-19 and provide a resource for identifying drug targets.",infectious diseases,fuzzy,100,100 -bioRxiv,10.1101/2020.11.06.369439,2020-11-06,https://biorxiv.org/cgi/content/short/2020.11.06.369439,Allosteric hotspots in the main protease of SARS-CoV-2,Léonie Strömich; Nan Wu; Mauricio Barahona; Sophia N Yaliraki,Imperial College London; Imperial College London; Imperial College London; Imperial College London,"AO_SCPLOWBSTRACTC_SCPLOWInhibiting the main protease of SARS-CoV-2 is of great interest in tackling the COVID-19 pandemic caused by the virus. Most efforts have been centred on inhibiting the binding site of the enzyme. However, considering allosteric sites, distant from the active or orthosteric site, broadens the search space for drug candidates and confers the advantages of allosteric drug targeting. Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites without a priori knowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. We further score the highest ranking sites against random sites in similar distances through statistical bootstrapping and identify four statistically significant putative allosteric sites as good candidates for alternative drug targeting.",bioinformatics,fuzzy,100,100 medRxiv,10.1101/2020.11.01.20224014,2020-11-04,https://medrxiv.org/cgi/content/short/2020.11.01.20224014,MODELLING PRESYMPTOMATIC INFECTIOUSNESS IN COVID-19,Russell Cheng; Christopher Dye; John Dagpunar; Brian Williams,University of Southampton; Oxford University; University of Southampton; Stellenbosch University,"This paper considers SEPIR, the extension of an existing parametric SEIR continuous simulation compartment model. Both models can be fitted to real data as they include parameters that can simply be estimated from the data. However SEPIR deploys an additional presymptomatic (also called asymptomatic) infectious stage that is not included in SEIR but which is known to exist in COVID-19. This stage is also parametrised and so can be fitted to data. Both SEPIR and the existing SEIR model assume a homogeneous mixing population, an idealisation that is unrealistic in practice when dynamically varying control strategies are deployed against virus. This means that if either model is to represent more than just a single period in the behaviour of the epidemic, then the parameters of the model will have to be time dependent. This issue is also discussed in this paper.",epidemiology,fuzzy,93,100 medRxiv,10.1101/2020.11.02.20223891,2020-11-04,https://medrxiv.org/cgi/content/short/2020.11.02.20223891,Performance characteristics of a rapid SARS-CoV-2 antigen detection assay at a public plaza testing site in San Francisco,Genay Pilarowski; Paul Lebel; Sara Sunshine; Jamin Liu; Emily Crawford; Carina Marquez; Luis Rubio; Gabriel Chamie; Jackie Martinez; James Peng; Douglas Black; Wesley Wu; John Pak; Matthew T Laurie; Diane Jones; Steve Miller; Jon Jacobo; Susana Rojas; Susy Rojas; Robert Nakamura; Valerie Tulier-Laiwa; Maya Petersen; Diane V Havlir; - The CLIAHUB Consortium; Joseph DeRisi,"Department of Pathology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA and Department of Microbiology and Immunology, University of California San Francisco, CA 94143; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA; Unidos en Salud, San Francisco, CA 94143, USA; Department of Laboratory Medicine, University of California San Francisco CA 94131, USA; Latino Task Force-COVID-19, San Francisco, CA 94110, USA; Latino Task Force-COVID-19, San Francisco, CA 94110, USA; Latino Task Force-COVID-19, San Francisco, CA 94110, USA; California Department of Public Health, Microbial Diseases Laboratory, Richmond, CA, 94804, USA; Latino Task Force-COVID-19, San Francisco, CA 94110, USA; Division of Epidemiology and Biostatistics, University of California, Berkeley, Berkeley, CA 94720, USA; Division of HIV, Infectious Diseases, and Global Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; ; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA and Department of Biochemistry and Biophysics, University of California San Francisco, CA 94143, USA","We evaluated the performance of the Abbott BinaxNOW Covid-19 rapid antigen test to detect virus among persons, regardless of symptoms, at a public plaza site of ongoing community transmission. Titration with cultured clinical SARS-CoV-2 yielded a human observable threshold between 1.6x104-4.3x104 viral RNA copies (cycle threshold (Ct) of 30.3-28.8 in this assay). Among 878 subjects tested, 3% (26/878) were positive by RT-PCR, of which 15/26 had a Ct<30, indicating high viral load. 40% (6/15) of Ct<30 were asymptomatic. Using this Ct<30 threshold for Binax-CoV2 evaluation, the sensitivity of the Binax-CoV2 was 93.3% (14/15), 95% CI: 68.1-99.8%, and the specificity was 99.9% (855/856), 95% CI: 99.4-99.9%.",infectious diseases,fuzzy,92,100 medRxiv,10.1101/2020.11.03.20220699,2020-11-04,https://medrxiv.org/cgi/content/short/2020.11.03.20220699,A prospective study of risk factors associated with seroprevalence of SARS-CoV-2 antibodies in healthcare workers at a large UK teaching hospital,Daniel J Cooper; Sara Lear; Laura Watson; Ashley Shaw; Mark Ferris; Rainer Doffinger; Rachel Bousfield; Katherine Sharrocks; Michael Weekes; Ben Warne; Dominic Sparkes; Nick K Jones; Lucy Rivett; Matthew Routledge; Afzal Chaudhry; Katherine Dempsey; Montgomery Matson; Adil Lakha; George Gathercole; Olivia O'Connor; Emily Wilson; Orthi Shahzad; Kieran Toms; Rachel Thompson; Ian Halsall; David Halsall; Sally Houghton; Sofia Papadia; Nathalie Kingston; Kathleen Stirrups; Barbara Graves; Neil Walker; Hannah Stark; - The CITIID-NIHR BioResource COVID-19 Collaboration; Daniela De Angelis; Shaun Seaman; John Bradley; M Estée Török; Ian G. Goodfellow; Stephen Baker,"Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR Cambridge Clinical Research Facility; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR Cambridge Clinical Research Facility.; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust; ; MRC Biostatistics Unit, University of Cambridge; MRC Biostatistics Unit, University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Department of pathology, Division of virology, University of Cambridge; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK","BackgroundThe COVID-19 pandemic continues to grow at an unprecedented rate. Healthcare workers (HCWs) are at higher risk of SARS-CoV-2 infection than the general population but risk factors for HCW infection are not well described. @@ -4665,7 +4607,6 @@ The decline from rounds 1 to 3 was largest in those who did not report a history DiscussionThese findings provide evidence of variable waning in antibody positivity over time such that, at the start of the second wave of infection in England, only 4.4% of adults had detectable IgG antibodies using an LFIA. Antibody positivity was greater in those who reported a positive PCR and lower in older people and those with asymptomatic infection. These data suggest the possibility of decreasing population immunity and increasing risk of reinfection as detectable antibodies decline in the population.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.10.26.20219485,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.26.20219485,Predicting the impact of COVID-19 interruptions on transmission of gambiense human African trypanosomiasis in two health zones of the Democratic Republic of Congo,Maryam Aliee; Soledad Castano; Christopher Davis; Swati Patel; Erick Mwamba Miaka; Simon EF Spencer; Matt J Keeling; Nakul Chitnis; Kat S Rock,"University of Warwick; Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute; University of Warwick; University of Warwick; Programme National de Lutte contre la Trypanosomiase Humaine Africaine, Kinshasa, the Democratic Republic of the Congo; University of Warwick; University of Warwick; Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Warwick","Many control programmes against neglected tropical diseases have been interrupted due to COVID-19 pandemic, including those that rely on active case finding. In this study we focus on gambiense human African trypanosomiasis (gHAT), where active screening was suspended in the Democratic Republic of Congo (DRC) due to the pandemic. We use two independent mathematical models to predict the impact of COVID-19 interruptions on transmission and reporting, and the achievement of 2030 elimination of transmission (EOT) goal for gHAT in two moderate-risk regions of DRC. We consider different interruption scenarios, including reduced passive surveillance in fixed health facilities, and whether this suspension lasts until the end of 2020 or 2021. Our models predict an increase in the number of new infections in the interruption period only if both active screening and passive surveillance were suspended, and with slowed reduction - but no increase - if passive surveillance remains fully functional. In all scenarios, the EOT may be slightly pushed back if no mitigation such as increased screening coverage is put in place. However, we emphasise that the biggest challenge will remain in the higher prevalence regions where EOT is already predicted to be behind schedule without interruptions unless interventions are bolstered.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.10.19.20214494,2020-10-21,https://medrxiv.org/cgi/content/short/2020.10.19.20214494,Attributes and predictors of Long-COVID: analysis of COVID cases and their symptoms collected by the Covid Symptoms Study App,Carole H Sudre; Benjamin Murray; Thomas Varsavsky; Mark S Graham; Rose S Penfold; Ruth C.E Bowyer; Joan Capdevila Pujol; Kerstin Klaser; Michela Antonelli; Liane S Canas; Erika Molteni; Marc Modat; M. Jorge Cardoso; Anna May; Sajaysurya Ganesh; Richard Davies; Long H Nguyen; David Alden Drew; Christina M Astley; Amit D. Joshi; Jordi Merino; Neli Tsereteli; Tove Fall; Maria F Gomez; Emma Duncan; Christina Menni; Frances MK Williams; Paul W Franks; Andrew T Chan; Jonathan Wolf; Sebastien Ourselin; Timothy Spector; Claire J Steves,KCL; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital; Boston Children's Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Lund University; Uppsala University; Lund University; King's College London; King's College London; King's College London; Lund University; Massachusetts General Hospital; Zoe Global Limited; King's College London; King's College London; King's College London,"Reports of ""Long-COVID"", are rising but little is known about prevalence, risk factors, or whether it is possible to predict a protracted course early in the disease. We analysed data from 4182 incident cases of COVID-19 who logged their symptoms prospectively in the COVID Symptom Study app. 558 (13.3%) had symptoms lasting >=28 days, 189 (4.5%) for >=8 weeks and 95 (2.3%) for >=12 weeks. Long-COVID was characterised by symptoms of fatigue, headache, dyspnoea and anosmia and was more likely with increasing age, BMI and female sex. Experiencing more than five symptoms during the first week of illness was associated with Long-COVID, OR=3.53 [2.76;4.50]. A simple model to distinguish between short and long-COVID at 7 days, which gained a ROC-AUC of 76%, was replicated in an independent sample of 2472 antibody positive individuals. This model could be used to identify individuals for clinical trials to reduce long-term symptoms and target education and rehabilitation services.",infectious diseases,fuzzy,94,100 medRxiv,10.1101/2020.10.15.20213108,2020-10-20,https://medrxiv.org/cgi/content/short/2020.10.15.20213108,FebriDx point-of-care test in patients with suspected COVID-19: a pooled diagnostic accuracy study,Samuel G Urwin; B Clare Lendrem; Jana Suklan; Kile Green; Sara Graziadio; Peter Buckle; Paul M Dark; Adam L Gordon; Daniel S Lasserson; Brian Nicholson; D Ashley Price; Charles Reynard; Mark H Wilcox; Gail Hayward; Graham Prestwich; Valerie Tate; Tristan W Clark; Raja V Reddy; Hamish Houston; Ankur Gupta-Wright; Laurence John; Richard Body; A Joy Allen,"NIHR Newcastle In Vitro Diagnostics Co-operative, Newcastle-upon-Tyne Hospitals Foundation Trust, Newcastle-upon-Tyne, UK; NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK; NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK; NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK; NIHR Newcastle In Vitro Diagnostics Co-operative, Newcastle-upon-Tyne Hospitals Foundation Trust, Newcastle-upon-Tyne, UK; Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, UK; Division of Infection, Immunity & Respiratory Medicine, University of Manchester, UK; School of Medicine, University of Nottingham, UK; NIHR Applied Research Collaboration East Midlands (ARC-EM), Nottingham, UK; NIHR Community Healthcare MedTech and In Vitro Diagnostics Cooperative, Oxford Health NHS Foundation Trust, Oxford, UK; Division of Health Sciences, University ; Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; NIHR Newcastle In Vitro Diagnostics Co-operative, Newcastle-upon-Tyne Hospitals Foundation Trust, Newcastle-upon-Tyne, UK; NIHR Doctoral Research Fellowship Programme, UK; Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK; Healthcare Associated Infections Research Group, NIHR Leeds In Vitro Diagnostics Co-operative, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds; NIHR Community Healthcare MedTech and In Vitro Diagnostics Co-operative, Oxford Health NHS Foundation Trust, Oxford, UK; Nuffield Department of Primary Care Hea; Yorkshire and Humber Academic Health Science Network, Wakefield, UK; Patient Public Involvement (PPI) Member, Precision Antimicrobial Prescribing PPI Group, NIHR Community Healthcare MedTech and In Vitro Diagnostics Cooperative, ; School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; Department of Infection, University Hospital Sout; Department of Respiratory Medicine, Kettering General Hospital NHS Foundation Trust, Kettering, UK; Northwick Park Hospital, London North West University Healthcare NHS Trust, Harrow, UK; Institute for Global Health, University College London, London, UK; Ealing Hospital, London North West University Healthcare NHS Trust, London, UK; Clinical Res; Northwick Park Hospital, London North West University Healthcare NHS Trust, Harrow, UK; Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, University of Manchester, UK; Emergency Department, Manchester Royal Infirmary, Ma; NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK","BackgroundWe conducted a systematic review and individual patient data (IPD) meta-analysis to evaluate the diagnostic accuracy of a commercial point-of-care test, the FebriDx lateral flow device (LFD), in adult patients with suspected COVID-19. The FebriDx LFD is designed to distinguish between viral and bacterial respiratory infection. MethodsWe searched MEDLINE, EMBASE, PubMed, Google Scholar, LitCovid, ClinicalTrials.gov and preprint servers on the 13th of January 2021 to identify studies reporting diagnostic accuracy of FebriDx (myxovirus resistance protein A component) versus real time reverse transcriptase polymerase chain reaction (RT-PCR) testing for SARS-CoV-2 in adult patients suspected of COVID-19. IPD were sought from studies meeting the eligibility criteria. Studies were screened for risk of bias using the QUADAS-2 tool. A bivariate linear mixed model was fitted to the data to obtain a pooled estimate of sensitivity and specificity with 95% confidence intervals (95% CIs). A summary receiver operating characteristic (SROC) curve of the model was constructed. A sub-group analysis was performed by meta-regression using the same modelling approach to compare pooled estimates of sensitivity and specificity between patients with a symptom duration of 0 to 7 days and >7 days, and patients aged between 16 to 73 years and >73 years. @@ -4856,17 +4797,6 @@ Results241,266, 41,198, 23,783 and 3,850 adults shared a household with 0, 1, 2, ConclusionBetween March and October 2020, living with young children was associated with an attenuated risk of any COVID-19 and COVID-19 requiring hospitalisation among adults living in healthcare worker households. There was no evidence that living with young children increased adults risk of COVID-19, including during the period after schools re-opened.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.09.17.20196436,2020-09-21,https://medrxiv.org/cgi/content/short/2020.09.17.20196436,Comparison of COVID-19 outcomes among shielded and non-shielded populations: A general population cohort study of 1.3 million,Bhautesh D Jani; Frederick K Ho; David J Lowe; Jamie P Traynor; Sean MacBride-Stewart; Patrick B Mark; Frances S Mair; Jill P Pell,University of Glasgow; University of Glasgow; NHS Greater Glasgow and Clyde; NHS Greater Glasgow and Clyde; NHS Greater Glasgow and Clyde; University of Glasgow; University of Glasgow; University of Glasgow,"Many western countries used shielding (extended self-isolation) of people presumed to be at high-risk from COVID-19 to protect them and reduce healthcare demand. To investigate the effectiveness of this strategy, we linked family practitioner, prescribing, laboratory, hospital and death records and compared COVID-19 outcomes among shielded and non-shielded individuals in the West of Scotland. Of the 1.3 million population, 27,747 (2.03%) were advised to shield, and 353,085 (26.85%) were classified a priori as moderate risk. COVID-19 testing was more common in the shielded (7.01%) and moderate risk (2.03%) groups, than low risk (0.73%). Referent to low-risk, the shielded group had higher confirmed infections (RR 8.45, 95% 7.44-9.59), case-fatality (RR 5.62, 95% CI 4.47-7.07) and population mortality (RR 57.56, 95% 44.06-75.19). The moderate-risk had intermediate confirmed infections (RR 4.11, 95% CI 3.82-4.42) and population mortality (RR 25.41, 95% CI 20.36-31.71) but, due to their higher prevalence, made the largest contribution to deaths (PAF 75.30%). Age [≥]70 years accounted for 49.55% of deaths. In conclusion, shielding has not been effective at preventing deaths in individuals at high risk. Also, to be effective as a population strategy, shielding criteria would need to be widely expanded to include other criteria, such as the elderly.",public and global health,fuzzy,100,100 -medRxiv,10.1101/2020.09.15.20194795,2020-09-18,https://medrxiv.org/cgi/content/short/2020.09.15.20194795,"Acute, non-COVID related medical admissions during the first wave of COVID-19: A retrospective comparison of changing patterns of disease",Bridget Riley; Mary Packer; Suzy Gallier; Elizabeth Sapey; Catherine Atkin,"University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; PIONEER Hub, University Hospitals Birmingham NHS Foundation Trust; PIONEER Hub, University of Birmingham; PIONEER Hub, University of Birmingham","BackgroundThe COVID-19 pandemic was associated with social restrictions in the UK from 16th March 2020. It was unclear if the lockdown period was associated with differences in the case-mix of non-COVID acute medical admissions compared with the previous year. - -MethodsRetrospective data were collected for 1st-30th April 2019 and 1st-30th April 2020 from University Hospitals Birmingham NHS Foundation Trust, one of the largest hospitals in the UK with over 2 million patient contacts per year. The latter time period was chosen to coincide with the peak of COVID-19 cases in the West Midlands. All patients admitted under acute medicine during these time periods were included. COVID-19 was confirmed by SARS-Cov-2 swab or a probable case of COVID-19 based on World Health Organization diagnostic parameters. Non-COVID patients were those with a negative SARS-Cov-2 swab and no suspicion of COVID-19. Data was sourced from UHBs in-house electronic health system (EHS). - -ResultsThe total number of acute medical admissions fell comparing April 2019 (n = 2409) to April 2020 (n = 1682). As a proportion of total admissions, those aged under 45 years decreased, while those aged 46 and over did not change. - -The number of admissions due to psychiatric conditions and overdoses was higher in April 2020 (p < 0.001). When viewed as a proportion of admissions, alcohol-related admissions (p = 0.004), psychiatric conditions and overdoses (p< 0.001) increased in April 2020 than in April 2019. The proportion of patients who were in hospital due to falls also increased in April 2020 (p< 0.001). In the same period, the absolute number and the proportion of admissions that were due to non-specific chest pain, to musculoskeletal complaints and patients who self-discharged prior to assessment decreased (p = 0.02, p = 0.01 and p = 0.002 respectively). - -There were no significant differences in non-COVID-related intensive care admissions or mortality between the same months in the two years. - -ConclusionIn this large, single-centre study, there was a change in hospitalised case-mix when comparing April 2019 with April 2020: an increase in conditions which potentially reflect social isolation (falls, drug and alcohol misuse and psychiatric illness) and a decrease in conditions which rarely require in-patient hospital treatment (musculoskeletal pain and non-cardiac chest pain) especially among younger adults. These results highlight two areas for further research; the impact of social isolation on health and whether younger adults could be offered alternative health services to avoid potentially unnecessary hospital assessment.",emergency medicine,fuzzy,100,100 medRxiv,10.1101/2020.09.17.20196469,2020-09-18,https://medrxiv.org/cgi/content/short/2020.09.17.20196469,Renin-angiotensin system inhibitors and susceptibility to COVID-19 in patients with hypertension: a propensity score-matched cohort study in primary care,Shamil Haroon; Anuradhaa Subramanian; Jennifer Cooper; Astha Anand; Krishna Gokhale; Nathan Byne; Samir Dhalla; Dionisio Acosta-Mena; Thomas Taverner; Kelvin Okoth; Jingya Wang; Joht Singh Chandan; Christopher Sainsbury; Dawit Tefra Zemedikun; G Neil Thomas; Dhruv Parekh; Tom Marshall; Elizabeth Sapey; Nicola J Adderley; Krishnarajah Nirantharakumar,"University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Cegedim Health Data, Cegedim Rx, London, UK; Cegedim Health Data, Cegedim Rx, London, UK; Cegedim Health Data, Cegedim Rx, London, UK; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham and Department of Diabetes, Gartnavel General Hospital, NHS Greater Glasgow and Clyde, UK; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham","Introduction A significant proportion of patients with Coronavirus Disease-19 (COVID-19) have hypertension and are treated with renin-angiotensin system (RAS) inhibitors, namely angiotensin-converting enzyme I inhibitors (ACE inhibitors) or angiotensin II type-1 receptor blockers (ARBs). These medications have been postulated to influence susceptibility to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). The objective of this study was to assess a possible association between prescription of RAS inhibitors and the incidence of COVID-19 and all-cause mortality. Methods We conducted a propensity-score matched cohort study to assess the incidence of COVID-19 among patients with hypertension who were prescribed ACE inhibitors or ARBs compared to patients treated with calcium channel blockers (CCBs) in a large UK-based primary care database (The Health Improvement Network). We estimated crude incidence rates for confirmed/suspected COVID-19 among those prescribed ACE inhibitors, ARBs and CCBs. We used a Cox proportional hazards model to produce adjusted hazard ratios for COVID-19 comparing patients prescribed ACE inhibitors or ARBs to those prescribed CCBs. We further assessed all-cause mortality as a secondary outcome and a composite of accidents, trauma or fractures as a negative control outcome to assess for residual confounding. Results In the propensity score matched analysis, 83 of 18,895 users (0.44%) of ACE inhibitors developed COVID-19 over 8,923 person-years, an incidence rate of 9.3 per 1000 person-years. 85 of 18,895 (0.45%) users of CCBs developed COVID-19 over 8,932 person-years, an incidence rate of 9.5 per 1000 person-years. The adjusted hazard ratio for suspected/confirmed COVID-19 for users of ACE inhibitors compared to CCBs was 0.92 (95% CI 0.68 to 1.26). 79 out of 10,623 users (0.74%) of ARBs developed COVID-19 over 5010 person-years, an incidence rate of 15.8 per 1000 person-years, compared to 11.6 per 1000 person-years among users of CCBs. The adjusted hazard ratio for suspected/confirmed COVID-19 for users of ARBs compared to CCBs was 1.38 (95% CI 0.98 to 1.95). There were no significant associations between use of ACE inhibitors or ARBs and all-cause mortality, compared to use of CCBs. We found no evidence of significant residual confounding with the negative control analysis. Conclusion Current use of ACE inhibitors was not associated with the risk of suspected or confirmed COVID-19 whereas use of ARBs was associated with a statistically non-significant 38% relative increase in risk compared to use of CCBs. However, no significant associations were observed between prescription of either ACE inhibitors or ARBs and all-cause mortality during the peak of the pandemic.",infectious diseases,fuzzy,100,100 bioRxiv,10.1101/2020.09.16.297945,2020-09-16,https://biorxiv.org/cgi/content/short/2020.09.16.297945,Characterisation of protease activity during SARS-CoV-2 infection identifies novel viral cleavage sites and cellular targets for drug repurposing,Bjoern Meyer; Jeanne Chiaravalli; Stacy Gellenoncourt; Philip Brownridge; Dominic P. Bryne; Leonard A. Daly; Arturas Grauslys; Marius Walter; Fabrice Agou; Lisa A. Chakrabarti; Charles S. Craik; Claire E. Eyers; Patrick A. Eyers; Yann Gambin; Andrew R Jones; Emma Sierecki; Eric Verdin; Marco Vignuzzi; Edward Emmott,Institut Pasteur; Institut Pasteur; Institut Pasteur; University of Liverpool; University of Liverpool; University of Liverpool; University of Liverpool; Buck Institute for Aging; Institut Pasteur; Institut Pasteur; UCSF; University of Liverpool; University of Liverpool; UNSW; University of Liverpool; UNSW; Buck Institute for Aging; Institut Pasteur; University of Liverpool,"SARS-CoV-2 is the causative agent behind the COVID-19 pandemic, and responsible for over 170 million infections, and over 3.7 million deaths worldwide. Efforts to test, treat and vaccinate against this pathogen all benefit from an improved understanding of the basic biology of SARS-CoV-2. Both viral and cellular proteases play a crucial role in SARS-CoV-2 replication, and inhibitors targeting proteases have already shown success at inhibiting SARS-CoV-2 in cell culture models. Here, we study proteolytic cleavage of viral and cellular proteins in two cell line models of SARS-CoV-2 replication using mass spectrometry to identify protein neo-N-termini generated through protease activity. We identify previously unknown cleavage sites in multiple viral proteins, including major antigenic proteins S and N, which are the main targets for vaccine and antibody testing efforts. We discovered significant increases in cellular cleavage events consistent with cleavage by SARS-CoV-2 main protease, and identify 14 potential high-confidence substrates of the main and papain-like proteases, validating a subset with in vitro assays. We showed that siRNA depletion of these cellular proteins inhibits SARS-CoV-2 replication, and that drugs targeting two of these proteins: the tyrosine kinase SRC and Ser/Thr kinase MYLK, showed a dose-dependent reduction in SARS-CoV-2 titres. Overall, our study provides a powerful resource to understand proteolysis in the context of viral infection, and to inform the development of targeted strategies to inhibit SARS-CoV-2 and treat COVID-19.",microbiology,fuzzy,100,100 medRxiv,10.1101/2020.09.12.20191973,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.12.20191973,Inequality in access to health and care services during lockdown - Findings from the COVID-19 survey in five UK national longitudinal studies,Constantin-Cristian Topriceanu; Andrew Wong; James C Moon; Alun Hughes; David Bann; Nishi Chaturvedi; Praveetha Patalay; Gabriella Conti; Gabriella Captur,University College London; UCL; UCL; UCL; University College London; UCL; University College London; UCL; University College London,"Background: Access to health services and adequate care is influenced by sex, ethnicity, socio-economic position (SEP) and burden of co-morbidities. However, it is unknown whether the COVID-19 pandemic further deepened these already existing health inequalities. Methods: Participants were from five longitudinal age-homogenous British cohorts (born in 2001, 1990, 1970, 1958 and 1946). A web and telephone-based survey provided data on cancelled surgical or medical appointments, and the number of care hours received during the UK COVID-19 national lockdown. Using binary or ordered logistic regression, we evaluated whether these outcomes differed by sex, ethnicity, SEP and having a chronic illness. Adjustment was made for study-design, non-response weights, psychological distress, presence of children or adolescents in the household, keyworker status, and whether participants had received a shielding letter. Meta-analyses were performed across the cohorts and meta-regression evaluated the effect of age as a moderator. Findings: 14891 participants were included. Females (OR 1.40, 95% confidence interval [1.27,1.55]) and those with a chronic illness (OR 1.84 [1.65-2.05]) experienced significantly more cancellations during lockdown (all p<0.0001). Ethnic minorities and those with a chronic illness required a higher number of care hours during the lockdown (both OR approx. 2.00, all p<0.002). Age was not independently associated with either outcome in meta-regression. SEP was not associated with cancellation or care hours. Interpretation: The UK government's lockdown approach during the COVID-19 pandemic appears to have deepened existing health inequalities, impacting predominantly females, ethnic-minorities and those with chronic illnesses. Public health authorities need to implement urgent policies to ensure equitable access to health and care for all in preparation for a second wave.",public and global health,fuzzy,100,100 @@ -4925,6 +4855,15 @@ MethodsIn this analysis of the Bug Watch prospective community cohort study, we ResultsThe baseline incidence of cough or fever in the UK is expected to rise rapidly from 154,554 (95%CI 103,083 - 231,725) cases per day in August 2020 to 250,708 (95%CI 181,095 - 347,080) in September, peaking at 444,660 (95%CI 353,084 - 559,988) in December. If 80% of baseline cough or fever cases request tests, average daily UK testing demand would exceed current capacity for five consecutive months (October 2020 to February 2021), with a peak demand of 147,240 (95%CI 73,978 - 239,502) tests per day above capacity in December 2020. ConclusionsOur results show that current national COVID-19 testing capacity is likely to be exceeded by demand due to baseline cough and fever alone. This study highlights that the UKs response to the COVID-19 pandemic must ensure that a high proportion of people with symptoms request tests, and that testing capacity is immediately scaled up to meet this high predicted demand.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.09.01.20185793,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.01.20185793,Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study,Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter,University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust,"ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection. + +MethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome. + +ResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold. + +ConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive. + +RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,fuzzy,100,100 medRxiv,10.1101/2020.09.02.20186502,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.02.20186502,Real-time monitoring of COVID-19 dynamics using automated trend fitting and anomaly detection,Thibaut Jombart; Stephane Ghozzi; Dirk Schumacher; Quentin Leclerc; Mark Jit; Stefan Flasche; Felix Greaves; Tom Ward; Rosalind M Eggo; Emily Nightingale; Sophie Meakin; Oliver J Brady; - Centre for Mathematical Modelling of Infectious Diseases COVID-19 Working Group; Graham Medley; Michael Hohle; John Edmunds,"London School of Hygiene and Tropical Medicine (LSHTM); Department of Epidemiology, Helmholtz Centre for Infection Research, Brunswick, Lower Saxony, Germany; R Epidemics Consortium; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; LSHTM; Joint Biosecurity Centre; Joint Biosecurity Centre; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; LSHTM; London School of Hygiene and Tropical Medicine; ; LSHTM; Department of Mathematics, Stockholm University, Sweden; LSHTM","As several countries gradually release social distancing measures, rapid detection of new localised COVID-19 hotspots and subsequent intervention will be key to avoiding large-scale resurgence of transmission. We introduce ASMODEE (Automatic Selection of Models and Outlier Detection for Epidemics), a new tool for detecting sudden changes in COVID-19 incidence. Our approach relies on automatically selecting the best (fitting or predicting) model from a range of user-defined time series models, excluding the most recent data points, to characterise the main trend in an incidence. We then derive prediction intervals and classify data points outside this interval as outliers, which provides an objective criterion for identifying departures from previous trends. We also provide a method for selecting the optimal breakpoints, used to define how many recent data points are to be excluded from the trend fitting procedure. The analysis of simulated COVID-19 outbreaks suggest ASMODEE compares favourably with a state-of-art outbreak-detection algorithm while being simpler and more flexible. We illustrate our method using publicly available data of NHS Pathways reporting potential COVID-19 cases in England at a fine spatial scale, for which we provide a template automated analysis pipeline. ASMODEE is implemented in the free R package trendbreaker.",health informatics,fuzzy,100,100 medRxiv,10.1101/2020.09.02.20186817,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.02.20186817,Revealing the extent of the COVID-19 pandemic in Kenya based on serological and PCR-test data,John Ojal; Samuel PC Brand; Vincent Were; Emelda A Okiro; Ivy Kadzo Kombe; Caroline Mburu; Rabia Aziza; Morris Ogero; Ambrose Agweyu; George M Warimwe; Sophie Uyoga; Ifedayo M. O Adetifa; John Anthony Scott; Edward Otieno; Lynette I Ochola-Oyier; Charles Nyaigoti Agoti; Kadondi Kasera; Patrick Amoth; Mercy Mwangangi; Rashid Aman; Wangari Ng'ang'a; Benjamin Tsofa; Philip Bejon; Edwine Barasa; Matt J Keeling; D James Nokes,"Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya and London School of Hygiene and Tropical Medicine; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK.; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; KEMRI Wellcome Trust Research Programme; KEMRI-Wellcome Trust Research Programme; London School of Hygiene & Tropical Medicine; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Ministry of Health, Government of Kenya, Kenya; Presidential Policy & Strategy Unit, The Presidency, Government of Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; Kenya Medical Research Institute -Wellcome Trust Research Programme, Kenya; KEMRI-Wellcome Trust Research Programme; The Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, UK; KEMRI-Wellcome Trust Research Programme, Kenya and School of Life Sciences, University of Warwick, UK","Policy makers in Africa need robust estimates of the current and future spread of SARS-CoV-2. Data suitable for this purpose are scant. We used national surveillance PCR test, serological survey and mobility data to develop and fit a county-specific transmission model for Kenya. We estimate that the SARS-CoV-2 pandemic peaked before the end of July 2020 in the major urban counties, with 34 - 41% of residents infected, and will peak elsewhere in the country within 2-3 months. Despite this penetration, reported severe cases and deaths are low. Our analysis suggests the COVID-19 disease burden in Kenya may be far less than initially feared. A similar scenario across sub-Saharan Africa would have implications for balancing the consequences of restrictions with those of COVID-19.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.09.01.20183822,2020-09-02,https://medrxiv.org/cgi/content/short/2020.09.01.20183822,Trust and Transparency in times of Crisis: Results from an Online Survey During the First Wave (April 2020) of the COVID-19 Epidemic in the UK,Luisa Enria; Naomi Waterlow; Nina Trivedy Rogers; Hannah Brindle; Sham Lal; Rosalind M Eggo; Shelley Lees; Chrissy h Roberts,London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; UCL; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine (LSHTM),"BackgroundThe success of a governments COVID-19 control strategy relies on public trust and broad acceptance of response measures. We investigated public perceptions of the UK governments COVID-19 response, focusing on the relationship between trust and transparency, during the first wave (April 2020) of the COVID-19 pandemic in the United Kingdom. @@ -5408,7 +5347,6 @@ ResultsSurvival curves show an increased proportion of deaths between 23rd March ConclusionsThe survival curves and increased HRs show a significantly increased risk of death in the 2020 study periods.",public and global health,fuzzy,100,100 bioRxiv,10.1101/2020.07.01.182709,2020-07-01,https://biorxiv.org/cgi/content/short/2020.07.01.182709,Genetic architecture of host proteins interacting with SARS-CoV-2,Maik Pietzner; Eleanor Wheeler; Julia Carrasco-Zanini; Johannes Raffler; Nicola D. Kerrison; Erin Oerton; Victoria P.W. Auyeung; Chris Finan; Juan P. Casas; Rachel Ostroff; Steve A. Williams; Gabi Kastenmüller; Markus Ralser; Eric G. Gamazon; Nicholas J. Wareham; Aroon Dinesh Hingorani; Claudia Langenberg,University of Cambridge; University of Cambridge; University of Cambridge; Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH); University of Cambridge; University of Cambridge; University of Cambridge; University College London; Harvard Medical School; SomaLogic Inc.; SomaLogic Inc.; Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH); The Francis Crick Institute; Vanderbilt University Medical Center; University of Cambridge; University College London; University of Cambridge,"Strategies to develop therapeutics for SARS-CoV-2 infection may be informed by experimental identification of viral-host protein interactions in cellular assays and measurement of host response proteins in COVID-19 patients. Identification of genetic variants that influence the level or activity of these proteins in the host could enable rapid in silico assessment in human genetic studies of their causal relevance as molecular targets for new or repurposed drugs to treat COVID-19. We integrated large-scale genomic and aptamer-based plasma proteomic data from 10,708 individuals to characterize the genetic architecture of 179 host proteins reported to interact with SARS-CoV-2 proteins or to participate in the host response to COVID-19. We identified 220 host DNA sequence variants acting in cis (MAF 0.01-49.9%) and explaining 0.3-70.9% of the variance of 97 of these proteins, including 45 with no previously known protein quantitative trait loci (pQTL) and 38 encoding current drug targets. Systematic characterization of pQTLs across the phenome identified protein-drug-disease links, evidence that putative viral interaction partners such as MARK3 affect immune response, and establish the first link between a recently reported variant for respiratory failure of COVID-19 patients at the ABO locus and hypercoagulation, i.e. maladaptive host response. Our results accelerate the evaluation and prioritization of new drug development programmes and repurposing of trials to prevent, treat or reduce adverse outcomes. Rapid sharing and dynamic and detailed interrogation of results is facilitated through an interactive webserver (https://omicscience.org/apps/covidpgwas/).",genomics,fuzzy,100,100 -medRxiv,10.1101/2020.06.29.20142448,2020-06-30,https://medrxiv.org/cgi/content/short/2020.06.29.20142448,Using past and current data to estimate potential crisis service use in mental healthcare after the COVID-19 lockdown: South London and Maudsley data,Robert Stewart; Matthew Broadbent,King's College London; South London and Maudsley NHS Foundation Trust,"The lockdown policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare with uncertain consequences over the 12 months ahead. Past activity may provide a means to predict future demand. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource at the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in south London), we carried out a range of descriptive analyses to inform the Trust on patient groups who might be most likely to require inpatient and home treatment team (HTT) crisis care. We considered the 12 months following UK COVID-19 lockdown policy on 16th March, drawing on comparable findings from previous years, and quantified levels of change in service delivery to those most likely to receive crisis care. For 12-month crisis days from 16th March in 2015-19, we found that most (over 80%) were accounted for by inpatient care (rather than HTT), most (around 75%) were used by patients who were current or recent Trust patients at the commencement of follow-up, and highest numbers were used by patients with a previously recorded schizophreniform disorder diagnosis. For current/recent patients on 16th March there had been substantial reductions in use of inpatient care in the following 31 days in 2020, more than previous years; changes in total non-inpatient contact numbers did not differ in 2020 compared to previous years, although there had been a marked switch from face-to-face to virtual contacts.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.06.28.20141986,2020-06-29,https://medrxiv.org/cgi/content/short/2020.06.28.20141986,Protocol for the development and evaluation of a tool for predicting risk of short-term adverse outcomes due to COVID-19 in the general UK population,Julia Hippisley-Cox; Ashley Kieran Clift; Carol AC Coupland; Ruth Keogh; Karla Diaz-Ordaz; Elizabeth Williamson; Ewen Harrison; Andrew Hayward; Harry Hemingway; Peter Horby; Nisha Mehta; Jonathan Kieran Benger; Kamlesh Khunti; David Spiegelhalter; Aziz Sheikh; Jonathan Valabhji; Ronan A Lyons; John Robson; Malcolm Gracie Semple; Frank Kee; Peter Johnson; Susan Jebb; Tony Williams; David Coggon,"University of Oxford; University of Oxford; University of Nottingham; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Edinburgh; University College London; University College London; University of Oxford; Department of Health and Social Care; NHS Digital; University of Leicester; University of Cambridge; University of Edinburgh; Imperial College London; Swansea University; Queen Mary University London; University of Liverpool; Queen's University Belfast; University of Southampton; University of Oxford; Working Fit, Ltd.; University of Southampton","IntroductionNovel coronavirus 2019 (COVID-19) has propagated a global pandemic with significant health, economic and social costs. Emerging emergence has suggested that several factors may be associated with increased risk from severe outcomes or death from COVID-19. Clinical risk prediction tools have significant potential to generate individualised assessment of risk and may be useful for population stratification and other use cases. Methods and analysisWe will use a prospective open cohort study of routinely collected data from 1205 general practices in England in the QResearch database. The primary outcome is COVID-19 mortality (in or out-of-hospital) defined as confirmed or suspected COVID-19 mentioned on the death certificate, or death occurring in a person with SARS-CoV-2 infection between 24th January and 30th April 2020. Our primary outcome in adults is COVID-19 mortality (including out of hospital and in hospital deaths). We will also examine COVID-19 hospitalisation in children. Time-to-event models will be developed in the training data to derive separate risk equations in adults (19-100 years) for males and females for evaluation of risk of each outcome within the 3-month follow-up period (24th January to 30th April 2020), accounting for competing risks. Predictors considered will include age, sex, ethnicity, deprivation, smoking status, alcohol intake, body mass index, pre-existing medical co-morbidities, and concurrent medication. Measures of performance (prediction errors, calibration and discrimination) will be determined in the test data for men and women separately and by ten-year age group. For children, descriptive statistics will be undertaken if there are currently too few serious events to allow development of a risk model. The final model will be externally evaluated in (a) geographically separate practices and (b) other relevant datasets as they become available. @@ -5569,6 +5507,15 @@ C_LI What do these findings mean?O_LIIndividuals with [≥]2 LTCs, especially if these are cardiometabolic in nature, should be particularly stringent in adhering to preventive measures, such as physical distancing and hand hygiene. C_LIO_LIOur findings have implications for clinicians, occupational health and employers when considering work-place environments, appropriate advice for patients, and adaptations that might be required to protect such staff, identified here, as higher risk. C_LI",epidemiology,fuzzy,100,91 +medRxiv,10.1101/2020.06.10.20127175,2020-06-11,https://medrxiv.org/cgi/content/short/2020.06.10.20127175,Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.,Amitava Banerjee; Suliang Chen; Laura Pasea; Alvina Lai; Michail Katsoulis; Spiros Denaxas; Vahe Nafilyan; Bryan Williams; Wai Keong Wong; Ameet Bakhai; Kamlesh Khunti; Deenan Pillay; Mahdad Noursadeghi; Honghan Wu; Nilesh Pareek; Daniel Bromage; Theresa Mcdonagh; Jonathan Byrne; James T Teo; Ajay Shah; Ben Humberstone; Liang V Tang; Anoop SV Shah; Andrea Rubboli; Yutao Guo; Yu Hu; Cathie LM Sudlow; Gregory YH Lip; Harry Hemingway,"University College London; University College London; University College London; University College London; UCL; University College London; Office for National Statistics; UCL; University College London Hospitals NHS Trust; Royal Free Hospitals NHS Trust; University of Leicester; UCL; UCL; UCL; King's College Hospital; Kings College London; Kings College London; Kings London NHS Trust; Kings College Hospital NHS Foundation Trust; King's College London; Office for National Statistics; Huazhong University of Science and Technology, Wuhan, China; University of Edinburgh; Ospedale S. Maria delle Croci, Ravenna, Italy; PLA General Hospital, Beijing, China.; Huazhong University of Science and Technology, Wuhan, China.; University of Edinburgh; University of Liverpool; UCL","BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both ""direct"", through infection, and ""indirect"", through changes in healthcare. + +MethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(""direct"" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For ""indirect"" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020. + +FindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths. + +InterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic. + +FundingNIHR, HDR UK, Astra Zeneca",cardiovascular medicine,fuzzy,100,100 bioRxiv,10.1101/2020.06.11.145920,2020-06-11,https://biorxiv.org/cgi/content/short/2020.06.11.145920,SARS-CoV-2 mRNA Vaccine Development Enabled by Prototype Pathogen Preparedness,Kizzmekia S. Corbett; Darin Edwards; Sarah R. Leist; Olubukola M. Abiona; Seyhan Boyoglu-Barnum; Rebecca A. Gillespie; Sunny Himansu; Alexandra Schafer; Cynthia T. Ziwawo; Anthony T. DiPiazza; Kenneth H. Dinnon; Sayda M. Elbashir; Christine A. Shaw; Angela Woods; Ethan J. Fritch; David R. Martinez; Kevin W. Bock; Mahnaz Minai; Bianca M. Nagata; Geoffrey B. Hutchinson; Kapil Bahl; Dario Garcia-Dominguez; LingZhi Ma; Isabella Renzi; Wing-Pui Kong; Stephen D. Schmidt; Lingshu Wang; Yi Zhang; Laura J. Stevens; Emily Phung; Lauren A. Chang; Rebecca J. Loomis; Nedim Emil Altaras; Elisabeth Narayanan; Mihir Metkar; Vlad Presnyak; Catherine Liu; Mark K. Louder; Wei Shi; Kwanyee Leung; Eun Sung Yang; Ande West; Kendra L. Gully; Nianshuang Wang; Daniel Wrapp; Nicole A. Doria-Rose; Guillaume Stewart-Jones; Hamilton Bennett; Martha C. Nason; Tracy J. Ruckwardt; Jason S. McLellan; Mark R. Denison; James D. Chappell; Ian N. Moore; Kaitlyn M. Morabito; John R. Mascola; Ralph S. Baric; Andrea Carfi; Barney S Graham,"Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Department of Epidemiology; University of North Carolina at Chapel Hill; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Department of Epidemiology; University of North Carolina at Chapel Hill; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Epidemiology; University of North Carolina at Chapel Hill; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill; Department of Epidemiology; University of North Carolina at Chapel Hill; National Institute of Allergy and Infectious Diseases; National Institutes of Health; National Institute of Allergy and Infectious Diseases; National Institutes of Health; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Pediatrics, Vanderbilt University Medical Center; Institute for Biomedical Sciences, George Washington University; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Moderna, Inc.; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Epidemiology; University of North Carolina at Chapel Hill; Department of Epidemiology; University of North Carolina at Chapel Hill; Department of Molecular Biosciences; University of Texas at Austin; Department of Molecular Biosciences; University of Texas at Austin; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Moderna, Inc.; Moderna, Inc.; Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Molecular Biosciences; University of Texas at Austin; Department of Pediatrics, Vanderbilt University Medical Center; Department of Pediatrics, Vanderbilt University Medical Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health; Department of Epidemiology; University of North Carolina at Chapel Hill; Department of Microbiology and Immunology, School of Medicine, University of North Caro; Moderna, Inc.; Vaccine Research Center, NIAID, NIH","A SARS-CoV-2 vaccine is needed to control the global COVID-19 public health crisis. Atomic-level structures directed the application of prefusion-stabilizing mutations that improved expression and immunogenicity of betacoronavirus spike proteins. Using this established immunogen design, the release of SARS-CoV-2 sequences triggered immediate rapid manufacturing of an mRNA vaccine expressing the prefusion-stabilized SARS-CoV-2 spike trimer (mRNA-1273). Here, we show that mRNA-1273 induces both potent neutralizing antibody and CD8 T cell responses and protects against SARS-CoV-2 infection in lungs and noses of mice without evidence of immunopathology. mRNA-1273 is currently in a Phase 2 clinical trial with a trajectory towards Phase 3 efficacy evaluation.",immunology,fuzzy,96,94 medRxiv,10.1101/2020.06.08.20120584,2020-06-09,https://medrxiv.org/cgi/content/short/2020.06.08.20120584,SARS-CoV-2 virus and antibodies in front-line Health Care Workers in an acute hospital in London: preliminary results from a longitudinal study,Catherine Houlihan; Nina Vora; Thomas Byrne; Dan Lewer; Judith Heaney; David A Moore; Rebecca Matthews; Sajida Adam; Louise Enfield; Abigail Severn; Angela McBride; Moira Jane Spyer; Rupert Beale; Peter Cherepanov; Kathleen Gaertner; Maryam Shahmanesh; - The SAFER Field Study Team; Kevin Ng; Georgina Cornish; Naomi Walker; Susan Michie; Ed Manley; Fabiana Lorencatto; - The Crick-COVID-Consortium; Richard Gilson; Sonia Gandhi; Steve Gamblin; George Kassiotis; Laura McCoy; Charles Swanton; Andrew Hayward; Eleni Nastouli,University College London Hospital; UCL; UCL; University College London; UCL; Francis Crick Institute; UCL; UCL; UCL; UCL; UCL; UCL; Francis Crick Institute; Francis Crick Institute; UCL; UCL; ; Francis Crick Institute; Francis Crick Institute; UCL; UCL; Leeds University; UCL; ; UCL; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; UCL; Francis Crick Institute; UCL; University College London,"BackgroundAlthough SARS-CoV-2 infection in Healthcare Workers (HCWs) is a public health concern, there is little description of their longitudinal antibody response in the presence or absence of SARS-CoV-2 and symptoms. We followed HCWs in an acute London hospital to measure seroconversion and RNA detection at the peak of the pandemic. @@ -5637,13 +5584,6 @@ Results106 abstracts were identified from the databases search, of which 16 were ConclusionIn these initial reporting studies for the first month of the pandemic, patients receiving IMV were older and had more pre-existing co-morbidities than those who did not require IMV. The mortality rate was high in COVID-19 patients who received IMV. Studies are needed to evaluate protocols and modalities of IMV to improve outcomes and identify the populations most likely to benefit from IMV.",intensive care and critical care medicine,fuzzy,100,100 medRxiv,10.1101/2020.06.01.20116608,2020-06-03,https://medrxiv.org/cgi/content/short/2020.06.01.20116608,Is death from Covid-19 a multistep process?,Neil Pearce; Giovenale Moirano; Milena Maule; Manolis Kogevinas; Xavier Rodo; Deborah Lawlor; Jan Vandenbroucke; Christina Vandenbroucke-Grauls; Fernando P Polack; Adnan Custovic,"London School of Hygiene and Tropical Medicine; University of Turin, Italy; University of Turin, Italy; ISGlobal; ISGlobal; University of Bristol; Leiden University Medical Center; Amsterdam UMC; Vanderbilt Unversity; Imperial College London","Covid-19 death has a different relationship with age than is the case for other severe respiratory pathogens. The Covid-19 death rate increases exponentially with age, and the main risk factors are age itself, as well as having underlying conditions such as hypertension, diabetes, cardiovascular disease, severe chronic respiratory disease and cancer. Furthermore, the almost complete lack of deaths in children suggests that infection alone is not sufficient to cause death; rather, one must have gone through a number of changes, either as a result of undefined aspects of aging, or as a result of chronic disease. These characteristics of Covid-19 death are consistent with the multistep model of disease, a model which has primarily been used for cancer, and more recently for amyotrophic lateral sclerosis (ALS). We applied the multi-step model to data on Covid-19 case fatality rates (CFRs) from China, South Korea, Italy, Spain and Japan. In all countries we found that a plot of ln (CFR) against ln (age) was approximately linear with a slope of about 5. As a comparison, we also conducted similar analyses for selected other respiratory diseases. SARS showed a similar log-log age-pattern to that of Covid-19, albeit with a lower slope, whereas seasonal and pandemic influenza showed quite different age-patterns. Thus, death from Covid-19 and SARS appears to follow a distinct age-pattern, consistent with a multistep model of disease that in the case of Covid-19 is probably defined by comorbidities and age producing immune-related susceptibility. Identification of these steps would be potentially important for prevention and therapy for SARS-COV-2 infection.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.06.01.20118943,2020-06-02,https://medrxiv.org/cgi/content/short/2020.06.01.20118943,"Greater risk of severe COVID-19 in non-White ethnicities is not explained by cardiometabolic, socioeconomic, or behavioural factors, or by 25(OH)-vitamin D status: study of 1,326 cases from the UK Biobank",Zahra Raisi-Estabragh; Celeste McCracken; Mae S Bethell; Jackie Cooper; Cyrus Cooper; Mark J Caulfield; Patricia B Munroe; Nicholas C Harvey; Steffen E Petersen,"William Harvey Research Institute; William Harvey Research Institute; North West Anglia NHS Foundation Trust; William Harvey Research Institute; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; William Harvey Research Institute; William Harvey Research Institute; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; William Harvey Research Institute","BackgroundWe examined whether the greater severity of coronavirus disease 2019 (COVID-19) amongst men and non-White ethnicities is explained by cardiometabolic, socio-economic, or behavioural factors. - -MethodsWe studied 4,510 UK Biobank participants tested for COVID-19 (positive, n = 1,326). Multivariate logistic regression models including age, sex, and ethnicity were used to test whether addition of: 1)cardiometabolic factors (diabetes, hypertension, high cholesterol, prior myocardial infarction, smoking, BMI); 2)25(OH)-vitamin D; 3)poor diet; 4)Townsend deprivation score; 5)housing (home type, overcrowding); or 6)behavioural factors (sociability, risk taking) attenuated sex/ethnicity associations with COVID-19 status. - -ResultsThere was over-representation of men and non-White ethnicities in the COVID-19 positive group. Non-Whites had, on average, poorer cardiometabolic profile, lower 25(OH)-vitamin D, greater material deprivation, and were more likely to live in larger households and flats/apartments. Male sex, non-White ethnicity, higher BMI, Townsend deprivation score, and household overcrowding were independently associated with significantly greater odds of COVID-19. The pattern of association was consistent for men and women; cardiometabolic, socio-demographic and behavioural factors did not attenuate sex/ethnicity associations. - -ConclusionsSex and ethnicity differential pattern of COVID-19 is not adequately explained by variations in cardiometabolic factors, 25(OH)-vitamin D levels, or socio-economic factors. Investigation of alternative biological pathways and different genetic susceptibilities is warranted.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.05.31.20118638,2020-06-02,https://medrxiv.org/cgi/content/short/2020.05.31.20118638,Respiratory Failure in Covid19 is associated with increased monocyte expression of complement receptor 3,Rajeev Gupta; Vanya A Gant; Bryan Williams; Tariq Enver,UCL Cancer Institute; UCL Hospitals NHS Trust; UCLH NHS Hospitals Foundation Trust; UCL Cancer Institute,"A key question in COVID-19 infection is why some previously healthy patients develop severe pulmonary failure and some ultimately die. Initial pulmonary failure does not exhibit classical features of ARDS; hypercoagulability is a common laboratory feature, and pulmonary thrombotic microangiopathy has been reported post mortem1,2,3. Biomarkers cannot robustly identify such patients pre-emptively and no specific interventions exist to mitigate clinical deterioration. Mononuclear phagocytic cells are key immune cells and bind fibrinogen through the CD11b/CD18 dimer CR3, whose activated form can initiate microthrombus formation. Accordingly, we profiled circulating monocyte CD11b/CD18 cell surface density from COVID-19 infected adults who were (i) symptomatic but breathless, (ii) requiring ventilatory support, and (iii) recovering following ICU care for hypoxia.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.05.31.20114520,2020-06-02,https://medrxiv.org/cgi/content/short/2020.05.31.20114520,Rapid point of care nucleic acid testing for SARS-CoV-2 in hospitalised patients: a clinical trial and implementation study,Dami A Collier; Sonny M Assennato; Nyarie Sithole; Katherine Sharrocks; Allyson Ritchie; Pooja Ravji; Matt Routledge; Dominic Sparkes; Jordan Skittrall; Ben Warne; Anna smielewska; ISOBEL RAMSEY; NEHA GOEL; MARTIN CURRAN; DAVID ENOCH; RHYS TASSELL; MICHELLE LINEHAM; DEVAN VAGHELA; CLARE LEONG; HOI PING MOK; JOHN BRADLEY; KENNETH GC SMITH; Vivien Mendoza; NIKOS DEMIRIS; MARTIN BESSER; GORDON DOUGAN; PAUL J LEHNER; Mark Siedner; HONGYI ZHANG; CLAIRE WADDINGTON; HELEN LEE; Ravindra K Gupta,UCL; DRW; CUH; CUH; DRW; CUH; cut; CUH; CUH; CUH; CUH; CUH; DRW; CUH; CUH; CUH; CUH; CUH; CUH; CUH; CAMBRIDGE UNIVERSITY; UNIVERSITY OF CAMBRIDGE; CUH; Athens University of Economics and Business; CUH; UNIVERSITY OF CAMBRIDGE; UNIVERSITY OF CAMBRIDGE; Harvard Medical School; CUH; CUH; DRW; University of Cambridge,"BackgroundThere is urgent need for safe and efficient triage protocols for hospitalized COVID-19 suspects to appropriate isolation wards. A major barrier to timely discharge of patients from the emergency room and hospital is the turnaround time for many SARS-CoV-2 nucleic acid tests. We validated a point of care nucleic acid amplification based platform SAMBA II for diagnosis of COVID-19 and performed an implementation study to assess its impact on patient disposition at a major academic hospital. @@ -5803,6 +5743,9 @@ RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe interaction bet Added value of this studyData from a large UK population who are users of a symptom reporting app during the pandemic supports the hypothesis that smokers are more likely to develop symptoms consistent with COVID-19 and that they have an increased symptom burden. Implications of all the available evidenceThese population data, combined with evidence of a worse outcome in smokers hospitalised with the condition, support the contention that smoking increases individual risk from COVID-19. Support to help people to quit smoking should therefore form part of efforts to deal with the pandemic.",respiratory medicine,fuzzy,94,100 +medRxiv,10.1101/2020.05.14.20101824,2020-05-19,https://medrxiv.org/cgi/content/short/2020.05.14.20101824,Changing travel patterns in China during the early stages of the COVID-19 pandemic,Hamish Gibbs; Yang Liu; Carl AB Pearson; Christopher I Jarvis; Chris Grundy; Billy J Quilty; Charlie Diamond; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigated the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020 and discussed their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower access to care. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and have not yet led to structural reorganisation of the transportation network at the time of this study. + +One sentence summaryUnderstanding travel before, during, and after the introduction of travel restrictions in China in response to the COVID-19 Pandemic.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.05.11.20098269,2020-05-18,https://medrxiv.org/cgi/content/short/2020.05.11.20098269,Accessibility and allocation of public parks and gardens during COVID-19 social distancing in England and Wales,Niloofar Shoari; Majid Ezzati; Jill Baumgartner; Diego Malacarne; Daniela Fecht,Imperial College London; Imperial College London; McGill University; Imperial College London; Imperial College London,"Visiting parks and gardens may attenuate the adverse physical and mental health impacts of social distancing implemented to reduce the spread of COVID-19. We quantified access to public parks and gardens in urban areas of England and Wales, and the potential for park crowdedness during periods of high use. We combined data from the Office for National Statistics and Ordnance Survey to quantify (i) the number of parks within 500 and 1,000 metres of urban postcodes (i.e., availability), (ii) the distance of postcodes to the nearest park (i.e., accessibility), and (iii) per-capita space in each park for people living within 1,000m. We examined how these measures vary by city and share of homes that are flats. Around 25.4 million people can access public parks or gardens within a ten-minute walk, while 3.8 million residents live farther away; of these 21% are children and 13% are elderly. Areas with a higher share of flats on average are closer to a park but people living in these areas are potentially less able to meet social distancing requirements while in parks during periods of high use. Cities in England and Wales can provide residents with access to green space that enables outdoor exercise and play during social distancing. Cities aiming to facilitate social distancing while keeping public green spaces open might require implementing measures such as dedicated park times for different age groups or entry allocation systems that, combined with smartphone apps or drones, can monitor and manage the total number of people using the park.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.05.12.20098921,2020-05-18,https://medrxiv.org/cgi/content/short/2020.05.12.20098921,Behavioural change towards reduced intensity physical activity is disproportionately prevalent among adults with serious health issues or self-perception of high risk during the UK COVID-19 lockdown.,Nina Trivedy Rogers; Naomi Waterlow; Hannah E Brindle; Luisa Enria; Rosalind M Eggo; Shelley Lees; Chrissy h Roberts,University College London (UCL); London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Bath; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"ImportanceThere are growing concerns that the UK COVID-19 lockdown has reduced opportunities to maintain health through physical activity, placing individuals at higher risk of chronic disease and leaving them more vulnerable to severe sequelae of COVID-19. @@ -6305,3 +6248,12 @@ Added value of this studyThis study uses a mathematical model to assess the feas Implications of all the available evidenceContact tracing and isolation may not contain outbreaks of 2019-nCoV unless very high levels of contact tracing are achieved. Even in this case, if there is asymptomatic transmission, or a high fraction of transmission before onset of symptoms, this strategy may not achieve control within three months.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.01.31.20019265,2020-02-02,https://medrxiv.org/cgi/content/short/2020.01.31.20019265,Effectiveness of airport screening at detecting travellers infected with 2019-nCoV,Billy Quilty; Sam Clifford; Stefan Flasche; Rosalind M Eggo,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"As the number of novel coronavirus cases grows both inside and outside of China, public health authorities require evidence on the effectiveness of control measures such as thermal screening of arrivals at airports. We evaluated the effectiveness of exit and entry screening for 2019-nCoV infection. In our baseline scenario, we estimated that 46.5% (95%CI: 35.9 to 57.7) of infected travellers would not be detected, depending on the incubation period, sensitivity of exit and entry screening, and the proportion of cases which are asymptomatic. Airport screening is unlikely to detect a sufficient proportion of 2019-nCoV infected travellers to avoid entry of infected travellers. We developed an online tool so that results can be updated as new information becomes available.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.01.31.20019901,2020-02-02,https://medrxiv.org/cgi/content/short/2020.01.31.20019901,Early dynamics of transmission and control of 2019-nCoV: a mathematical modelling study,Adam J Kucharski; Timothy W Russell; Charlie Diamond; Yang Liu; CMMID nCoV working group; John Edmunds; Sebastian Funk; Rosalind M Eggo,London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine,"BackgroundAn outbreak of the novel coronavirus SARS-CoV-2 has led to 46,997 confirmed cases as of 13th February 2020. Understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas. + +MethodsWe combined a stochastic transmission model with data on cases of novel coronavirus disease (COVID-19) in Wuhan and international cases that originated in Wuhan to estimate how transmission had varied over time during January and February 2020. Based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas. + +FindingsWe estimated that the median daily reproduction number, Rt, declined from 2.35 (95% CI: 1.15-4.77) one week before travel restrictions were introduced on 23rd January to 1.05 (95% CI: 0.413-2.39) one week after. Based on our estimates of Rt,we calculated that in locations with similar transmission potential as Wuhan in early January, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population. + +InterpretationOur results show that COVID-19 transmission likely declined in Wuhan during late January 2020, coinciding with the introduction of control measures. As more cases arrive in international locations with similar transmission potential to Wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually. + +FundingWellcome Trust (206250/Z/17/Z, 210758/Z/18/Z), HDR UK (MR/S003975/1), Gates Foundation (INV-003174), NIHR (16/137/109)",infectious diseases,fuzzy,100,100 diff --git a/data/covid/preprints.exact.csv b/data/covid/preprints.exact.csv index 52115685..250537bb 100644 --- a/data/covid/preprints.exact.csv +++ b/data/covid/preprints.exact.csv @@ -739,13 +739,6 @@ MethodsData were collected as a part of the RADAR-CNS (Remote Assessment of Dise ResultsParticipants with MDD (N=255) and MS (N=214) were included in the analyses. Overall, depressive symptoms remained stable across the three periods in both groups. Lower mean HR and HR variation were observed between pre and during lockdown during the day for MDD and during the night for MS. HR variation during rest periods also decreased between pre-and post-lockdown in both clinical conditions. We observed a reduction of physical activity for MDD and MS upon the introduction of lockdowns. The group with MDD exhibited a net increase in social interaction via social network apps over the three periods. ConclusionsBehavioral response to the lockdown measured by social activity, physical activity and HR may reflect changes in stress in people with MDD and MS.",psychiatry and clinical psychology,exact,100,100 -medRxiv,10.1101/2022.05.06.22274658,2022-05-07,https://medrxiv.org/cgi/content/short/2022.05.06.22274658,"STIMULATE-ICP-CAREINEQUAL - Defining usual care and examining inequalities in Long Covid support: protocol for a mixed-methods study (part of STIMULATE-ICP: Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways).",Mel Ramasawmy; Yi Mu; Donna Clutterbuck; Marija Pantelic; Gregory Y.H. Lip; Christina Van der Feltz-Cornelis; Dan Wootton; Nefyn H Williams; Hugh Montgomery; Rita Mallinson Cookson; Emily Attree; Mark Gabbay; Melissa J Heightman; Nisreen A Alwan; Amitava Banerjee; Paula Lorgelly; - STIMULATE-ICP consortium,"Institute of Health Informatics, University College London; Institute of Health Informatics, University College London; School of Primary Care, Population Sciences and Medical Education, University of Southampton; Brighton and Sussex Medical School, University of Sussex; Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, United Kingdom; and Department of Clinical; Department of Health Sciences, HYMS, University of York, and Institute of Health Informatics, University College London; Institute of Infection Veterinary and Ecological Sciences, University of Liverpool; Department of Primary Care and Mental Health, University of Liverpool; Centre for Human Health and Performance, Department of Medicine, University College London; PPIE Representative; PPIE Representative; Department of Primary Care and Mental Health, University of Liverpool; University College London Hospitals NHS Trust; School of Primary Care, Population Sciences and Medical Education, University of Southampton; NIHR Southampton Biomedical Research Centre, University of Southam; Institute of Health Informatics, University College London; School of Population Health and Department of Economics, University of Auckland; ","IntroductionIndividuals with Long Covid represent a new and growing patient population. In England, fewer than 90 Long Covid clinics deliver assessment and treatment informed by NICE guidelines. However, a paucity of clinical trials or longitudinal cohort studies means that the epidemiology, clinical trajectory, healthcare utilisation and effectiveness of current Long Covid care are poorly documented, and that neither evidence-based treatments nor rehabilitation strategies exist. In addition, and in part due to pre-pandemic health inequalities, access to referral and care varies, and patient experience of the Long Covid care pathways can be poor. - -In a mixed methods study, we therefore aim to: (1) describe the usual healthcare, outcomes and resource utilisation of individuals with Long Covid; (2) assess the extent of inequalities in access to Long Covid care, and specifically to understand Long Covid patients experiences of stigma and discrimination. - -Methods and analysisA mixed methods study will address our aims. Qualitative data collection from patients and health professionals will be achieved through surveys, interviews and focus group discussions, to understand their experience and document the function of clinics. A patient cohort study will provide an understanding of outcomes and costs of care. Accessible data will be further analysed to understand the nature of Long Covid, and the care received. - -Ethics and disseminationEthical approval was obtained from South Central - Berkshire Research Ethics Committee (reference 303958). The dissemination plan will be decided by the patient and public involvement and engagement (PPIE) group members and study Co-Is, but will target 1) policy makers, and those responsible for commissioning and delivering Long Covid services, 2) patients and the public, and 3) academics.",health systems and quality improvement,exact,100,100 medRxiv,10.1101/2022.04.28.22273177,2022-04-29,https://medrxiv.org/cgi/content/short/2022.04.28.22273177,Occupational differences in SARS-CoV-2 infection: Analysis of the UK ONS Coronavirus (COVID-19) Infection Survey,Sarah Rhodes; Jack Wilkinson; Neil Pearce; Will Mueller; Mark Cherrie; Katie Stocking; Matthew Gittins; Srinivasa Vittal Katikireddi; Martie van Tongeren,University of Manchester; University of Manchester; London School of Hygiene and Tropical Medicine; Institute of Occupational Medicine; Institute of Occupational Medicine; University of Manchester; University of Manchester; University of Glasgow; University of Manchester,"BackgroundConsiderable concern remains about how occupational SARS-CoV-2 risk has evolved during the COVID-19 pandemic. We aimed to ascertain which occupations had the greatest risk of SARS-CoV-2 infection and explore how relative differences varied over the pandemic. MethodsAnalysis of cohort data from the UK Office of National Statistics Coronavirus (COVID-19) Infection Survey from April 2020 to November 2021. This survey is designed to be representative of the UK population and uses regular PCR testing. Cox and multilevel logistic regression to compare SARS-CoV-2 infection between occupational/sector groups, overall and by four time periods with interactions, adjusted for age, sex, ethnicity, deprivation, region, household size, urban/rural neighbourhood and current health conditions. @@ -814,23 +807,6 @@ TRIAL REGISTRATIONClinicalTrials.gov no. NCT04579640 SUMMARY BOXO_ST_ABSWhat is already known on this topic?C_ST_ABSVitamin D metabolites support innate immune responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory pathogens. Sub-optimal vitamin D status (25-hydroxyvitamin D <75 nmol/L) associates with increased susceptibility to all-cause acute respiratory infections (ARI) and coronavirus disease 2019 (COVID-19). Phase 3 randomised controlled trials of vitamin D to prevent COVID-19 have not yet reported. What this study addsThis phase 3 randomised controlled trial, including 6200 participants, shows that implementation of a population-level test-and-treat approach to oral vitamin D replacement at a dose of 800 IU or 3200 IU per day did not reduce risk of all-cause ARI or COVID-19 among adults with a high baseline prevalence of sub-optimal vitamin D status.",infectious diseases,exact,100,100 -medRxiv,10.1101/2022.03.22.22272775,2022-03-23,https://medrxiv.org/cgi/content/short/2022.03.22.22272775,Risk of death following SARS-CoV-2 infection or COVID-19 vaccination in young people in England: a self-controlled case series study,Vahe Nafilyan; Charlotte Bermingham; Isobel L Ward; Jasper Morgan; Francesco Zaccardi; Kamlesh Khunti; Julie Stanborough; Amitava Banerjee,"Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Real World Evidence Unit, Diabetes Research Centre, University of Leicester; Real World Evidence Unit, Diabetes Research Centre, University of Leicester; Office for National Statistics; Institute of Health Informatics, University College London","ObjectivesTo assess whether there is a change in the incidence of cardiac and all-cause death in young people following COVID-19 vaccination or SARS-CoV-2 infection in unvaccinated individuals. - -DesignSelf-controlled case series. - -SettingNational, linked electronic health record data in England. - -Study populationIndividuals aged 12-29 who had received at least one dose of COVID-19 vaccination and died between 8 December 2020 and 2 February 2022 and registered by 16 February 2022 within 12 weeks of COVID-19 vaccination; Individuals aged 12-29 who died within 12 weeks of testing positive for SARS-CoV-2. - -Main outcome measuresCardiac and all-cause deaths occurring within 12 weeks of vaccination or SARS-CoV-2 infection. - -ResultsCompared to the baseline period, there was no evidence of a change in the incidence of cardiac death in the six weeks after vaccination, whether for each of weeks 1 to 6 or the whole six-week period. There was a decrease in the risk of all-cause death in the first week after vaccination and no change in each of weeks 2 to 6 after vaccination or whole six-week period after vaccination. Subgroup analyses by sex, age, vaccine type, and last dose also showed no change in the risk of death in the first six weeks after vaccination. There was a large increase in the incidence of cardiac and all-cause death in the overall risk period after SARS-CoV-2 infection among the unvaccinated. - -ConclusionThere is no evidence of an association between COVID-19 vaccination and an increased risk of death in young people. By contrast, SARS-CoV-2 infection was associated with substantially higher risk of cardiac related death and all-cause death. - -What is already known on this topicSeveral studies have highlighted the association between COVID-19 vaccination and the risk of myocarditis, myopericarditis, and other cardiac problems, especially in young people, but associated risk of mortality is unclear. Since younger people have lower risk of COVID-19 hospitalisation and mortality, the mortality risk associated with vaccination is potentially more important to them in balancing the risk and benefit of vaccination. - -What this study addsAlthough there is a risk of myocarditis or myopericarditis with COVID-19, there is no evidence of increased risk of cardiac or all-cause mortality following COVID-19 vaccination in young people aged 12 to 29. Given the increased risk of mortality following SARS-CoV-2 infection in this group, the risk-benefit analysis favours COVID-19 vaccination for this age group.",epidemiology,exact,100,100 medRxiv,10.1101/2022.03.18.22272607,2022-03-21,https://medrxiv.org/cgi/content/short/2022.03.18.22272607,"Multi-organ impairment and Long COVID: a 1-year prospective, longitudinal cohort study",Andrea Dennis; Daniel J Cuthbertson; Dan Wootton; Michael Crooks; Mark Gabbay; Nicole Eichert; Sofia Mouchti; Michele Pansini; Adriana Roca-Fernandez; Helena Thomaides-Brears; Matt Kelly; Matthew Robson; Lyth Hishmeh; Emily Attree; Melissa J Heightman; Rajarshi Banerjee; Amitava Banerjee,Perspectum Ltd; University of Liverpool; University of Liverpool; University of Hull; University of Liverpool; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Perspectum Diagnostics; Perspectum Ltd; Perspectum Ltd; Perspectum Ltd; Long COVID SoS; UKDoctors#Longcovid; UCLH; Perspectum Ltd; University College London,"ImportanceMulti-organ impairment associated with Long COVID is a significant burden to individuals, populations and health systems, presenting challenges for diagnosis and care provision. Standardised assessment across multiple organs over time is lacking, particularly in non-hospitalised individuals. ObjectiveTo determine the prevalence of organ impairment in Long COVID patients at 6 and at 12 months after initial symptoms and to explore links to clinical presentation. @@ -1048,6 +1024,7 @@ MethodTrial emulation was conducted by pooling results from six cohorts whose re ResultsAcross six cohorts, there were a total of 21,283 participants who were eligible and vaccinated with either ChAdOx1 (n = 13,813) or BNT162b2 (n = 7,470) with a median follow-up time of 266 days (IQR: 235 - 282). By November 12th 2021, 750 (5.4%) adults who had ChAdOx1 as their vaccine experienced a SARS-CoV-2 infection, compared to 296 (4.0%) who had BNT162b2. We found that people who received ChAdOx1 vaccinations had 10.54 per 1000 people higher cumulative incidence for SARS-CoV-2 infection compared to BNT162b2 for infections during a maximum of 315 days of follow-up. When adjusted for age at vaccination, sex, minority ethnic status, index of multiple deprivation, and clinical vulnerability status, we found a pooled adjusted hazard ratio of 1.35 [HR: 1.35, 95%CI: 1.15 - 1.58], demonstrating a 35% increase in SARS-CoV-2 infections in people who received ChAdOx1 compared to BNT162b2. DiscussionWe found evidence of greater effectiveness of receiving BNT162b2 compared to ChAdOx1 vaccines against SARS-CoV-2 infection in England and Wales during a time period when Delta became the most prevalent variant of concern. Our findings demonstrate the importance of booster (third) doses to maintain protection and suggest that these should be prioritised to those who received ChAdOx1 as their primary course.",epidemiology,exact,100,100 +bioRxiv,10.1101/2021.12.17.473248,2021-12-21,https://biorxiv.org/cgi/content/short/2021.12.17.473248,"SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion",Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta,"University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge","The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.",microbiology,exact,100,100 medRxiv,10.1101/2021.12.20.21268098,2021-12-21,https://medrxiv.org/cgi/content/short/2021.12.20.21268098,"Therapies for Long COVID in non-hospitalised individuals - from symptoms, patient-reported outcomes, and immunology to targeted therapies (The TLC Study): Study protocol",Shamil Haroon; Krishnarajah Nirantharakumar; Sarah Hughes; Anuradhaa Subramanian; Olalekan Lee Aiyegbusi; Elin Haf Davies; Puja Myles; Tim Williams; Grace Turner; Joht Singh Chandan; Christel McMullan; Janet Lord; David Wraith; Kirsty McGee; Alastair Denniston; Tom Taverner; Louise Jackson; Elizabeth Sapey; Georgios Gkoutos; Krishna Gokhale; Edward Leggett; Clare Iles; Christopher Frost; Gary McNamara; Amy Bamford; Tom Marshall; Dawit Zemedikun; Gary Price; Steven Marwaha; Nikita Simms-Williams; Kirsty Brown; Anita Walker; Karen Jones; Karen Matthews; Jennifer Camaradou; Michael Saint-Cricq; Sumita Kumar; Yvonne Alder; David Stanton; Lisa Agyen; Megan Baber; Hannah Blaize; Melanie Calvert,University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Aparito; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; University of Birmingham; University ofBirmingham; University of Birmingham; Medicines and Healthcare Products Regulatory Agency; Medicines and Healthcare Products Regulatory Agency; Aparito; Aparito; University Hospitals Birmingham NHS Foundation Trust; University of Birmingham; University of Birmingham; N/A; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; University of Birmingham; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; Not applicable; University ofBirmingham,"IntroductionIndividuals with COVID-19 frequently experience symptoms and impaired quality of life beyond 4-12 weeks, commonly referred to as Long COVID. Whether Long COVID is one or several distinct syndromes is unknown. Establishing the evidence base for appropriate therapies is needed. We aim to evaluate the symptom burden and underlying pathophysiology of Long COVID syndromes in non-hospitalised individuals and evaluate potential therapies. Methods and analysisA cohort of 4000 non-hospitalised individuals with a past COVID-19 diagnosis and 1000 matched controls will be selected from anonymised primary care records from the Clinical Practice Research Datalink (CPRD) and invited by their general practitioners to participate on a digital platform (Atom5). Individuals will report symptoms, quality of life, work capability, and patient reported outcome measures. Data will be collected monthly for one year. @@ -1162,27 +1139,6 @@ Results15,621 participants were included in the primary analysis, of whom 639 we ConclusionsThese findings indicate that for patients assessed in A&E, pulse oximetry remote monitoring may be a clinically effective and safe model for early detection of hypoxia and escalation, leading to increased subsequent A&E attendance and admissions, and reduced critical care requirement and mortality.",health systems and quality improvement,exact,100,100 bioRxiv,10.1101/2021.11.24.469860,2021-11-26,https://biorxiv.org/cgi/content/short/2021.11.24.469860,Nanopore ReCappable Sequencing maps SARS-CoV-2 5' capping sites and provides new insights into the structure of sgRNAs,Camilla Ugolini; Logan Mulroney; Adrien Leger; Matteo Castelli; Elena Criscuolo; Maia Kavanagh Williamson; Andrew D Davidson; Abdulaziz Almuqrin; Roberto Giambruno; Miten Jain; Gianmaria Frigè; Hugh Olsen; George Tzertzinis; Ira Schildkraut; Madalee F Wulf; Ivan R. Corrêa Jr.; Laurence Ettwiller; Nicola Clementi; Massimo Clementi; Nicasio Mancini; Ewan Birney; Mark Akeson; Francesco Nicassio; David A Matthews; Tommaso Leonardi,Italian Institute of Technology; Italian Institute of Technology; Oxford Nanopore Technologies; Vita-Salute San Raffaele University; Vita-Salute San Raffaele University; University of Bristol; University of Bristol; University of Bristol; Istituto Italiano di Tecnologia; University of California Santa Cruz; Istituto Europeo di Oncologia; University of California Santa Cruz; New England Biolabs; New England Biolabs; New England Biolabs; New England Biolabs; New England Biolabs Inc; Vita-Salute San Raffaele University; Vita-Salute San Raffaele University; Università Vita-Salute San Raffaele; European Bioinformatics Institute; University of California Santa Cruz; Istituto Italiano di Tecnologia; University of Bristol; Italian Institute of Technology,"The SARS-CoV-2 virus has a complex transcriptome characterised by multiple, nested sub genomic RNAs used to express structural and accessory proteins. Long-read sequencing technologies such as nanopore direct RNA sequencing can recover full-length transcripts, greatly simplifying the assembly of structurally complex RNAs. However, these techniques do not detect the 5' cap, thus preventing reliable identification and quantification of full-length, coding transcript models. Here we used Nanopore ReCappable Sequencing (NRCeq), a new technique that can identify capped full-length RNAs, to assemble a complete annotation of SARS-CoV-2 sgRNAs and annotate the location of capping sites across the viral genome. We obtained robust estimates of sgRNA expression across cell lines and viral isolates and identified novel canonical and non-canonical sgRNAs, including one that uses a previously un-annotated leader-to-body junction site. The data generated in this work constitute a useful resource for the scientific community and provide important insights into the mechanisms that regulate the transcription of SARS-CoV-2 sgRNAs.",genomics,exact,100,100 -medRxiv,10.1101/2021.11.22.21266512,2021-11-24,https://medrxiv.org/cgi/content/short/2021.11.22.21266512,Association of COVID-19 with arterial and venous vascular diseases: a population-wide cohort study of 48 million adults in England and Wales,Rochelle Knight; Venexia Walker; Samantha Ip; Jennifer A Cooper; Thomas Bolton; Spencer Keene; Rachel Denholm; Ashley Akbari; Hoda Abbasizanjani; Fatemeh Torabi; Efosa Omigie; Sam Hollings; Teri-Louise North; Renin Toms; Emanuele Di Angelantonio; Spiros Denaxas; Johan H Thygesen; Christopher Tomlinson; Ben Bray; Craig J Smith; Mark Barber; George Davey Smith; Nishi Chaturvedi; Cathie Sudlow; William N Whiteley; Angela Wood; Jonathan A C Sterne; - CVD-COVID-UK/COVID-IMPACT consortium; - Longitudinal Health and Wellbeing COVID-19 National Core Study,University of Bristol; University of Bristol; University of Cambridge; University of Bristol; University of Cambridge; University of Cambridge; University of Bristol; Swansea University; Swansea University; Swansea University; NHS Digital; NHS Digital; University of Bristol; University of Bristol; University of Cambridge; University College London; University College London; University College London; Kings College London; University of Manchester; Glasgow Caledonian University; University of Bristol; University College London; Health Data Research UK; University of Edinburgh; University of Cambridge; University of Bristol; ; ,"ImportanceThe long-term effects of COVID-19 on the incidence of vascular diseases are unclear. - -ObjectiveTo quantify the association between time since diagnosis of COVID-19 and vascular disease, overall and by age, sex, ethnicity, and pre-existing disease. - -DesignCohort study based on population-wide linked electronic health records, with follow up from January 1st to December 7th 2020. - -Setting and participantsAdults registered with an NHS general practice in England or Wales and alive on January 1st 2020. - -ExposuresTime since diagnosis of COVID-19 (categorised as 0-6 days, 1-2 weeks, 3-4, 5-8, 9-12, 13-26 and 27-49 weeks since diagnosis), with and without hospitalisation within 28 days of diagnosis. - -Main outcomes and measuresPrimary outcomes were arterial thromboses (mainly acute myocardial infarction and ischaemic stroke) and venous thromboembolic events (VTE, mainly pulmonary embolism and lower limb deep vein thrombosis). We also studied other vascular events (transient ischaemic attack, haemorrhagic stroke, heart failure and angina). Hazard ratios were adjusted for demographic characteristics, previous disease diagnoses, comorbidities and medications. - -ResultsAmong 48 million adults, 130,930 were and 1,315,471 were not hospitalised within 28 days of COVID-19. In England, there were 259,742 first arterial thromboses and 60,066 first VTE during 41.6 million person-years follow-up. Adjusted hazard ratios (aHRs) for first arterial thrombosis compared with no COVID-19 declined rapidly from 21.7 (95% CI 21.0-22.4) to 3.87 (3.58-4.19) in weeks 1 and 2 after COVID-19, 2.80 (2.61-3.01) during weeks 3-4 then to 1.34 (1.21-1.48) during weeks 27-49. aHRs for first VTE declined from 33.2 (31.3-35.2) and 8.52 (7.59-9.58) in weeks 1 and 2 to 7.95 (7.28-8.68) and 4.26 (3.86-4.69) during weeks 3-4 and 5-8, then 2.20 (1.99-2.44) and 1.80 (1.50-2.17) during weeks 13-26 and 27-49 respectively. aHRs were higher, for longer after diagnosis, after hospitalised than non-hospitalised COVID-19. aHRs were also higher among people of Black and Asian than White ethnicity and among people without than with a previous event. Across the whole population estimated increases in risk of arterial thromboses and VTEs were 2.5% and 0.6% respectively 49 weeks after COVID-19, corresponding to 7,197 and 3,517 additional events respectively after 1.4 million COVID-19 diagnoses. - -Conclusions and RelevanceHigh rates of vascular disease early after COVID-19 diagnosis decline more rapidly for arterial thromboses than VTEs but rates remain elevated up to 49 weeks after COVID_19. These results support continued policies to avoid COVID-19 infection with effective COVID-19 vaccines and use of secondary preventive agents in high-risk patients. - -Key pointsO_ST_ABSQuestionC_ST_ABSIs COVID-19 associated with higher long-term incidence of vascular diseases? - -FindingsIn this cohort study of 48 million adults in England and Wales, COVID-19 was associated with higher incidence, that declined with time since diagnosis, of both arterial thromboses [week 1: adjusted HR [aHR] 21.7 (95% CI 21.0-22.4) weeks 27-49: aHR 1.34 (1.21-1.48)] and venous thromboembolism [week 1: aHR 33.2 (31.3-35.2), weeks 27-49 1.80 (1.50-2.17)]. aHRs were higher, for longer, after hospitalised than non-hospitalised COVID-19. The estimated excess number of arterial thromboses and venous thromboembolisms was 10,500. - -MeaningAvoidance of COVID-19 infection through vaccination, and use of secondary preventive agents after infection in high-risk patients, may reduce post-COVID-19 acute vascular diseases.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.11.15.21266264,2021-11-16,https://medrxiv.org/cgi/content/short/2021.11.15.21266264,Association of COVID-19 employment disruption with mental and social wellbeing: evidence from nine UK longitudinal studies,Jacques Wels; Charlotte Booth; Bozena Wielgoszewska; Michael J Green; Giorgio Di Gessa; Charlotte F Huggins; Gareth J Griffith; Alex Siu Fung Kwong; Ruth C E Bowyer; Jane Maddock; Praveetha Patalay; Richard J Silverwood; Emla Fitzsimons; Richard John Shaw; Ellen J Thompson; Andrew Steptoe; Alun Hughes; Nishi Chaturvedi; Claire J Steves; Srinivasa Vittal Katikireddi; George B Ploubidis,University College London; University College London; University College London; University of Glasgow; University College London; University of Edinburgh; University of Bristol; University of Bristol; King's College London; University College London; University College London; University College London; University College London; University of Glasgow; Kings College London; University College London; University College London; University College London; King's College London; University of Glasgow; University College London,"BackgroundThe COVID-19 pandemic has led to major economic disruptions. In March 2020, the UK implemented the Coronavirus Job Retention Scheme - known as furlough - to minimize the impact of job losses. We investigate associations between change in employment status and mental and social wellbeing during the early stages of the pandemic. MethodsData were from 25,670 respondents, aged 17 to 66, across nine UK longitudinal studies. Furlough and other employment changes were defined using employment status pre-pandemic and during the first lockdown (April-June 2020). Mental and social wellbeing outcomes included psychological distress, life satisfaction, self-rated health, social contact, and loneliness. Study-specific modified Poisson regression estimates, adjusting for socio-demographic characteristics and pre-pandemic mental and social wellbeing measures, were pooled using meta-analysis. @@ -1224,13 +1180,6 @@ Research in ContextO_ST_ABSEvidence before the studyC_ST_ABSWe searched PubMed o Added value of this studyTo our knowledge, this is the first study providing a comprehensive view of COVID-19 across pandemic waves using national data and focusing on severity, vaccination, and patient trajectories. Drawing on linked electronic health record (EHR) data on a national scale (56.6 million people alive and registered with GP in England), we describe key demographic factors, frequency of comorbidities, impact of the two main waves in England, and effect of full vaccination on COVID-19 severities. Additionally, we identify and describe patient trajectory networks which illustrate the main transition pathways of COVID-19 patients in the healthcare system. Finally, we provide reproducible COVID-19 phenotyping algorithms reflecting clinically relevant stages of disease severity i.e. positive tests, primary care diagnoses, hospitalisation, critical care treatments (e.g. ventilatory support) and mortality. Implications of all the available evidenceThe COVID-19 phenotypes and trajectory analysis framework outlined produce a reproducible, extensible and repurposable means to generate national-scale data to support critical policy decision making. By modelling patient trajectories as a series of interactions with healthcare systems, and linking these to demographic and outcome data, we provide a means to identify and prioritise care pathways associated with adverse outcomes and highlight healthcare system touch points which may act as tangible targets for intervention.",public and global health,exact,100,100 -medRxiv,10.1101/2021.11.08.21265380,2021-11-08,https://medrxiv.org/cgi/content/short/2021.11.08.21265380,Describing the population experiencing COVID-19 vaccine breakthrough following second vaccination in England: A cohort study from OpenSAFELY,Amelia CA Green; Helen J Curtis; William J Hulme; Elizabeth J Williamson; Helen I McDonald; Krishnan Bhaskaran; Christopher T Rentsch; Anna Schultze; Brian MacKenna; Viyaasan Mahalingasivam; Laurie Tomlinson; Alex J Walker; Louis Fisher; Jon Massey; Colm D Andrews; Lisa E M Hopcroft; Caroline E Morton; Richard Croker; Jessica Morley; Amir Mehrkar; Sebastian CJ Bacon; David Evans; Peter Inglesby; George Hickman; Tom Ward; Simon Davy; Rohini Mathur; John Tazare; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; Christopher Bates; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Ian J Douglas; Stephen JW Evans; Liam Smeeth; Ben Goldacre,University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Bristol; TPP; TPP; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundWhile the vaccines against COVID-19 are considered to be highly effective, COVID-19 vaccine breakthrough is likely and a small number of people will still fall ill, be hospitalised, or die from COVID-19, despite being fully vaccinated. With the continued increase in numbers of positive SARS-CoV-2 tests, describing the characters of individuals who have experienced a COVID-19 vaccine breakthrough could be hugely important in helping to determine who may be at greatest risk. - -MethodWith the approval of NHS England we conducted a retrospective cohort study using routine clinical data from the OpenSAFELY TPP database of fully vaccinated individuals, linked to secondary care and death registry data, and described the characteristics of those experiencing a COVID-19 vaccine breakthrough. - -ResultsAs of 01st November 2021, a total of 15,436,455 individuals were identified as being fully vaccinated against COVID-19, with a median follow-up time of 149 days (IQR: 107-179). From within this population, a total of 577245 (<4%) individuals reported a positive SARS-CoV-2 test. For every 1000 years of patient follow-up time, the corresponding incidence rate was 98.02 (95% CI 97.9-98.15). There were 16,120 COVID-19-related hospital admissions, 1,100 COVID-19 critical care admission patients and 3,925 COVID-19-related deaths; corresponding incidence rates of 2.72 (95% C 2.7-2.74), 0.19 (95% C 0.18-0.19) and 0.66 (95% C 0.65-0.67), respectively. When broken down by the initial priority group, higher rates of hospitalisation and death were seen in those in care homes and those over 80 years of age. Comorbidities with the highest rates of breakthrough COVID-19 included chronic kidney disease, dialysis, transplant, haematological malignancy, and immunocompromised. - -ConclusionThe majority of COVID-19 vaccine breakthrough cases in England were mild with relatively few fully vaccinated individuals being hospitalised or dying as a result. However, some concerning differences in rates of breakthrough cases were identified in several clinical and demographic groups. While it is important to note that these findings are simply descriptive and cannot be used to answer why certain groups have higher rates of COVID-19 breakthrough than others, the emergence of the Omicron variant of COVID-19 coupled with the continued increase in numbers of positive SARS-CoV-2 tests are concerning. As numbers of fully vaccinated individuals increases and follow-up time lengthens, so too will the number of COVID-19 breakthrough cases. Additional analyses, aimed at identifying individuals at higher risk, are therefore required.",epidemiology,exact,100,100 medRxiv,10.1101/2021.11.04.21265918,2021-11-05,https://medrxiv.org/cgi/content/short/2021.11.04.21265918,Longitudinal Changes of Cardiac and Aortic Imaging Phenotypes Following COVID-19 in the UK Biobank Cohort,Wenjia Bai; Betty Raman; Steffen E Peterson; Stefan Neubauer; Zahra Raisi-Estabragh; Nay Aung; Nicholas C Harvey; Naomi Allen; Rory Collins; Paul M Matthews,"Department of Brain Sciences, Imperial College London and British Heart Foundation Centre for Research Excellence, Imperial College London, London, UK; University of Oxford; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford and British Heart Foundation; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London; William Harvey Research Institute, NIHR Barts Biomedical Research Centre, Queen Mary University of London; MRC Lifecourse Epidemiology Centre, University of Southampton and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital; Nuffield Department of Population Health, University of Oxford, Oxford, UK and UK Biobank, Stockport, UK; Nuffield Department of Population Health, University of Oxford, Oxford, UK and UK Biobank, Stockport, UK; Imperial College, London","Case studies conducted after recovery from acute infection with SARS-CoV-2 have frequently identified abnormalities on CMR imaging, suggesting the possibility that SARS-CoV-2 infection commonly leads to cardiac pathology. However, these observations have not been able to distinguish between associations that reflect pre-existing cardiac abnormalities (that might confer a greater likelihood of more severe infection) from those that arise as consequences of infection. To address this question, UK Biobank volunteers (n=1285; 54.5% women; mean age at baseline, 59.8 years old; 96.3% white) who attended an imaging assessment including cardiac magnetic resonance (CMR) before the start of the COVID-19 pandemic were invited to attend a second imaging assessment in 2021. Cases with evidence of previous SARS-CoV-2 infection were identified through linkage to PCR-testing or other medical records, or a positive antibody lateral flow test; n=640 in data available on 22 Sep 2021) and were matched to controls with no evidence of previous infection (n=645). The majority of these infections were milder and did not involve hospitalisation. Measures of cardiac and aortic structure and function were derived from the CMR images obtained on the cases before and after SARS-CoV-2 infection from images for the controls obtained over the same time interval using a previously validated, automated algorithm. Cases and controls had similar cardiac and aortic imaging phenotypes at their first imaging assessment. Changes between CMR imaging measures in cases before and after infection were not significantly different from those in the matched control group. Additional adjustment for comorbidities made no material difference to the results. While these results are preliminary and limited to imaging metrics derived from automated analyses, they do not suggest clinically significant persistent cardiac pathology in the UK Biobank population after generally milder (non-hospitalised) SARS-CoV-2 infection.",neurology,exact,100,100 medRxiv,10.1101/2021.11.02.21265767,2021-11-03,https://medrxiv.org/cgi/content/short/2021.11.02.21265767,Determinants of pre-vaccination antibody responses to SARS-CoV-2: a population-based longitudinal study (COVIDENCE UK),Mohammad Talaei; Sian Faustini; Hayley Holt; David A. Jolliffe; Giulia Vivaldi; Matthew Greenig; Natalia Perdek; Sheena Maltby; Carola M Bigogno; Jane Symons; Gwyneth A. Davies; Ronan A. Lyons; Christopher J Griffiths; Frank Kee; Aziz Sheikh; Alex G. Richter; Seif O. Shaheen; Adrian R Martineau,Queen Mary University of London; University of Birmingham; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Jane Symons Media; Swansea University Medical School; Swansea University Medical School; Queen Mary University of London; Queens University Belfast; University of Edinburgh; University of Birminghan; Queen Mary University of London; Queen Mary University of London,"BackgroundProspective population-based studies investigating multiple determinants of pre-vaccination antibody responses to SARS-CoV-2 are lacking. @@ -1329,6 +1278,7 @@ ResultsThe trial opened on April 2, 2020, with randomisation to colchicine start ConclusionsColchicine did not improve time to recovery in people at higher risk of complications with COVID-19 in the community. Trial registrationISRCTN86534580.",infectious diseases,exact,100,100 +medRxiv,10.1101/2021.09.13.21263487,2021-09-16,https://medrxiv.org/cgi/content/short/2021.09.13.21263487,SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population,Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.09.09.21263026,2021-09-13,https://medrxiv.org/cgi/content/short/2021.09.09.21263026,The clinically extremely vulnerable to COVID: Identification and changes in health care while self-isolating (shielding) during the coronavirus pandemic,Jessica Erin Butler; Mintu Nath; Dimitra Blana; William P Ball; Nicola Beech; Corri Black; Graham Osler; Sebastien Peytrignet; Katie Wilde; Artur Wozniak; Simon Sawhney,University of Aberdeen; University of Aberdeen; University of Aberdeen; University of Aberdeen; NHS Grampian; NHS Grampian and University of Aberdeen; NHS Grampian; Health Foundation; University of Aberdeen; University of Aberdeen; NHS Grampian and University of Aberdeen,"BackgroundIn March 2020, the government of Scotland identified people deemed clinically extremely vulnerable to COVID due to their pre-existing health conditions. These people were advised to strictly self-isolate (shield) at the start of the pandemic, except for necessary healthcare. We examined who was identified as clinically extremely vulnerable, how their healthcare changed during isolation, and whether this process exacerbated healthcare inequalities. MethodsWe linked those on the shielding register in NHS Grampian, a health authority in Scotland, to healthcare records from 2015-2020. We described the source of identification, demographics, and clinical history of the cohort. We measured changes in out-patient, in-patient, and emergency healthcare during isolation in the shielding population and compared to the general non-shielding population. @@ -1638,6 +1588,9 @@ MethodsWorking on behalf of NHS England, we used OpenSAFELY data encompassing 96 ResultsLong COVID was recorded for 23,273 people. Coding was unevenly distributed amongst practices, with 26.7% of practices having not used the codes at all. Regional variation was high, ranging between 20.3 per 100,000 people for East of England (95% confidence interval 19.3-21.4) and 55.6 in London (95% CI 54.1-57.1). The rate was higher amongst women (52.1, 95% CI 51.3-52.9) compared to men (28.1, 95% CI 27.5-28.7), and higher amongst practices using EMIS software (53.7, 95% CI 52.9-54.4) compared to TPP software (20.9, 95% CI 20.3-21.4). ConclusionsLong COVID coding in primary care is low compared with early reports of long COVID prevalence. This may reflect under-coding, sub-optimal communication of clinical terms, under-diagnosis, a true low prevalence of long COVID diagnosed by clinicians, or a combination of factors. We recommend increased awareness of diagnostic codes, to facilitate research and planning of services; and surveys of clinicians experiences, to complement ongoing patient surveys.",epidemiology,exact,100,100 +medRxiv,10.1101/2021.05.05.21256668,2021-05-09,https://medrxiv.org/cgi/content/short/2021.05.05.21256668,COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland,Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz,The University of Edinburgh; The University of Edinburgh; The University of Edinburgh,"The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively. + +Clinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.",health informatics,exact,100,100 medRxiv,10.1101/2021.05.04.21256507,2021-05-06,https://medrxiv.org/cgi/content/short/2021.05.04.21256507,Describing the burden of the COVID-19 pandemic in people with psoriasis: findings from a global cross-sectional study,Satveer K Mahil; Mark Yates; Zenas Z Yiu; Sinead M Langan; Teresa Tsakok; Nick Dand; Kayleigh J Mason; Helen McAteer; Freya Meynall; Bolaji Coker; Alexandra Vincent; Dominic Urmston; Amber Vesty; Jade Kelly; Camille Lancelot; Lucy Moorhead; Herve Bachelez; Francesca Capon; Claudia R Contreras; Claudia De La Cruz; Paola Di Meglio; Paolo Gisondi; Denis Jullien; Jo Lambert; Luigi Naldi; Sam Norton; Luis Puig; Phyllis Spuls; Tiago Torres; Richard B Warren; Hoseah Waweru; John Weinman; Matt A Brown; James B Galloway; Christopher M Griffiths; Jonathan N Barker; Catherine H Smith,"St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; Faculty of Epidemiology, and Population Health, London School of Hygiene and Tropical Medicine, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; The Psoriasis Association, Northampton, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; The Psoriasis Association, Northampton, UK; The Psoriasis Association, Northampton, UK; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; Department of Dermatology, AP-HP Hopital Saint-Louis, Paris, France; King's College London; Catedra de Dermatologia, Hospital de Clinicas, Facultad de Ciencias Medicas, Universidad Nacional de Asuncion, Paraguay; Clinica Dermacross, Santiago, Chile; King's College London; Section of Dermatology and Venereology, University of Verona, Verona, Italy; Department of Dermatology, Edouard Herriot Hospital, Hospices Civils de Lyon, University of Lyon, Lyon, France; Department of Dermatology, Ghent University, Ghent, Belgium; Centro Studi GISED, Bergamo, Italy; Psychology Department, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, UK; Department of Dermatology, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Catalonia, Spain; Department of Dermatology, Amsterdam Public Health/Infection and Immunology, Amsterdam University Medical Centers, Location AMC, Amsterdam, The Netherlands; Department of Dermatology, Centro Hospitalar do Porto, Portugal; Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Rese; International Federation of Psoriasis Associations; School of Cancer and Pharmaceutical Sciences, Kings College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; Centre for Rheumatic Diseases, King's College London, London, UK; 3Dermatology Centre, Salford Royal NHS Foundation Trust, The University of Manchester, Manchester Academic Health Science Centre, NIHR Manchester Biomedical Res; NIHR Biomedical Research Centre at Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK; St Johns Institute of Dermatology, Guys and St Thomas NHS Foundation Trust and Kings College London, London, UK","BackgroundIndirect excess morbidity has emerged as a major concern in the COVID-19 pandemic. People with psoriasis may be particularly vulnerable to this because of prevalent anxiety and depression, multimorbidity and therapeutic use of immunosuppression. ObjectiveCharacterise the factors associated with worsening psoriasis in the COVID-19 pandemic, using mental health status (anxiety and depression) as the main exposure of interest. @@ -1669,6 +1622,13 @@ What this study addsO_LIIn 70,464 people with atrial fibrillation, at the thresh C_LIO_LIThis might be explained by OACs preventing severe COVID-19 outcomes, or more cautious behaviours and environmental factors reducing the risk of SARS-CoV-2 infection in those taking OACs. C_LIO_LIIn 372,746 people with non-valvular atrial fibrillation, there was no evidence of a higher risk of severe COVID-19 outcomes associated with warfarin compared with DOACs. C_LI",epidemiology,exact,100,100 +medRxiv,10.1101/2021.04.26.21255732,2021-04-28,https://medrxiv.org/cgi/content/short/2021.04.26.21255732,Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales,Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative,"University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ","BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation. + +MethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period. + +ResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods. + +ConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.",epidemiology,exact,100,100 medRxiv,10.1101/2021.04.21.21255807,2021-04-27,https://medrxiv.org/cgi/content/short/2021.04.21.21255807,A randomised clinical trial of azithromycin versus standard care in ambulatory COVID-19 - the ATOMIC2 trial,Timothy SC Hinks; Lucy Cureton; Ruth Knight; Ariel Wang; Jennifer L Cane; Vicki S Barber; Joanna Black; Susan J Dutton; James Melhorn; Maisha Jabeen; Phil Moss; Rajendar Garlapati; Tanya Baron; Graham Johnson; Fleur Cantle; David Clarke; Samer Elkhodair; Jonathan Underwood; Daniel Lasserson; Ian D Pavord; Sophie B Morgan; Duncan Richards,"University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; St George's Hospital, London; East Lancashire NHS Hospitals; Oxford University Hospitals NHS Trust; Royal Derby Hospital; Kings College Hospital, London; Royal Berkshire Hospital; University College London Hospital; Cardiff University; Oxford University Hospitals NHS Trust; University of Oxford; University of Oxford; University of Oxford","BackgroundThe antibacterial, anti-inflammatory and antiviral properties of azithromycin suggest therapeutic potential against COVID-19. Randomised data in mild-moderate disease are lacking. We assessed whether azithromycin is effective in reducing hospitalisation in patients with mild-moderate COVID-19. MethodsThis open-label, randomised superiority clinical trial at 19 centres in the United Kingdom enrolled adults, [≥]18 years, presenting to hospitals with clinically-diagnosed highly-probable or confirmed COVID-19 infection, with <14 days symptoms, considered suitable for initial ambulatory management. Patients were randomised (1:1) to azithromycin (500 mg daily orally for 14 days) or to standard care without macrolides. The primary outcome was the difference in proportion of participants with death or hospital admission from any cause over the 28 days from randomisation, assessed according to intention-to-treat (ITT). Trial registration: ClinicalTrials.gov, NCT04381962, Study closed. @@ -1843,21 +1803,6 @@ What this study addsO_LI3,102,674 surgical procedures were performed in England C_LIO_LIOver 1.5 million procedures were not performed, with this deficit likely to continue to grow to 2.3 million by the end of 2021 C_LIO_LIThis deficit is the equivalent of more than 6 months of pre-pandemic surgical activity, requiring a monumental financial and logistic challenge to manage C_LI",surgery,exact,100,100 -medRxiv,10.1101/2021.02.23.21251975,2021-02-25,https://medrxiv.org/cgi/content/short/2021.02.23.21251975,The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH): Protocol for a prospective longitudinal cohort study of healthcare and ancillary workers in UK healthcare settings,Katherine Woolf; Carl Melbourne; Luke Bryant; Anna Louise Guyatt; Ian Christopher McManus; Amit Gupta; Robert C Free; Laura Nellums; Sue Carr; Catherine John; Christopher A Martin; Louise V Wain; Laura J Gray; Claire Garwood; Vishant Modhwadia; Keith Abrams; Martin D Tobin; Kamlesh Khunti; Manish Pareek; - UK-REACH Study Collaborative Group,"University College London; University of Leicester; University of Leicester; University of Leicester; University College London; University Hospitals Oxford NHS Foundation Trust; University of Leicester; University of Nottingham; General Medical Council, University Hospitals Leicester NHS Trust; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of York; University of Leicester; University of Leicester; University of Leicester; ","IntroductionThe COVID-19 pandemic has resulted in significant morbidity and mortality, and has devastated economies in many countries. Amongst the groups identified as being at increased risk from COVID-19 are healthcare workers (HCWs) and ethnic minority groups. Emerging evidence suggests HCWs from ethnic minority groups are at increased risk of adverse COVID-19-related physical and mental health outcomes. To date there has been no large-scale analysis of these risks in UK healthcare workers or ancillary workers in healthcare settings, stratified by ethnicity or occupation type, and adjusted for potential confounders. This paper reports the protocol for a prospective longitudinal questionnaire study of UK HCWs, as part of the UK-REACH programme (The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers). - -Methods and analysisA baseline questionnaire with follow-up questionnaires at 4 and 8 months will be administered to a national cohort of UK healthcare workers and ancillary workers in healthcare settings, and those registered with UK healthcare regulators. With consent, data will be linked to health records, and participants followed up for 25 years. - -Univariate associations between ethnicity and primary outcome measures (clinical COVID-19 outcomes, and physical and mental health) and key confounders/explanatory variables will be tested, followed by multivariable analyses to test for associations between ethnicity and key outcomes adjusted for the confounder/explanatory variables, with interactions included as appropriate. Using follow-up data, multilevel models will be used to model changes over time by ethnic group, facilitating understanding of absolute and relative risks in different ethnic groups, and generalisability of findings. - -Ethics and disseminationThe study is approved by Health Research Authority (reference 20/HRA/4718), and carries minimal risk to participants. We aim to manage the small risk of participant distress due to being asked questions on sensitive topics by clearly indicating on the participant information sheet that the questionnaire covers sensitive topics and that participants are under no obligation to answer these, or indeed any other, questions, and by providing links to support organisations. Results will be disseminated with reports to Government and papers uploaded to pre-print servers and submitted to peer reviewed journals. - -Registration detailsTrial ID: ISRCTN11811602 - -STRENGTHS AND LIMITATIONS OF THIS STUDYO_LINational, UK-wide, study, aiming to capture variety of healthcare worker job roles including ancillary workers in healthcare settings. -C_LIO_LILongitudinal study including three waves of questionnaire data collection, and linkage to administrative data over 25 years, with consent. -C_LIO_LIUnique support from all major UK healthcare worker regulators, relevant healthcare worker organisations, and a Professional Expert Panel to increase participant uptake and the validity of findings. -C_LIO_LIPotential for self-selection bias and low response rates, and the use of electronic invitations and online data collection makes it harder to reach ancillary workers without regular access to work email addresses. -C_LI",infectious diseases,exact,100,100 medRxiv,10.1101/2021.02.16.21251853,2021-02-19,https://medrxiv.org/cgi/content/short/2021.02.16.21251853,Mortality in COVID-19 amongst women on Hormone Replacement Therapy or Combined Oral Contraception: A cohort study,Hajira Dambha-Miller; William Hinton; Mark Joy; Michael Feher; Simon de Lusignan,University of Southampton; University of Oxford; University of Surrey; University of Oxford; University of Oxford,"ObjectiveTo investigate the association between Hormone Replacement Therapy (HRT) or Combined Oral Contraception (COCP) use, and the likelihood of death in women with COVID-19. DesignA cohort study @@ -2108,7 +2053,6 @@ ResultsMuch activity recorded in general practice declined to some extent during ConclusionsWe successfully delivered an open source software framework to describe trends and variation in clinical activity across an unprecedented scale of primary care data. The COVD-19 pandemic led to a substantial change in healthcare activity. Most laboratory tests showed substantial reduction, largely recovering to near-normal levels by September 2020, with some important tests less affected. Records of respiratory infections decreased with the exception of codes related to COVID-19, whilst activity of other respiratory disease codes was mixed. We are expanding the NHS Service Restoration Observatory in collaboration with clinicians, commissioners and researchers and welcome feedback.",health systems and quality improvement,exact,100,100 medRxiv,10.1101/2020.12.30.20248603,2021-01-01,https://medrxiv.org/cgi/content/short/2020.12.30.20248603,SARS-CoV-2 positivity in asymptomatic-screened dental patients,David I Conway; Shauna Culshaw; Maura Edwards; Claire Clark; Chris Watling; Chris Robertson; Raymond Braid; Emma O'Keefe; Niall McGoldrick; Jacky Burns; Stacey Provan; Harper VanSteenhouse; Jodie Hay; Rory Gunson; - Dental COVID-19 Surveillance Survey Group,University of Glasgow and Public Health Scotland; University of Glasgow; NHS Ayrshire and Arran; Public Health Scotland; Public Health Scotland; Strathclyde University and Public Health Scotland; Public Health Scotland; NHS Fife; NHS Fife; NHS Fife; NHS Greater Glasgow & Clyde; BioClavis Ltd; University of Glasgow; NHS Greater Glasgow & Clyde; ,"Enhanced community surveillance is a key pillar of the public health response to COVID-19. Asymptomatic carriage of SARS-CoV-2 is a potentially significant source of transmission, yet remains relatively poorly understood. Disruption of dental services continues with significantly reduced capacity. Ongoing precautions include pre- and/or at appointment COVID-19 symptom screening and use of enhanced personal protective equipment (PPE). This study aimed to investigate SARS-CoV-2 infection in dental patients to inform community surveillance and improve understanding of risks in the dental setting. Thirty-one dental care centres across Scotland invited asymptomatic screened patients over 5-years-old to participate. Following verbal consent and completion of sociodemographic and symptom history questionnaire, trained dental teams took a combined oropharyngeal and nasal swab sample using standardised VTM-containing testkits. Samples were processed by the Lighthouse Lab and patients informed of their results by SMS/e-mail with appropriate self-isolation guidance in the event of a positive test. Over a 13-week period (from 3August to 31October2020) n=4,032 patients, largely representative of the population, were tested. Of these n=22 (0.5%; 95%CI 0.5%, 0.8%) tested positive for SARS-CoV-2. The positivity rate increased over the period, commensurate with uptick in community prevalence identified across all national testing monitoring data streams. All positive cases were successfully followed up by the national contact tracing program. To the best of our knowledge this is the first report of a COVID-19 testing survey in asymptomatic-screened patients presenting in a dental setting. The positivity rate in this patient group reflects the underlying prevalence in community at the time. These data are a salient reminder, particularly when community infection levels are rising, of the importance of appropriate ongoing Infection Prevention Control and PPE vigilance, which is relevant as healthcare team fatigue increases as the pandemic continues. Dental settings are a valuable location for public health surveillance.",dentistry and oral medicine,exact,100,100 -bioRxiv,10.1101/2020.12.23.424229,2020-12-25,https://biorxiv.org/cgi/content/short/2020.12.23.424229,Patterns of within-host genetic diversity in SARS-CoV-2,Gerry Tonkin-Hill; Inigo Martincorena; Roberto Amato; Andrew R J Lawson; Moritz Gerstung; Ian Johnston; David K Jackson; Naomi R Park; Stefanie V Lensing; Michael A Quail; Sónia Gonçalves; Cristina Ariani; Michael Spencer Chapman; William L Hamilton; Luke W Meredith; Grant Hall; Aminu S Jahun; Yasmin Chaudhry; Myra Hosmillo; Malte L Pinckert; Iliana Georgana; Anna Yakovleva; Laura G Caller; Sarah L Caddy; Theresa Feltwell; Fahad A Khokhar; Charlotte J Houldcroft; Martin D Curran; Surendra Parmar; - The COVID-19 Genomics UK (COG-UK) Consortium; Alex Alderton; Rachel Nelson; Ewan Harrison; John Sillitoe; Stephen D Bentley; Jeffrey C Barrett; M. Estee Torok; Ian G Goodfellow; Cordelia Langford; Dominic Kwiatkowski; - Wellcome Sanger Institute COVID-19 Surveillance Team,"Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge and The Francis Crick Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge and Cambridge Institute of Therapeutic Immunology and Infectious Disease; Department of Medicine, University of Cambridge; Public Health England; Public Health England; COG-UK; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute and European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute and Oxford University; ","Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1,181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within and between host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.",genomics,exact,100,100 medRxiv,10.1101/2020.12.18.20248477,2020-12-20,https://medrxiv.org/cgi/content/short/2020.12.18.20248477,Face covering adherence is positively associated with better mental health and wellbeing: a longitudinal analysis of the CovidLife surveys,Drew M Altschul; Chloe Fawns-Ritchie; Alex Kwong; Louise Hartley; Clifford Nangle; Rachel Edwards; Rebecca Dawson; Christie Levein; Archie Campbell; Robin Flaig; Andrew McIntosh; Ian Deary; Riccardo Marioni; Caroline Hayward; Cathie Sudlow; Elaine Douglas; David Bell; David Porteous,The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; University of Stirling; University of Stirling; The University of Edinburgh,"Face masks or coverings are effective at reducing airborne infection rates, yet pandemic mitigation measures, including wearing face coverings, have been suggested to contribute to reductions in quality of life and poorer mental health. Longitudinal analyses of more than 11,000 participants across the UK found no association between lower adherence to face covering guidelines and poorer mental health. The opposite appears to be true. Even after controlling for behavioral, social, and psychological confounds, including measures of pre-pandemic mental health, individuals who wore face coverings ""most of the time"" or ""always"" had better mental health and wellbeing than those who did not. These results suggest that wearing face coverings more often will not negatively impact mental health.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2020.12.10.20247155,2020-12-14,https://medrxiv.org/cgi/content/short/2020.12.10.20247155,Self-harm presentations to Emergency Departments and Place of Safety during the first wave of the UK COVID-19 pandemic: South London and Maudsley data on service use from February to June 2020.,Eleanor Nuzum; Evangelia Martin; Gemma Morgan; Rina Dutta; Christoph Mueller; Catherine Polling; Megan Pritchard; Sumithra Velupillai; Robert Stewart,South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic has had a substantial impact on both mental health service delivery, and the ways in which people are accessing these services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for around 1.2m residents in South London) have highlighted increased use of virtual contacts by mental health teams, with dropping numbers of face-to-face contacts over the first wave of the pandemic. There has been concern that the impact of the COVID-19 pandemic would lead to higher mental health emergencies, particularly instances of self-harm. However, with people advised to stay at home during the first wave lockdown, it is as yet unclear whether this impacted mental health service presentations. Taking advantage of SLaMs Clinical Records Interactive Search (CRIS) data resource with daily updates of information from its electronic mental health records, this paper describes overall presentations to Emergency Department (ED) mental health liaison teams, and those with self-harm. The paper focussed on three periods: i) a pre-lockdown period 1st February to 15th March, ii) a lockdown period 16th March to 10th May and iii) a post-lockdown period 11th May to 28th June. In summary, all attendances to EDs for mental health support decreased during the lockdown period, including those with self-harm. All types of self-harm decreased during lockdown, with self-poisoning remaining the most common. Attendances to EDs for mental health support increased post-lockdown, although were only just approaching pre-lockdown levels by the end of June 2020.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2020.12.07.20245183,2020-12-07,https://medrxiv.org/cgi/content/short/2020.12.07.20245183,"Indicators of COVID-19 status in a cohort study of university staff and post-graduate research students, including results from home antibody testing",Katrina A S Davis; Ewan Carr; Daniel Leightley; Valentina Vitiello; Gabriella Bergin Cartwright; Grace Lavelle; Alice Wickersham; Michael H Malim; Carolin Oetzmann; Catherine Polling; Sharon A.M. Stevelink; Reza Razavi; Matthew Hotopf; - KCL-CHECK research team,"KCL Institute of Psychiatry, Psychology and Neuroscience; KCL Institute of Psychiatry Psychology and Neuroscience; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; ","Background Definitive diagnosis of COVID-19 requires resources frequently restricted to the severely ill. Cohort studies must rely on surrogate indicators to define cases of COVID-19 in the community. We describe the prevalence and overlap of potential indicators including self-reported symptoms, suspicion, and routine test results, plus home antibody testing. Methods An occupational cohort of 2807 staff and postgraduate students at a large London university. Repeated surveys covering March to June 2020. Antibody test results from 'lateral flow' IgG/IgM cassettes in June 2020. Results 1882 participants had valid antibody test results, and 124 (7%) were positive. Core symptoms of COVID-19 were common (770 participants positive, 41%), although fewer met criteria on a symptom algorithm (n=297, 16%). Suspicion of COVID-19 (n=509, 27%) was much higher than positive external tests (n=39, 2%). Positive antibody tests were rare in people who had no suspicion (n=4, 1%) or no core symptoms (n=10, 2%). In those who reported external antibody tests, 15% were positive on the study antibody test, compared with 24% on earlier external antibody tests. Discussion Our results demonstrate the agreement between different COVID indicators. Antibody testing using lateral flow devices at home can detect asymptomatic cases and provide greater certainty to self-report; but due to weak and waning antibody responses to mild infection, may under-ascertain. Multiple indicators used in combination can provide a more complete story than one used alone. Cohort studies need to consider how they deal with different, sometimes conflicting, indicators of COVID-19 illness to understand its long-term outcomes.",epidemiology,exact,100,100 @@ -2144,6 +2088,7 @@ C_LIO_LIOptimal symptom combinations maximise case capture considering available C_LIO_LIImplications for COVID-19 vaccine efficacy trials and wider public health C_LI",health informatics,exact,100,100 medRxiv,10.1101/2020.11.19.20234120,2020-11-23,https://medrxiv.org/cgi/content/short/2020.11.19.20234120,Actionable druggable genome-wide Mendelian randomization identifies repurposingopportunities for COVID-19,Liam Gaziano; Claudia Giambartolomei; Alexandre C Pereira; Anna Gaulton; Daniel C Posner; Sonja A Swanson; Yuk Lam Ho; Sudha K Iyengar; Nicole M Kosik; Marijana Vujkovic; David R Gagnon; A Patricia Bento; Pedro Beltrao; Inigo Barrio Hernandez; Lars Ronnblom; Niklas Hagberg; Christian Lundtoft; Claudia Langenberg; Maik Pietzner; Dennis Valentine; Elias Allara; Praveen Surendran; Stephen Burgess; Jing Hua Zhao; James E Peters; Bram P Prins; John Danesh; Poornima Devineni; Yunling Shi; Kristine E Lynch; Scott L DuVall; Helene Garcon; Lauren Thomann; Jin J Zhou; Bryan R Gorman; Jennifer E Huffman; Christopher J O'Donnell; Philip S Tsao; Jean C Beckham; Saiju Pyarajan; Sumitra Muralidhar; Grant D Huang; Rachel Ramoni; Adriana M Hung; Kyong-Mi Chang; Yan V Sun; Jacob Joseph; Andrew R Leach; Todd L Edwards; Kelly Cho; J Michael Gaziano; Adam S Butterworth; Juan P Casas,"VA Boston Healthcare System, University of Cambridge; Instituto Italiano di Tecnologia, University of California Los Angeles; University of Sao Paulo, Harvard University; European Molecular Biology Laboratory, European Bioinformatics Institute; VA Boston Healthcare System; Erasmus Medical Center; VA Boston Healthcare System; Case Western Reserve University and Louis Stoke Cleveland VAMC; VA Boston Healthcare System; The Corporal Michael J. Crescenz VA Medical Center, the University of Pennsylvania Perelman School of Medicine; Boston University, VA Boston Healthcare System; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; European Molecular Biology Laboratory, European Bioinformatics Institute; Uppsala University; Uppsala University; Uppsala University; Charite University Medicine Berlin, Universityof Cambridge; Universityof Cambridge; University College London; University of Cambridge; Wellcome Genome Campus and University of Cambridge; University of Cambridge; University of Cambridge; Imperial College London; Wellcome Genome Campus and University of Cambridge; University of Cambridge; VA Boston Healthcare System; VA Boston Healthcare System; VA Salt Lake City Health Care System, University of Utah; VA Salt Lake City Health Care System, University of Utah; VA Boston Healthcare System; VA Boston Healthcare System; University of Arizona, Phoenix VA Health Care System; VA Boston Healthcare System; VA Boston Healthcare System; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Palo Alto Health Care System, Stanford University School of Medicine; Durham VA Medical Center, Duke University School of Medicine; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs; Department of Veterans Affairs, Vanderbilt University; The Corporal Michael J. Crescenz VA Medical Center, University of Pennsylvania; Atlanta VA Health Care System, Emory University Rollins School of Public Health; VA Boston Healthcare System and Brigham & Women's Hospital; European Molecular Biology Laboratory, European Bioinformatics Institute; Department of Veterans Affairs Tennessee Valley Healthcare System, Vanderbilt Genetics Institute Vanderbilt University Medical Center; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School; University of Cambridge, Wellcome Genome Campus and University of Cambridge; VA Boston Healthcare System, Brigham and Women's Hospital, Harvard Medical School","Drug repurposing provides a rapid approach to meet the urgent need for therapeutics to address COVID-19. To identify therapeutic targets relevant to COVID-19, we conducted Mendelian randomization (MR) analyses, deriving genetic instruments based on transcriptomic and proteomic data for 1,263 actionable proteins that are targeted by approved drugs or in clinical phase of drug development. Using summary statistics from the Host Genetics Initiative and the Million Veteran Program, we studied 7,554 patients hospitalized with COVID-19 and >1 million controls. We found significant Mendelian randomization results for three proteins (ACE2: P=1.6x10-6, IFNAR2: P=9.8x10-11, and IL-10RB: P=1.9x10-14) using cis-eQTL genetic instruments that also had strong evidence for colocalization with COVID-19 hospitalization. To disentangle the shared eQTL signal for IL10RB and IFNAR2, we conducted phenome-wide association scans and pathway enrichment analysis, which suggested that IFNAR2 is more likely to play a role in COVID-19 hospitalization. Our findings prioritize trials of drugs targeting IFNAR2 and ACE2 for early management of COVID-19.",epidemiology,exact,100,100 +medRxiv,10.1101/2020.11.19.20234849,2020-11-22,https://medrxiv.org/cgi/content/short/2020.11.19.20234849,Community factors and excess mortality in first wave of the COVID-19 pandemic.,Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.",epidemiology,exact,100,100 medRxiv,10.1101/2020.11.06.20227108,2020-11-07,https://medrxiv.org/cgi/content/short/2020.11.06.20227108,Primary school staff reflections on school closures due to COVID-19 and recommendations for the future: a national qualitative survey,Emily Marchant; Charlotte Todd; Michaela James; Tom Crick; Russell Dwyer; Sinead Brophy,Swansea University; Swansea University; Swansea University; Swansea University; St Thomas Community Primary School; Swansea University,"School closures due to the COVID-19 global pandemic are likely to have a range of negative consequences spanning the domains of child development, education and health, in addition to the widening of inequalities and inequities. Research is required to improve understanding of the impact of school closures on the education, health and wellbeing of pupils and school staff, the challenges posed during reopening and importantly to identify how countries can return to in-school education and to inform policy. This qualitative study aimed to reflect on the perspectives and experiences of primary school staff (pupils aged 3-11) in Wales regarding school closures and the initial reopening of schools and to identify recommendations for the future. A total of 208 school staff completed a national online survey through the HAPPEN primary school network, consisting of questions about school closures (March to June 2020), the phased reopening of schools (June to July 2020) and a return to full-time education. Thematic analysis of survey responses highlighted that primary school staff perceive that gaps in learning, health and wellbeing have increased and inequalities have widened during school closures. Findings from this study identified five recommendations; (i) prioritise the health and wellbeing of pupils and staff; (ii) focus on enabling parental engagement and support; (iii) improve digital competence amongst pupils, teachers and parents; (iv) consider opportunities for smaller class sizes and additional staffing; and (v) improve the mechanism of communication between schools and families, and between government and schools.",public and global health,exact,100,100 medRxiv,10.1101/2020.11.03.20220699,2020-11-04,https://medrxiv.org/cgi/content/short/2020.11.03.20220699,A prospective study of risk factors associated with seroprevalence of SARS-CoV-2 antibodies in healthcare workers at a large UK teaching hospital,Daniel J Cooper; Sara Lear; Laura Watson; Ashley Shaw; Mark Ferris; Rainer Doffinger; Rachel Bousfield; Katherine Sharrocks; Michael Weekes; Ben Warne; Dominic Sparkes; Nick K Jones; Lucy Rivett; Matthew Routledge; Afzal Chaudhry; Katherine Dempsey; Montgomery Matson; Adil Lakha; George Gathercole; Olivia O'Connor; Emily Wilson; Orthi Shahzad; Kieran Toms; Rachel Thompson; Ian Halsall; David Halsall; Sally Houghton; Sofia Papadia; Nathalie Kingston; Kathleen Stirrups; Barbara Graves; Neil Walker; Hannah Stark; - The CITIID-NIHR BioResource COVID-19 Collaboration; Daniela De Angelis; Shaun Seaman; John Bradley; M Estée Török; Ian G. Goodfellow; Stephen Baker,"Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR Cambridge Clinical Research Facility; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR Cambridge Clinical Research Facility.; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; University of Cambridge School of Clinical Medicine; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, NIHR Cambridge Biomedical Research Centre; NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust; ; MRC Biostatistics Unit, University of Cambridge; MRC Biostatistics Unit, University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Cambridge University Hospitals NHS Foundation Trust; Department of pathology, Division of virology, University of Cambridge; Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK","BackgroundThe COVID-19 pandemic continues to grow at an unprecedented rate. Healthcare workers (HCWs) are at higher risk of SARS-CoV-2 infection than the general population but risk factors for HCW infection are not well described. @@ -2358,17 +2303,6 @@ Main outcomesCOVID-19 requiring hospitalisation, and any COVID-19 (any positive Results241,266, 41,198, 23,783 and 3,850 adults shared a household with 0, 1, 2, and 3 or more young children respectively. Over the study period, the risk of COVID-19 requiring hospitalisation was reduced progressively with increasing numbers of household children - fully adjusted hazard ratio (aHR) 0.93 per child (95% CI 0.79-1.10). The risk of any COVID-19 was similarly reduced, with the association being statistically significant (aHR per child 0.93; 95% CI 0.88-0.98). After schools reopened to all children in August 2020, no association was seen between exposure to young children and risk of any COVID-19 (aHR per child 1.03; 95% CI 0.92-1.14). ConclusionBetween March and October 2020, living with young children was associated with an attenuated risk of any COVID-19 and COVID-19 requiring hospitalisation among adults living in healthcare worker households. There was no evidence that living with young children increased adults risk of COVID-19, including during the period after schools re-opened.",epidemiology,exact,100,100 -medRxiv,10.1101/2020.09.15.20194795,2020-09-18,https://medrxiv.org/cgi/content/short/2020.09.15.20194795,"Acute, non-COVID related medical admissions during the first wave of COVID-19: A retrospective comparison of changing patterns of disease",Bridget Riley; Mary Packer; Suzy Gallier; Elizabeth Sapey; Catherine Atkin,"University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; PIONEER Hub, University Hospitals Birmingham NHS Foundation Trust; PIONEER Hub, University of Birmingham; PIONEER Hub, University of Birmingham","BackgroundThe COVID-19 pandemic was associated with social restrictions in the UK from 16th March 2020. It was unclear if the lockdown period was associated with differences in the case-mix of non-COVID acute medical admissions compared with the previous year. - -MethodsRetrospective data were collected for 1st-30th April 2019 and 1st-30th April 2020 from University Hospitals Birmingham NHS Foundation Trust, one of the largest hospitals in the UK with over 2 million patient contacts per year. The latter time period was chosen to coincide with the peak of COVID-19 cases in the West Midlands. All patients admitted under acute medicine during these time periods were included. COVID-19 was confirmed by SARS-Cov-2 swab or a probable case of COVID-19 based on World Health Organization diagnostic parameters. Non-COVID patients were those with a negative SARS-Cov-2 swab and no suspicion of COVID-19. Data was sourced from UHBs in-house electronic health system (EHS). - -ResultsThe total number of acute medical admissions fell comparing April 2019 (n = 2409) to April 2020 (n = 1682). As a proportion of total admissions, those aged under 45 years decreased, while those aged 46 and over did not change. - -The number of admissions due to psychiatric conditions and overdoses was higher in April 2020 (p < 0.001). When viewed as a proportion of admissions, alcohol-related admissions (p = 0.004), psychiatric conditions and overdoses (p< 0.001) increased in April 2020 than in April 2019. The proportion of patients who were in hospital due to falls also increased in April 2020 (p< 0.001). In the same period, the absolute number and the proportion of admissions that were due to non-specific chest pain, to musculoskeletal complaints and patients who self-discharged prior to assessment decreased (p = 0.02, p = 0.01 and p = 0.002 respectively). - -There were no significant differences in non-COVID-related intensive care admissions or mortality between the same months in the two years. - -ConclusionIn this large, single-centre study, there was a change in hospitalised case-mix when comparing April 2019 with April 2020: an increase in conditions which potentially reflect social isolation (falls, drug and alcohol misuse and psychiatric illness) and a decrease in conditions which rarely require in-patient hospital treatment (musculoskeletal pain and non-cardiac chest pain) especially among younger adults. These results highlight two areas for further research; the impact of social isolation on health and whether younger adults could be offered alternative health services to avoid potentially unnecessary hospital assessment.",emergency medicine,exact,100,100 medRxiv,10.1101/2020.09.12.20191973,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.12.20191973,Inequality in access to health and care services during lockdown - Findings from the COVID-19 survey in five UK national longitudinal studies,Constantin-Cristian Topriceanu; Andrew Wong; James C Moon; Alun Hughes; David Bann; Nishi Chaturvedi; Praveetha Patalay; Gabriella Conti; Gabriella Captur,University College London; UCL; UCL; UCL; University College London; UCL; University College London; UCL; University College London,"Background: Access to health services and adequate care is influenced by sex, ethnicity, socio-economic position (SEP) and burden of co-morbidities. However, it is unknown whether the COVID-19 pandemic further deepened these already existing health inequalities. Methods: Participants were from five longitudinal age-homogenous British cohorts (born in 2001, 1990, 1970, 1958 and 1946). A web and telephone-based survey provided data on cancelled surgical or medical appointments, and the number of care hours received during the UK COVID-19 national lockdown. Using binary or ordered logistic regression, we evaluated whether these outcomes differed by sex, ethnicity, SEP and having a chronic illness. Adjustment was made for study-design, non-response weights, psychological distress, presence of children or adolescents in the household, keyworker status, and whether participants had received a shielding letter. Meta-analyses were performed across the cohorts and meta-regression evaluated the effect of age as a moderator. Findings: 14891 participants were included. Females (OR 1.40, 95% confidence interval [1.27,1.55]) and those with a chronic illness (OR 1.84 [1.65-2.05]) experienced significantly more cancellations during lockdown (all p<0.0001). Ethnic minorities and those with a chronic illness required a higher number of care hours during the lockdown (both OR approx. 2.00, all p<0.002). Age was not independently associated with either outcome in meta-regression. SEP was not associated with cancellation or care hours. Interpretation: The UK government's lockdown approach during the COVID-19 pandemic appears to have deepened existing health inequalities, impacting predominantly females, ethnic-minorities and those with chronic illnesses. Public health authorities need to implement urgent policies to ensure equitable access to health and care for all in preparation for a second wave.",public and global health,exact,100,100 medRxiv,10.1101/2020.09.13.20193730,2020-09-14,https://medrxiv.org/cgi/content/short/2020.09.13.20193730,Mental health service activity during COVID-19 lockdown among individuals with Personality Disorders: South London and Maudsley data on services and mortality from January to May 2020,Eleanor Nuzum; Evangelia Martin; Matthew Broadbent; Robert Stewart,South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic is likely to have a widespread impact on mental healthcare for both services themselves and the people accessing those services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in South London) highlighted a shift to virtual contacts among those accessing community mental health and home treatment teams and an increase in deaths over the pandemics first wave. However, there is a need to understand this further for specific groups, including those diagnosed with a personality disorder who might have particular vulnerabilities. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource with 24-hourly updates of electronic mental health records data, this paper describes daily caseloads and contact numbers (face-to-face and virtual) for individuals with personality disorders across community, specialist, crisis and inpatient services. The report focussed on the period 1st January to 31st May 2020. We also report on daily accepted and discharged trust referrals, total trust caseloads and daily inpatient admissions and discharges for individuals with personality disorders. In addition, daily deaths are described for all current and previous SLaM service users with personality disorder over this period. In summary, comparing periods before and after 16th March 2020 there was a shift from face-to-face contacts to virtual contacts across all teams. Liaison and Older Adult teams showed the largest drop in caseloads, whereas Early Intervention in Psychosis service caseloads remained the same. Reduced accepted referrals and inpatient admissions were observed and there was a 28% increase in average daily deaths in the period after 16th March, compared to the period 1st January to 15th March.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2020.09.10.20191841,2020-09-11,https://medrxiv.org/cgi/content/short/2020.09.10.20191841,The King's College London Coronavirus Health and Experiences of Colleagues at King's Study: SARS-CoV-2 antibody response in an occupational sample,Daniel Leightley; Valentina Vitiello; Gabriella Bergin-Cartwright; Alice Wickersham; Katrina A S Davis; Sharon Stevelink; Matthew Hotopf; Reza Razavi; - On behalf of the KCL CHECK research team,"Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London.; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; Department of Psychological Medicine, Institute of Psychiatry Psychology and Neuroscience, King's College London; The School of Biomedical Engineering and Imaging Sciences, Faculty of Life Sciences and Medicine, King's College London; ","We report test results for SARS-CoV-2 antibodies in an occupational group of postgraduate research students and current members of staff at Kings College London. Between June and July 2020, antibody testing kits were sent to n=2296 participants; n=2004 (86.3%) responded, of whom n=1882 (93.9%) returned valid test results. Of those that returned valid results, n=124 (6.6%) tested positive for SARS-CoV-2 antibodies, with initial comparisons showing variation by age group and clinical exposure.",epidemiology,exact,100,100 @@ -2396,6 +2330,15 @@ At the recommended threshold, PMEWS and the WHO criteria showed good sensitivity ConclusionCURB-65, PMEWS and NEWS2 provide good but not excellent prediction for adverse outcome in suspected COVID-19, and predicted death without organ support better than receipt of organ support. PMEWS, the WHO criteria and NEWS2 (using a lower threshold than usually recommended) provide good sensitivity at the expense of specificity. +RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,exact,100,100 +medRxiv,10.1101/2020.09.01.20185793,2020-09-03,https://medrxiv.org/cgi/content/short/2020.09.01.20185793,Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study,Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter,University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust,"ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection. + +MethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome. + +ResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold. + +ConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive. + RegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533",emergency medicine,exact,100,100 medRxiv,10.1101/2020.08.26.20182279,2020-09-01,https://medrxiv.org/cgi/content/short/2020.08.26.20182279,COVID-19 infection dynamics in care homes in the East of England: a retrospective genomic epidemiology study,William L Hamilton; Gerry Tonkin-Hill; Emily Smith; Dinesh Aggarwal; Charlotte Houldcroft; Ben Warne; Colin Brown; Luke Meredith; Myra Hosmillo; Aminu Jahun; Martin Curran; Surendra Parmar; Laura Caller; Sarah Caddy; Fahad Khokhar; Anna Yakovleva; Grant Hall; Theresa Feltwell; Malte Pinckert; Iliana Georgana; Yasmin Chaudhry; Nicholas Brown; Sonia Goncalves; Roberto Amato; Ewan Harrison; Mathew Beale; Michael Spencer Chapman; David Jackson; Ian Johnston; Alex Alderton; John Sillitoe; Cordelia Langford; Gordon Dougan; Sharon Peacock; Dominic Kwiatowski; Ian Goodfellow; M. Estee Torok; - COVID-19 Genomics Consortium UK,"University of Cambridge; Wellcome Sanger Institute; Cambridgeshire County Council, UK; Public Health England; University of Cambridge; Cambridge University Hospitals NHS Foundation Trust; Public Health England; University of Cambridge; University of Cambridge; University of Cambridge; Public Health England; Public Health England; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; Public Health England; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; University of Cambridge; University of Cambridge; ","COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1,167 residents from 337 care homes were identified from a dataset of 6,600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns - outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population. @@ -2680,7 +2623,6 @@ ResultsSurvival curves show an increased proportion of deaths between 23rd March ConclusionsThe survival curves and increased HRs show a significantly increased risk of death in the 2020 study periods.",public and global health,exact,100,100 bioRxiv,10.1101/2020.07.01.182709,2020-07-01,https://biorxiv.org/cgi/content/short/2020.07.01.182709,Genetic architecture of host proteins interacting with SARS-CoV-2,Maik Pietzner; Eleanor Wheeler; Julia Carrasco-Zanini; Johannes Raffler; Nicola D. Kerrison; Erin Oerton; Victoria P.W. Auyeung; Chris Finan; Juan P. Casas; Rachel Ostroff; Steve A. Williams; Gabi Kastenmüller; Markus Ralser; Eric G. Gamazon; Nicholas J. Wareham; Aroon Dinesh Hingorani; Claudia Langenberg,University of Cambridge; University of Cambridge; University of Cambridge; Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH); University of Cambridge; University of Cambridge; University of Cambridge; University College London; Harvard Medical School; SomaLogic Inc.; SomaLogic Inc.; Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH); The Francis Crick Institute; Vanderbilt University Medical Center; University of Cambridge; University College London; University of Cambridge,"Strategies to develop therapeutics for SARS-CoV-2 infection may be informed by experimental identification of viral-host protein interactions in cellular assays and measurement of host response proteins in COVID-19 patients. Identification of genetic variants that influence the level or activity of these proteins in the host could enable rapid in silico assessment in human genetic studies of their causal relevance as molecular targets for new or repurposed drugs to treat COVID-19. We integrated large-scale genomic and aptamer-based plasma proteomic data from 10,708 individuals to characterize the genetic architecture of 179 host proteins reported to interact with SARS-CoV-2 proteins or to participate in the host response to COVID-19. We identified 220 host DNA sequence variants acting in cis (MAF 0.01-49.9%) and explaining 0.3-70.9% of the variance of 97 of these proteins, including 45 with no previously known protein quantitative trait loci (pQTL) and 38 encoding current drug targets. Systematic characterization of pQTLs across the phenome identified protein-drug-disease links, evidence that putative viral interaction partners such as MARK3 affect immune response, and establish the first link between a recently reported variant for respiratory failure of COVID-19 patients at the ABO locus and hypercoagulation, i.e. maladaptive host response. Our results accelerate the evaluation and prioritization of new drug development programmes and repurposing of trials to prevent, treat or reduce adverse outcomes. Rapid sharing and dynamic and detailed interrogation of results is facilitated through an interactive webserver (https://omicscience.org/apps/covidpgwas/).",genomics,exact,100,100 -medRxiv,10.1101/2020.06.29.20142448,2020-06-30,https://medrxiv.org/cgi/content/short/2020.06.29.20142448,Using past and current data to estimate potential crisis service use in mental healthcare after the COVID-19 lockdown: South London and Maudsley data,Robert Stewart; Matthew Broadbent,King's College London; South London and Maudsley NHS Foundation Trust,"The lockdown policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare with uncertain consequences over the 12 months ahead. Past activity may provide a means to predict future demand. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource at the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in south London), we carried out a range of descriptive analyses to inform the Trust on patient groups who might be most likely to require inpatient and home treatment team (HTT) crisis care. We considered the 12 months following UK COVID-19 lockdown policy on 16th March, drawing on comparable findings from previous years, and quantified levels of change in service delivery to those most likely to receive crisis care. For 12-month crisis days from 16th March in 2015-19, we found that most (over 80%) were accounted for by inpatient care (rather than HTT), most (around 75%) were used by patients who were current or recent Trust patients at the commencement of follow-up, and highest numbers were used by patients with a previously recorded schizophreniform disorder diagnosis. For current/recent patients on 16th March there had been substantial reductions in use of inpatient care in the following 31 days in 2020, more than previous years; changes in total non-inpatient contact numbers did not differ in 2020 compared to previous years, although there had been a marked switch from face-to-face to virtual contacts.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2020.06.28.20141986,2020-06-29,https://medrxiv.org/cgi/content/short/2020.06.28.20141986,Protocol for the development and evaluation of a tool for predicting risk of short-term adverse outcomes due to COVID-19 in the general UK population,Julia Hippisley-Cox; Ashley Kieran Clift; Carol AC Coupland; Ruth Keogh; Karla Diaz-Ordaz; Elizabeth Williamson; Ewen Harrison; Andrew Hayward; Harry Hemingway; Peter Horby; Nisha Mehta; Jonathan Kieran Benger; Kamlesh Khunti; David Spiegelhalter; Aziz Sheikh; Jonathan Valabhji; Ronan A Lyons; John Robson; Malcolm Gracie Semple; Frank Kee; Peter Johnson; Susan Jebb; Tony Williams; David Coggon,"University of Oxford; University of Oxford; University of Nottingham; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Edinburgh; University College London; University College London; University of Oxford; Department of Health and Social Care; NHS Digital; University of Leicester; University of Cambridge; University of Edinburgh; Imperial College London; Swansea University; Queen Mary University London; University of Liverpool; Queen's University Belfast; University of Southampton; University of Oxford; Working Fit, Ltd.; University of Southampton","IntroductionNovel coronavirus 2019 (COVID-19) has propagated a global pandemic with significant health, economic and social costs. Emerging emergence has suggested that several factors may be associated with increased risk from severe outcomes or death from COVID-19. Clinical risk prediction tools have significant potential to generate individualised assessment of risk and may be useful for population stratification and other use cases. Methods and analysisWe will use a prospective open cohort study of routinely collected data from 1205 general practices in England in the QResearch database. The primary outcome is COVID-19 mortality (in or out-of-hospital) defined as confirmed or suspected COVID-19 mentioned on the death certificate, or death occurring in a person with SARS-CoV-2 infection between 24th January and 30th April 2020. Our primary outcome in adults is COVID-19 mortality (including out of hospital and in hospital deaths). We will also examine COVID-19 hospitalisation in children. Time-to-event models will be developed in the training data to derive separate risk equations in adults (19-100 years) for males and females for evaluation of risk of each outcome within the 3-month follow-up period (24th January to 30th April 2020), accounting for competing risks. Predictors considered will include age, sex, ethnicity, deprivation, smoking status, alcohol intake, body mass index, pre-existing medical co-morbidities, and concurrent medication. Measures of performance (prediction errors, calibration and discrimination) will be determined in the test data for men and women separately and by ten-year age group. For children, descriptive statistics will be undertaken if there are currently too few serious events to allow development of a risk model. The final model will be externally evaluated in (a) geographically separate practices and (b) other relevant datasets as they become available. @@ -2746,6 +2688,15 @@ MethodsWe investigated staff reports regarding the impact of the COVID-19 pandem Results2,180 staff from a range of sectors, professions and specialties participated. Immediate infection control concerns were highly salient for inpatient staff, new ways of working for community staff. Multiple rapid adaptations and innovations in response to the crisis were described, especially remote working. This was cautiously welcomed but found successful in only some clinical situations. Staff had specific concerns about many groups of service users, including people whose conditions are exacerbated by pandemic anxieties and social disruptions; people experiencing loneliness, domestic abuse and family conflict; those unable to understand and follow social distancing requirements; and those who cannot engage with remote care. ConclusionThis overview of staff concerns and experiences in the early COVID-19 pandemic suggests directions for further research and service development: we suggest that how to combine infection control and a therapeutic environment in hospital, and how to achieve effective and targeted tele-health implementation in the community, should be priorities. The limitations of our convenience sample must be noted.",psychiatry and clinical psychology,exact,100,100 +medRxiv,10.1101/2020.06.10.20127175,2020-06-11,https://medrxiv.org/cgi/content/short/2020.06.10.20127175,Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.,Amitava Banerjee; Suliang Chen; Laura Pasea; Alvina Lai; Michail Katsoulis; Spiros Denaxas; Vahe Nafilyan; Bryan Williams; Wai Keong Wong; Ameet Bakhai; Kamlesh Khunti; Deenan Pillay; Mahdad Noursadeghi; Honghan Wu; Nilesh Pareek; Daniel Bromage; Theresa Mcdonagh; Jonathan Byrne; James T Teo; Ajay Shah; Ben Humberstone; Liang V Tang; Anoop SV Shah; Andrea Rubboli; Yutao Guo; Yu Hu; Cathie LM Sudlow; Gregory YH Lip; Harry Hemingway,"University College London; University College London; University College London; University College London; UCL; University College London; Office for National Statistics; UCL; University College London Hospitals NHS Trust; Royal Free Hospitals NHS Trust; University of Leicester; UCL; UCL; UCL; King's College Hospital; Kings College London; Kings College London; Kings London NHS Trust; Kings College Hospital NHS Foundation Trust; King's College London; Office for National Statistics; Huazhong University of Science and Technology, Wuhan, China; University of Edinburgh; Ospedale S. Maria delle Croci, Ravenna, Italy; PLA General Hospital, Beijing, China.; Huazhong University of Science and Technology, Wuhan, China.; University of Edinburgh; University of Liverpool; UCL","BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both ""direct"", through infection, and ""indirect"", through changes in healthcare. + +MethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(""direct"" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For ""indirect"" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020. + +FindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths. + +InterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic. + +FundingNIHR, HDR UK, Astra Zeneca",cardiovascular medicine,exact,100,100 medRxiv,10.1101/2020.06.08.20120584,2020-06-09,https://medrxiv.org/cgi/content/short/2020.06.08.20120584,SARS-CoV-2 virus and antibodies in front-line Health Care Workers in an acute hospital in London: preliminary results from a longitudinal study,Catherine Houlihan; Nina Vora; Thomas Byrne; Dan Lewer; Judith Heaney; David A Moore; Rebecca Matthews; Sajida Adam; Louise Enfield; Abigail Severn; Angela McBride; Moira Jane Spyer; Rupert Beale; Peter Cherepanov; Kathleen Gaertner; Maryam Shahmanesh; - The SAFER Field Study Team; Kevin Ng; Georgina Cornish; Naomi Walker; Susan Michie; Ed Manley; Fabiana Lorencatto; - The Crick-COVID-Consortium; Richard Gilson; Sonia Gandhi; Steve Gamblin; George Kassiotis; Laura McCoy; Charles Swanton; Andrew Hayward; Eleni Nastouli,University College London Hospital; UCL; UCL; University College London; UCL; Francis Crick Institute; UCL; UCL; UCL; UCL; UCL; UCL; Francis Crick Institute; Francis Crick Institute; UCL; UCL; ; Francis Crick Institute; Francis Crick Institute; UCL; UCL; Leeds University; UCL; ; UCL; Francis Crick Institute; Francis Crick Institute; Francis Crick Institute; UCL; Francis Crick Institute; UCL; University College London,"BackgroundAlthough SARS-CoV-2 infection in Healthcare Workers (HCWs) is a public health concern, there is little description of their longitudinal antibody response in the presence or absence of SARS-CoV-2 and symptoms. We followed HCWs in an acute London hospital to measure seroconversion and RNA detection at the peak of the pandemic. MethodsWe enrolled 200 patient-facing HCWs between 26 March and 8 April 2020 and collected twice-weekly self-administered nose and throat swabs, symptom data and monthly blood samples. Swabs were tested for SARS-CoV-2 by PCR, and serum for antibodies to spike protein by ELISA and flow cytometry. diff --git a/data/covid/preprints.exact.json b/data/covid/preprints.exact.json index 21da51ff..79715fa7 100644 --- a/data/covid/preprints.exact.json +++ b/data/covid/preprints.exact.json @@ -1133,20 +1133,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.05.06.22274658", - "date": "2022-05-07", - "link": "https://medrxiv.org/cgi/content/short/2022.05.06.22274658", - "title": "STIMULATE-ICP-CAREINEQUAL - Defining usual care and examining inequalities in Long Covid support: protocol for a mixed-methods study (part of STIMULATE-ICP: Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways).", - "authors": "Mel Ramasawmy; Yi Mu; Donna Clutterbuck; Marija Pantelic; Gregory Y.H. Lip; Christina Van der Feltz-Cornelis; Dan Wootton; Nefyn H Williams; Hugh Montgomery; Rita Mallinson Cookson; Emily Attree; Mark Gabbay; Melissa J Heightman; Nisreen A Alwan; Amitava Banerjee; Paula Lorgelly; - STIMULATE-ICP consortium", - "affiliations": "Institute of Health Informatics, University College London; Institute of Health Informatics, University College London; School of Primary Care, Population Sciences and Medical Education, University of Southampton; Brighton and Sussex Medical School, University of Sussex; Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, United Kingdom; and Department of Clinical; Department of Health Sciences, HYMS, University of York, and Institute of Health Informatics, University College London; Institute of Infection Veterinary and Ecological Sciences, University of Liverpool; Department of Primary Care and Mental Health, University of Liverpool; Centre for Human Health and Performance, Department of Medicine, University College London; PPIE Representative; PPIE Representative; Department of Primary Care and Mental Health, University of Liverpool; University College London Hospitals NHS Trust; School of Primary Care, Population Sciences and Medical Education, University of Southampton; NIHR Southampton Biomedical Research Centre, University of Southam; Institute of Health Informatics, University College London; School of Population Health and Department of Economics, University of Auckland; ", - "abstract": "IntroductionIndividuals with Long Covid represent a new and growing patient population. In England, fewer than 90 Long Covid clinics deliver assessment and treatment informed by NICE guidelines. However, a paucity of clinical trials or longitudinal cohort studies means that the epidemiology, clinical trajectory, healthcare utilisation and effectiveness of current Long Covid care are poorly documented, and that neither evidence-based treatments nor rehabilitation strategies exist. In addition, and in part due to pre-pandemic health inequalities, access to referral and care varies, and patient experience of the Long Covid care pathways can be poor.\n\nIn a mixed methods study, we therefore aim to: (1) describe the usual healthcare, outcomes and resource utilisation of individuals with Long Covid; (2) assess the extent of inequalities in access to Long Covid care, and specifically to understand Long Covid patients experiences of stigma and discrimination.\n\nMethods and analysisA mixed methods study will address our aims. Qualitative data collection from patients and health professionals will be achieved through surveys, interviews and focus group discussions, to understand their experience and document the function of clinics. A patient cohort study will provide an understanding of outcomes and costs of care. Accessible data will be further analysed to understand the nature of Long Covid, and the care received.\n\nEthics and disseminationEthical approval was obtained from South Central - Berkshire Research Ethics Committee (reference 303958). The dissemination plan will be decided by the patient and public involvement and engagement (PPIE) group members and study Co-Is, but will target 1) policy makers, and those responsible for commissioning and delivering Long Covid services, 2) patients and the public, and 3) academics.", - "category": "health systems and quality improvement", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.04.28.22273177", @@ -1259,20 +1245,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.03.22.22272775", - "date": "2022-03-23", - "link": "https://medrxiv.org/cgi/content/short/2022.03.22.22272775", - "title": "Risk of death following SARS-CoV-2 infection or COVID-19 vaccination in young people in England: a self-controlled case series study", - "authors": "Vahe Nafilyan; Charlotte Bermingham; Isobel L Ward; Jasper Morgan; Francesco Zaccardi; Kamlesh Khunti; Julie Stanborough; Amitava Banerjee", - "affiliations": "Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Real World Evidence Unit, Diabetes Research Centre, University of Leicester; Real World Evidence Unit, Diabetes Research Centre, University of Leicester; Office for National Statistics; Institute of Health Informatics, University College London", - "abstract": "ObjectivesTo assess whether there is a change in the incidence of cardiac and all-cause death in young people following COVID-19 vaccination or SARS-CoV-2 infection in unvaccinated individuals.\n\nDesignSelf-controlled case series.\n\nSettingNational, linked electronic health record data in England.\n\nStudy populationIndividuals aged 12-29 who had received at least one dose of COVID-19 vaccination and died between 8 December 2020 and 2 February 2022 and registered by 16 February 2022 within 12 weeks of COVID-19 vaccination; Individuals aged 12-29 who died within 12 weeks of testing positive for SARS-CoV-2.\n\nMain outcome measuresCardiac and all-cause deaths occurring within 12 weeks of vaccination or SARS-CoV-2 infection.\n\nResultsCompared to the baseline period, there was no evidence of a change in the incidence of cardiac death in the six weeks after vaccination, whether for each of weeks 1 to 6 or the whole six-week period. There was a decrease in the risk of all-cause death in the first week after vaccination and no change in each of weeks 2 to 6 after vaccination or whole six-week period after vaccination. Subgroup analyses by sex, age, vaccine type, and last dose also showed no change in the risk of death in the first six weeks after vaccination. There was a large increase in the incidence of cardiac and all-cause death in the overall risk period after SARS-CoV-2 infection among the unvaccinated.\n\nConclusionThere is no evidence of an association between COVID-19 vaccination and an increased risk of death in young people. By contrast, SARS-CoV-2 infection was associated with substantially higher risk of cardiac related death and all-cause death.\n\nWhat is already known on this topicSeveral studies have highlighted the association between COVID-19 vaccination and the risk of myocarditis, myopericarditis, and other cardiac problems, especially in young people, but associated risk of mortality is unclear. Since younger people have lower risk of COVID-19 hospitalisation and mortality, the mortality risk associated with vaccination is potentially more important to them in balancing the risk and benefit of vaccination.\n\nWhat this study addsAlthough there is a risk of myocarditis or myopericarditis with COVID-19, there is no evidence of increased risk of cardiac or all-cause mortality following COVID-19 vaccination in young people aged 12 to 29. Given the increased risk of mortality following SARS-CoV-2 infection in this group, the risk-benefit analysis favours COVID-19 vaccination for this age group.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.03.18.22272607", @@ -1567,6 +1539,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2021.12.17.473248", + "date": "2021-12-21", + "link": "https://biorxiv.org/cgi/content/short/2021.12.17.473248", + "title": "SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion", + "authors": "Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta", + "affiliations": "University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge", + "abstract": "The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.", + "category": "microbiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.20.21268098", @@ -1749,20 +1735,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.11.22.21266512", - "date": "2021-11-24", - "link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266512", - "title": "Association of COVID-19 with arterial and venous vascular diseases: a population-wide cohort study of 48 million adults in England and Wales", - "authors": "Rochelle Knight; Venexia Walker; Samantha Ip; Jennifer A Cooper; Thomas Bolton; Spencer Keene; Rachel Denholm; Ashley Akbari; Hoda Abbasizanjani; Fatemeh Torabi; Efosa Omigie; Sam Hollings; Teri-Louise North; Renin Toms; Emanuele Di Angelantonio; Spiros Denaxas; Johan H Thygesen; Christopher Tomlinson; Ben Bray; Craig J Smith; Mark Barber; George Davey Smith; Nishi Chaturvedi; Cathie Sudlow; William N Whiteley; Angela Wood; Jonathan A C Sterne; - CVD-COVID-UK/COVID-IMPACT consortium; - Longitudinal Health and Wellbeing COVID-19 National Core Study", - "affiliations": "University of Bristol; University of Bristol; University of Cambridge; University of Bristol; University of Cambridge; University of Cambridge; University of Bristol; Swansea University; Swansea University; Swansea University; NHS Digital; NHS Digital; University of Bristol; University of Bristol; University of Cambridge; University College London; University College London; University College London; Kings College London; University of Manchester; Glasgow Caledonian University; University of Bristol; University College London; Health Data Research UK; University of Edinburgh; University of Cambridge; University of Bristol; ; ", - "abstract": "ImportanceThe long-term effects of COVID-19 on the incidence of vascular diseases are unclear.\n\nObjectiveTo quantify the association between time since diagnosis of COVID-19 and vascular disease, overall and by age, sex, ethnicity, and pre-existing disease.\n\nDesignCohort study based on population-wide linked electronic health records, with follow up from January 1st to December 7th 2020.\n\nSetting and participantsAdults registered with an NHS general practice in England or Wales and alive on January 1st 2020.\n\nExposuresTime since diagnosis of COVID-19 (categorised as 0-6 days, 1-2 weeks, 3-4, 5-8, 9-12, 13-26 and 27-49 weeks since diagnosis), with and without hospitalisation within 28 days of diagnosis.\n\nMain outcomes and measuresPrimary outcomes were arterial thromboses (mainly acute myocardial infarction and ischaemic stroke) and venous thromboembolic events (VTE, mainly pulmonary embolism and lower limb deep vein thrombosis). We also studied other vascular events (transient ischaemic attack, haemorrhagic stroke, heart failure and angina). Hazard ratios were adjusted for demographic characteristics, previous disease diagnoses, comorbidities and medications.\n\nResultsAmong 48 million adults, 130,930 were and 1,315,471 were not hospitalised within 28 days of COVID-19. In England, there were 259,742 first arterial thromboses and 60,066 first VTE during 41.6 million person-years follow-up. Adjusted hazard ratios (aHRs) for first arterial thrombosis compared with no COVID-19 declined rapidly from 21.7 (95% CI 21.0-22.4) to 3.87 (3.58-4.19) in weeks 1 and 2 after COVID-19, 2.80 (2.61-3.01) during weeks 3-4 then to 1.34 (1.21-1.48) during weeks 27-49. aHRs for first VTE declined from 33.2 (31.3-35.2) and 8.52 (7.59-9.58) in weeks 1 and 2 to 7.95 (7.28-8.68) and 4.26 (3.86-4.69) during weeks 3-4 and 5-8, then 2.20 (1.99-2.44) and 1.80 (1.50-2.17) during weeks 13-26 and 27-49 respectively. aHRs were higher, for longer after diagnosis, after hospitalised than non-hospitalised COVID-19. aHRs were also higher among people of Black and Asian than White ethnicity and among people without than with a previous event. Across the whole population estimated increases in risk of arterial thromboses and VTEs were 2.5% and 0.6% respectively 49 weeks after COVID-19, corresponding to 7,197 and 3,517 additional events respectively after 1.4 million COVID-19 diagnoses.\n\nConclusions and RelevanceHigh rates of vascular disease early after COVID-19 diagnosis decline more rapidly for arterial thromboses than VTEs but rates remain elevated up to 49 weeks after COVID_19. These results support continued policies to avoid COVID-19 infection with effective COVID-19 vaccines and use of secondary preventive agents in high-risk patients.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSIs COVID-19 associated with higher long-term incidence of vascular diseases?\n\nFindingsIn this cohort study of 48 million adults in England and Wales, COVID-19 was associated with higher incidence, that declined with time since diagnosis, of both arterial thromboses [week 1: adjusted HR [aHR] 21.7 (95% CI 21.0-22.4) weeks 27-49: aHR 1.34 (1.21-1.48)] and venous thromboembolism [week 1: aHR 33.2 (31.3-35.2), weeks 27-49 1.80 (1.50-2.17)]. aHRs were higher, for longer, after hospitalised than non-hospitalised COVID-19. The estimated excess number of arterial thromboses and venous thromboembolisms was 10,500.\n\nMeaningAvoidance of COVID-19 infection through vaccination, and use of secondary preventive agents after infection in high-risk patients, may reduce post-COVID-19 acute vascular diseases.", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.11.15.21266264", @@ -1833,20 +1805,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.11.08.21265380", - "date": "2021-11-08", - "link": "https://medrxiv.org/cgi/content/short/2021.11.08.21265380", - "title": "Describing the population experiencing COVID-19 vaccine breakthrough following second vaccination in England: A cohort study from OpenSAFELY", - "authors": "Amelia CA Green; Helen J Curtis; William J Hulme; Elizabeth J Williamson; Helen I McDonald; Krishnan Bhaskaran; Christopher T Rentsch; Anna Schultze; Brian MacKenna; Viyaasan Mahalingasivam; Laurie Tomlinson; Alex J Walker; Louis Fisher; Jon Massey; Colm D Andrews; Lisa E M Hopcroft; Caroline E Morton; Richard Croker; Jessica Morley; Amir Mehrkar; Sebastian CJ Bacon; David Evans; Peter Inglesby; George Hickman; Tom Ward; Simon Davy; Rohini Mathur; John Tazare; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; Christopher Bates; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Ian J Douglas; Stephen JW Evans; Liam Smeeth; Ben Goldacre", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Bristol; TPP; TPP; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford", - "abstract": "BackgroundWhile the vaccines against COVID-19 are considered to be highly effective, COVID-19 vaccine breakthrough is likely and a small number of people will still fall ill, be hospitalised, or die from COVID-19, despite being fully vaccinated. With the continued increase in numbers of positive SARS-CoV-2 tests, describing the characters of individuals who have experienced a COVID-19 vaccine breakthrough could be hugely important in helping to determine who may be at greatest risk.\n\nMethodWith the approval of NHS England we conducted a retrospective cohort study using routine clinical data from the OpenSAFELY TPP database of fully vaccinated individuals, linked to secondary care and death registry data, and described the characteristics of those experiencing a COVID-19 vaccine breakthrough.\n\nResultsAs of 01st November 2021, a total of 15,436,455 individuals were identified as being fully vaccinated against COVID-19, with a median follow-up time of 149 days (IQR: 107-179). From within this population, a total of 577245 (<4%) individuals reported a positive SARS-CoV-2 test. For every 1000 years of patient follow-up time, the corresponding incidence rate was 98.02 (95% CI 97.9-98.15). There were 16,120 COVID-19-related hospital admissions, 1,100 COVID-19 critical care admission patients and 3,925 COVID-19-related deaths; corresponding incidence rates of 2.72 (95% C 2.7-2.74), 0.19 (95% C 0.18-0.19) and 0.66 (95% C 0.65-0.67), respectively. When broken down by the initial priority group, higher rates of hospitalisation and death were seen in those in care homes and those over 80 years of age. Comorbidities with the highest rates of breakthrough COVID-19 included chronic kidney disease, dialysis, transplant, haematological malignancy, and immunocompromised.\n\nConclusionThe majority of COVID-19 vaccine breakthrough cases in England were mild with relatively few fully vaccinated individuals being hospitalised or dying as a result. However, some concerning differences in rates of breakthrough cases were identified in several clinical and demographic groups. While it is important to note that these findings are simply descriptive and cannot be used to answer why certain groups have higher rates of COVID-19 breakthrough than others, the emergence of the Omicron variant of COVID-19 coupled with the continued increase in numbers of positive SARS-CoV-2 tests are concerning. As numbers of fully vaccinated individuals increases and follow-up time lengthens, so too will the number of COVID-19 breakthrough cases. Additional analyses, aimed at identifying individuals at higher risk, are therefore required.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.11.04.21265918", @@ -1987,6 +1945,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.09.13.21263487", + "date": "2021-09-16", + "link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263487", + "title": "SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population", + "authors": "Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford", + "abstract": "We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.09.09.21263026", @@ -2561,6 +2533,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.05.05.21256668", + "date": "2021-05-09", + "link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256668", + "title": "COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland", + "authors": "Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz", + "affiliations": "The University of Edinburgh; The University of Edinburgh; The University of Edinburgh", + "abstract": "The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively.\n\nClinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.", + "category": "health informatics", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.05.04.21256507", @@ -2589,6 +2575,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.04.26.21255732", + "date": "2021-04-28", + "link": "https://medrxiv.org/cgi/content/short/2021.04.26.21255732", + "title": "Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales", + "authors": "Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative", + "affiliations": "University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ", + "abstract": "BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation.\n\nMethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period.\n\nResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods.\n\nConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.04.21.21255807", @@ -2869,20 +2869,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.23.21251975", - "date": "2021-02-25", - "link": "https://medrxiv.org/cgi/content/short/2021.02.23.21251975", - "title": "The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH): Protocol for a prospective longitudinal cohort study of healthcare and ancillary workers in UK healthcare settings", - "authors": "Katherine Woolf; Carl Melbourne; Luke Bryant; Anna Louise Guyatt; Ian Christopher McManus; Amit Gupta; Robert C Free; Laura Nellums; Sue Carr; Catherine John; Christopher A Martin; Louise V Wain; Laura J Gray; Claire Garwood; Vishant Modhwadia; Keith Abrams; Martin D Tobin; Kamlesh Khunti; Manish Pareek; - UK-REACH Study Collaborative Group", - "affiliations": "University College London; University of Leicester; University of Leicester; University of Leicester; University College London; University Hospitals Oxford NHS Foundation Trust; University of Leicester; University of Nottingham; General Medical Council, University Hospitals Leicester NHS Trust; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of York; University of Leicester; University of Leicester; University of Leicester; ", - "abstract": "IntroductionThe COVID-19 pandemic has resulted in significant morbidity and mortality, and has devastated economies in many countries. Amongst the groups identified as being at increased risk from COVID-19 are healthcare workers (HCWs) and ethnic minority groups. Emerging evidence suggests HCWs from ethnic minority groups are at increased risk of adverse COVID-19-related physical and mental health outcomes. To date there has been no large-scale analysis of these risks in UK healthcare workers or ancillary workers in healthcare settings, stratified by ethnicity or occupation type, and adjusted for potential confounders. This paper reports the protocol for a prospective longitudinal questionnaire study of UK HCWs, as part of the UK-REACH programme (The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers).\n\nMethods and analysisA baseline questionnaire with follow-up questionnaires at 4 and 8 months will be administered to a national cohort of UK healthcare workers and ancillary workers in healthcare settings, and those registered with UK healthcare regulators. With consent, data will be linked to health records, and participants followed up for 25 years.\n\nUnivariate associations between ethnicity and primary outcome measures (clinical COVID-19 outcomes, and physical and mental health) and key confounders/explanatory variables will be tested, followed by multivariable analyses to test for associations between ethnicity and key outcomes adjusted for the confounder/explanatory variables, with interactions included as appropriate. Using follow-up data, multilevel models will be used to model changes over time by ethnic group, facilitating understanding of absolute and relative risks in different ethnic groups, and generalisability of findings.\n\nEthics and disseminationThe study is approved by Health Research Authority (reference 20/HRA/4718), and carries minimal risk to participants. We aim to manage the small risk of participant distress due to being asked questions on sensitive topics by clearly indicating on the participant information sheet that the questionnaire covers sensitive topics and that participants are under no obligation to answer these, or indeed any other, questions, and by providing links to support organisations. Results will be disseminated with reports to Government and papers uploaded to pre-print servers and submitted to peer reviewed journals.\n\nRegistration detailsTrial ID: ISRCTN11811602\n\nSTRENGTHS AND LIMITATIONS OF THIS STUDYO_LINational, UK-wide, study, aiming to capture variety of healthcare worker job roles including ancillary workers in healthcare settings.\nC_LIO_LILongitudinal study including three waves of questionnaire data collection, and linkage to administrative data over 25 years, with consent.\nC_LIO_LIUnique support from all major UK healthcare worker regulators, relevant healthcare worker organisations, and a Professional Expert Panel to increase participant uptake and the validity of findings.\nC_LIO_LIPotential for self-selection bias and low response rates, and the use of electronic invitations and online data collection makes it harder to reach ancillary workers without regular access to work email addresses.\nC_LI", - "category": "infectious diseases", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.02.16.21251853", @@ -3191,20 +3177,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "bioRxiv", - "doi": "10.1101/2020.12.23.424229", - "date": "2020-12-25", - "link": "https://biorxiv.org/cgi/content/short/2020.12.23.424229", - "title": "Patterns of within-host genetic diversity in SARS-CoV-2", - "authors": "Gerry Tonkin-Hill; Inigo Martincorena; Roberto Amato; Andrew R J Lawson; Moritz Gerstung; Ian Johnston; David K Jackson; Naomi R Park; Stefanie V Lensing; Michael A Quail; S\u00f3nia Gon\u00e7alves; Cristina Ariani; Michael Spencer Chapman; William L Hamilton; Luke W Meredith; Grant Hall; Aminu S Jahun; Yasmin Chaudhry; Myra Hosmillo; Malte L Pinckert; Iliana Georgana; Anna Yakovleva; Laura G Caller; Sarah L Caddy; Theresa Feltwell; Fahad A Khokhar; Charlotte J Houldcroft; Martin D Curran; Surendra Parmar; - The COVID-19 Genomics UK (COG-UK) Consortium; Alex Alderton; Rachel Nelson; Ewan Harrison; John Sillitoe; Stephen D Bentley; Jeffrey C Barrett; M. Estee Torok; Ian G Goodfellow; Cordelia Langford; Dominic Kwiatkowski; - Wellcome Sanger Institute COVID-19 Surveillance Team", - "affiliations": "Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge and The Francis Crick Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge and Cambridge Institute of Therapeutic Immunology and Infectious Disease; Department of Medicine, University of Cambridge; Public Health England; Public Health England; COG-UK; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute and European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute and Oxford University; ", - "abstract": "Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1,181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within and between host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.", - "category": "genomics", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.12.18.20248477", @@ -3303,6 +3275,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.19.20234849", + "date": "2020-11-22", + "link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234849", + "title": "Community factors and excess mortality in first wave of the COVID-19 pandemic.", + "authors": "Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott", + "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London", + "abstract": "Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.06.20227108", @@ -3667,20 +3653,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.09.15.20194795", - "date": "2020-09-18", - "link": "https://medrxiv.org/cgi/content/short/2020.09.15.20194795", - "title": "Acute, non-COVID related medical admissions during the first wave of COVID-19: A retrospective comparison of changing patterns of disease", - "authors": "Bridget Riley; Mary Packer; Suzy Gallier; Elizabeth Sapey; Catherine Atkin", - "affiliations": "University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; PIONEER Hub, University Hospitals Birmingham NHS Foundation Trust; PIONEER Hub, University of Birmingham; PIONEER Hub, University of Birmingham", - "abstract": "BackgroundThe COVID-19 pandemic was associated with social restrictions in the UK from 16th March 2020. It was unclear if the lockdown period was associated with differences in the case-mix of non-COVID acute medical admissions compared with the previous year.\n\nMethodsRetrospective data were collected for 1st-30th April 2019 and 1st-30th April 2020 from University Hospitals Birmingham NHS Foundation Trust, one of the largest hospitals in the UK with over 2 million patient contacts per year. The latter time period was chosen to coincide with the peak of COVID-19 cases in the West Midlands. All patients admitted under acute medicine during these time periods were included. COVID-19 was confirmed by SARS-Cov-2 swab or a probable case of COVID-19 based on World Health Organization diagnostic parameters. Non-COVID patients were those with a negative SARS-Cov-2 swab and no suspicion of COVID-19. Data was sourced from UHBs in-house electronic health system (EHS).\n\nResultsThe total number of acute medical admissions fell comparing April 2019 (n = 2409) to April 2020 (n = 1682). As a proportion of total admissions, those aged under 45 years decreased, while those aged 46 and over did not change.\n\nThe number of admissions due to psychiatric conditions and overdoses was higher in April 2020 (p < 0.001). When viewed as a proportion of admissions, alcohol-related admissions (p = 0.004), psychiatric conditions and overdoses (p< 0.001) increased in April 2020 than in April 2019. The proportion of patients who were in hospital due to falls also increased in April 2020 (p< 0.001). In the same period, the absolute number and the proportion of admissions that were due to non-specific chest pain, to musculoskeletal complaints and patients who self-discharged prior to assessment decreased (p = 0.02, p = 0.01 and p = 0.002 respectively).\n\nThere were no significant differences in non-COVID-related intensive care admissions or mortality between the same months in the two years.\n\nConclusionIn this large, single-centre study, there was a change in hospitalised case-mix when comparing April 2019 with April 2020: an increase in conditions which potentially reflect social isolation (falls, drug and alcohol misuse and psychiatric illness) and a decrease in conditions which rarely require in-patient hospital treatment (musculoskeletal pain and non-cardiac chest pain) especially among younger adults. These results highlight two areas for further research; the impact of social isolation on health and whether younger adults could be offered alternative health services to avoid potentially unnecessary hospital assessment.", - "category": "emergency medicine", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.09.12.20191973", @@ -3765,6 +3737,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.09.01.20185793", + "date": "2020-09-03", + "link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185793", + "title": "Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study", + "authors": "Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter", + "affiliations": "University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust", + "abstract": "ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection.\n\nMethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome.\n\nResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold.\n\nConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive.\n\nRegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533", + "category": "emergency medicine", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.08.26.20182279", @@ -4213,20 +4199,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.06.29.20142448", - "date": "2020-06-30", - "link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142448", - "title": "Using past and current data to estimate potential crisis service use in mental healthcare after the COVID-19 lockdown: South London and Maudsley data", - "authors": "Robert Stewart; Matthew Broadbent", - "affiliations": "King's College London; South London and Maudsley NHS Foundation Trust", - "abstract": "The lockdown policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare with uncertain consequences over the 12 months ahead. Past activity may provide a means to predict future demand. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource at the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in south London), we carried out a range of descriptive analyses to inform the Trust on patient groups who might be most likely to require inpatient and home treatment team (HTT) crisis care. We considered the 12 months following UK COVID-19 lockdown policy on 16th March, drawing on comparable findings from previous years, and quantified levels of change in service delivery to those most likely to receive crisis care. For 12-month crisis days from 16th March in 2015-19, we found that most (over 80%) were accounted for by inpatient care (rather than HTT), most (around 75%) were used by patients who were current or recent Trust patients at the commencement of follow-up, and highest numbers were used by patients with a previously recorded schizophreniform disorder diagnosis. For current/recent patients on 16th March there had been substantial reductions in use of inpatient care in the following 31 days in 2020, more than previous years; changes in total non-inpatient contact numbers did not differ in 2020 compared to previous years, although there had been a marked switch from face-to-face to virtual contacts.", - "category": "psychiatry and clinical psychology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.06.28.20141986", @@ -4339,6 +4311,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.06.10.20127175", + "date": "2020-06-11", + "link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127175", + "title": "Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.", + "authors": "Amitava Banerjee; Suliang Chen; Laura Pasea; Alvina Lai; Michail Katsoulis; Spiros Denaxas; Vahe Nafilyan; Bryan Williams; Wai Keong Wong; Ameet Bakhai; Kamlesh Khunti; Deenan Pillay; Mahdad Noursadeghi; Honghan Wu; Nilesh Pareek; Daniel Bromage; Theresa Mcdonagh; Jonathan Byrne; James T Teo; Ajay Shah; Ben Humberstone; Liang V Tang; Anoop SV Shah; Andrea Rubboli; Yutao Guo; Yu Hu; Cathie LM Sudlow; Gregory YH Lip; Harry Hemingway", + "affiliations": "University College London; University College London; University College London; University College London; UCL; University College London; Office for National Statistics; UCL; University College London Hospitals NHS Trust; Royal Free Hospitals NHS Trust; University of Leicester; UCL; UCL; UCL; King's College Hospital; Kings College London; Kings College London; Kings London NHS Trust; Kings College Hospital NHS Foundation Trust; King's College London; Office for National Statistics; Huazhong University of Science and Technology, Wuhan, China; University of Edinburgh; Ospedale S. Maria delle Croci, Ravenna, Italy; PLA General Hospital, Beijing, China.; Huazhong University of Science and Technology, Wuhan, China.; University of Edinburgh; University of Liverpool; UCL", + "abstract": "BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both \"direct\", through infection, and \"indirect\", through changes in healthcare.\n\nMethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(\"direct\" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For \"indirect\" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020.\n\nFindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths.\n\nInterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic.\n\nFundingNIHR, HDR UK, Astra Zeneca", + "category": "cardiovascular medicine", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.06.08.20120584", diff --git a/data/covid/preprints.json b/data/covid/preprints.json index 150004f9..53bb9762 100644 --- a/data/covid/preprints.json +++ b/data/covid/preprints.json @@ -2099,20 +2099,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.05.06.22274658", - "date": "2022-05-07", - "link": "https://medrxiv.org/cgi/content/short/2022.05.06.22274658", - "title": "STIMULATE-ICP-CAREINEQUAL - Defining usual care and examining inequalities in Long Covid support: protocol for a mixed-methods study (part of STIMULATE-ICP: Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways).", - "authors": "Mel Ramasawmy; Yi Mu; Donna Clutterbuck; Marija Pantelic; Gregory Y.H. Lip; Christina Van der Feltz-Cornelis; Dan Wootton; Nefyn H Williams; Hugh Montgomery; Rita Mallinson Cookson; Emily Attree; Mark Gabbay; Melissa J Heightman; Nisreen A Alwan; Amitava Banerjee; Paula Lorgelly; - STIMULATE-ICP consortium", - "affiliations": "Institute of Health Informatics, University College London; Institute of Health Informatics, University College London; School of Primary Care, Population Sciences and Medical Education, University of Southampton; Brighton and Sussex Medical School, University of Sussex; Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, United Kingdom; and Department of Clinical; Department of Health Sciences, HYMS, University of York, and Institute of Health Informatics, University College London; Institute of Infection Veterinary and Ecological Sciences, University of Liverpool; Department of Primary Care and Mental Health, University of Liverpool; Centre for Human Health and Performance, Department of Medicine, University College London; PPIE Representative; PPIE Representative; Department of Primary Care and Mental Health, University of Liverpool; University College London Hospitals NHS Trust; School of Primary Care, Population Sciences and Medical Education, University of Southampton; NIHR Southampton Biomedical Research Centre, University of Southam; Institute of Health Informatics, University College London; School of Population Health and Department of Economics, University of Auckland; ", - "abstract": "IntroductionIndividuals with Long Covid represent a new and growing patient population. In England, fewer than 90 Long Covid clinics deliver assessment and treatment informed by NICE guidelines. However, a paucity of clinical trials or longitudinal cohort studies means that the epidemiology, clinical trajectory, healthcare utilisation and effectiveness of current Long Covid care are poorly documented, and that neither evidence-based treatments nor rehabilitation strategies exist. In addition, and in part due to pre-pandemic health inequalities, access to referral and care varies, and patient experience of the Long Covid care pathways can be poor.\n\nIn a mixed methods study, we therefore aim to: (1) describe the usual healthcare, outcomes and resource utilisation of individuals with Long Covid; (2) assess the extent of inequalities in access to Long Covid care, and specifically to understand Long Covid patients experiences of stigma and discrimination.\n\nMethods and analysisA mixed methods study will address our aims. Qualitative data collection from patients and health professionals will be achieved through surveys, interviews and focus group discussions, to understand their experience and document the function of clinics. A patient cohort study will provide an understanding of outcomes and costs of care. Accessible data will be further analysed to understand the nature of Long Covid, and the care received.\n\nEthics and disseminationEthical approval was obtained from South Central - Berkshire Research Ethics Committee (reference 303958). The dissemination plan will be decided by the patient and public involvement and engagement (PPIE) group members and study Co-Is, but will target 1) policy makers, and those responsible for commissioning and delivering Long Covid services, 2) patients and the public, and 3) academics.", - "category": "health systems and quality improvement", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.05.05.22273234", @@ -2239,20 +2225,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "bioRxiv", - "doi": "10.1101/2022.04.20.488895", - "date": "2022-04-20", - "link": "https://biorxiv.org/cgi/content/short/2022.04.20.488895", - "title": "Emergence of new subgenomic mRNAs in SARS-CoV-2", - "authors": "Harriet V Mears; George R Young; Theo Sanderson; Ruth Harvey; Margaret Crawford; Daniel M Snell; Ashley S Fowler; Saira Hussain; Jerome Nicod; Edward Emmott; Katja Finsterbusch; Jakub Luptak; Emma Wall; Bryan Williams; Sonia Gandhi; Charles Swanton; David LV Bauer", - "affiliations": "RNA Virus Replication Laboratory, The Francis Crick Institute, London, UK; RNA Virus Replication Laboratory & Bioinformatics and Biostatistics STP, The Francis Crick Institute, London, UK; Malaria Biochemistry Laboratory, The Francis Crick Institute, London, UK; Worldwide Influenza Centre, The Francis Crick Institute, London, UK; Advanced Sequencing Facility, The Francis Crick Institute, London, UK; Advanced Sequencing Facility, The Francis Crick Institute, London, UK; Advanced Sequencing Facility, The Francis Crick Institute, London, UK; RNA Virus Replication Laboratory, The Francis Crick Institute, London, UK; Advanced Sequencing Facility, The Francis Crick Institute, London, UK; Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems Molecular & Integrative Biology, University of Liverpool, Liver; Immunoregulation Laboratory, The Francis Crick Institute, London, UK; MRC Laboratory of Molecular Biology, Cambridge, UK; Crick/UCLH Legacy Study, The Francis Crick Institute, London, UK; and National Institute for Health Research (NIHR) University College London Hospitals (UCLH) B; University College London; and National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre, London, UK; Neurodegeneration Biology Laboratory, The Francis Crick Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; RNA Virus Replication Laboratory, The Francis Crick Institute, London, UK", - "abstract": "Two mutations occurred in SARS-CoV-2 early during the COVID-19 pandemic that have come to define circulating virus lineages1: first a change in the spike protein (D614G) that defines the B.1 lineage and second, a double substitution in the nucleocapsid protein (R203K, G204R) that defines the B.1.1 lineage, which has subsequently given rise to three Variants of Concern: Alpha, Gamma and Omicron. While the latter mutations appear unremarkable at the protein level, there are dramatic implications at the nucleotide level: the GGG[->]AAC substitution generates a new Transcription Regulatory Sequence (TRS) motif, driving SARS-CoV-2 to express a novel subgenomic mRNA (sgmRNA) encoding a truncated C-terminal portion of nucleocapsid (N.iORF3), which is an inhibitor of type I interferon production. We find that N.iORF3 also emerged independently within the Iota variant, and further show that additional TRS motifs have convergently evolved to express novel sgmRNAs; notably upstream of Spike within the nsp16 coding region of ORF1b, which is expressed during human infection. Our findings demonstrate that SARS-CoV-2 is undergoing evolutionary changes at the functional RNA level in addition to the amino acid level, reminiscent of eukaryotic evolution. Greater attention to this aspect in the assessment of emerging strains of SARS-CoV-2 is warranted.", - "category": "microbiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.04.14.22273903", @@ -2423,14 +2395,14 @@ }, { "site": "medRxiv", - "doi": "10.1101/2022.03.22.22272775", + "doi": "10.1101/2022.03.23.22272804", "date": "2022-03-23", - "link": "https://medrxiv.org/cgi/content/short/2022.03.22.22272775", - "title": "Risk of death following SARS-CoV-2 infection or COVID-19 vaccination in young people in England: a self-controlled case series study", - "authors": "Vahe Nafilyan; Charlotte Bermingham; Isobel L Ward; Jasper Morgan; Francesco Zaccardi; Kamlesh Khunti; Julie Stanborough; Amitava Banerjee", - "affiliations": "Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Real World Evidence Unit, Diabetes Research Centre, University of Leicester; Real World Evidence Unit, Diabetes Research Centre, University of Leicester; Office for National Statistics; Institute of Health Informatics, University College London", - "abstract": "ObjectivesTo assess whether there is a change in the incidence of cardiac and all-cause death in young people following COVID-19 vaccination or SARS-CoV-2 infection in unvaccinated individuals.\n\nDesignSelf-controlled case series.\n\nSettingNational, linked electronic health record data in England.\n\nStudy populationIndividuals aged 12-29 who had received at least one dose of COVID-19 vaccination and died between 8 December 2020 and 2 February 2022 and registered by 16 February 2022 within 12 weeks of COVID-19 vaccination; Individuals aged 12-29 who died within 12 weeks of testing positive for SARS-CoV-2.\n\nMain outcome measuresCardiac and all-cause deaths occurring within 12 weeks of vaccination or SARS-CoV-2 infection.\n\nResultsCompared to the baseline period, there was no evidence of a change in the incidence of cardiac death in the six weeks after vaccination, whether for each of weeks 1 to 6 or the whole six-week period. There was a decrease in the risk of all-cause death in the first week after vaccination and no change in each of weeks 2 to 6 after vaccination or whole six-week period after vaccination. Subgroup analyses by sex, age, vaccine type, and last dose also showed no change in the risk of death in the first six weeks after vaccination. There was a large increase in the incidence of cardiac and all-cause death in the overall risk period after SARS-CoV-2 infection among the unvaccinated.\n\nConclusionThere is no evidence of an association between COVID-19 vaccination and an increased risk of death in young people. By contrast, SARS-CoV-2 infection was associated with substantially higher risk of cardiac related death and all-cause death.\n\nWhat is already known on this topicSeveral studies have highlighted the association between COVID-19 vaccination and the risk of myocarditis, myopericarditis, and other cardiac problems, especially in young people, but associated risk of mortality is unclear. Since younger people have lower risk of COVID-19 hospitalisation and mortality, the mortality risk associated with vaccination is potentially more important to them in balancing the risk and benefit of vaccination.\n\nWhat this study addsAlthough there is a risk of myocarditis or myopericarditis with COVID-19, there is no evidence of increased risk of cardiac or all-cause mortality following COVID-19 vaccination in young people aged 12 to 29. Given the increased risk of mortality following SARS-CoV-2 infection in this group, the risk-benefit analysis favours COVID-19 vaccination for this age group.", - "category": "epidemiology", + "link": "https://medrxiv.org/cgi/content/short/2022.03.23.22272804", + "title": "Waning effectiveness of BNT162b2 and ChAdOx1 COVID-19 vaccines over six months since second dose: a cohort study using linked electronic health records", + "authors": "Elsie MF Horne; William J Hulme; Ruth H Keogh; Tom M Palmer; Elizabeth J Williamson; Edward PK Parker; Amelia Green; Venexia Walker; Alex J Walker; Helen Curtis; Louis Fisher; Brian MacKenna; Richard Croker; Lisa Hopcroft; Robin Y Park; Jon Massey; Jessica Morely; Amir Mehrkar; Sebastian Bacon; David Evans; Peter Inglesby; Caroline E Morton; George Hickman; Simon Davy; Tom Ward; Iain Dillingham; Ben Goldacre; Miguel A Hernan; Jonathan AC Sterne", + "affiliations": "University of Bristol; Univeristy of Oxford; London School of Hygiene and Tropical Medicine; University of Bristol; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Univeristy of Oxford; University of Bristol; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Univeristy of Oxford; Harvard University; University of Bristol", + "abstract": "BackgroundThe rate at which COVID-19 vaccine effectiveness wanes over time is crucial for vaccination policies, but is incompletely understood with conflicting results from different studies.\n\nMethodsThis cohort study, using the OpenSAFELY-TPP database and approved by NHS England, included individuals without prior SARS-CoV-2 infection assigned to vaccines priority groups 2-12 defined by the UK Joint Committee on Vaccination and Immunisation. We compared individuals who had received two doses of BNT162b2 or ChAdOx1 with unvaccinated individuals during six 4-week comparison periods, separately for subgroups aged 65+ years; 16-64 years and clinically vulnerable; 40-64 years and 18-39 years. We used Cox regression, stratified by first dose eligibility and geographical region and controlled for calendar time, to estimate adjusted hazard ratios (aHRs) comparing vaccinated with unvaccinated individuals, and quantified waning vaccine effectiveness as ratios of aHRs per-4-week period. The outcomes were COVID-19 hospitalisation, COVID-19 death, positive SARS-CoV-2 test, and non-COVID-19 death.\n\nFindingsThe BNT162b2, ChAdOx1 and unvaccinated groups comprised 1,773,970, 2,961,011 and 2,433,988 individuals, respectively. Waning of vaccine effectiveness was similar across outcomes and vaccine brands: e.g. in the 65+ years subgroup ratios of aHRs versus unvaccinated for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test ranged from 1.23 (95% CI 1.15-1.32) to 1.27 (1.20-1.34) for BNT162b2 and 1.16 (0.98-1.37) to 1.20 (1.14-1.27) for ChAdOx1. Despite waning, rates of COVID-19 hospitalisation and COVID-19 death were substantially lower among vaccinated individuals compared to unvaccinated individuals up to 26 weeks after second dose, with estimated aHRs <0.20 (>80% vaccine effectiveness) for BNT162b2, and <0.26 (>74%) for ChAdOx1. By weeks 23-26, rates of SARS-CoV-2 infection in fully vaccinated individuals were similar to or higher than those in unvaccinated individuals: aHRs ranged from 0.85 (0.78-0.92) to 1.53 (1.07-2.18) for BNT162b2, and 1.21 (1.13-1.30) to 1.99 (1.94-2.05) for ChAdOx1.\n\nInterpretationThe rate at which estimated vaccine effectiveness waned was strikingly consistent for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test, and similar across subgroups defined by age and clinical vulnerability. If sustained to outcomes of infection with the Omicron variant and to booster vaccination, these findings will facilitate scheduling of booster vaccination doses.", + "category": "infectious diseases", "match_type": "fuzzy", "author_similarity": 100, "affiliation_similarity": 100 @@ -2799,20 +2771,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.01.28.22270013", - "date": "2022-01-29", - "link": "https://medrxiv.org/cgi/content/short/2022.01.28.22270013", - "title": "Agility and sustainability: A qualitative evaluation of COVID-19 Non-pharmaceutical Interventions (NPIs) in the UK logistics sector", - "authors": "Hua Wei; Sarah A Daniels; Carl A Whitfield; Yang Han; David W Denning; Ian Hall; Martyn Regan; Arpana Verma; Martie J van Tongeren", - "affiliations": "The University of Manchester; The University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester", - "abstract": "BackgroundThe emergence of SARS-CoV-2 triggered a chain of public health responses that radically changed our way of living and working. Non-healthcare sectors, such as the logistics sector, play a key role in such responses. This research aims to qualitatively evaluate the non-pharmaceutical interventions (NPIs) implemented in the UK logistics sector during the COVID-19 pandemic.\n\nMethodsWe conducted nine semi-structured interviews in July-August 2020 and May-June 2021. In total 11 interviewees represented six companies occupying a range of positions in the UKs logistics sector, including takeaway food delivery, large and small goods delivery and home appliance installation, and logistics technology providers. Inductive thematic analysis was completed using NVivo12 to generate emerging themes and subthemes. Themes/subthemes relevant to interventions were mapped deductively onto an adapted Hierarchy of Control (HoC) framework, focusing on delivery workers. Themes/subthemes relevant to the process of implementation were analyzed to understand the barriers and facilitators of rapid responses.\n\nResultsHoC analysis suggests the sector has implemented a wide range of risk mitigation measures, with each company developing their own portfolio of measures. Contact-free delivery was the most commonly implemented measure and perceived effective. In addition, a broad range of measures were implemented, including social distancing, internal contact tracing, communication and collaboration with other key stakeholders of the sector. Process evaluation identified facilitators of rapid responses including capacity to develop interventions internally, localized government support, overwhelming external mandates, effective communication, leadership support and financial support for self-isolation, while barriers included unclear government guidance, shortage of testing capacity and supply, high costs and diversified language and cultural backgrounds. Main sustainability issues included compliance fatigue, and the possible mental health impacts of a prolonged rapid response.\n\nConclusionsThis research identified drivers and obstacles of rapid implementation of NPIs in response to a respiratory infection pandemic. Existing implementation process models do not consider speed to respond and the absence or lack of guidance in emergency situations such as the COVID-19. We recommend the development of a rapid response model to inform the design of effective and sustainable infection prevention and control policies and to focus future research priorities.\n\nContributions to the fieldO_LIThe study offered important insights into the process of the UK logistics sectors response to the COVID-19 pandemic.\nC_LIO_LIThe Hierarchy of Control (HoC) framework was adapted for the evaluation of a collection of non-pharmaceutical interventions (NPIs) implemented in a non-healthcare sector.\nC_LIO_LIThematic analysis of qualitative data generated themes that were relevant to the process of rapid implementation of NPIs during a public health emergency.\nC_LIO_LIBarriers, facilitators and sustainability issues of the sectors rapid response to the COVID-19 pandemic have been highlighted to inform future research on implementation strategies.\nC_LI", - "category": "occupational and environmental health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.01.26.22269901", @@ -3079,6 +3037,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2021.12.17.473248", + "date": "2021-12-21", + "link": "https://biorxiv.org/cgi/content/short/2021.12.17.473248", + "title": "SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion", + "authors": "Bo Meng; Isabella Ferreira; Adam Abdullahi; Niluka Goonawardane; Akatsuki Saito; Izumi Kimura; Daichi Yamasoba; Steven A Kemp; Guido Papa; Saman Fatihi; Surabhi Rathore; Pehuen Perera Gerba; Terumasa Ikeda; Mako Toyoda; Toong Seng Tan; Jin Kuramochi; Shigeki Mitsunaga; Takamasa Ueno; Oscar Charles; Dami Collier; - CITIID-NIHR BioResource COVID-19 Collaboration; - The Genotype to Phenotype Japan (G2P-Japan) Consortium; - Ecuador-COVID19 Consortium; John Bradley; Jinwook Choi; Kenneth Smith; Elo Madissoon; Kerstin Meyer; Petra Mlcochova; Rainer Doffinger; Sarah A Teichmann; Leo James; Joo Hyeon Lee; Teresa Brevini; Matteo Pizzuto; Myra Hosmillo; Donna Mallery; Samantha Zepeda; Alexandra Walls; Anshu Joshi; John Bowen; John Briggs; Alex Sigal; Laurelle Jackson; Sandile Cele; Anna De Marco; Fotios Sampaziotis; Davide Corti; David Veesler; Nicholas Matheson; Ian Goodfellow; Lipi Thukral; Kei Sato; Ravindra K Gupta", + "affiliations": "University of Cambridge; University of Cambridge; University of Cambridge; University of Cambridge; University of Miyazaki; The University of Tokyo; Kumamoto University; University of Cambridge; LMB Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; CSIR Institute of Genomics and Integrative Biology, Delhi, India; University of Cambridge; Kumamoto Univ; Kumamoto University, Kumamoto; Kuramochi Clinic Interpark; Kuramochi Clinic Interpark; National Institute of Genetics, Mishima, Shizuoka; Kumamoto University, Kumamoto; University College London; University of Cambridge; -; -; -; University of Cambridge; University of Cambridge; University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute; University of Cambridge; Cambridge University Hospitals NHS Trust; Cambridge University; MRC LMB; University of Cambridge; University of Cambridge; Humabs Biomed SA; University of Cambridge; MRC LMB Cambridge; University of Washington; University of Washington; University of Washington; University of Washington; University of Heidelberg; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Africa Health Research Institute, Durban, South Africa; Humabs Biomed SA; University of Cambridge; Humabs Biomed SA; University of Washington; University of Cambridge; University of Cambridge; CSIR Institute of Genomics and Integrative Biology, Delhi, India; The University of Tokyo; University of Cambridge", + "abstract": "The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.", + "category": "microbiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.20.21268098", @@ -3205,6 +3177,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.12.13.21267368", + "date": "2021-12-15", + "link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267368", + "title": "Acute COVID-19 severity and 16-month mental morbidity trajectories in patient populations of six nations", + "authors": "Ingibjorg Magnusdottir; Aniko Lovik; Anna Bara Unnarsdottir; Daniel L. McCartney; Helga Ask; Kadri Koiv; Lea Arregui Nordahl Christoffersen; Sverre Urnes Johnson; Andrew M McIntosh; Anna K. Kahler; Archie Campbell; Arna Hauksdottir; Chloe Fawns-Ritchie; Christian Erikstrup; Dorte Helenius; Drew Altschul; Edda Bjork Thordardottir; Elias Eythorsson; Emma M. Frans; Gunnar Tomasson; Harpa Lind Jonsdottir; Harpa Runarsdottir; Henrik Hjalgrim; Hronn Hardardottir; Juan Gonzalez-Hijon; Karina Banasik; Khoa Manh Dinh; Li Lu; Lili Milani; Lill Trogstad; Maria Didriksen; Omid V. Ebrahimi; Patrick F. Sullivan; Per Minor Magnus; Qing Shen; Ragnar Nesvag; Reedik Magi; Runolfur Palsson; Sisse Rye Ostrowski; Thomas Werge; Asle Hoffart; David J. Porteous; Fang Fang; Johanna Jakobsdottir; Kelli Lehto; Ole A. Andreassen; Ole B.V. Pedersen; Thor Aspelund; Unnur Anna Valdimarsdottir", + "affiliations": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Division of Psychiatry, University of Edinburgh, Edinburgh, UK; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Edinburgh, Edinburgh, UK; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Faculty of Psychology, University of Iceland School of Health Sciences, Reykjavik, Iceland; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Danish Cancer Society Research Center, Copenhagen, Denmark; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark; Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA; Centre of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway.; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland; Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark; Department of Psychology, University of Oslo, Oslo, Norway; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK; Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia; NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Clinical Immunology, Zealand University Hospital, Denmark; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland; Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland", + "abstract": "BACKGROUNDThe aim of this multinational study was to assess the development of adverse mental health symptoms among individuals diagnosed with COVID-19 in the general population by acute infection severity up to 16 months after diagnosis.\n\nMETHODSParticipants consisted of 247 249 individuals from seven cohorts across six countries (Denmark, Estonia, Iceland, Norway, Scotland, and Sweden) recruited from April 2020 through August 2021. We used multivariable Poisson regression to contrast symptom-prevalence of depression, anxiety, COVID-19 related distress, and poor sleep quality among individuals with and without a diagnosis of COVID-19 at entry to respective cohorts by time (0-16 months) from diagnosis. We also applied generalised estimating equations (GEE) analysis to test differences in repeated measures of mental health symptoms before and after COVID-19 diagnosis among individuals ever diagnosed with COVID-19 over time.\n\nFINDINGSA total of 9979 individuals (4%) were diagnosed with COVID-19 during the study period and presented overall with a higher symptom burden of depression (prevalence ratio [PR] 1{middle dot}18, 95% confidence interval [95% CI] 1{middle dot}03-1{middle dot}36) and poorer sleep quality (1{middle dot}13, 1{middle dot}03-1{middle dot}24) but not with higher levels of symptoms of anxiety or COVID-19 related distress compared with individuals without a COVID-19 diagnosis. While the prevalence of depression and COVID-19 related distress attenuated with time, the trajectories varied significantly by COVID-19 acute infection severity. Individuals diagnosed with COVID-19 but never bedridden due to their illness were consistently at lower risks of depression and anxiety (PR 0{middle dot}83, 95% CI 0{middle dot}75-0{middle dot}91 and 0{middle dot}77, 0{middle dot}63-0{middle dot}94, respectively), while patients bedridden for more than 7 days were persistently at higher risks of symptoms of depression and anxiety (PR 1{middle dot}61, 95% CI 1{middle dot}27-2{middle dot}05 and 1{middle dot}43, 1{middle dot}26-1{middle dot}63, respectively) throughout the 16-month study period.\n\nCONCLUSIONAcute infection severity is a key determinant of long-term mental morbidity among COVID-19 patients.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 92 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.14.21267460", @@ -3375,13 +3361,13 @@ }, { "site": "medRxiv", - "doi": "10.1101/2021.11.22.21266512", + "doi": "10.1101/2021.11.22.21266692", "date": "2021-11-24", - "link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266512", - "title": "Association of COVID-19 with arterial and venous vascular diseases: a population-wide cohort study of 48 million adults in England and Wales", - "authors": "Rochelle Knight; Venexia Walker; Samantha Ip; Jennifer A Cooper; Thomas Bolton; Spencer Keene; Rachel Denholm; Ashley Akbari; Hoda Abbasizanjani; Fatemeh Torabi; Efosa Omigie; Sam Hollings; Teri-Louise North; Renin Toms; Emanuele Di Angelantonio; Spiros Denaxas; Johan H Thygesen; Christopher Tomlinson; Ben Bray; Craig J Smith; Mark Barber; George Davey Smith; Nishi Chaturvedi; Cathie Sudlow; William N Whiteley; Angela Wood; Jonathan A C Sterne; - CVD-COVID-UK/COVID-IMPACT consortium; - Longitudinal Health and Wellbeing COVID-19 National Core Study", - "affiliations": "University of Bristol; University of Bristol; University of Cambridge; University of Bristol; University of Cambridge; University of Cambridge; University of Bristol; Swansea University; Swansea University; Swansea University; NHS Digital; NHS Digital; University of Bristol; University of Bristol; University of Cambridge; University College London; University College London; University College London; Kings College London; University of Manchester; Glasgow Caledonian University; University of Bristol; University College London; Health Data Research UK; University of Edinburgh; University of Cambridge; University of Bristol; ; ", - "abstract": "ImportanceThe long-term effects of COVID-19 on the incidence of vascular diseases are unclear.\n\nObjectiveTo quantify the association between time since diagnosis of COVID-19 and vascular disease, overall and by age, sex, ethnicity, and pre-existing disease.\n\nDesignCohort study based on population-wide linked electronic health records, with follow up from January 1st to December 7th 2020.\n\nSetting and participantsAdults registered with an NHS general practice in England or Wales and alive on January 1st 2020.\n\nExposuresTime since diagnosis of COVID-19 (categorised as 0-6 days, 1-2 weeks, 3-4, 5-8, 9-12, 13-26 and 27-49 weeks since diagnosis), with and without hospitalisation within 28 days of diagnosis.\n\nMain outcomes and measuresPrimary outcomes were arterial thromboses (mainly acute myocardial infarction and ischaemic stroke) and venous thromboembolic events (VTE, mainly pulmonary embolism and lower limb deep vein thrombosis). We also studied other vascular events (transient ischaemic attack, haemorrhagic stroke, heart failure and angina). Hazard ratios were adjusted for demographic characteristics, previous disease diagnoses, comorbidities and medications.\n\nResultsAmong 48 million adults, 130,930 were and 1,315,471 were not hospitalised within 28 days of COVID-19. In England, there were 259,742 first arterial thromboses and 60,066 first VTE during 41.6 million person-years follow-up. Adjusted hazard ratios (aHRs) for first arterial thrombosis compared with no COVID-19 declined rapidly from 21.7 (95% CI 21.0-22.4) to 3.87 (3.58-4.19) in weeks 1 and 2 after COVID-19, 2.80 (2.61-3.01) during weeks 3-4 then to 1.34 (1.21-1.48) during weeks 27-49. aHRs for first VTE declined from 33.2 (31.3-35.2) and 8.52 (7.59-9.58) in weeks 1 and 2 to 7.95 (7.28-8.68) and 4.26 (3.86-4.69) during weeks 3-4 and 5-8, then 2.20 (1.99-2.44) and 1.80 (1.50-2.17) during weeks 13-26 and 27-49 respectively. aHRs were higher, for longer after diagnosis, after hospitalised than non-hospitalised COVID-19. aHRs were also higher among people of Black and Asian than White ethnicity and among people without than with a previous event. Across the whole population estimated increases in risk of arterial thromboses and VTEs were 2.5% and 0.6% respectively 49 weeks after COVID-19, corresponding to 7,197 and 3,517 additional events respectively after 1.4 million COVID-19 diagnoses.\n\nConclusions and RelevanceHigh rates of vascular disease early after COVID-19 diagnosis decline more rapidly for arterial thromboses than VTEs but rates remain elevated up to 49 weeks after COVID_19. These results support continued policies to avoid COVID-19 infection with effective COVID-19 vaccines and use of secondary preventive agents in high-risk patients.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSIs COVID-19 associated with higher long-term incidence of vascular diseases?\n\nFindingsIn this cohort study of 48 million adults in England and Wales, COVID-19 was associated with higher incidence, that declined with time since diagnosis, of both arterial thromboses [week 1: adjusted HR [aHR] 21.7 (95% CI 21.0-22.4) weeks 27-49: aHR 1.34 (1.21-1.48)] and venous thromboembolism [week 1: aHR 33.2 (31.3-35.2), weeks 27-49 1.80 (1.50-2.17)]. aHRs were higher, for longer, after hospitalised than non-hospitalised COVID-19. The estimated excess number of arterial thromboses and venous thromboembolisms was 10,500.\n\nMeaningAvoidance of COVID-19 infection through vaccination, and use of secondary preventive agents after infection in high-risk patients, may reduce post-COVID-19 acute vascular diseases.", + "link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266692", + "title": "Serological responses to COVID-19 booster vaccine in England", + "authors": "Georgina Ireland; Heather Whitaker; Shamez N Ladhani; Frances Baawuah; Vani Subbarao; Ezra Linley; Lenesha Warrener; Michelle O'Brien; Corrine Whillock; Paul Moss; Mary E Ramsay; Gayatri Amirthalingam; Kevin E Brown", + "affiliations": "UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency; Brondesbury Medical Centre, Kilburn, London, United Kingdom; UK Health Security Agency; University of Birmingham; UK Health Security Agency; UK Health Security Agency; UK Health Security Agency", + "abstract": "IntroductionThere are limited data on immune responses after COVID-19 vaccine boosters in individuals receiving primary immunisation with BNT162b2 (Pfizer-BioNTech) or AZD1222 (AstraZeneca).\n\nMethodsA prospective, cohort study to assess SARS-CoV-2 antibody responses before and after booster vaccination with BNT162b2 in adults receiving either (i) two BNT162b2 doses <30 days apart (BNT162b2-control), (ii) two BNT162b2 doses [≥]30 days apart (BNT162b2-extended) or (iii) two AZD1222 doses [≥]30 days apart (AZD1222-extended) in London, England. SARS-CoV-2 spike protein antibody geometric mean titres (GMTs) before and 2-4 weeks after booster were compared.\n\nResultsOf 750 participants, 626 provided serum samples for up to 38 weeks after their second vaccine dose. Antibody GMTs peaked at 2-4 weeks after the second dose, before declining by 68% at 36-38 weeks after dose 2 for BNT162b2-control participants, 85% at 24-29 weeks for BNT162b2-extended participants and 78% at 24-29 weeks for AZD1222-extended participants. Antibody GMTs was highest in BNT162b2-extended participants (942 [95%CI, 797-1113]) than AZD1222-extended (183 [124-268]) participants at 24-29 weeks or BNT162b2-control participants at 36-38 weeks (208; 95%CI, 150-289). At 2-4 weeks after booster, GMTs were significantly higher than after primary vaccination in all three groups: 18,104 (95%CI, 13,911-23,560; n=47) in BNT162b2-control (76.3-fold), 13,980 (11,902-16,421; n=118) in BNT162b2-extended (15.9-fold) and 10,799 (8,510-13,704; n=43) in AZD1222-extended (57.2-fold) participants. BNT162b2-control participants (median:262 days) had a longer interval between primary and booster doses than BNT162b2-extended or AZD1222-extended (both median:186 days) participants.\n\nConclusionsWe observed rapid serological responses to boosting with BNT162b2, irrespective of vaccine type or schedule used for primary immunisation, with higher post-booster responses with longer interval between primary immunisation and boosting. Boosters will not only provide additional protection for those at highest risk of severe COVID-19 but also prevent infection and, therefore, interrupt transmission, thereby reducing infections rates in the population. Ongoing surveillance will be important for monitoring the duration of protection after the booster.", "category": "infectious diseases", "match_type": "fuzzy", "author_similarity": 100, @@ -3541,20 +3527,6 @@ "author_similarity": 96, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.11.08.21265380", - "date": "2021-11-08", - "link": "https://medrxiv.org/cgi/content/short/2021.11.08.21265380", - "title": "Describing the population experiencing COVID-19 vaccine breakthrough following second vaccination in England: A cohort study from OpenSAFELY", - "authors": "Amelia CA Green; Helen J Curtis; William J Hulme; Elizabeth J Williamson; Helen I McDonald; Krishnan Bhaskaran; Christopher T Rentsch; Anna Schultze; Brian MacKenna; Viyaasan Mahalingasivam; Laurie Tomlinson; Alex J Walker; Louis Fisher; Jon Massey; Colm D Andrews; Lisa E M Hopcroft; Caroline E Morton; Richard Croker; Jessica Morley; Amir Mehrkar; Sebastian CJ Bacon; David Evans; Peter Inglesby; George Hickman; Tom Ward; Simon Davy; Rohini Mathur; John Tazare; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; Christopher Bates; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Ian J Douglas; Stephen JW Evans; Liam Smeeth; Ben Goldacre", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Bristol; TPP; TPP; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford", - "abstract": "BackgroundWhile the vaccines against COVID-19 are considered to be highly effective, COVID-19 vaccine breakthrough is likely and a small number of people will still fall ill, be hospitalised, or die from COVID-19, despite being fully vaccinated. With the continued increase in numbers of positive SARS-CoV-2 tests, describing the characters of individuals who have experienced a COVID-19 vaccine breakthrough could be hugely important in helping to determine who may be at greatest risk.\n\nMethodWith the approval of NHS England we conducted a retrospective cohort study using routine clinical data from the OpenSAFELY TPP database of fully vaccinated individuals, linked to secondary care and death registry data, and described the characteristics of those experiencing a COVID-19 vaccine breakthrough.\n\nResultsAs of 01st November 2021, a total of 15,436,455 individuals were identified as being fully vaccinated against COVID-19, with a median follow-up time of 149 days (IQR: 107-179). From within this population, a total of 577245 (<4%) individuals reported a positive SARS-CoV-2 test. For every 1000 years of patient follow-up time, the corresponding incidence rate was 98.02 (95% CI 97.9-98.15). There were 16,120 COVID-19-related hospital admissions, 1,100 COVID-19 critical care admission patients and 3,925 COVID-19-related deaths; corresponding incidence rates of 2.72 (95% C 2.7-2.74), 0.19 (95% C 0.18-0.19) and 0.66 (95% C 0.65-0.67), respectively. When broken down by the initial priority group, higher rates of hospitalisation and death were seen in those in care homes and those over 80 years of age. Comorbidities with the highest rates of breakthrough COVID-19 included chronic kidney disease, dialysis, transplant, haematological malignancy, and immunocompromised.\n\nConclusionThe majority of COVID-19 vaccine breakthrough cases in England were mild with relatively few fully vaccinated individuals being hospitalised or dying as a result. However, some concerning differences in rates of breakthrough cases were identified in several clinical and demographic groups. While it is important to note that these findings are simply descriptive and cannot be used to answer why certain groups have higher rates of COVID-19 breakthrough than others, the emergence of the Omicron variant of COVID-19 coupled with the continued increase in numbers of positive SARS-CoV-2 tests are concerning. As numbers of fully vaccinated individuals increases and follow-up time lengthens, so too will the number of COVID-19 breakthrough cases. Additional analyses, aimed at identifying individuals at higher risk, are therefore required.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "bioRxiv", "doi": "10.1101/2021.11.05.467529", @@ -3709,20 +3681,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.10.13.21264937", - "date": "2021-10-18", - "link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264937", - "title": "Comparative effectiveness of ChAdOx1 versus BNT162b2 COVID-19 vaccines in Health and Social Care workers in England: a cohort study using OpenSAFELY", - "authors": "William J Hulme; Elizabeth J Williamson; Amelia CA Green; Krishnan Bhaskaran; Helen I McDonald; Christopher T Rentsch; Anna Schultze; John Tazare; Helen J Curtis; Alex J Walker; Laurie Tomlinson; Tom M Palmer; Elsie Horne; Brian MacKenna; Caroline E Morton; Amir Mehrkar; Louis Fisher; Sebastian CJ Bacon; David Evans; Peter Inglesby; George Hickman; Simon Davy; Tom Ward; Richard Croker; Rosalind M Eggo; Angel YS Wong; Rohini Mathur; Kevin Wing; Harriet Forbes; Daniel J Grint; Ian J Douglas; Stephen JW Evans; Liam Smeeth; Christopher Bates; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Jonathan AC Sterne; Miguel A Hernan; Ben Goldacre", - "affiliations": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; London School of Hygiene and Tropical Medicine, London, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; London School of Hygiene and Tropical Medicine, London, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; London School of Hygiene and Tropical Medicine, London, UK; TPP, Horsforth, Leeds, UK; TPP, Horsforth, Leeds, UK; TPP, Horsforth, Leeds, UK; TPP, Horsforth, Leeds, UK; TPP, Horsforth, Leeds, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Bristol, Biomedical Research Centre, Bristol, UK; CAUSALab, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Departments of Epidemiology and Biostatistics, Harvard T.H. Chan School of Public Health, ; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK", - "abstract": "ObjectivesTo compare the effectiveness of the BNT162b2 mRNA (Pfizer-BioNTech) and the ChAdOx1 (Oxford-AstraZeneca) COVID-19 vaccines against infection and COVID-19 disease in health and social care workers.\n\nDesignCohort study, emulating a comparative effectiveness trial.\n\nSettingLinked primary care, hospital, and COVID-19 surveillance records available within the OpenSAFELY-TPP research platform.\n\nParticipants317,341 health and social care workers vaccinated between 4 January and 28 February 2021, registered with a GP practice using the TPP SystmOne clinical information system in England, and not clinically extremely vulnerable.\n\nInterventionsVaccination with either BNT162b2 or ChAdOx1 administered as part of the national COVID-19 vaccine roll-out.\n\nMain outcome measuresRecorded SARS-CoV-2 positive test, or COVID-19 related Accident and Emergency attendance or hospital admission occurring within 20 weeks of vaccination.\n\nResultsThe cumulative incidence of each outcome was similar for both vaccines during the first 20 weeks post-vaccination. The cumulative incidence of recorded SARS-CoV-2 infection 6 weeks after vaccination with BNT162b2 was 19.2 per 1000 people (95%CI 18.6 to 19.7) and with ChAdOx1 was 18.9 (95%CI 17.6 to 20.3), representing a difference of -0.24 per 1000 people (95%CI -1.71 to 1.22). The difference in the cumulative incidence per 1000 people of COVID-19 accident and emergency attendance at 6 weeks was 0.01 per 1000 people (95%CI -0.27 to 0.28). For COVID-19 hospital admission, this difference was 0.03 per 1000 people (95%CI -0.22 to 0.27).\n\nConclusionsIn this cohort of healthcare workers where we would not anticipate vaccine type to be related to health status, we found no substantial differences in the incidence of SARS-CoV-2 infection or COVID-19 disease up to 20 weeks after vaccination. Incidence dropped sharply after 3-4 weeks and there were very few COVID-19 hospital attendance and admission events after this period. This is in line with expected onset of vaccine-induced immunity, and suggests strong protection against COVID-19 disease for both vaccines.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.10.13.21264956", @@ -3877,6 +3835,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.09.13.21263487", + "date": "2021-09-16", + "link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263487", + "title": "SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population", + "authors": "Jia Wei; Koen B. Pouwels; Nicole Stoesser; Philippa C. Matthews; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John I Bell; John N Newton; Jeremy Farrar; Alison Howarth; Brian D. Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W. Crook; Tim E.A. Peto; A.Sarah Walker; David W. Eyre", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford", + "abstract": "We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.09.13.21262360", @@ -4269,6 +4241,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.07.20.21260558", + "date": "2021-07-22", + "link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260558", + "title": "Intentions to participate in cervical and colorectal cancer screening during the COVID-19 pandemic: a mixed-methods study", + "authors": "Rebecca Wilson; Harriet Quinn-Scoggins; Yvonne Moriarty; Jacqueline Hughes; Mark Goddard; Rebecca Cannings-John; Victoria Whitelock; Katriina L Whitaker; Detelina Grozeva; Julia Townson; Kirstie Osborne; Stephanie Smits; Michael Robling; Julie Hepburn; Graham Moore; Ardiana Gjini; Kate Brain; Jo Waller", + "affiliations": "Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cardiff University; Cancer Research UK; University of Surrey; Cardiff University; Cardiff University; Cancer Research UK; Cardiff University; Cardiff University; Public Involvement Community, Health and Care Research Wales; Cardiff University; Public Health Wales; Cardiff University; Kings College London", + "abstract": "Worldwide, cancer screening faced significant disruption in 2020 due to the COVID-19 pandemic. If this has led to changes in public attitudes towards screening and reduced intention to participate, there is a risk of long-term adverse impact on cancer outcomes. In this study, we examined previous participation and future intentions to take part in cervical and colorectal cancer (CRC) screening following the first national lockdown in the UK.\n\nOverall, 7543 adults were recruited to a cross-sectional online survey in August-September 2020. Logistic regression analyses were used to identify correlates of strong screening intentions among 2,319 participants eligible for cervical screening and 2,502 eligible for home-based CRC screening. Qualitative interviews were conducted with a sub-sample of 30 participants. Verbatim transcripts were analysed thematically.\n\nOf those eligible, 74% of survey participants intended to attend cervical screening and 84% intended to complete home-based CRC screening when next invited. Thirty percent and 19% of the cervical and CRC samples respectively said they were less likely to attend a cancer screening appointment now than before the pandemic. Previous non-participation was the strongest predictor of low intentions for cervical (aOR 26.31, 95% CI: 17.61-39.30) and CRC (aOR 67.68, 95% CI: 33.91-135.06) screening. Interview participants expressed concerns about visiting healthcare settings but were keen to participate when screening programmes resumed.\n\nIntentions to participate in future screening were high and strongly associated with previous engagement in both programmes. As screening services recover, it will be important to monitor participation and to ensure people feel safe to attend.", + "category": "oncology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 98 + }, { "site": "medRxiv", "doi": "10.1101/2021.07.19.21260782", @@ -4591,20 +4577,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.06.21.21259104", - "date": "2021-06-28", - "link": "https://medrxiv.org/cgi/content/short/2021.06.21.21259104", - "title": "Models of COVID-19 vaccine prioritisation: a systematic literature search and narrative review", - "authors": "Nuru Saadi; Y-Ling Chi; Srobana Ghosh; Rosalind M Eggo; Ciara McCarthy; Matthew Quaife; Jeanette Dawa; Mark Jit; Anna Vassall", - "affiliations": "London School of Hygiene and Tropical Medicine; International Decision Support Inititative, Center for Global Health and Development; International Decision Support Inititative, Center for Global Health and Development; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine; Washington State University - Global Health Program, Nairobi, Kenya. Center for Epidemiological Modelling and Analysis, University of Nairobi, Nairobi, Kenya; Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine", - "abstract": "BackgroundHow best to prioritise COVID-19 vaccination within and between countries has been a public health and an ethical challenge for decision-makers globally. We systematically reviewed epidemiological and economic modelling evidence on population priority groups to minimise COVID-19 mortality, transmission and morbidity outcomes.\n\nMethodsWe searched the National Institute of Health iSearch COVID-19 Portfolio (a database of peer-reviewed and pre-print articles), Econlit, the Centre for Economic Policy Research and the National Bureau of Economic Research for mathematical modelling studies evaluating the impact of prioritising COVID-19 vaccination to population target groups. We narratively synthesised the main study conclusions on prioritisation and the conditions under which the conclusions changed.\n\nFindingsThe search identified 1820 studies. 36 studies met the inclusion criteria and were narratively synthesised. 83% of studies described outcomes in high-income countries. We found that for countries seeking to minimise deaths, prioritising vaccination of senior adults was the optimal strategy and for countries seeking to minimise cases the young were prioritised. There were several exceptions to the main conclusion, notably reductions in deaths could be increased, if groups at high risk of both transmission and death could be further identified. Findings were also sensitive to the level of vaccine coverage.\n\nInterpretationThe evidence supports WHO SAGE recommendations on COVID-19 vaccine prioritisation. There is however an evidence gap on optimal prioritisation for low- and middle-income countries, studies that included an economic evaluation, and studies that explore prioritisation strategies if the aim is to reduce overall health burden including morbidity.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.06.24.21259107", @@ -4815,6 +4787,20 @@ "author_similarity": 95, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.06.08.21258533", + "date": "2021-06-12", + "link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258533", + "title": "The impact of co-circulating pathogens on SARS-CoV-2/COVID-19 surveillance. How concurrent epidemics may decrease true SARS-CoV-2 percent positivity.", + "authors": "Aleksandra Kovacevic; Rosalind M Eggo; Marc Baguelin; Matthieu Domenech de Cell\u00e8s; Lulla Opatowski", + "affiliations": "Institut Pasteur; London School of Hygiene & Tropical Medicine; Imperial College London; Max Planck Institute for Infection Biology; Univ Versailles Saint Quentin / Institut Pasteur / Inserm", + "abstract": "BackgroundCirculation of non-SARS-CoV-2 respiratory viruses during the COVID-19 pandemic may alter quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures. Here, we assess the impact of an increased circulation of other respiratory viruses on the monitoring of positivity rates of SARS-CoV-2 and interpretation of surveillance data.\n\nMethodsUsing a multi-pathogen Susceptible-Exposed-Infectious-Recovered (SEIR) transmission model formalizing co-circulation of SARS-CoV-2 and another respiratory we assess how an outbreak of secondary virus may inflate the number of SARS-CoV-2 tests and affect the interpretation of COVID-19 surveillance data. Using simulation, we assess to what extent the use of multiplex PCR tests on a subsample of symptomatic individuals can support correction of the observed SARS-CoV-2 percent positive during other virus outbreaks and improve surveillance quality.\n\nResultsModel simulations demonstrated that a non-SARS-CoV-2 epidemic creates an artificial decrease in the observed percent positivity of SARS-CoV-2, with stronger effect during the growth phase, until the peak is reached. We estimate that performing one multiplex test for every 1,000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percent positive.\n\nConclusionsThis study highlights that co-circulating respiratory viruses can disrupt SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.\n\nSummaryCOVID-19 surveillance indicators may be impacted by increased co-circulation of other respiratory viruses delaying control measure implementation. Continued surveillance through multiplex PCR testing in a subsample of the symptomatic population may play a role in fixing this problem.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.06.08.21258546", @@ -4927,20 +4913,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.27.21257032", - "date": "2021-05-31", - "link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257032", - "title": "How immunity from and interaction with seasonal coronaviruses can shape SARS-CoV-2 epidemiology", - "authors": "Naomi R Waterlow; Edwin Van Leeuwen; Nicholas G Davies; - CMMID COVID-19 working group; Stefan Flasche; Rosalind M Eggo", - "affiliations": "London School of Hygiene and Tropical Medicine; Public Health England; London School of Hygiene and Tropical Medicine; ; LSHTM; London School of Hygiene & Tropical Medicine", - "abstract": "We hypothesised that cross-protection from seasonal epidemics of human coronaviruses (HCoVs) could have affected SARS-CoV-2 transmission, including generating reduced susceptibility in children. To determine what the pre-pandemic distribution of immunity to HCoVs was, we fitted a mathematical model to 6 years of seasonal coronavirus surveillance data from England and Wales. We estimated a duration of immunity to seasonal HCoVs of 7.3 years (95%CI 6.8 - 7.9) and show that, while cross-protection between HCoV and SARS-CoV-2 may contribute to the age distribution, it is insufficient to explain the age pattern of SARS-CoV-2 infections in the first wave of the pandemic in England and Wales. Projections from our model illustrate how different strengths of cross-protection between circulating coronaviruses could determine the frequency and magnitude of SARS-CoV-2 epidemics over the coming decade, as well as the potential impact of cross-protection on future seasonal coronavirus transmission.\n\nSignificance statementCross-protection from seasonal epidemics of human coronaviruses (HCoVs) has been hypothesised to contribute to the relative sparing of children during the early phase of the pandemic. Testing this relies on understanding the pre-pandemic age-distribution of recent HCoV infections, but little is known about their dynamics. Using England and Wales as a case study, we use a transmission model to estimate the duration of immunity to seasonal coronaviruses, and show how cross-protection could have affected the age distribution of susceptibility during the first wave, and alter SARS-CoV-2 transmission patterns over the coming decade.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.22.21257633", @@ -4969,20 +4941,6 @@ "author_similarity": 94, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.25.21257505", - "date": "2021-05-25", - "link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257505", - "title": "Plitidepsin has a positive therapeutic index in adult patients with COVID-19 requiring hospitalization.", - "authors": "Jose F. Varona; Pedro Landete; Jose A Lopez-Martin; Vicente Estrada; Roger Paredes; Pablo Guisado-Vasco; Lucia Fernandez de Orueta; Miguel Torralba; Jesus Fortun; Roberto Vates; Jose Barberan; Bonaventura Clotet; Julio Ancochea; Daniel Carnevali; Noemi Cabello; Lourdes Porras; Paloma Gijon; Alfonso Monereo; Daniel Abad; Sonia Zu\u00f1iga; Isabel Sola; Jordi Rodon; Nuria Izquierdo-Useros; Salvador Fudio; Maria Jose Pontes; Beatriz de Rivas; Patricia Giron de Velasco; Belen Sopesen; Antonio Nieto; Javier Gomez; Pablo Aviles; Rubin Lubomirov; Kris M White; Romel Rosales; Soner Yildiz; Ann-Kathrin Reuschl; Lucy G. Thorne; Clare Jolly; Greg J. Towers; Lorena Zuliani-Alvarez; Mehdi Bouhaddou; Kirsten Obernier; Luis Enjuanes; Jose M Fernandez-Sousa; - Plitidepsin COVID Study Group; Nevan J Krogan; Jose M. Jimeno; Adolfo Garcia-Sastre", - "affiliations": "Departamento de Medicina Interna, Hospital Universitario HM Monteprincipe, HM Hospitales, Madrid, Spain. Facultad de Medicina, Universidad San Pablo-CEU, Madrid; Hospital Universitario de La Princesa. Madrid, Spain. Universidad Autonoma de Madrid, Madrid, Spain.; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain.; Hospital Clinico San Carlos, Madrid, Spain. Universidad Complutense de Madrid, Madrid, Spain.; IrsiCaixa AIDS Research Institute; Internal Medicine Department, Hospital Universitario Quironsalud, Madrid, Spain. Universidad Europea, Madrid, Spain.; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain. European University of Madrid, Madrid, Spain.; Internal Medicine, Guadalajara University Hospital, Guadalajara, Spain. University of Alcala, Madrid, Spain.; Hospital Universitario Ramon y Cajal, Madrid, Spain.; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain.; Hospital Universitario HM Monteprincipe, Madrid, Spain. Facultad de Medicina San Pablo CEU, Madrid, Spain.; Head of Infectious Diseases Department, Director of the Research Lab, IrsiCaixa, Barcelone, Spain. Professor of the UAB and the UVIC-UCC, Barcelone, Spain.; Hospital Universitario La Princesa, Madrid, Spain. Centro de Investigacion en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII; Hospital Universitario Quironsalud, Madrid, Spain Universidad Europea, Madrid, Spain.; Infectious Diseases Department, San Carlos University Hospital. Madrid Spain.; Internal Medicine, Hospital General de Ciudad Real, Ciudad Real, Spain.; Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Mara\u00f1on, Instituto de Investigacion Sanitaria Gregorio Mara\u00f1on; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain; Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain. European University of Madrid, Madrid, Spain.; Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNBCSIC), Madrid, Spain.; Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNBCSIC), Madrid, Spain.; IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, Bellaterra, Spain; IrsiCaixa AIDS Research Institute, 08916, Badalona, Spain. Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, 08916, Badalona, Spain.; PharmaMar - Clinical Pharmacology Unit. Colmenar Viejo, Madrid, Spain; PharmaMar - Medical Affairs Unit. Colmenar Viejo. Madrid, Spain.; PharmaMar - Medical Affairs Unit. Colmenar Viejo, Madrid, Spain.; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain.; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain. Sylentis, S.A.U., Tres Cantos, Madrid, Spain. Biocross, S.L., Valladolid, Spain.; PharmaMar - Statistics Unit. Colmenar Viejo, Madrid, Spain.; PharmaMar - Statistics Unit. Colmenar Viejo, Madrid, Spain.; PharmaMar - Preclinical Unit. Colmenar Viejo, Madrid, Spain; PharmaMar - Clinical Pharmacology Unit. Colmenar Viejo, Madrid, Spain; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom.; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom.; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom.; Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G; Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G; Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain.; PharmaMar, S.A., Colmenar Viejo, Madrid, Spain.; ; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. ; PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain.; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at ", - "abstract": "Plitidepsin is a marine-derived cyclic-peptide that inhibits SARS-CoV-2 replication at low nanomolar concentrations by the targeting of host protein eEF1A (eukaryotic translation-elongation-factor-1A). We evaluated a model of intervention with plitidepsin in hospitalized COVID-19 adult patients where three doses were assessed (1.5, 2 and 2.5 mg/day for 3 days, as a 90-minute intravenous infusion) in 45 patients (15 per dose-cohort). Treatment was well tolerated, with only two Grade 3 treatment-related adverse events observed (hypersensitivity and diarrhea). The discharge rates by Days 8 and 15 were 56.8% and 81.8%, respectively, with data sustaining dose-effect. A mean 4.2 log10 viral load reduction was attained by Day 15. Improvement in inflammation markers was also noted in a seemingly dose-dependent manner. These results suggest that plitidepsin impacts the outcome of patients with COVID-19.\n\nOne-Sentence SummaryPlitidepsin, an inhibitor of SARS-Cov-2 in vitro, is safe and positively influences the outcome of patients hospitalized with COVID-19.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.18.21257396", @@ -5025,6 +4983,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.05.18.21257267", + "date": "2021-05-18", + "link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257267", + "title": "Colchicine in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", + "authors": "Peter W Horby; Mark Campbell; Enti Spata; Jonathan R Emberson; Natalie Staplin; Guilherme Pessoa-Amorim; Leon Peto; Martin Wiselka; Laura Wiffen; Simon Tiberi; Ben Caplin; Caroline Wroe; Christopher Green; Paul Hine; Benjamin Prudon; Tina George; Andrew Wight; J Kenneth Baillie; Buddha Basnyat; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Faust; Raph L Hamers; Thomas Jaki; Edmund Juszczak; Katie Jeffery; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray", + "affiliations": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and International Severe Acute Res; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and Nuffield Department of Populat; Department of Infectious Diseases, University Hospital Leicester, Leicester, United Kingdom; Portsmouth Hospitals University NHS Foundation Trust, Portsmouth, United Kingdom; Department of Infection, Barts Health NHS Trust, London, United Kingdom; Department of Renal Medicine, University College London, London, United Kingdom and Royal Free London NHS Trust, London, United Kingdom; James Cook University Hospital, Middlesbrough, United Kingdom; University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom; Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom; North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom; Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom; Wirral University Teaching Hospital NHS Foundation Trust, Birkenhead, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Oxford University Clinical Research Unit -Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Course Sciences, King?s College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia and Faculty of Medicine, University of Indonesia, Jakarta, Indonesia and Centre for Tropical Medicine ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom and MRC Biostatistics Unit, University of Cambridge, Cambridge, United; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom and Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Notting; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un", + "abstract": "BackgroundColchicine has been proposed as a treatment for COVID-19 on the basis of its anti-inflammatory actions.\n\nMethodsIn this randomised, controlled, open-label trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care alone or usual standard of care plus colchicine twice daily for 10 days or until discharge (or one of the other treatment arms) using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 27 November 2020 and 4 March 2021, 5610 patients were randomly allocated to receive colchicine and 5730 patients to receive usual care alone. Overall, 1173 (21%) patients allocated to colchicine and 1190 (21%) patients allocated to usual care died within 28 days (rate ratio 1.01; 95% confidence interval [CI] 0.93-1.10; p=0.77). Consistent results were seen in all pre-specified subgroups of patients. There was no significant difference in duration of hospitalisation (median 10 days vs. 10 days) or the proportion of patients discharged from hospital alive within 28 days (70% vs. 70%; rate ratio 0.98; 95% CI 0.94-1.03; p=0.44). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (25% vs. 25%; risk ratio 1.02; 95% CI 0.96-1.09; p=0.47).\n\nInterpretationIn adults hospitalised with COVID-19, colchicine was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056). Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.05.17.21256818", @@ -5193,6 +5165,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.05.05.21256668", + "date": "2021-05-09", + "link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256668", + "title": "COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland", + "authors": "Sofia de la Fuente Garcia; Fasih Haider; Saturnino Luz", + "affiliations": "The University of Edinburgh; The University of Edinburgh; The University of Edinburgh", + "abstract": "The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively.\n\nClinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.", + "category": "health informatics", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.05.05.21256649", @@ -5249,6 +5235,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.04.26.21255732", + "date": "2021-04-28", + "link": "https://medrxiv.org/cgi/content/short/2021.04.26.21255732", + "title": "Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales", + "authors": "Sarah Beale; Isobel Braithwaite; Annalan MD Navaratnam; Pia Hardelid; Alison Rodger; Anna Aryee; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Vincent Nguyen; Parth Patel; Madhumita Shrotri; Robert W Aldridge; Andrew C Hayward; - Virus Watch Collaborative", + "affiliations": "University College London; University College London; University College London; University College London; University College London; Royal Free London NHS Foundation Trust,; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; ", + "abstract": "BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation.\n\nMethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period.\n\nResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods.\n\nConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.04.24.21255968", @@ -5333,20 +5333,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.04.12.21255275", - "date": "2021-04-19", - "link": "https://medrxiv.org/cgi/content/short/2021.04.12.21255275", - "title": "Children develop strong and sustained cross-reactive immune responses against spike protein following SARS-CoV-2 infection", - "authors": "Alexander C Dowell; Megan S. Butler; Elizabeth Jinks; Gokhan Tut; Tara Lancaster; Panagiota Sylla; Jusnara Begum; Rachel Bruton; Hayden Pearce; Kriti Verma; Nicola Logan; Grace Tyson; Eliska Spalkova; Sandra Margielewska-Davies; Graham S. Taylor; Eleni Syrimi; Frances Baawuah; Joanne Beckmann; Ifeanyichukwu Okike; Shazaad Ahmad; Joanna Garstang; Andrew Brent; Bernadette Brent; Georgina Ireland; Felicity Aiano; Zahin Amin-Chowdhury; Samuel Jones; Ray Borrow; Ezra Linley; Rafaq Azad; John Wright; Dagmar Waiblinger; Chris Davis; Emma C Thomson; Massimo Palmarini; Brian James Willett; Wendy S Barclay; John Poh; Vanessa Saliba; Gayatri Amirthalingam; Kevin Brown; Mary Ramsay; Jianmin Zuo; Paul Moss; Shamez Ladhani", - "affiliations": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; University of Birmingham; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; University of Birmingham; MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61-1QH, UK; MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61-1QH, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; East London NHS Foundation Trust, 9 Allie Street, London E1 8DE, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK 4.\tUniversity Hospitals of Derby and Burton NHS Foundation Trust, Uttoxeter New Road, Derby; Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9WL, UK; Birmingham Community Healthcare NHS Trust, Holt Street, Aston B7 4BN, UK; Oxford University Hospitals NHS Foundation Trust, Old Road, Oxford OX3 7HE University of Oxford, Wellington Square, Oxford OX1 2JD, UK; Oxford University Hospitals NHS Foundation Trust, Old Road, Oxford OX3 7HE; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, Manchester Royal Infirmary, Manchester, United Kingdom; Public Health England, Manchester Royal Infirmary, Manchester, United Kingdom; Bradford Teaching Hospitals NHS Foundation Trust; Bradford Teaching Hospitals NHS Foundation Trust; Bradford Teaching Hospitals NHS Foundation Trust; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; Imperial College, London; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK", - "abstract": "SARS-CoV-2 infection is generally mild or asymptomatic in children but the biological basis for this is unclear. We studied the profile of antibody and cellular immunity in children aged 3-11 years in comparison with adults. Antibody responses against spike and receptor binding domain (RBD) were high in children and seroconversion boosted antibody responses against seasonal Beta-coronaviruses through cross-recognition of the S2 domain. Seroneutralisation assays against alpha, beta and delta SARS-CoV-2 variants demonstrated comparable neutralising activity between children and adults. T cell responses against spike were >2-fold higher in children compared to adults and displayed a TH1 cytokine profile. SARS-CoV-2 spike-specific T cells were also detected in many seronegative children, revealing pre-existing responses that were cross-reactive with seasonal Alpha and Beta-coronaviruses. Importantly, all children retained high antibody titres and cellular responses at 6 months after infection whilst relative antibody waning was seen in adults. Spike-specific responses in children also remained broadly stable beyond 12 months. Children thus distinctly generate robust, cross-reactive and sustained immune responses after SARS-CoV-2 infection with focussed specificity against spike protein. These observations demonstrate novel features of SARS-CoV-2-specific immune responses in children and may provide insight into their relative clinical protection. Furthermore, this information will help to guide the introduction of vaccination regimens in the paediatric population.", - "category": "allergy and immunology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.04.08.21255100", @@ -5417,20 +5403,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.04.08.21255128", - "date": "2021-04-10", - "link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255128", - "title": "Changing patterns of sickness absence among healthcare workers in England during the COVID-19 pandemic.", - "authors": "Rhiannon Edge; Diana A van der Plaat; Vaughan Parsons; David Coggon; Martie J van Tongeren; Rupert Muiry; Ira Madan; Paul Cullinan", - "affiliations": "Lancaster University; National Heart and Lung Institute (NHLI), Imperial College London; Guys and St Thomas NHS Foundation Trust; MRC Lifecourse Epidemiology Unit, University of Southampton; Centre for Occupational and Environmental Health, University of Manchester; Guys and St Thomas NHS Foundation Trust; Guy's and St Thomas' NHS Foundation Trust; National Heart and Lung Institute (NHLI), Imperial College London", - "abstract": "ObjectiveTo explore impacts of the COVID-19 pandemic on patterns of sickness absence among staff employed by the National Health Service (NHS) in England.\n\nMethodsWe analysed prospectively collected, pseudonymised data on 959,356 employees who were continuously employed by NHS trusts during 1 January 2019 to 31 July 2020, comparing the frequency of new sickness absence in 2020 with that at corresponding times in 2019.\n\nResultsAfter exclusion of episodes directly related to COVID-19, the overall incidence of sickness absence during the initial 10 weeks of the pandemic (March-May 2020) was more than 20% lower than in corresponding weeks of 2019, but trends for specific categories of illness varied. Marked increases were observed for asthma (122%), infectious diseases (283%) and mental illness (42.3%), while reductions were apparent for gastrointestinal problems (48.4%), genitourinary/gynaecological disorders (33.8%), eye problems (42.7%), injury and fracture (27.7%), back problems (19.6%), other musculoskeletal disorders (29.3%), disorders of ear, nose and throat (32.7%), cough/flu (24.5%) and cancer (24.1%). A doubling of new absences for pregnancy-related disorders during 18 May to 19 July of 2020 was limited to women with earlier COVID-19 sickness absence.\n\nConclusionsVarious factors will have contributed to the large and divergent changes that were observed. The findings add to concerns regarding delays in diagnosis and treatment of cancers, and support a need to plan for a large backlog of treatment for many other diseases. Further research should explore the rise in absence for pregnancy-related disorders among women with earlier COVID-19 sickness absence.\n\nO_TEXTBOX1. What is already known about this subject?\n\nHistorically, rates of sickness absence among the NHS workforce in England have been relatively high but stable. Reports of a marked increase during the first wave of the COVID-19 pandemic have not distinguished between different categories of underlying illness.\n\n2. What are the new findings?\n\nDuring the first wave of COVID-19, incidence of sickness-absence changed markedly when compared to the previous year, with major increases for some categories of illness, and large declines for many others, including cancer.\n\n3. How might this impact on policy or clinical practice in the foreseeable future?\n\nThe findings support a need to plan for effects from delayed diagnosis and treatment of cancer, and to manage a large backlog of treatment for many other diseases.\n\nC_TEXTBOX", - "category": "occupational and environmental health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.04.07.21255072", @@ -5795,6 +5767,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.12.21253484", + "date": "2021-03-13", + "link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253484", + "title": "Limits of lockdown: characterising essential contacts during strict physical distancing", + "authors": "Amy C Thomas; Leon Danon; Hannah Christensen; Kate Northstone; Daniel Smith; Emily J Nixon; Adam Trickey; Gibran Hemani; Sarah Sauchelli; Adam Finn; Nicholas J Timpson; Ellen Brooks-Pollock", + "affiliations": "University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; NIHR Bristol Biomedical Research Centre, University of Bristol; University of Bristol; University of Bristol; University of Bristol", + "abstract": "COVID-19 has exposed health inequalities within countries and globally. The fundamental determining factor behind an individuals risk of infection is the number of social contacts they make. In many countries, physical distancing measures have been implemented to control transmission of SARS-CoV-2, reducing social contacts to a minimum. Characterising unavoidable social contacts is key for understanding the inequalities behind differential risks and planning vaccination programmes. We utilised an existing English longitudinal birth cohort, which is broadly representative of the wider population (n=6807), to explore social contact patterns and behaviours when strict physical distancing measures were in place during the UKs first lockdown in March-May 2020. Essential workers, specifically those in healthcare, had 4.5 times as many contacts as non-essential workers [incident rate ratio = 4.42 (CI95%: 3.88-5.04)], whilst essential workers in other sectors, mainly teaching and the police force had three times as many contacts [IRR = 2.84 (2.58-3.13)]. The number of individuals in a household, which is conflated by number of children, increases essential social contacts by 40%. Self-isolation effectively reduces numbers of contacts outside of the home, but not entirely. Together, these findings will aid the interpretation of epidemiological data and impact the design of effective SARS-CoV-2 control strategies, such as vaccination, testing and contact tracing.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.10.21253173", @@ -6047,20 +6033,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.02.23.21251975", - "date": "2021-02-25", - "link": "https://medrxiv.org/cgi/content/short/2021.02.23.21251975", - "title": "The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH): Protocol for a prospective longitudinal cohort study of healthcare and ancillary workers in UK healthcare settings", - "authors": "Katherine Woolf; Carl Melbourne; Luke Bryant; Anna Louise Guyatt; Ian Christopher McManus; Amit Gupta; Robert C Free; Laura Nellums; Sue Carr; Catherine John; Christopher A Martin; Louise V Wain; Laura J Gray; Claire Garwood; Vishant Modhwadia; Keith Abrams; Martin D Tobin; Kamlesh Khunti; Manish Pareek; - UK-REACH Study Collaborative Group", - "affiliations": "University College London; University of Leicester; University of Leicester; University of Leicester; University College London; University Hospitals Oxford NHS Foundation Trust; University of Leicester; University of Nottingham; General Medical Council, University Hospitals Leicester NHS Trust; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of York; University of Leicester; University of Leicester; University of Leicester; ", - "abstract": "IntroductionThe COVID-19 pandemic has resulted in significant morbidity and mortality, and has devastated economies in many countries. Amongst the groups identified as being at increased risk from COVID-19 are healthcare workers (HCWs) and ethnic minority groups. Emerging evidence suggests HCWs from ethnic minority groups are at increased risk of adverse COVID-19-related physical and mental health outcomes. To date there has been no large-scale analysis of these risks in UK healthcare workers or ancillary workers in healthcare settings, stratified by ethnicity or occupation type, and adjusted for potential confounders. This paper reports the protocol for a prospective longitudinal questionnaire study of UK HCWs, as part of the UK-REACH programme (The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers).\n\nMethods and analysisA baseline questionnaire with follow-up questionnaires at 4 and 8 months will be administered to a national cohort of UK healthcare workers and ancillary workers in healthcare settings, and those registered with UK healthcare regulators. With consent, data will be linked to health records, and participants followed up for 25 years.\n\nUnivariate associations between ethnicity and primary outcome measures (clinical COVID-19 outcomes, and physical and mental health) and key confounders/explanatory variables will be tested, followed by multivariable analyses to test for associations between ethnicity and key outcomes adjusted for the confounder/explanatory variables, with interactions included as appropriate. Using follow-up data, multilevel models will be used to model changes over time by ethnic group, facilitating understanding of absolute and relative risks in different ethnic groups, and generalisability of findings.\n\nEthics and disseminationThe study is approved by Health Research Authority (reference 20/HRA/4718), and carries minimal risk to participants. We aim to manage the small risk of participant distress due to being asked questions on sensitive topics by clearly indicating on the participant information sheet that the questionnaire covers sensitive topics and that participants are under no obligation to answer these, or indeed any other, questions, and by providing links to support organisations. Results will be disseminated with reports to Government and papers uploaded to pre-print servers and submitted to peer reviewed journals.\n\nRegistration detailsTrial ID: ISRCTN11811602\n\nSTRENGTHS AND LIMITATIONS OF THIS STUDYO_LINational, UK-wide, study, aiming to capture variety of healthcare worker job roles including ancillary workers in healthcare settings.\nC_LIO_LILongitudinal study including three waves of questionnaire data collection, and linkage to administrative data over 25 years, with consent.\nC_LIO_LIUnique support from all major UK healthcare worker regulators, relevant healthcare worker organisations, and a Professional Expert Panel to increase participant uptake and the validity of findings.\nC_LIO_LIPotential for self-selection bias and low response rates, and the use of electronic invitations and online data collection makes it harder to reach ancillary workers without regular access to work email addresses.\nC_LI", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.02.24.21252338", @@ -6285,6 +6257,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.02.02.21251043", + "date": "2021-02-05", + "link": "https://medrxiv.org/cgi/content/short/2021.02.02.21251043", + "title": "COVID-19 infection and subsequent thromboembolism: A self-controlled case series analysis of a population cohort", + "authors": "Frederick Ho; Kenneth Man; Mark Toshner; Colin Church; Carlos Celis-Morales; Ian Wong; Colin Berry; Naveed Sattar; Jill Pell", + "affiliations": "University of Glasgow; UCL; University of Cambridge; NHS Greater Glasgow and Clyde; University of Glasgow; UCL; University of Glasgow; University of Glasgow; University of Glasgow", + "abstract": "ObjectiveAn unexpectedly large number of people infected with Covid-19 had experienced a thrombotic event. This study aims to assess the associations between Covid-19 infection and thromboembolism including myocardial infarction (MI), ischaemic stroke, deep-vein thrombosis (DVT), and pulmonary embolism (PE).\n\nPatients and MethodsA self-controlled case-series study was conducted covering the whole of Scotlands general population. The study population comprised individuals with confirmed (positive test) Covid-19 and at least one thromboembolic event between March 2018 and October 2020. Their incidence rates during the risk interval (5 days before to 56 days after the positive test) and the control interval (the remaining periods) were compared intra-personally.\n\nResultsAcross Scotland, 1,449 individuals tested positive for Covid-19 and experienced a thromboembolic event. The risk of thromboembolism was significantly elevated over the whole risk period but highest in the 7 days following the positive test (IRR 12.01, 95% CI 9.91-14.56) in all included individuals. The association was also present in individuals not originally hospitalised for Covid-19 (IRR 4.07, 95% CI 2.83-5.85). Risk of MI, stroke, PE and DVT were all significantly higher in the week following a positive test. The risk of PE and DVT was particularly high and remained significantly elevated even 56 days following the test.\n\nConclusionConfirmed Covid-19 infection was associated with early elevations in risk with MI, ischaemic stroke, and substantially stronger and prolonged elevations with DVT and PE both in hospital and community settings. Clinicians should consider thromboembolism, especially PE, among people with Covid-19 in the community.", + "category": "cardiovascular medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.02.03.21251004", @@ -6467,6 +6453,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2021.01.25.428136", + "date": "2021-01-25", + "link": "https://biorxiv.org/cgi/content/short/2021.01.25.428136", + "title": "mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge", + "authors": "Michelle Meyer; Yuan Wang; Darin Edwards; Gregory R Smith; Aliza B Rubenstein; Palaniappan Ramanathan; Chad E Mire; Colette Pietzsch; Xi Chen; Yongchao Ge; Wan Sze Cheng; Carole Henry; Angela Woods; LingZhi Ma; Guillaume B. E. Stewart-Jones; Kevin W Bock; Minai Mahnaz; Bianca M Nagata; Sivakumar Periasamy; Pei-Yong Shi; Barney S Graham; Ian N Moore; Irene Ramos; Olga G. Troyanskaya; Elena Zaslavsky; Andrea Carfi; Stuart C Sealfon; Alexander Bukreyev", + "affiliations": "University of Texas Medical Branch; Princeton University; Moderna Inc; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch; University of Texas Medical Branch; University of Texas Medical Branch; Flatiron Institute, Simons Foundation; Icahn School of Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; Moderna Inc; Moderna Inc; Moderna Inc; Moderna Inc; National Institute of Health; National Institutes of Health; National Institutes of Health; University of Texas Medical Branch; University of Texas Medical Branch; National Institutes of Health; National Institutes of Health; Icahn School of Medicine at Mount Sinai; Princeton University; Icahn School of Medicine at Mount Sinai; Moderna Inc; Icahn School of Medicine at Mount Sinai; University of Texas Medical Branch at Galveston", + "abstract": "The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.", + "category": "immunology", + "match_type": "fuzzy", + "author_similarity": 96, + "affiliation_similarity": 94 + }, { "site": "medRxiv", "doi": "10.1101/2021.01.21.20240887", @@ -6677,20 +6677,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "bioRxiv", - "doi": "10.1101/2020.12.23.424229", - "date": "2020-12-25", - "link": "https://biorxiv.org/cgi/content/short/2020.12.23.424229", - "title": "Patterns of within-host genetic diversity in SARS-CoV-2", - "authors": "Gerry Tonkin-Hill; Inigo Martincorena; Roberto Amato; Andrew R J Lawson; Moritz Gerstung; Ian Johnston; David K Jackson; Naomi R Park; Stefanie V Lensing; Michael A Quail; S\u00f3nia Gon\u00e7alves; Cristina Ariani; Michael Spencer Chapman; William L Hamilton; Luke W Meredith; Grant Hall; Aminu S Jahun; Yasmin Chaudhry; Myra Hosmillo; Malte L Pinckert; Iliana Georgana; Anna Yakovleva; Laura G Caller; Sarah L Caddy; Theresa Feltwell; Fahad A Khokhar; Charlotte J Houldcroft; Martin D Curran; Surendra Parmar; - The COVID-19 Genomics UK (COG-UK) Consortium; Alex Alderton; Rachel Nelson; Ewan Harrison; John Sillitoe; Stephen D Bentley; Jeffrey C Barrett; M. Estee Torok; Ian G Goodfellow; Cordelia Langford; Dominic Kwiatkowski; - Wellcome Sanger Institute COVID-19 Surveillance Team", - "affiliations": "Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge and The Francis Crick Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge and Cambridge Institute of Therapeutic Immunology and Infectious Disease; Department of Medicine, University of Cambridge; Public Health England; Public Health England; COG-UK; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute and European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute and Oxford University; ", - "abstract": "Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1,181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within and between host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.", - "category": "genomics", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.12.21.20248607", @@ -7041,6 +7027,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.19.20234849", + "date": "2020-11-22", + "link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234849", + "title": "Community factors and excess mortality in first wave of the COVID-19 pandemic.", + "authors": "Bethan Davies; Brandon L Parkes; James Bennett; Daniela Fecht; Marta Blangiardo; Majid Ezzati; Paul Elliott", + "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London", + "abstract": "Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.18.20233932", @@ -7069,6 +7069,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.18.20225029", + "date": "2020-11-20", + "link": "https://medrxiv.org/cgi/content/short/2020.11.18.20225029", + "title": "The Invasive Respiratory Infection Surveillance (IRIS) Initiative reveals significant reductions in invasive bacterial infections during the COVID-19 pandemic", + "authors": "Angela B Brueggemann; Melissa J Jansen van Rensburg; David Shaw; Noel D McCarthy; Keith A Jolley; Martin CJ Maiden; Mark PG van der Linden", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Warwick; University of Oxford; University of Oxford; University Hospital RWTH Aachen", + "abstract": "BackgroundStreptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis are leading causes of invasive diseases including bacteraemic pneumonia and meningitis, and of secondary infections post-viral respiratory disease. They are typically transmitted via respiratory droplets. We investigated rates of invasive disease due to these pathogens during the early phase of the COVID-19 pandemic.\n\nMethodsLaboratories in 26 countries across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae and N meningitidis from 1 January 2018 to 31 May 2020. Weekly cases in 2020 vs 2018-2019 were compared. Streptococcus agalactiae data were collected from nine laboratories for comparison to a non-respiratory pathogen. The stringency of COVID-19 containment measures was quantified by the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed by Google COVID-19 Community Mobility Reports. Interrupted time series modelling quantified changes in rates of invasive disease in 2020 relative to when containment measures were imposed.\n\nFindingsAll countries experienced a significant, sustained reduction in invasive diseases due to S pneumoniae, H influenzae and N meningitidis, but not S agalactiae, in early 2020, which coincided with the introduction of COVID-19 containment measures in each country. Similar impacts were observed across most countries despite differing stringency in COVID-19 control policies. There was no evidence of a specific effect due to enforced school closures.\n\nInterpretationThe introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of these bacterial respiratory pathogens, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.18.20234369", @@ -7209,20 +7223,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "bioRxiv", - "doi": "10.1101/2020.11.06.369439", - "date": "2020-11-06", - "link": "https://biorxiv.org/cgi/content/short/2020.11.06.369439", - "title": "Allosteric hotspots in the main protease of SARS-CoV-2", - "authors": "L\u00e9onie Str\u00f6mich; Nan Wu; Mauricio Barahona; Sophia N Yaliraki", - "affiliations": "Imperial College London; Imperial College London; Imperial College London; Imperial College London", - "abstract": "AO_SCPLOWBSTRACTC_SCPLOWInhibiting the main protease of SARS-CoV-2 is of great interest in tackling the COVID-19 pandemic caused by the virus. Most efforts have been centred on inhibiting the binding site of the enzyme. However, considering allosteric sites, distant from the active or orthosteric site, broadens the search space for drug candidates and confers the advantages of allosteric drug targeting. Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites without a priori knowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. We further score the highest ranking sites against random sites in similar distances through statistical bootstrapping and identify four statistically significant putative allosteric sites as good candidates for alternative drug targeting.", - "category": "bioinformatics", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.11.01.20224014", @@ -7503,20 +7503,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.10.19.20214494", - "date": "2020-10-21", - "link": "https://medrxiv.org/cgi/content/short/2020.10.19.20214494", - "title": "Attributes and predictors of Long-COVID: analysis of COVID cases and their symptoms collected by the Covid Symptoms Study App", - "authors": "Carole H Sudre; Benjamin Murray; Thomas Varsavsky; Mark S Graham; Rose S Penfold; Ruth C.E Bowyer; Joan Capdevila Pujol; Kerstin Klaser; Michela Antonelli; Liane S Canas; Erika Molteni; Marc Modat; M. Jorge Cardoso; Anna May; Sajaysurya Ganesh; Richard Davies; Long H Nguyen; David Alden Drew; Christina M Astley; Amit D. Joshi; Jordi Merino; Neli Tsereteli; Tove Fall; Maria F Gomez; Emma Duncan; Christina Menni; Frances MK Williams; Paul W Franks; Andrew T Chan; Jonathan Wolf; Sebastien Ourselin; Timothy Spector; Claire J Steves", - "affiliations": "KCL; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; Zoe Global Limited; Zoe Global Limited; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital; Boston Children's Hospital; Massachusetts General Hospital; Massachusetts General Hospital; Lund University; Uppsala University; Lund University; King's College London; King's College London; King's College London; Lund University; Massachusetts General Hospital; Zoe Global Limited; King's College London; King's College London; King's College London", - "abstract": "Reports of \"Long-COVID\", are rising but little is known about prevalence, risk factors, or whether it is possible to predict a protracted course early in the disease. We analysed data from 4182 incident cases of COVID-19 who logged their symptoms prospectively in the COVID Symptom Study app. 558 (13.3%) had symptoms lasting >=28 days, 189 (4.5%) for >=8 weeks and 95 (2.3%) for >=12 weeks. Long-COVID was characterised by symptoms of fatigue, headache, dyspnoea and anosmia and was more likely with increasing age, BMI and female sex. Experiencing more than five symptoms during the first week of illness was associated with Long-COVID, OR=3.53 [2.76;4.50]. A simple model to distinguish between short and long-COVID at 7 days, which gained a ROC-AUC of 76%, was replicated in an independent sample of 2472 antibody positive individuals. This model could be used to identify individuals for clinical trials to reduce long-term symptoms and target education and rehabilitation services.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 94, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.10.15.20213108", @@ -7909,20 +7895,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.09.15.20194795", - "date": "2020-09-18", - "link": "https://medrxiv.org/cgi/content/short/2020.09.15.20194795", - "title": "Acute, non-COVID related medical admissions during the first wave of COVID-19: A retrospective comparison of changing patterns of disease", - "authors": "Bridget Riley; Mary Packer; Suzy Gallier; Elizabeth Sapey; Catherine Atkin", - "affiliations": "University Hospitals Birmingham NHS Foundation Trust; University Hospitals Birmingham NHS Foundation Trust; PIONEER Hub, University Hospitals Birmingham NHS Foundation Trust; PIONEER Hub, University of Birmingham; PIONEER Hub, University of Birmingham", - "abstract": "BackgroundThe COVID-19 pandemic was associated with social restrictions in the UK from 16th March 2020. It was unclear if the lockdown period was associated with differences in the case-mix of non-COVID acute medical admissions compared with the previous year.\n\nMethodsRetrospective data were collected for 1st-30th April 2019 and 1st-30th April 2020 from University Hospitals Birmingham NHS Foundation Trust, one of the largest hospitals in the UK with over 2 million patient contacts per year. The latter time period was chosen to coincide with the peak of COVID-19 cases in the West Midlands. All patients admitted under acute medicine during these time periods were included. COVID-19 was confirmed by SARS-Cov-2 swab or a probable case of COVID-19 based on World Health Organization diagnostic parameters. Non-COVID patients were those with a negative SARS-Cov-2 swab and no suspicion of COVID-19. Data was sourced from UHBs in-house electronic health system (EHS).\n\nResultsThe total number of acute medical admissions fell comparing April 2019 (n = 2409) to April 2020 (n = 1682). As a proportion of total admissions, those aged under 45 years decreased, while those aged 46 and over did not change.\n\nThe number of admissions due to psychiatric conditions and overdoses was higher in April 2020 (p < 0.001). When viewed as a proportion of admissions, alcohol-related admissions (p = 0.004), psychiatric conditions and overdoses (p< 0.001) increased in April 2020 than in April 2019. The proportion of patients who were in hospital due to falls also increased in April 2020 (p< 0.001). In the same period, the absolute number and the proportion of admissions that were due to non-specific chest pain, to musculoskeletal complaints and patients who self-discharged prior to assessment decreased (p = 0.02, p = 0.01 and p = 0.002 respectively).\n\nThere were no significant differences in non-COVID-related intensive care admissions or mortality between the same months in the two years.\n\nConclusionIn this large, single-centre study, there was a change in hospitalised case-mix when comparing April 2019 with April 2020: an increase in conditions which potentially reflect social isolation (falls, drug and alcohol misuse and psychiatric illness) and a decrease in conditions which rarely require in-patient hospital treatment (musculoskeletal pain and non-cardiac chest pain) especially among younger adults. These results highlight two areas for further research; the impact of social isolation on health and whether younger adults could be offered alternative health services to avoid potentially unnecessary hospital assessment.", - "category": "emergency medicine", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.09.17.20196469", @@ -8063,6 +8035,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.09.01.20185793", + "date": "2020-09-03", + "link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185793", + "title": "Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study", + "authors": "Katie Biggs; Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Matthew Bursnall; Amanda Loban; Simon Waterhouse; Richard Simmonds; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter", + "affiliations": "University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust", + "abstract": "ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection.\n\nMethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome.\n\nResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold.\n\nConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive.\n\nRegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533", + "category": "emergency medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.09.02.20186502", @@ -8903,20 +8889,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.06.29.20142448", - "date": "2020-06-30", - "link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142448", - "title": "Using past and current data to estimate potential crisis service use in mental healthcare after the COVID-19 lockdown: South London and Maudsley data", - "authors": "Robert Stewart; Matthew Broadbent", - "affiliations": "King's College London; South London and Maudsley NHS Foundation Trust", - "abstract": "The lockdown policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare with uncertain consequences over the 12 months ahead. Past activity may provide a means to predict future demand. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource at the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in south London), we carried out a range of descriptive analyses to inform the Trust on patient groups who might be most likely to require inpatient and home treatment team (HTT) crisis care. We considered the 12 months following UK COVID-19 lockdown policy on 16th March, drawing on comparable findings from previous years, and quantified levels of change in service delivery to those most likely to receive crisis care. For 12-month crisis days from 16th March in 2015-19, we found that most (over 80%) were accounted for by inpatient care (rather than HTT), most (around 75%) were used by patients who were current or recent Trust patients at the commencement of follow-up, and highest numbers were used by patients with a previously recorded schizophreniform disorder diagnosis. For current/recent patients on 16th March there had been substantial reductions in use of inpatient care in the following 31 days in 2020, more than previous years; changes in total non-inpatient contact numbers did not differ in 2020 compared to previous years, although there had been a marked switch from face-to-face to virtual contacts.", - "category": "psychiatry and clinical psychology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.06.28.20141986", @@ -9197,6 +9169,20 @@ "author_similarity": 100, "affiliation_similarity": 91 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.06.10.20127175", + "date": "2020-06-11", + "link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127175", + "title": "Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.", + "authors": "Amitava Banerjee; Suliang Chen; Laura Pasea; Alvina Lai; Michail Katsoulis; Spiros Denaxas; Vahe Nafilyan; Bryan Williams; Wai Keong Wong; Ameet Bakhai; Kamlesh Khunti; Deenan Pillay; Mahdad Noursadeghi; Honghan Wu; Nilesh Pareek; Daniel Bromage; Theresa Mcdonagh; Jonathan Byrne; James T Teo; Ajay Shah; Ben Humberstone; Liang V Tang; Anoop SV Shah; Andrea Rubboli; Yutao Guo; Yu Hu; Cathie LM Sudlow; Gregory YH Lip; Harry Hemingway", + "affiliations": "University College London; University College London; University College London; University College London; UCL; University College London; Office for National Statistics; UCL; University College London Hospitals NHS Trust; Royal Free Hospitals NHS Trust; University of Leicester; UCL; UCL; UCL; King's College Hospital; Kings College London; Kings College London; Kings London NHS Trust; Kings College Hospital NHS Foundation Trust; King's College London; Office for National Statistics; Huazhong University of Science and Technology, Wuhan, China; University of Edinburgh; Ospedale S. Maria delle Croci, Ravenna, Italy; PLA General Hospital, Beijing, China.; Huazhong University of Science and Technology, Wuhan, China.; University of Edinburgh; University of Liverpool; UCL", + "abstract": "BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both \"direct\", through infection, and \"indirect\", through changes in healthcare.\n\nMethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(\"direct\" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For \"indirect\" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020.\n\nFindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths.\n\nInterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic.\n\nFundingNIHR, HDR UK, Astra Zeneca", + "category": "cardiovascular medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "bioRxiv", "doi": "10.1101/2020.06.11.145920", @@ -9337,20 +9323,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.06.01.20118943", - "date": "2020-06-02", - "link": "https://medrxiv.org/cgi/content/short/2020.06.01.20118943", - "title": "Greater risk of severe COVID-19 in non-White ethnicities is not explained by cardiometabolic, socioeconomic, or behavioural factors, or by 25(OH)-vitamin D status: study of 1,326 cases from the UK Biobank", - "authors": "Zahra Raisi-Estabragh; Celeste McCracken; Mae S Bethell; Jackie Cooper; Cyrus Cooper; Mark J Caulfield; Patricia B Munroe; Nicholas C Harvey; Steffen E Petersen", - "affiliations": "William Harvey Research Institute; William Harvey Research Institute; North West Anglia NHS Foundation Trust; William Harvey Research Institute; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; William Harvey Research Institute; William Harvey Research Institute; MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK; William Harvey Research Institute", - "abstract": "BackgroundWe examined whether the greater severity of coronavirus disease 2019 (COVID-19) amongst men and non-White ethnicities is explained by cardiometabolic, socio-economic, or behavioural factors.\n\nMethodsWe studied 4,510 UK Biobank participants tested for COVID-19 (positive, n = 1,326). Multivariate logistic regression models including age, sex, and ethnicity were used to test whether addition of: 1)cardiometabolic factors (diabetes, hypertension, high cholesterol, prior myocardial infarction, smoking, BMI); 2)25(OH)-vitamin D; 3)poor diet; 4)Townsend deprivation score; 5)housing (home type, overcrowding); or 6)behavioural factors (sociability, risk taking) attenuated sex/ethnicity associations with COVID-19 status.\n\nResultsThere was over-representation of men and non-White ethnicities in the COVID-19 positive group. Non-Whites had, on average, poorer cardiometabolic profile, lower 25(OH)-vitamin D, greater material deprivation, and were more likely to live in larger households and flats/apartments. Male sex, non-White ethnicity, higher BMI, Townsend deprivation score, and household overcrowding were independently associated with significantly greater odds of COVID-19. The pattern of association was consistent for men and women; cardiometabolic, socio-demographic and behavioural factors did not attenuate sex/ethnicity associations.\n\nConclusionsSex and ethnicity differential pattern of COVID-19 is not adequately explained by variations in cardiometabolic factors, 25(OH)-vitamin D levels, or socio-economic factors. Investigation of alternative biological pathways and different genetic susceptibilities is warranted.", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.05.31.20118638", @@ -9561,6 +9533,20 @@ "author_similarity": 94, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.05.14.20101824", + "date": "2020-05-19", + "link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101824", + "title": "Changing travel patterns in China during the early stages of the COVID-19 pandemic", + "authors": "Hamish Gibbs; Yang Liu; Carl AB Pearson; Christopher I Jarvis; Chris Grundy; Billy J Quilty; Charlie Diamond; Rosalind M Eggo", + "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine", + "abstract": "Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigated the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020 and discussed their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower access to care. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and have not yet led to structural reorganisation of the transportation network at the time of this study.\n\nOne sentence summaryUnderstanding travel before, during, and after the introduction of travel restrictions in China in response to the COVID-19 Pandemic.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.05.11.20098269", @@ -10372,5 +10358,19 @@ "match_type": "fuzzy", "author_similarity": 100, "affiliation_similarity": 100 + }, + { + "site": "medRxiv", + "doi": "10.1101/2020.01.31.20019901", + "date": "2020-02-02", + "link": "https://medrxiv.org/cgi/content/short/2020.01.31.20019901", + "title": "Early dynamics of transmission and control of 2019-nCoV: a mathematical modelling study", + "authors": "Adam J Kucharski; Timothy W Russell; Charlie Diamond; Yang Liu; CMMID nCoV working group; John Edmunds; Sebastian Funk; Rosalind M Eggo", + "affiliations": "London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine", + "abstract": "BackgroundAn outbreak of the novel coronavirus SARS-CoV-2 has led to 46,997 confirmed cases as of 13th February 2020. Understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas.\n\nMethodsWe combined a stochastic transmission model with data on cases of novel coronavirus disease (COVID-19) in Wuhan and international cases that originated in Wuhan to estimate how transmission had varied over time during January and February 2020. Based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas.\n\nFindingsWe estimated that the median daily reproduction number, Rt, declined from 2.35 (95% CI: 1.15-4.77) one week before travel restrictions were introduced on 23rd January to 1.05 (95% CI: 0.413-2.39) one week after. Based on our estimates of Rt,we calculated that in locations with similar transmission potential as Wuhan in early January, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population.\n\nInterpretationOur results show that COVID-19 transmission likely declined in Wuhan during late January 2020, coinciding with the introduction of control measures. As more cases arrive in international locations with similar transmission potential to Wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually.\n\nFundingWellcome Trust (206250/Z/17/Z, 210758/Z/18/Z), HDR UK (MR/S003975/1), Gates Foundation (INV-003174), NIHR (16/137/109)", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 } ] \ No newline at end of file diff --git a/data/covid/raw-preprints.json b/data/covid/raw-preprints.json index 0392d573..5d688cf7 100644 --- a/data/covid/raw-preprints.json +++ b/data/covid/raw-preprints.json @@ -5,7 +5,7 @@ "rel_date": "2024-01-06", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.05.574360", - "rel_abs": "Upon infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), patients with critical coronavirus disease 2019 (COVID-19) present with life-threatening respiratory distress, pulmonary damage and cytokine storm. One unexplored hub in COVID-19 is the neuropeptide calcitonin gene-related peptide (CGRP), which is highly abundant in the airways and could converge in multiple aspects of COVID-19-related pulmonary pathophysiology. Whether CGRP affects SARS-CoV-2 infection directly remains elusive. We show that in critical COVID-19 patients, CGRP is increased in both plasma and lungs. Importantly, CGRP pulmonary levels are elevated in early SARS-CoV-2-positive patients, and restore to baseline upon subsequent viral clearance in SARS-CoV-2-negative patients. We further show that CGRP and its stable analogue SAX directly inhibit infection of bronchial Calu-3 epithelial cells with SARS-CoV-2 Omicron and Alpha variants in a dose-dependent manner. Both pre- and post-infection treatment with GRRP and/or SAX is enough to block SARS-CoV-2 productive infection of Calu3 cells. CGRP-mediated inhibition occurs via activation of the CGRP receptor and involves down-regulation of SARS-CoV-2 entry receptors at the surface of Calu-3 cells. Together, we propose that increased pulmonary CGRP mediates beneficial viral clearance in critical COVID-19 patients, by directly inhibiting SARS-CoV-2 infection. Hence, CGRP-based interventions could be harnessed for management of COVID-19.", + "rel_abs": "Upon infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), patients with critical coronavirus disease 2019 (COVID-19) present with life-threatening respiratory distress, pulmonary damage and cytokine storm. One unexplored hub in COVID-19 is the neuropeptide calcitonin gene-related peptide (CGRP), which is highly abundant in the airways and could converge in multiple aspects of COVID-19-related pulmonary pathophysiology. Whether CGRP affects SARS-CoV-2 infection directly remains elusive. We show that in critical COVID-19 patients, CGRP is increased in both plasma and lungs. Importantly, CGRP pulmonary levels are elevated in early SARS-CoV-2-positive patients, and restore to baseline upon subsequent viral clearance in SARS-CoV-2-negative patients. We further show that CGRP and its stable analogue SAX directly inhibit infection of bronchial Calu-3 epithelial cells with SARS-CoV-2 Omicron and Alpha variants in a dose-dependent manner. Both pre- and post-infection treatment with GRRP and/or SAX is enough to block SARS-CoV-2 productive infection of Calu3 cells. CGRP-mediated inhibition occurs via activation of the CGRP receptor and involves down-regulation of SARS-CoV-2 entry receptors at the surface of Calu-3 cells. Together, we propose that increased pulmonary CGRP mediates beneficial viral clearance in critical COVID-19 patients, by directly inhibiting SARS-CoV-2 infection. Hence, CGRP-based interventions could be harnessed for management of COVID-19.\n\nBrief summaryPulmonary levels of the neuropeptide CGRP are increased in critical COVID-19 patients, and could clear virus by directly inhibiting SRAS-CoV-2 infection of bronchial epithelia cells.", "rel_num_authors": 14, "rel_authors": [ { @@ -76,7 +76,7 @@ "rel_date": "2024-01-06", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.05.574420", - "rel_abs": "Previous studies have linked the evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic variants to persistent infections in people with immunocompromising conditions, but the evolutionary processes underlying these observations are incompletely understood. Here we used high-throughput, single-genome amplification and sequencing (HT-SGS) to obtain up to ~103 SARS-CoV-2 spike gene sequences in each of 184 respiratory samples from 22 people with HIV (PWH) and 25 people without HIV (PWOH). Twelve of 22 PWH had advanced HIV infection, defined by peripheral blood CD4 T cell counts (i.e., CD4 counts) <200 cells/L. In PWOH and PWH with CD4 counts [≥]200 cells/L, most single-genome spike sequences in each person matched one haplotype that predominated throughout the infection. By contrast, people with advanced HIV showed elevated intra-host spike diversity with a median of 46 haplotypes per person (IQR 14-114). Higher intra-host spike diversity immediately after COVID-19 symptom onset predicted longer SARS-CoV-2 RNA shedding among PWH, and intra-host spike diversity at this timepoint was significantly higher in people with advanced HIV than in PWOH. Composition of spike sequence populations in people with advanced HIV fluctuated rapidly over time, with founder sequences often replaced by groups of new haplotypes. These population-level changes were associated with a high total burden of intra-host mutations and positive selection at functionally important residues. In several cases, delayed emergence of detectable serum binding to spike was associated with positive selection for presumptive antibody-escape mutations. Taken together, our findings show remarkable intra-host genetic diversity of SARS-CoV-2 in advanced HIV infection and suggest that adaptive intra-host SARS-CoV-2 evolution in this setting may contribute to the emergence of new variants of concern (VOCs).", + "rel_abs": "Previous studies have linked the evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic variants to persistent infections in people with immunocompromising conditions1-4, but the evolutionary processes underlying these observations are incompletely understood. Here we used high-throughput, single-genome amplification and sequencing (HT-SGS) to obtain up to [~]103 SARS-CoV-2 spike gene sequences in each of 184 respiratory samples from 22 people with HIV (PWH) and 25 people without HIV (PWOH). Twelve of 22 PWH had advanced HIV infection, defined by peripheral blood CD4 T cell counts (i.e., CD4 counts) <200 cells/L. In PWOH and PWH with CD4 counts [≥]200 cells/L, most single-genome spike sequences in each person matched one haplotype that predominated throughout the infection. By contrast, people with advanced HIV showed elevated intra-host spike diversity with a median of 46 haplotypes per person (IQR 14-114). Higher intra-host spike diversity immediately after COVID-19 symptom onset predicted longer SARS-CoV-2 RNA shedding among PWH, and intra-host spike diversity at this timepoint was significantly higher in people with advanced HIV than in PWOH. Composition of spike sequence populations in people with advanced HIV fluctuated rapidly over time, with founder sequences often replaced by groups of new haplotypes. These population-level changes were associated with a high total burden of intra-host mutations and positive selection at functionally important residues. In several cases, delayed emergence of detectable serum binding to spike was associated with positive selection for presumptive antibody-escape mutations. Taken together, our findings show remarkable intra-host genetic diversity of SARS-CoV-2 in advanced HIV infection and suggest that adaptive intra-host SARS-CoV-2 evolution in this setting may contribute to the emergence of new variants of concern (VOCs).", "rel_num_authors": 21, "rel_authors": [ { @@ -175,7 +175,7 @@ "rel_date": "2024-01-05", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.02.573936", - "rel_abs": "Patients present a wide range of clinical severities in response SARS-CoV-2 infection, but the underlying molecular and cellular reasons why clinical outcomes vary so greatly within the population remains unknown. Here, we report that negative clinical outcomes in severely ill patients were associated with divergent RNA transcriptome profiles in peripheral immune cells compared with mild cases during the first weeks after disease onset. Protein-protein interaction analysis indicated that early-responding cytotoxic NK cells were associated with an effective clearance of the virus and a less severe outcome. This innate immune response was associated with the activation of select cytokine-cytokine receptor pathways and robust Th1/Th2 cell differentiation profiles. In contrast, severely ill patients exhibited a dysregulation between innate and adaptive responses affiliated with divergent Th1/Th2 profiles and negative outcomes. This knowledge forms the basis of clinical triage that may be used to preemptively detect high-risk patients before life-threatening outcomes ensue.", + "rel_abs": "Patients present a wide range of clinical severities in response SARS-CoV-2 infection, but the underlying molecular and cellular reasons why clinical outcomes vary so greatly within the population remains unknown. Here, we report that negative clinical outcomes in severely ill patients were associated with divergent RNA transcriptome profiles in peripheral immune cells compared with mild cases during the first weeks after disease onset. Protein-protein interaction analysis indicated that early-responding cytotoxic NK cells were associated with an effective clearance of the virus and a less severe outcome. This innate immune response was associated with the activation of select cytokine-cytokine receptor pathways and robust Th1/Th2 cell differentiation profiles. In contrast, severely ill patients exhibited a dysregulation between innate and adaptive responses affiliated with divergent Th1/Th2 profiles and negative outcomes. This knowledge forms the basis of clinical triage that may be used to preemptively detect high-risk patients before life-threatening outcomes ensue.\n\nHighlights- Mild COVID-19 patients presented an early compromise with NK cell function, whereas severe patients do so with neutrophil function.\n- The identified co-expressed genes give insights into a coordinated transcriptional program of NK cell cytotoxic activity being associated with mild patients.\n- Key checkpoints of NK cell cytotoxicity that were enriched in mild patients include: KLRD1, CD247, and IFNG.\n- The early innate immune response related to NK cells connects with the Th1/Th2 adaptive immune responses, supporting their relevance in COVID-19 progression.", "rel_num_authors": 13, "rel_authors": [ { @@ -34560,7 +34560,7 @@ "rel_date": "2023-09-25", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.22.23295541", - "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@5b5e50org.highwire.dtl.DTLVardef@8ce6c8org.highwire.dtl.DTLVardef@837cc2org.highwire.dtl.DTLVardef@73a6de_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Our understanding of the quality of cellular and humoral immunity conferred by COVID-19 vaccination alone versus vaccination plus SARS-CoV-2 breakthrough (BT) infection remains incomplete. While the current (2023) SARS-CoV-2 immune landscape of Canadians is complex, in late 2021 most Canadians had either just received a third dose of COVID-19 vaccine, or had received their two dose primary series and then experienced an Omicron BT. Herein we took advantage of this coincident timing to contrast cellular and humoral immunity conferred by three doses of vaccine versus two doses plus BT. Our results show that mild BT infection induces cell-mediated immune responses to variants comparable to an intramuscular vaccine booster dose. In contrast, BT subjects had higher salivary IgG and IgA levels against the Omicron Spike and enhanced reactivity to the ancestral Spike for the IgA isotype, which also reacted with SARS-CoV-1. Serum neutralizing antibody levels against the ancestral strain and the variants were also higher after BT infection. Our results support the need for mucosal vaccines to emulate the enhanced mucosal and humoral immunity induced by Omicron without exposing individuals to the risks associated with SARS-CoV-2 infection.\n\nONE SENTENCE SUMMARYOmicron breakthrough elicits cross-reactive systemic and mucosal immune responses in fully vaccinated adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC=\"FIGDIR/small/23295541v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@16781b4org.highwire.dtl.DTLVardef@745d73org.highwire.dtl.DTLVardef@1a3576aorg.highwire.dtl.DTLVardef@bff724_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 22, "rel_authors": [ { @@ -223504,6 +223504,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.26.22279242", + "rel_title": "A survey of patient and public perceptions and awareness of SARS-CoV-2-related risks among participants in India and South Africa", + "rel_date": "2022-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.26.22279242", + "rel_abs": "A cross-sectional survey was performed among the adult population of participating countries, India and South Africa. The purpose of this study was to explore perceptions and awareness of SARS-CoV-2-related risks in the relevant countries. The main outcome measures were the proportion of participants aware of SARS-CoV-2, and their perception of infection risks.\n\nSelf-administered questionnaires were used to collect data via a web- and paper-based survey over three months. For data capturing, Microsoft Excel was employed, and descriptive statistics used for presenting data. Pearsons Chi-squared test was used to assess relationships between variables, and a p-value less than 0.05 was considered significant.\n\nThere were 844 respondents (India: n=660, South Africa: n=184; response rate 87.6%), with a 61.1% vs 38.3% female to male ratio. Post-high-school or university education was the lowest qualification reported by most respondents in India (77.3%) and South Africa (79.3%). Sources of information about the pandemic were usually media and journal publications (73.2%), social media (64.6%), family and friends (47.7%) and government websites (46.2%). Most respondents correctly identified infection prevention measures (such as physical distancing, mask use), with 90.0% reporting improved hand hygiene practices since the pandemic. Hesitancy or refusal to accept the SARS-CoV-2 vaccine was reported among 17.9% and 50.9% of respondents in India and South Africa, respectively. Reasons cited included rushed vaccine development and the futility of vaccines for what respondents considered a self-limiting flu-like illness.\n\nRespondents identified public health promotion measures for SARS-CoV-2. Reported hesitancy to the up-take of SARS-CoV-2 vaccines was much higher in South Africa. Vaccination campaigns should consider robust public engagement and contextually fit communication strategies with multimodal, participatory online and offline initiatives to address public concerns, specifically towards vaccines developed for this pandemic and general vaccine hesitancy.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Oluchi N Mbamalu", + "author_inst": "University of Cape Town Faculty of Health Sciences" + }, + { + "author_name": "Surya Surendran", + "author_inst": "The George Institute for Global Health India" + }, + { + "author_name": "Vrinda Nampoothiri", + "author_inst": "Amrita Institute of Medical Sciences" + }, + { + "author_name": "Candice Bonaconsa", + "author_inst": "University of Cape Town Faculty of Health Sciences" + }, + { + "author_name": "Fabia Edathadathil", + "author_inst": "Amrita Institute of Medical Sciences" + }, + { + "author_name": "Nina Zhu", + "author_inst": "Imperial College London Faculty of Medicine - South Kensington Campus: Imperial College London Faculty of Medicine" + }, + { + "author_name": "Vanessa Carter", + "author_inst": "Health Communication and Social Media" + }, + { + "author_name": "Helen Lambert", + "author_inst": "University of Bristol Medical School" + }, + { + "author_name": "Carolyn Tarrant", + "author_inst": "University of Leicester Department of Health Sciences" + }, + { + "author_name": "Raheelah Ahmad", + "author_inst": "City University of London" + }, + { + "author_name": "Adrian Brink", + "author_inst": "University of Cape Town Faculty of Health Sciences" + }, + { + "author_name": "Ebrahim Steenkamp", + "author_inst": "University of Cape Town Department of Statistical Sciences" + }, + { + "author_name": "Alison Holmes", + "author_inst": "Imperial College London Faculty of Medicine - South Kensington Campus: Imperial College London Faculty of Medicine" + }, + { + "author_name": "Sanjeev Singh", + "author_inst": "Amrita Institute of Medical Sciences" + }, + { + "author_name": "Esmita Charani", + "author_inst": "Imperial College London Faculty of Medicine - South Kensington Campus: Imperial College London Faculty of Medicine" + }, + { + "author_name": "Marc Mendelson", + "author_inst": "University of Cape Town Faculty of Health Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.25.22279238", "rel_title": "Evaluation of Secondary Chemistry due to Disinfection of Indoor Air with Germicidal Ultraviolet Lamps", @@ -225192,51 +225271,39 @@ "category": "epidemiology" }, { - "rel_doi": "10.1101/2022.08.23.504798", - "rel_title": "Integrated Immunopeptidomics and Proteomics Study Reveals Imbalanced Innate and Adaptive Immune Responses to SARS-Cov-2 Infection", + "rel_doi": "10.1101/2022.08.23.505031", + "rel_title": "New Insights into How JUUL Electronic Cigarette Aerosols and Aerosol Constituents Affect SARS-CoV-2 Infection of Human Bronchial Epithelial Cells", "rel_date": "2022-08-24", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.23.504798", - "rel_abs": "We present an integrated immunopeptidomics and proteomics study of SARS-Cov-2 infection to comprehensively decipher the changes in host cells in response to viral infection. Our results indicated that innate immune response in Calu-3 cells was initiated by TLR3, followed by activation of interferon signaling pathway. Host cells also present viral antigens to the cell surface through both Class I and Class II MHC system for recognition by adaptive immune system. SARS-Cov-2 infection led to the disruption of antigen presentation as demonstrated by higher level of HLA proteins from the flow-through of MHC immunoprecipitation. Glycosylation analysis of HLA proteins from the elution and flow-through of immunoprecipitation revealed that the synthesis and degradation of HLA protein was affected by SARS-Cov-2 infection. This study provided many useful information to study the host response to SARS-Cov-2 infection and would be helpful for the development of therapeutics and vaccine for Covid-19 and future pandemic.", - "rel_num_authors": 8, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.23.505031", + "rel_abs": "BackgroundThe relationship between the use of tobacco products and SARS-CoV-2 infection is poorly understood and controversial. Most studies have been done with tobacco cigarettes, while few have examined the effect of electronic cigarettes (ECs) on SARS-CoV-2 infection. We tested the hypothesis that EC fluids and aerosols with high concentrations of nicotine promote SARS-COV-2 infection by increasing viral entry into human respiratory epithelial cells.\n\nMethodsResponses of BEAS-2B cells to authentic JUUL aerosols or their individual constituents (propylene glycol (PG)/vegetable glycerin (VG) and nicotine) were compared using three exposure platforms: submerged culture, air-liquid-interface (ALI) exposure in a cloud chamber, and ALI exposure in a Cultex(R) system, which produces authentic heated EC aerosols. SARS-CoV-2 infection machinery was assessed using immunohistochemistry and Western blotting. Specifically, the levels of the SARS-CoV-2 receptor ACE2 (angiotensin converting enzyme 2) and a spike modifying enzyme, TMPRSS2 (transmembrane serine protease 2), were evaluated. Following each exposure, lentivirus pseudoparticles with spike protein and a green-fluorescent reporter were used to test viral penetration and the susceptibility of BEAS-2B cells to infection.\n\nResultsNicotine, EC fluids, and authentic JUUL aerosols increased both ACE2 levels and TMPRSS2 activity, which in turn increased viral particle entry into cells. While most data were in good agreement across the three exposure platforms, cells were more responsive to treatments when exposed at the ALI in the Cultex system, even though the exposures were brief and intermittent. In the Cultex system, PG/VG, PG/VG/nicotine, and JUUL aerosols significantly increased infection above clean air controls. However, both the PG/VG and JUUL treatments were significantly lower than nicotine/PG/VG. PG/VG increased infection only in the Cultex(R) system, which produces heated aerosol.\n\nConclusionOur data are consistent with the conclusion that authentic JUUL aerosols or their individual constituents (nicotine or PG/VG) increase SARS-CoV-2 infection. The strong effect produced by nicotine was modulated in authentic JUUL aerosols, demonstrating the importance of studying mixtures and aerosols from actual EC products. These data support the idea that vaping increases the likelihood of contracting COVID-19.", + "rel_num_authors": 5, "rel_authors": [ { - "author_name": "Rui Chen", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Kelly M Fulton", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Anh Tran", - "author_inst": "National Reseach Council Canada" - }, - { - "author_name": "Diana Duque", - "author_inst": "National Research Council Canada" + "author_name": "Rattapol Phandthong", + "author_inst": "University of California, Riverside" }, { - "author_name": "Kevin Kovalchik", - "author_inst": "CHU Sainte-Justine Research Center" + "author_name": "Man Wong", + "author_inst": "University of California, Riverside" }, { - "author_name": "Etienne Caron", - "author_inst": "CHU Sainte-Justine Research Center" + "author_name": "Ann Song", + "author_inst": "University of California, Riverside" }, { - "author_name": "Susan M Twine", - "author_inst": "National Research Council Canada" + "author_name": "Teresa Martinez", + "author_inst": "University of California, Riverside" }, { - "author_name": "Jianjun Li", - "author_inst": "National Research Council Canada" + "author_name": "Prue Talbot", + "author_inst": "University of California, Riverside" } ], "version": "1", "license": "cc_by_nc_nd", "type": "new results", - "category": "immunology" + "category": "cell biology" }, { "rel_doi": "10.1101/2022.08.24.22279160", @@ -227058,61 +227125,45 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.08.19.22278876", - "rel_title": "Seroprevalence of anti-SARS-CoV-2 IgG antibodies in admitted patients at a tertiary referral centre in North India", + "rel_doi": "10.1101/2022.08.21.22279044", + "rel_title": "SARS-CoV-2 IgM and IgG serology and clinical outcomes in COVID-19 patients", "rel_date": "2022-08-22", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.19.22278876", - "rel_abs": "BackgroundSeroprevalence of IgG antibodies against SARS-CoV-2 is an important tool to estimate true burden of infection in a given population. Serosurveys, though being conducted in different parts of India, are not readily published in entirety and often do not report on the different characteristics of the population studied. In this present study, we aimed to serially estimate the seroprevalence of anti-SARS-CoV-2 IgG antibody over 11 months at one of the largest government hospital in India.\n\nMethodIn this cross-sectional study which was conducted between between 9th June 2020 and 27th April 2021, consecutive patients admitted to medicine wards or intensive care units, who were negative for SARS-CoV-2 by RT-PCR or CBNAAT were included. The 2linic-demographic features of the subjects were recorded in pre-formed questionnaires. Anti-SARS-CoV2 antibody levels targeting recombinant spike receptor-binding domain (RBD) protein of SARS CoV-2 were estimated in serum sample by the ELISA method.\n\nResultsA total of 916 patients were recruited over 11 months with mean age({+/-}SD) 39.79{+/-}14.9 of years and 55% of population being males. In total 264(28.8%) patients were found to be seropositive. Residency in Delhi and non-smoking status conferred a higher risk for seropositivity. The adjusted odds ratio for seropositivity with regards to no smoking and residence out of Delhi were .31{+/-}.09 (Odds ratio {+/-} S.E) and .65 {+/-} .1 (Odds ratio {+/-} S.E) respectively. No other factors like age, socio-economic status, contact history etc showed significant relationship with seropositivity.\n\nConclusionThe seropositivity rate among hospitalized patients was found to increase with time (from 8.45% to 38%) over a period of 9 months. Residence in Delhi and non-smokers had higher risk for seropositivity on multivariate analysis.", - "rel_num_authors": 12, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.21.22279044", + "rel_abs": "BackgroundThe SARS-CoV-2 virus has become pandemic for the last 2 years. Inflammatory response to the virus leads to organ dysfunction and death. Predicting the severity of inflammatory response helps in managing critical patients using serology tests IgG and IgM. We conducted a longitudinal study to correlate serum SARS-CoV-2 IgM and IgG serology with clinical outcomes in COVID-19 patients.\n\nMethodsWe analyzed patient data from March to December of 2020 for those who were admitted at AIIMS Rishikesh. Clinical and laboratory data of these patients were collected from the e-hospital portal and analysed. Correlation was seen with clinical outcomes and was assessed using MS Excel 2010 and SPSS software.\n\nResultsOut of 494 patients, the mean age of patients was 48.95 {+/-} 16.40 years and there were more male patients in the study (66.0%). The patients were classified into 4 groups; mild-moderate 328 (67.1%), severe 131 (26.8%) and critical 30 (6.1%). The mean duration from symptom onset to serology testing was 19.87 {+/-} 30.53 days. In-hospital mortality was observed in 25.1% patients. The seropositivity rate (i.e., either IgG or IgM >10 AU) was 50%. There was a significant difference between the 2 groups in terms of IgM Levels (AU/mL) (W = 33428.000, p = <0.001) and IgG Levels (AU/mL) (W = 39256.500, p = <0.001), with the median IgM/ IgG Levels (AU/mL) being highest in the RT-PCR-Positive group. There was no significant difference between the groups in terms of IgM Levels and IgG levels with all other clinical outcomes (disease severity, septic shock, Intensive care admission, mechanical ventilation and mortality).\n\nConclusionSerology (IgM and IgG) levels are high in RTPCR positive group compared to clinical COVID-19. However, serology cannot be useful for the prediction of disease outcomes except few situations. The study also highlights the importance of doing serology at a particular time as antibody titres vary with the duration of the disease.", + "rel_num_authors": 8, "rel_authors": [ { - "author_name": "Animesh Ray", - "author_inst": "All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Komal Singh", - "author_inst": "All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Farha Mehdi", - "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana" - }, - { - "author_name": "Souvick Chattopadhyay", - "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana" - }, - { - "author_name": "Ranveer Singh Jadon", - "author_inst": "All India Institute of Medical Sciences, New Delhi" + "author_name": "Mohan S", + "author_inst": "AIIMS Rishikesh" }, { - "author_name": "Neeraj Nischal", - "author_inst": "All India Institute of Medical Sciences, New Delhi" + "author_name": "Pratap Kumar", + "author_inst": "AIIMS Rishikesh" }, { - "author_name": "Manish Soneja", - "author_inst": "All India Institute of Medical Sciences, New Delhi" + "author_name": "Prasan Kumar Panda", + "author_inst": "AIIMS Rishikesh" }, { - "author_name": "Prayas Sethi", - "author_inst": "All India Institute of Medical Sciences, New Delhi" + "author_name": "Vikram Jain", + "author_inst": "AIIMS Rishikesh" }, { - "author_name": "Ved Prakash Meena", - "author_inst": "All India Institute of Medical Sciences, New Delhi" + "author_name": "Rohit Raina", + "author_inst": "AIIMS Rishikesh" }, { - "author_name": "Anjan Trikha", - "author_inst": "All India Institute of Medical Sciences, New Delhi" + "author_name": "Sarama Saha", + "author_inst": "AIIMS Rishikesh" }, { - "author_name": "Gaurav Batra", - "author_inst": "Translational Health Science and Technology Institute, Faridabad, Haryana" + "author_name": "Vivekandan S", + "author_inst": "AIIMS Rishikesh" }, { - "author_name": "Naveet Wig", - "author_inst": "All India Institute of Medical Sciences, New Delhi" + "author_name": "Balram J Omar", + "author_inst": "AIIMS Rishikesh" } ], "version": "1", @@ -228848,55 +228899,43 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.08.18.504268", - "rel_title": "A syntenin inhibitor blocks endosomal entry of SARS-CoV-2 and a panel of RNA viruses", + "rel_doi": "10.1101/2022.08.17.504362", + "rel_title": "Ancestral lineage of SARS-CoV-2 is more stable in human biological fluids than Alpha, Beta and Omicron variants of concern", "rel_date": "2022-08-19", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.18.504268", - "rel_abs": "Viruses are dependent on interactions with host factors in order to efficiently establish an infection and replicate. Targeting such interactions provides an attractive strategy to develop novel antivirals. Syntenin is a protein known to regulate the architecture of cellular membranes by its involvement in protein trafficking, and has previously been shown to be important for HPV infection. Here we show that a highly potent and metabolically stable peptide inhibitor that binds to the PDZ1 domain of syntenin inhibits SARS-CoV-2 infection by blocking the endosomal entry of the virus. Furthermore, we found that the inhibitor also hampered chikungunya infection, and strongly reduced flavivirus infection, which are completely dependent on receptor mediated endocytosis for their entry. In conclusion, we have identified a novel pan-viral inhibitor that efficiently target a broad range of RNA viruses.", - "rel_num_authors": 9, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.17.504362", + "rel_abs": "SARS-CoV-2 is a zoonotic virus which was first identified in 2019, and has quickly spread worldwide. The virus is primarily transmitted through respiratory droplets from infected persons; however, the virus-laden excretions can contaminate surfaces which can serve as a potential source of infection. Since the beginning of the pandemic, SARS-CoV-2 has continued to evolve and accumulate mutations throughout its genome leading to the emergence of variants of concern (VOCs) which exhibit increased fitness, transmissibility, and/or virulence. However, the stability of SARS-CoV-2 VOCs in biological fluids has not been thoroughly investigated so far. The aim of this study was to determine and compare the stability of different SARS-CoV-2 strains in human biological fluids. Here, we demonstrate that the ancestral strain of Wuhan-like lineage A was more stable than the Alpha VOC B.1.1.7, and the Beta VOC B.1.351 strains in human liquid nasal mucus and sputum. In contrast, there was no difference in stability among the three strains in dried biological fluids. Furthermore, we also show that the Omicron VOC B.1.1.529 strain was less stable than the ancestral Wuhan-like strain in liquid nasal mucus. These studies provide insight into the effect of the molecular evolution of SARS-CoV-2 on environmental virus stability, which is important information for the development of countermeasures against SARS-CoV-2.\n\nImportanceGenetic evolution of SARS-CoV-2 leads to the continuous emergence of novel variants, posing a significant concern to global public health. Five of these variants have been classified so far into variants of concern (VOCs); Alpha, Beta, Gamma, Delta, and Omicron. Previous studies investigated the stability of SARS-CoV-2 under various conditions, but there is a gap of knowledge on the survival of SARS-CoV-2 VOCs in human biological fluids which are clinically relevant. Here, we present evidence that Alpha, Beta, and Omicron VOCs were less stable than the ancestral Wuhan-like strain in human biological fluids. Our findings highlight the potential risk of contaminated human biological fluids in SARS-CoV-2 transmission and contribute to the development of countermeasures against SARS-CoV-2.", + "rel_num_authors": 6, "rel_authors": [ { - "author_name": "Richard Lindqvist", - "author_inst": "Umea University" - }, - { - "author_name": "Caroline Benz", - "author_inst": "Uppsala University" - }, - { - "author_name": "Vita Sereikaite", - "author_inst": "Copenhagen University" - }, - { - "author_name": "Lars Maassen", - "author_inst": "Uppsala University" + "author_name": "Taeyong Kwon", + "author_inst": "Kansas State University" }, { - "author_name": "Louise Laursen", - "author_inst": "Uppsala University" + "author_name": "Natasha N Gaudreault", + "author_inst": "Kansas State University" }, { - "author_name": "Per Jemth", - "author_inst": "Uppsala University" + "author_name": "David Meekins", + "author_inst": "Kansas State University" }, { - "author_name": "Kristian Stromgaard", - "author_inst": "University of Copenhagen" + "author_name": "Chester McDowell", + "author_inst": "Kansas State Univeristy" }, { - "author_name": "Ylva Ivarsson", - "author_inst": "Uppsala University" + "author_name": "Konner Cool", + "author_inst": "Kansas State University" }, { - "author_name": "Anna K Overby", - "author_inst": "Umea university" + "author_name": "Juergen A Richt", + "author_inst": "Kansas State University" } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc_by_nd", "type": "new results", - "category": "biochemistry" + "category": "microbiology" }, { "rel_doi": "10.1101/2022.08.17.504313", @@ -230526,49 +230565,77 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.08.12.22278567", - "rel_title": "Performance of the Cue COVID-19 Molecular Test for Point of Care: Insights from a multi-site clinic service model", + "rel_doi": "10.1101/2022.08.13.22278740", + "rel_title": "Demographic and Viral-Genetic Analyses of COVID-19 Severity in Bahrain Identify Local Risk Factors and a Protective Effect of Polymerase Mutations", "rel_date": "2022-08-16", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.12.22278567", - "rel_abs": "The COVID-19 pandemic highlighted the critical need for rapid and accurate molecular diagnostic testing. The Cue COVID-19 Point of Care Test (Cue POCT) is a nucleic acid amplification test (NAAT), authorized by Health Canada and FDA as a POCT for SARS-CoV-2 detection. Cue POCT was deployed at a network of clinics in Ontario, Canada with n=13,848 patrons tested between July 17, 2021 to January 31, 2022. The clinical performance and operational experience with Cue POCT was examined for this testing population composed mostly of asymptomatic individuals (93.7%). A head-to-head prospective clinical verification was performed between July 17 to October 4 for all POCT service clients (n= 3037) with paired COVID-19 testing by Cue and RT-PCR. Prospective verification demonstrated a clinical sensitivity of 100% and clinical specificity of 99.4% for Cue COVID-19 POCT. The lack of false negatives and low false positive rate (0.64%), underscores the high accuracy (99.4%) of Cue POCT to provide rapid PCR quality results. Low error rates (cancellation rate of 0% and invalid rate of 0.63%) with the current software version were additionally noted. Together these findings highlight the value of accurate molecular COVID-19 POCT in a distributed service delivery model to rapidly detect cases in the community with the potential to curb transmission in high exposure settings (i.e. in-flight, congregate workplace and social events). The insights gleaned from this operational implementation are readily transferable to future POCT diagnostic services.", - "rel_num_authors": 9, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.13.22278740", + "rel_abs": "A multitude of demographic, health, and genetic factors are associated with the risk of developing severe COVID-19 following infection by the SARS-CoV-2. There is a need to perform studies across human societies and to investigate the full spectrum of genetic variation of the virus. Using data from 869 COVID-19 patients in Bahrain between March 2020 and March 2021, we analyzed paired viral sequencing and non-genetic host data to understand host and viral determinants of severe COVID-19. We estimated the effects of demographic variables specific to the Bahrain population and found that the impact of health factors are largely consistent with other populations. To extend beyond the common variants of concern in the Spike protein analyzed by previous studies, we used a viral burden approach and detected a protective effect of low-frequency missense viral mutations in the RNA-dependent RNA polymerase (Pol) gene on disease severity. Our results contribute to the survey of severe COVID-19 in diverse populations and highlight the benefits of studying rare viral mutations.", + "rel_num_authors": 16, "rel_authors": [ { - "author_name": "Any Rebbapragada", - "author_inst": "FH Health" + "author_name": "Evan M Koch", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Justin Du", + "author_inst": "Yale University" + }, + { + "author_name": "Michelle Dressner", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Hashmeya Erahim Alwasti", + "author_inst": "Bahrain Ministry of Health" }, { - "author_name": "Lane Cariazo", - "author_inst": "FH Health" + "author_name": "Zahra Al Taif", + "author_inst": "Bahrain Ministry of Health" }, { - "author_name": "David Elchuk", - "author_inst": "FH Health" + "author_name": "Fatima Shehab", + "author_inst": "Bahrain Ministry of Health" }, { - "author_name": "Hossam Abdelrahman", - "author_inst": "FH Health" + "author_name": "Afaf Merza Mohamed", + "author_inst": "Bahrain Ministry of Health" }, { - "author_name": "Dang Pham", - "author_inst": "FH Health" + "author_name": "Amani Alhajeri", + "author_inst": "Salmaniya Medical Complex" }, { - "author_name": "Nirochile Joseph", - "author_inst": "FH Health" + "author_name": "Amna Alawadhi", + "author_inst": "Salmaniya Medical Complex" }, { - "author_name": "Elena Gouzenkova", - "author_inst": "FH Health" + "author_name": "Nabeel Almoamen", + "author_inst": "Salmaniya Medical Complex" }, { - "author_name": "Harpreet Gill", - "author_inst": "FH Health" + "author_name": "Khulood Ashoor", + "author_inst": "Salmaniya Medical Complex" + }, + { + "author_name": "Sara Hasan", + "author_inst": "Salmaniya Medical Complex" + }, + { + "author_name": "Amjad Ghanem", + "author_inst": "Bahrain Ministry of Health" + }, + { + "author_name": "Alireza Haghighi", + "author_inst": "Brigham and Womens Hospital" }, { - "author_name": "Peter Blecher", - "author_inst": "FH Health" + "author_name": "Shamil Sunyaev", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Maha Farhat", + "author_inst": "Harvard Medical School" } ], "version": "1", @@ -232384,43 +232451,175 @@ "category": "epidemiology" }, { - "rel_doi": "10.1101/2022.08.10.22278643", - "rel_title": "Open Science and COVID-19 Randomized Controlled Trials: Examining Open Access, Preprinting, and Data Sharing-Related Practices During the Pandemic", + "rel_doi": "10.1101/2022.08.08.22278550", + "rel_title": "Cohort Study Protocol of the Brazilian Collaborative Research Network on COVID-19: strengthening WHO global data", "rel_date": "2022-08-11", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.10.22278643", - "rel_abs": "The COVID-19 pandemic has brought substantial attention to the systems used to communicate biomedical research. In particular, the need to rapidly and credibly communicate research findings has led many stakeholders to encourage researchers to adopt open science practices such as posting preprints and sharing data. To examine the degree to which this has led to the adoption of such practices, we examined the \"openness\" of a sample of 539 published papers describing the results of randomized controlled trials testing interventions to prevent or treat COVID-19. The majority (56%) of the papers in this sample were free to read at the time of our investigation and 23.56% were preceded by preprints. However, there is no guarantee that the papers without an open license will be available without a subscription in the future, and only 49.61% of the preprints we identified were linked to the subsequent peer-reviewed version. Of the 331 papers in our sample with statements identifying if (and how) related datasets were available, only a paucity indicated that data was available in a repository that facilitates rapid verification and reuse. Our results demonstrate that, while progress has been made, there is still a significant mismatch between aspiration and the practice of open science in an important area of the COVID-19 literature.\n\nOpen MaterialsWe are committed to making the details of our research process as open as possible. The data and code that underlie our analyses are archived and published through the Dryad Data Repository (https://doi.org/10.5061/dryad.mkkwh7137). Documentation and instructions for manuscript screening and data extraction are available on Protocols.io (https://dx.doi.org/10.17504/protocols.io.x54v9jx7zg3e/v1). Author contributions are outlined in Supplementary Table 1.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@774764org.highwire.dtl.DTLVardef@f03612org.highwire.dtl.DTLVardef@6e16ccorg.highwire.dtl.DTLVardef@19ac3eborg.highwire.dtl.DTLVardef@1b47f40_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOSupplementary Table 1.C_FLOATNO O_TABLECAPTIONAuthor Information and Contributions\n\nC_TABLECAPTION C_TBL", - "rel_num_authors": 6, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.08.22278550", + "rel_abs": "IntroductionWith the COVID-19 pandemic, hospitals in low-income countries were faced with a triple challenge. First, a large number of patients required hospitalization because of the infections more severe symptoms. Second, there was a lack of systematic and broad testing policies for early identification of cases. Third, there were weaknesses in the integration of information systems, which led to the need to search for available information from the hospital information systems. Accordingly, it is also important to state that relevant aspects of COVID-19s natural history had not yet been fully clarified. The aim of this research protocol is to present the strategies of a Brazilian network of hospitals to perform systematized data collection on COVID-19 through the World Health Organization (WHO) Platform.\n\nMethods and AnalysisThis is a multicenter project among Brazilian hospitals to provide data on COVID-19 through the WHO global platform, which integrates patient care information from different countries. From October 2020 to March 2021, a committee worked on defining a flowchart for this platform, specifying the variables of interest, data extraction standardization and analysis.\n\nEthics and DisseminationThis protocol was approved by the Research Ethics Committee (CEP) of the Research Coordinating Center of Brazil (CEP of the Hospital Nossa Senhora da Conceicao), on January 29, 2021, under approval No. 4.515.519 and by the National Research Ethics Commission (CONEP), on February 5, 2021, under approval No. 4.526.456. The project results will be explained in WHO reports and published in international peer-reviewed journals, and summaries will be provided to the funders of the study.\n\nStrengths and limitations of this studyAs the study involves a convenience and non-probabilistic sample of patients hospitalized in health units, it may not represent the population of patients with COVID-19 hospitalized in the country. However, the information generated by this research can serve as a basis for the development of maps of the evolution of SARS-CoV-2 infection and public policies to face pandemics. It is a study that uses secondary data, and therefore, information bias may occur, but on the other hand, it has a low cost and facilitates a population-based study with national coverage.\n\nArticle SummaryThis is a multicenter project among Brazilian hospitals to provide data on COVID-19 through the WHO global platform.\n\nIt is expected to deepen knowledge about the pandemic scenario and help hospital institutions to develop preventive measures, health service protocols and strengthen the training of teams in the existing complications.", + "rel_num_authors": 39, "rel_authors": [ { - "author_name": "John A Borghi", - "author_inst": "Stanford University" + "author_name": "Fernando Anschau", + "author_inst": "Conceicao Hospitalar Group" }, { - "author_name": "Cheyenne Payne", - "author_inst": "Stanford University" + "author_name": "Natalia Del' Angelo Aredes", + "author_inst": "Universidade Federal de Goias, Nursing School Goiania, Goias, BR" }, { - "author_name": "Lily Ren", - "author_inst": "Stanford University" + "author_name": "Ludovic Reveiz", + "author_inst": "Pan American Health Organization, DC, USA" }, { - "author_name": "Amanda L Woodward", - "author_inst": "Stanford University" + "author_name": "Monica Padilla", + "author_inst": "Pan American Health Organization Brazil Brasilia, DF, BR" }, { - "author_name": "Connie Wong", - "author_inst": "Stanford University" + "author_name": "Rosane de Mendonca Gomes", + "author_inst": "Pan American Health Organization Brazil Brasilia, DF, BR" }, { - "author_name": "Christopher Stave", - "author_inst": "Stanford University" + "author_name": "Wellington Mendes Carvalho", + "author_inst": "Pan American Health Organization Brazil Brasilia, DF, BR" + }, + { + "author_name": "Fernando Antonio Gomes Leles", + "author_inst": "Pan American Health Organization Brazil Brasilia, DF, BR" + }, + { + "author_name": "Fernanda Baeumle Reese", + "author_inst": "Complexo Hospitalar do Trabalhador Curitiba, PR, BR" + }, + { + "author_name": "Andre Hostilio Hubert", + "author_inst": "Complexo Hospitalar do Trabalhador Curitiba, Parana, BR" + }, + { + "author_name": "Elisandrea Sguario Kemper", + "author_inst": "Hospital da Crianca de Brasilia Distrito Federal, BR" + }, + { + "author_name": "Renilson Rehem de Souza", + "author_inst": "Hospital da Crianca de Brasilia, Distrito Federal, BR" + }, + { + "author_name": "Cristiane Feitosa Salviano", + "author_inst": "Hospital da Crianca de Brasilia, DF, BR" + }, + { + "author_name": "Hevelin Silveira e Silva", + "author_inst": "Hospital da Crianca de Brasilia, DF, BR" + }, + { + "author_name": "Eduardo Barbosa Coelho", + "author_inst": "Brazilian Company of Hospital Services Belo Horizonte, Minas Gerais, BR" + }, + { + "author_name": "Giuseppe Cesare Gatto", + "author_inst": "Brazilian Company of Hospital Services Belo Horizonte, Minas Gerais, BR" + }, + { + "author_name": "Rafael Freitas de Morais", + "author_inst": "Brazilian Company of Hospital Services Brasilia, Distrito Federal, BR" + }, + { + "author_name": "Leonardo Nunes Alegre", + "author_inst": "Brazilian Company of Hospital Services Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Rodrigo Citton Padilha dos Reis", + "author_inst": "Universidade Federal do Rio Grande do Sul, Graduate Program in Epidemiology Porto Alegre, RS, BR" + }, + { + "author_name": "Joaquim Francisco dos Santos Neto", + "author_inst": "Universidade Federal do Rio Grande do Sul, Graduate Program in Epidemiology Porto Alegre, RS, BR" + }, + { + "author_name": "Cesar Perdomo Purper", + "author_inst": "Grupo Hospitalar Conceicao, Gerencia de Ensino e Pesquisa Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Veridian Baldon dos Santos", + "author_inst": "Grupo Hospitalar Conceicao, Rio Grande do Sul, BR" + }, + { + "author_name": "Andressa Fontoura Garbini", + "author_inst": "Grupo Hospitalar Conceicao, Rio Grande do Sul, BR" + }, + { + "author_name": "Rafaela dos Santos Charao de Almeida,", + "author_inst": "Grupo Hospitalar Conceicao, Rio Grande do Sul, BR" + }, + { + "author_name": "Bruna Donida", + "author_inst": "Grupo Hospitalar Conceicao, Rio Grande do Sul, BR" + }, + { + "author_name": "Rogerio Farias Bitencourt", + "author_inst": "Grupo Hospitalar Conceicao, Gerencia de Ensino e Pesquisa Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Luciane Kopittke", + "author_inst": "Grupo Hospitalar Conceicao, Gerencia de Ensino e Pesquisa Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Fernanda Costa dos Santos", + "author_inst": "Grupo Hospitalar Conceicao Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Raquel Lutkmeier", + "author_inst": "Grupo Hospitalar Conceicao Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Daniela dos Reis Carazai", + "author_inst": "Grupo Hospitalar Conceicao Porto Alegre, Rio Grande do Sul, BR" + }, + { + "author_name": "Virginia Angelica Silveira Reis", + "author_inst": "Instituto de Saude e Gestao Hospitalar Fortaleza, CE, BR" + }, + { + "author_name": "Flavio Clemente Deulefeu,", + "author_inst": "Instituto de Saude e Gestao Hospitalar Fortaleza, CE, BR" + }, + { + "author_name": "Fernanda Gadelha Severino", + "author_inst": "Instituto de Saude e Gestao Hospitalar Fortaleza, CE, BR" + }, + { + "author_name": "Jose Gustavo da Costa Neto", + "author_inst": "Instituto de Saude e Gestao Hospitalar Fortaleza, CE, BR" + }, + { + "author_name": "Nirvania do Vale Carvalho", + "author_inst": "Health Department of the State of Piaui, Hospital Getulio Vargas Teresina, Piaui, BR" + }, + { + "author_name": "Andre Jamson Rocha de Andrade", + "author_inst": "Health Department of the State of Piaui, Hospital Getulio Vargas Teresina, Piaui, BR" + }, + { + "author_name": "Adriana Melo Teixeira", + "author_inst": "Brazilian Ministry of Health, Department of Hospital, Home, and Emergency Care (DAHU) of the Specialized Health Care Office (SAES) Brasilia, Distrito Federal, B" + }, + { + "author_name": "Olavo Braga Neto", + "author_inst": "Brazilian Ministry of Health, Department of Hospital, Home, and Emergency Care (DAHU) of the Specialized Health Care Office (SAES) Brasilia, Distrito Federal, B" + }, + { + "author_name": "Gabriel Cardozo Muller", + "author_inst": "Universidade Federal do Rio Grande do Sul, Graduate Program in Epidemiology Porto Alegre, RS, BR" + }, + { + "author_name": "Ricardo de Souza Kuchenbecker", + "author_inst": "Universidade Federal do Rio Grande do Sul, Graduate Program in Epidemiology Porto Alegre, RS, BR" } ], "version": "1", - "license": "cc_by", + "license": "cc_no", "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" + "category": "epidemiology" }, { "rel_doi": "10.1101/2022.08.05.22278487", @@ -234714,101 +234913,49 @@ "category": "pharmacology and toxicology" }, { - "rel_doi": "10.1101/2022.08.08.503239", - "rel_title": "A replicon RNA vaccine induces durable protective immunity from SARS-CoV-2 in nonhuman primates after neutralizing antibodies have waned", + "rel_doi": "10.1101/2022.08.08.503231", + "rel_title": "Vitamin B12 attenuates leukocyte inflammatory signature in COVID-19 via methyl-dependent changes in epigenetic marks", "rel_date": "2022-08-09", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.08.503239", - "rel_abs": "The global SARS-CoV-2 pandemic prompted rapid development of COVID-19 vaccines. Although several vaccines have received emergency approval through various public health agencies, the SARS-CoV-2 pandemic continues. Emergent variants of concern, waning immunity in the vaccinated, evidence that vaccines may not prevent transmission and inequity in vaccine distribution have driven continued development of vaccines against SARS-CoV-2 to address these public health needs. In this report, we evaluated a novel self-amplifying replicon RNA vaccine against SARS-CoV-2 in a pigtail macaque model of COVID-19 disease. We found that this vaccine elicited strong binding and neutralizing antibody responses. While binding antibody responses were sustained, neutralizing antibody waned to undetectable levels after six months but were rapidly recalled and conferred protection from disease when the animals were challenged 7 months after vaccination as evident by reduced viral replication and pathology in the lower respiratory tract, reduced viral shedding in the nasal cavity and lower concentrations of pro-inflammatory cytokines in the lung. Cumulatively, our data demonstrate in pigtail macaques that a self-amplifying replicon RNA vaccine can elicit durable and protective immunity to SARS-CoV-2 infection. Furthermore, these data provide evidence that this vaccine can provide durable protective efficacy and reduce viral shedding even after neutralizing antibody responses have waned to undetectable levels.", - "rel_num_authors": 21, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.08.503231", + "rel_abs": "COVID-19 induces chromatin remodeling in host immune cells, and it had previously been shown that vitamin B12 downregulates some inflammatory genes via methyl-dependent epigenetic mechanisms. In this work, whole blood cultures from moderate or severe COVID-19 patients were used to assess the potential of B12 as adjuvant drug. The vitamin normalized the expression of a panel of inflammatory genes still dysregulated in the leukocytes despite glucocorticoid therapy during hospitalization. B12 also increased the flux of the sulfur amino acid pathway, raising the bioavailability of methyl. Accordingly, B12-induced downregulation of CCL3 strongly and negatively correlated with the hypermethylation of CpGs in its regulatory regions. Transcriptome analysis revealed that B12 attenuates the effects of COVID-19 on most inflammation-related pathways affected by the disease. As far as we are aware, this is the first study to demonstrate that pharmacological modulation of epigenetic marks in leukocytes favorably regulates central components of COVID-19 physiopathology.\n\nTeaserB12 has great potential as an adjuvant drug for alleviating inflammation in COVID-19.", + "rel_num_authors": 8, "rel_authors": [ { - "author_name": "David W. Hawman", - "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain La" - }, - { - "author_name": "Kimberly Meade-White", - "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain La" - }, - { - "author_name": "Shanna Leventhal", - "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain La" - }, - { - "author_name": "Wenjun Song", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center (Seattle, Washington)" - }, - { - "author_name": "Samantha Randall", - "author_inst": "HDT Bio (1616 Eastlake Ave E #280, Seattle, Washington)" - }, - { - "author_name": "Jacob Archer", - "author_inst": "HDT Bio (1616 Eastlake Ave E #280, Seattle, Washington)" - }, - { - "author_name": "Thomas B. Lewis", - "author_inst": "Department of Microbiology, University of Washington (750 Republican St., Seattle, Washington)" - }, - { - "author_name": "Brieann Brown", - "author_inst": "Department of Microbiology, University of Washington (750 Republican St., Seattle, Washington)" - }, - { - "author_name": "Naoto Iwayama", - "author_inst": "Washington National Primate Research Center, University of Washington (1705 NE Pacific Street, Seattle, Washington)" - }, - { - "author_name": "Chul Ahrens", - "author_inst": "Washington National Primate Research Center, University of Washington (1705 NE Pacific Street, Seattle, Washington)" - }, - { - "author_name": "William Garrison", - "author_inst": "Washington National Primate Research Center, University of Washington (1705 NE Pacific Street, Seattle, Washington)" - }, - { - "author_name": "Solomon Wangari", - "author_inst": "Washington National Primate Research Center, University of Washington (1705 NE Pacific Street, Seattle, Washington)" - }, - { - "author_name": "Kathryn A. Guerriero", - "author_inst": "Washington National Primate Research Center, University of Washington (1705 NE Pacific Street, Seattle, Washington)" - }, - { - "author_name": "Patrick Hanley", - "author_inst": "Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky M" + "author_name": "Vanessa C Silva", + "author_inst": "Universidade Federal de Sao Paulo" }, { - "author_name": "Jamie Lovaglio", - "author_inst": "Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky M" + "author_name": "Marina S Oliveira", + "author_inst": "FIOCRUZ" }, { - "author_name": "Greg Saturday", - "author_inst": "Rocky Mountain Veterinary Branch, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky M" + "author_name": "Barbara V O Prado", + "author_inst": "Hospital Metropolitano Dr. Celio de Castro" }, { - "author_name": "Paul T. Edlefsen", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center (Seattle, Washington)" + "author_name": "Cristianne G Cardoso", + "author_inst": "Hospital Metropolitano Dr. Celio de Castro" }, { - "author_name": "Amit Khandhar", - "author_inst": "HDT Bio (1616 Eastlake Ave E #280, Seattle, Washington)" + "author_name": "Anna C M Salim", + "author_inst": "FIOCRUZ" }, { - "author_name": "Heinz Feldmann", - "author_inst": "Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain La" + "author_name": "Gloria R Franco", + "author_inst": "Universidade Federal de Minas Gerais" }, { - "author_name": "Deborah Heydenburg Fuller", - "author_inst": "Department of Microbiology, University of Washington (750 Republican St., Seattle, Washington)" + "author_name": "Saionara C Francisco", + "author_inst": "Hospital Metropolitano Dr. Celio de Castro" }, { - "author_name": "Jesse H. Erasmus", - "author_inst": "HDT Bio (1616 Eastlake Ave E #280, Seattle, Washington)" + "author_name": "Roney S Coimbra", + "author_inst": "FIOCRUZ" } ], "version": "1", - "license": "cc_no", + "license": "cc_by", "type": "new results", "category": "immunology" }, @@ -236736,35 +236883,67 @@ "category": "biophysics" }, { - "rel_doi": "10.1101/2022.08.04.22278404", - "rel_title": "A Plagiarism Paperdemic - Plagiarism in infection journals in the era of COVID-19", + "rel_doi": "10.1101/2022.08.06.22278449", + "rel_title": "Severity Predictors of COVID-19 in SARS-CoV-2 Variant, Delta and Omicron Period; Single Center Study", "rel_date": "2022-08-08", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.04.22278404", - "rel_abs": "BackgroundThe COVID-19 pandemic has caused drastic changes in the publishing framework in order to quickly review and publish vital information during this public health emergency. The quality of the academic work being published may have been compromised. One area of concern is plagiarism, where the work of others is directly copied and represented as ones own. The purpose of this study is to determine the presence of plagiarism in infection journals in papers relating to the COVID-19 pandemic.\n\nMethodsConsecutively occurring original research or reviews relating to the COVID-19 pandemic, published in infection journals as ranked by SCOPUS Journal finder were collected. Each manuscript was optimized and uploaded to the Turnitin program. Similarity reports were then manually checked for true plagiarism within the text, where any sentence with more than 80% copying was deemed plagiarised.\n\nResultsA total of 310 papers were analyzed in this cross-sectional study. Papers from a total of 23 journals among 4 quartiles were examined. Of the papers we examined, 41.6% were deemed plagiarised (n=129). Among the plagiarised papers, the average number of copied sentences was 5.42{+/-}9.18. The highest recorded similarity report was 60%, and the highest number of copied sentences was 85. Plagiarism was higher in papers published in the year 2020. The most problematic area in the manuscripts was the discussion section. Self plagiarism was identified in 31 papers. Average time to judge all manuscripts was 2.45{+/-}3.09. Among all the plagiarized papers 72% belonged to papers where the similarity report was [≤]15% (n=93). Papers published from core anglosphere speaking countries were not associated with higher rates of plagiarism. No significant differences were found with regards to plagiarism events among the quartiles.\n\nConclusionPlagiarism is prevalent in COVID19 related publications in infection journals among various quartiles. It is not enough to rely only on similarity reports. Such reports must be accompanied by manual curation of the results with an appropriate threshold to be able to appropriately determine if plagiarism is occurring. The majority of plagiarism is occurring in reports of less than 15% similarity, and this is a blind spot. Incorporating a manual judge could save future time in avoiding retractions and improving the quality of papers in these journals.\n\n\"A poor original is better than a good imitation.\"\n\n-- Ella Wheeler Wilcox", - "rel_num_authors": 4, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.06.22278449", + "rel_abs": "BackgroundThe outcomes of coronavirus disease 2019 (COVID-19) treatment have improved due to vaccination and the establishment of better treatment regimens. However, the emergence of variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes COVID-19, and the corresponding changes in the characteristics of the disease present new challenges in patient management. This study aimed to analyze predictors of COVID-19 severity caused by the delta and omicron variants of SARS-CoV-2.\n\nMethodsWe retrospectively analyzed the data of patients who were admitted for COVID-19 at Yokohama City University Hospital from August 2021 to March 2022.\n\nResultsA total of 141 patients were included in this study. Of these, 91 had moderate COVID-19, whereas 50 had severe COVID-19. There were significant differences in sex, vaccination status, dyspnea, sore throat symptoms, and body mass index (BMI) (p <0.0001, p <0.001, p <0.001, p=0.02, p< 0.0001, respectively) between the moderate and severe COVID-19 groups. Regarding comorbidities, smoking habit and renal dysfunction were significantly different between the two groups (p=0.007 and p=0.01, respectively). Regarding laboratory data, only LDH level on the first day of hospitalization was significantly different between the two groups (p<0.001). Multiple logistic regression analysis revealed that time from the onset of COVID-19 to hospitalization, BMI, smoking habit, and LDH level were significantly different between the two groups (p<0.03, p=0.039, p=0.008, p<0.001, respectively). The cut-off value for the time from onset of COVID-19 to hospitalization was four days (sensitivity, 0.73; specificity, 0.70).\n\nConclusionsTime from the onset of COVID-19 to hospitalization is the most important factor in the prevention of the aggravation of COVID-19 caused by the delta and omicron SARS-CoV-2 variants. Appropriate medical management within four days after the onset of COVID-19 is essential for preventing the progression of COVID-19, especially in patients with smoking habits.", + "rel_num_authors": 12, "rel_authors": [ { - "author_name": "Rahma Menshawey", - "author_inst": "Cairo University Kasr al Ainy Faculty of Medicine" + "author_name": "Fumihiro Ogawa", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Yasufumi Oi", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Hiroshi Honzawa", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Naho Misawa", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" }, { - "author_name": "Esraa Menshawey", - "author_inst": "Cairo University Kasr Al Ainy School of Medicine" + "author_name": "Tomoaki Takeda", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" }, { - "author_name": "Ahmed Mitkees", - "author_inst": "Cairo University Kasr al Ainy Faculty of Medicine" + "author_name": "Yushi Kikuchi", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" }, { - "author_name": "Bilal A Mahamud", - "author_inst": "Cairo University Kasr al Ainy Faculty of Medicine" + "author_name": "Ryosuke Fukui", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Katsushi Tanaka", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Daiki Kano", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Hideaki Kato", + "author_inst": "Yokohama City University Hospital, Infection prevention and control department" + }, + { + "author_name": "Takeru Abe", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" + }, + { + "author_name": "Ichiro Takeuchi", + "author_inst": "Yokohama City University Hospital: Yokohama Shiritsu Daigaku Fuzoku Byoin" } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc_by", "type": "PUBLISHAHEADOFPRINT", - "category": "medical ethics" + "category": "infectious diseases" }, { "rel_doi": "10.1101/2022.08.07.499047", @@ -238958,59 +239137,91 @@ "category": "epidemiology" }, { - "rel_doi": "10.1101/2022.08.03.22278392", - "rel_title": "Association of mortality and aspirin use for COVID-19 residents at VA Community Living Center Nursing Homes", + "rel_doi": "10.1101/2022.08.03.22278363", + "rel_title": "Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is common in post-acute sequelae of SARS-CoV-2 infection (PASC): Results from a post-COVID-19 multidisciplinary clinic.", "rel_date": "2022-08-04", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.03.22278392", - "rel_abs": "Background/ObjectivesCoronavirus disease 2019 (COVID-19) is associated with a hypercoagulable state and increased thrombotic risk in infected individuals. Several complex and varied coagulation abnormalities were proposed for this association1. Acetylsalicylic acid(ASA, aspirin) is known to have inflammatory, antithrombotic properties and its use was reported as having potency to reduce RNA synthesis and replication of some types of coronaviruses including human coronavirus-299E (CoV-229E) and Middle East Respiratory Syndrome (MERS)-CoV 2,3. We hypothesized that chronic low dose aspirin use may decrease COVID-19 mortality relative to ASA non-users.\n\nMethodsThis is a retrospective, observational cohort analysis of residents residing at Veterans Affairs Community Living Centers from December 13, 2020, to September 18, 2021, with a positive SARS-CoV-2 PCR test. Low dose aspirin users had low dose (81mg) therapy (10 of 14 days) prior to the positive COVID date and were compared to aspirin non-users (no ASA in prior 14 days). The primary outcome was mortality at 30 and 56 days post positive test and hospitalization.\n\nResultsWe identified 1.823 residents who had SARS-CoV-2 infection and 1,687 residents were eligible for the study. Aspirin use was independently associated with a reduced risk of 30 days of mortality (adjusted HR, 0.60, 95% CI, 0.40-0.90) and 56 days of mortality (adjusted HR, 0.67, 95% CI, 0.47-0.95)\n\nConclusionChronic low dose aspirin use for primary or secondary prevention of cardiovascular events is associated with lower COVID-19 mortality. Although additional randomized controlled trials are required to understand these associations and the potential implications more fully for improving care, aspirin remains a medication with known side effects and clinical practice should not change based on these findings.", - "rel_num_authors": 10, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.03.22278363", + "rel_abs": "BackgroundThe global prevalence of PASC is estimated to be present in 0{middle dot}43 and based on the WHO estimation of 470 million worldwide COVID-19 infections, corresponds to around 200 million people experiencing long COVID symptoms. Despite this, its clinical features are not well defined.\n\nMethodsWe collected retrospective data from 140 patients with PASC in a post-COVID-19 clinic on demographics, risk factors, illness severity (graded as one-mild to five-severe), functional status, and 29 symptoms and principal component symptoms cluster analysis. The Institute of Medicine (IOM) 2015 criteria were used to determine the ME/CFS phenotype.\n\nFindingsThe median age was 47 years, 59{middle dot}0% were female; 49{middle dot}3% White, 17{middle dot}2% Hispanic, 14{middle dot}9% Asian, and 6{middle dot}7% Black. Only 12{middle dot}7% required hospitalization. Seventy-two (53{middle dot}5%) patients had no known comorbid conditions. Forty-five (33{middle dot}9%) were significantly debilitated. The median duration of symptoms was 285{middle dot}5 days, and the number of symptoms was 12. The most common symptoms were fatigue (86{middle dot}5%), post-exertional malaise (82{middle dot}8%), brain fog (81{middle dot}2%), unrefreshing sleep (76{middle dot}7%), and lethargy (74{middle dot}6%). Forty-three percent fit the criteria for ME/CFS.\n\nInterpretationsMost PASC patients evaluated at our clinic had no comorbid condition and were not hospitalized for acute COVID-19. One-third of patients experienced a severe decline in their functional status. About 43% had the ME/CFS subtype.\n\nFundingThe study did not received funding.", + "rel_num_authors": 18, "rel_authors": [ { - "author_name": "Yasin Abul", - "author_inst": "Center of Innovation in Long Term Services and Supports, Providence VA Medical Center, Providence, RI and Division of Geriatric and Palliative Medicine, Warren " + "author_name": "Hector Bonilla", + "author_inst": "Stanford University" }, { - "author_name": "Frank Devone", - "author_inst": "Center of Innovation in Long Term Services and Supports, Providence VA Medical Center, Providence, RI" + "author_name": "Tom Quach", + "author_inst": "Stanford University" }, { - "author_name": "Thomas Bayer", - "author_inst": "Center of Innovation in Long Term Services and Supports, Providence VA Medical Center, Providence, RI" + "author_name": "Anushri Tiwari", + "author_inst": "Stanford University" }, { - "author_name": "Christopher Halladay", - "author_inst": "Center of Innovation in Long Term Services and Supports, Providence VA Medical Center, Providence, RI" + "author_name": "Andres Bonilla", + "author_inst": "University of Michigan" }, { - "author_name": "Kevin McConeghy", - "author_inst": "Center of Innovation in Long Term Services and Supports, Providence VA Medical Center, Providence, RI" + "author_name": "Mitchell G Miglis", + "author_inst": "Stanford University" }, { - "author_name": "Nadia Mujahid", - "author_inst": "Division of Geriatric and Palliative Medicine, Warren Alpert Medical School of Brown University, Providence, RI" + "author_name": "Phillip Yang", + "author_inst": "Stanford University" }, { - "author_name": "Mriganka Singh", - "author_inst": "Division of Geriatric and Palliative Medicine, Warren Alpert Medical School of Brown University, Providence, RI" + "author_name": "Lauren Eggert", + "author_inst": "Stanford University" }, { - "author_name": "Ciera Leeder", - "author_inst": "Division of Geriatric and Palliative Medicine, Warren Alpert Medical School of Brown University, Providence, RI" + "author_name": "Husham Sharifi", + "author_inst": "Stanford University" }, { - "author_name": "Stefan Gravenstein", - "author_inst": "Center of Innovation in Long Term Services and Supports, Providence VA Medical Center, Providence, RI and Division of Geriatric and Palliative Medicine, Warren " + "author_name": "Audra Horomanski", + "author_inst": "Stanford University" }, { - "author_name": "James L Rudolph", - "author_inst": "Center of Innovation in Long Term Services and Supports, Providence VA Medical Center, Providence, RI and Division of Geriatric and Palliative Medicine, Warren " + "author_name": "Aruna K Subramanian", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Liza Smirnoff", + "author_inst": "Stanford University" + }, + { + "author_name": "Norah Simpson", + "author_inst": "Stanford University" + }, + { + "author_name": "Houssam Halawi", + "author_inst": "Stanford University" + }, + { + "author_name": "Oliver Sum-Ping", + "author_inst": "Stanford University" + }, + { + "author_name": "Agnieszka Kalinowski", + "author_inst": "Stanford University" + }, + { + "author_name": "Zara Patel", + "author_inst": "Stanford University" + }, + { + "author_name": "Robert William Shafer", + "author_inst": "Stanford University" + }, + { + "author_name": "Linda Geng", + "author_inst": "Stanford University" } ], "version": "1", "license": "cc_no", "type": "PUBLISHAHEADOFPRINT", - "category": "geriatric medicine" + "category": "infectious diseases" }, { "rel_doi": "10.1101/2022.08.03.22278386", @@ -240596,97 +240807,117 @@ "category": "primary care research" }, { - "rel_doi": "10.1101/2022.08.01.502390", - "rel_title": "SARS-CoV-2 Omicron BA.1 and BA.2 are attenuated in rhesus macaques as compared to Delta", + "rel_doi": "10.1101/2022.08.02.502439", + "rel_title": "Serological surveillance for wild rodent infection with SARS-CoV-2 in Europe", "rel_date": "2022-08-02", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.01.502390", - "rel_abs": "Since the emergence of SARS-CoV-2, five different variants of concern (VOCs) have been identified: Alpha, Beta, Gamma, Delta, and Omicron. Due to confounding factors in the human population, such as pre-existing immunity, comparing severity of disease caused by different VOCs is challenging. Here, we investigate disease progression in the rhesus macaque model upon inoculation with the Delta, Omicron BA.1, and Omicron BA.2 VOCs. Disease severity in rhesus macaques inoculated with Omicron BA.1 or BA.2 was lower than those inoculated with Delta and resulted in significantly lower viral loads in nasal swabs, bronchial cytology brush samples, and lung tissue in rhesus macaques. Cytokines and chemokines were upregulated in nasosorption samples of Delta animals compared to Omicron BA.1 and BA.2 animals. Overall, these data suggests that in rhesus macaques, Omicron replicates to lower levels than the Delta VOC, resulting in reduced clinical disease.", - "rel_num_authors": 21, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.02.502439", + "rel_abs": "We report serological surveillance for exposure to SARS-CoV-2 in 1,237 wild rodents and other small mammals across Europe. All samples were negative with the possible exception of one. Given the ongoing circulation of this virus in humans and potential host jumps, we suggest such surveillance be continued.", + "rel_num_authors": 26, "rel_authors": [ { - "author_name": "Neeltje van Doremalen", - "author_inst": "NIH" + "author_name": "Vincent Bourret", + "author_inst": "University of Helsinki, INRAE" }, { - "author_name": "Manmeet Singh", - "author_inst": "NIH" + "author_name": "Lara Dutra", + "author_inst": "University of Helsinki" }, { - "author_name": "Taylor Saturday", - "author_inst": "NIH" + "author_name": "Hussein Alburkat", + "author_inst": "University of Helsinki" }, { - "author_name": "Kwe Claude Yinda", - "author_inst": "NIH" + "author_name": "Sanna Maki", + "author_inst": "University of Helsinki" }, { - "author_name": "Lizzette Perez-Perez", - "author_inst": "NIH" + "author_name": "Ella Lintunen", + "author_inst": "University of Helsinki" }, { - "author_name": "W. Forrest Bohler", - "author_inst": "NIH" + "author_name": "Marine Wasniewski", + "author_inst": "ANSES" }, { - "author_name": "Zack Weishampel", - "author_inst": "NIH" + "author_name": "Ravi Kant", + "author_inst": "University of Helsinki" }, { - "author_name": "Matthew Lewis", - "author_inst": "NIH" + "author_name": "Maciej Grzybek", + "author_inst": "Medical University of Gdansk" }, { - "author_name": "Jonathan Schulz", - "author_inst": "NIH" + "author_name": "Vinaya Venkat", + "author_inst": "University of Helsinki" }, { - "author_name": "Brandi Williamson", - "author_inst": "NIH" + "author_name": "Hayder Asad", + "author_inst": "University of Helsinki" }, { - "author_name": "Kimberly Meade-White", - "author_inst": "NIAID/NIH" + "author_name": "Julien Pradel", + "author_inst": "INRAE" }, { - "author_name": "Shane Gallogly", - "author_inst": "NIH" + "author_name": "Marie Bouilloud", + "author_inst": "IRD" }, { - "author_name": "Atsushi Okumura", - "author_inst": "NIAID/NIH" + "author_name": "Herwig Leirs", + "author_inst": "University of Antwerp" }, { - "author_name": "Friederike Feldmann", - "author_inst": "NIAID/NIH" + "author_name": "Valeria Carolina Colombo", + "author_inst": "University of Antwerp, CONICET" }, { - "author_name": "Jamie Lovaglio", - "author_inst": "National Institute of Allergy and Infectious Diseases" + "author_name": "Vincent Sluydts", + "author_inst": "University of Antwerp" }, { - "author_name": "Patrick Hanley", - "author_inst": "National Institute of Allergy and Infectious Diseases" + "author_name": "Peter Stuart", + "author_inst": "Munster Technological University" }, { - "author_name": "Carl Shaia", - "author_inst": "NIAID/NIH" + "author_name": "Andrew McManus", + "author_inst": "Munster Technological University" }, { - "author_name": "Heinz Feldmann", - "author_inst": "NIAID, NIH" + "author_name": "Jana A. Eccard", + "author_inst": "University of Potsdam" }, { - "author_name": "Emmie de Wit", - "author_inst": "NIAID, NIH" + "author_name": "Jasmin Firozpoor", + "author_inst": "University of Potsdam" }, { - "author_name": "Vincent Munster", - "author_inst": "NIAID" + "author_name": "Christian Imholt", + "author_inst": "Julius Kuhn Institute" }, { - "author_name": "Kyle Rosenke", - "author_inst": "NIAID" + "author_name": "Joanna Nowicka", + "author_inst": "Medical University of Gdansk" + }, + { + "author_name": "Aleksander Goll", + "author_inst": "Medical University of Gdansk" + }, + { + "author_name": "Nathan Ranc", + "author_inst": "INRAE" + }, + { + "author_name": "Guillaume Castel", + "author_inst": "INRAE" + }, + { + "author_name": "Nathalie Charbonnel", + "author_inst": "INRAE" + }, + { + "author_name": "Tarja Sironen", + "author_inst": "University of Helsinki" } ], "version": "1", @@ -242474,39 +242705,71 @@ "category": "health policy" }, { - "rel_doi": "10.1101/2022.07.30.22278240", - "rel_title": "Modelling the role of quarantine escapees on COVID-19 dynamics", + "rel_doi": "10.1101/2022.07.30.22278213", + "rel_title": "Higher Perceived Stress during the COVID-19 pandemic increased Menstrual Dysregulation and Menopause Symptoms", "rel_date": "2022-07-31", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.30.22278240", - "rel_abs": "The recent outbreak of the novel coronavirus (COVID-19) pandemic which originated from the Wuhan City of China has devastated many parts of the globe. At present, non-pharmaceutical interventions are the widely available measures being used in combating and controlling this disease. There is great concern over the rampant unaccounted cases of individuals skipping the border during this critical period in time. We develop a deterministic compartmental model to investigate the impact of escapees on the transmission dynamics of COVID-19 in Zimbabwe. A suitable Lyapunov function has been used to show that the disease-free equilibrium is globally asymptotically stable provided [R]0 < 1. We performed global sensitivity analysis using the Latin-hyper cube sampling method and partial rank correlation coefficients to determine the most influential model parameters on the short and long term dynamics of the pandemic, so as to minimize uncertainties associated with our variables and parameters. Results confirm that there is a positive correlation between the number of escapees and the reported number of COVID-19 cases. It is shown that escapees are largely responsible for the rapid increase in local transmissions. Also, the results from sensitivity analysis show that an increase in the governmental role actions and a reduction in immigration rate will help to control and contain the disease spread.", - "rel_num_authors": 5, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.30.22278213", + "rel_abs": "ObjectiveThe increased stress the globe has experienced with the COVID-19 pandemic has affected mental health, disproportionately affecting women. However, how perceived stress in the first year affected menstrual and menopausal symptoms has not yet been investigated.\n\nMethodsResidents in British Columbia, Canada, were surveyed online as part of the COVID-19 Rapid Evidence Study of a Provincial Population-Based Cohort for Gender and Sex (RESPPONSE). A subgroup (n=4171) who were assigned female sex at birth (age 25-69) and were surveyed within the first 6-12 months of the pandemic (August 2020-February 2021), prior to the widespread rollout of vaccines, were retrospectively asked if they noticed changes in their menstrual or menopausal symptoms, as well as completing validated measures of stress, depression, and anxiety.\n\nResultsWe found that 27.8% reported menstrual cycle disturbances and 6.7% reported increased menopause symptoms. Those who scored higher on perceived stress, depression, and anxiety scales were more likely to have reproductive cycle disturbances. Free text responses revealed that reasons for disturbances were perceived to be related to the pandemic.\n\nConclusionsThe COVID-19 pandemic has highlighted the need to research womens health issues, such as menstruation. Our data indicates that in the first year of the pandemic, almost a third of the menstruating population reported disturbances in their cycle, which is approximately two times higher than in non-pandemic situations and four times higher than any reported changes in menopausal symptoms across that first year of the pandemic.\n\nSummary SentencesWomen+ with higher anxiety, depression or perceived stress scores during the first year of the pandemic were more likely to have experienced menstrual cycle phase disturbance or menopausal status disruption. Younger women were particularly prone to disturbances in their reproductive cycles.", + "rel_num_authors": 13, "rel_authors": [ { - "author_name": "Josaih Mushanyu", - "author_inst": "University of Zimbabwe" + "author_name": "Romina Garcia de Leon", + "author_inst": "University of British Columbia" }, { - "author_name": "Chinwendu Emilian Madubueze", - "author_inst": "University of Agriculture, Makurdi" + "author_name": "Alexandra Baaske", + "author_inst": "Women's Health Research Institute" }, { - "author_name": "Zviiteyi Chazuka", - "author_inst": "Department of Mathematics and Applied Mathematics, University of Johannesburg, Auckland Park 2006, South Africa" + "author_name": "Arianne Albert", + "author_inst": "Women's Health Research Institute" }, { - "author_name": "Williams Chukwu", - "author_inst": "University of Johannesburg" + "author_name": "Amy Booth", + "author_inst": "University of British Columbia" }, { - "author_name": "Chisara Ogbogbo", - "author_inst": "Department of Mathematics, University of Ghana, Ghana" + "author_name": "C. Sarai Racey", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Shanlea Gordon", + "author_inst": "Womens Health Research Institute" + }, + { + "author_name": "Laurie Smith", + "author_inst": "BC Cancer" + }, + { + "author_name": "Anna Gottschlich", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Manish Sadarangani", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Angela Kaida", + "author_inst": "Simon Fraser University" + }, + { + "author_name": "Gina Ogilvie", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Lori Brotto", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Liisa A.M Galea", + "author_inst": "University of British Columbia" } ], "version": "1", - "license": "cc_by_nc", + "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" + "category": "sexual and reproductive health" }, { "rel_doi": "10.1101/2022.07.29.22278186", @@ -244320,39 +244583,107 @@ "category": "epidemiology" }, { - "rel_doi": "10.1101/2022.07.27.501726", - "rel_title": "Sequential in vitro enzymatic N-glycoprotein modification reveals site-specific rates of glycoenzyme processing", + "rel_doi": "10.1101/2022.07.27.501719", + "rel_title": "Development of Equine Polyclonal Antibodies as a Broad-Spectrum Therapy Against SARS-CoV-2 Variants", "rel_date": "2022-07-28", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.27.501726", - "rel_abs": "N-glycosylation is an essential eukaryotic post-translational modification that affects various glycoprotein properties, including folding, solubility, protein-protein interactions, and half-life. N-glycans are processed in the secretory pathway to form varied ensembles of structures, and diversity at a single site on a glycoprotein is termed microheterogeneity. To understand the factors that influence glycan microheterogeneity, we hypothesized that local steric and electrostatic factors surrounding each site influences glycan availability to enzymatic modification. We tested this hypothesis by expression of a panel of reporter N-linked glycoproteins in MGAT1- null HEK293 cells to produce immature Man5GlcNAc2 glycoforms (38 glycan sites total). These glycoproteins were then sequentially modified in vitro from high-mannose to hybrid and on to biantennary, core fucosylated, complex structures by a panel of N-glycosylation enzymes and each reaction time-course was quantified by LC-MS/MS. Substantial differences in rates of in vitro enzymatic modification were observed between glycan sites on the same protein and differences in modification rates varied depending on the glycoenzyme being evaluated. By comparison, proteolytic digestion of the reporters prior to N-glycan processing eliminated differences in in vitro enzymatic modification. Comparison of in vitro rates of enzymatic modification with the glycan structures found on the mature reporters expressed in wild type cells correlate well with the enzymatic bottlenecks found in vitro. These data suggest that higher-order local structures surrounding each glycosylation site contribute to the efficiency of modification both in vitro and in vivo to establish the spectrum of site-specific microheterogeneity found on N-linked glycoproteins.", - "rel_num_authors": 5, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.27.501719", + "rel_abs": "The Coronavirus disease 19 (COVID-19) pandemic has accumulated over 550 million confirmed cases and more than 6.34 million deaths worldwide. Although vaccinations has largely protected the population through the last two years, the effect of vaccination has been increasingly challenged by the emerging SARS-CoV-2 variants. Although several therapeutics including both monoclonal antibodies and small molecule drugs have been used clinically, high cost, viral escape mutations, and potential side effects have reduced their efficacy. There is an urgent need to develop a low cost treatment with wide-spectrum effect against the novel variants of SARS-CoV-2.\n\nHere we report a product of equine polyclonal antibodies that showed potential broad spectrum neutralization effect against the major variants of SARS-CoV-2. The equine polyclonal antibodies were generated by horse immunization with the receptor binding domain (RBD) of SARS-CoV-2 spike protein and purified from equine serum. A high binding affinity between the generated equine antibodies and the RBD was observed. Although designed against the RBD of the early wild type strain sequenced in 2020, the equine antibodies also showed a highly efficient neutralization capacity against the major variants of SARS-CoV-2, including the recent BA.2 Omicron variant (IC50 =1.867g/ml) in viral neutralization assay in Vero E6 cells using live virus cultured. The broad-spectrum neutralization capacity of the equine antibodies was further confirmed using pseudovirus neutralization assay covering the major SARS-CoV-2 variants including wild type, alpha, beta, delta, and omicron, showing effective neutralization against all the tested strains. Ex vivo reconstructed human respiratory organoids representing nasal, bronchial, and lung epitheliums were employed to test the treatment efficacy of the equine antibodies. Antibody treatment protected the human nasal, bronchial, and lung epithelial organoids against infection of the novel SARS-CoV-2 variants challenging public health, the Delta and Omicron BA.2 isolates, by reducing >95% of the viral load. The equine antibodies were further tested for potential side effects in a mouse model by inhalation and no significant pathological feature was observed.\n\nEquine antibodies, as a mature medical product, have been widely applied in the treatment of infectious diseases for more than a century, which limits the potential side effects and are capable of large scale production at a low cost. A cost-effective, wide-spectrum equine antibody therapy effective against the major SARS-CoV-2 variants can contribute as an affordable therapy to cover a large portion of the world population, and thus potentially reduce the transmission and mutation of SARS-CoV-2.", + "rel_num_authors": 22, "rel_authors": [ { - "author_name": "Trevor M Adams", - "author_inst": "University of Georgia" + "author_name": "Shumin Liao", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China; The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China" }, { - "author_name": "Peng Zhao", - "author_inst": "University of Georgia" + "author_name": "Yunjiao He", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" }, { - "author_name": "Digantkumar Chapla", - "author_inst": "University of Georgia" + "author_name": "Jing Qu", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" }, { - "author_name": "Kelley W Moremen", - "author_inst": "University of Georgia" + "author_name": "Yue Shi", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" }, { - "author_name": "Lance Wells", - "author_inst": "University of Georgia" + "author_name": "Yingzi Liu", + "author_inst": "Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, China; School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Keli Zhao", + "author_inst": "Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, China" + }, + { + "author_name": "Junhui Chen", + "author_inst": "Peking University Shenzhen Hospital, No. 1120, Lianhua Road, Futian District, Shenzhen, China" + }, + { + "author_name": "Yue Jing", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd., Jiangxi, China; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen, China; Haina" + }, + { + "author_name": "Clifton Kwang-Fu Shen", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd.Jiangxi; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen; Hainan Institute of P" + }, + { + "author_name": "Chong Ji", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd., Jiangxi, China; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen, China; Haina" + }, + { + "author_name": "Guxun Luo", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd., Jiangxi, China; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen, China; Haina" + }, + { + "author_name": "Xusheng Zhao", + "author_inst": "Jiangxi Institute of Biological Products Co. Ltd., Jiangxi, China; Jiangxi Institute of Biological Products Shenzhen R&D Center Co. Ltd., Shenzhen, China; Haina" + }, + { + "author_name": "Shuo Li", + "author_inst": "Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China; The Sixth Affiliated Hospital of Shenzhen University Health Science Cent" + }, + { + "author_name": "Yunping Fan", + "author_inst": "Department of Otolaryngology, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China" + }, + { + "author_name": "Ziquan Lv", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Shisong Fang", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Yaqing He", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Chunli Wu", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Renli Zhang", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Xuan Zou", + "author_inst": "Shenzhen Center for Disease Control and Prevention, No. 8, Longyuan Road, Nanshan District, Shenzhen, Guangdong Province, China" + }, + { + "author_name": "Peng Wang", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" + }, + { + "author_name": "Liang Li", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China; Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced T" } ], "version": "1", - "license": "cc_by", + "license": "cc_no", "type": "new results", - "category": "biochemistry" + "category": "immunology" }, { "rel_doi": "10.1101/2022.07.27.501708", @@ -245990,99 +246321,31 @@ "category": "cardiovascular medicine" }, { - "rel_doi": "10.1101/2022.07.24.22277978", - "rel_title": "Genomic epidemiology and phylodynamics for county-to-county transmission of SARS-CoV-2 in Minnesota, from 19A to Omicron", + "rel_doi": "10.1101/2022.07.24.22277968", + "rel_title": "Effects of wearing FFP2 masks on SARS-CoV-2 infection rates in classrooms", "rel_date": "2022-07-25", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.24.22277978", - "rel_abs": "SARS-CoV-2 has had an unprecedented impact on human health and highlights the need for genomic epidemiology studies to increase our understanding of virus evolution and spread, and to inform policy decisions. We sequenced viral genomes from over 22,000 patient samples tested at Mayo Clinic Laboratories between 2020-2022 and use Bayesian phylodynamics to describe county and regional spread in Minnesota.\n\nThe earliest introduction into Minnesota was to Hennepin County from a domestic source around January 22, 2020; six weeks before the first confirmed case in the state. This led to the virus spreading to Northern Minnesota, and eventually, the rest of the state. International introductions were most abundant in Hennepin (home to the Minneapolis/St. Paul International (MSP) airport) totaling 45 (out of 107) over the two-year period. Southern Minnesota counties were most common for domestic introductions with 19 (out of 64), potentially driven by bordering states such as Iowa and Wisconsin as well as Illinois which is nearby. Hennepin also was, by far, the most dominant source of in-state transmissions to other Minnesota locations (n=772) over the two-year period.\n\nWe also analyzed the diversity of the location source of SARS-CoV-2 viruses in each county and noted the timing of state-wide policies as well as trends in clinical cases. Neither the number of clinical cases or major policy decisions, such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, appeared to have impact on virus diversity across each individual county.\n\nImportanceWe analyzed over 22,000 SARS-CoV-2 genomes of patient samples tested at Mayo Clinic Laboratories during a two-year period in the COVID-19 pandemic that included Alpha, Delta, and Omicron VoCs to examine the roles and relationships of Minnesota virus transmission.\n\nWe found that Hennepin County, the most populous county, drove the transmission of SARS-CoV-2 viruses in the state after including the formation of earlier clades including 20A, 20C, and 20G, as well as variants of concern Alpha and Delta. We also found that Hennepin County was the source for most of the county-to-county introductions after its initial introduction with the virus in early 2020 from an international source, while other counties acted as transmission \"sinks\". In addition, major policies such as the end of the lockdown period in 2020 or the end of all restrictions in 2021, did not appear to have an impact on virus diversity across individual counties.", - "rel_num_authors": 20, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.24.22277968", + "rel_abs": "ImportanceDifferent mitigation measures are mandated in schools worldwide to control the spread of SARS-CoV-2. The efficacy of most measures, however, has not been investigated thus far.\n\nObjectiveTo investigate the usefulness of FFP-2 masks in classrooms to prevent the spread of SARS-CoV-2.\n\nDesignA retrospective comparative cohort study of infection rates (evaluated by PCR screening in school) in students wearing FFP-2 masks continuously and students in sports classes with limited face mask use.\n\nSettingA single-center evaluation comparing classes (middle school: age 10-16 years, 4-year high school: age 14-20 years) with a high sports focus (SF), with regular classes during the Delta and Omicron waves (September 2021-April 2022).\n\nParticipantsIn total, 616 children/families were invited to participate in the comparative evaluation, and 614 (99.7%) followed this invitation by providing relevant information concerning their SARS-CoV-2 infection status. A total of 213 legal guardians (for children < 14 years) and 401 adolescents ([≥]14 years) reported SARS-CoV-2 infections during the 2021/22 school year.\n\nMain Outcomes and MeasuresA comparative analysis of cumulative SARS-CoV-2 infection rates in sports and non-sports classes (the 7-day classroom incidence of SARS-CoV-2 infections, and potential secondary infections among school classmates).\n\nResultsCumulative SARS-CoV-2 infection rates were clearly higher in sports classes (with limited mask use) than in non-sports classes (continuous mask use). After the relaxation of the mitigation measures, students in non-sports classes, however, showed a clear \"catch-up\" of infections, leading to a higher incidence of infections during this phase. By the end of the observation period (April 30, 2022), only a small difference in cumulative SARS-CoV-2 infection rates (p=0.037, {varphi}=0.09) was detected between classes with a sports focus and those without a sports focus.\n\nConclusions and RelevanceWearing FFP2 face masks reduces the risk of SARS-CoV-2 infection if strict mitigation measures are applied. Following the relaxation of strict measures, previously \"protected\" students show a significant \"catch-up\" infection rate. Thus, continuous face mask use postpones rather than avoids SARS-CoV-2 infection in many cases. Therefore, the advantage of reduced transmission must be carefully balanced against the disadvantages associated with mask wearing throughout schools.", + "rel_num_authors": 3, "rel_authors": [ { - "author_name": "Matthew Scotch", - "author_inst": "Arizona State University" - }, - { - "author_name": "Kimberly Lauer", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Eric D Wieben", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Yesesri Cherukuri", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Julie M Cunningham", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Eric W Klee", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Jonathan J Harrington", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Julie S Lau", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Samantha J McDonough", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Mark Mutawe", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "John C O'Horo", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Chad E Rentmeester", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Nicole R Schlicher", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Valerie T White", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Susan K Schneider", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Peter T Vedell", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Xiong Wang", - "author_inst": "Minnesota Department of Health" - }, - { - "author_name": "Joseph D Yao", - "author_inst": "Mayo Clinic" + "author_name": "Gerald Jarnig", + "author_inst": "Institute of Human Movement Science, Sport and Health, University of Graz, Graz, Austria" }, { - "author_name": "Bobbi S Pritt", - "author_inst": "Mayo Clinic" + "author_name": "Reinhold Kerbl", + "author_inst": "Department of Pediatrics and Adolescent Medicine, LKH Hochsteiermark/Leoben, Austria" }, { - "author_name": "Andrew P Norgan", - "author_inst": "Mayo Clinic" + "author_name": "Mireille van Poppel", + "author_inst": "Institute of Human Movement Science, Sport and Health, University of Graz, Graz, Austria" } ], "version": "1", "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" + "category": "public and global health" }, { "rel_doi": "10.1101/2022.07.20.22277718", @@ -247732,75 +247995,59 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.07.20.500860", - "rel_title": "A linear DNA vaccine candidate encoding the SARS-CoV-2 Receptor Binding Domain elicits protective immunity in domestic cats", + "rel_doi": "10.1101/2022.07.21.501010", + "rel_title": "Durability of the Neutralizing Antibody Response to mRNA Booster Vaccination Against SARS-CoV-2 BA.2.12.1 and BA.4/5 Variants", "rel_date": "2022-07-22", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.20.500860", - "rel_abs": "Since its first detection in China in late 2019, SARS-CoV-2, the etiologic agent of COVID-19 pandemic, has infected a wide range of animal species, especially mammals, all over the world. Indeed, as reported by the American Veterinary Medical Association, besides human-to-human transmission, human-to-animal transmission has been observed in some wild animals and pets, especially in cats. With animal models as an invaluable tool in the study of infectious diseases combined with the fact that the intermediate animal source of SARS-CoV-2 is still unknown, researchers have demonstrated that cats are permissive to COVID-19 and are susceptible to airborne infections. Given the high transmissibility potential of SARS-CoV-2 to different host species and the close contact between humans and animals, it is crucial to find mechanisms to prevent the transmission chain and reduce the risk of spillover to susceptible species. Here, we show results from a randomized Phase I/II clinical study conducted in domestic cats to assess safety and immunogenicity of a linear DNA (\"linDNA\") vaccine encoding the RBD domain of SARS-CoV-2. No significant adverse events occurred and both RBD-specific binding/neutralizing antibodies and T cells were detected. These findings demonstrate the safety and immunogenicity of a genetic vaccine against COVID-19 administered to cats and strongly support the development of vaccines for preventing viral spread in susceptible species, especially those in close contact with humans.", - "rel_num_authors": 14, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.21.501010", + "rel_abs": "The recent emergence of the SARS-CoV-2 BA.4/5 and BA.2.12.1 variants has led to rising COVID-19 case numbers and concerns over the continued efficacy of mRNA booster vaccination. Here we examine the durability of neutralizing antibody (nAb) responses against these SARS-CoV-2 Omicron subvariants in a cohort of health care workers 1-40 weeks after mRNA booster dose administration. Neutralizing antibody titers fell by [~]1.5-fold 4-6 months and by [~]2.5-fold 7-9 months after booster dose, with average nAb titers falling by 11-15% every 30 days, far more stable than two dose induced immunity. Notably, nAb titers from booster recipients against SARS-CoV-2 BA.1, BA.2.12.1, and BA.4/5 variants were [~]4.7-, 7.6-, and 13.4-fold lower than against the ancestral D614G spike. However, the rate of waning of booster dose immunity was comparable across variants. Importantly, individuals reporting prior infection with SARS-CoV-2 exhibited significantly higher nAb titers compared to those without breakthrough infection. Collectively, these results highlight the broad and stable neutralizing antibody response induced by mRNA booster dose administration, implicating a significant role of virus evolution to evade nAb specificity, versus waning humoral immunity, in increasing rates of breakthrough infection.", + "rel_num_authors": 10, "rel_authors": [ { - "author_name": "Antonella Conforti", - "author_inst": "Evvivax" - }, - { - "author_name": "Elisa Sanchez", - "author_inst": "Veterinary Oncology Services" - }, - { - "author_name": "Erika Salvatori", - "author_inst": "Takis Biotech" - }, - { - "author_name": "Lucia Lione", - "author_inst": "Takis Biotech" - }, - { - "author_name": "Mirco Compagnone", - "author_inst": "Neomatrix Biotech" + "author_name": "PANKE QU", + "author_inst": "The Ohio State University" }, { - "author_name": "Eleonora Pinto", - "author_inst": "Takis Biotech" + "author_name": "Julia N. Faraone", + "author_inst": "The Ohio State University" }, { - "author_name": "Fabio Palombo", - "author_inst": "Neomatrix Biotech" + "author_name": "John P. Evans", + "author_inst": "The Ohio State University" }, { - "author_name": "Yuhua Sun", - "author_inst": "ADNAS" + "author_name": "Yi-Min Zheng", + "author_inst": "The Ohio State University" }, { - "author_name": "Brian Viscount", - "author_inst": "ADNAS" + "author_name": "Claire Carlin", + "author_inst": "The Ohio State University" }, { - "author_name": "James Hayward", - "author_inst": "ADNAS" + "author_name": "Gerard Lozanski", + "author_inst": "The Ohio State University" }, { - "author_name": "Clay Shorrock", - "author_inst": "ADNAS" + "author_name": "Linda J. Saif", + "author_inst": "The Ohio State University" }, { - "author_name": "Diego G Diel", - "author_inst": "Cornell University" + "author_name": "Eugene M. Oltz", + "author_inst": "The Ohio State University" }, { - "author_name": "Joseph A Impellizeri", - "author_inst": "Veterinary Oncology Services" + "author_name": "Richard J. Gumina", + "author_inst": "The Ohio State University" }, { - "author_name": "Luigi Aurisicchio", - "author_inst": "Evvivax" + "author_name": "Shan-Lu Liu", + "author_inst": "The Ohio State University" } ], "version": "1", - "license": "cc_no", + "license": "cc_by_nc", "type": "new results", - "category": "immunology" + "category": "microbiology" }, { "rel_doi": "10.1101/2022.07.21.501023", @@ -249522,87 +249769,39 @@ "category": "immunology" }, { - "rel_doi": "10.1101/2022.07.18.499583", - "rel_title": "Discovering host protein interactions specific for SARS-CoV-2 RNA genome", + "rel_doi": "10.1101/2022.07.18.22277694", + "rel_title": "Determinants of healthcare employee preference to continue teleworking after the COVID-19 pandemic: a cross-sectional study using hierarchical regression", "rel_date": "2022-07-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.18.499583", - "rel_abs": "SARS-CoV-2, a positive single-stranded RNA virus, interacts with host cell proteins throughout its life cycle. These interactions are necessary for the host to recognize and hinder the replication of SARS-CoV-2. For the virus, to translate, transcribe and replicate its genetic material. However, many details of these interactions are still missing. We focused on the proteins binding to the highly structured 5 and 3 end regions of SARS-CoV-2 RNA that were predicted by the catRAPID algorithm to attract numerous proteins, exploiting RNA-Protein Interaction Detection coupled with Mass Spectrometry (RaPID-MS) technology. The validated interactors, which agreed with our predictions, include pseudouridine synthase PUS7 that binds to both ends of the viral RNA. Nanopore direct-RNA sequencing confirmed that the RNA virus is heavily modified, and PUS7 consensus regions were found in both SARS-CoV-2 RNA end regions. Notably, a modified site was detected in the viral Transcription Regulatory Sequence - Leader (TRS-L) and can influence the viral RNA structure and interaction propensity. Overall, our data map host protein interactions within SARS-CoV-2 UTR regions, pinpointing to a potential role of pseudouridine synthases and post-transcriptional modifications in the viral life cycle. These findings contribute to understanding virus-host dynamics and may guide the development of targeted therapies.", - "rel_num_authors": 17, + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.18.22277694", + "rel_abs": "Employees post-pandemic telework preference is an important consideration for navigating post-pandemic work arrangements and can inform organizational planning and workforce management. A cross-sectional survey of employees (n=400, participation rate =36.4%) of a regional health authority who teleworked during the COVID-19 pandemic was conducted. The most common post-pandemic telework preference was all the time (52%) followed by over half but not all the time (32%) and less than half the time or not at all (16%). Using hierarchical multinomial logistic regression models and less than half the time or not at all as the reference outcome, being a provider of direct patient care and productivity while teleworking were strong determinants of post-pandemic telework preference while two or more weekly teleconference hours, work-life balance and having one or more people over five years of age in the home while teleworking were moderate determinants.", + "rel_num_authors": 5, "rel_authors": [ { - "author_name": "Roberto Giambruno", - "author_inst": "Institute of Biomedical Technologies, National Research Council, ITB - CNR; Istituto Italiano di Tecnologia - IIT" - }, - { - "author_name": "Elsa Zacco", - "author_inst": "Italian Institute of Technology - IIT" - }, - { - "author_name": "Camilla Ugolini", - "author_inst": "Italian Institute of Technology - IIT" - }, - { - "author_name": "Andrea Vandelli", - "author_inst": "Italian Institute of Technology - IIT" - }, - { - "author_name": "Logan Mulroney", - "author_inst": "Italian Institute of Technology - IIT; European Molecular Biology Laboratory - EMBL" - }, - { - "author_name": "Manfredi D'Onghia", - "author_inst": "Italian Institute of Technology - IIT" - }, - { - "author_name": "Bianca Giuliani", - "author_inst": "Italian Institute of Technology - IIT" - }, - { - "author_name": "Elena Criscuolo", - "author_inst": "Vita-Salute San Raffaele University" - }, - { - "author_name": "Matteo Castelli", - "author_inst": "Vita-Salute San Raffaele University" - }, - { - "author_name": "Nicola Clementi", - "author_inst": "Vita-Salute San Raffaele University; IRCCS San Raffaele Scientific Institute" - }, - { - "author_name": "Massimo Clementi", - "author_inst": "Vita-Salute San Raffaele University; IRCCS San Raffaele Scientific Institute" - }, - { - "author_name": "Nicasio Mancini", - "author_inst": "Universita Vita-Salute San Raffaele; IRCCS San Raffaele Scientific Institute" - }, - { - "author_name": "Tiziana Bonaldi", - "author_inst": "European Institute of Oncology; University of Milan" + "author_name": "Andrea Marie Jones", + "author_inst": "University of British Columbia" }, { - "author_name": "Stefano Gustincich", - "author_inst": "IIT- Center for Human Technologies (CHT)" + "author_name": "Jonathan Fan", + "author_inst": "University of British Columbia" }, { - "author_name": "Tommaso Leonardi", - "author_inst": "Italian Institute of Technology - IIT" + "author_name": "Leah Thomas-Olson", + "author_inst": "Fraser Health Authority" }, { - "author_name": "Gian Gaetano Tartaglia", - "author_inst": "Italian Institute of Technology - IIT" + "author_name": "Wei Zhang", + "author_inst": "University of British Columbia/ Centre for Health Evaluation and Outcome Sciences" }, { - "author_name": "Francesco Nicassio", - "author_inst": "Italian Institute of Technology - IIT" + "author_name": "Christopher B McLeod", + "author_inst": "University of British Columbia" } ], "version": "1", "license": "cc_no", - "type": "new results", - "category": "molecular biology" + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" }, { "rel_doi": "10.1101/2022.07.19.22277747", @@ -251396,37 +251595,41 @@ "category": "allergy and immunology" }, { - "rel_doi": "10.1101/2022.07.15.22277696", - "rel_title": "Ethnic homophily affects vaccine prioritization strategies", + "rel_doi": "10.1101/2022.07.15.22277497", + "rel_title": "Global patterns and drivers of influenza decline during the COVID-19 pandemic", "rel_date": "2022-07-17", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.15.22277696", - "rel_abs": "People are more likely to interact with other people of their ethnicity--a phenomenon known as ethnic homophily. In the United States, people of color are known to hold proportionately more high-contact jobs and are thus more at risk of virus infection. At the same time, these ethnic groups are on average younger than the rest of the population. This gives rise to interesting disease dynamics and non-trivial trade-offs that should be taken into consideration when developing prioritization strategies for future mass vaccine roll-outs.\n\nHere, we study the spread of COVID-19 through the U.S. population, stratified by age, ethnicity, and occupation, using a detailed, previously-developed compartmental disease model. Based on historic data from the U.S. mass COVID-19 vaccine roll-out that began in December 2020, we show, (i) how ethnic homophily affects the choice of optimal vaccine allocation strategy, (ii) that, notwithstanding potential ethical concerns, differentiating by ethnicity in these strategies can improve outcomes (e.g., fewer deaths), and (iii) that the most likely social context in the United States is very different from the standard assumptions made by models which do not account for ethnicity and this difference affects which allocation strategy is optimal.\n\nHighlightsO_LIA social mixing model accounting for ethnic homophily and variable job-related risk level is developed.\nC_LIO_LIA scenario that differs strongly from standard homogeneous mixing assumptions best matches U.S. ethnicity-specific death and case counts.\nC_LIO_LITwo trade-offs are explored: Should (i) old or young, and (ii) people of color or White and Asian people first receive COVID-19 vaccines?\nC_LIO_LIExhaustive simulation of a compartmental disease model identifies the optimal allocation strategy for different demographic groups.\nC_LIO_LIOptimal strategies depend on the underlying mixing pattern and strategies that differentiate vaccine access by ethnicity outperform others.\nC_LI", - "rel_num_authors": 5, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.15.22277497", + "rel_abs": "Influenza circulation declined during the COVID-19 pandemic. The timing and extent of decline and its association with interventions against COVID-19 were described for some regions. Here, we provide a global analysis of the influenza decline between March 2020 and September 2021 and investigate its potential drivers. We computed influenza change by country and trimester relative to the 2014-2019 period using the number of samples in the FluNet database. We used random forests to determine important predictors in a list of 20 covariates including demography, weather, pandemic preparedness, COVID-19 incidence, and COVID-19 pandemic response. With a regression tree we then classified observations according to these predictors. We found that influenza circulation decreased globally, with COVID-19 incidence and pandemic preparedness being the two most important predictors of this decrease. The regression tree showed interpretable groups of observations by country and trimester: Europe and North America clustered together in spring 2020, with limited influenza decline despite strong COVID-19 restrictions; in the period afterwards countries of temperate regions, with high pandemic preparedness, high COVID-19 incidence and stringent social restrictions grouped together having strong influenza decline. Conversely, countries in the tropics, with altogether low pandemic preparedness, low reported COVID-19 incidence and low strength of COVID-19 response showed low influenza decline overall. A final group singled out four \"zero-Covid\" countries, with the lowest residual influenza levels. The spatiotemporal decline of influenza during the COVID-19 pandemic was global, yet heterogeneous. The sociodemographic context and stage of the COVID-19 pandemic showed non-linear associations with this decline. Zero-Covid countries maintained the lowest levels of reduction with strict border controls and despite close-to-normal social activity. These results suggest that the resurgence of influenza could take equally diverse paths. It also emphasises the importance of influenza reseeding in driving countries seasonal influenza epidemics.", + "rel_num_authors": 6, "rel_authors": [ { - "author_name": "Claus Kadelka", - "author_inst": "Iowa State University" + "author_name": "Francesco Bonacina", + "author_inst": "Sorbonne Universit\u00e9" }, { - "author_name": "Md Rafiul Islam", - "author_inst": "Iowa State University" + "author_name": "Pierre-Yves Bo\u00eblle", + "author_inst": "Sorbonne Universit\u00e9" }, { - "author_name": "Audrey McCombs", - "author_inst": "Iowa State University" + "author_name": "Vittoria Colizza", + "author_inst": "INSERM" }, { - "author_name": "Jake Alston", - "author_inst": "Iowa State University" + "author_name": "Olivier Lopez", + "author_inst": "Sorbonne Universit\u00e9" }, { - "author_name": "Noah Morton", - "author_inst": "Iowa State University" + "author_name": "Maud Thomas", + "author_inst": "Sorbonne Universit\u00e9" + }, + { + "author_name": "Chiara Poletto", + "author_inst": "INSERM and Sorbonne Universit\u00e9" } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc_by_nd", "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, @@ -253606,57 +253809,53 @@ "category": "epidemiology" }, { - "rel_doi": "10.1101/2022.07.14.22277616", - "rel_title": "SARS-CoV-2 infection dynamics and genomic surveillance reveals early variant transmission in urban wastewater", + "rel_doi": "10.1101/2022.07.13.22277575", + "rel_title": "SARS-CoV-2 infections during Omicron (BA.1) dominant wave and subsequent population immunity in Gauteng, South Africa", "rel_date": "2022-07-15", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.14.22277616", - "rel_abs": "Environmental surveillance (ES) of a pathogen is crucial for understanding the community load of disease. As an early warning system, ES for SARS-CoV-2 has complemented routine diagnostic surveillance by capturing near real-time virus circulation at a population level. In this longitudinal study in 28 sewershed sites in Bangalore city, we quantified SARS-CoV-2 RNA to track infection dynamics and provide evidence of change in the relative abundance of emerging variants. We describe an early warning system using the exponentially weighted moving average control chart and demonstrate how SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 8-14 days earlier in wastewater than in clinical data. This was further corroborated by showing that the estimated number of infections is strongly correlated with SARS-CoV-2 RNA copies detected in the wastewater. Using a deconvolution matrix, we detected emerging variants of concern up to two months earlier in wastewater samples. In addition, we found a huge diversity in variants detected in wastewater compared to clinical samples. Our study highlights that quantifying viral titres, correlating it with a known number of cases in the area, and combined with genomic surveillance helps in tracking VOCs over time and space, enabling timely and making informed policy decisions.", - "rel_num_authors": 11, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.13.22277575", + "rel_abs": "BackgroundThe B.1.1.529 (Omicron BA.1) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global resurgence of coronavirus disease 2019 (Covid-19). The contribution of BA.1 infection to population immunity and its effect on subsequent resurgence of B.1.1.529 sub-lineages warrant investigation.\n\nMethodsWe conducted an epidemiologic survey to determine the sero-prevalence of SARS-CoV-2 IgG from March 1 to April 11, 2022, after the BA.1-dominant wave had subsided in Gauteng (South Africa), and prior to a resurgence of Covid-19 dominated by the BA.4 and BA.5 (BA.4/BA.5) sub-lineages. Population-based sampling included households in an earlier survey from October 22 to December 9, 2021 preceding the BA.1 dominant wave. Dried-blood-spot samples were quantitatively tested for IgG against SARS-CoV-2 spike protein and nucleocapsid protein. Epidemiologic trends in Gauteng for cases, hospitalizations, recorded deaths, and excess deaths were evaluated from the inception of the pandemic to the onset of the BA.1 dominant wave (pre-BA.1), during the BA.1 dominant wave, and for the BA.4/BA.5 dominant wave through June 6, 2022.\n\nResultsThe 7510 participants included 2420 with paired samples from the earlier survey. Despite only 26.7% (1995/7470) of individuals having received a Covid-19 vaccine, the overall sero-prevalence was 90.9% (95% confidence interval [CI], 90.2 to 91.5), including 89.5% in Covid-19 unvaccinated individuals. Sixty-four percent (95%CI, 61.8-65.9) of individuals with paired samples had serological evidence of SARS-CoV-2 infection during the BA.1 dominant wave. Of all cumulative recorded hospitalisations and deaths, 14.1% and 5.9% were contributed by the BA.1 dominant wave, and 5.1% and 1.6% by the BA.4/BA.5 dominant wave. The SARS-CoV-2 infection fatality risk was lower in the BA.1 compared with pre-BA.1 waves for recorded deaths (0.02% vs. 0.33%) and Covid-19 attributable deaths based on excess mortality estimates (0.03% vs. 0.67%).\n\nConclusionsGauteng province experienced high levels of infections in the BA.1 -dominant wave against a backdrop of high (73%) sero-prevalence. Covid-19 hospitalizations and deaths were further decoupled from infections during BA.4/BA.5 dominant wave than that observed during the BA.1 dominant wave.\n\n(Funded by the Bill and Melinda Gates Foundation.)", + "rel_num_authors": 10, "rel_authors": [ { - "author_name": "Sanjay Lamba", - "author_inst": "Tata Institute for Genetics and Society" - }, - { - "author_name": "Sutharan G.", - "author_inst": "Tata Institute for Genetics and Society" + "author_name": "Shabir Madhi", + "author_inst": "University of the Witwatersrand" }, { - "author_name": "Namrta Daroch", - "author_inst": "Tata Institute for Genetics and Society" + "author_name": "Gaurav Kwatra", + "author_inst": "University of the Witwatersrand" }, { - "author_name": "Kiran Paul", - "author_inst": "Tata Institute for Genetics and Society" + "author_name": "Jonathan E. Myers", + "author_inst": "University of Cape Town" }, { - "author_name": "Soumya Gopal Joshi", - "author_inst": "Tata Institute for Genetics and Society" + "author_name": "Waasila Jassat", + "author_inst": "National institute for communicable diseases of South Africa" }, { - "author_name": "Darshan S", - "author_inst": "National Centre for Biological Sciences" + "author_name": "Nisha Dhar", + "author_inst": "University of the Witwatersrand" }, { - "author_name": "Annamalai N", - "author_inst": "Tata Institute for Genetics and Society" + "author_name": "Christian K. Mukendi", + "author_inst": "University of the Witwatersrand" }, { - "author_name": "Vishwanath S", - "author_inst": "Biome Environmental Trust" + "author_name": "Lucille Blumberg", + "author_inst": "National institute for communicable diseases of South Africa" }, { - "author_name": "Rakesh K Mishra", - "author_inst": "Tata Institute for Genetics and Society" + "author_name": "Richard Welch", + "author_inst": "National institute for communicable diseases of South Africa" }, { - "author_name": "Uma Ramakrishnan", - "author_inst": "National Centre for Biological Sciences" + "author_name": "Alane Izu", + "author_inst": "University of the Witwatersrand" }, { - "author_name": "Farah Ishtiaq", - "author_inst": "Tata Institute for Genetics and Society" + "author_name": "Portia C. Mutevedzi", + "author_inst": "University of the Witwatersrand" } ], "version": "1", @@ -255220,129 +255419,45 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.07.11.22277481", - "rel_title": "Age stratified seroprevalence of antibodies against SARS CoV 2 in the pre and post vaccination era, February 2020 to March 2022, Japan", + "rel_doi": "10.1101/2022.07.10.22277467", + "rel_title": "Development of an Accurate and Rapid Antigen Assay for COVID-19 Diagnostics Using Saliva", "rel_date": "2022-07-12", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.11.22277481", - "rel_abs": "Japan has reported a small number of COVID-19 cases relative to other countries. Because not all infected people receive diagnostic tests for COVID-19, the reported number of COVID-19 cases must be lower than the actual number of infections. Assessments of the presence of antibodies against the spike protein of SARS-CoV-2 can retrospectively determine the history of natural infection and vaccination. In this study, we assessed SARS-CoV-2 seroprevalence by analyzing over 60,000 samples collected in Japan from February 2020 to March 2022. The results showed that about 5% of the Japanese population had been infected with the virus by January 2021. The seroprevalence increased with the administration of vaccinations to adults; however, among the elderly, it was not as high as the vaccination rate, probably due to poor immune responses to the vaccines and waning immunity. The infection was spread during the epidemic waves caused by the SARS-CoV-2 Delta and Omicron variants among children who were not eligible for vaccination. Nevertheless, their seroprevalence was as low as 10% as of March 2022. Our study underscores the low incidence of SARS-CoV-2 infection in Japan and the effects of vaccination on immunity at the population level.", - "rel_num_authors": 28, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.10.22277467", + "rel_abs": "The global outbreak of COVID-19 highlighted the need for rapid and accurate diagnostic testing to control the spread of this highly contagious disease (1-5). Here, we describe the nCoVega COVID-19 antigen rapid test ([~] 15min) that can detect the presence of the SARS-COV-2 virus particles from saliva sample on a portable device. The portable reader instrument, the Vega-200, has a small footprint and is designed for use at point of care settings. The test detects the fluorescence signal using wide-field illumination from antigen-antibody complexes captured on a special filter matrix (6). Results of this clinical evaluation of 183 subjects demonstrates that the nCoVega COVID-19 test performs at par with qRT-PCR tests (7) (gold standard) for both symptomatic and asymptomatic patients, with a strong inverse correlation between RFU (relative fluorescence units) and Ct counts (from RT-PCR) maintaining detection accuracy even at very low viral loads. The test has an analytical performance of 15.3 TCID50/mL, and 100% specificity for COVID-19 as compared to other human respiratory viruses, including other human coronaviruses. The working principle of this assay and test system can be used for developing other rapid, inexpensive antigen assays and it can offer an end-to-end, point-of-care solution to meet the continuous demand in tackling existing and emerging infectious diseases across the globe.", + "rel_num_authors": 7, "rel_authors": [ { - "author_name": "Seiya Yamayoshi", - "author_inst": "University of Tokyo" + "author_name": "Camille Troup", + "author_inst": "Kaya17 Inc" }, { - "author_name": "Kiyoko Iwatsuki-Horimoto", - "author_inst": "University of Tokyo" + "author_name": "Debnath Mukhopadhyay", + "author_inst": "Kaya17 Inc" }, { - "author_name": "Moe Okuda", - "author_inst": "University of Tokyo" + "author_name": "Tania Chakrabarty", + "author_inst": "Kaya17 Inc" }, { - "author_name": "Michiko Ujie", - "author_inst": "University of Tokyo" + "author_name": "Anup Madan", + "author_inst": "Kaya17 Inc" }, { - "author_name": "Atsuhiro Yasuhara", - "author_inst": "University of Tokyo" + "author_name": "Sri Satyanarayana", + "author_inst": "Kaya17, inc" }, { - "author_name": "Jurika Murakami", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Calvin Duong", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Taiki Hamabata", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Mutsumi Ito", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Shiho Chiba", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Ryo Kobayashi", - "author_inst": "Sapporo Medical University Hospital" - }, - { - "author_name": "Satoshi Takahash", - "author_inst": "Sapporo Medical University School of Medicine" - }, - { - "author_name": "Keiko Mitamura", - "author_inst": "Eiju General Hospital" + "author_name": "Shreefal Mehta", + "author_inst": "Kaya17 Inc" }, { - "author_name": "Masao Hagihara", - "author_inst": "Eiju General Hospital" - }, - { - "author_name": "Akimichi Shibata", - "author_inst": "Japanese Red Cross Ashikaga Hospital" - }, - { - "author_name": "Yoshifumi Uwamino", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Naoki Hasegawa", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Toshiaki Ebina", - "author_inst": "Yokohama City University Medical Center" - }, - { - "author_name": "Akihiko Izumi", - "author_inst": "Yokohama City University Medical Center" - }, - { - "author_name": "Hideaki Kato", - "author_inst": "Yokohama City University Hospital" - }, - { - "author_name": "Hideaki Nakajima", - "author_inst": "Yokohama City University Graduate School of Medicine" - }, - { - "author_name": "Norio Sugaya", - "author_inst": "Keio University School of Medicine" - }, - { - "author_name": "Yuki Seki", - "author_inst": "Keiyu Hospital" - }, - { - "author_name": "Asef Iqbal", - "author_inst": "National Hospital Organization Saitama Hospital" - }, - { - "author_name": "Isamu Kamimaki", - "author_inst": "National Hospital Organization Saitama Hospital" - }, - { - "author_name": "Masahiko Yamazaki", - "author_inst": "Zama Childrens Clinic" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "University of Tokyo" - }, - { - "author_name": "Yuki Furuse", - "author_inst": "Nagasaki University" + "author_name": "Sulatha Dwarakanath", + "author_inst": "Kaya17 Inc" } ], "version": "1", - "license": "cc_by_nd", + "license": "cc_by", "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, @@ -257358,53 +257473,105 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.07.07.22277391", - "rel_title": "Modeling the impact of the Omicron infection wave in Germany", + "rel_doi": "10.1101/2022.07.05.22277189", + "rel_title": "Class switch towards non-inflammatory IgG isotypes after repeated SARS-CoV-2 mRNA vaccination", "rel_date": "2022-07-10", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.07.22277391", - "rel_abs": "BACKGROUNDIn November 2021, the first case of SARS-CoV-2 \"variant of concern\" (VOC) B.1.1.529 (\"Omicron\") was reported in Germany, alongside global reports of reduced vaccine efficacy against infections with this variant. The potential threat posed by the rapid spread of this variant in Germany remained, at the time, elusive.\n\nMETHODSWe developed a variant-dependent population-averaged susceptible-exposed-infected-recovered (SEIR) infectious disease model. The model was calibrated on the observed fixation dynamics of the Omicron variant in December 2021, and allowed us to estimate potential courses of upcoming infection waves in Germany, focusing on the corresponding burden on intensive care units (ICUs) and the efficacy of contact reduction strategies.\n\nRESULTSA maximum median incidence of approximately 300 000 (50% PI in 1000: [181,454], 95% PI in 1000: [55,804]) reported cases per day was expected with the median peak occurring in the mid of February 2022, reaching a cumulative Omicron case count of 16.5 million (50% PI in mio: [11.4, 21.3], 95% PI in mio: [4.1, 27.9]) until Apr 1, 2022. These figures were in line with the actual Omicron waves that were subsequently observed in Germany with respective peaks occurring in mid February (peak: 191k daily new cases) and mid March (peak: 230k daily new cases), cumulatively infecting 14.8 million individuals during the study period. The model peak incidence was observed to be highly sensitive to variations in the assumed generation time and decreased with shorter generation time. Low contact reductions were expected to lead to containment. Early, strict, and short contact reductions could have led to a strong \"rebound\" effect with high incidences after the end of the respective non-pharmaceutical interventions. Higher vaccine uptake would have led to a lower outbreak size. To ensure that ICU occupancy remained below maximum capacity, a relative risk of requiring ICU care of 10%-20% was necessary (after infection with Omicron vs. infection with Delta).\n\nCONCLUSIONSWe expected a large cumulative number of infections with the VOC Omicron in Germany with ICU occupancy likely remaining below capacity nevertheless, even without additional non-pharmaceutical interventions. Our estimates were in line with the retrospectively observed waves. The results presented here informed legislation in Germany. The methodology developed in this study might be used to estimate the impact of future waves of COVID-19 or other infectious diseases.", - "rel_num_authors": 9, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.05.22277189", + "rel_abs": "Repeated mRNA vaccinations are an efficient tool to combat the SARS-CoV-2 pandemic. High levels of neutralizing SARS-CoV-2-antibodies are an important component of vaccine-induced immunity. Shortly after the first or second mRNA vaccine dose, the IgG response mainly consists of the pro-inflammatory isotypes IgG1 and IgG3 and is driven by T helper (Th) 1 cells. Here, we report that several months after the second vaccination, SARS-CoV-2-specific antibodies were increasingly composed of non-inflammatory IgG2 and particularly IgG4, which were further boosted by a third mRNA vaccination and/or SARS-CoV-2 variant breakthrough infections. While IgG antibodies were affinity matured and of high neutralization capacity, the switch in constant domains caused changes in fragment crystallizable (Fc)-receptor mediated effector functions, including a decreased capacity to facilitate phagocytosis. IgG4 induction was neither induced by Th2 cells nor observed after homologous or heterologous SARS-CoV-2 vaccination with adenoviral vectors. In addition, IgG2- and IgG4-producing memory B cells were phenotypically indistinguishable from IgG1- or IgG3-producing cells. Since Fc-mediated effector functions are critical for antiviral immunity, the described class switch towards non-inflammatory IgG isotypes, which otherwise rarely occurs after vaccination or viral infection, may have consequences for the choice and timing of vaccination regimens using mRNA vaccines.", + "rel_num_authors": 22, "rel_authors": [ { - "author_name": "Benjamin F Maier", - "author_inst": "Robert Koch Institute" + "author_name": "Pascal Irrgang", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," }, { - "author_name": "Angelique Burdinski", - "author_inst": "Robert Koch Institute" + "author_name": "Juliane Gerling", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," }, { - "author_name": "Marc Wiedermann", - "author_inst": "Robert Koch Institute" + "author_name": "Katharina Kocher", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" }, { - "author_name": "Annika H Rose", - "author_inst": "Robert Koch Institute" + "author_name": "Dennis Lapuente", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," }, { - "author_name": "Matthias an der Heiden", - "author_inst": "Robert Koch Institute" + "author_name": "Philipp Steininger", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," }, { - "author_name": "Ole Wichmann", - "author_inst": "Robert Koch Institute" + "author_name": "Monika Wytopil", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," }, { - "author_name": "Thomas Harder", - "author_inst": "Robert Koch Institute" + "author_name": "Simon Sch\u00e4fer", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," }, { - "author_name": "Frank Schlosser", - "author_inst": "Robert Koch Institute" + "author_name": "Katharina Habenicht", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," }, { - "author_name": "Dirk Brockmann", - "author_inst": "Robert Koch Institute" + "author_name": "Jahn Zhong", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," + }, + { + "author_name": "George Ssebyatika", + "author_inst": "Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Thomas Krey", + "author_inst": "Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck, Luebeck, Germany" + }, + { + "author_name": "Valeria Falcone", + "author_inst": "Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany" + }, + { + "author_name": "Christine Sch\u00fclein", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Antonia Sophia Peter", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Krystelle Nganou-Makamdop", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Hartmut Hengel", + "author_inst": "Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany" + }, + { + "author_name": "J\u00fcrgen Held", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Christian Bogdan", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Klaus \u00dcberla", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," + }, + { + "author_name": "Kilian Schober", + "author_inst": "Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlange" + }, + { + "author_name": "Thomas H Winkler", + "author_inst": "Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-University Erlangen-Nuremberg (FAU), Erlangen," + }, + { + "author_name": "Matthias Tenbusch", + "author_inst": "Institut fuer klinische und molekulare Virologie, Universitaetsklinikum Erlangen und Friedrich-Alexander-Universitaet (FAU) Erlangen-Nuernberg, Schlossgarten 4," } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc_no", "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, @@ -259516,67 +259683,27 @@ "category": "epidemiology" }, { - "rel_doi": "10.1101/2022.07.07.22277360", - "rel_title": "Racial Disparities in Hesitancy and Utilization of Monoclonal Antibody Infusion Treatment of COVID-19", + "rel_doi": "10.1101/2022.07.06.22277303", + "rel_title": "Quantifying the impact of vaccines and booster doses on COVID-19 in the U.S.", "rel_date": "2022-07-07", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.07.22277360", - "rel_abs": "Background and MethodsWe conducted a single center cross-sectional study to investigate racial disparities in the hesitancy and utilization of monoclonal antibody (mAb) treatment of COVID-19 among treatment eligible patients who were referred to the infusion center between January 4, 2021 and May 14, 2021.\n\nResultsAmong the 2,406 eligible participants, African Americans were significantly more likely to underutilize mAb treatment (OR 1.8; 95% CI 1.5-2.1) and miss treatment opportunities due to monoclonal hesitancy (OR 1.7, 95% CI 1.3-2.1).\n\nConclusionAddressing racial disparities in mAb delivery is an opportunity to bridge the racial inequities in COVID-19 care.", - "rel_num_authors": 12, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.06.22277303", + "rel_abs": "The COVID-19 pandemic continues to have a devastating impact on health systems and economies across the globe. Implementing public health measures in tandem with effective vaccination strategies have been instrumental in curtailing the burden of the pandemic. With the three vaccines authorized for use in the U.S. having varying efficacies and waning effects against major COVID-19 strains, understanding the impact of these vaccines on COVID-19 incidence and fatalities is critical. Here, we formulate and use mathematical models to assess the impact of vaccine type, vaccination and booster uptake, and waning of natural and vaccine-induced immunity on the incidence and fatalities of COVID-19 and to predict future trends of the disease in the U.S. when existing control measures are reinforced or relaxed. Results of the study show a 5, 1.8, and 2 times reduction in the reproduction number during the period in which vaccination, first booster, and second booster uptake started, respectively, compared to the previous period. Due to waning of vaccine-induced immunity, vaccinating up to 96% of the U.S. population might be required to attain herd immunity, if booster uptake is low. Additionally, vaccinating and boosting more people from the onset of vaccination and booster uptake, especially with mRNA vaccines (which confer superior protection than the Johnson & Johnson vaccine) would have led to a significant reduction in COVID-19 cases and deaths in the U.S. Furthermore, adopting natural immunity-boosting measures is important in fighting COVID-19 and transmission rate reduction measures such as mask-use are critical in combating COVID-19. The emergence of a more transmissible COVID-19 variant, or early relaxation of existing control measures can lead to a more devastating wave, especially if transmission rate reduction measures and vaccination are relaxed simultaneously, while chances of containing the pandemic are enhanced if both vaccination and transmission rate reduction measures are reinforced simultaneously. We conclude that maintaining or improving existing control measures and boosting with mRNA vaccines are critical in curtailing the burden of the pandemic in the U.S.", + "rel_num_authors": 2, "rel_authors": [ { - "author_name": "Yahya Shaikh", - "author_inst": "MITRE Corporation, Baltimore, Maryland, USA" - }, - { - "author_name": "Ishaan Gupta", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Sophia Purekal", - "author_inst": "Baltimore Convention Center Field Hospital, Baltimore, Maryland, USA" - }, - { - "author_name": "MaryJane E. Vaeth", - "author_inst": "Baltimore Convention Center Field Hospital, Baltimore, Maryland, USA" - }, - { - "author_name": "Maisha Foyez", - "author_inst": "Baltimore Convention Center Field Hospital, Baltimore, Maryland, USA" - }, - { - "author_name": "Charles D. Callahan", - "author_inst": "Department of Population Health, University of Maryland Medical Center, Baltimore, Maryland, USA" - }, - { - "author_name": "Maryam Elhabashy", - "author_inst": "University of Maryland, Baltimore County, Maryland, USA" - }, - { - "author_name": "James R Ficke", - "author_inst": "Department of Orthopaedic Surgery, Johns Hopkins University, Baltimore, Maryland, USA" - }, - { - "author_name": "Albert W. Wu", - "author_inst": "Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA" - }, - { - "author_name": "Paul Auwaerter", - "author_inst": "The Sherrilyn and Ken Fisher Center for Environmental Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA" - }, - { - "author_name": "Melinda E. Kantsiper", - "author_inst": "Division of Hospital Medicine, Johns Hopkins Bayview Medical Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA" + "author_name": "Calistus N. Ngonghala", + "author_inst": "Department of Mathematics, University of Florida, Gainesville, FL 32611, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA." }, { - "author_name": "Zishan K. Siddiqui", - "author_inst": "Department of Medicine, Johns Hopkins University, Baltimore, Maryland, USA" + "author_name": "Michael Asare-Baah", + "author_inst": "Department of Epidemiology, University of Florida, 2004 Mowry Road, Gainesville, FL 32610, USA; Emerging Pathogens Institute, University of Florida, Gainesville" } ], "version": "1", - "license": "cc_by_nc", + "license": "cc_no", "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" + "category": "epidemiology" }, { "rel_doi": "10.1101/2022.07.02.22277181", @@ -262522,23 +262649,47 @@ "category": "epidemiology" }, { - "rel_doi": "10.1101/2022.07.02.22276577", - "rel_title": "Revisiting biological sex as a risk factor for COVID-19: a fact or mirage of numbers?", + "rel_doi": "10.1101/2022.07.03.22277196", + "rel_title": "Leveraging Serosurveillance and Postmortem Surveillance to Quantify the Impact of COVID-19 in Africa", "rel_date": "2022-07-05", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.02.22276577", - "rel_abs": "Biological sex is considered a risk factor for COVID-19. The prevailing view supposes males are about two-fold more impacted than females based on early-stage studies. The observed higher male deaths in COVID-19 are purportedly a result of biological differences that make males more vulnerable to adverse outcomes in infectious diseases. Research and policy paradigms seem to follow a similar line of thought to mitigate COVID-19 impact on populations. The analysis of sex-disaggregated data could help us evaluate the veracity of assertions for a preferred evidence-guided response. The analysis of the sex-disaggregated data available for the top 70 countries contributing about 80% of total deaths (as of 15 September 2021; on average two waves of infections experienced) indicates average Case Sex (Male: Female) ratio (CSR) of 1.09{+/-}0.35 (marginally more male cases) and Death Sex ratio (DSR) of 1.48{+/-} 0.47. Consideration of only laboratory-confirmed cases indicates the mortality sex ratio (MSR) in COVID-19 (MSR-COVID) to be 1.37{+/-}0.30. The prevailing MSR for the same countries was 1.758{+/-}0.409. The relative change in the mortality rate for males as compared to females in COVID-19 (ratio: MSR-COVID/prevailing MSR-PP) was 0.818{+/-}0.261 much lower than anticipated (2 or higher). Overall, over three-fold more countries (51/70) experienced a higher rate of female mortality than male mortality (15/70). Together, it suggests a more disproportionately severe impact of COVID-19 on females than on males, contrary to the prevailing view. Identification and analysis of country-specific factors contributing to differential impact on sexes, whether biological or environmental, seem warranted.", - "rel_num_authors": 1, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.03.22277196", + "rel_abs": "BackgroundThe COVID-19 pandemic has had a devastating impact on global health, the magnitude of which appears to differ intercontinentally: for example, reports suggest 271,900 per million people have been infected in Europe versus 8,800 per million people in Africa. While Africa is the second largest continent by population, its reported COVID-19 cases comprise <3% of global cases. Although social, environmental, and environmental explanations have been proposed to clarify this discrepancy, systematic infection underascertainment may be equally responsible.\n\nMethodsWe seek to quantify magnitude of underascertainment in COVID-19s cumulative incidence in Africa. Using serosurveillance and postmortem surveillance, we constructed multiplicative factors estimating ratios of true infections to reported cases in African nations since March 2020.\n\nResultsMultiplicative factors derived from serology data - in a subset of 12 nations - suggested a range of COVID-19 reporting rates, from 1 in 630 infections reported in Kenya (May 2020) to 1 in 15 infections reported in South Africa (November 2021). The largest multiplicative factor, 3,795, corresponded to Malawi (June 2020), suggesting <0.05% of infections captured. A similar set of multiplicative factors for all nations derived from postmortem data points toward the same conclusion: reported COVID-19 cases are unrepresentative of true infections, suggesting a key reason for low case burden in many African nations is significant underdetection and underreporting.\n\nConclusionsWhile estimating COVID-19s exact burden is challenging, the multiplicative factors we present provide incidence curves reflecting likely-to-worst-case ranges of infection. Our results stress the need for expansive surveillance to allocate resources in areas experiencing severe discrepancies between reported cases, projected infections, and deaths.\n\nSummaryHere we present a range of estimates quantifying the extent of underascertainment of COVID-19 cumulative incidence in Africa. These estimates, constructed from serology and mortality data, suggest that systematic underdetection and underreporting may be contributing to the seemingly low burden of COVID-19 reported in Africa.", + "rel_num_authors": 7, "rel_authors": [ { - "author_name": "Samer Singh", - "author_inst": "Banaras Hindu University" + "author_name": "Nicole Kogan", + "author_inst": "Harvard T. H. Chan School of Public Health | Northeastern University" + }, + { + "author_name": "Shae Gantt", + "author_inst": "Harvard T. H. Chan School of Public Health" + }, + { + "author_name": "David Swerdlow", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Cecile Viboud", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Muhammed Semakula", + "author_inst": "Rwanda Biomedical Centre" + }, + { + "author_name": "Marc Lipsitch", + "author_inst": "Harvard T. H. Chan School of Public Health | CDC" + }, + { + "author_name": "Mauricio Santillana", + "author_inst": "Northeastern University | Harvard T. H. Chan School of Public Health" } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc_no", "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" + "category": "infectious diseases" }, { "rel_doi": "10.1101/2022.06.29.498117", @@ -264540,43 +264691,91 @@ "category": "epidemiology" }, { - "rel_doi": "10.1101/2022.07.01.22277108", - "rel_title": "Self-Reported Use of COVID-19 Immunologic Test Results to Inform Decisions About Daily Activities and COVID-19 Vaccination", + "rel_doi": "10.1101/2022.07.01.22277163", + "rel_title": "Phase 2 randomised placebo-controlled trial of spironolactone and dexamethasone versus dexamethasone in COVID-19 hospitalised patients in Delhi", "rel_date": "2022-07-02", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.01.22277108", - "rel_abs": "ImportanceDespite widespread use of clinical diagnostic tests to assess prior exposure to SARS-CoV-2, limited evidence exists regarding how test results affect patient behaviors and decision-making.\n\nObjectiveTo understand the rationale behind ordering diagnostic T-cell receptor (TCR) immunosequencing for assessment of prior SARS-CoV-2 infection and evaluate how test results affect patient behaviors, including day-to-day activities and decisions about vaccination.\n\nDesignMandatory demographic information and clinical characteristics were collected for all individuals ordering T-Detect COVID. Study participants completed a one-time survey that included additional questions about demographics and clinical characteristics, relevant interactions with healthcare providers, reasons for ordering diagnostic TCR immunosequencing, and the utility of test results.\n\nSettingUS participants ordering T-Detect COVID between February 2021 and March 2022.\n\nParticipantsOf the 806 individuals who underwent diagnostic TCR immunosequencing, provided informed consent, and were sent the email survey, 718 completed the survey (response rate, 89.1%). At the time of receiving the test report, 25.5% of participants had been vaccinated against COVID-19, 29.7% reported a previous COVID-19 infection, and 25.6% were immunocompromised.\n\nMain Outcome(s) and Measure(s)Patient demographics and clinical characteristics were reported using descriptive statistics. Additional analyses explored trends in reported data over time and evaluated reasons for ordering diagnostic TCR immunosequencing and behaviors among participant subgroups (vaccinated or unvaccinated individuals and those with positive or negative test results). Logistic regression analysis evaluated factors that increased the likelihood of post-test vaccination.\n\nResultsStudy participants ordered diagnostic TCR immunosequencing to understand their health status (55.0%) and to inform decision-making about daily activities (43.6%) and vaccination (38.3%). Most participants (92.1%) ordered diagnostic TCR immunosequencing for themselves without consulting their physician. Testing negative for prior SARS-CoV-2 infection was associated with increased likelihood of subsequent COVID-19 vaccination (31.0% vs 6.9%; median time to vaccination, 17.0 days vs 47.5 days), which was confirmed by logistic regression analysis.\n\nConclusions and RelevanceThis report presents patient-reported clinical utility of a commercial COVID-19 assay based on an immune response readout. Our findings suggest that participants used diagnostic TCR immunosequencing results to inform decisions about daily activities and COVID-19 vaccination.\n\nTrial RegistrationNot applicable.\n\nKEY POINTSO_LIWe aimed to understand the factors driving immunologic testing for SARS-CoV-2 and characterize the actions and decisions spurred by test results.\nC_LIO_LIResults of this study suggest that individuals frequently ordered immunologic testing for themselves to understand their health status and to inform decision-making about daily activities and vaccination.\nC_LIO_LIAmong unvaccinated participants, testing negative for prior SARS-CoV-2 infection was associated with increased likelihood of undergoing vaccination and shorter time to vaccination.\nC_LIO_LIThis study provides the first real-world evidence of patient-perceived utility of a COVID-19 immunologic test for decision-making related to vaccination and lifestyle.\nC_LI", - "rel_num_authors": 6, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.01.22277163", + "rel_abs": "BackgroundIn this phase 2 randomised placebo-controlled clinical trial, we hypothesised that blocking mineralocorticoid receptors with spironolactone in patients with COVID-19 is safe and may reduce illness severity.\n\nMethodsHospitalised patients with confirmed COVID-19 were randomly allocated to low dose oral spironolactone (50mg day 1, then 25mg once daily for 21 days) or standard care in a 2:1 ratio. Both groups received dexamethasone 6mg for 10 days. Group allocation was blinded to the patient and research team. Primary outcomes were time to recovery, defined as the number of days until patients achieved WHO Ordinal Scale (OS) category [≤] 3, and the effect of spironolactone on aldosterone, D-dimer, angiotensin II and Von Willebrand Factor (VWF).\n\nResults120 patients were recruited in Delhi from 01 February to 30 April 2021. 74 were randomly assigned to spironolactone and dexamethasone (SpiroDex), and 46 to dexamethasone alone (Dex). There was no significant difference in the time to recovery between SpiroDex and Dex groups (SpiroDex median 4.5 days, Dex median 5.5 days, p = 0.055). SpiroDex patients had lower aldosterone levels on day 7 and lower D-dimer levels on days 4 and 7 (day 7 D-dimer mean SpiroDex 1.15{micro}g/mL, Dex 3.15 {micro}g/mL, p = 0.0004). There was no increase in adverse events in patients receiving SpiroDex. Post hoc analysis demonstrated reduced clinical deterioration (pre specified as escalating to WHO OS category >4) in the SpiroDex group vs Dex group (5.4% vs 19.6%).\n\nConclusionLow dose oral spironolactone in addition to dexamethasone was safe and reduced D-Dimer and aldosterone. Although time to recovery was not significantly reduced, fewer patients progressed to severe disease. Phase 3 randomised controlled trials with spironolactone should be considered.", + "rel_num_authors": 18, "rel_authors": [ { - "author_name": "Miao Jiang", - "author_inst": "Adaptive Biotechnologies" + "author_name": "Bharti Wadhwa", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" }, { - "author_name": "Nicholas K. Akers", - "author_inst": "Adaptive Biotechnologies" + "author_name": "Vikas Malhotra", + "author_inst": "Department of ENT & Head and Neck Surgery, Maulana Azad Medical College & Associated Hospitals, New Delhi, India" }, { - "author_name": "Darcy B. Gill", - "author_inst": "Adaptive Biotechnologies" + "author_name": "Sukhyanti Kerai", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" }, { - "author_name": "Benjamin Eckhert", - "author_inst": "Adaptive Biotechnologies" + "author_name": "Farah Husain", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" }, { - "author_name": "Emily Svejnoha", - "author_inst": "Adaptive Biotechnologies" + "author_name": "Nalini Bala Pandey", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" }, { - "author_name": "Harlan S Robins", - "author_inst": "Adaptive Biotechnologies" + "author_name": "Kirti N Saxena", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Vinay Singh", + "author_inst": "Department of Anaesthesia, Maulana Azad Medical College, New Delhi, India" + }, + { + "author_name": "Tom Michael Quinn", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Feng Li", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Erin Gaughan", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Manu Shankar-Hari", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Bethany Mills", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Jean Antonelli", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Annya Bruce", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Keith Finlayson", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Anne Moore", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Kevin Dhaliwal", + "author_inst": "Centre for Inflammation Research, The Queens Medical Research Institute, The University of Edinburgh,UK" + }, + { + "author_name": "Christopher Edwards", + "author_inst": "Imperial College, Hammersmith Campus, UK" } ], "version": "1", "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" + "category": "respiratory medicine" }, { "rel_doi": "10.1101/2022.06.30.498338", @@ -266194,63 +266393,35 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.06.28.22276794", - "rel_title": "Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine, KD-414, in healthy adult and elderly subjects: a randomized, double-blind, placebo-controlled, phase 1/2 clinical study in Japan", + "rel_doi": "10.1101/2022.06.29.22277010", + "rel_title": "Exploring the Role of Superspreading Events in SARS-CoV-2 Outbreaks", "rel_date": "2022-06-29", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.28.22276794", - "rel_abs": "BackgroundIn the current protracted COVID-19 pandemic, SARS-CoV-2 vaccines that have the ability to be used safely and to prevent onset or severe disease are still highly needed. A Phase 1/2 study was conducted in healthy adults and the elderly in Japan to evaluate the immunogenicity, safety, and tolerability of an inactivated whole-virus vaccine (KD-414) that is under development.\n\nMethodsIn this double-blind, randomized, placebo-controlled, Phase 1/2 study, adults aged 20 to 64 years and elderly participants aged 65 years or older without a history of COVID-19 were randomly allocated to the following groups: the L group (2.5 g/dose), M group (5 g/dose), or H group (10 g/dose) with KD-414, or the placebo group (2:2:2:1). The participants received KD-414 or the placebo intramuscularly twice at intervals of 28 days. To determine the go-forward dose, safety after the first dosing and neutralizing antibody titers against SARS-CoV-2 at 28 days after the second dosing were evaluated for each group. Additionally, after unblinding, participants in the H group received a third dose of KD-414 (H) approximately 6 months after the second dosing for an exploratory evaluation of the safety and neutralizing antibody titers to be conducted.\n\nResultsA total of 210 participants were enrolled: 105 adults aged 20 to 64 years, and 105 elderly participants aged 65 years or older. Of these participants, 105 adults and 104 elderly participants completed the second dosing, and 28 adults and 31 elderly participants in the H group received a third dose of KD-414 (H). The incidence of adverse reactions from the first dosing to 28 days after the second dosing was 19 of 30 (63.3%), 22 of 31 (71.0%), 22 of 29 (75.9%), and six of 15 (40.0%) for adults, and 14 of 30 (46.7%), 14 of 29 (48.3%), 15 of 31 (48.4%), and six of 15 (40.0%) for elderly participants in the L, M, H, and placebo groups, respectively. No differences in incidence were shown among the KD-414 groups. The most common adverse reaction was injection site pain. Fever that resolved the following day was observed in only 1 adult in the H group after the second dosing; this was a sole Grade 3 or higher adverse reaction. For immunogenicity, the neutralizing antibody seroconversion rate (95% confidence intervals [CI]) against SARS-CoV-2 (vaccine strain) 28 days after the second dosing was 36.7% (19.9-56.1), 38.7% (21.8-57.8), and 72.4% (52.8-87.3) in adults, and 33.3% (17.3-52.8), 31.0% (15.3-50.8), and 45.2% (27.3-64.0) in elderly participants in the L, M, and H groups, respectively, showing a dose response by KD-414. The stratified analysis by age-range for the H group, which observed the highest immunogenicity, also showed an age dependency in the neutralizing antibody responses. Based on these results up to the second dosing, the H (10 g/dose) dosage was determined as the recommended dosage for further clinical development of KD-414. In addition, there was no particular difference between the incidence of adverse reactions after the third dosing and that after the second dosing with KD-414 (H) in participants. Moreover, the geometric mean neutralizing antibody titers (GMTs) against SARS-CoV-2 (vaccine strain) 28 days after the third dosing were 2-fold higher than those at 28 days after the second dosing, and the GMTs 13 weeks after the third dosing were 3-fold higher than those at 13 weeks after the second dosing. The stratified analysis by age-range of Pseudovirus SARS-CoV-2 (D614) spike protein neutralizing antibody titers showed 100.0% neutralizing antibody seroconversion rate and high neutralizing antibody titers in participants aged [≤] 40 years.\n\nConclusionKD-414 was well tolerated in healthy adults and the elderly at all doses evaluated. In view of the dose-response and age-dependency of the immunogenicity of KD-414 (H) (10 g/dose), it is expected to induce high neutralizing antibody titers, particularly in the age range of 20 to 40 years. A Phase 2/3 study (Japan Registry of Clinical Trials [jRCT] 2071210081), a Phase 3 study (jRCT 2031210679), and a Phase 2/3 study in pediatric participants aged 6 months to 17 years (jRCT 2031220032) using KD-414 (H) are ongoing.", - "rel_num_authors": 11, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.29.22277010", + "rel_abs": "The novel coronavirus SARS-CoV-2 emerged in 2019 and subsequently spread throughout the world, causing over 529 million cases and 6 million deaths thus far. In this study, we formulate a continuous-time Markov chain model to investigate the influence of superspreading events (SSEs), defined here as public or social events that result in multiple infections over a short time span, on SARS-CoV-2 outbreak dynamics. Using Gillespies direct algorithm, we simulate a continuous-time Markov chain model for SARS-CoV-2 spread under multiple scenarios: first, with neither hospitalisation nor quarantine; second, with hospitalisation, quarantine, premature hospital discharge, and quarantine violation; and third, with hospitalisation and quarantine but neither premature hospital discharge nor quarantine violation. We also vary quarantine violation rates. Results indicate that, in most cases, SSE-dominated outbreaks are more variable but less severe than non-SSE-dominated outbreaks, though the most severe SSE-dominated outbreaks are more severe than the most severe non-SSE-dominated outbreaks. SSE-dominated outbreaks are outbreaks with relatively higher SSE rates. In all cases, SSE-dominated outbreaks are more sensitive to control measures, with premature hospital discharge and quarantine violation substantially reducing control measure effectiveness.", + "rel_num_authors": 4, "rel_authors": [ { - "author_name": "Mitsuyoshi Tanishima", - "author_inst": "KM Biologics Co., Ltd. (KM Biologics), Kumamoto, Japan" - }, - { - "author_name": "Kayo Ibaraki", - "author_inst": "KM Biologics Co., Ltd. (KM Biologics), Kumamoto, Japan" - }, - { - "author_name": "Keishi Kido", - "author_inst": "KM Biologics Co., Ltd. (KM Biologics), Kumamoto, Japan" - }, - { - "author_name": "Shun Nakayama", - "author_inst": "KM Biologics Co., Ltd. (KM Biologics), Kumamoto, Japan" - }, - { - "author_name": "Shun Nakayama", - "author_inst": "KM Biologics Co., Ltd. (KM Biologics), Kumamoto, Japan" - }, - { - "author_name": "Kohei Ata", - "author_inst": "KM Biologics Co., Ltd. (KM Biologics), Kumamoto, Japan" - }, - { - "author_name": "Hideki Nakamura", - "author_inst": "KM Biologics Co., Ltd. (KM Biologics), Kumamoto, Japan" - }, - { - "author_name": "Yasuhiko Shinmura", - "author_inst": "KM Biologics Co., Ltd. (KM Biologics), Kumamoto, Japan" + "author_name": "Jordan Bramble", + "author_inst": "University of Kansas" }, { - "author_name": "Kengo Sonoda", - "author_inst": "KM Biologics Co., Ltd. (KM Biologics), Kumamoto, Japan" + "author_name": "Alexander Fulk", + "author_inst": "University of Kansas" }, { - "author_name": "Kohji Ueda", - "author_inst": "Professor emeritus, Kyushu University, Fukuoka, Japan" + "author_name": "Raul Saenz", + "author_inst": "University of Kansas Medical Center" }, { - "author_name": "Yoshiaki Oda", - "author_inst": "KM Biologics Co., Ltd. (KM Biologics), Kumamoto, Japan" + "author_name": "Folashade Agusto", + "author_inst": "University of Kansas" } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc_no", "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" + "category": "epidemiology" }, { "rel_doi": "10.1101/2022.06.27.497749", @@ -268016,71 +268187,43 @@ "category": "public and global health" }, { - "rel_doi": "10.1101/2022.06.23.22276820", - "rel_title": "IMMUNE PROFILES TO DISTINGUISH HOSPITALIZED VERSUS AMBULATORY COVID-19 CASES IN OLDER PATIENTS", + "rel_doi": "10.1101/2022.06.24.22276852", + "rel_title": "Compliant citizens, defiant rebels or neither? Exploring changing COVID-19 vaccine attitudes and decisions in Bradford, UK: Findings from a follow-up qualitative study", "rel_date": "2022-06-27", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.23.22276820", - "rel_abs": "BackgroundA fraction of COVID-19 patients develops severe disease requiring hospitalization, while the majority, including high-risk individuals, experience mild symptoms. Severe disease has been associated with higher levels of antibodies and inflammatory cytokines, but the association has often resulted from comparison of patients with diverse demographics and comorbidity status. This study examined patients with defined demographic risk factors for severe COVID-19 who developed mild vs. severe COVID-19.\n\nMethodsThis study evaluated hospitalized vs. ambulatory COVID-19 patients in the James J. Peters VA Medical Center, Bronx, NY. This cohort presented demographic risk factors for severe COVID-19: median age of 63, >80% male, >85% black and/or Hispanic. Sera were collected four to 243 days after symptom onset and evaluated for binding and functional antibodies as well as 48 cytokines/chemokines.\n\nFindingsAmbulatory and hospitalized patients showed no difference in SARS-CoV-2-specific antibody levels and functions. However, a strong correlation between anti-S2 antibody levels and the other antibody parameters was observed in hospitalized but not in ambulatory cases. Cytokine/chemokine levels also revealed differences, with notably higher IL-27 levels in hospitalized patients. Hence, among the older, mostly male patients studied here, SARS-CoV-2-specific antibody levels and functions did not distinguish hospitalized and ambulatory cases but a discordance in S2-specific antibody responses was noted in ambulatory patients, and elevated levels of specific cytokines were maintained in convalescent sera of hospitalized cases.\n\nInterpretationThe data indicate that antibodies against the relatively conserved S2 spike subunit and immunoregulatory cytokines such as IL-27 are potential immune determinants of COVID-19.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSPrevious studies demonstrated that high levels of SARS-CoV-2 spike binding antibodies and neutralizing antibodies were associated with COVID-19 disease severity. However, the comparisons were often made without considering demographics and comorbidities. Correlation was similarly shown between severe disease and marked elevation of several plasma cytokines but again, most analyses of cytokine responses to COVID-19 were conducted by comparison of patient cohorts with diverse demographic characteristics and risk factors.\n\nAdded value of this studyWe evaluated here a comprehensive profile of SARS-CoV-2-specific antibodies (total Ig, isotypes/subtypes, Fab- and Fc-mediated functions) and a panel of 48 cytokines and chemokines in serum samples from a cohort of SARS-CoV-2-infected patients with demographic risk factors for severe COVID-19: 81% were male, 79% were >50 years old (median of 63), and 85% belonged to US minority groups (black and/or Hispanic). Comparison of hospitalized vs. ambulatory patients within this cohort revealed two features that differed between severe vs. mild COVID-19 cases: a discordant Ab response to the S2 subunit of the viral spike protein in the mild cases and an elevated response of specific cytokines and chemokines, notably IL-27, in the severe cases.\n\nImplications of all the available evidenceData from the study identified key immunologic markers for severe vs. mild COVID-19 that provide a path forward for investigations of their roles in minimizing or augmenting disease severity.", - "rel_num_authors": 13, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.24.22276852", + "rel_abs": "BackgroundCOVID-19 vaccines have been the central pillar of the public health response to the pandemic, intended to enable us to live with Covid. It is important to understand COVID-19 vaccines attitudes and decisions in order to maximise uptake through an empathetic lens.\n\nObjectiveTo explore the factors that influenced peoples COVID-19 vaccines decisions and how attitudes towards the vaccines had changed in an eventful year.\n\nDesign and participantsThis is a follow up study that took place in Bradford, UK one year after the original study, between October 2021 and January 2022. In-depth phone interviews were conducted with 12 (of the 20 originally interviewed) people from different ethnic groups and areas of Bradford. Reflexive thematic analysis was conducted.\n\nResults11 of the 12 participants interviewed had received both doses of the COVID-19 vaccine and most intended to have a booster dose. Participants described a variety of reasons why they had decided to have the vaccines, including: feeling at increased risk at work; protecting family and others in their communities, unrestricted travel and being influenced by the vaccine decisions of family, friends and colleagues. All participants discussed ongoing interaction with COVID-19 misinformation and for some this meant they were uneasy about their decision to have the vaccine. They described feeling overloaded by and disengaged from COVID-19 information, which they often found contradictory and some felt mistrustful of the UK governments motives and decisions during the pandemic.\n\nConclusionsThe majority of participants had managed to navigate an overwhelming amount of circulating COVID-19 misinformation and chosen to have two or more COVID-19 vaccines, even if they had been previously said they were unsure. However, these decisions were complicated, and demonstrate the continuum of vaccine hesitancy and acceptance. This follow up study underlines that vaccine attitudes are changeable and contextual.\n\nPatient or Public ContributionThe original study was developed through a rapid community and stakeholder engagement process in 2020. Discussion with the Bradford Council Public Health team and the public through the Bradford COVID-19 Community Insights Group was undertaken in 2021 to identify important priorities for this follow up study.", + "rel_num_authors": 6, "rel_authors": [ { - "author_name": "Jeromine Klingler", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Gregory S Lambert", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Juan C Bandres", - "author_inst": "James J. Peters VA Medical Center" + "author_name": "Bridget Lockyer", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust" }, { - "author_name": "Rozita Emami-Gorizi", - "author_inst": "James J. Peters VA Medical Center" + "author_name": "Rachael H Moss", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust" }, { - "author_name": "Arthur Nadas", - "author_inst": "NYU School of Medicine" + "author_name": "Charlotte Endacott", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust" }, { - "author_name": "Kasopefoluwa Y Oguntuyo", - "author_inst": "Icahn School of Medicine at Mount Sinai" + "author_name": "Shahid Islam", + "author_inst": "Bradford Institute for Health Research, Bradford Teaching Hospitals Foundation Trust" }, { - "author_name": "Fatima Amanat", - "author_inst": "Icahn School of Medicine at Mount Sinai" + "author_name": "Laura Sheard", + "author_inst": "Bradford Teaching Hospitals Foundation Trust" }, { - "author_name": "- PARIS Study Team", + "author_name": "- Bradford Institute for Health Research Covid-19 Scientific Advisory Group", "author_inst": "" - }, - { - "author_name": "Viviana Simon", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Benhur Lee", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Susan Zolla-Pazner", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Chitra Upadhyay", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Catarina E Hioe", - "author_inst": "Icahn School of Medicine at Mount Sinai" } ], "version": "1", "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" + "category": "public and global health" }, { "rel_doi": "10.1101/2022.06.22.22276744", @@ -269666,95 +269809,55 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.06.24.22276703", - "rel_title": "A Bivalent Omicron-containing Booster Vaccine Against Covid-19", - "rel_date": "2022-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.24.22276703", - "rel_abs": "BackgroundUpdated vaccination strategies against acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern are needed. Interim results of the safety and immunogenicity of the bivalent omicron-containing mRNA-1273.214 booster candidate are presented.\n\nMethodsIn this ongoing, phase 2/3 trial, the 50-g bivalent vaccine mRNA-1273.214 (25-g each ancestral Wuhan-Hu-1 and omicron B.1.1.529 spike SARS-CoV-2 mRNAs) was compared to the authorized 50-g mRNA-1273 booster in adults who previously received 2-dose primary series of 100-g mRNA-1273 and a first booster dose of 50-g mRNA-1273 at least 3 months prior. Primary objectives were safety and reactogenicity, and immunogenicity of 50-g mRNA-1273.214 compared with 50-g mRNA-1273. Immunogenicity data 28 days after the booster dose are presented.\n\nResultsFour hundred thirty-seven and 377 participants received 50-g of mRNA-1273.214, or mRNA-1273, respectively. Median time between first and second booster doses of mRNA-1273.214 and mRNA-1273 were similar (136 and 134 days, respectively). In participants with no prior SARS-CoV-2 infection, observed omicron neutralizing antibody geometric mean titers (GMTs [95% confidence interval]) after the mRNA-1273.214 and mRNA-1273 booster doses, were 2372.4 (2070.6-2718.2) and 1473.5 (1270.8-1708.4) respectively and the model-based GMT ratio (97.5% confidence interval) was 1.75 (1.49-2.04). All pre-specified non-inferiority (ancestral SARS-CoV-2 with D614G mutation [D614G] GMT ratio; ancestral SARS-CoV-2 [D614G] and omicron seroresponse rates difference) and superiority primary objectives (omicron GMT ratio) for mRNA-1273.214 compared to mRNA-1273 were met. Additionally, mRNA-1273.214 50-g induced a potent neutralizing antibody response against omicron subvariants BA.4/BA.5 and higher binding antibody responses against alpha, beta, gamma, delta and omicron variants. Safety and reactogenicity profiles were similar and well-tolerated for both vaccines groups.\n\nConclusionThe bivalent vaccine mRNA-1273.214 50-g was well-tolerated and elicited a superior neutralizing antibody response against omicron, compared to mRNA-1273 50-g, and a non-inferior neutralizing antibody response against the ancestral SARS-CoV-2 (D614G), 28 days after immunization, creating a new tool as we respond to emerging SARS-CoV-2 variants.", - "rel_num_authors": 19, + "rel_doi": "10.1101/2022.06.23.497376", + "rel_title": "Monitoring SARS-CoV-2 infection using a double reporter-expressing virus", + "rel_date": "2022-06-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.23.497376", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the highly contagious agent responsible for the coronavirus disease 2019 (COVID-19) pandemic. An essential requirement for understanding SARS-CoV-2 fundamental biology and the impact of anti-viral therapeutics are robust methods to detect for the presence of the virus in infected cells or animal models. Despite the development and successful generation of recombinant (r)SARS-CoV-2 expressing fluorescent or luciferase reporter genes, knowledge acquired from their use in in vitro assays and/or in live animals are limited to the properties of the fluorescent or luciferase reporter genes. Herein, for the first time, we engineered a replication-competent rSARS-CoV-2 that expresses both fluorescent (mCherry) and luciferase (Nluc) reporter genes (rSARS-CoV-2/mCherry-Nluc) to overcome limitations associated with the use of a single reporter gene. In cultured cells, rSARS-CoV-2/mCherry-Nluc displayed similar viral fitness as rSARS-CoV-2 expressing single reporter fluorescent and luciferase genes (rSARS-CoV-2/mCherry and rSARS-CoV-2/Nluc, respectively), or wild-type (WT) rSARS-CoV-2, while maintaining comparable expression levels of both reporter genes. In vivo, rSARS-CoV-2/mCherry-Nluc has similar pathogenicity in K18 human angiotensin converting enzyme 2 (hACE2) transgenic mice than rSARS-CoV-2 expressing individual reporter genes, or WT rSARS-CoV-2. Importantly, rSARS-CoV-2/mCherry-Nluc facilitates the assessment of viral infection and transmission in golden Syrian hamsters using in vivo imaging systems (IVIS). Altogether, this study demonstrates the feasibility of using this novel bireporter-expressing rSARS-CoV-2 for the study SARS-CoV-2 in vitro and in vivo.\n\nIMPORTANCEDespite the availability of vaccines and antivirals, the coronavirus disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to ravage health care institutions worldwide. Previously, we have generated replication-competent recombinant (r)SARS-CoV-2 expressing fluorescent or luciferase reporter proteins to track viral infection in vitro and/or in vivo. However, these rSARS-CoV-2 are restricted to express only a single fluorescent or a luciferase reporter gene, limiting or preventing their use to specific in vitro assays and/or in vivo studies. To overcome this limitation, we have engineered a rSARS-CoV-2 expressing both fluorescent (mCherry) and luciferase (Nluc) genes and demonstrated its feasibility to study the biology of SARS-CoV-2 in vitro and/or in vivo, including the identification and characterization of neutralizing antibodies and/or antivirals. Using rodent models, we visualize SARS-CoV-2 infection and transmission through in vivo imaging systems (IVIS).", + "rel_num_authors": 9, "rel_authors": [ { - "author_name": "Spyros Chalkias", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Charles Harper", - "author_inst": "Meridian Clinical Research" - }, - { - "author_name": "Keith Vrbicky", - "author_inst": "Meridian Clinical Research" - }, - { - "author_name": "Stephen R Walsh", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Brandon Essink", - "author_inst": "Meridian Clinical Research" - }, - { - "author_name": "Adam Brosz", - "author_inst": "Meridian Clinical Research" - }, - { - "author_name": "Nichole McGhee", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Joanne E Tomassini", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Xing Chen", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Ying Chang", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Andrea Sutherland", - "author_inst": "Moderna, Inc." + "author_name": "Kevin Chiem", + "author_inst": "Texas Biomedical Research Institute" }, { - "author_name": "David C Montefiori", - "author_inst": "Duke University" + "author_name": "Jun-Gyu Park", + "author_inst": "Texas Biomedical Research Institute" }, { - "author_name": "Bethany Girard", - "author_inst": "Moderna, Inc." + "author_name": "Desarey Morales Vasquez", + "author_inst": "Texas Biomedical Research Institute" }, { - "author_name": "Darin K Edwards", - "author_inst": "Moderna, Inc." + "author_name": "Richard K. Plemper", + "author_inst": "Georgia State University" }, { - "author_name": "Jing Feng", - "author_inst": "Moderna, Inc." + "author_name": "Jordi B Torrelles", + "author_inst": "Texas Biomedical Research Institute" }, { - "author_name": "Honghong Zhou", - "author_inst": "Moderna, Inc." + "author_name": "James Kobie", + "author_inst": "University of Alabama at Birmingham" }, { - "author_name": "Lindsey R Baden", - "author_inst": "Brigham and Women's Hospital" + "author_name": "Mark R Walter", + "author_inst": "University of Alabama at Birmingham" }, { - "author_name": "Jacqueline M Miller", - "author_inst": "Moderna, Inc." + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" }, { - "author_name": "Rituparna Das", - "author_inst": "Moderna, Inc." + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" } ], "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" + "license": "cc_no", + "type": "new results", + "category": "microbiology" }, { "rel_doi": "10.1101/2022.06.23.497404", @@ -271488,45 +271591,41 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.06.20.22276662", - "rel_title": "Multiple cohort study of hospitalized SARS-CoV-2 in-host infection dynamics: parameter estimates, sensitivity and the eclipse phase profile", + "rel_doi": "10.1101/2022.06.21.22276724", + "rel_title": "COVID-19 rebound after Paxlovid and Molnupiravir during January-June 2022", "rel_date": "2022-06-22", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.20.22276662", - "rel_abs": "Within-host SARS-CoV-2 modelling studies have been published throughout the COVID-19 pandemic. These studies contain highly variable numbers of individuals and capture varying timescales of pathogen dynamics; some studies capture the time of disease onset, the peak viral load and subsequent heterogeneity in clearance dynamics across individuals, while others capture late-time post-peak dynamics. In this study, we curate multiple previously published SARS-CoV-2 viral load data sets, fit these data with a consistent modelling approach, and estimate the variability of in-host parameters including the basic reproduction number, R0. We find that fitted dynamics can be highly variable across data sets, and highly variable within data sets, particularly when key components of the dynamic trajectories (e.g. peak viral load) are not represented in the data. Further, we investigated the role of the eclipse phase time distribution in fitting SARS-CoV-2 viral load data. By varying the shape parameter of an Erlang distribution, we demonstrate that models with either no eclipse phase, or with an exponentially-distributed eclipse phase, offer significantly worse fits to these data, whereas models with less dispersion around the mean eclipse time (shape parameter two or more) offered the best fits to the available data.", - "rel_num_authors": 7, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.21.22276724", + "rel_abs": "ImportanceRecent case reports document that some patients who were treated with Paxlovid experienced rebound COVID-19 infections and symptoms 2 to 8 days after completing a 5-day course of Paxlovid. The Centers for Disease Control and Prevention (CDC) has recently issued a Health Alert Network Health Advisory to update the public on the potential for COVID-19 rebound after Paxlovid treatments. However, the rates of COVID-19 rebound in a real-world population or whether rebound is unique to Paxlovid remains unknown.\n\nObjectivesTo examine the rates and relative risks of COVID-19 rebound in patients treated with Paxlovid or with Molnupiravir and to compare characteristics of patients who experienced COVID-19 rebound to those who did not.\n\nDesign, Setting, and ParticipantsRetrospective cohort study of electronic health records (EHRs) of 92 million patients from a multicenter and nationwide database in the US. The study population comprised 13,644 patients age [≥] 18 years who contracted COVID-19 between 1/1/2022-6/8/2022 and were treated with Paxlovid (n =11,270) or with Molnupiravir (n =2,374) within 5 days of their COVID-19 infection.\n\nExposuresPaxlovid or Molnupiravir.\n\nMain Outcomes and MeasuresThree types of COVID-19 rebound outcomes (COVID-19 infections, COVID-19 related symptoms, and hospitalizations) were examined. Hazard ratios and 95% confidence interval (CI) of 7-day and 30-day risk for COVID-19 rebound between patients treated with Paxlovid and patients treated with Molnupiravir were calculated before and after propensity-score matching.\n\nResultsThe 7-day and 30-day COVID-19 rebound rates after Paxlovid treatment were 3.53% and 5.40% for COVID-19 infection, 2.31% and 5.87% for COVID-19 symptoms, and 0.44% and 0.77% for hospitalizations. The 7-day and 30-day COVID-19 rebound rates after Molnupiravir treatment were 5.86% and 8.59% for COVID-19 infection, 3.75% and 8.21% for COVID-19 symptoms, and 0.84% and 1.39% for hospitalizations. After propensity-score matching, there were no significant differences in COVID-19 rebound risks between Paxlovid and Molnupiravir: infection (HR 0.90, 95% CI: 0.73-1.11), COVID-19 symptoms (HR: 1.03, 95% CI: 0.83-1.27), or hospitalizations (HR: 0.92, 95% CI: 0.56-1.55). Patients with COVID-19 rebound had significantly higher prevalence of underlying medical conditions than those without.\n\nConclusions and RelevanceCOVID-19 rebound occurred both after Paxlovid and Molnupiravir, especially in patients with underlying medical conditions. This indicates that COVID-19 rebound is not unique to Paxlovid and the risks were similar for Paxlovid and Molnupiravir. For both drugs the rates of COVID-19 rebound increased with time after treatments. Our results call for continuous surveillance of COVID-19 rebound after Paxlovid and Molnupiravir treatments. Studies are necessary to determine the mechanisms underlying COVID-19 rebounds and to test dosing and duration regimes that might prevent such rebounds in vulnerable patients.", + "rel_num_authors": 6, "rel_authors": [ { - "author_name": "Chapin S. Korosec", - "author_inst": "York University" - }, - { - "author_name": "Matthew I. Betti", - "author_inst": "Mount Allison University" + "author_name": "Lindsey Wang", + "author_inst": "Case Western Reserve University" }, { - "author_name": "David W Dick", - "author_inst": "York University" + "author_name": "Nathan A Berger", + "author_inst": "Case Western Reserve University" }, { - "author_name": "Hsu Kiang Ooi", - "author_inst": "National Research Council Canada" + "author_name": "Pamela B Davis", + "author_inst": "Case Western Reserve University" }, { - "author_name": "Iain R. Moyles", - "author_inst": "York University" + "author_name": "David C Kaelber", + "author_inst": "MetroHealth" }, { - "author_name": "Lindi M. Wahl", - "author_inst": "Western University" + "author_name": "Nora Volkow", + "author_inst": "NIH/NIDA" }, { - "author_name": "Jane M Heffernan", - "author_inst": "York University" + "author_name": "Rong Xu", + "author_inst": "Case Western Reserve University" } ], "version": "1", - "license": "cc_by_nd", + "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, @@ -273462,23 +273561,115 @@ "category": "public and global health" }, { - "rel_doi": "10.1101/2022.06.15.22276447", - "rel_title": "Ventilation Requirements and Recommendations for Controlling SARS-CoV-2 and Variants Outbreaks in Indoor Gathering Places with Close Contact", + "rel_doi": "10.1101/2022.06.20.22276596", + "rel_title": "Kinetics of neutralising antibodies against Omicron variant in Vietnamese healthcare workers after primary immunisation with ChAdOx1-S and booster with BNT162b2", "rel_date": "2022-06-21", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.15.22276447", - "rel_abs": "Unexpected rapid infection involving SARS-CoV-2 variant Omicron known as the fifth wave of outbreak occurred since early January 2022 in Hong Kong. Almost 1.2 million citizens were infected in three months. Ventilation provisions in some gathering places with close contact such as restaurants were found to be lower than requirements, believed to be one of the main causes of transmission in these indoor spaces. At the end of the fifth outbreak in mid-May 2022, group infections were still found in several such gathering places including restaurants and pubs due to inadequate ventilation provisions. There are worries about triggering the sixth wave of outbreak.\n\nKey points related to ventilation requirements in such gathering places are discussed in this paper. Adequate ventilation of 6 air changes per hour minimum must be provided to avoid direct air transmission of virus. Indoor aerodynamics induced by ventilation system must be considered too. However, it is difficult to measure ventilation rate quickly and accurately. A control scheme on virus outbreaks is proposed on installing mechanical ventilation energy use meters and carbon dioxide sensors for checking ventilation provisions adequacy quickly.", - "rel_num_authors": 1, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.20.22276596", + "rel_abs": "We studied the development and persistence of neutralising antibodies against SARS-CoV-2 ancestral strain, and Delta and Omicron (BA.1 and BA.2) variants in Vietnamese healthcare workers (HCWs) up to 15 weeks after booster vaccination. We included 47 HCWs with different pre-existing immune statuses (group 1 (G1): n=21, and group 2 (G2): n=26 without and with prior breakthrough Delta variant infection, respectively). The study participants had completed primary immunisation with ChAdOx1-S and booster vaccination with BNT162b2. Neutralising antibodies were measured using a surrogate virus neutralisation assay. Of the 21 study participants in G1, neutralising antibodies against ancestral strain, Delta variant, BA.1 and BA.2 were (almost) abolished at month 8 after the second dose, but all had detectable neutralising antibodies to the study viruses at week two post booster dose. Of the 26 study participants in G2, neutralising antibody levels to BA.1 and BA.2 were significantly higher than those to the corresponding viruses measured at week 2 post breakthrough infection and before the booster dose. At week 15 post booster vaccination, neutralising antibodies to BA.1 and BA.2 dropped significantly, with more profound changes observed in those without breakthrough Delta variant infection. Booster vaccination enhanced neutralising activities against ancestral strain and Delta variant, as compared to those induced by primary vaccination. These responses were maintained at high levels for at least 15 weeks. Our findings emphasise the importance of the first booster dose in producing cross-neutralising antibodies against Omicron variant. A second booster dose might be needed to maintain long-term protection against Omicron variant.", + "rel_num_authors": 24, "rel_authors": [ { - "author_name": "W.K. Chow", - "author_inst": "The Hong Kong Polytechnic University" + "author_name": "Nguyen Van Vinh Chau", + "author_inst": "Department of Health, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Lam Anh Nguyet", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thanh Dung", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Vo Minh Quang", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thanh Truong", + "author_inst": "Tan Phu Hospital, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Mau Toan", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Manh Hung", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Dinh Nguyen Huy Man", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Dao Bach Khoa", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thanh Phong", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nghiem My Ngoc", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Huynh Phuong Thao", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Dinh Thi Bich Ty", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Pham Ba Thanh", + "author_inst": "Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thi Han Ny", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Kim Thanh", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Cao Thu Thuy", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen To Anh", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Nguyen Thi Thu Hong", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Nguyen Truc Nhu", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Lam Minh Yen", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Guy Thwaites", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Tran Tan Thanh", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "Le Van Tan", + "author_inst": "OUCRU-VN" } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc_by", "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" + "category": "infectious diseases" }, { "rel_doi": "10.1101/2022.06.14.22276397", @@ -275344,81 +275535,105 @@ "category": "psychiatry and clinical psychology" }, { - "rel_doi": "10.1101/2022.06.16.22276480", - "rel_title": "Immunogenicity following two doses of BBIBP-CorV vaccine and a third booster dose with viral vector and mRNA COVID-19 vaccines against delta and omicron variants in prime immunized adults with two doses of BBIBP-CorV vaccine", + "rel_doi": "10.1101/2022.06.16.22276392", + "rel_title": "COVID-19 redux: clinical, virologic, and immunologic evaluation of clinical rebound after nirmatrelvir/ritonavir", "rel_date": "2022-06-17", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.16.22276480", - "rel_abs": "Coronavirus disease 2019 (COVID-19) booster vaccination is being comprehensively evaluated globally due to waning immunity and the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. Therefore, this study aimed to evaluate antibody responses in individuals vaccinated with two doses of BBIBP-CorV vaccine and to explore the boosting effect of the different vaccine platforms in BBIBP-CorV-primed healthy adults, including viral vector vaccine (AZD122) and mRNA vaccines (BNT162b2 and mRNA-1273). The results showed that, in the BBIBP-CorV prime group, the total receptor-binding domain (RBD) immuno-globulin (Ig) and anti-RBD IgG levels waned significantly at 3 months after receiving the second dose. However, after the booster, RBD-specific binding antibody levels increased. Neutralizing antibody measured by a surrogate neutralization test showed of inhibition over 90% against the SARS-CoV-2 delta variant but less than 70% against omicron variant after the third dose on day 28. All booster vaccines could induce the total IFN-{square} T-cell response. The reactogenicity was acceptable and well tolerated without serious adverse events. This study supported administration of the third dose with either viral vector or mRNA vaccine for the BBIBP-CorV-primed individuals to stimulate antibody and T cell responses.", - "rel_num_authors": 16, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.16.22276392", + "rel_abs": "Clinical rebound of COVID-19 after nirmatrelvir/ritonavir treatment has been reported. We performed clinical, virologic, and immune measurements in seven patients with symptomatic rebound, six after nirmatrelvir/ritonavir treatment and one without previous treatment. There was no evidence of severe disease or impaired antibody and T-cell responses in people with rebound symptoms.", + "rel_num_authors": 22, "rel_authors": [ { - "author_name": "Jira Chansaenroj", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Brian P Epling", + "author_inst": "National Institute of Allergy and Infectious Diseases" }, { - "author_name": "Nungruthai Suntronwong", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Joseph M Rocco", + "author_inst": "National Institute of Allergy and Infectious Diseases" }, { - "author_name": "Sitthichai Kanokudom", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Kristin L Boswell", + "author_inst": "National Institute of Allergy and Infectious Diseases" }, { - "author_name": "Suvichada Assawakosri", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Elizabeth Laidlaw", + "author_inst": "National Institute of Allergy and Infectious Diseases" }, { - "author_name": "Ritthideach Yorsaeng", - "author_inst": "Faculty of Medicine, Chulalongkorn University" + "author_name": "Frances Galindo", + "author_inst": "National Institute of Allergy and Infectious Diseases" }, { - "author_name": "Preeyaporn Vichaiwattana", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Anela Kellogg", + "author_inst": "Leidos Biomedical Research" }, { - "author_name": "Sirapa Klinfueng", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Sanchita Das", + "author_inst": "National Institutes of Health" }, { - "author_name": "Lakana Wongsrisang", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Allison Roder", + "author_inst": "National Institute of Allergy and Infectious Diseases" }, { - "author_name": "Donchida Srimuan", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Elodie Ghedin", + "author_inst": "National Institute of Allergy and Infectious Diseases" }, { - "author_name": "Thaksaporn Thatsanatorn", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Allie Kreitman", + "author_inst": "National Institute of Allergy and Infectious Diseases" }, { - "author_name": "Thanunrat Thongmee", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Robin L Dewar", + "author_inst": "Frederick National Laboratory" }, { - "author_name": "Chompoonut Auphimai", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Sophie E. M. Kelly", + "author_inst": "National Institute of Biomedical Imaging and Bioengineering" }, { - "author_name": "Pornjarim Nilyanimit", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Heather Kalish", + "author_inst": "National Institute of Biomedical Imaging and Bioengineering" }, { - "author_name": "Nasamon Wanlapakorn", - "author_inst": "Division of Academic Affairs, Faculty of Medicine, Chulalongkorn University" + "author_name": "Tauseef Rehman", + "author_inst": "Frederick National Laboratory" }, { - "author_name": "Natthinee Sudhinaraset", - "author_inst": "Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University" + "author_name": "Jeroen Highbarger", + "author_inst": "Frederick National Laboratory" }, { - "author_name": "yong Poovorawan", - "author_inst": "Chulalongkorn University" + "author_name": "Adam Rupert", + "author_inst": "Frederick National Laboratory" + }, + { + "author_name": "Gregory Kocher", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Michael R Holbrook", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Andrea Lisco", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Maura Manion", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Richard A Koup", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Irini Sereti", + "author_inst": "National Institute of Allergy and Infectious Diseases" } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc0", "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, @@ -277178,79 +277393,67 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.06.14.22276166", - "rel_title": "Overt and occult hypoxemia in patients hospitalized with novel coronavirus disease 2019", + "rel_doi": "10.1101/2022.06.13.22276339", + "rel_title": "Effects of hydrometeorological and other factors on SARS-CoV-2 reproduction number in three contiguous countries of Tropical Andean South America: a spatiotemporally disaggregated time series analysis.", "rel_date": "2022-06-16", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.14.22276166", - "rel_abs": "BackgroundProgressive hypoxemia is the predominant mode of deterioration in COVID-19. Among hypoxemia measures, the ratio of the partial pressure of arterial oxygen to the fraction of inspired oxygen (P/F ratio) has optimal construct validity but poor availability because it requires arterial blood sampling. Pulse oximetry reports oxygenation continuously, but occult hypoxemia can occur in Black patients because the technique is affected by skin color. Oxygen dissociation curves allow non-invasive estimation of P/F ratios (ePFR) but this approach remains unproven.\n\nResearch QuestionCan ePFRs measure overt and occult hypoxemia?\n\nStudy Design and methodsWe retrospectively studied COVID-19 hospital encounters (n=5319) at two academic centers (University of Virginia [UVA] and Emory University). We measured primary outcomes (death or ICU transfer within 24 hours), ePFR, conventional hypoxemia measures, baseline predictors (age, sex, race, comorbidity), and acute predictors (National Early Warning Score (NEWS) and Sepsis-3). We updated predictors every 15 minutes. We assessed predictive validity using adjusted odds ratios (AOR) and area under receiver operating characteristics curves (AUROC). We quantified disparities (Black vs non-Black) in empirical cumulative distributions using the Kolmogorov-Smirnov (K-S) two-sample test.\n\nResultsOvert hypoxemia (low ePFR) predicted bad outcomes (AOR for a 100-point ePFR drop: 2.7 [UVA]; 1.7 [Emory]; p<0.01) with better discrimination (AUROC: 0.76 [UVA]; 0.71 [Emory]) than NEWS (AUROC: 0.70 [UVA]; 0.70 [Emory]) or Sepsis-3 (AUROC: 0.68 [UVA]; 0.65 [Emory]). We found racial differences consistent with occult hypoxemia. Black patients had better apparent oxygenation (K-S distance: 0.17 [both sites]; p<0.01) but, for comparable ePFRs, worse outcomes than other patients (AOR: 2.2 [UVA]; 1.2 [Emory], p<0.01).\n\nInterpretationThe ePFR was a valid measure of overt hypoxemia. In COVID-19, it may outperform multi-organ dysfunction models like NEWS and Sepsis-3. By accounting for biased oximetry as well as clinicians real-time responses to it (supplemental oxygen adjustment), ePFRs may enable statistical modelling of racial disparities in outcomes attributable to occult hypoxemia.", - "rel_num_authors": 15, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.13.22276339", + "rel_abs": "BackgroundThe COVID-19 pandemic has caused societal disruption globally and South America has been hit harder than other lower-income regions. This study modeled effects of 6 weather variables on district-level SARS-CoV-2 reproduction numbers (Rt) in three contiguous countries of Tropical Andean South America (Colombia, Ecuador, and Peru), adjusting for environmental, policy, healthcare infrastructural and other factors.\n\nMethodsDaily time-series data on SARS-CoV-2 infections were sourced from health authorities of the three countries at the smallest available administrative level. Rt values were calculated and merged by date and unit ID with variables from a Unified COVID-19 dataset and other publicly available sources for May - December 2020. Generalized additive mixed effects models were fitted.\n\nFindingsRelative humidity and solar radiation were inversely associated with SARS-CoV-2 Rt. Days with radiation above 1,000 KJ/m2 saw a 1.3%, and those with humidity above 50%, a 1.0% reduction in Rt. Transmission was highest in densely populated districts, and lowest in districts with poor healthcare access and on days with least population mobility. Temperature, region, aggregate government policy response and population age structure had little impact. The fully adjusted model explained 3.9% of Rt variance.\n\nInterpretationDry atmospheric conditions of low humidity increase, and higher solar radiation decrease district-level SARS-CoV-2 reproduction numbers, effects that are comparable in magnitude to population factors like lockdown compliance. Weather monitoring could be incorporated into disease surveillance and early warning systems in conjunction with more established risk indicators and surveillance measures.\n\nFundingNASAs Group on Earth Observations Work Programme (16-GEO16-0047).", + "rel_num_authors": 12, "rel_authors": [ { - "author_name": "Shrirang Mukund Gadrey", - "author_inst": "University of Virginia" - }, - { - "author_name": "Piyus Mohanty", - "author_inst": "Emory University" - }, - { - "author_name": "Sean P Haughey", - "author_inst": "University of Virginia" - }, - { - "author_name": "Beck A Jacobsen", - "author_inst": "University of Virginia" + "author_name": "Josh M Colston", + "author_inst": "University of Virginia School of Medicine" }, { - "author_name": "Kira J Dubester", + "author_name": "Patrick Hinson", "author_inst": "University of Virginia" }, { - "author_name": "Katherine M Webb", + "author_name": "Nhat-Lan H Nguyen", "author_inst": "University of Virginia" }, { - "author_name": "Rebecca L Kowalski", - "author_inst": "University of Virginia" + "author_name": "Yen Ting Chen", + "author_inst": "Chi-Mei Medical Center" }, { - "author_name": "Jessica J Dreicer", - "author_inst": "University of Virginia" + "author_name": "Hamada S. Badr", + "author_inst": "Johns Hopkins University" }, { - "author_name": "Robert T Andris", - "author_inst": "University of Virginia" + "author_name": "Gaige H Kerr", + "author_inst": "George Washington University" }, { - "author_name": "Matthew T Clark", - "author_inst": "Nihon Kohden Digital Health Solutions Inc" + "author_name": "Lauren Marie Gardner", + "author_inst": "Johns Hopkins University" }, { - "author_name": "Christopher C Moore", - "author_inst": "University of Virginia" + "author_name": "David N Martin", + "author_inst": "University of Virginia School of Medicine" }, { - "author_name": "Andre Holder", - "author_inst": "Emory University" + "author_name": "Antonio M Quispe", + "author_inst": "Universidad Continental" }, { - "author_name": "Rishi Kamaleswaran", - "author_inst": "Emory University" + "author_name": "Francesca Schiaffino", + "author_inst": "Universidad Peruana Cayetano Heredia" }, { - "author_name": "Sarah J Ratcliffe", + "author_name": "Margaret N Kosek", "author_inst": "University of Virginia" }, { - "author_name": "J Randall Moorman", - "author_inst": "University of Virginia" + "author_name": "Benjamin F Zaitchik", + "author_inst": "Johns Hopkins University" } ], "version": "1", "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" + "category": "epidemiology" }, { "rel_doi": "10.1101/2022.06.15.22276436", @@ -279416,33 +279619,81 @@ "category": "health informatics" }, { - "rel_doi": "10.1101/2022.06.09.22275881", - "rel_title": "Effect of HIV disease and the associated moderators on COVID-19 related Mortality", + "rel_doi": "10.1101/2022.06.09.22276030", + "rel_title": "Immunogenicity and safety of coadministration of COVID-19 and influenza vaccination among healthcare workers", "rel_date": "2022-06-14", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.09.22275881", - "rel_abs": "IntroductionEstablished predictors for COVID 19 related mortalities are diverse. The impact of these several risk factors on coronavirus mortality have been previously reported in several meta-analyses limited by small sample sizes and premature data. The objective of this systematic review and meta-analysis coupled with meta-regression was to evaluate the updated evidence on the risk of COVID 19 related mortality by HIV serostatus using published data, and account for possible moderators.\n\nMethodElectronic databases including Google Scholar, Cochrane Library, Web of Sciences (WOS), EMBASE, Medline/PubMed, COVID 19 Research Database, and Scopus, were systematically searched till 30th February, 2022. All human studies were included irrespective of publication date or region. Twenty-two studies with a total of 19,783,097 patients detailing COVID 19 related mortality were included. To pool the estimate, a random effects model with risk ratio as the effect measure was used. Moreover, publication bias and sensitivity analysis were evaluated followed by meta-regression. The trial was registered (CRD42021264761) on the PROSPERO register.\n\nResultsThe findings were consistent in stating the contribution of HIV infection for COVID-19 related mortality. The cumulative COVID-19 related mortality was 110270 (0.6%) and 48863 (2.4%) with total events of 2010 (3.6%), 108260 (0.5%) among HIV-positive and negative persons respectively. HIV infection showed an increased risk of COVID-19 related mortality [RR=1.19, 95% CI (1.02, 1.39) (P=0.00001)] with substantial heterogeneity (I squared > 80%). The true effects size in 95% of all the comparable populations fell between 0.64 to 2.22. Multiple Centre studies and COVID-19 mortality with HIV infection showed a significant association [RR = 1.305, 95% CI (1.092, 1.559) (P = 0.003)], similar to studies conducted in America (RR=1.422, 95% CI 1.233, 1.639) and South Africa (RR=202;1.123, 95% CI 1.052, 1.198). HIV infection showed a risk for ICU admission [(P=0.00001) (I squared = 0%)] and mechanical ventilation [(P=0.04) (I squared = 0%)] which are predictors of COVID-19 severity prior to death. Furthermore, risk of COVID 19 related mortality is influenced by the region of study (R squared = 0.60). The variance proportion explained by covariates was significant (I squared = 87.5%, Q = 168.02, df = 21, p = 0.0000) (R squared = 0.67).\n\nConclusionOur updated meta-analysis indicated that HIV infection was significantly associated with an increased risk for both COVID 19 mortality, which might be modulated by the regions. We believe the updated data further will contribute to more substantiation of the findings reported by similar earlier studies (Dong et al., 2021; K. W. Lee et al., 2021; Massarvva, 2021; Mellor et al., 2021; Ssentongo et al., 2021)", - "rel_num_authors": 4, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.09.22276030", + "rel_abs": "BackgroundA third dose of COVID-19 vaccination ( COVID booster vaccination) has become established as an important measure to strengthen the immune response against SARS-CoV-2. In contrast, seasonal influenza vaccination has been an important infection prevention measure for years, especially among highly exposed healthcare workers (HCWs). Coadministration of vaccines against COVID-19 and seasonal influenza could be an efficient strategy to protect HCWs from two major viral respiratory infections. Yet, the immunogenicity and safety of coadministration remains to be evaluated.\n\nMethodsThis study examines the differences in Anti-SARS-CoV-2-Spike IgG antibody formation as well as side effects based on a digital questionnaire after a third COVID-19 vaccination with or without coadministration of a seasonal quadrivalent influenza vaccine (Influvac Tetra vaccine 2021/2022). 1,231 HCWs were recruited who received a mRNA-based booster COVID-19 vaccination (mRNA-1273 or BNT162b2mRNA) after basic immunisation with BNT162b2mRNA twice. Anti-SARS-CoV-2-Spike IgG levels were determined at least 14 days after vaccination by SERION ELISA agile SARS-CoV-2 IgG.\n\nFindingsAnti-SARS-CoV-2-Spike IgG concentrations were by 25{middle dot}4% lower in individuals with coadministration of the seasonal quadrivalent influenza vaccination than without (p<0{middle dot}01). There was no statistically significant difference in the reported side effects. The concentration of Anti-SARS-CoV-2-Spike IgG was higher in HCWs who had received the influenza vaccine concomitantly with mRNA-1273 than with BNT162b2mRNA as third COVID-19 vaccine (p<0{middle dot}0001).\n\nInterpretationCoadministration of the seasonal quadrivalent influenza vaccine significantly limits the levels in Anti-SARS-CoV-2-Spike IgG levels, with a more restricted elevation in case of a BNT162b2mRNA booster vaccination compared with mRNA-1273 vaccine. The reduced humoral immune response in case of coadministration needs to be considered in seasonal vaccination recommendations, although the consequences of lower Anti-SARS-CoV-2-Spike IgG levels for the protection against SARS-CoV-2 infection and severe COVID-19 disease course are currently unknown. An augmented mRNA-based COVID-19 vaccine dosage may compensate for the restricted immunogenicity in case of coadministration.\n\nFundingThis study was funded by the Federal Ministry for Education and Science (BMBF) through a grant provided to the University Hospital of Wuerzburg by the Network University Medicine on COVID-19 (B-FAST, grant-No 01KX2021) as well as by the Free State of Bavaria with COVID-research funds provided to the University of Wuerzburg, Germany. Nils Petri is supported by the German Research Foundation (DFG) funded scholarship UNION CVD.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSFor evaluation of the previously published evidence, PubMed and medRxiv were searched for the terms \"influenza vaccination\", \"influenza vaccine\", \"influenza\", \"flu\", \"seasonality\", combined with \"coadministration\", \"concomitant\", \"COVID-19 vaccination\", \"COVID-19 vaccine\", \"SARS-CoV-2\", in title or abstract, published between 1st of January 2020 and 18th of May 2022.\n\nTo date, it is unclear if coadministration of COVID-19 and influenza vaccine is effective and safe, particularly in the cohort of healthcare workers (HCWs) as key public health stakeholders. For the subunit COVID-19 vaccine NVX-CoV2373, an impairment of Anti-SARS-CoV-2-Spike IgG levels has been shown in individuals coadministered with a seasonal influenza vaccine. The two previously published studies on coadministration of a mRNA-based COVID-19 and a seasonal quadrivalent influenza vaccine have reported a restriction of humoral Anti-SARS-CoV-2-Spike immune response in the coadministration group. These examinations were conducted with limited correspondence to real-life conditions and in smaller cohorts. Additionally, these former studies do not consider the important aspect of side effects as a possible direct effect of the prevention measure on the availability of public health care in combination with Anti-SARS-CoV-2-Spike IgG levels. In summary, the humoral immunogenicity and side effects of a coadministered third COVID-19 and a seasonal influenza vaccine are still unclear and the limited available data is not transferable to the general public.\n\nAdded value of this studyWe performed the first large-scale real-life evaluation of humoral immunogenicity and side effects of COVID-19 and influenza vaccine coadministration in HCWs. Anti-SARS-CoV-2-Spike IgG levels were significantly lower in the coadministered cohort compared to the not coadministered control group, stratified by third COVID-19 vaccine (BNT162b2mRNA or mRNA-1273). Anti-SARS-CoV-2-Spike IgG post-vaccine elevation was lower among BNT162b2mRNA vaccinated HCWs than in those vaccinated with mRNA-1273 as a third COVID-19 vaccination. The influence of the seasonal quadrivalent influenza vaccine is evaluated in a cohort including 1,231 HCWs in total, covering a broad age range. Coadministration did not lead to an increase in side effects, which is a central requirement for considering the option of coadministration, given the role of HCWs as key personnel in maintaining health care capacities.\n\nImplications of all the available evidenceOur data suggest, that coadministration of third mRNA-based COVID-19 and quadrivalent seasonal influenza vaccine is safe and immunogenic, although it leads to a slightly reduced Anti-SARS-CoV-2-Spike antibody formation. While the clinical impact of the observed reduction in humoral Anti-SARS-CoV-2-Spike immune response for protection against SARS-CoV-2 infection and severe COVID-19 disease is still unclear, influenza vaccination remains an important infection prevention measure, especially among highly exposed HCWs. The coadministration does not increase side effects but may improve vaccination rate. A higher-dosed mRNA-based COVID-19 vaccine may compensate for the restricted immunogenicity in case of seasonal influenza vaccine coadministration. Our results will support the development of public health recommendations for coadministration of COVID-19 and influence vaccines in anticipation of the imminent infection waves in the coming winter season.", + "rel_num_authors": 16, "rel_authors": [ { - "author_name": "JOHN KYALO MUTHUKA", - "author_inst": "KENYA MEDICAL TRAINING COLLEGE" + "author_name": "Isabell Wagenh\u00e4user", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" }, { - "author_name": "Francis Wambura", - "author_inst": "Kenya MedicalTraining College" + "author_name": "Julia Reusch", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" }, { - "author_name": "Kelly Oluoch", - "author_inst": "Kenya Medical Training College" + "author_name": "Alexander Gabel", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Anna H\u00f6hn", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Thi\u00ean-Tr\u00ed L\u00e2m", + "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Giovanni Almanzar", + "author_inst": "Paediatric Rheumatology/Special Immunology, Department of Paediatrics, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Martina Prelog", + "author_inst": "Paediatric Rheumatology/Special Immunology, Department of Paediatrics, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Lukas B. Krone", + "author_inst": "Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; University Hospital of Psychiatry and Psychotherapy, University of Bern, Bern," + }, + { + "author_name": "Anna Frey", + "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Alexandra Schubert-Unkmeir", + "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Lars D\u00f6lken", + "author_inst": "Institute for Virology and Immunobiology, University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Stefan Frantz", + "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Oliver Kurzai", + "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg; Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knoell-I" }, { - "author_name": "Japeth Nzioki Mativo", - "author_inst": "Jumeira University, UAE" + "author_name": "Ulrich Vogel", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg; Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg," + }, + { + "author_name": "Nils Petri", + "author_inst": "Department of Internal Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Manuel Krone", + "author_inst": "Infection Control and Antimicrobial Stewardship Unit, University Hospital Wuerzburg; Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg," } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc_no", "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, @@ -281310,47 +281561,107 @@ "category": "public and global health" }, { - "rel_doi": "10.1101/2022.06.12.495816", - "rel_title": "Two ligand-binding sites on SARS-CoV-2 non-structural protein 1 revealed by fragment-based x-ray screening", + "rel_doi": "10.1101/2022.06.12.495779", + "rel_title": "An attenuated vaccinia vaccine encoding the SARS-CoV-2 spike protein elicits broad and durable immune responses, and protects cynomolgus macaques and human ACE2 transgenic mice from SARS-CoV-2 and its variants", "rel_date": "2022-06-13", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.12.495816", - "rel_abs": "The regular reappearance of coronavirus (CoV) outbreaks over the past 20 years has caused significant health consequences and financial burdens worldwide. The most recent and still ongoing novel CoV pandemic, caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) has brought a range of devastating consequences. Due to the exceptionally fast development of vaccines, the mortality rate of the virus has been curbed to a significant extent. However, the limitations of vaccination efficiency and applicability, coupled with the still high infection rate, emphasise the urgent need for discovering safe and effective antivirals against SARS-CoV-2 through suppressing its replication and or attenuating its virulence. Non-structural protein 1 (nsp1), a unique viral and conserved leader protein, is a crucial virulence factor for causing host mRNA degradation, suppressing interferon (IFN) expression and host antiviral signalling pathways. In view of the essential role of nsp1 in the CoV life cycle, it is regarded as an exploitable target for antiviral drug discovery. Here, we report a variety of fragment hits against SARS-CoV-2 nsp1 identified by fragment-based screening via X-ray crystallography. We also determined the structure of nsp1 at atomic resolution (0.95 [A]). Binding affinities of hits against nsp1 were determined by orthogonal biophysical assays such as microscale thermophoresis and thermal sift assays. We identified two ligand-binding sites on nsp1, one deep and one shallow pocket, which are not conserved between the three medially relevant SARS, SARS-CoV-2 and MERS coronaviruses. Our study provides an excellent starting point for the development of more potent nsp1-targeting inhibitors and functional studies on SARS-CoV-2 nsp1.", - "rel_num_authors": 7, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.12.495779", + "rel_abs": "As long as the coronavirus disease 2019 (COVID-19) pandemic continues, new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with altered antigenicity will emerge. The development of vaccines that elicit robust, broad, and durable protection against SARS-CoV-2 variants is urgently needed. We have developed a vaccine (rDIs-S) consisting of the attenuated vaccinia virus DIs strain platform carrying the SARS-CoV-2 S gene. rDIs-S induced neutralizing antibody and T-lymphocyte responses in cynomolgus macaques and human angiotensin converting enzyme 2 (hACE2) transgenic mice, and showed broad protection against SARS-CoV-2 isolates ranging from the early-pandemic strain (WK-521) to the recent Omicron BA. 1 variant (TY38-839). Using a tandem mass tag (TMT) -based quantitative proteomic analysis of lung homogenates from hACE2 transgenic mice, we found that, among mice subjected to challenge infection with WK-521, vaccination with rDIs-S prevented protein expression related to the severe pathogenic effects of SARS-CoV-2 infection (tissue destruction, inflammation, coagulation, fibrosis, and angiogenesis) and restored protein expression related to immune responses (antigen presentation and cellular response to stress). Furthermore, long-term studies in mice showed that rDIs-S maintains S protein-specific antibody titers for at least 6 months after a 1st vaccination. Thus, rDIs-S appears to provide broad and durable protective immunity against SARS-CoV-2, including current and possibly future variants.", + "rel_num_authors": 22, "rel_authors": [ { - "author_name": "Shumeng Ma", - "author_inst": "UCL School of Pharmacy" + "author_name": "Hirohito Ishigaki", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" }, { - "author_name": "Shymaa Damfo", - "author_inst": "UCL School of Pharmacy" + "author_name": "Fumihiko Yasui", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" }, { - "author_name": "Jiaqi Lou", - "author_inst": "UCL School of Pharmacy" + "author_name": "Misako Nakayama", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" }, { - "author_name": "Nikos Pinotsis", - "author_inst": "Birkbeck College" + "author_name": "Akinori Endo", + "author_inst": "Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science" }, { - "author_name": "Matthew W Bowler", - "author_inst": "European Molecular Biology Laboratory" + "author_name": "Naoki Yamamoto", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" }, { - "author_name": "Shozeb Haider", - "author_inst": "University College London School of Pharmacy" + "author_name": "Kenzaburo Yamaji", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" }, { - "author_name": "Frank Gerhard Kozielski", - "author_inst": "University College London" + "author_name": "Cong Thanh Nguyen", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Yoshinori Kitagawa", + "author_inst": "Division of Microbiology and Infectious Diseases, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Takahiro Sanada", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Tomoko Honda", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Tsubasa Munakata", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Masahiko Higa", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Sakiko Toyama", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Risa Kono", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Asako Takagi", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Yusuke Matsumoto", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Kaori Hayashi", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Masanori Shiohara", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Koji Ishii", + "author_inst": "Department of Quality Assurance and Radiological Protection, National Institute of Infectious Diseases" + }, + { + "author_name": "Yasushi Saeki", + "author_inst": "Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science" + }, + { + "author_name": "Yasushi Itoh", + "author_inst": "Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science" + }, + { + "author_name": "Michinori Kohara", + "author_inst": "Department of Microbiology and Cell Biology, Tokyo Metropolitan Institute of Medical Science" } ], "version": "1", "license": "cc_no", "type": "new results", - "category": "biochemistry" + "category": "microbiology" }, { "rel_doi": "10.1101/2022.06.13.495912", @@ -282880,53 +283191,25 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.06.07.493653", - "rel_title": "COVID-MVP: an interactive visualization for tracking SARS-CoV-2 mutations, variants, and prevalence, enabled by curated functional annotations and portable genomics workflow", + "rel_doi": "10.1101/2022.06.07.495170", + "rel_title": "Single-cell Multi-omics Integration for Unpaired Data by a Siamese Network with Graph-based Contrastive Loss", "rel_date": "2022-06-08", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.07.493653", - "rel_abs": "The SARS-CoV-2 pandemic has reemphasized the importance of genomic epidemiology to track the evolution of the virus, dynamics of epidemics, geographic origins, and the emerging variants. It is vital in understanding the epidemiological spread of the virus on global, national, and local scales. Several analytical (bioinformatics) resources have been developed for molecular surveillance. However, a resource that combines genetic mutations and functional annotations on the impact of these mutations has been lacking in SARS-CoV-2 genomics surveillance. COVID-MVP provides an interactive visualization application that summarizes the mutations and their prevalence in SARS-CoV-2 viral lineages and provides functional annotations from the literature curated in an ongoing effort, Pokay. COVID-MVP is a tool that can be used for routine surveillance including spatio-temporal analyses. We have powered the visualization through a scalable and reproducible genomic analysis workflow nf-ncov-voc wrapped in Nextflow. COVID-MVP allows users to interactively explore data and download summarized surveillance reports. COVID-MVP, Pokay, and nf-ncov-voc are open-source tools available under the Massachusetts Institute of Technology (MIT) and GPL-3.0 licenses. COVID-MVP source code is available at https://github.com/cidgoh/COVID-MVP and an instance is hosted at https://covidmvp.cidgoh.ca.", - "rel_num_authors": 9, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.07.495170", + "rel_abs": "Single-cell omics technology is being rapidly developed to measure the epigenome, genome, and transcriptome across a range of cell types. However, integrating omics data from different modalities is still challenging. Here, we propose a variation of the Siamese neural network framework called MinNet, which is trained to integrate multi-omics data on the single-cell resolution by utilizing graph-based contrastive loss. By training the model and testing it on several benchmark datasets, we showed its accuracy and generalizability in integrating scRNA-seq with scATAC-seq, and scRNA-seq with epitopes data. Further evaluation demonstrated our models unique capacity in removing the batch effect, which is a common problem in actual practice. To show how the integration impacts downstream analysis, we established model-based smoothing and cis-regulatory element inferring method and validated it with external pcHi-C evidence. Finally, the framework was applied to a COVID-19 dataset to compensate the original work with integration-based analysis, showing its necessity in single-cell multi-omics research.", + "rel_num_authors": 2, "rel_authors": [ { - "author_name": "Muhammad Zohaib Anwar", - "author_inst": "Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada" - }, - { - "author_name": "Ivan S Gill", - "author_inst": "Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada" - }, - { - "author_name": "Madeline Iseminger", - "author_inst": "Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada" - }, - { - "author_name": "Anoosha Sehar", - "author_inst": "Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada" - }, - { - "author_name": "Kenyi D Igwacho", - "author_inst": "Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada" - }, - { - "author_name": "Khushi Vora", - "author_inst": "Centre for Health Genomics and Informatics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada" - }, - { - "author_name": "Gary Van Domselaar", - "author_inst": "National Microbiology Laboratory, Public health Agency of Canada, Winnipeg, MB, Canada" - }, - { - "author_name": "Paul M. K. Gordon", - "author_inst": "Centre for Health Genomics and Informatics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada" + "author_name": "Chaozhong Liu", + "author_inst": "Baylor College of Medicine" }, { - "author_name": "William WL Hsiao", - "author_inst": "Centre for Infectious Disease Genomics and One Health, Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada" + "author_name": "Linhua Wang", + "author_inst": "Baylor College of Medicine" } ], "version": "1", - "license": "cc_by", + "license": "cc_by_nc_nd", "type": "new results", "category": "bioinformatics" }, @@ -284946,103 +285229,39 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.06.05.494897", - "rel_title": "Discovery of Chlorofluoroacetamide-Based Covalent Inhibitors for SARS-CoV-2 3CL Protease", + "rel_doi": "10.1101/2022.06.05.494856", + "rel_title": "A uniquely stable trimeric model of SARS-CoV-2 spike transmembrane domain", "rel_date": "2022-06-06", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.05.494897", - "rel_abs": "The pandemic of coronavirus disease 2019 (COVID-19) has urgently necessitated the development of antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The 3C-like protease (3CLpro) is a promising target for COVID-19 treatment. Here, we report the new class of covalent inhibitors for 3CLpro possessing chlorofluoroacetamide (CFA) as a cysteine reactive warhead. Based on the aza-peptide scaffold, we synthesized the series of CFA derivatives in enantiopure form and evaluated their biochemical efficiencies. The data revealed that 8a (YH-6) with R configuration at the CFA unit strongly blocks the SARS-CoV-2 replication in the infected cells and this potency is comparable to that of nirmatrelvir. The X-ray structural analysis shows that 8a (YH-6) forms a covalent bond with Cys145 at the catalytic center of 3CLpro. The strong antiviral activity and sufficient pharmacokinetics property of 8a (YH-6) suggest its potential as a lead compound for treatment of COVID-19.", - "rel_num_authors": 21, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.05.494856", + "rel_abs": "The spike (S) protein of SARS-CoV-2 effectuates membrane fusion and virus entry into target cells. Its transmembrane domain (TMD) represents a homotrimer of -helices anchoring the spike in the viral envelope. Although S-protein models available to date include the TMD, its precise configuration was given brief consideration. Understanding viral fusion entails realistic TMD models, while no reliable approaches towards predicting the 3D structure of transmembrane (TM) trimers exist. Here, we propose a comprehensive computational framework to model the spike TMD (S-TMD) based solely on its primary structure. First, we performed amino acid sequence pattern matching and compared molecular hydrophobicity potential (MHP) distribution on the helix surface against TM homotrimers with known 3D structures and thus selected the TMD of the tumour necrosis factor receptor 1 (TNFR-1) for subsequent template-based modelling. We then iteratively built an all-atom homotrimer model of S-TMD based on \"dynamic MHP portraits\" and residue variability motifs. In this model each helix possessed two overlapping interfaces interacting with either of the remaining helices, which include conservative residues I1216, F1220, I1227, M1229, and M1233. Finally, the stability of this and several alternative models (including a recent NMR structure) and a set of mutant forms was tested in all-atom molecular dynamics (MD) simulations in a POPC bilayer mimicking the viral envelope membrane. Unlike other configurations, our model trimer remained extraordinarily tightly packed over a microsecond-range MD and retained its stability when palmitoylated in accordance with experimental data. Palmitoylation had no significant impact on the TMD conformation nor the way in which the lipid bilayer was perturbed in the presence of the trimer. Overall, the resulting model of S-TMD conforms to known basic principles of TM helix packing and will be further used to explore the complex machinery of membrane fusion from a broader perspective beyond the TMD.", + "rel_num_authors": 5, "rel_authors": [ { - "author_name": "Yuya Hirose", - "author_inst": "Kyushu University" - }, - { - "author_name": "Naoya Shindo", - "author_inst": "Kyushu University" - }, - { - "author_name": "Makiko Mori", - "author_inst": "Kyushu University" - }, - { - "author_name": "Satsuki Onitsuka", - "author_inst": "Kyushu University" - }, - { - "author_name": "Hikaru Isogai", - "author_inst": "Kyushu University" - }, - { - "author_name": "Rui Hamada", - "author_inst": "Kyushu University" - }, - { - "author_name": "Tadanari Hiramoto", - "author_inst": "Kyushu University" - }, - { - "author_name": "Jinta Ochi", - "author_inst": "Kyushu University" - }, - { - "author_name": "Daisuke Takahashi", - "author_inst": "Kyushu University" - }, - { - "author_name": "Tadashi Ueda", - "author_inst": "Kyushu University" - }, - { - "author_name": "Jose M. M. Caaveiro", - "author_inst": "Kyushu University" - }, - { - "author_name": "Yuya Yoshida", - "author_inst": "Kyushu University" - }, - { - "author_name": "Shigehiro Ohdo", - "author_inst": "Kyushu University" - }, - { - "author_name": "Naoya Matsunaga", - "author_inst": "Kyushu University" - }, - { - "author_name": "Shinsuke Toba", - "author_inst": "Hokkaido University, Shionogi & Co. Ltd." + "author_name": "Elena T. Aliper", + "author_inst": "MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia" }, { - "author_name": "Michihito Sasaki", - "author_inst": "Hokkaido University" + "author_name": "Nikolay A. Krylov", + "author_inst": "MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia" }, { - "author_name": "Yasuko Orba", - "author_inst": "Hokkaido University" + "author_name": "Dmitry E. Nolde", + "author_inst": "MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia" }, { - "author_name": "Hirofumi Sawa", - "author_inst": "Hokkaido University, Global Virus Network" + "author_name": "Anton A. Polyansky", + "author_inst": "Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna Biocenter 5, A-1030, Vienna, Austria" }, { - "author_name": "Akihiko Sato", - "author_inst": "Hokkaido University, Shionogi & Co. Ltd." - }, - { - "author_name": "Eiji Kawanishi", - "author_inst": "Kyushu University" - }, - { - "author_name": "Akio Ojida", - "author_inst": "Kyushu University" + "author_name": "Roman G. Efremov", + "author_inst": "MM Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia" } ], "version": "1", "license": "cc_by_nc_nd", "type": "new results", - "category": "biochemistry" + "category": "bioinformatics" }, { "rel_doi": "10.1101/2022.06.05.493249", @@ -286660,159 +286879,43 @@ "category": "epidemiology" }, { - "rel_doi": "10.1101/2022.06.02.22275932", - "rel_title": "Distinct smell and taste disorder phenotype of post-acute COVID-19 sequelae", + "rel_doi": "10.1101/2022.06.03.22275964", + "rel_title": "Indian Female Migrants Face Greater Barriers to Post-Covid Recovery than Males: Evidence from a Panel Study", "rel_date": "2022-06-03", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.02.22275932", - "rel_abs": "BackgroundOlfactory dysfunction (OD) often accompanies acute coronavirus disease 2019 (COVID-19) and its sequelae. Herein, we investigated OD during COVID-19 recovery in the context of other symptoms, quality of life, physical and mental health.\n\nMethodsSymptom recovery patterns were analyzed in a bi-national, ambulatory COVID-19 survey (n = 906, [≥] 90 days follow-up) and a multi-center observational cross-sectional cohort of ambulatory and hospitalized individuals (n = 108, 360 days follow-up) with multi-dimensional scaling, association rule mining and partitioning around medoids clustering.\n\nResultsBoth in the ambulatory collective (72%, n = 655/906) and the cross-sectional ambulatory and hospitalized cohort (41%, n = 44/108) self-reported OD was frequent during acute COVID-19, displayed a slow recovery pace (ambulatory: 28 days, cross-sectional: 90 days median recovery time) and commonly co-occurred with taste disorders. In the ambulatory collective, a predominantly young, female, comorbidity-free group of convalescents with persistent OD and taste disorder (>90 days) was identified. This post-acute smell and taste disorder phenotype was characterized by a low frequency of other leading post-acute symptoms including fatigue, respiratory and neurocognitive complaints. Despite a protracted smell and taste dysfunction, this subset had high ratings of physical performance, mental health, and quality of life.\n\nConclusionOur results underline the clinical heterogeneity of post-acute COVID-19 sequelae calling for tailored management strategies. The persistent smell and taste disorder phenotype may represent a distinct COVID-19 recovery pathway characterized by a good recovery of other COVID-19 related symptoms.\n\nStudy registrationClinicalTrials.gov: NCT04661462 (ambulatory collective), NCT04416100 (cross-sectional cohort).", - "rel_num_authors": 35, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.03.22275964", + "rel_abs": "BackgroundIndias abrupt nationwide Covid-19 lockdown internally displaced millions of urban migrants, who made arduous journeys to distant rural homes. Documenting their labor market reintegration is a critical aspect of understanding the economic costs of the pandemic for Indias poor. In a country marked by low and declining female labor force participation, identifying gender gaps in labor market reintegration - as a marker of both womens vulnerability at times of crisis and setbacks in womens agency - is especially important. Yet most studies of pandemic-displaced Indian migrants are small, rely on highly selected convenience samples, and lack a gender focus.\n\nMethodsBeginning in April 2020 we enrolled roughly 4,600 displaced migrants who had returned to two of Indias poorest states into a panel survey, which tracked enrollees through July 2021. Survey respondents were randomly selected from the states official databases of return migrants, with sampling stratified by state and gender. 85 percent of enrollees (3,950) were working in urban areas prior to the pandemic. Our analysis focuses on a balanced panel of 1,780 workers who were interviewed three times through July 2021, considering labor market re-entry, earnings, and measures of vulnerability by gender.\n\nFindingsBoth men and women struggle to remigrate - by July 2021 (over a year after the nationwide lockdown ended), no more than 63 percent (95% CI [60,66]) of men and 55 percent [51,59] of women had left their home villages since returning. Initially, returning migrants transition from non-agricultural urban employment into agriculture and unemployment in rural areas. Alongside, incomes plummet, with both genders earning roughly 17 percent of their pre-lockdown incomes in July 2020. Remigration is critical to regaining income - male re-migrants report earnings on par with their pre-lockdown incomes by January 2021, while men remaining in rural areas earn only 23 percent [19,27] of their pre-pandemic income. Remigration benefits women to a lesser extent - female remigrants regain no more than 65 percent [57,73] of their pre-pandemic income at any point. This contrast reflects significantly higher rates of unemployment among women, both among those remaining in rural areas (9 percentage points [6,13] higher than men across waves) and among those who remigrate (13 percentage points [9,17] higher than men across waves). As a result, we observe gender gaps in well-being: female migrants were 7 percentage points [4,10] more likely to report reduced consumption of essential goods and fare 6 percentage points [4,7] worse on a food security index.\n\nInterpretationReturn migrants of both genders experienced persistent hardships for over a year after the initial pandemic lockdown. Female migrants fare worse, driven by both lower rates of remigration and lower rates of labor market re-entry both inside and outside home villages. Some women drop out of the labor force entirely, but most unemployed report seeking or being available to work. In short, pandemic-induced labor market displacement has far-reaching, long-term consequences for migrant workers, especially women.\n\nFundingSurvey costs were funded by research grants from IZA/FCDO Gender, Growth, and Labour Markets in Low Income Countries Programme, J-PAL Jobs and Opportunity Initiative, and the Evidence-based Measures of Empowerment for Research on Gender Equality (EMERGE) program at University of California San Diego. Funders had no role in study design, study implementation, data analysis, or manuscript preparation.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSMost research documenting the experience of displaced domestic migrants during the pandemic is focused on difficulties faced in returning to their home villages and the immediate consequences of this displacement. Existing evidence has found high levels of short-run economic and psychological distress, especially among women and children, and under-coverage of government programs designed to ease the lockdowns sudden economic shock.\n\nAdded value of this studyThis study contributes to existing literature by surveying a large sample of male and female workers, designed to be broadly representative of returned migrants in two of Indias poorest states. Our work takes a longer-term view, tracking study participants efforts to remigrate and reintegrate into the labor force over 15 months. We document sustained difficulties attaining pre-pandemic levels of income and consumption insecurity, especially among women, who struggle even after remigrating.\n\nImplications of all the available evidenceTaken as a whole, the evidence underscores that displaced Indian migrants are a vulnerable and underserved social group, who have faced (and will likely continue to face) lasting negative effects of the Covid-19 pandemic. Displaced migrants - and especially women - would likely benefit from programs designed to facilitate re-entry into urban labor markets; wrap around services that address other effects of the pandemic (e.g. psychological distress) may be particularly valuable.", + "rel_num_authors": 6, "rel_authors": [ { - "author_name": "Verena Rass", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Piotr Tymoszuk", - "author_inst": "Data Analytics As a Service Tirol, Innsbruck, Austria" - }, - { - "author_name": "Sabina Sahanic", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck Austria" - }, - { - "author_name": "Beatrice Heim", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Dietmar Ausserhofer", - "author_inst": "Institute of General Practice and Public Health, Claudiana College of Health Professions, Bolzano, Italy" - }, - { - "author_name": "Anna Lindner", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Mario Kofler", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Philipp Mahlknecht", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Anna Boehm", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck Austria" - }, - { - "author_name": "Katharina H\u00fcfner", - "author_inst": "Department of Psychiatry, Psychotherapy, Psychosomatics and Medical Psychology, University Hospital for Psychiatry II, Medical University of Innsbruck, Innsbruc" - }, - { - "author_name": "Alex Pizzini", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck Austria" - }, - { - "author_name": "Thomas Sonnweber", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck Austria" - }, - { - "author_name": "Katharina Kurz", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck Austria" - }, - { - "author_name": "Bernhard Pfeifer", - "author_inst": "Tyrolean Federal Institute for Integrated Care, Innsbruck, Austria" - }, - { - "author_name": "Stefan Kiechl", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Marina Peball", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Philipp Kindl", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Lauma Putnina", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Elena Fava", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Atbin Djamshidian", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Andreas Huber", - "author_inst": "Tyrolean Federal Institute for Integrated Care, Innsbruck, Austria" - }, - { - "author_name": "Christian J Wiedermann", - "author_inst": "Institute of General Practice and Public Health, Claudiana College of Health Professions, Bolzano, Italy" - }, - { - "author_name": "Barbara Sperner-Unterweger", - "author_inst": "Department of Psychiatry, Psychotherapy, Psychosomatics and Medical Psychology, University Hospital for Psychiatry II, Medical University of Innsbruck, Innsbruc" + "author_name": "Jenna Allard", + "author_inst": "MacMillan Center, Yale University" }, { - "author_name": "Ewald W\u00f6ll", - "author_inst": "Department of Internal Medicine, St. Vinzenz Hospital, Zams, Austria" - }, - { - "author_name": "Ronny Beer", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Alois Josef Schiefecker", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Rosa Bellmann-Weiler", - "author_inst": "Department of Internal Medicine, St. Vinzenz Hospital, Zams, Austria" - }, - { - "author_name": "Herbert Bachler", - "author_inst": "Institute of General Medicine, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Ivan Tancevski", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck Austria" - }, - { - "author_name": "Bettina Pfausler", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Giuliano Piccoliori", - "author_inst": "Institute of General Practice and Public Health, Claudiana College of Health Professions, Bolzano, Italy" + "author_name": "Maulik Jagnani", + "author_inst": "University of Colorado Denver" }, { - "author_name": "Klaus Seppi", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" + "author_name": "Yusuf Neggers", + "author_inst": "University of Michigan" }, { - "author_name": "G\u00fcnter Weiss", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck Austria" + "author_name": "Rohini Pande", + "author_inst": "Economic Growth Center, Yale University" }, { - "author_name": "Judith L\u00f6ffler-Ragg", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck Austria" + "author_name": "Simone Schaner", + "author_inst": "Center for Economic and Social Research, University of Southern California" }, { - "author_name": "Raimund Helbok", - "author_inst": "Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria" + "author_name": "Charity Troyer Moore", + "author_inst": "MacMillan Center, Yale University" } ], "version": "1", "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" + "category": "public and global health" }, { "rel_doi": "10.1101/2022.06.02.22275918", @@ -288610,59 +288713,55 @@ "category": "bioengineering" }, { - "rel_doi": "10.1101/2022.06.01.494101", - "rel_title": "Antiviral immune responses, cellular metabolism and adhesion are differentially modulated by SARS-CoV-2 ORF7a or ORF7b", + "rel_doi": "10.1101/2022.05.31.22274501", + "rel_title": "Severe acute respiratory syndrome coronavirus 2 breakthrough infections in healthcare workers vaccinees with BNT162b2 (Pfizer-BioNtech) in Bogota, Colombia", "rel_date": "2022-06-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.01.494101", - "rel_abs": "SARS-CoV-2, the causative agent of the present COVID-19 pandemic, possesses eleven accessory proteins encoded in its genome, and some have been implicated in facilitating infection and pathogenesis through their interaction with cellular components. Among these proteins, accessory protein ORF7a and ORF7b functions are poorly understood. In this study, A549 cells were transduced to express ORF7a and ORF7b, respectively, to explore more in depth the role of each accessory protein in the pathological manifestation leading to COVID-19. Bioinformatic analysis and integration of transcriptome results identified defined canonical pathways and functional groupings revealing that after expression of ORF7a or ORF7b, the lung cells are potentially altered to create conditions more favorable for SARS-CoV-2, by inhibiting the IFN-I response, increasing proinflammatory cytokines release, and altering cell metabolic activity and adhesion. Based on these results, it is reasonable to suggest that ORF7a and ORF7b could be targeted by new therapies or used as future biomarkers during this pandemic.", - "rel_num_authors": 10, + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.31.22274501", + "rel_abs": "The healthcare workers are considered as a high-risk group for infection with SARS-CoV-2, so they were included in the first stage of the National Plan for Vaccination against COVID-19 in Colombia.\n\nAn ongoing prospective cohort study to evaluate immune response to vaccination included 490 workers from health institutions in Bogota, Colombia, vaccinated between March and June 2021 with BNT162b2 (Pfizer-BioNtech). Multiple samples were collected during a follow-up period of 6 months after immunization. We report cases of asymptomatic and symptomatic SARS-CoV-2 infections detected in this cohort. For each participant demographic data, vaccination dates, results for SARS-CoV-2 RT-PCR, and detection of antibody (IgG) tests during the follow-up period were collected.\n\nSARS-CoV-2 infection was detected in 38 (7.7 %) volunteers. Of these, 81.6% had a positive RT-PCR for SARS-CoV-2, and 18.4% were confirmed by detection of IgG anti-SARS-CoV-2 nucleoprotein; 76.3% of infections occurred after 7 days of second dose. A total of 57.9% of the cases were asymptomatic. No hospitalizations or deaths were registered. When infection occurred, 81.6% of infected participants had presence of IgG anti-S antibodies. In 12 samples in which genomic characterization was achieved, 83.4% corresponded to the variant Mu, 8.3% Gamma, and 8.3% Delta.\n\nAll findings agree with other reports in different studies that show the benefit of COVID-19 vaccines, protecting specially against severe disease but not against infection or re-infection.", + "rel_num_authors": 9, "rel_authors": [ { - "author_name": "Transito Garcia-Garcia", - "author_inst": "Immunogenomics and Molecular Pathogenesis BIO365 Group, Department of Genetics, University of Cordoba, Cordoba, Spain" - }, - { - "author_name": "Raul Fernandez-Rodriguez", - "author_inst": "Immunogenomics and Molecular Pathogenesis BIO365 Group, Department of Genetics, University of Cordoba, Cordoba, Spain" + "author_name": "Pilar Tavera-Rodriguez", + "author_inst": "Instituto Nacional de Salud Colombia" }, { - "author_name": "Natalia Redondo", - "author_inst": "Molecular Biomedicine Department, Centro de Investigaciones Biologicas Margarita Salas (CIB), CSIC, Madrid, Spain" + "author_name": "Juliana Barbosa-Ramirez", + "author_inst": "Instituto Nacional de Salud" }, { - "author_name": "Ana de Lucas-Rius", - "author_inst": "Molecular Biomedicine Department, Centro de Investigaciones Biologicas Margarita Salas (CIB), CSIC, Madrid, Spain" + "author_name": "Andrea Bermudez-Forero", + "author_inst": "Instituto Nacional de Salud" }, { - "author_name": "Sara Zaldivar-Lopez", - "author_inst": "Immunogenomics and Molecular Pathogenesis BIO365 Group, Department of Genetics, University of Cordoba, Cordoba, Spain" + "author_name": "Diego Prada-Cardozo", + "author_inst": "Instituto Nacional de Salud" }, { - "author_name": "Blanca Dies Lopez-Ayllon", - "author_inst": "Molecular Biomedicine Department, Centro de Investigaciones Biologicas Margarita Salas (CIB), CSIC, Madrid, Spain" + "author_name": "Jhonnatan Reales-Gonzalez", + "author_inst": "Instituto Nacional de Salud" }, { - "author_name": "Jose M. Suarez-Cardenas", - "author_inst": "Immunogenomics and Molecular Pathogenesis BIO365 Group, Department of Genetics, University of Cordoba, Cordoba, Spain" + "author_name": "Dioselina Pelaez-Carvajal", + "author_inst": "Instituto Nacional de Salud" }, { - "author_name": "Angeles Jimenez-Marin", - "author_inst": "Immunogenomics and Molecular Pathogenesis BIO365 Group, Department of Genetics, University of Cordoba, Cordoba, Spain" + "author_name": "Diana Malo-Sanchez", + "author_inst": "Instituto Nacional de Salud" }, { - "author_name": "Maria Montoya", - "author_inst": "Molecular Biomedicine Department, Centro de Investigaciones Biologicas Margarita Salas (CIB), CSIC, Madrid, Spain" + "author_name": "Maria-Ximena Meneses-Gil", + "author_inst": "Instituto Nacional de Salud" }, { - "author_name": "Juan J. Garrido", - "author_inst": "Immunogenomics and Molecular Pathogenesis BIO365 Group, Department of Genetics, University of Cordoba, Cordoba, Spain" + "author_name": "Marcela Mercado-Reyes", + "author_inst": "Instituto Nacional de Salud" } ], "version": "1", "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" }, { "rel_doi": "10.1101/2022.05.31.22275746", @@ -290236,53 +290335,73 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.05.27.22275630", - "rel_title": "Incidence of SARS-CoV-2 infection among unvaccinated US adults during the Omicron wave", + "rel_doi": "10.1101/2022.05.29.22275277", + "rel_title": "Investigation of a SARS-CoV-2 outbreak in a Texas summer camp resulting from a single introduction", "rel_date": "2022-05-30", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.27.22275630", - "rel_abs": "As of 4/20/2022, approximately 23% of the eligible US population was unvaccinated. We studied COVID-19 infections during the Omicron (B.1.1.529) wave in unvaccinated US adults, stratified by pre-Omicron antibody levels. Anti-spike serologic testing was performed prior to the Omicron wave in the United States (9/23/21-11/5/21) and participants were surveilled to determine incident COVID-19. Only 12% of those who entered the wave with antibodies reported a test-confirmed COVID-19 infection, compared to 35% of those without antibodies prior to the Omicron wave. Effectiveness of these anti-RBD antibodies in this unvaccinated population was 67%. Among people with antibodies, titer did not appear to be associated with risk of test-confirmed Omicron infection.", - "rel_num_authors": 9, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.29.22275277", + "rel_abs": "SARS-CoV-2 is the etiological agent responsible for the COVID-19 pandemic. It is estimated that only 10 aerosol-borne virus particles are sufficient to establish a secondary infection with SARS-CoV-2. However, the dispersal pattern of SARS-CoV-2 is highly variable and only 10- 20% of cases are responsible for up 80% of secondary infections. The heterogeneous nature of SARS-CoV-2 transmission suggests that super-spreader events play an important role in viral transmission. Super-spreader events occur when a single person is responsible for an unusually high number of secondary infections due to a combination of biological, environmental, and/or behavioral factors. While super-spreader events have been identified as a significant factor driving SARS-CoV-2 transmission, epidemiologic studies have consistently shown that education settings do not play a major role in community transmission. However, an outbreak of SARS-CoV-2 was recently reported among 186 children (aged 10-17) and adults (aged 18 +) after attending an overnight summer camp in Texas in June 2021. To understand the transmission dynamics of the outbreak, RNA was isolated from 36 nasopharyngeal swabs collected from patients that attended the camp and 19 control patients with no known connection to the outbreak. Genome sequencing on the Oxford Nanopore platform was performed using the ARTIC approaches for library preparation and bioinformatic analysis. SARS-CoV-2 amplicons were produced from all RNA samples and >70% of the viral genome was successfully reconstructed with >10X coverage for 46 samples. Phylogenetic methods were used to estimate the transmission history and suggested that the outbreak was the result of a single introduction. We also found evidence for secondary transmission from campers to the community. Together, these findings demonstrate that super-spreader events may occur during large gatherings of children.", + "rel_num_authors": 14, "rel_authors": [ { - "author_name": "Jennifer L Alejo", - "author_inst": "Johns Hopkins Medical Institutions" + "author_name": "Daniele Michele Swetnam", + "author_inst": "University of Texas Medical Branch" }, { - "author_name": "Teresa Po-Yu Chiang", - "author_inst": "Johns Hopkins Medical Institutions" + "author_name": "Rojelio Elias Alvarado", + "author_inst": "University of Texas Medical Branch" }, { - "author_name": "Jonathan Mitchell", - "author_inst": "Johns Hopkins Medical Institutions" + "author_name": "Stephanea Sotcheff", + "author_inst": "University of Texas Medical Branch" }, { - "author_name": "Aura T Abedon", - "author_inst": "Johns Hopkins Medical Institutions" + "author_name": "Brooke M Mitchell", + "author_inst": "University of Texas Medical Branch" }, { - "author_name": "Alexa Jefferis", - "author_inst": "Johns Hopkins Medical Institutions" + "author_name": "Allan McConnell", + "author_inst": "University of Texas Medical Branch" }, { - "author_name": "William A Werbel", - "author_inst": "Johns Hopkins Medical Institutions" + "author_name": "Rafael R.G. Machado", + "author_inst": "University of Texas Medical Branch" }, { - "author_name": "Allan B Massie", - "author_inst": "NYU Langone Medical Center" + "author_name": "Nehad Saada", + "author_inst": "University of Texas Medical Branch" }, { - "author_name": "Martin A Makary", - "author_inst": "Johns Hopkins Medical Institutions" + "author_name": "Florence P Haseltine", + "author_inst": "University of Texas at Arlington" }, { - "author_name": "Dorry L Segev", - "author_inst": "NYU Langone Medical Center" + "author_name": "Sara Maknojia", + "author_inst": "Galveston County Health District" + }, + { + "author_name": "Anajane Smith", + "author_inst": "University of Texas at Arlington" + }, + { + "author_name": "Ping Ren", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Philip Keiser", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Scott Weaver", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Andrew L Routh", + "author_inst": "University of Texas Medical Branch" } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc_by_nd", "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, @@ -291910,91 +292029,119 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.05.25.22273991", - "rel_title": "Development and scaling of a sequencing pipeline for genomic surveillance of SARS-CoV-2 in New York City", + "rel_doi": "10.1101/2022.05.27.493682", + "rel_title": "Structural basis of a two-antibody cocktail exhibiting highly potent and broadly neutralizing activities against SARS-CoV-2 variants including diverse Omicron sublineages", "rel_date": "2022-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.25.22273991", - "rel_abs": "In the ongoing COVID-19 pandemic, detecting the appearance and spread of variants of concern (VOC) is a critical capability in the fight to quell the virus and return to normalcy. Genomic surveillance of the emergence, propagation, and geographical spread of VOCs is thus an important tool for public health officials and government leaders to make policy decisions and advise the public. As part of our role as a major SARS-CoV-2 diagnostic testing facility in New York City, the Pandemic Response Lab (PRL) has been performing genomic surveillance on the large number of positive samples processed by the facility on a daily basis from throughout the New York metropolitan area. Here we describe the development and optimization of a high-throughput SARS-CoV-2 genome sequencing facility at PRL serving New York City.", - "rel_num_authors": 18, + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.27.493682", + "rel_abs": "SARS-CoV-2 variants of concern (VOCs), especially the latest Omicron, have exhibited severe antibody evasion. Broadly neutralizing antibodies with high potency against Omicron are urgently needed for understanding working mechanisms and developing therapeutic agents. In this study, we characterized previously reported F61, which was isolated from convalescent patients infected with prototype SARS-CoV-2, as a broadly neutralizing antibody against all VOCs including Omicron BA.1, BA.1.1, BA.2, BA.3 and BA.4 sublineages by utilizing antigen binding and cell infection assays. We also identified and characterized another broadly neutralizing antibody D2 with epitope distinct from that of F61. More importantly, we showed that a combination of F61 with D2 exhibited synergy in neutralization and protecting mice from SARS-CoV-2 Delta and Omicron BA.1 variants. Cryo-EM structures of the spike-F61 and spike-D2 binary complexes revealed the distinct epitopes of F61 and D2 at atomic level and the structural basis for neutralization. Cryo-EM structure of the Omicron-spike-F61-D2 ternary complex provides further structural insights into the synergy between F61 and D2. These results collectively indicated F61 and F61-D2 cocktail as promising therapeutic antibodies for combating SARS-CoV-2 variants including diverse Omicron sublineages.", + "rel_num_authors": 25, "rel_authors": [ { - "author_name": "Michael J Hammerling", - "author_inst": "Pandemic Response Lab" + "author_name": "Xiaoman Li", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" }, { - "author_name": "Shinyoung Clair Kang", - "author_inst": "Cultivarium" + "author_name": "Yongbing Pan", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" }, { - "author_name": "William Ward", - "author_inst": "Pandemic Response Lab" + "author_name": "Qiangling Yin", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" }, { - "author_name": "Isabel Fernandez Escapa", - "author_inst": "Pandemic Response Lab" + "author_name": "Zejun Wang", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" }, { - "author_name": "Pradeep Bugga", - "author_inst": "Kern Systems" + "author_name": "Sisi Shan", + "author_inst": "NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Ts" }, { - "author_name": "Cybill Del Castillo", - "author_inst": "Pandemic Response Lab" + "author_name": "Laixing Zhang", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" }, { - "author_name": "Melissa Hopkins", - "author_inst": "Pandemic Response Lab" + "author_name": "Jinfang Yu", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" }, { - "author_name": "Steven Chase", - "author_inst": "Pandemic Response Lab" + "author_name": "Yuanyuan Qu", + "author_inst": "Institution of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen 518107, China" }, { - "author_name": "Sol Rey", - "author_inst": "Pandemic Response Lab" + "author_name": "Lina Sun", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" }, { - "author_name": "Dylan Law", - "author_inst": "Pandemic Response Lab" + "author_name": "Fang Gui", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" }, { - "author_name": "Alexander Carpio", - "author_inst": "Pandemic Response Lab" + "author_name": "Jia Lu", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" }, { - "author_name": "Kate Nelson", - "author_inst": "Pandemic Response Lab" + "author_name": "Zhaofei Jing", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" }, { - "author_name": "Simran Chhabria", - "author_inst": "Pandemic Response Lab" + "author_name": "Wei Wu", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" }, { - "author_name": "Simran Gupta", - "author_inst": "Pandemic Response Lab" + "author_name": "Tao Huang", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" }, { - "author_name": "Tiara Rivera", - "author_inst": "Pandemic Response Lab" + "author_name": "Xuanling Shi", + "author_inst": "NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Ts" }, { - "author_name": "Jon M Laurent", - "author_inst": "Pandemic Response Lab" + "author_name": "Jiandong Li", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" }, { - "author_name": "Haiping Hao", - "author_inst": "Pandemic Response Lab" + "author_name": "Xinguo Li", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Dexin Li", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Shiwen Wang", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" + }, + { + "author_name": "Maojun Yang", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" + }, + { + "author_name": "Linqi Zhang", + "author_inst": "NexVac Research Center, Comprehensive AIDS Research Center, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Ts" + }, + { + "author_name": "Kai Duan", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Mifang Liang", + "author_inst": "State Key Laboratory for Molecular Virology and Genetic Engineering, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Con" }, { - "author_name": "Henry H Lee", - "author_inst": "Cultivarium" + "author_name": "Xiaoming Yang", + "author_inst": "National Engineering Technology Research Center for Combined Vaccines, Wuhan Institute of Biological Products Co. Ltd., Wuhan 430070, China" + }, + { + "author_name": "Xinquan Wang", + "author_inst": "The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Bio" } ], "version": "1", "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" + "type": "new results", + "category": "biochemistry" }, { "rel_doi": "10.1101/2022.05.27.493400", @@ -294328,43 +294475,47 @@ "category": "microbiology" }, { - "rel_doi": "10.1101/2022.05.26.22275585", - "rel_title": "Long Covid stigma: estimating burden and validating scale in a UK-based sample", + "rel_doi": "10.1101/2022.05.26.493529", + "rel_title": "The emergence of variants with increased fitness accelerates the slowdown of genome sequence heterogeneity in the SARS CoV 2 coronavirus", "rel_date": "2022-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.26.22275585", - "rel_abs": "BackgroundStigma can be experienced as perceived or actual disqualification from social and institutional acceptance on the basis of one or more physical, behavioural or other attributes deemed to be undesirable. Long Covid is a predominantly multisystem condition that occurs in people with a history of SARSCoV2 infection, often resulting in functional disability.\n\nAimTo develop and validate a Long Covid Stigma Scale (LCSS); and to quantify the burden of Long Covid stigma.\n\nDesign and SettingFollow-up of a co-produced community-based Long Covid online survey using convenience non-probability sampling.\n\nMethodThirteen questions on stigma were designed to develop the LCSS capturing three domains - enacted (overt experiences of discrimination), internalised (internalising negative associations with Long Covid and accepting them as self-applicable) and anticipated (expectation of bias/poor treatment by others) stigma. Confirmatory factor analysis tested whether LCSS consisted of the three hypothesised domains. Model fit was assessed and prevalence was calculated.\n\nResults966 UK-based participants responded (888 for stigma questions), with mean age 48 years (SD: 10.7) and 85% female. Factor loadings for enacted stigma were 0.70-0.86, internalised 0.75-0.84, anticipated 0.58-0.87, and model fit was good. The prevalence of experiencing stigma at least sometimes and often/always was 95% and 76% respectively. Anticipated and internalised stigma were more frequently experienced than enacted stigma. Those who reported having a clinical diagnosis of Long Covid had higher stigma prevalence than those without.\n\nConclusionThis study establishes a scale to measure Long Covid stigma and highlights common experiences of stigma in people living with Long Covid.", - "rel_num_authors": 6, + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.26.493529", + "rel_abs": "Since the outbreak of the COVID-19 pandemic, the SARS-CoV-2 coronavirus has accumulated an important amount of genetic and genomic variability through mutation and recombination events. To test evolutionary trends that could inform us on the adaptive process of the virus to its human host, we summarize all this sequence variability by computing the Sequence Compositional Complexity (SCC) in more than 23,000 high-quality coronavirus genome sequences from across the globe, covering the period spanning from the start of the pandemic in December 2019 to March 2022. In early samples, we found no statistical support for any trend in SCC values over time, although the virus as a whole appears to evolve faster than Brownian Motion expectation. However, in samples taken after the first Variant of Concern (VoC) with higher transmissibility (Alpha) emerges, and controlling for phylogenetic and sampling effects, we were able to detect a statistically significant trend for decreased SCC values over time. SARS-CoV-2 evolution towards lower values of genome heterogeneity is further intensified by the emergence of successive, widespread VoCs. Concomitantly to the temporal reduction in SCC, its absolute evolutionary rate kept increasing toward the present, meaning that the SCC decrease itself accelerated over time. As compared to Alpha or Delta variants, the currently dominant VoC, Omicron, shows much stronger trends in both SCC values and rates over time. These results indicate that the increases in fitness of variant genomes associated to a higher transmissibility leads to a reduction of their genome sequence heterogeneity, thus explaining the general slowdown of SCC along with the pandemic course.", + "rel_num_authors": 7, "rel_authors": [ { - "author_name": "Marija Pantelic", - "author_inst": "University of Sussex" + "author_name": "Jos\u00e9 L. Oliver", + "author_inst": "Professor of Genetics, Facultad de Ciencias, Universidad de Granada, Spain" }, { - "author_name": "Nida Ziauddeen", - "author_inst": "University of Southampton" + "author_name": "Pedro Bernaola-Galv\u00e1n", + "author_inst": "Professor of Applied Physics, E.T.S. de Ingenieria de Telecomunicacion, Universidad de Malaga, Spain" }, { - "author_name": "Mark Boyes", - "author_inst": "Curtin University" + "author_name": "Francisco Perfectti", + "author_inst": "Professor of Genetics, Grupo de Genetica Evolutiva, Departamento de Genetica and Research Unit Modeling Nature Evoflor, Unidad Asociada al CSIC, Universidad de" }, { - "author_name": "Margaret E O'Hara", - "author_inst": "Long Covid Support" + "author_name": "Cristina G\u00f3mez-Mart\u00edn", + "author_inst": "Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Center Amsterdam, Amsterdam, Netherlands" }, { - "author_name": "Claire Hastie", - "author_inst": "Long Covid Support" + "author_name": "Pasquale Raia", + "author_inst": "Dip.to DiSTAR, Napoli Universita di Napoli Federico II, Dipartimento di Scienze della Terra, dell Ambiente e delle Risorse, Italy" }, { - "author_name": "Nisreen A Alwan", - "author_inst": "University of Southampton" + "author_name": "Miguel Verd\u00fa", + "author_inst": "Centro de Investigaciones sobre Desertificacion, Consejo Superior de Investigaciones Cientificas (CSIC), University of Valencia and Generalitat Valenciana, 4611" + }, + { + "author_name": "Andr\u00e9s Moya", + "author_inst": "Professor of Genetics, University of Valencia Chair, Institutional Professorship FISABIO - University of Valencia, Spain" } ], "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" }, { "rel_doi": "10.1101/2022.05.21.22275421", @@ -296214,53 +296365,21 @@ "category": "biochemistry" }, { - "rel_doi": "10.1101/2022.05.23.22275442", - "rel_title": "Assessment of subtle cognitive impairments in patients with post-COVID syndrome with the tablet-based Oxford Cognitive Screen-Plus (OCS-Plus).", + "rel_doi": "10.1101/2022.05.20.22275407", + "rel_title": "Social divisions and risk perception can drive divergent epidemic dynamics and large second and third waves", "rel_date": "2022-05-23", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.23.22275442", - "rel_abs": "Background and objectivesCognitive symptoms persisting beyond three months following COVID-19 present a considerable disease burden. We aimed to establish a domain-specific cognitive profile of post-COVID syndrome (PCS) and relationships with subjective cognitive complaints and clinical variables to provide relevant information for the understanding of cognitive dysfunction and its predictors in a clinical cohort with PCS.\n\nMethodsIn this cross-sectional study, we compared cognitive performance on the clinically viable Oxford Cognitive Screen-Plus between a large post-COVID cohort (n = 282) and a socio-demographically matched healthy control group (n = 52). We assessed group differences in terms of fatigue and depression as well as relationships between cognitive dysfunction and clinical and patient-reported outcomes.\n\nResultsOn a group-level, patients scored significantly lower on delayed verbal memory (non-parametric effect size r = .13), attention (r = .1), and executive functioning (r=.1) than healthy controls. In each of these domains, 10-20% of patients performed more than 1.5 SD below the healthy control mean. Delayed Memory was particularly affected and a small proportion of its variance was explained by hospitalisation ({beta} = -.72, p < .01) and age ({beta} = -.03, p < .05; R2adj. = .08). Attention scores were significantly predicted by hospitalisation ({beta} = -.78, p < .01) and fatigue ({beta} = -.04, p < .05; R2adj. = .06).\n\nDiscussionPCS is associated with long-term cognitive dysfunction, particularly in delayed verbal memory, attention, and executive functioning. Deficits in delayed memory performance seem to be of particular relevance to patients subjective experience of impairment. Initial disease severity, current level of fatigue, and age seem to predict cognitive performance, while time since infection, depression, and pre-existing conditions do not. Longitudinal data are needed to map long-term course of cognitive dysfunction in PCS.", - "rel_num_authors": 10, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.20.22275407", + "rel_abs": "During infectious disease outbreaks, individuals may adopt protective measures like vaccination and physical distancing in response to awareness of disease burden. Prior work showed how feedback between epidemic intensity and awareness-based behavior shapes disease dynamics (e.g., producing plateaus and oscillations). These models often overlook social divisions, where population subgroups may be disproportionately impacted by a disease and more responsive to the effects of disease within their group. We hypothesize that socially divided awareness-based behavior could fundamentally alter epidemic dynamics and shift disease burden between groups.\n\nWe develop a compartmental model of disease transmission in a population split into two groups to explore the impacts of awareness separation (relatively greater in-versus out-group awareness of epidemic severity) and mixing separation (relatively greater in-versus out-group contact rates). Protective measures are adopted based on awareness of recent disease-linked mortality. Using simulations, we show that groups that are more separated in awareness have smaller differences in mortality. Fatigue-driven abandonment of protective behavior can drive additional infection waves that can even exceed the size of the initial wave, particularly if uniform awareness drives early protection in one group, leaving that group largely susceptible to future infection. Finally, vaccine or infection-acquired immunity that is more protective against transmission and mortality may indirectly lead to more infections by reducing perceived risk of infection, and thereby reducing vaccine uptake. The dynamics of awareness-driven protective behavior, including relatively greater awareness of epidemic conditions in ones own group, can dramatically impact protective behavior uptake and the course of epidemics.", + "rel_num_authors": 2, "rel_authors": [ { - "author_name": "Valeska Kozik", - "author_inst": "Jena University Hospital" - }, - { - "author_name": "Philipp Reuken", - "author_inst": "Department of Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital, Jena, Germany" - }, - { - "author_name": "Isabelle Utech", - "author_inst": "Department of Neurology, Jena University Hospital Jena, Germany" - }, - { - "author_name": "Judith Gramlich", - "author_inst": "Department of Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital, Jena, Germany" - }, - { - "author_name": "Zoe Stallmach", - "author_inst": "Department of Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital, Jena, Germany" - }, - { - "author_name": "Nele Demeyere", - "author_inst": "Department of Experimental Psychology, University of Oxford, Radcliffe Observatory Quarter, Oxford OX2 6GG, UK" - }, - { - "author_name": "Florian Rakers", - "author_inst": "Department of Neurology, Jena University Hospital Jena, Germany" - }, - { - "author_name": "Matthias Schwab", - "author_inst": "Department of Neurology, Jena University Hospital Jena, Germany" - }, - { - "author_name": "Andreas Stallmach", - "author_inst": "Department of Internal Medicine IV (Gastroenterology, Hepatology and Infectious Diseases), Jena University Hospital, Jena, Germany; Center for Sepsis Control an" + "author_name": "Mallory J Harris", + "author_inst": "Biology Department, Stanford University, Stanford, CA 94301" }, { - "author_name": "Kathrin Finke", - "author_inst": "Department of Neurology, Jena University Hospital, Jena, Germany; Department of Psychology, Ludwig-Maximilians-University, Munich" + "author_name": "Erin A. Mordecai", + "author_inst": "Biology Department, Stanford University, Stanford, CA 94301" } ], "version": "1", @@ -298392,39 +298511,59 @@ "category": "nephrology" }, { - "rel_doi": "10.1101/2022.05.18.22275217", - "rel_title": "Bias-adjusted predictions of county-level vaccination coverage from the COVID-19 Trends and Impact Survey", + "rel_doi": "10.1101/2022.05.18.22275283", + "rel_title": "BNT162b2 induces robust cross-variant SARS-CoV-2 immunity in children", "rel_date": "2022-05-21", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.18.22275217", - "rel_abs": "The potential for bias in non-representative, large-scale, low-cost survey data can limit their utility for population health measurement and public health decision-making. We developed a multi-step regression framework to bias-adjust vaccination coverage predictions from the large-scale US COVID-19 Trends and Impact Survey that included post-stratification to the American Community Survey and secondary normalization to an unbiased reference indicator. As a case study, we applied this framework to generate county-level predictions of long-run vaccination coverage among children ages 5 to 11 years. Our vaccination coverage predictions suggest a low ceiling on long-term national coverage (46%), detect substantial geographic heterogeneity (ranging from 11% to 91% across counties in the US), and highlight widespread disparities in the pace of scale-up in the three months following Emergency Use Authorization of COVID-19 vaccination for 5 to 11 year-olds. Generally, our analysis demonstrates an approach to leverage differing strengths of multiple sources of information to produce estimates on the time-scale and geographic-scale necessary for proactive decision-making. The utility of large-scale, low-cost survey data for improving population health measurement is amplified when these data are combined with other representative sources of data.", - "rel_num_authors": 5, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.18.22275283", + "rel_abs": "Currently available mRNA vaccines are extremely safe and effective to prevent severe SARS-CoV-2 infections. However, the emergence of novel variants of concerns has highlighted the importance of high population-based vaccine rates to effectively suppress viral transmission and breakthrough infections. While initially left out from vaccine efforts, children have become one of the most affected age groups and are key targets to stop community and household spread. Antibodies are central for vaccine induced protection and emerging data points to the importance of additional Fc effector functions like opsononophagocytosis or cytotoxicity, particularly in the context of variants of concern that escape neutralizing antibodies. Here, we observed delayed induction and reduced magnitude of vaccine induced antibody titers in children 5-11 years receiving two doses of the age recommended 10 g dose of the Pfizer SARS-CoV-2 BNT162b2 vaccine compared to adolescents (12-15 years) or adults receiving the 30 g dose. Conversely, children mounted equivalent or more robust neutralization and opsonophagocytic functions at peak immunogenicity, pointing to a qualitatively more robust humoral functional response in children. Moreover, broad cross-variants of concern responses were observed across children, with enhanced IgM and parallel IgG cross-reactivity to variants of concern (VOCs) in children compared to adults. Collectively, these data argue that despite the lower magnitude of the BNT162b2 induced antibody response in children, vaccine induced immunity in children target VOCs broadly and exhibit enhanced functionality that may contribute to attenuation of disease.", + "rel_num_authors": 10, "rel_authors": [ { - "author_name": "Marissa B Reitsma", - "author_inst": "Stanford University" + "author_name": "Yannic C Bartsch", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" }, { - "author_name": "Sherri Rose", - "author_inst": "Stanford University" + "author_name": "Jessica W Chen", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" }, { - "author_name": "Alex Reinhart", - "author_inst": "Carnegie Mellon University" + "author_name": "Jaewon Kang", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" }, { - "author_name": "Jeremy D Goldhaber-Fiebert", - "author_inst": "Stanford University" + "author_name": "Madeline D Burns", + "author_inst": "Massachusetts General Hospital Department of Pediatrics" }, { - "author_name": "Joshua A Salomon", - "author_inst": "Stanford University" + "author_name": "Kerri J St.Denis", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Maegan L Sheehan", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Jameson P Davis", + "author_inst": "Massachusetts General Hospital Department of Pediatrics" + }, + { + "author_name": "Alejandro B Balazs", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Lael M Yonker", + "author_inst": "Massachusetts General Hospital Department of Pediatrics" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" } ], "version": "1", "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" + "category": "infectious diseases" }, { "rel_doi": "10.1101/2022.05.18.22275240", @@ -300202,107 +300341,47 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.05.18.22275209", - "rel_title": "Reduced antibody acquisition with increasing age following vaccination with BNT162b2: results from a large study performed in the general population aged 12 to 92 years", + "rel_doi": "10.1101/2022.05.14.22275075", + "rel_title": "Self-medication practices and associated factors among COVID-19 recovered patients to prevent future infections: A web-based survey in Bangladesh", "rel_date": "2022-05-19", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.18.22275209", - "rel_abs": "Vaccine-induced protection of the population against severe COVID-19, hospitalization and death is of utmost importance, especially in the elderly. However, limited data are available on humoral immune responses following COVID-19 vaccination in the general population across a broad age range. We performed an integrated analysis of the effect of age, sex and prior SARS-CoV-2 infection on Spike S1-specific (S1) IgG concentrations up to three months post BNT162b2 vaccination. 1{middle dot}735 persons, eligible for COVID-19 vaccination through the national program, were recruited from the general population (12 to 92 years old). Sixty percent were female and the median vaccination interval was 35 days (interquartile range, IQR: 35-35). All participants had seroconverted to S1 one month after two doses of vaccine. S1 IgG was higher in participants with a history of SARS-CoV-2 infection (median: 4{middle dot}535 BAU/ml, IQR: 2{middle dot}341-7{middle dot}205) compared to infection-naive persons (1{middle dot}842 BAU/ml, 1{middle dot}019-3{middle dot}116) after two doses, p<0.001. In infection-naive persons, linear mixed effects regression showed a strong negative association between age and S1 IgG one month after the first vaccination (p<0.001) across the entire age range. The association was still present after the second vaccination, but less pronounced. Females had higher S1 IgG than males after both the first and second vaccination (p<0.001); although this difference was lower after the second dose. In persons with an infection history, age nor sex was associated with peak S1 IgG. As IgG decreased with age and time since vaccination, older persons may become at risk of infection, especially with escape variants such as Omicron.", - "rel_num_authors": 22, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.14.22275075", + "rel_abs": "BackgroundHuman health is largely affected by self-medication in both ways, adversely and favorably, as evidenced by the COVID-19 pandemic. The fear of spreading COVID-19 among health workers and hospital environments has led many Bangladeshi people to practice self-medicate for as a preventive strategy against this disease. Consequently, this practice entails an improper and injudicious use of medicine to cure self-recognized symptoms. To date, the COVID-19 has no effective treatment. The lack of a cure for COVID-19 and the continual progression of the diseases in educational settings induce a substantial population to practice self-medication. Therefore a study of self-medication practices is necessary for the framework of the pandemic. This study aimed to estimate the prevalence and factors associated with self-medication to prevent or manage future COVID-19 infections among recovered COVID-19 patients.\n\nMethodsThis cross-sectional study was conducted from September 2020 to February 2021 using an e-survey along with 360 participants. Data were collected using a pre-tested self-reported questionnaire. Descriptive statistics and correlations analysis were performed in the study.\n\nResultsAmong 360 participants, males were 69.7%, and females 30.3%. The prevalence of self-medication is 11%, and monthly family income, residence, education, occupation, and previous history of SM are the associated factors. Among the participants, 29.7% use antibiotics, and 30% use herbal products or drugs as medication.\n\nConclusionThe present study found SMP is moderately prevalent among COVID-19 recovered patients. To minimize the rate of SMP, adequate health care access systems and public education should be introduced, and media & community should be engaged in rational use of medication.", + "rel_num_authors": 7, "rel_authors": [ { - "author_name": "Lotus Leonie van den Hoogen", - "author_inst": "RIVM" - }, - { - "author_name": "Mardi C. Boer", - "author_inst": "RIVM" - }, - { - "author_name": "Abigail Postema", - "author_inst": "RIVM" - }, - { - "author_name": "Lia de Rond", - "author_inst": "RIVM" - }, - { - "author_name": "Mary-lene de Zeeuw-Brouwer", - "author_inst": "RIVM" - }, - { - "author_name": "Inge Pronk", - "author_inst": "RIVM" - }, - { - "author_name": "Alienke J. Wijmenga-Monsuur", - "author_inst": "RIVM" - }, - { - "author_name": "Elske Bijvank", - "author_inst": "RIVM" - }, - { - "author_name": "Caitlyn Kruiper", - "author_inst": "RIVM" - }, - { - "author_name": "Lisa Beckers", - "author_inst": "RIVM" - }, - { - "author_name": "Marjan Bogaard-van Maurik", - "author_inst": "RIVM" - }, - { - "author_name": "Ilse Zutt", - "author_inst": "RIVM" - }, - { - "author_name": "Jeffrey van Vliet", - "author_inst": "RIVM" - }, - { - "author_name": "Rianne van Bergen", - "author_inst": "RIVM" - }, - { - "author_name": "Marjan Kuijer", - "author_inst": "RIVM" - }, - { - "author_name": "Gaby Smits", - "author_inst": "RIVM" + "author_name": "Md. Safaet Hossain Sujan", + "author_inst": "Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh" }, { - "author_name": "W.M. Monique Verschuren", - "author_inst": "RIVM" + "author_name": "Atefehsadat Haghighathoseini", + "author_inst": "Department of Health Administration and Policy, George Mason University" }, { - "author_name": "H. Susan J. Picavet", - "author_inst": "RIVM" + "author_name": "Rafia Tasnim", + "author_inst": "Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh; Centre for Advanced Research Excellence in Public Health, " }, { - "author_name": "Fiona R.M. van der Klis", - "author_inst": "RIVM" + "author_name": "Md. Saiful Islam", + "author_inst": "Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh" }, { - "author_name": "Gerco den Hartog", - "author_inst": "RIVM" + "author_name": "Sarif Mahammad Salauddin", + "author_inst": "Sir Salimullah Medical College, Dhaka-1212, Bangladesh" }, { - "author_name": "Robert S. van Binnendijk", - "author_inst": "RIVM" + "author_name": "Mohammad Mohiuddin Hasan", + "author_inst": "Hospital Services Management, DGHS, Mohakhali, Dhaka-1212, Bangladesh" }, { - "author_name": "Anne-Marie Buisman", - "author_inst": "RIVM" + "author_name": "Muhammad Ramiz Uddin", + "author_inst": "Department of Chemistry and Biochemistry, The university of Oklahoma, Norman, USA" } ], "version": "1", "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" + "category": "epidemiology" }, { "rel_doi": "10.1101/2022.05.17.22275154", @@ -301884,27 +301963,71 @@ "category": "immunology" }, { - "rel_doi": "10.1101/2022.05.15.22275107", - "rel_title": "WHAT ARE EFFECTIVE STRATEGY TO CONSTRAIN COVID-19 PANDEMIC CRISIS? LESSONS LEARNED FROM A COMPARATIVE POLICY ANALYSIS BETWEEN ITALIAN REGIONS TO COPE WITH NEXT PANDEMIC IMPACT", + "rel_doi": "10.1101/2022.05.17.22275027", + "rel_title": "A Randomized Phase 2/3 Study of Ensitrelvir, a Novel Oral SARS-CoV-2 3C-like Protease Inhibitor, in Japanese Patients With Mild-to-Moderate COVID-19 or Asymptomatic SARS-CoV-2 Infection: Results of the Phase 2a Part", "rel_date": "2022-05-17", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.15.22275107", - "rel_abs": "The pandemic of Coronavirus Disease 2019 (COVID-19) and its variants is rapidly spreading all over the world, generating a high number of infections, deaths and negative impact on socioeconomic system of countries. As vaccines and appropriate drugs for treatment of the COVID-19 can reduce the effectiveness in the presence of variants and/or new viral agents, one of the questions in social studies of medicine is effective public policy responses to reduce the impact of COVID-19 global pandemic and similar infectious diseases on health of people and on economies. This study analyzes public policy responses to the pandemic crisis across Italian regions that were the first areas to experience a rapid increase in confirmed cases and deaths of COVID-19. The analysis of regional strategies, from January to July 2020, reveals differences in public policy responses to delay and reduce the height of epidemic peak and to afford health-care systems more time to expand and respond to this new emergency. Veneto Region in North-East Italy has managed health policy responses with: a) a timely and widespread testing of individuals, b) units of epidemiological investigation for tracing all contacts of infected people in an effective contact tracing system. This public policy response has reduced total deaths and the final size of COVID-19 pandemic on health of people. Other regions have done public interventions without a clear strategy and goals to cope with diffusion of COVID-19 and as a consequence, they have had a higher negative impact on public health. Lesson learned can be important to design an effective public policy that can be generalized in different regional and national systems to prevent and/or reduce future epidemics or pandemics similar to the COVID-19.", - "rel_num_authors": 2, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.17.22275027", + "rel_abs": "For the treatment of coronavirus disease 2019 (COVID-19), antiviral agents that can achieve rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reduction are warranted. This double-blind, phase 2a part of a phase 2/3 study assessed the efficacy and safety of ensitrelvir, a novel oral SARS-CoV-2 3C-like protease inhibitor, in Japanese patients with mild-to-moderate COVID-19 or asymptomatic SARS-CoV-2 infection. Sixty-nine patients enrolled from 56 sites were randomized (1:1:1) to orally receive 5-day ensitrelvir fumaric acid (375 mg on day 1 followed by 125 mg daily or 750 mg on day 1 followed by 250 mg daily) or placebo and followed up until day 28. The primary outcome was change from baseline in SARS-CoV-2 viral titer. A total of 16, 14, and 17 patients in the ensitrelvir 125 mg, ensitrelvir 250 mg, and placebo groups, respectively, were included in the intention-to-treat population (mean age: 38.8, 40.4, and 38.0 years, respectively). On day 4, the change from baseline in SARS-CoV-2 viral titer (log10 50% tissue culture infectious dose/mL) in patients with positive viral titer and viral RNA at baseline was greater with ensitrelvir 125 mg (mean [standard deviation], -2.42 [1.42]; P = 0.0712) and 250 mg (-2.81 [1.21]; P = 0.0083) versus placebo (-1.54 [0.74]), and ensitrelvir treatment reduced SARS-CoV-2 RNA by -1.4 to -1.5 log10 copies/mL versus placebo. All adverse events were mild to moderate. Ensitrelvir treatment demonstrated rapid SARS-CoV-2 clearance and was well tolerated in patients with mild-to-moderate COVID-19 or asymptomatic SARS-CoV-2 infection (Japan Registry of Clinical Trials identifier: jRCT2031210350).", + "rel_num_authors": 13, "rel_authors": [ { - "author_name": "Mario Coccia", - "author_inst": "National Research Council of Italy" + "author_name": "Hiroshi Mukae", + "author_inst": "Nagasaki University Graduate School of Biomedical Sciences" }, { - "author_name": "Igor Benati", - "author_inst": "IRCRES-CNR Italy" + "author_name": "Hiroshi Yotsuyanagi", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Yohei Doi", + "author_inst": "University of Pittsburgh School of Medicine/Fujita Health University School of Medicine" + }, + { + "author_name": "Takumi Imamura", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Takuhiro Sonoyama", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Takahiro Fukuhara", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Genki Ichihashi", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Takao Sanaki", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Keiko Baba", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Yosuke Takeda", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Yuko Tsuge", + "author_inst": "Shionogi & Co., Ltd." + }, + { + "author_name": "Takeki Uehara", + "author_inst": "Shionogi & Co., Ltd." } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc_no", "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" + "category": "infectious diseases" }, { "rel_doi": "10.1101/2022.05.16.22275163", @@ -303562,51 +303685,103 @@ "category": "psychiatry and clinical psychology" }, { - "rel_doi": "10.1101/2022.05.11.22274952", - "rel_title": "Assessment of oxidative stress markers in elderly patients with SARS-CoV-2 infection and potential prognostic implications. An observational study", + "rel_doi": "10.1101/2022.05.14.491911", + "rel_title": "SARS-CoV-2 Omicron Variant Wave in India: Advent, Phylogeny and Evolution", "rel_date": "2022-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.11.22274952", - "rel_abs": "The aim of the study was to evaluate the correlation of plasma levels of thiobarbituric acid reactive substances (TBARS) and reduced thiols with morbidity, mortality and immune response in SARS-CoV-2 infection. This was an observational study that included inpatients with SARS-CoV-2 infection greater than 65 years old. Individuals were followed up until 12 months after hospital discharge. Demographic, clinical and laboratory variables were collected. Plasma levels of TBARS and reduced thiols were quantified as a measure of lipid and protein oxidation, respectively. Events of interest (fatal and non-fatal) were quantified at hospital discharge, third, sixth and twelfth-month post-discharge. The outcomes were differences in oxidative stress markers between groups of interest and time to a negative RT-qPCR and to significant anti-SARS-CoV-2 IgM titers. There were 61 patients (57% women) with a mean age of 83 years old. Patients with higher levels of TBARS and lower levels of reduced thiols had more risk of fatal and non-fatal events between admission and the first 12 months post-discharge. The presence of any event (fatal or non-fatal) at the end of the first 12 months post-discharge was correlated with TBARS levels, anti-SARS-CoV-2 IgM titers, lactate dehydrogenase, platelet count and neutrophil and lymphocyte count. We found a correlation between plasma reduced thiols and time to achieve significant anti-SARS-CoV-2 IgM titers. Assessment of some parameters related to oxidative stress could help to identify groups of patients with a higher risk of morbidity and mortality during and after SARS-CoV-2 infection.", - "rel_num_authors": 8, + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.14.491911", + "rel_abs": "SARS-CoV-2 evolution has continued to generate variants, responsible for new pandemic waves locally and globally. Varying disease presentation and severity has been ascribed to inherent variant characteristics and vaccine immunity. This study analyzed genomic data from 305 whole genome sequences from SARS-CoV-2 patients before and through the third wave in India. Delta variant was responsible for disease in patients without comorbidity(97%), while Omicron BA.2 caused disease primarily in those with comorbidity(77%). Tissue adaptation studies brought forth higher propensity of Omicron variants to bronchial tissue than lung, contrary to observation in Delta variants from Delhi. Study of codon usage pattern distinguished the prevalent variants, clustering them separately, Omicron BA.2 isolated in February grouped away from December strains, and all BA.2 after December acquired a new mutation S959P in ORF1b (44.3% of BA.2 in the study) indicating ongoing evolution. Loss of critical spike mutations in Omicron BA.2 and gain of immune evasion mutations including G142D, reported in Delta but absent in BA.1, and S371F instead of S371L in BA.1 could possibly be due to evolutionary trade-off and explain very brief period of BA.1 in December 2021, followed by complete replacement by BA.2.", + "rel_num_authors": 21, "rel_authors": [ { - "author_name": "Nestor Vazquez-Agra", - "author_inst": "University Hospital of Santiago de Compostela: Complejo Hospitalario Universitario de Santiago de Compostela" + "author_name": "Urvashi B Singh", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Sushanta Deb", + "author_inst": "All India institute of medical sciences" + }, + { + "author_name": "Rama Chaudhry", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Kiran Bala", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Lata Rani", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Ritu Gupta", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Lata Kumari", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Jawed Ahmed", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Sudesh Gaurav", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Sowjanya Perumalla", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Md. Nizam", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Anwita Mishra", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "J. Stephenraj", + "author_inst": "All India Institute Of Medical Sciences" + }, + { + "author_name": "Jyoti Shukla", + "author_inst": "All India Institute Of Medical Sciences" }, { - "author_name": "Ana-Teresa Marques-Afonso", - "author_inst": "University Hospital of Santiago de Compostela: Complejo Hospitalario Universitario de Santiago de Compostela" + "author_name": "Deepika Bhardwaj", + "author_inst": "All India Institute Of Medical Sciences" }, { - "author_name": "Anton Cruces-Sande", - "author_inst": "University of Santiago de Compostela: Universidade de Santiago de Compostela" + "author_name": "Jamshed Nayer", + "author_inst": "All India Institute Of Medical Sciences" }, { - "author_name": "Ignacio Novo-Veleiro", - "author_inst": "University Hospital of Santiago de Compostela: Complejo Hospitalario Universitario de Santiago de Compostela" + "author_name": "Praveen Aggarwal", + "author_inst": "All India Institute Of Medical Sciences" }, { - "author_name": "Antonio Pose-Reino", - "author_inst": "University Hospital of Santiago de Compostela: Complejo Hospitalario Universitario de Santiago de Compostela" + "author_name": "Madhulika Kabra", + "author_inst": "All India Institute Of Medical Sciences" }, { - "author_name": "Estefania Mendez-Alvarez", - "author_inst": "University of Santiago de Compostela: Universidade de Santiago de Compostela" + "author_name": "Vineet Ahuja", + "author_inst": "All India Institute Of Medical Sciences" }, { - "author_name": "Ramon Soto-Otero", - "author_inst": "University of Santiago de Compostela: Universidade de Santiago de Compostela" + "author_name": "Subrata Sinha", + "author_inst": "All India Institute of Medical Sciences" }, { - "author_name": "alvaro hermida-Ameijeiras", - "author_inst": "University Hospital of Santiago de Compostela: Complejo Hospitalario Universitario de Santiago de Compostela" + "author_name": "Randeep Guleria", + "author_inst": "All India Institute of Medical Sciences" } ], "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "geriatric medicine" + "license": "cc_no", + "type": "new results", + "category": "genomics" }, { "rel_doi": "10.1101/2022.05.13.491763", @@ -305144,39 +305319,47 @@ "category": "microbiology" }, { - "rel_doi": "10.1101/2022.05.10.491349", - "rel_title": "Biochemical Characterization of Emerging SARS-CoV-2 Nsp15 Endoribonuclease Variants", + "rel_doi": "10.1101/2022.05.10.491351", + "rel_title": "The SARS-CoV-2 Spike Protein Activates the Epidermal Growth Factor Receptor-Mediated Signaling", "rel_date": "2022-05-12", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.10.491349", - "rel_abs": "Global sequencing efforts from the ongoing COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, continue to provide insight into the evolution of the viral genome. Coronaviruses encode 16 nonstructural proteins, within the first two-thirds of their genome, that facilitate viral replication and transcription as well as evasion of the host immune response. However, many of these viral proteins remain understudied. Nsp15 is a uridine-specific endoribonuclease conserved across all coronaviruses. The nuclease activity of Nsp15 helps the virus evade triggering an innate immune response. Understanding how Nsp15 has changed over the course of the pandemic, and how mutations affect its RNA processing function, will provide insight into the evolution of an oligomerization-dependent endoribonuclease and inform drug design. In combination with previous structural data, bioinformatics analyses of 1.9+ million SARS-CoV-2 sequences revealed mutations across Nsp15s three structured domains (N-terminal, Middle, EndoU). Selected Nsp15 variants were characterized biochemically and compared to wild type Nsp15. We found that mutations to important catalytic residues decreased cleavage activity but increased the hexamer/monomer ratio of the recombinant protein. Many of the highly prevalent variants we analyzed led to decreased nuclease activity as well as an increase in the inactive, monomeric form. Overall, our work establishes how Nsp15 variants seen in patient samples affect nuclease activity and oligomerization, providing insight into the effect of these variants in vivo.", - "rel_num_authors": 5, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.10.491351", + "rel_abs": "ObjectivesThe coronavirus disease-19 (COVID-19) pandemic is caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). At the molecular and cellular levels, the SARS-Cov-2 uses its envelope glycoprotein, the spike S protein, to infect the target cells in the lungs via binding with their transmembrane receptor, the angiotensin-converting enzyme 2 (ACE2). Here, we wanted to invesitgate if other molecular targets and pathways may be used by SARS-Cov-2.\n\nMethodsWe investigated the possibility for the spike 1 S protein and its receptor-binding domain (RBD) to target the epidermal growth factor receptor (EGFR) and its downstream signaling pathway in vitro using the lung cancer cell line (A549 cells). Protein expression and phosphorylation was examined upon cell treatment with the recombinant full spike 1 S protein or RBD.\n\nResultsWe demonstrate for the first time the activation of EGFR by the Spike 1 protein associated with the phosphorylation of the canonical ERK1/2 and AKT kinases and an increase of survivin expression controlling the survival pathway.\n\nConclusionsOur study suggests the putative implication of EGFR and its related signaling pathways in SARS-CoV-2 infectivity and Covid-19 pathology. This may open new perspectives in the treatment of Covid-19 patients by targeting EGFR.", + "rel_num_authors": 7, "rel_authors": [ { - "author_name": "Isha M Wilson", - "author_inst": "National Institute of Environmental Health Sciences" + "author_name": "Abdulrasheed Palakkott", + "author_inst": "The United Arab Emirates University" }, { - "author_name": "Meredith N Frazier", - "author_inst": "National Institute of Environmental Health Sciences" + "author_name": "Aysha Alneyadi", + "author_inst": "The United Arab Emirates University" }, { - "author_name": "Jian-Liang N Li", - "author_inst": "National Institute of Environmental Health Sciences" + "author_name": "Khalid Muhammad", + "author_inst": "The United Arab Emirates University" }, { - "author_name": "Thomas A. Randall", - "author_inst": "National Institute of Environmental Health Sciences, NIH" + "author_name": "Eid H Ali", + "author_inst": "Qatar University" }, { - "author_name": "Robin E Stanley", - "author_inst": "National Institute of Environmental Health Sciences" + "author_name": "Khaled Amiri", + "author_inst": "The United Arab Emirates University" + }, + { + "author_name": "Mohammed Akli Ayoub", + "author_inst": "The United Arab Emirates University" + }, + { + "author_name": "Rabah Iratni", + "author_inst": "The United Arab Emirates University" } ], "version": "1", - "license": "cc0", + "license": "cc_no", "type": "new results", - "category": "microbiology" + "category": "cell biology" }, { "rel_doi": "10.1101/2022.05.12.491597", @@ -307158,59 +307341,51 @@ "category": "epidemiology" }, { - "rel_doi": "10.1101/2022.05.09.22274838", - "rel_title": "Socio-economic determinants of SARS-CoV-2 infection: results from a population-based serosurvey in Geneva, Switzerland", + "rel_doi": "10.1101/2022.05.09.22274714", + "rel_title": "Mental-health before and during the COVID-19 pandemic in adults with neurodevelopmental disorders.", "rel_date": "2022-05-10", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274838", - "rel_abs": "BackgroundSARS-CoV-2 infection and its health consequences have disproportionally affected disadvantaged socio-economic groups globally. This study aimed to analyze the association between socio-economic conditions and having developed anti-SARS-CoV-2 antibodies in a population-based sample in the canton of Geneva, Switzerland.\n\nMethodsData was obtained from a population-based serosurvey of adults in Geneva and their household members, between November and December, 2020, towards the end of the second pandemic wave in the canton. Participants were tested for anti-SARS-CoV-2 antibodies. Socio-economic conditions representing different dimensions were self-reported. Mixed effects logistic regressions were conducted for each predictor to test its association with seropositive status as the main outcome.\n\nResults2,889 adults completed the study questionnaire and were included in the final analysis. Retired participants and those living in suburban areas had lower odds of a seropositive result when compared to employed participants (OR 0.42, 95% CI - 0.20 - 0.87) and those living in urban areas (OR 0.67, 95% CI - 0.46 - 0.97), respectively. People facing financial hardship for less than a year had higher odds of a seropositive result compared to those who had never faced them (OR 2.23, 95% CI - 1.01 - 4.95). Educational level, occupational position and household income were not associated with being seropositive, nor were ethnicity or country of birth.\n\nDiscussionWhile traditional measures of socio-economic position did not seem to be related to the risk of being infected in this sample, this study sheds lights on the importance of examining the broader social determinants of health when evaluating the differential impact of the pandemic within the population.", - "rel_num_authors": 10, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.09.22274714", + "rel_abs": "The COVID-19 pandemic negatively impacted mental health globally. Individuals with neurodevelopmental disorders (NDDs), including autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD), are at elevated risk of mental health difficulties. Therefore, we investigated the impact of the pandemic on anxiety, depression and mental wellbeing in adults with NDDs using longitudinal data from the Avon Longitudinal Study of Parents and Children study (n=3,058). Mental health data were collected pre-pandemic (age 21-25) and at three timepoints during the pandemic (ages 27-28) using the Short Mood and Feelings Questionnaire, Generalised Anxiety Disorder Assessment-7, and Warwick Edinburgh Mental Wellbeing Scale. ADHD and ASD were defined using validated cut-points of the Strengths and Difficulties Questionnaire and Autism Spectrum Quotient, self-reported at age 25. We used multi-level mixed-effects models to investigate changes in mental health in those with ADHD and ASD compared to those without. Prevalences of depression, anxiety and poor mental wellbeing were higher at all timepoints (pre-pandemic and during pandemic) in those with ADHD and ASD compared to those without. Anxiety increased to a greater extent in those with ADHD ({beta}=0.8 [0.2,1.4], p=0.01) and ASD ({beta}=1.2 [-0.1,2.5], p=0.07), while depression symptoms decreased, particularly in females with ASD ({beta}=-3.1 [-4.6,-1.5], p=0.0001). On average, mental wellbeing decreased in all, but to a lesser extent in those with ADHD ({beta}=1.3 [0.2,2.5], p=0.03) and females with ASD ({beta}=3.0 [0.2,5.9], p=0.04). To conclude, anxiety disproportionately increased in adults with NDDs during the pandemic, however, the related lockdowns may have provided a protective environment for depressive symptoms in the same individuals.", + "rel_num_authors": 8, "rel_authors": [ { - "author_name": "Hugo Alejandro Santa-Ramirez", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care, Geneva University Hospitals" - }, - { - "author_name": "Ania Wisniak", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care, Geneva University Hospitals - Institute of Global Health, Faculty of Medicine, University of Geneva," - }, - { - "author_name": "Nick Pullen", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care, Geneva University Hospitals" + "author_name": "Amy Shakeshaft", + "author_inst": "Cardiff University" }, { - "author_name": "Maria Eugenia Zaballa", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care, Geneva University Hospitals" + "author_name": "Rachel Blakey", + "author_inst": "University of Bristol" }, { - "author_name": "Francesco Pennacchio", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care, Geneva University Hospitals" + "author_name": "Alex Siu Fung Kwong", + "author_inst": "University of Bristol" }, { - "author_name": "Elsa Lorthe", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care, Geneva University Hospitals" + "author_name": "Lucy Riglin", + "author_inst": "Cardiff University" }, { - "author_name": "Roxane Dumont", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care, Geneva University Hospitals" + "author_name": "George Davey Smith", + "author_inst": "University of Bristol" }, { - "author_name": "Helene Baysson", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care, Geneva University Hospitals" + "author_name": "Evie Stergiakouli", + "author_inst": "University of Bristol" }, { - "author_name": "Idris Guessous", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care, Geneva University Hospitals - Department of Health and Community Medicine, Faculty of Medicine, Unive" + "author_name": "Kate Tilling", + "author_inst": "University of Bristol" }, { - "author_name": "Silvia Stringhini", - "author_inst": "Unit of Population Epidemiology, Division of Primary Care, Geneva University Hospitals - Department of Health and Community Medicine, Faculty of Medicine, Unive" + "author_name": "Anita Thapar", + "author_inst": "Cardiff University" } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc_by", "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" + "category": "psychiatry and clinical psychology" }, { "rel_doi": "10.1101/2022.05.10.22272976", @@ -308912,87 +309087,59 @@ "category": "neurology" }, { - "rel_doi": "10.1101/2022.05.06.22274658", - "rel_title": "STIMULATE-ICP-CAREINEQUAL - Defining usual care and examining inequalities in Long Covid support: protocol for a mixed-methods study (part of STIMULATE-ICP: Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways).", + "rel_doi": "10.1101/2022.05.06.22274782", + "rel_title": "Post-acute health care burden after SARS-CoV-2 infection: A retrospective cohort study among 530,892 adults", "rel_date": "2022-05-07", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.06.22274658", - "rel_abs": "IntroductionIndividuals with Long Covid represent a new and growing patient population. In England, fewer than 90 Long Covid clinics deliver assessment and treatment informed by NICE guidelines. However, a paucity of clinical trials or longitudinal cohort studies means that the epidemiology, clinical trajectory, healthcare utilisation and effectiveness of current Long Covid care are poorly documented, and that neither evidence-based treatments nor rehabilitation strategies exist. In addition, and in part due to pre-pandemic health inequalities, access to referral and care varies, and patient experience of the Long Covid care pathways can be poor.\n\nIn a mixed methods study, we therefore aim to: (1) describe the usual healthcare, outcomes and resource utilisation of individuals with Long Covid; (2) assess the extent of inequalities in access to Long Covid care, and specifically to understand Long Covid patients experiences of stigma and discrimination.\n\nMethods and analysisA mixed methods study will address our aims. Qualitative data collection from patients and health professionals will be achieved through surveys, interviews and focus group discussions, to understand their experience and document the function of clinics. A patient cohort study will provide an understanding of outcomes and costs of care. Accessible data will be further analysed to understand the nature of Long Covid, and the care received.\n\nEthics and disseminationEthical approval was obtained from South Central - Berkshire Research Ethics Committee (reference 303958). The dissemination plan will be decided by the patient and public involvement and engagement (PPIE) group members and study Co-Is, but will target 1) policy makers, and those responsible for commissioning and delivering Long Covid services, 2) patients and the public, and 3) academics.", - "rel_num_authors": 17, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.06.22274782", + "rel_abs": "ImportanceThe SARS-CoV-2 pandemic portends a significant increase in health care use related to post-acute COVID sequelae, but the magnitude is not known.\n\nObjectiveTo assess the burden of post-acute health care use after a positive versus negative polymerase chain reaction (PCR) test for SARS-CoV-2.\n\nDesign, Setting, and ParticipantsRetrospective cohort study of community-dwelling adults January 1, 2020 to March 31, 2021 in Ontario, Canada, using linked population-based health data. Follow-up began 56 days after PCR testing.\n\nExposuresIndividuals with a positive SARS-CoV-2 PCR test were matched 1:1 to individuals who tested negative based on hospitalization, test date, public health unit, sex, and a propensity score of socio-demographic and clinical characteristics.\n\nMain Outcomes and MeasuresThe health care utilization rate was the number of outpatient clinical encounters, homecare encounters, emergency department visits, days hospitalized, and days in long-term care per person-year. Mean health care utilization for test-positive versus negative individuals was compared using negative binomial regression, and rates at 95th and 99th percentiles were compared. Outcomes were also stratified by sex.\n\nResultsAmong 530,232 unique, matched individuals, mean age was 44 years (sd 17), 51% were female, and 0.6% had received [≥]1 COVID-19 vaccine dose. The mean rate of health care utilization was 11% higher in test-positive individuals (RR 1.11, 95% confidence interval [CI] 1.10-1.13). At the 95th percentile, test-positive individuals had 2.1 (95% CI 1.5-2.6) more health care encounters per person-year, and at the 99th percentile 71.9 (95% CI 57.6-83.2) more health care encounters per person-year. At the 95th percentile, test-positive women had 3.8 (95% CI 2.8-4.8) more health care encounters per person-year while there was no difference for men. At the 99th percentile, test-positive women had 76.7 (95% CI 56.3-89.6) more encounters per person-year, compared to 37.6 (95% CI 16.7-64.3) per person-year for men.\n\nConclusions and RelevancePost-acute health care utilization after a positive SARS-CoV-2 PCR test is significantly higher compared to matched test-negative individuals. Given the number of infections worldwide, this translates to a tremendous increase in use of health care resources. Stakeholders can use these findings to prepare for health care demand associated with long COVID.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow does the burden of health care use [≥]56 days after a positive SARS-CoV-2 polymerase chain reaction (PCR) test compare to matched individuals who tested negative?\n\nFindingsAfter accounting for multiple factors, the mean burden of post-acute health care use was 11% higher among those who tested positive, with higher rates of outpatient encounters, days hospitalized, and days in long-term care. Rates of homecare use were higher for test-positive women but lower for men.\n\nFor perspective, for every day in January 2022 with 100,000 or more infections, this translates to an estimated 72,000 additional post-acute health care encounters per year for the 1% of people who experienced the most severe complications of SARS-CoV-2; among those in the top 50% of health care use, this translates to 245,000 additional health care encounters per year. This increase will occur in the context of an ongoing pandemic and, in many health care systems, a depleted workforce and backlogs of care. Unless addressed, this increase is likely to exacerbate existing health inequities.\n\nMeaningGiven the large number of people infected, stakeholders can use these findings to plan for health care use associated with long COVID.", + "rel_num_authors": 10, "rel_authors": [ { - "author_name": "Mel Ramasawmy", - "author_inst": "Institute of Health Informatics, University College London" - }, - { - "author_name": "Yi Mu", - "author_inst": "Institute of Health Informatics, University College London" - }, - { - "author_name": "Donna Clutterbuck", - "author_inst": "School of Primary Care, Population Sciences and Medical Education, University of Southampton" - }, - { - "author_name": "Marija Pantelic", - "author_inst": "Brighton and Sussex Medical School, University of Sussex" - }, - { - "author_name": "Gregory Y.H. Lip", - "author_inst": "Liverpool Centre for Cardiovascular Science, University of Liverpool and Liverpool Heart & Chest Hospital, Liverpool, United Kingdom; and Department of Clinical" - }, - { - "author_name": "Christina Van der Feltz-Cornelis", - "author_inst": "Department of Health Sciences, HYMS, University of York, and Institute of Health Informatics, University College London" - }, - { - "author_name": "Dan Wootton", - "author_inst": "Institute of Infection Veterinary and Ecological Sciences, University of Liverpool" - }, - { - "author_name": "Nefyn H Williams", - "author_inst": "Department of Primary Care and Mental Health, University of Liverpool" + "author_name": "Candace D McNaughton", + "author_inst": "ICES, Sunnybrook Research Institute, and University of Toronto" }, { - "author_name": "Hugh Montgomery", - "author_inst": "Centre for Human Health and Performance, Department of Medicine, University College London" + "author_name": "Peter C Augstin", + "author_inst": "ICES, Sunnybrook Research Institute, Institute of Health Policy, Management and Evaluation, University of Toronto" }, { - "author_name": "Rita Mallinson Cookson", - "author_inst": "PPIE Representative" + "author_name": "Atul Sivaswamy", + "author_inst": "ICES" }, { - "author_name": "Emily Attree", - "author_inst": "PPIE Representative" + "author_name": "Jiming Fang", + "author_inst": "ICES" }, { - "author_name": "Mark Gabbay", - "author_inst": "Department of Primary Care and Mental Health, University of Liverpool" + "author_name": "Husam Abdel-Qadir", + "author_inst": "ICES, Institute of Health Policy, Management and Evaluation, University of Toronto, Peter Munk Cardiac Centre, Toronto General Hospital, Division of Cardiology," }, { - "author_name": "Melissa J Heightman", - "author_inst": "University College London Hospitals NHS Trust" + "author_name": "Nick Daneman", + "author_inst": "ICES, Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, University of Toronto" }, { - "author_name": "Nisreen A Alwan", - "author_inst": "School of Primary Care, Population Sciences and Medical Education, University of Southampton; NIHR Southampton Biomedical Research Centre, University of Southam" + "author_name": "Jacob Allan Udell", + "author_inst": "Women's College Hospital" }, { - "author_name": "Amitava Banerjee", - "author_inst": "Institute of Health Informatics, University College London" + "author_name": "Walter Wodchis", + "author_inst": "ICES, Sunnybrook Research Institute" }, { - "author_name": "Paula Lorgelly", - "author_inst": "School of Population Health and Department of Economics, University of Auckland" + "author_name": "Ivona Mostarac", + "author_inst": "Sunnybrook Research Institute" }, { - "author_name": "- STIMULATE-ICP consortium", - "author_inst": "" + "author_name": "Clare L Atzema", + "author_inst": "ICES, Sunnybrook Research Institute, Institute of Health Policy, Management and Evaluation, University of Toronto" } ], "version": "1", - "license": "cc_by_nc", + "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" + "category": "epidemiology" }, { "rel_doi": "10.1101/2022.05.05.22273234", @@ -310642,67 +310789,51 @@ "category": "pediatrics" }, { - "rel_doi": "10.1101/2022.05.04.22274659", - "rel_title": "What innovations can address inequalities experienced by women and girls due to the COVID-19 pandemic across the different areas of life/domains: work, health, living standards, personal security, participation and education? Rapid Review", + "rel_doi": "10.1101/2022.05.02.22274456", + "rel_title": "Change in stroke presentations during COVID-19 pandemic in South-Western Sydney.", "rel_date": "2022-05-05", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.04.22274659", - "rel_abs": "TOPLINE SUMMARYO_ST_ABSWhat is a Rapid Review?C_ST_ABSOur rapid reviews use a variation of the systematic review approach, abbreviating or omitting some components to generate the evidence to inform stakeholders promptly whilst maintaining attention to bias. They follow the methodological recommendations and minimum standards for conducting and reporting rapid reviews, including a structured protocol, systematic search, screening, data extraction, critical appraisal and evidence synthesis to answer a specific question and identify key research gaps. They take one to two months, depending on the breadth and complexity of the research topic/question(s), the extent of the evidence base and type of analysis required for synthesis.\n\nBackground / Aim of Rapid ReviewThe COVID-19 pandemic has led to differential economic, health and social impacts illuminating prevailing gender inequalities (WEN Wales, 2020). This rapid review investigated evidence for effectiveness of interventions to address gender inequalities across the domains of work, health, living standards, personal security, participation, and education.\n\nKey FindingsO_ST_ABSExtent of the evidence baseC_ST_ABSO_LI21 studies were identified: 7 reviews, 6 commentaries and 8 primary studies\nC_LIO_LILimited evidence for the effectiveness of identified innovations in minority groups\nC_LIO_LIA lack of evaluation data for educational interventions\nC_LIO_LIA lack of evidence for cost-effectiveness of the identified interventions\nC_LIO_LI14 additional articles were identified in the grey literature but not used to inform findings (apart from the Education domain, where there was a lack of peer-reviewed evidence).\nC_LI\n\nRecency of the evidence baseO_LIAll studies were published in 2020-2021\nC_LI\n\nSummary of findingsSome evidence supported interventions/innovations related to work: O_LIPermanent contracts, full-time hours, and national childcare programmes to increase income for women and thereby decrease the existing gender wage gap.\nC_LIO_LIMore frequent use of online platforms in the presentation of professional work can reduce gender disparities due to time saved in travel away from home.\nC_LI Some evidence supported interventions/innovations related to health: O_LILeadership in digital health companies could benefit from women developing gender-friendly technology that meets the health needs of women.\nC_LIO_LICreate authentic partnerships with black women and female-led organisations to reduce maternal morbidity and mortality (Bray & McLemore, 2021).\nC_LI Some evidence supported interventions/innovations related to living standards including: O_LIMulti-dimensional care provided to women and their children experiencing homelessness.\nC_LI Limited evidence supported interventions/innovations related to personal security including: O_LISpecific training of social workers, psychologists and therapists to empower women to use coping strategies and utilise services to gain protection from abusive partners.\nC_LIO_LIHelplines, virtual safe spaces smart phone applications and online counselling to address issues of violence and abuse for women and girls.\nC_LI Very limited evidence supported interventions/innovations related to participation including: O_LIUse of online platforms to reduce gender disparities in the presentation of academic/professional work.\nC_LIO_LIEnsuring equal representation, including women and marginalised persons, in pandemic response and recovery planning and decision-making.\nC_LI Limited evidence from the grey literature described interventions/innovations related to education including: O_LITeacher training curricula development to empower teachers to understand and challenge gender stereotypes in learning environments.\nC_LIO_LIEducation for girls to enable participation in STEM.\nC_LI\n\nPolicy ImplicationsThis evidence can be used to map against existing policies to identify which are supported by the evidence, which are not in current policy and could be implemented and where further research/evaluation is needed.\n\nFurther research is needed to evaluate the effectiveness of educational innovations, the effectiveness of the innovations in minority groups and the social value gained from interventions to address gender inequalities.\n\nStrength of EvidenceOne systematic review on mobile interventions targeting common mental disorders among pregnant and postpartum women was rated as high quality (Saad et al., 2021). The overall confidence in the strength of evidence was rated as low due to study designs. Searches did not include COVID specific resources or pre-prints. There may be additional interventions/innovations that have been implemented to reduce inequalities experienced by women and girls due to the COVID-19 pandemic but have not been evaluated or published in the literature and are therefore not included here.", - "rel_num_authors": 12, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.02.22274456", + "rel_abs": "BackgroundAustralia managed relatively well during the global COVID-19 pandemic owing to our swift mandated public health response. During the NSW lockdown restrictions, we noted a decrease in acute stroke presentations at our institution, similar to what was subsequently reported worldwide.\n\nAimsWe aimed to test our hypothesis that (i) the true numbers of ischaemic strokes did not change, however patients were presenting later and (ii) the proportion of TIAs decreased.\n\nMethodsWe conducted a retrospective audit of all stroke and TIA presentations in 2020 and compared these with data from 2019. We collected information about stroke subtype, severity, time from stroke/TIA onset to presentation and acute reperfusion therapies.\n\nResultsBetween January-February and April-March 2020, there was a 15% drop in acute stroke presentations (128 vs. 109). In the same period \"stroke mimic\" presentations dropped by 22%. The proportion of patients attending the emergency department within 4.5hrs was only 36% compared with 48% over the similar period in 2019.\n\nConclusionsAlthough the raw numbers of ischemic stroke presentations remained stable during NSW Covid lockdown, the proportion of patients presenting within time window for acute reperfusion therapies fell. The number of TIAs similarly fell suggesting COVID-19 discouraged patients from presenting to hospital which placed them at higher risk of disabling stroke. The opportunity cost of lockdown restrictions on stroke outcome should be considered in future policy directives.", + "rel_num_authors": 8, "rel_authors": [ { - "author_name": "Llinos Haf Spencer", - "author_inst": "Bangor University" - }, - { - "author_name": "Ned Hartfiel", - "author_inst": "Bangor University" - }, - { - "author_name": "Annie Hendry", - "author_inst": "Bangor University" + "author_name": "James Thomas", + "author_inst": "Liverpool Hospital" }, { - "author_name": "Bethany Fern Anthony", - "author_inst": "Bangor University" + "author_name": "Dennis Cordato", + "author_inst": "Liverpool Hospital" }, { - "author_name": "Abraham Makanjuola", - "author_inst": "Bangor University" + "author_name": "David Manser", + "author_inst": "Liverpool Hospital" }, { - "author_name": "Kalpa Pisavadia", - "author_inst": "Bangor University" + "author_name": "Paul M Middleton", + "author_inst": "Liverpool Hospital" }, { - "author_name": "Jacob Davies", - "author_inst": "Bangor University" + "author_name": "Cecilia Cappelen-Smith", + "author_inst": "Liverpool Hospital" }, { - "author_name": "Nathan Bray", - "author_inst": "Bangor University" + "author_name": "Alan McDougall", + "author_inst": "Liverpool Hospital" }, { - "author_name": "Dyfrig A. Hughes", - "author_inst": "Bangor University" - }, - { - "author_name": "Clare Wilkinson", - "author_inst": "Bangor University" - }, - { - "author_name": "Deborah Fitzsimmons", - "author_inst": "Swansea University" + "author_name": "Peter Thomas", + "author_inst": "Liverpool Hospital" }, { - "author_name": "Rhiannon Tudor Edwards", - "author_inst": "Bangor University" + "author_name": "Nicholas Moore", + "author_inst": "Liverpool Hospital" } ], "version": "1", - "license": "cc_no", + "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" + "category": "neurology" }, { "rel_doi": "10.1101/2022.05.04.22274657", @@ -312840,39 +312971,23 @@ "category": "allergy and immunology" }, { - "rel_doi": "10.1101/2022.05.01.22274540", - "rel_title": "Keeping it close: The role of a Campus COVID Support Team (CCST) in sustaining a safe and healthy university campus during COVID-19", + "rel_doi": "10.1101/2022.05.01.490203", + "rel_title": "SARS-CoV-2 Main Protease: a Kinetic Approach", "rel_date": "2022-05-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.01.22274540", - "rel_abs": "It has been over 24 months since the start of the COVID-19 pandemic forced university campuses to shut down and then reopen under new safety guidelines. Now as we move into the subsequent years of the pandemic, we can look back and evaluate what has worked, improvements to be made, and plans for providing a sustained response for a campus community. In this article we detail one campus response to the COVID-19 pandemic and directions being taken to ensure a sustained campus COVID support team (CCST) is in hand to ensure the health and safety of the university community. The CCST was created to serve as a one-stop-shop to help the university community navigate COVID-19 policies and procedures. The responsibilities of the CCST include conducting case investigations for any positive COVID-19 tests within the university community, contact tracing for authorized university affiliates, epidemiological surveillance and mitigation efforts, and communication through real-time analysis and dashboards. Continuous monitoring procedures demonstrated the CCST conducted all case investigations within the post-testing 24-hour window, thus keeping the university test-positivity rate below 3%. Quality improvement surveys demonstrated a high level of satisfaction with the CCST efforts and provided areas for improvement and sustainability. Having a public health faculty led CCST enabled the university to act swiftly when COVID-19 positive cases were emerging and deter widespread campus COVID-19 outbreaks. The CCST timeliness and connectivity to the campus has demonstrated benefits to the health and safety of the campus.\n\nHighlightsO_LIUniversities are their own communities and having on campus COVID support teams can mitigate potential COVID-19 outbreaks.\nC_LIO_LIHaving a public health driven Campus COVID Support Team that can conduct case investigations within 24 hours of a positive test result has demonstrated benefits to taking responsive measures.\nC_LIO_LIContinuous quality improvement efforts including surveys of the Campus COVID Support Team should be implemented for any COVID service efforts.\nC_LI", - "rel_num_authors": 5, + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.01.490203", + "rel_abs": "In this article, I present a new model of the interaction of the main protease (Mpro) from SARS-CoV-2 virus with its substrate. The reaction scheme used to describe this mechanism is an extension of the well-known Michaelis-Menten model proposed in 1913 by Leonor Michaelis and Maud Menten [1]. The model I present here takes into account that one Mpro enzyme monomer interacts with another Mpro monomer in the presence of the substrate, leading to the formation of an enzyme dimer bound to one substrate molecule. Indeed, this dimer is formed by the sequentially binding of one Mpro enzyme monomer to one molecule of substrate, followed by another Mpro enzyme monomer binding to this Mpro-substrate complex. This reaction mechanism is also known in the literature as substrate-induced dimerization [3]. Starting from this new reaction scheme established for this catalytic mechanism, I derived a mathematical expression describing the catalytic rate of the active Mpro enzyme dimer as a function of the substrate concentration [S]. The plot corresponding to this substrate-induced dimerization reaction shows a function f ([S]) that is not monotonic, i.e. not strictly increasing or decreasing, but with a second derivative initially negative and then becoming positive after having passed the Vmax point. This is typically a type of curve showing a phenomenon like the one of substrate inhibition (for instance, inhibition by excess-substrate [7]). The graphical representation of this process shows an interesting behaviour: from zero M/s, the reaction rate increases progressively, similar to the kind of curve described by the Michaelis-Menten model. However, after having reached its maximum catalytic rate, Vmax, the reaction rate decreases progressively as we continue to increase the substrate concentration. I propose an explanation to this interesting behavior. At the moment where Vcat is maximum, we can assume that, in theory, every single substrate molecule in solution is bound to two enzyme monomers (i.e. to one active dimer). The catalytic rate is thus theoretically maximized. At the time where the reaction rate begins to decrease, we observe a new phenomenon that appears: the enzyme monomers begin to be \"diluted\" in the solution containing the excess substrate. The dimers begin to dissociate and to bind increasingly to the substrate as inactive monomers instead of active dimers. Hence, it is more and more unlikely for the enzyme monomers to sequentially bind twice to the same substrate molecule (here, [E] << [S]). Thus, at this stage, the substrate-induced dimerization occurs less often. At the limit, when the substrate is in high excess, there is virtually no more dimerization which occurs. This is one example of excess-substrate inhibition. Furthermore, after having established this fact, I wanted to see if this catalytic behavior was also observed in vitro. Therefore, I conducted an experiment where I measured the catalytic rate of the Mpro dimer for different substrate concentrations. The properties of my substrate construct were such, that I could determine the catalytic rate of the enzyme dimer by directly measuring the spectrophotometric absorbance of the cleaved substrate at{lambda} = 405 nm. The results show explicitly -- within a margin of error -- that the overall shape of the experimental curve looks like the one of the theoretical curve. I thus conclude that the biochemical behavior of the Mpro in vitro follows a new path when it is in contact with its substrate: an excess substrate concentration decreases the activity of the enzyme by the phenomenon of a type of excess-substrate inhibition. This finding could open a new door in the discovery of drugs directed against the Mpro enzyme of the SARS-CoV-2 virus, acting on the inhibition by excess-substrate of the Mpro enzyme, this protein being a key component in the metabolism of the virus. Furthermore, I have established that the maximum of the fitted curve, Vmax, depends only on [E]T and not on [S]. [Formula] exhibits the same dependence pattern. Therefore, if I keep [E]T close to zero, the catalytic rate of the enzyme will also be greatly reduced, which can be understood intuitively. Finally, if we dilute the enzyme sufficiently in the host cell by injecting a suitably high concentration of the octapeptide substrate AVLQSGFR (an inhibitor of the original substrate), this artificial substrate will bind to the \"intermediate\" dimer from the polypeptide and prevent the precursor Mpro from auto-cleaving and dimerizing due to the \"distorted key\" effect of the octapeptide on the \"intermediate\" dimer. The precursor peptide Mpro will auto-cleave to a lesser extent than in the absence of the artificial octapeptide and thus the concentration of the total enzyme [E]T will be lowered in the cell. It would therefore be possible to control the virulence of the virus by adjusting the concentration of the artificial inhibitory octapeptide. However, this is only speculation and has yet to be verified in practice.", + "rel_num_authors": 1, "rel_authors": [ { - "author_name": "Karen A McDonnell", - "author_inst": "The George Washington University, Milken Institute School of Public Health" - }, - { - "author_name": "Amanda D Castel", - "author_inst": "The George Washington University Milken Institute School of Public Health" - }, - { - "author_name": "Amita B Vyas", - "author_inst": "The George Washington University, Milken Institute School of Public Health" - }, - { - "author_name": "Nitasha C Nagaraj", - "author_inst": "The George Washington University, Milken Institute School of Public Health" - }, - { - "author_name": "Megan Landry", - "author_inst": "The George Washington University, Milken Institute School of Public Health" + "author_name": "Thierry Rebetez", + "author_inst": "ETHZ" } ], "version": "1", "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" + "type": "new results", + "category": "biophysics" }, { "rel_doi": "10.1101/2022.04.30.489997", @@ -314862,55 +314977,103 @@ "category": "occupational and environmental health" }, { - "rel_doi": "10.1101/2022.04.28.489859", - "rel_title": "Argon plasma-modified bacterial cellulose filters for protection against respiratory pathogens", + "rel_doi": "10.1101/2022.04.28.489942", + "rel_title": "Immediate myeloid depot for SARS-CoV-2 in the human lung", "rel_date": "2022-04-29", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.28.489859", - "rel_abs": "Due to the global spread of the SARS-CoV-2 virus and the resultant pandemic, there has been a major surge in the demand for surgical masks, respirators, and other air filtration devices. Unfortunately, the fact that these filters are made of petrochemical-derived, non-biodegradable polymers means that the surge in production has also led to a surge in plastic waste. In this work, we present novel, sustainable filters based on bacterial cellulose (BC) functionalized with low-pressure argon plasma (LPP-Ar). The \"green\" production process involved BC biosynthesis by Komagataeibacter xylinus, followed by simple purification, homogenization, lyophilization, and finally LPP-Ar treatment. The obtained LPP-Ar-functionalized BC-based material (LPP-Ar-BC-bM) showed excellent antimicrobial and antiviral properties, with no cytotoxicity versus murine fibroblasts in vitro. Further, filters consisting of three layers of LPP-Ar-BC-bM had >99% bacterial and viral filtration efficiency, while maintaining sufficiently low airflow resistance (6 mbar at an airflow of 95 L/min). Finally, as a proof-of-concept, we were able to prepare 80 masks with LPP-Ar-BC-bM filter and ~85% of volunteer medical staff assessed them as good or very good in terms of comfort. We conclude that our novel sustainable, biobased, biodegradable filters are suitable for respiratory personal protective equipment (PPE), such as surgical masks and respirators. Further, with scale-up, they may be adapted for indoor air handling filtration in hospitals or schools.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC=\"FIGDIR/small/489859v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (46K):\norg.highwire.dtl.DTLVardef@99ae8dorg.highwire.dtl.DTLVardef@192c4eforg.highwire.dtl.DTLVardef@bf2acborg.highwire.dtl.DTLVardef@92907a_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 9, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.28.489942", + "rel_abs": "In the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, considerable focus has been placed on a model of viral entry into host epithelial populations, with a separate focus upon the responding immune system dysfunction that exacerbates or causes disease. We developed a precision-cut lung slice model to investigate very early host-viral pathogenesis and found that SARS-CoV-2 had a rapid and specific tropism for myeloid populations in the human lung. Infection of alveolar macrophages was partially dependent upon their expression of ACE2, and the infections were productive for amplifying virus, both findings which were in contrast with their neutralization of another pandemic virus, Influenza A virus (IAV). Compared to IAV, SARS-CoV-2 was extremely poor at inducing interferon-stimulated genes in infected myeloid cells, providing a window of opportunity for modest titers to amplify within these cells. Endotracheal aspirate samples from humans with the acute respiratory distress syndrome (ARDS) from COVID-19 confirmed the lung slice findings, revealing a persistent myeloid depot. In the early phase of SARS-CoV-2 infection, myeloid cells may provide a safe harbor for the virus with minimal immune stimulatory cues being generated, resulting in effective viral colonization and quenching of the immune system.", + "rel_num_authors": 21, "rel_authors": [ { - "author_name": "Anna Zywicka", - "author_inst": "Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin" + "author_name": "Melia Magnen", + "author_inst": "UCSF" + }, + { + "author_name": "Ran You", + "author_inst": "UCSF" }, { - "author_name": "Daria Ciecholewska-Jusko", - "author_inst": "West Pomeranian University of Technology in Szczecin" + "author_name": "Arjun A Rao", + "author_inst": "UCSF" }, { - "author_name": "Magdalena Szymanska", - "author_inst": "Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin" + "author_name": "Ryan T Davis", + "author_inst": "UCSF" }, { - "author_name": "Radoslaw Drozd", - "author_inst": "Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin" + "author_name": "Lauren Rodriguez", + "author_inst": "UCSF" }, { - "author_name": "Peter Sobolewski", - "author_inst": "Department of Polymer and Biomaterials Science, West Pomeranian University of Technology in Szczecin, Faculty of Chemical Technology and Engineering" + "author_name": "Camille R Simoneau", + "author_inst": "UCSF" }, { - "author_name": "Adam Junka", - "author_inst": "Department of Pharmaceutical Microbiology and Parasitology, Faculty of Pharmacy, Wroclaw Medical University" + "author_name": "Lisiena Hysenaj", + "author_inst": "UCSF" + }, + { + "author_name": "Kenneth H Hu", + "author_inst": "UCSF" }, { - "author_name": "Selestina Gorgieva", - "author_inst": "Institute of Engineering Materials and Design, Faculty of Mechanical Engineering, University of Maribor" + "author_name": "- The UCSF COMET Consortium", + "author_inst": "-" }, { - "author_name": "Miroslawa El Fray", - "author_inst": "Department of Polymer and Biomaterials Science, West Pomeranian University of Technology in Szczecin, Faculty of Chemical Technology and Engineering" + "author_name": "Christina Love", + "author_inst": "UCSF" + }, + { + "author_name": "Prescott G Woodruff", + "author_inst": "UCSF" + }, + { + "author_name": "David J Erle", + "author_inst": "UCSF" + }, + { + "author_name": "Carolyn M Hendrickson", + "author_inst": "UCSF" + }, + { + "author_name": "Carolyn S Calfee", + "author_inst": "UCSF" + }, + { + "author_name": "Michael A Matthay", + "author_inst": "UCSF" }, { - "author_name": "Karol Fijalkowski", - "author_inst": "Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin" + "author_name": "Jeroen P Roose", + "author_inst": "UCSF" + }, + { + "author_name": "Anita Sil", + "author_inst": "UCSF" + }, + { + "author_name": "Melanie Ott", + "author_inst": "UCSF" + }, + { + "author_name": "Charles R Langelier", + "author_inst": "UCSF" + }, + { + "author_name": "Matthew F Krummel", + "author_inst": "UCSF" + }, + { + "author_name": "Mark R Looney", + "author_inst": "UCSF" } ], "version": "1", "license": "cc_by_nc_nd", "type": "new results", - "category": "bioengineering" + "category": "immunology" }, { "rel_doi": "10.1101/2022.04.26.22274264", @@ -316804,65 +316967,57 @@ "category": "bioinformatics" }, { - "rel_doi": "10.1101/2022.04.27.489747", - "rel_title": "Two types of human TCR differentially regulate reactivity to self and non-self antigens", + "rel_doi": "10.1101/2022.04.28.489850", + "rel_title": "GM-CSF-activated human dendritic cells promote type1 T follicular helper cells (Tfh1) polarization in a CD40-dependent manner", "rel_date": "2022-04-28", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.27.489747", - "rel_abs": "Based on analyses of TCR sequences from over 1,000 individuals, we report that the TCR repertoire is composed of two ontogenically and functionally distinct types of TCRs. Their production is regulated by variations in thymic output and terminal deoxynucleotidyl transferase (TDT) activity. Neonatal TCRs derived from TDT-negative progenitors persist throughout life, are highly shared among subjects, and are polyreactive to self and microbial antigens. Thus, >50% of cord blood TCRs are responsive to SARS-CoV2 and other common pathogens. TDT- dependent TCRs present distinct structural features and are less shared among subjects. TDT- dependent TCRs are produced in maximal numbers during infancy when thymic output and TDT activity reach a summit, are more abundant in subjects with AIRE mutations, and seem to play a dominant role in graft-versus-host disease. Factors decreasing thymic output (age, male sex) negatively impact TCR diversity. Males compensate for their lower repertoire diversity via hyperexpansion of selected TCR clonotypes.", - "rel_num_authors": 12, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.28.489850", + "rel_abs": "T follicular helper (Tfh) cells are specialized CD4+ T cells that regulate humoral immunity by providing B cell help. Tfh1 sub-population was recently identified and associated with severity in infection and autoimmune diseases. The cellular and molecular requirements to induce human Tfh1 differentiation are unknown. Our work investigated the role of human dendritic cells (DC) in promoting Tfh1 differentiation and their physiopathological implication in mycobacterium tuberculosis and mild COVID-19 infection.\n\nActivated human blood CD1c+ DC were cocultured with allogeneic naive CD4+ T cells. Single-cell RNA sequencing was then used alongside protein validation to define the induced Tfh lineage. DC signature and correlation with Tfh1 cells in infected patients was established through bioinformatic analysis.\n\nOur results show that GM-CSF-activated DC drove the differentiation of Tfh1 cells, displaying typical Tfh molecular features, including 1) high levels of PD-1, CXCR5, and ICOS expression; 2) BCL6 and TBET co-expression; 3) IL-21 and IFN-{gamma} secretion. Mechanistically, GM-CSF triggered the emergence of two distinct DC sub-populations defined by their differential expression of CD40 and ICOS-ligand (ICOS-L), and distinct phenotype, morphology, transcriptomic signature, and function. We showed that Tfh1 differentiation was efficiently and specifically induced by CD40highICOS-Llow DC in a CD40-dependent manner. Tfh1 cells were positively associated with a CD40highICOS-LLow DC signature in patients with latent mycobacterium tuberculosis and mild COVID-19 infection.\n\nOur study uncovers a novel CD40-dependent human Tfh1 axis. Immunotherapy modulation of Tfh1 activity might contribute to control diseases where Tfh1 are known to play a key role, such as infections.\n\nSignificance StatementDendritic cells (DC) play a central role in triggering the adaptive immune response due to their T cell priming functions. Among different T cell subsets, it is still not clear how human type1 T follicular helper cells (Tfh1) differentiate. Tfh1 cells are implicated in several physiopathological conditions, including infections. Here we show that GM-CSF induces diversification of human DC. Only CD40highICOS-LLow DC were able to drive Tfh1 cell differentiation. We found that CD40highICOS-LLow DC signature was associated to Tfh1 cells in mycobacterium tuberculosis and COVID-19 patients. Our data reveal a previously undescribed pathway leading to human Tfh1 cell differentiation and highlight the importance of GM-CSF and CD40 as potential targets for the design of anti-infective therapies.", + "rel_num_authors": 10, "rel_authors": [ { - "author_name": "Assya Trofimov", - "author_inst": "Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Research Operations - University of Montreal" - }, - { - "author_name": "Philippe Brouillard", - "author_inst": "Department of Computer Science and Research Operations - University of Montreal" - }, - { - "author_name": "Jean-David Larouche", - "author_inst": "Institute for Research in Immunology and Cancer (IRIC), Department of Medicine - University of Montreal" + "author_name": "Sarantis Korniotis", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis, F-75010, Paris, France" }, { - "author_name": "Jonathan Seguin", - "author_inst": "Institute for Research in Immunology and Cancer (IRIC)" + "author_name": "Melissa Saichi", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" }, { - "author_name": "Jean-Philippe Laverdure", - "author_inst": "Institute for Research in Immunology and Cancer (IRIC)" + "author_name": "Coline Trichot", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" }, { - "author_name": "Ann Brasey", - "author_inst": "Maisonneuve-Rosemont Hospital" + "author_name": "Caroline Hoffmann", + "author_inst": "Institut Curie, INSERM U932 Research Unit, Immunity and Cancer, F-75005 Paris, France" }, { - "author_name": "Gregory Ehx", - "author_inst": "Institute for Research in Immunology and Cancer (IRIC), Interdisciplinary Cluster for Applied Geno-Proteomics (GIGA-I3) - University of Liege" + "author_name": "Elise Amblard", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" }, { - "author_name": "Denis-Claude Roy", - "author_inst": "Maisonneuve-Rosemont Hospital" + "author_name": "Annick Viguier", + "author_inst": "Institut Curie, INSERM U932 Research Unit, Immunity and Cancer, F-75005 Paris, France" }, { - "author_name": "Lambert Busque", - "author_inst": "Maisonneuve-Rosemont Hospital" + "author_name": "Sophie Grondin", + "author_inst": "Institut Curie, INSERM U932 Research Unit, Immunity and Cancer, F-75005 Paris, France" }, { - "author_name": "Silvy Lachance", - "author_inst": "Department of Medicine - University of Montreal, Maisonneuve-Rosemont Hospital" + "author_name": "Floriane Noel", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" }, { - "author_name": "Sebastien Lemieux", - "author_inst": "Institute for Research in Immunology and Cancer (IRIC), Department of Computer Science and Research Operations - University of Montreal, Department of Biochemis" + "author_name": "Hamid Mattoo", + "author_inst": "Immunology and Inflammation Therapeutic Area, Sanofi, Cambridge MA, USA" }, { - "author_name": "Claude Perreault", - "author_inst": "Institute for Research in Immunology and Cancer (IRIC), Department of Medicine - University of Montreal, Maisonneuve-Rosemont Hospital" + "author_name": "Vassili Soumelis", + "author_inst": "University of Paris, Inserm U976 HIPI Unit, Institut de Recherche Saint-Louis" } ], "version": "1", - "license": "cc_by", + "license": "cc_no", "type": "new results", "category": "immunology" }, @@ -318474,107 +318629,63 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.04.20.22274076", - "rel_title": "Safety, tolerability and immunogenicity of Biological Es CORBEVAX vaccine in children and adolescents: A Prospective, Randomised, Double-blind, Placebo controlled, Phase-2/3 Study.", + "rel_doi": "10.1101/2022.04.23.22274192", + "rel_title": "Excess all-cause mortality across counties in the United States, March 2020 to December 2021", "rel_date": "2022-04-26", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.20.22274076", - "rel_abs": "BackgroundAfter establishing safety and immunogenicity of Biological Es CORBEVAX vaccine in adult population (18-80 years) in Phase 1-3 studies, vaccine is further tested in children and adolescents in this study.\n\nMethodsThis is a phase-2/3 prospective, randomised, double-blind, placebo controlled, study evaluating safety, reactogenicity, tolerability and immunogenicity of CORBEVAX vaccine in children and adolescents of either gender between <18 to [≥]12 years of age in Phase-II and <18 to [≥]5 years of age in Phase-III with placebo as a control. This study has two age sub groups; age subgroup-1 with subjects <18 to [≥]12 years of age and age subgroup-2 with subjects <12 to [≥]5 years of age. In both age sub groups eligible subjects (SARS-CoV-2 RT-PCR negative and seronegative at baseline) were randomized to receive either CORBEVAX vaccine or Placebo in 3: 1 ratio.\n\nFindingsThe safety profile of CORBEVAX vaccine in both pediatric cohorts was comparable to the placebo control group. Majority of reported adverse events (AEs) were mild in nature. No severe or serious AEs, medically attended AEs (MAAEs) or AEs of special interest (AESI) were reported during the study period and all the reported AEs resolved without any sequelae. In both pediatric age groups, CORBEVAX vaccinated subjects showed significant improvement in humoral immune-responses in terms of anti-RBD-IgG concentrations, anti-RBD-IgG1 titers, neutralizing antibody (nAb)-titers against Ancestral Wuhan and Delta strains. Significantly high interferon gamma immune response (cellular) was elicited by CORBEVAX vaccinated subjects with minimal effect on IL-4 cytokine secretion.\n\nInterpretationsThe safety profile of CORBEVAX vaccine in <18 to [≥]5 years children and adolescents was found to be safe and tolerable. The adverse event profile was also found to be acceptable. Significant increase in anti-RBD IgG and nAb titers and IFN-gamma immune responses were observed post vaccination in both pediatric age sub groups. Both humoral and cellular immune responses were found to be non-inferior to the immune responses induced by CORBEVAX vaccine in adult population. This study shows that CORBEVAX vaccine is highly immunogenic and can be safely administered to pediatric population as young as 5 years old.\n\nThe study was prospectively registered with clinical trial registry of India-CTRI/2021/10/037066", - "rel_num_authors": 22, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.23.22274192", + "rel_abs": "Excess mortality is the difference between expected and observed mortality in a given period and has emerged as a leading measure of the overall impact of the Covid-19 pandemic that is not biased by differences in testing or cause-of-death assignment. Spatially and temporally granular estimates of excess mortality are needed to understand which areas have been most impacted by the pandemic, evaluate exacerbating and mitigating factors, and inform response efforts, including allocating resources to affected communities. We estimated all-cause excess mortality for the United States from March 2020 through February 2022 by county and month using a Bayesian hierarchical model trained on data from 2015 to 2019. An estimated 1,159,580 excess deaths occurred during the first two years of the pandemic (first: 620,872; second: 538,708). Overall, excess mortality decreased in large metropolitan counties, but increased in nonmetro counties, between the first and second years of the pandemic. Despite the initial concentration of mortality in large metropolitan Northeast counties, beginning in February 2021, nonmetro South counties had the highest cumulative relative excess mortality. These results highlight the need for investments in rural health as the pandemics disproportionate impact on rural areas continues to grow.", + "rel_num_authors": 11, "rel_authors": [ { - "author_name": "Subhash Thuluva", - "author_inst": "Biological E. Limited" - }, - { - "author_name": "Vikram Paradkar", - "author_inst": "Biological E Limited" - }, - { - "author_name": "Subbareddy Gunneri", - "author_inst": "Biological E Limited" - }, - { - "author_name": "Vijay Yerroju", - "author_inst": "Biological E Limited" - }, - { - "author_name": "Rammohan Mogulla", - "author_inst": "Biological E Limited" - }, - { - "author_name": "Suneetha Venkata Pothakamuri", - "author_inst": "Biological E Limited" - }, - { - "author_name": "Kishore Turaga", - "author_inst": "Biological E Limited" - }, - { - "author_name": "Mahesh Kyasani", - "author_inst": "Biological E Limited" - }, - { - "author_name": "Senthilkumar Manoharan", - "author_inst": "Biological E Limited" - }, - { - "author_name": "Srikanth Adabala", - "author_inst": "Biological E Limited" - }, - { - "author_name": "Aditya Sri Javvadi", - "author_inst": "Biological E Limited" - }, - { - "author_name": "Guruprasad R Medigeshi", - "author_inst": "Translational Health Science and Technology Institute" + "author_name": "Eugenio Paglino", + "author_inst": "University of Pennsylvania" }, { - "author_name": "Janmejay Singh", - "author_inst": "Translational Health Science and Technology Institute" + "author_name": "Dielle J. Lundberg", + "author_inst": "Boston University School of Public Health" }, { - "author_name": "Heena Shaman", - "author_inst": "Translational Health Science and Technology Institute" + "author_name": "Zhenwei Zhou", + "author_inst": "Boston University School of Public Health" }, { - "author_name": "Akshay Binayke", - "author_inst": "Translational Health Science and Technology Institute" + "author_name": "Joe A. Wasserman", + "author_inst": "RTI International" }, { - "author_name": "Zaheer Aymaan", - "author_inst": "Translational Health Science and Technology Institute" + "author_name": "Rafeya Raquib", + "author_inst": "Boston University School of Public Health" }, { - "author_name": "Amit Awasthi", - "author_inst": "Translational Health Science and Technology Institute" + "author_name": "Anneliese N. Luck", + "author_inst": "University of Pennsylvania" }, { - "author_name": "Manish Narang", - "author_inst": "Guru Teg Bahadur Hospital" + "author_name": "Katherine Hempstead", + "author_inst": "The Robert Wood Johnson Foundation" }, { - "author_name": "Pradeep N", - "author_inst": "Cheluvamba Hospital, Mysore" + "author_name": "Jacob Bor", + "author_inst": "Boston University School of Public Health" }, { - "author_name": "Niranjan Mahantshetti", - "author_inst": "KLES Dr. Prabhakar Kore Hospital & Medical Research Centre, Belagavi" + "author_name": "Samuel H. Preston", + "author_inst": "University of Pennsylvania" }, { - "author_name": "Bishan Swarup Garg", - "author_inst": "Mahatma Gandhi Institute of Medical Sciences (MGIMS), Wardha" + "author_name": "Irma T. Elo", + "author_inst": "University of Pennsylvania" }, { - "author_name": "Mandal Ravi", - "author_inst": "ESIC Medical College & Hospital, Faridabad" + "author_name": "Andrew C. Stokes", + "author_inst": "Boston University School of Public Health" } ], "version": "1", - "license": "cc_no", + "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" + "category": "epidemiology" }, { "rel_doi": "10.1101/2022.04.22.22274058", @@ -320252,85 +320363,25 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.04.21.22274060", - "rel_title": "Effectiveness of the neutralizing antibody sotrovimab among high-risk patients with mild to moderate SARS-CoV-2 in Qatar", + "rel_doi": "10.1101/2022.04.21.22274155", + "rel_title": "Usage and awareness of antiviral medications for COVID-19", "rel_date": "2022-04-22", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.21.22274060", - "rel_abs": "Effectiveness of sotrovimab against severe, critical, or fatal COVID-19 was investigated in Qatar using a case-control study design at a time when BA.2 Omicron subvariant dominated incidence. Adjusted odds ratio of progression to severe, critical, or fatal COVID-19, comparing those sotrovimab-treated to those untreated, was 2.67-fold higher (95% CI: 0.60-11.91).", - "rel_num_authors": 17, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.21.22274155", + "rel_abs": "We surveyed people that recently tested positive for SARS-CoV-2 to assess the frequency and correlates of early treatment seeking behavior. Among high risk respondents, 66.0% were aware of treatment for COVID-19 and 36.3% had sought treatment, however only 1.7% reported use of an antiviral for SARS-CoV-2 infection. More public outreach is needed to raise awareness of the benefits of treatment for COVID-19.", + "rel_num_authors": 2, "rel_authors": [ { - "author_name": "Ahmed Zaqout", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Muna A. Almaslamani", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hiam Chemaitelly", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Samar A. Hashim", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ajithkumar Ittaman", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Abeir Alimam", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Fatma Rustom", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Joanne Daghfal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Mohammed Abukhattab", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Sawsan AlMukdad", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Anvar Hassan Kaleeckal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ali Nizar Latif", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Adeel A Butt", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Roberto Bertollini", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Abdullatif Al-Khal", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ali S. Omrani", - "author_inst": "Hamad Medical Corporation" + "author_name": "Noah Kojima", + "author_inst": "UCLA" }, { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Weill Cornell Medicine-Qatar" + "author_name": "Jeffrey D Klausner", + "author_inst": "USC" } ], "version": "1", - "license": "cc_no", + "license": "cc_by_nd", "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, @@ -323690,87 +323741,75 @@ "category": "microbiology" }, { - "rel_doi": "10.1101/2022.04.20.488895", - "rel_title": "Emergence of new subgenomic mRNAs in SARS-CoV-2", + "rel_doi": "10.1101/2022.04.20.488873", + "rel_title": "Uncovering the structural flexibility of SARS-CoV-2 glycoprotein spike variants", "rel_date": "2022-04-20", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.20.488895", - "rel_abs": "Two mutations occurred in SARS-CoV-2 early during the COVID-19 pandemic that have come to define circulating virus lineages1: first a change in the spike protein (D614G) that defines the B.1 lineage and second, a double substitution in the nucleocapsid protein (R203K, G204R) that defines the B.1.1 lineage, which has subsequently given rise to three Variants of Concern: Alpha, Gamma and Omicron. While the latter mutations appear unremarkable at the protein level, there are dramatic implications at the nucleotide level: the GGG[->]AAC substitution generates a new Transcription Regulatory Sequence (TRS) motif, driving SARS-CoV-2 to express a novel subgenomic mRNA (sgmRNA) encoding a truncated C-terminal portion of nucleocapsid (N.iORF3), which is an inhibitor of type I interferon production. We find that N.iORF3 also emerged independently within the Iota variant, and further show that additional TRS motifs have convergently evolved to express novel sgmRNAs; notably upstream of Spike within the nsp16 coding region of ORF1b, which is expressed during human infection. Our findings demonstrate that SARS-CoV-2 is undergoing evolutionary changes at the functional RNA level in addition to the amino acid level, reminiscent of eukaryotic evolution. Greater attention to this aspect in the assessment of emerging strains of SARS-CoV-2 is warranted.", - "rel_num_authors": 17, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.20.488873", + "rel_abs": "The severe acute respiratory syndrome CoV-2 rapidly spread worldwide, causing a pandemic. After a period of evolutionary stasis, a set of SARS-CoV-2 mutations has arisen in the spike, the leading glycoprotein at the viral envelope and the primary antigenic candidate for vaccines against the 2019 CoV disease (COVID-19). Here, we present comparative biochemical data of the glycosylated full-length ancestral and D614G spike together with three other highly transmissible strains classified by the World Health Organization as variants of concern (VOC): beta, gamma, and delta. By showing that only D614G early variant has less hydrophobic surface exposure and trimer persistence at mid-temperatures, we place D614G with features that support a model of temporary fitness advantage for virus spillover worldwide. Further, during the SARS-CoV-2 adaptation, the spike accumulates alterations leading to less structural rigidity. The decreased trimer stability observed for the ancestral and the gamma strain and the presence of D614G uncoupled conformations mean higher ACE-2 affinities when compared to the beta and delta strains. Mapping the energetic landscape and flexibility of spike variants is necessary to improve vaccine development.", + "rel_num_authors": 14, "rel_authors": [ { - "author_name": "Harriet V Mears", - "author_inst": "RNA Virus Replication Laboratory, The Francis Crick Institute, London, UK" + "author_name": "Hiam R. S. Arruda", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "George R Young", - "author_inst": "RNA Virus Replication Laboratory & Bioinformatics and Biostatistics STP, The Francis Crick Institute, London, UK" + "author_name": "Tulio M. Lima", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "Theo Sanderson", - "author_inst": "Malaria Biochemistry Laboratory, The Francis Crick Institute, London, UK" + "author_name": "Renata G. F. Alvim", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "Ruth Harvey", - "author_inst": "Worldwide Influenza Centre, The Francis Crick Institute, London, UK" + "author_name": "Fernanda B. A. Victorio", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "Margaret Crawford", - "author_inst": "Advanced Sequencing Facility, The Francis Crick Institute, London, UK" + "author_name": "Daniel P. B. Abreu", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "Daniel M Snell", - "author_inst": "Advanced Sequencing Facility, The Francis Crick Institute, London, UK" + "author_name": "Federico F. Marsili", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "Ashley S Fowler", - "author_inst": "Advanced Sequencing Facility, The Francis Crick Institute, London, UK" + "author_name": "Karen D. Cruz", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "Saira Hussain", - "author_inst": "RNA Virus Replication Laboratory, The Francis Crick Institute, London, UK" + "author_name": "Patricia Sosa-Acosta", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "Jerome Nicod", - "author_inst": "Advanced Sequencing Facility, The Francis Crick Institute, London, UK" + "author_name": "Mauricio Quinones-Vega", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "Edward Emmott", - "author_inst": "Centre for Proteome Research, Department of Biochemistry & Systems Biology, Institute of Systems Molecular & Integrative Biology, University of Liverpool, Liver" + "author_name": "Jessica S. Guedes", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "Katja Finsterbusch", - "author_inst": "Immunoregulation Laboratory, The Francis Crick Institute, London, UK" + "author_name": "F\u00e1bio C. S. Nogueira", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "Jakub Luptak", - "author_inst": "MRC Laboratory of Molecular Biology, Cambridge, UK" + "author_name": "Jerson L. Silva", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "Emma Wall", - "author_inst": "Crick/UCLH Legacy Study, The Francis Crick Institute, London, UK; and National Institute for Health Research (NIHR) University College London Hospitals (UCLH) B" + "author_name": "Leda R. Castilho", + "author_inst": "Federal University of Rio de Janeiro: Universidade Federal do Rio de Janeiro" }, { - "author_name": "Bryan Williams", - "author_inst": "University College London; and National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre, London, UK" - }, - { - "author_name": "Sonia Gandhi", - "author_inst": "Neurodegeneration Biology Laboratory, The Francis Crick Institute, London, UK" - }, - { - "author_name": "Charles Swanton", - "author_inst": "Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK" - }, - { - "author_name": "David LV Bauer", - "author_inst": "RNA Virus Replication Laboratory, The Francis Crick Institute, London, UK" + "author_name": "Guilherme A. P. de Oliveira", + "author_inst": "Federal University of Rio de Janeiro" } ], "version": "1", "license": "cc_by", "type": "new results", - "category": "microbiology" + "category": "biochemistry" }, { "rel_doi": "10.1101/2022.04.20.22274061", @@ -325352,43 +325391,51 @@ "category": "microbiology" }, { - "rel_doi": "10.1101/2022.04.16.22273937", - "rel_title": "Global reports of takotsubo (stress) cardiomyopathy following COVID-19 vaccination: First systematic review and meta-analysis", - "rel_date": "2022-04-19", + "rel_doi": "10.1101/2022.04.14.22273868", + "rel_title": "Effectiveness of Four Vaccines in Preventing SARS-CoV-2 Infection in Kazakhstan", + "rel_date": "2022-04-18", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.16.22273937", - "rel_abs": "Concerns have been raised recently about takotsubo cardiomyopathy (TCM) after receiving COVID-19 vaccines, particularly the messenger RNA (mRNA) vaccines. The goal of this study was to compile case reports to provide a comprehensive overview of takotsubo cardiomyopathy (TCM) associated with COVID-19 vaccines. A systematic literature search was conducted in PubMed, Scopus, Embase, Web of Science, and Google Scholar between 2020 and June 1, 2022. The study included individuals who developed cardiac takotsubo cardiomyopathy from receiving COVID-19 vaccinations. Ten studies, including 10 cases, participated in the current systematic review. The mean age was 61.8 years; 90% were female, while 10% were male. 80% of the patients received the mRNA COVID-19 vaccine, while 20% received other types. In addition, takotsubo cardiomyopathy (TCM) occurred in 50% of patients receiving the first dose and another 40% after the second dose of COVID-19 vaccines. Moreover, the mean number of days to the onset of symptoms was 2.62 days. All cases had an elevated troponin test and abnormal ECG findings. The left ventricular ejection fraction (LVEF) was lower than 50% in 90% of patients. In terms of the average length of hospital stay, 50% stayed for 10.2 days, and all cases recovered from their symptoms. In conclusion, takotsubo (stress) cardiomyopathy (TCM) complications associated with COVID-19 vaccination are rare but can be life-threatening. Chest pain should be considered an alarming symptom, especially in those who have received the first and second doses of the COVID-19 vaccine.", - "rel_num_authors": 6, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.14.22273868", + "rel_abs": "BACKGROUNDIn February 2021 Kazakhstan began offering COVID-19 vaccines to adults. Breakthrough SARS-CoV-2 infections raised concerns about real-world vaccine effectiveness. We aimed to evaluate effectiveness of four vaccines against SARS-CoV-2 infection.\n\nMETHODSWe conducted a retrospective cohort analysis among adults in Almaty using aggregated vaccination data and individual-level breakthrough COVID-19 cases ([≥]14 days from 2nd dose) using national surveillance data. We ran time-adjusted Cox-proportional-hazards model with sensitivity analysis accounting for varying entry into vaccinated cohort to assess vaccine effectiveness for each vaccine (measured as 1-adjusted hazard ratios) using the unvaccinated population as reference (N=565,390). We separately calculated daily cumulative hazards for COVID-19 breakthrough among vaccinated persons by age and vaccine month.\n\nRESULTSFrom February 22 to Sept 1, 2021 in Almaty, 747,558 (57%) adults were fully vaccinated (received 2 doses) and 108,324 COVID-19 cases (11,472 breakthrough) were registered. Vaccine effectiveness against infection was 78% (sensitivity estimates: 74-82%) for QazVac, 77% (72- 81%) for Sputnik V, 71% (69-72%) for Hayat-Vax, and 69% (64-72%) for CoronaVac. Among vaccinated persons, the 90-day follow-up cumulative hazard for breakthrough infection was 2.2%. Cumulative hazard was 2.9% among people aged [≥]60 years versus 1.9% among persons aged 18-39 years (p<0.001), and 1.2% for people vaccinated in February-May versus 3.3% in June-August (p<0.001).\n\nCONCLUSIONOur analysis demonstrates high effectiveness of COVID-19 vaccines against infection in Almaty similar to other observational studies. Higher cumulative hazard of breakthrough among people >60 years of age and during variant surges warrants targeted booster vaccination campaigns.\n\nWhat is already known on this topicO_LIPlenty of data are published on effectiveness of mRNA vaccines; however, these vaccines were not widely available in many low- and middle-income countries in 2021.\nC_LIO_LIThere are no real-world effectiveness studies on several vaccines available in the Central Asia region, including QazVac vaccine, an inactivated vaccine developed by Kazakhstan.\nC_LIO_LIUnderstanding how these vaccines are performing outside of clinical trials is critical for the COVID-19 response and lack of published data can contribute to vaccine hesitancy.\nC_LI\n\nWhat this study addsO_LIOur study demonstrated that at the population-level the four vaccines against COVID-19 used in Kazakhstan were effective at preventing SARS-CoV-2 infection.\nC_LIO_LIVaccination reduced the risk of infection by 76% and prevented over 100,000 cases of SARS-CoV-2 infection in Almaty, the countrys most populous city.\nC_LIO_LIThis is also the first study that demonstrated high vaccine effectiveness in real-world conditions of QazVac, developed in Kazakhstan.\nC_LI\n\nHow this study might affect research, practice or policyO_LIPolicy makers in Kazakhstan and the Central Asia region need data on vaccines provided in the region to update evidence-based vaccine guidelines for different populations.\nC_LI", + "rel_num_authors": 8, "rel_authors": [ { - "author_name": "Sirwan Khalid Ahmed", - "author_inst": "Department of Emergency, Rania Pediatric & Maternity Teaching Hospital, Rania, Sulaimani, Kurdistan-region, Iraq" + "author_name": "Dilyara NABIROVA", + "author_inst": "U.S. Centers for Disease Control and Prevention, Central Asia Regional Office" }, { - "author_name": "Mona Gamal Mohamed", - "author_inst": "Department of Adult Nursing, RAK Medical and Health Sciences University, Ras Al Khaimah, UAE" + "author_name": "Roberta Horth", + "author_inst": "U.S. Centers for Disease Control and Prevention, Central Asia Regional Office" }, { - "author_name": "Rawand Abdulrahman Essa", - "author_inst": "Department of Emergency, Rania Pediatric & Maternity Teaching Hospital, Rania, Sulaimani, Kurdistan-region, Iraq" + "author_name": "Manar Smagul", + "author_inst": "Scientific and practical center of sanitary-epidemiological examination and monitoring, branch of the National Center for Public Health, Almaty, Kazakhstan" }, { - "author_name": "Eman Abdelazizi Ahmed Rashad Dabou", - "author_inst": "Department of Adult Nursing, RAK Medical and Health Sciences University, Ras Al Khaimah, UAE" + "author_name": "Gaukhar Nukenova", + "author_inst": "Scientific and practical center of sanitary-epidemiological examination and monitoring, branch of the National Center for Public Health, Almaty, Kazakhstan" + }, + { + "author_name": "Aizhan Yesmagambetova", + "author_inst": "Ministry of Healthcare of the Republic of Kazakhstan" }, { - "author_name": "Salar Omar Abdulqadir", - "author_inst": "Department of Nursing, University of Raparin, Ranya, Sulaimani, Kurdistan-region, Iraq" + "author_name": "Daniel Singer", + "author_inst": "U.S. Centers for Disease Control and Prevention, Central Asia Regional Office" }, { - "author_name": "Rukhsar Muhammad Omar", - "author_inst": "Department of Nursing, University of Raparin, Ranya, Sulaimani, Kurdistan-region, Iraq" + "author_name": "Alden Henderson", + "author_inst": "U.S. Centers for Disease Control and Prevention, Atlanta, USA" + }, + { + "author_name": "Alexey Tsoy", + "author_inst": "Ministry of Healthcare of the Republic of Kazakhstan" } ], "version": "1", - "license": "cc_by", + "license": "cc0", "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" + "category": "public and global health" }, { "rel_doi": "10.1101/2022.04.13.22273837", @@ -327046,51 +327093,51 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.04.15.22273907", - "rel_title": "Multi-faceted analysis of COVID-19 epidemic in the Republic of Korea considering Omicron variant: Mathematical modeling-based study", + "rel_doi": "10.1101/2022.04.18.22273970", + "rel_title": "A comparative analysis of pediatric mental health-related emergency department utilization in Montreal, Canada before and during the COVID-19 pandemic", "rel_date": "2022-04-18", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.15.22273907", - "rel_abs": "BackgroundThe most recent variant of concern, Omicron (B.1.1.529), has caused numerous cases worldwide including the Republic of Korea due to its fast transmission and reduced vaccine effectiveness.\n\nMethodsA mathematical model considering age-structure, vaccine, antiviral treatment, and influx of the Omicron variant was developed. We estimated transmission rates among age groups using maximum likelihood estimation for the age-structured model. The impact of nonpharmaceutical interventions (in community and border), quantified by a parameter in the force of infection, and vaccination were examined through a multi-faceted analysis. A theory-based endemic equilibrium study was performed to find the manageable number of cases according to Omicron-and healthcare-related factors.\n\nResultsBy fitting the model to the available data, the estimated values of ranged from 0.31 to 0.73, representing the intensity of nonpharmaceutical interventions such as social distancing level. If < 0.55 and 300,000 booster shots were administered daily from February 3, 2022, the number of severe cases was forecasted to exceed the severe bed capacity. Moreover, the number of daily cases is reduced as the timing of screening measures is delayed. If screening measure was intensified as early as November 24, 2021 and the number of overseas entrant cases was contained to 1 case per 10 days, simulations showed that the daily incidence by February 3, 2022 could have been reduced by 87%. Furthermore, we found that the incidence number in mid-December 2021 exceeded the theory-driven manageable number of daily cases.\n\nConclusionNonpharmaceutical interventions, vaccination, and antiviral therapy influence the spread of Omicron and number of severe cases in the Republic of Korea. Intensive and early screening measures during the emergence of a new variant is key in controlling the epidemic size. Using the endemic equilibrium of the model, a formula for the manageable daily cases depending on the severity rate and average length of hospital stay was derived so that the number of severe cases does not surpass the severe bed capacity.", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.18.22273970", + "rel_abs": "BackgroundReports on longitudinal trends in mental health-related (MHR) emergency department (ED) utilization spanning the pre- and post-pandemic periods are lacking, along with evidence comparing healthcare services utilization by sociodemographic subgroups. The aim of this study was to evaluate COVID-19-associated changes in MHR ED utilization among youth overall and by age, sex, and socioeconomic status (SES).\n\nMethodsThis retrospective cross-sectional study analyzed MHR ED utilization before and during the COVID-19 pandemic at a large urban pediatric tertiary care hospital in Montreal, Canada. All ED visits for children (5-11 years) and adolescents (12-17 years) between April 1, 2016 and November 30, 2021 were included. The main outcome was the monthly count of MHR ED visits. Pre-pandemic and pandemic periods were compared using an interrupted time series design. The effect of seasonality (in months), age (in years), sex (male or female), and SES (low, average, high) were compared using a generalized additive model.\n\nResultsThere were a total of 437,147 ED visits (204,215 unique patients) during the five-year study period of which 9,748 (5.8%) were MHR visits (7,686 unique patients). We observed an increase of 69% (95% CI, +53% to +85%; p = .001) in the mean monthly count of MHR ED visits during the pandemic period, which remained significant after adjusting for seasonality (44% increase, 95% CI, +38% to +51%; p = .001). The chance of presenting for a MHR ED visit increased non-linearly with age. There were increased odds of presenting for a MHR ED visit among girls between the pre-pandemic and pandemic periods (OR 1.42, 95% CI 1.29-1.56). No difference by SES group during and before the COVID-19 pandemic was found (OR 1.01, 95% CI 0.89-1.15 [low]; OR 1.09, 95% CI 0.96-1.25 [high]).\n\nConclusionsOur study shows important increases in MHR ED utilization among youth, and especially among girls, during the first 20 months of the COVID-19 pandemic, highlighting the need for sustained, targeted and scalable mental health resources to support youth mental health during the current and future crises.", "rel_num_authors": 8, "rel_authors": [ { - "author_name": "Youngsuk Ko", - "author_inst": "Department of Mathematics, Konkuk University, Seoul, Korea" + "author_name": "Gabrielle Beaudry", + "author_inst": "Department of Psychiatry, University of Oxford, Oxford (UK)" }, { - "author_name": "Victoria May Mendoza", - "author_inst": "Department of Mathematics, Konkuk University, Seoul, Korea" + "author_name": "Olivier Drouin", + "author_inst": "Sainte-Justine Hospital Research Center, Montreal, Quebec (Canada)" }, { - "author_name": "Renier Mendoza", - "author_inst": "Department of Mathematics, Konkuk University, Seoul, Korea" + "author_name": "Jocelyn Gravel", + "author_inst": "Sainte-Justine Hospital Research Center, Montreal, Quebec (Canada)" }, { - "author_name": "Yu Bin Seo", - "author_inst": "Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea" + "author_name": "Anna Smyrnova", + "author_inst": "Sainte-Justine Hospital Research Center, Montreal, Quebec (Canada)" }, { - "author_name": "Jacob Lee", - "author_inst": "Division of Infectious Disease, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul, Korea" + "author_name": "Andreas Bender", + "author_inst": "Department of Statistics, LMU Munich, Munich (Germany)" }, { - "author_name": "Jonggul Lee", - "author_inst": "Division of Public Health Emergency Response Research, Korea Disease Control and Prevention Agency, Cheongju, Korea" + "author_name": "Massimiliano Orri", + "author_inst": "McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec (Canada)" }, { - "author_name": "Donghyok Kwon", - "author_inst": "Division of Public Health Emergency Response Research, Korea Disease Control and Prevention Agency, Cheongju, Korea" + "author_name": "Marie-Claude Geoffroy", + "author_inst": "McGill Group for Suicide Studies, Douglas Mental Health University Institute, Department of Psychiatry, McGill University, Montreal, Quebec (Canada)" }, { - "author_name": "Eunok Jung", - "author_inst": "Department of Mathematics, Konkuk University, Seoul, Korea" + "author_name": "Nicholas Chadi", + "author_inst": "Sainte-Justine Hospital Research Center, Montreal, Quebec (Canada)" } ], "version": "1", - "license": "cc_no", + "license": "cc_by", "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" + "category": "psychiatry and clinical psychology" }, { "rel_doi": "10.1101/2022.04.15.22273460", @@ -328712,27 +328759,51 @@ "category": "public and global health" }, { - "rel_doi": "10.1101/2022.04.11.22273599", - "rel_title": "The dynamic reproduction index: accurate determination from incidence and application for an early warning system", + "rel_doi": "10.1101/2022.04.11.22273702", + "rel_title": "Making maternity and neonatal care personalised in the COVID-19 pandemic: results from the Babies Born Better Survey in the UK and the Netherlands", "rel_date": "2022-04-16", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.11.22273599", - "rel_abs": "Two methods of calculating the reproduction index from daily new infection data are considered, one by using the generation time tG as a shift (RG), and an incidence-based method directly derived from the differential equation system of an SIR epidemic dynamics model (RI). While the former is shown to have few in common with the true reproduction index, we find that the latter provides a sensitive detection device for intervention effects and other events affecting the epidemic, making it well-suited for diagnostic purposes in policy making. Furthermore, we introduce a similar quantity, [Formula], which can be calculated directly from RG. It shows largely the same behaviour as RI, with less fine structure. However, it is accurate in particular in the vicinity of R = 1, where accuracy is important for the corrrect prediction of epidemic dynamics. We introduce an entirely new, self-consistent method to derive, from both quantities, an improved [Formula] which is both accurate and contains the details of the epidemic spreading dynamics. Hence we obtain R accurately from data on daily new infections (incidence) alone. Moreover, by using RI instead of RG in plots of R versus incidence, orbital trajectories of epidemic waves become visible in a particularly insightful way, demonstrating that the widespread use of only incidence as a diagniostic tool is clearly inappropriate.\n\nPACS numbers:", - "rel_num_authors": 2, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.11.22273702", + "rel_abs": "Structured abstractO_ST_ABSBackgroundC_ST_ABSThe COVID-19 pandemic had a severe impact on womens birth experiences. To date, there are no studies that use both quantitative and qualitative data to compare womens birth experiences before and during the pandemic, across more than one country.\n\nAimTo examine womens birth experiences during the COVID-19 pandemic and to compare the experiences of women who gave birth in the United Kingdom (UK) or the Netherlands (NL) either before or during the pandemic.\n\nMethodThis study is based on analyses of quantitative and qualitative data from the online Babies Born Better survey. Responses recorded by women giving birth in the UK and the NL between June and December 2020 have been used, encompassing women who gave birth between 2017 and 2020. Quantitative data were analysed descriptively, and chi-squared tests were performed to compare women who gave birth pre- versus during pandemic and separately by country. Qualitative data was analysed by inductive thematic analysis.\n\nFindingsRespondents in both the UK and the NL who gave birth during the pandemic were as likely, or, if they had a self-reported above average standard of life, more likely to rate their labour and birth experience positively when compared to women who gave birth pre-pandemic. This was despite the fact that those labouring in the pandemic reported less support and choice. Two potential explanatory themes emerged from the qualitative data: respondents had lower expectations during the pandemic, and they appreciated that care providers tried hard to personalise care.\n\nConclusionOur study implies that many women labouring during the COVID-19 pandemic experienced restrictions, but their experience was mitigated by staff actions. However, personalised care should not be maintained by the good will of care providers, but should be a priority in maternity care policy to benefit all service users equitably.", + "rel_num_authors": 8, "rel_authors": [ { - "author_name": "Robert N.J. Conradt", - "author_inst": "CONRADT Mess- und Regeltechnik" + "author_name": "Lauri M.M. van den Berg", + "author_inst": "Amsterdam UMC Locatie VUmc" + }, + { + "author_name": "Naseerah Akooji", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "Gill Thomson", + "author_inst": "University of Central Lancashire" }, { - "author_name": "Stephan Herminghaus", - "author_inst": "Max Planck Institute for Dynamics and Self-Organization (MPI-DS), Goettingen, Germany" + "author_name": "Ank de Jonge", + "author_inst": "Amsterdam UMC Locatie VUmc" + }, + { + "author_name": "Marie-Clare Balaam", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "Anastasia Topalidou", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "Soo Downe", + "author_inst": "University of Central Lancashire" + }, + { + "author_name": "the ASPIRE COVID-19 research team", + "author_inst": "" } ], "version": "1", - "license": "cc_by_nc_nd", + "license": "cc_by", "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" + "category": "obstetrics and gynecology" }, { "rel_doi": "10.1101/2022.04.15.22273412", @@ -330334,25 +330405,16 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.04.12.22273792", - "rel_title": "Health behaviours the month prior to COVID-19 infection and the development of self-reported long COVID and specific long COVID symptoms: A longitudinal analysis of 1,811 UK adults", + "rel_doi": "10.1101/2022.04.12.22273804", + "rel_title": "Nowcasting and Forecasting COVID-19 Waves: The Recursive and Stochastic Nature of Transmission", "rel_date": "2022-04-13", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.12.22273792", - "rel_abs": "BackgroundDemographic and infection-related characteristics have been identified as risk factors for long COVID, but research on the influence of health behaviours (e.g., exercise, smoking) immediately preceding the index infection is lacking.\n\nMethods1,811 UK adults from the UCL COVID-19 Social Study and who had previously been infected with COVID-19 were analysed. Health behaviours in the month before infection were weekly exercise frequency, days of fresh air per week, sleep quality, smoking, consuming more than the number of recommended alcoholic drinks per week (>14), and the number of mental health care behaviours (e.g., online mental health programme). Logistic regressions controlling for covariates (e.g., COVID-19 infection severity and pre-existing health conditions) examined the impact of health behaviours on long COVID and three long COVID symptoms (difficulty with mobility, cognition, and self-care).\n\nResultsIn the month before infection with COVID-19, poor quality sleep increased the odds of long COVID (odds ratio [OR]: 3.53; (95% confidence interval [CI]: 2.01 to 6.21), as did average quality sleep (OR: 2.44; 95% CI: 1.44 to 4.12). Having smoked (OR: 8.39; 95% CI: 1.86 to 37.91) increased and meeting recommended weekly physical activity guidelines (3+ hours) (OR: 0.05; 95% CI: 0.01 to 0.39) reduced the likelihood of difficulty with self-care (e.g., washing all over or dressing) amongst those with long COVID.\n\nConclusionResults point to the importance of sleep quality for long COVID, potentially helping to explain previously demonstrated links between stress and long COVID. Results also suggest that exercise and smoking may be modifiable risk factors for preventing the development of difficulty with self-care.\n\nFundingThe Nuffield Foundation [WEL/FR-000022583], the MARCH Mental Health Network funded by the Cross-Disciplinary Mental Health Network Plus initiative supported by UK Research and Innovation [ES/S002588/1], and the Wellcome Trust [221400/Z/20/Z and 205407/Z/16/Z].\n\nWhat is already known on the topicLong COVID is rapidly becoming a public health concern. Although existing evidence to date has identified health characteristics such as obesity as risk factors, hardly any research on modifiable risk factors such as health behaviours has been conducted.\n\nWhat this study addsThis study adds to the dearth of evidence on modifiable risk factors occurring before COVID-19 infection. Findings suggest a role of poor sleep quality for the development of long COVID, and for meeting physical activity guidelines (3+ hours per week) and not smoking as modifiable risk factors for self-care difficulties amongst those with long COVID.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Elise Paul", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - } - ], + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.12.22273804", + "rel_abs": "We propose a parsimonious, yet effective, susceptible-exposed-infected-removed-type model that incorporates the time change in the transmission and death rates. The model is calibrated by Tikhonov-type regularization from official reports from New York City (NYC), Chicago, the State of Sao Paulo, in Brazil, and British Columbia, in Canada. To forecast, we propose different ways to extend the transmission parameter, considering its estimated values. The forecast accuracy is then evaluated using real data from the above referred places. All the techniques accurately provided forecast scenarios for periods 15 days long. One of the models effectively predicted the magnitude of the four waves of infections in NYC, including the one caused by the Omicron variant for periods of 45 days long using out-of-sample data.", + "rel_num_authors": 0, + "rel_authors": null, "version": "1", - "license": "cc_by", + "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, @@ -332041,103 +332103,71 @@ "category": "epidemiology" }, { - "rel_doi": "10.1101/2022.04.11.22272784", - "rel_title": "Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual.", - "rel_date": "2022-04-12", + "rel_doi": "10.1101/2022.04.07.22273561", + "rel_title": "The effect of the COVID-19 lockdown on mental health care use in South Africa: an interrupted time series analysis", + "rel_date": "2022-04-11", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.11.22272784", - "rel_abs": "Prolonged infections in immunocompromised individuals may be a source for novel SARS-CoV-2 variants, particularly when both the immune system and antiviral therapy fail to clear the infection, thereby promoting adaptation. Here we describe an approximately 16-month case of SARS-CoV-2 infection in an immunocompromised individual. Following monotherapy with the monoclonal antibody Bamlanivimab, the individuals virus was resistant to this antibody via a globally unique Spike amino acid variant (E484T) that evolved from E484A earlier in infection. With the emergence and spread of the Omicron Variant of Concern, which also contains Spike E484A, E484T may arise again as an antibody-resistant derivative of E484A.", - "rel_num_authors": 21, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.07.22273561", + "rel_abs": "AimsIn March 2020, South Africa introduced a lockdown in response to the COVID-19 pandemic, entailing the suspension of all non-essential activities and a complete ban of tobacco and alcohol sales. We studied the effect of the lockdown on mental health care utilisation rates in private-sector care in South Africa.\n\nMethodsWe did an interrupted time series analysis using insurance claims from January 1, 2017, to June 1, 2020 of beneficiaries 18 years or older from a large private sector medical aid scheme. We calculated weekly outpatient consultation and hospital admission rates for organic mental disorders, substance use disorders, serious mental disorders, depression, anxiety, other mental disorders, any mental disorder, and alcohol withdrawal syndrome. We calculated adjusted odds ratios (OR) for the effect of the lockdown on weekly outpatient consultation and hospital admission rates and the weekly change in rates during the lockdown until June 1, 2020.\n\nResults710,367 persons were followed up for a median of 153 weeks. Hospital admission rates (OR 0.38; 95% CI 0.33-0.44) and outpatient consultation rates (OR 0.74; 95% CI 0.63-0.87) for any mental disorder decreased substantially after the lockdown and did not recover to pre-lockdown levels until June 1, 2020. Health care utilisation rates for alcohol withdrawal syndrome doubled after the introduction of the lockdown, but the statistical uncertainty around the estimates was large (OR 2.24; 95% CI 0.69-7.24).\n\nConclusionsReduced mental health care contact rates during the COVID-19 lockdown likely reflect a substantial unmet need for mental health services with potential long-term consequences for mental health patients and their families. Steps to ensure access and continuity of mental health services during future lockdowns should be considered.", + "rel_num_authors": 13, "rel_authors": [ { - "author_name": "Peter Halfmann", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Nicholas R. Minor", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Luis A. Haddock III", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Robert Maddox", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Gage K. Moreno", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Katarina Braun", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "David Baker", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Kasen Riemersma", - "author_inst": "University of Wisconsin, Madison" - }, - { - "author_name": "Ankur Prasad", - "author_inst": "University of Wisconsin Hospitals and Clinics" + "author_name": "Anja Elisabeth Wettstein", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Switzerland and Graduate School for Health Sciences, University of Bern, Switzerland" }, { - "author_name": "Kirsten J. Alman", - "author_inst": "University of Wisconsin Hospitals and Clinics" + "author_name": "Mpho Tlali", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa" }, { - "author_name": "Matthew C. Lambert", - "author_inst": "University of Wisconsin Hospitals and Clinics" + "author_name": "John A Joska", + "author_inst": "HIV Mental Health Research Unit, Department of Psychiatry and Mental Health, Neuroscience Institute, Cape Town, South Africa" }, { - "author_name": "Kelsey Florek", - "author_inst": "Wisconsin State Laboratory of Hygiene" + "author_name": "Morna Cornell", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa" }, { - "author_name": "Allen Bateman", - "author_inst": "University of Wisconsin-Madison" + "author_name": "Veronika W Skrivankova", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" }, { - "author_name": "Ryan Westergaard", - "author_inst": "University of Wisconsin-Madison" + "author_name": "Soraya Seedat", + "author_inst": "Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa" }, { - "author_name": "Nasia Safdar", - "author_inst": "University of Wisconsin-Madison" + "author_name": "Johannes P Mouton", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa and Division of Clinical Pharmacology, Department of M" }, { - "author_name": "David R. Andes", - "author_inst": "University of Wisconsin-Madison" + "author_name": "Leigh L van den Heuvel", + "author_inst": "Department of Psychiatry, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa" }, { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "University of Wisconsin-Madison" + "author_name": "Nicola Maxwell", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa" }, { - "author_name": "Madiha Fida", - "author_inst": "Mayo Clinic" + "author_name": "Mary-Ann Davies", + "author_inst": "Centre for Infectious Disease Epidemiology and Research, University of Cape Town, Cape Town, South Africa" }, { - "author_name": "Joseph D. Yao", - "author_inst": "Mayo Clinic" + "author_name": "Gary Maartens", + "author_inst": "Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa" }, { - "author_name": "Thomas Friedrich", - "author_inst": "University of Wisconsin Madison" + "author_name": "Matthias Egger", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland; Centre for Infectious Disease Epidemiology and Research, University of Cape " }, { - "author_name": "David H. O'Connor", - "author_inst": "University of Wisconsin-Madison" + "author_name": "Andreas D Haas", + "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" } ], "version": "1", - "license": "cc_by_nc", + "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" + "category": "epidemiology" }, { "rel_doi": "10.1101/2022.04.07.22273593", @@ -333615,45 +333645,85 @@ "category": "immunology" }, { - "rel_doi": "10.1101/2022.04.07.487415", - "rel_title": "The Delta variant SARS-CoV-2 spike protein uniquely promotes aggregation of pseudotyped viral particles", + "rel_doi": "10.1101/2022.04.07.487520", + "rel_title": "Hippo Signaling Pathway Activation during SARS-CoV-2 Infection Contributes to Host Antiviral Response", "rel_date": "2022-04-08", "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.07.487415", - "rel_abs": "Individuals infected with the SARS-CoV-2 Delta variant, lineage B.1.617.2, exhibit faster initial infection with a higher viral load than prior variants, and pseudotyped particles bearing the SARS-CoV-2 Delta variant spike protein induce a faster initial infection rate of target cells compared to those bearing other SARS-CoV-2 variant spikes. Here, we show that pseudotyped particles bearing the Delta variant spike form unique aggregates, as evidenced by negative stain and cryogenic electron microscopy (EM), flow cytometry, and nanoparticle tracking analysis. Viral particles pseudotyped with other SARS-CoV-2 spike variants do not show aggregation by any of these criteria. The contribution to infection kinetics of the Delta spikes unique property to aggregate is discussed with respect to recent evidence for collective infection by other viruses. Irrespective of this intriguing possibility, spike-dependent aggregation is a new functional parameter of spike-expressing viral particles to evaluate in future spike protein variants.", - "rel_num_authors": 7, + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.07.487520", + "rel_abs": "SARS-CoV-2, responsible for the COVID-19 pandemic, causes respiratory failure and damage to multiple organ systems. The emergence of viral variants poses a risk of vaccine failures and prolongation of the pandemic. However, our understanding of the molecular basis of SARS-CoV-2 infection and subsequent COVID-19 pathophysiology is limited. In this study, we have uncovered a critical role for the evolutionarily conserved Hippo signaling pathway in COVID-19 pathogenesis. Given the complexity of COVID-19 associated cell injury and immunopathogenesis processes, we investigated Hippo pathway dynamics in SARS-CoV-2 infection by utilizing COVID-19 lung samples, and human cell models based on pluripotent stem cell-derived cardiomyocytes (PSC-CMs) and human primary lung air-liquid interface (ALI) cultures. SARS-CoV-2 infection caused activation of the Hippo signaling pathway in COVID-19 lung and in vitro cultures. Both parental and Delta variant of concern (VOC) strains induced Hippo pathway. The chemical inhibition and gene knockdown of upstream kinases MST1/2 and LATS1 resulted in significantly enhanced SARS-CoV-2 replication, indicating antiviral roles. Verteporfin a pharmacological inhibitor of the Hippo pathway downstream transactivator, YAP, significantly reduced virus replication. These results delineate a direct antiviral role for Hippo signaling in SARS-CoV-2 infection and the potential for this pathway to be pharmacologically targeted to treat COVID-19.", + "rel_num_authors": 17, "rel_authors": [ { - "author_name": "Jennifer D Petersen", - "author_inst": "Section on Integrative Biophysics, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Developme" + "author_name": "Gustavo Garcia Jr.", + "author_inst": "University of California, Los Angeles" }, { - "author_name": "Jianming Lu", - "author_inst": "Codex BioSolutions, Inc., 12358 Parklawn Dr., Suite 250, North Bethesda, MD" + "author_name": "Yijie Wang", + "author_inst": "University of California, Los Angeles" }, { - "author_name": "Wendy Fitzgerald", - "author_inst": "Section on Intercellular Interactions, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Devel" + "author_name": "Joseph Ignatius Irudayam", + "author_inst": "University of California, Los Angeles" }, { - "author_name": "Fei Zhou", - "author_inst": "Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Nat" + "author_name": "Arjit Vijey Jeyachandran", + "author_inst": "University of California, Los Angeles" }, { - "author_name": "Paul S Blank", - "author_inst": "Section on Integrative Biophysics, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Developme" + "author_name": "Sebastian Castillo Cario", + "author_inst": "University of California, Los Angeles" }, { - "author_name": "Doreen Matthies", - "author_inst": "Unit on Structural Biology, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Nat" + "author_name": "Chandani Sen", + "author_inst": "University of California, Los Angeles" }, { - "author_name": "Joshua Zimmerberg", - "author_inst": "Section on Integrative Biophysics, Division of Basic and Translational Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Developme" + "author_name": "Shen Li", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Yunfeng Li", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Ashok Kumar", + "author_inst": "Wayne State University" + }, + { + "author_name": "Karin Nielsen-Saines", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Samuel W. French", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Priya S. Shah", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Kouki Morizono", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Brigitte Gomperts", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Arjun Deb", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Arunachalam Ramaiah", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Vaithilingaraja Arumugaswami", + "author_inst": "University of California, Los Angeles" } ], "version": "1", - "license": "cc0", + "license": "cc_by", "type": "new results", "category": "microbiology" }, @@ -335593,51 +335663,115 @@ "category": "infectious diseases" }, { - "rel_doi": "10.1101/2022.04.05.22273434", - "rel_title": "Analysis of immunization, adverse events, and efficacy of a fourth dose of BNT162b2 vaccine", + "rel_doi": "10.1101/2022.04.06.22273080", + "rel_title": "Serious underlying medical conditions and COVID-19 vaccine hesitancy.", "rel_date": "2022-04-06", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.05.22273434", - "rel_abs": "ImportanceScarce information exists concerning the seroconversion and adverse events after immunization (AEFI) of the fourth dose of a SARS-COV-2 vaccine.\n\nObjectiveCorrelate the magnitude of the antibody response to vaccination with previous clinical conditions and AEFI of the fourth dose of BNT162b2 mRNA.\n\nDesignObservational study where SARS-CoV-2 spike 1-2 IgG antibodies IgG titers were measured 21-28 days after the exposition of the first, and second dose, three months after the second dose, 1-7 days after the third dose, before the fourth dose, and 21-28 days after the fourth dose of BNT162b2 mRNA.\n\nSettingThe study was conducted on healthcare workers of a private hospital in Northern Mexico.\n\nParticipantsInclusion criteria were healthcare workers of both genders, any age, who planned to conclude the immunization regimen. The exclusion criteria were previously given any SARS-CoV-2 vaccine prior to study entry.\n\nInterventionSubjects were exposed to four doses of the BNT162b2 mRNA vaccine.\n\nMain Outcome and Measures:\n\nThe anti-S1 and anti-S2 IgG antibodies against SARS-CoV-2 in plasma samples were measured with chemiluminescence immunoassay developed by DiaSorin.\n\nResultsWe recruited 112 subjects [43 (SD 9) years old, 74% women].\n\nAfter the first dose, subjects had a median (IQR) AU/ml IgG of 122(1904), with an increase to 1875 (2095) after the second dose, 3020 (2330) after the third dose, and 4230 (3393) after 21-28 of a fourth dose (p<0.01). The number (%) of any AEFI between doses was 90 (80.4), 89(79), 65(58), 69 (61.5), after first, second, third, and fourth, respectively, p<0.001. After the fourth dose, the most frequent AEFI was pain at the injection site (87%). Fever was slightly more frequent after the third and fourth doses, 9 (13.8) and 8 (11.4%) cases, respectively, and adenopathy was more frequent after the fourth dose [in11(15.7%) cases]. There was a correlation between AEFI in the fourth dose with gender and antibody levels (p<0.05). The highest proportion of AEFI was considered mild after the fourth dose. During the Omicron outbreak, 6 (5.3%) had mild SARS-CoV-2 during 8-28 days of the fourth dose.\n\nConclusions and RelevanceThe fourth dose of BNT162b2mRNA increases S1/S2 IgG 33.6 times with mild adverse events.\n\nRegistration numberNCT05228912\n\nKey pointsO_ST_ABSQuestionC_ST_ABSWhat is the magnitude of antibody response to vaccination and adverse events after immunization (AEFI) of a fourth dose of BNT162b2 mRNA?\n\nFindingsThis cohort included 112 healthcare workers. We measured S1/S2 IgG vs. SARS-CoV-2 after the first, second, third and fourth dose. Compared to the first dose, antibodies increased 33.6 times the antibody levels after the fourth dose. We found minimal to moderate adverse events. The change in antibodies correlated with AEFI. During the Omicron outbreak 6 (5.3%) had mild SARS-CoV-2.\n\nMeaningA fourth dose of BNT162b2mRNA increases S1/S2 IgG with mild to moderate adverse events.", - "rel_num_authors": 8, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.06.22273080", + "rel_abs": "ObjectiveTo examine vaccine uptake, hesitancy and explanatory factors amongst people with serious and/or chronic health conditions, including the impact of underlying disease on attitudes to vaccination.\n\nDesignCross-sectional survey.\n\nSettingTen Australian health services.\n\nParticipants4683 patients (3560 cancer, 842 diabetes and 281 multiple sclerosis) receiving care at the health services participated in the 42-item survey, between June 30 to October 5, 2021.\n\nMain outcome measuresSociodemographic and disease-related characteristics, COVID-19 vaccine uptake, and the scores of three validated scales which measured vaccine hesitancy and vaccine-related beliefs generally and specific to the participants disease, including the Oxford COVID-19 Vaccine Hesitancy Scale, the Oxford COVID-19 Vaccine Confidence and Complacency Scale and the Disease Influenced Vaccine Acceptance Scale. Multivariable logistic regression was used to determine the associations between scale scores and vaccine uptake.\n\nResultsOf all participants, 81.5% reported having at least one COVID-19 vaccine. Unvaccinated status was associated with younger age, female sex, lower education and income, English as a second language, and residence in regional areas (all p<0.05). Unvaccinated participants were more likely to report greater vaccine hesitancy and more negative perceptions toward vaccines (all p<0.05). Disease-related vaccine concerns were associated with unvaccinated status and hesitancy, including greater complacency about COVID-19 infection, and concerns relating to vaccine efficacy and impact on their disease and/or treatment (all p<0.05).\n\nConclusionsDisease-specific concerns impact COVID-19 vaccine-related behaviours and beliefs in people with serious and/or chronic health conditions. This highlights the need to develop targeted strategies and education about COVID-19 vaccination to support medically vulnerable populations and health professionals.\n\nTrial registrationACTRN12621001467820", + "rel_num_authors": 24, "rel_authors": [ { - "author_name": "Maria Elena Romero-Ibarguengoitia", - "author_inst": "Hospital Clinica Nova" + "author_name": "Daphne Day", + "author_inst": "Monash Health" }, { - "author_name": "Arnulfo Gonzalez-Cantu", - "author_inst": "Hospital Clinica Nova" + "author_name": "Lisa Grech", + "author_inst": "Monash University" }, { - "author_name": "Diego Rivera-Salinas", - "author_inst": "Hospital Clinica Nova" + "author_name": "Mike Nguyen", + "author_inst": "Monash Health" }, { - "author_name": "Yodira Guadalupe Hernandez-Ruiz", - "author_inst": "Hospital Clinica Nova" + "author_name": "Nathan Bain", + "author_inst": "Monash Health" }, { - "author_name": "Ana Gabriela Armendariz-Vazquez", - "author_inst": "Hospital Clinica Nova" + "author_name": "Alastair Kwok", + "author_inst": "Monash Health" }, { - "author_name": "Irene Antonieta Barco-Flores", - "author_inst": "Hospital Clinica Nova" + "author_name": "Sam Harris", + "author_inst": "Bendigo Health" }, { - "author_name": "Rosalinda Gonzalez-Facio", - "author_inst": "Hospital Clinica Nova" + "author_name": "Hieu Chau", + "author_inst": "Latrobe Regional Hospital" }, { - "author_name": "Miguel Angel Sanz-Sanchez", - "author_inst": "Hospital Clinica Nova" + "author_name": "Bryan Chan", + "author_inst": "Sunshine Coast Hospital and Health Service" + }, + { + "author_name": "Richard Blennerhassett", + "author_inst": "Central Coast Haematology" + }, + { + "author_name": "Louise Nott", + "author_inst": "Icon Cancer Centre Hobart" + }, + { + "author_name": "Nada Hamad", + "author_inst": "St Vincent's Hospital Sydney" + }, + { + "author_name": "Annette Tognela", + "author_inst": "Campbelltown Hospital" + }, + { + "author_name": "David Hoffman", + "author_inst": "Dr David Hoffman" + }, + { + "author_name": "Amelia McCartney", + "author_inst": "Monash Health" + }, + { + "author_name": "Kate Webber", + "author_inst": "Monash Health" + }, + { + "author_name": "Jennifer Wong", + "author_inst": "Monash Health" + }, + { + "author_name": "Craig Underhill", + "author_inst": "Border Medical Oncology" + }, + { + "author_name": "Brett Sillars", + "author_inst": "Sunshine Coast Hospital and Health Service" + }, + { + "author_name": "Antony Winkel", + "author_inst": "Sunshine Coast Hospital and Health Service" + }, + { + "author_name": "Mark Savage", + "author_inst": "Bendigo Health" + }, + { + "author_name": "Bao Sheng Loe", + "author_inst": "Cambridge University" + }, + { + "author_name": "Daniel Freeman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Eva Segelov", + "author_inst": "Monash Health" + }, + { + "author_name": "- CANVACCS, DIABVACCS, and MSVACCS investigators", + "author_inst": "" } ], "version": "1", "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" + "category": "public and global health" }, { "rel_doi": "10.1101/2022.04.06.22273512", @@ -337259,39 +337393,39 @@ "category": "pharmacology and therapeutics" }, { - "rel_doi": "10.1101/2022.03.31.22273181", - "rel_title": "Cannabis potential effects to prevent or attenuate SARS-COV2 contagion", + "rel_doi": "10.1101/2022.03.29.22273148", + "rel_title": "Modeling behavior change and underreporting in the early phase of COVID-19 pandemic in Metro Manila, Philippines", "rel_date": "2022-04-05", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273181", - "rel_abs": "Medical cannabis has gained an exponential interest in recent years. Therapeutic targets have been broadened from specific applications over pain control, chemotherapy side effects, treatment-resistant epilepsies and multiple sclerosis, among others. Several in vitro and animal studies, along with few human controlled studies, suggest cannabinoids have a potential therapeutic role over medical conditions comporting inflammatory mechanisms. Given the tremendous world-wide impact of the COVID-19 pandemic, research efforts are converging towards the use of cannabinoids to attenuate severe or fatal forms of the disease. The present survey aims to explore possible correlations between cannabis use, either recreational or medical, over the presence of SARS-COV-2 contagion, along with the symptoms severity. 4026 surveys were collected via electronic form. Results suggest a relation between any type of cannabis use and a lower risk of SARS-COV-2 contagion (p=0,004; OR=0,689, IC95% 0,534-0,889). Despite several methodological limitations, the present survey steps up the urge to expand our understanding on cannabinoids potential use on human controlled studies, that can better arm us in the fight against the current COVID-19 pandemic.", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.29.22273148", + "rel_abs": "IntroductionAt the start of the pandemic, the Philippine capital Metro Manila was placed under a strict lockdown termed Enhanced Community Quarantine (ECQ). When ECQ was eased to General Community Quarantine (GCQ) after three months, healthcare systems were soon faced with a surge of COVID-19 cases, putting most facilities at high or critical risk and prompting a return to a stricter policy.\n\nMethodsWe developed a mathematical model considering behavior changes and underreporting to represent the first major epidemic wave in Metro Manila. Key parameters were fitted to the cumulative cases in the capital from March to September 2020. A bi-objective optimization problem was formulated that allows easing of restrictions at an earlier time and minimizes the necessary additional beds to ensure sufficient capacity in healthcare facilities once ECQ was lifted.\n\nResultsIf behavior was changed one to four weeks earlier before GCQ, then the cumulative number of cases can be reduced by up to 55% and the peak delayed by up to four weeks. Increasing the reporting ratio during ECQ threefold may increase the reported cases by 23% but can reduce the total cases, including the unreported, by 61% on June 2020. If GCQ began on May 28, 2020, 48 beds should have been added per day to keep the capacity only at high-risk (75% occupancy). Among the optimal solutions, the peak of cases is lowest if ECQ was lifted on May 20, 2020 and with at least 56 additional beds per day.\n\nConclusionSince infectious diseases are likely to reemerge, the formulated model can be used as a decision support tool to improve existing policies and plan effective strategies that can minimize the socioeconomic impact of strict lockdown measures and ensure adequate healthcare capacity.", "rel_num_authors": 5, "rel_authors": [ { - "author_name": "Paula Herrera-Gomez", - "author_inst": "Universidad Tecnologica de Pereira" + "author_name": "Victoria May P. Mendoza", + "author_inst": "Institute of Mathematics, University of the Philippines Diliman" }, { - "author_name": "Luis Felipe Echeveri-Catano", - "author_inst": "Fundacion Universitaria de las Americas, Pereira Colombia" + "author_name": "Renier Mendoza", + "author_inst": "Institute of Mathematics, University of the Philippines Diliman" }, { - "author_name": "Yerson Andres Ruiz Colorado", - "author_inst": "Universidad Tecnologica de Pereira, Colombia" + "author_name": "Youngsuk Ko", + "author_inst": "Department of Mathematics, Konkuk University" }, { - "author_name": "Sebastian Giraldo Galeano", - "author_inst": "Universidad Tecnologica de Pereira, Colombia" + "author_name": "Jongmin Lee", + "author_inst": "Department of Mathematics, Konkuk University" }, { - "author_name": "Alberto Velez van Meerbeke", - "author_inst": "Universidad del Rosario, Bogota Colombia" + "author_name": "Eunok Jung", + "author_inst": "Department of Mathematics, Konkuk University" } ], "version": "1", - "license": "cc_no", + "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" + "category": "public and global health" }, { "rel_doi": "10.1101/2022.04.03.22273370", @@ -339293,39 +339427,83 @@ "category": "immunology" }, { - "rel_doi": "10.1101/2022.03.31.22273239", - "rel_title": "Epidemiological topology data analysis links severe COVID-19 to RAAS andhyperlipidemia associated metabolic syndrome conditions", + "rel_doi": "10.1101/2022.04.02.22273333", + "rel_title": "High rate of BA.1, BA.1.1 and BA.2 in triple vaccinated", "rel_date": "2022-04-03", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273239", - "rel_abs": "The emergence of COVID19 created incredible worldwide challenges but offers unique opportunities to understand the physiology of its risk factors and their interactions with complex disease conditions, such as metabolic syndrome. Epidemiological analysis powered by topological data analysis (TDA) is a novel approach to uncover these clinically relevant interactions. Here TDA utilized Explorys data to discover associations among severe COVID19 and metabolic syndrome, and it explored the probative value of drug prescriptions to capture the involvement of RAAS and hypertension with COVID19 as well as modification of risk factor impact by hyperlipidemia on severe COVID19.", - "rel_num_authors": 5, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.02.22273333", + "rel_abs": "BackgroundBooster vaccine doses offer protection against severe COVID-19 caused by omicron but are less effective against infection. Characteristics such as serological correlates of protection, viral abundance, and clearance of omicron infection in triple vaccinated individuals are scarce.\n\nMethodsWe conducted a 4-week twice-weekly SARS-CoV-2 qPCR screening shortly after an mRNA vaccine booster in 368 healthcare workers. Spike-specific IgG levels and neutralization titers were determined at study start. qPCR-positive participants were sampled repeatedly for two weeks and monitored for symptoms.\n\nResultIn total 81 (cumulative incidence 22%) omicron infections were detected, divided between BA.1, BA.1.1 and BA.2. Increasing post-booster antibody titers were protective against infection (p<0.05), linked to reduced viral load (p<0.01) and time to viral clearance (p<0.05). Only 10% of infected participants remained asymptomatic through the course of their infection. Viral load peaked at day 3 and live virus could be detected for up to 9 days after first PCR-positive sample. Presence of symptoms correlated to elevated viral load (p<0.0001), but despite resolution of symptoms most participants showed Ct levels <30 at day 9. No significant differences were observed for viral load and time to viral clearance between BA.1, BA.1.1 and BA.2 infected individuals.\n\nConclusionWe report a high incidence of omicron infection despite recent booster vaccination in triple vaccinated individuals. Increasing levels of vaccine-induced spike-specific WT antibodies entail increased protection against infection and reduce viral load if infected. High viral load and secretion of live virus for up to nine days may facilitate transmission in a triple vaccinated population.", + "rel_num_authors": 16, "rel_authors": [ { - "author_name": "Daniel E. Platt", - "author_inst": "IBM Research, Yorktown Heights, NY" + "author_name": "Ulrika Marking", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" }, { - "author_name": "Aritra Bose", - "author_inst": "IBM Research, Yorktown Heights, NY" + "author_name": "Sebastian Havervall", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" }, { - "author_name": "Chaya Levovitz", - "author_inst": "IBM Research, Yorktown Heights, NY" + "author_name": "Nina Greilert Norin", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" }, { - "author_name": "Kahn Rhrissorrakrai", - "author_inst": "IBM Research, Yorktown Heights, NY" + "author_name": "Oscar Bladh", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Wanda Christ", + "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Max Gordon", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Henry Ng", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Kim Blom", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" + }, + { + "author_name": "Mia Phillipson", + "author_inst": "Department of Medical Cell Biology and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Sara Mangsbo", + "author_inst": "Department of Pharmacy and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Anna Smed-Sorensen", + "author_inst": "Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden." + }, + { + "author_name": "Peter Nilsson", + "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Sophia Hober", + "author_inst": "Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden" + }, + { + "author_name": "Mikael Aberg", + "author_inst": "Department of Medical Sciences, Clinical Chemistry and SciLifeLab, Uppsala University, Uppsala, Sweden" + }, + { + "author_name": "Jonas Klingstrom", + "author_inst": "Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden" }, { - "author_name": "LAXMI PARIDA", - "author_inst": "IBM Research, Yorktown Heights, NY" + "author_name": "Charlotte Thalin", + "author_inst": "Department of Clinical Sciences, Karolinska Institutet Danderyd Hospital, Stockholm, Sweden" } ], "version": "1", - "license": "cc_by", + "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" + "category": "infectious diseases" }, { "rel_doi": "10.1101/2022.03.31.22273111", @@ -340927,45 +341105,61 @@ "category": "health informatics" }, { - "rel_doi": "10.1101/2022.03.31.22273208", - "rel_title": "COVID-19 in people with neurofibromatosis 1, neurofibromatosis 2, or schwannomatosis", + "rel_doi": "10.1101/2022.03.31.22273262", + "rel_title": "Emulation of epidemics via Bluetooth-based virtual safe virus spread: experimental setup, software, and data", "rel_date": "2022-04-01", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273208", - "rel_abs": "PurposePeople with pre-existing conditions may be more susceptible to severe Coronavirus disease 2019 (COVID-19) when infected by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The relative risk and severity of SARS-CoV-2 infection in people with rare diseases like neurofibromatosis (NF) type 1 (NF1), neurofibromatosis type 2 (NF2), or schwannomatosis (SWN) is unknown.\n\nMethodsWe investigated the proportions of SARS-CoV-2 positive or COVID-19 patients in people with NF1, NF2, or SWN in the National COVID Collaborative Cohort (N3C) electronic health record dataset.\n\nResultsThe cohort sizes in N3C were 2,501 (NF1), 665 (NF2), and 762 (SWN). We compared these to N3C cohorts of other rare disease patients (98 - 9844 individuals) and the general non-NF population of 5.6 million. The site- and age-adjusted proportion of people with NF1, NF2, or SWN who tested positive for SARS-CoV-2 or were COVID-19 patients (collectively termed positive cases) was not significantly higher than in individuals without NF or other selected rare diseases. There were no severe outcomes reported in the NF2 or SWN cohorts. The proportion of patients experiencing severe outcomes was no greater for people with NF1 than in cohorts with other rare diseases or the general population.\n\nConclusionHaving NF1, NF2, or SWN does not appear to increase the risk of being SARS-CoV-2 positive or of being a COVID-19 patient, or of developing severe complications from SARS-CoV-2.", - "rel_num_authors": 8, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273262", + "rel_abs": "We describe an experimental setup and a currently running experiment for evaluating how physical interactions over time and between individuals affect the spread of epidemics. Our experiment involves the voluntary use of the Safe Blues Android app by participants at The University of Auckland (UoA) City Campus in New Zealand. The app spreads multiple virtual safe virus strands via Bluetooth depending on the social and physical proximity of the subjects. The evolution of the virtual epidemics is recorded as they spread through the population. The data is presented as a real-time (and historical) dashboard. A simulation model is applied to calibrate strand parameters. Participants locations are not recorded, but participants are rewarded based on the duration of participation within a geofenced area, and aggregate participation numbers serve as part of the data. Once the experiment is complete, the data will be made available as an open-source anonymized dataset.\n\nThis paper outlines the experimental setup, software, subject-recruitment practices, ethical considerations, and dataset description. The paper also highlights current experimental results in view of the lockdown that started in New Zealand at 23:59 on August 17, 2021. The experiment was initially planned in the New Zealand environment, expected to be free of COVID and lockdowns after 2020. However, a COVID Delta strain lockdown shuffled the cards and the experiment is currently extended into 2022.\n\nAuthor summaryIn this paper, we describe the Safe Blues Android app experimental setup and a currently running experiment at the University of Auckland City Campus. This experiment is designed to evaluate how physical interactions over time and between individuals affect the spread of epidemics.\n\nThe Safe Blues app spreads multiple virtual safe virus strands via Bluetooth based on the subjects unobserved social and physical proximity. The app does not record the participants locations, but participants are rewarded based on the duration of participation within a geofenced area, and aggregate participation numbers serve as part of the data. When the experiment is finished, the data will be released as an open-source anonymized dataset.\n\nThe experimental setup, software, subject recruitment practices, ethical considerations, and dataset description are all described in this paper. In addition, we present our current experimental results in view of the lockdown that started in New Zealand at 23:59 on August 17, 2021. The information we provide here may be useful to other teams planning similar experiments in the future.", + "rel_num_authors": 12, "rel_authors": [ { - "author_name": "Jineta Banerjee", - "author_inst": "Sage Bionetworks, Seattle, WA" + "author_name": "Azam Asanjarani", + "author_inst": "The University of Auckland" }, { - "author_name": "Jan M Friedman", - "author_inst": "University of British Columbia, Vancouver, BC" + "author_name": "Aminath Shausan", + "author_inst": "The University of Queensland" }, { - "author_name": "Laura J Klesse", - "author_inst": "University of Texas Southwestern Medical Center, Dallas, TX" + "author_name": "Keng Chew", + "author_inst": "The University of Queensland" }, { - "author_name": "Kaleb Yohay", - "author_inst": "Comprehensive Neurofibromatosis Center at NYU Langone Health, New York, NY" + "author_name": "Thomas Graham", + "author_inst": "The University of Queensland" }, { - "author_name": "Justin T Jordan", - "author_inst": "Massachusetts General Hospital, Boston, MA" + "author_name": "Kirsty R. Short", + "author_inst": "The University of Queensland" }, { - "author_name": "Scott Plotkin", - "author_inst": "Massachusetts General Hospital, Boston, MA" + "author_name": "Yoni Nazarathy", + "author_inst": "The University of Queensland" }, { - "author_name": "Robert J Allaway", - "author_inst": "Sage Bionetworks, Seattle, WA" + "author_name": "Shane G. Henderson", + "author_inst": "Cornell University" }, { - "author_name": "Jaishri O Blakeley", - "author_inst": "Johns Hopkins University School of Medicine, Baltimore, MD" + "author_name": "Hermanus M. Jansen", + "author_inst": "Delft University of Technology" + }, + { + "author_name": "Peter G. Taylor", + "author_inst": "The University of melbourne" + }, + { + "author_name": "Aapeli Vuorinen", + "author_inst": "Columbia University" + }, + { + "author_name": "Yuvraj Yadav", + "author_inst": "Indian Institute of Technology Delhi" + }, + { + "author_name": "Ilze Ziedins", + "author_inst": "The University of Auckland" } ], "version": "1", @@ -342873,35 +343067,67 @@ "category": "epidemiology" }, { - "rel_doi": "10.1101/2022.03.31.22273238", - "rel_title": "Size of societal volunteering predicts COVID-19 mortality", + "rel_doi": "10.1101/2022.03.31.22273226", + "rel_title": "Cross-talk between red blood cells and plasma influences blood flow and omics phenotypes in severe COVID-19", "rel_date": "2022-03-31", "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273238", - "rel_abs": "IntroductionDifferent countries responded differently to the COVID-19 pandemic in terms of timing and stringency of measures, and in types of policies adopted. Typically, policy makers tried to balance the capacity of healthcare systems to take care of the ill (as determined by ICU capacity, availability of nurses, etc.), with safeguarding economic output (preventing total lockdown of the labor force, etc.). Later on, also a broader array of considerations such as impact on schooling or the need for social contact were taken into account to varying degrees.\n\nThe broad and relatively fast availability of data on healthcare and economic capacity, together with the political estimate that these were the most critical determinants for maintaining societal structure and compliance with the measures taken, in many countries prioritized decision-making. What received far less attention, in part due to the difficulty of obtaining reliable data in a timely manner, was the opposite question: to what extent do societal structures - besides healthcare and economic systems - contribute to a countrys resilience during catastrophes such as the pandemic? While it is commonly understood that the impact of a pandemic goes beyond its death count, perhaps the death count itself is impacted by the way societies are structured.\n\nOne example of such societal structure is the contribution of volunteers during the COVID-19 response. Volunteers may contribute to well-functioning societies in different ways, both through practical actions (e.g. knitting face masks) as by strengthening societal cohesion (e.g. encouraging fellow citizens to comply with measures). This paper quantifies the association between COVID-19 mortality and the size of societal volunteering, using the unique context of the COVID-19 crisis with its intensity, sudden onset and global spread.", - "rel_num_authors": 4, + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273226", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and can affect multiple organs, among which is the circulatory system. Inflammation and mortality risk markers were previously detected in COVID-19 plasma and red blood cells (RBCs) metabolic and proteomic profiles. Additionally, biophysical properties, such as deformability, were found to be changed during the infection. Based on such data, we aim to better characterize RBC functions in COVID-19. We evaluate the flow properties of RBCs in severe COVID-19 patients admitted to the intensive care unit by using in vitro microfluidic techniques and automated methods, including artificial neural networks, for an unbiased RBC analysis. We find strong flow and RBC shape impairment in COVID-19 samples and demonstrate that such changes are reversible upon suspension of COVID-19 RBCs in healthy plasma. Vice versa, healthy RBCs immediately resemble COVID-19 RBCs when suspended in COVID-19 plasma. Proteomics and metabolomics analyses allow us to detect the effect of plasma exchanges on both plasma and RBCs and demonstrate a new role of RBCs in maintaining plasma equilibria at the expense of their flow properties. Our findings provide a framework for further investigations of clinical relevance for therapies against COVID-19 and possibly other infectious diseases.", + "rel_num_authors": 12, "rel_authors": [ { - "author_name": "Fritz Schiltz", - "author_inst": "Belgian Red Cross, Mechelen, Belgium" + "author_name": "Steffen M. Recktenwald", + "author_inst": "Saarland University" + }, + { + "author_name": "Greta Simionato", + "author_inst": "Saarland University" + }, + { + "author_name": "Marcelle G.M. Lopes", + "author_inst": "Cysmic GmbH" + }, + { + "author_name": "Fabia Gamboni", + "author_inst": "University of Colorado Denver" + }, + { + "author_name": "Monika Dzieciatkowska", + "author_inst": "University of Colorado Denver" + }, + { + "author_name": "Patrick Meybohm", + "author_inst": "University Hospital Wuerzburg" + }, + { + "author_name": "Kai Zacharowski", + "author_inst": "University Hospital Frankfurt" }, { - "author_name": "Hans Van Remoortel", - "author_inst": "Centre for Evidence-Based Practice, Belgian Red Cross, Mechelen, Belgium; Department of Public Health and Primary Care, Leuven Institute for Healthcare Policy, " + "author_name": "Andreas von Knethen", + "author_inst": "University Hospital Frankfurt" }, { - "author_name": "Hans Scheers", - "author_inst": "Centre for Evidence-Based Practice, Belgian Red Cross, Mechelen, Belgium; Department of Public Health and Primary Care, Leuven Institute for Healthcare Policy, " + "author_name": "Christian Wagner", + "author_inst": "saarland University" }, { - "author_name": "Philippe Vandekerckhove", - "author_inst": "Belgian Red Cross, Mechelen, Belgium; Department of Public Health and Primary Care, Leuven Institute for Healthcare Policy, KU Leuven, Leuven, Belgium; Centre f" + "author_name": "Lars Kaestner", + "author_inst": "Saarland University" + }, + { + "author_name": "Angelo D'Alessandro", + "author_inst": "University of Colorado Denver" + }, + { + "author_name": "Stephan Quint", + "author_inst": "Cysmic GmbH" } ], "version": "1", "license": "cc_by_nc_nd", "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" + "category": "hematology" }, { "rel_doi": "10.1101/2022.03.30.22273206", @@ -345474,6 +345700,199 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.29.22273120", + "rel_title": "Adherence to and enforcement of non-pharmaceutical interventions (NPIs) for COVID-19 prevention in Nigeria, Rwanda, and Zambia: A mixed-methods analysis", + "rel_date": "2022-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.29.22273120", + "rel_abs": "IntroductionIn the early parts of the COVID-19 pandemic, non-pharmaceutical interventions (NPIs) were implemented worldwide, including in sub-Saharan Africa, to prevent and control SARS-CoV-2 transmission. This mixed-methods study examines adherence to and enforcement of NPIs implemented to curb COVID-19 in Nigeria, Rwanda, and Zambia, leading up to the 10,000th case of laboratory-confirmed COVID-19 in each country. Additionally, we aim to evaluate the relationship between levels and changes of NPIs over time and changes in COVID-19 cases and deaths.\n\nMethodsThis mixed-methods analysis utilized semi-structured interviews and a quantitative dataset constructed using multiple open data sources, including the Oxford COVID-19 Government Response Tracker. To understand potential barriers and facilitators in implementing and enforcing NPIs qualitative data were collected from those involved in the COVID-19 response and analyzed using NVivo. Quantitative results were analyzed using descriptive statistics, plots, ANOVA, and post hoc Tukey.\n\nResultsIndividual indicator scores varied with the COVID-19 response in all three countries. Nigeria had sustained levels of strict measures for containment and closure NPIs, while in Rwanda there was substantial variation in NPI score as it transitioned through the different case windows for the same measures. Zambia implemented moderate stringency throughout the pandemic using gathering restrictions and business/school closure measures but maintained low levels of strictness for other containment and closure measures. Rwanda had far more consistent and stringent measures compared to Nigeria and Zambia. Rwandas success in implementing COVID-related measures was partly due to strong enforcement and having a population that generally obeys its government.\n\nConclusionVarious forces either facilitated or hindered adherence and compliance to COVID-19 control measures. This research highlights important lessons, including the need to engage communities early and create buy-in, as well as the need for preparation to ensure that response efforts are proactive rather than reactive when faced with an emergency.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hiwote Solomon", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Donald M. Thea", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Sandro Galea", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Lora L. Sabin", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Daniel R. Lucey", + "author_inst": "Georgetown University School of Medicine" + }, + { + "author_name": "Davidson H. Hamer", + "author_inst": "Boston University School of Public Health" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, + { + "rel_doi": "10.1101/2022.03.26.22272613", + "rel_title": "Persistent health issues, adverse events of significant concern, and effectiveness of COVID-19 vaccination- findings from a real-world cohort study of healthcare workers in north India", + "rel_date": "2022-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.26.22272613", + "rel_abs": "BackgroundThere is paucity of real-world data on COVID-19 vaccine effectiveness and safety from cohort designs. The current study aimed to evaluate vaccine performance during second wave in India. It also aimed to determine adverse events of significant concern (AESCs), and to ascertain the effect of vaccination on persistent health issues in individuals post COVID-19.\n\nMethodsA cohort study was conducted from July-2021 to December-2021 in a tertiary hospital of north India. The primary outcome was vaccine-effectiveness against COVID-19. Secondary outcomes were AESCs, and persistent health issues in those receiving vaccine. Regression analyses were performed to determine risk factors.\n\nResultsIn 2760 healthcare workers (HCWs) included, 1033 COVID-19 events were reported. Around 6-17% vaccine effectiveness was observed against COVID-19 occurrence. One dose-recipients were at 1.6-times increased risk of COVID-19. Prior SARS-CoV-2 infection was a strong independent protective factor against COVID-19 (aOR 0.66). Full vaccination reduced moderate-severe COVID-19 by 57%. Those with lung disease were at 2.5-times increased risk of moderate-severe COVID-19. AESCs were observed in 1.3% including one case each of myocarditis and severe hypersensitivity. Individuals with hypothyroidism were at 5-times and those receiving vaccine after recovery from COVID-19 were at 3-times higher risk of persistent health issues.\n\nConclusionCOVID-19 vaccination reduced COVID-19 severity but offered marginal protection against occurrence. Relationship of asthma and hypothyroidism with COVID-19 outcomes necessitates focused research. Independent protection of prior SARS-CoV-2 infection was high and persistent health issues were common in individuals receiving vaccine post COVID-19. Recommendations of vaccinating those recovered from COVID-19 need further studies.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Upinder Kaur", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Sapna Bala", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Aditi Joshi", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Noti Taruni Srija Reddy", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Chetan Japur", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Mayank Chauhan", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Nikitha Pedapanga", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Shubham Kumar", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Anurup Mukherjee", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Vaibhav Mishra", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Dolly Talda", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Rohit Singh", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Rohit Kumar Gupta", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Ashish Kumar Yadav", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Poonam Jyoti Rana", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Jyoti Srivastava", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Shobha Bhat K", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Anup Singh", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Naveen Kumar PG", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Manoj Pandey", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Kishor Patwardhan", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Sangeeta Kansal", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Sankha Shubhra Chakrabarti", + "author_inst": "Institute of Medical Sciences, Banaras Hindu University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2022.03.28.22273068", + "rel_title": "SARS-CoV-2 spike-binding antibody longevity and protection from re-infection with antigenically similar SARS-CoV-2 variants", + "rel_date": "2022-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.28.22273068", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe PARIS (Protection Associated with Rapid Immunity to SARS-CoV-2) cohort follows health care workers with and without documented coronavirus disease 2019 (COVID-19) since April 2020. We report our findings regarding SARS-CoV-2 spike binding antibody stability and protection from infection in the pre-variant era. We analyzed data from 400 healthcare workers (150 seropositive and 250 seronegative at enrollment) for a median of 84 days. The SARS-CoV-2 spike binding antibody titers were highly variable with antibody levels decreasing over the first three months, followed by a relative stabilization. We found that both more advanced age (>40 years) and female sex were associated with higher antibody levels (1.6-fold and 1.4-fold increases, respectively). Only six percent of the initially seropositive participants \"seroreverted\". We documented a total of 11 new SARS-CoV-2 infections (ten naive participants, one previously infected participant without detectable antibodies, p<0.01) indicating that spike antibodies limit the risk of re-infection. These observations, however, only apply to SARS-CoV-2 variants antigenically similar to the ancestral SARS-CoV-2 ones. In conclusion, SARS-CoV-2 antibody titers mounted upon infection are stable over several months in most people and provide protection from infection with antigenically similar viruses.\n\nsummaryThe levels of SARS-CoV-2 spike binding antibodies mounted upon infection with ancestral SARS-CoV-2 variants are highly variable, stabilize at an individual level after three months and provide protection from infection with homologous virus.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "John Kubale", + "author_inst": "University of Michigan School of Public Health" + }, + { + "author_name": "Charles R Gleason", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Juan Manuel Carre\u00f1o", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Komal Srivastava", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "- PARIS Study Team", + "author_inst": "" + }, + { + "author_name": "Aubree Gordon", + "author_inst": "University of Michigan" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Viviana Simon", + "author_inst": "Icahn School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.29.22273041", "rel_title": "Emerging Therapies for COVID-19: the value of information from more clinical trials", @@ -345513,6 +345932,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2022.03.29.486173", + "rel_title": "A mosaic-type trimeric RBD-based COVID-19 vaccine candidate induces potent neutralization against Omicron and other SARS-CoV-2 variants", + "rel_date": "2022-03-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.29.486173", + "rel_abs": "Large-scale populations in the world have been vaccinated with COVID-19 vaccines, however, breakthrough infections of SARS-CoV-2 are still growing rapidly due to the emergence of immune-evasive variants, especially Omicron. It is urgent to develop effective broad-spectrum vaccines to better control the pandemic of these variants. Here, we present a mosaic-type trimeric form of spike receptor-binding domain (mos-tri-RBD) as a broad-spectrum vaccine candidate, which carries the key mutations from Omicron and other circulating variants. Tests in rats showed that the designed mos-tri-RBD, whether used alone or as a booster shot, elicited potent cross-neutralizing antibodies against not only Omicron but also other immune-evasive variants. Neutralizing antibody titers induced by mos-tri-RBD were substantially higher than those elicited by homo-tri-RBD (containing homologous RBDs from prototype strain) or the inactivated vaccine BBIBP-CorV. Our study indicates that mos-tri-RBD is highly immunogenic, which may serve as a broad-spectrum vaccine candidate in combating SARS-CoV-2 variants including Omicron.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Jing Zhang", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Zi Bo Han", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Yu Liang", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Xue Feng Zhang", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Yu Qin Jin", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Li Fang Du", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Shuai Shao", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Hui Wang", + "author_inst": "Beijing Institute of Biological Products Company Limited" + }, + { + "author_name": "Jun Wei Hou", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Ke Xu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC)" + }, + { + "author_name": "Ze Hua Lei", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Zhao Ming Liu", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Jin Zhang", + "author_inst": "Beijing Institute of Biological Products Company Limited" + }, + { + "author_name": "Ya Nan Hou", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Ning Liu", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Fu Jie Shen", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Jin Juan Wu", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Xiang Zheng", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Xin Yu Li", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Xin Li", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Wei Jin Huang", + "author_inst": "National Institute for Food and Drug Control (NIFDC)" + }, + { + "author_name": "Gui Zhen Wu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC)" + }, + { + "author_name": "Ji Guo Su", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + }, + { + "author_name": "Qi Ming Li", + "author_inst": "National Vaccine and Serum Institute (NVSI)" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.29.486253", "rel_title": "Discovery of a druggable copper-signaling pathway that drives cell plasticity and inflammation", @@ -347732,173 +348262,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.03.24.22272915", - "rel_title": "Inconsistent directions of change in case severity across successive SARS-CoV-2 variant waves suggests an unpredictable future", - "rel_date": "2022-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.24.22272915", - "rel_abs": "ObjectiveTo determine how the severity of successively dominant SARS-CoV-2 variants changed over the course of the COVID-19 pandemic.\n\nDesignRetrospective cohort analysis.\n\nSettingCommunity- and hospital-sequenced COVID-19 cases in the NHS Greater Glasgow and Clyde (NHS GG&C) Health Board.\n\nParticipantsAll sequenced non-nosocomial adult COVID-19 cases in NHS GG&C infected with the relevant SARS-CoV-2 lineages during analysis periods. B.1.177/Alpha: 1st November 2020 - 30th January 2021 (n = 1640). Alpha/Delta: 1st April - 30th June 2021 (n = 5552). AY.4.2 Delta/non-AY.4.2 Delta: 1st July - 31st October 2021 (n = 9613). Non-AY.4.2 Delta/Omicron: 1st - 31st December 2021 (n = 3858).\n\nMain outcome measuresAdmission to hospital, ICU, or death within 28 days of positive COVID-19 test\n\nResultsFor B.1.177/Alpha, 300 of 807 B.1.177 cases were recorded as hospitalised or worse, compared to 232 of 833 Alpha cases. After adjustment, the cumulative odds ratio was 1.51 (95% CI: 1.08-2.11) for Alpha versus B.1.177. For Alpha/Delta, 113 of 2104 Alpha cases were recorded as hospitalised or worse, compared to 230 of 3448 Delta cases. After adjustment, the cumulative odds ratio was 2.09 (95% CI: 1.42-3.08) for Delta versus Alpha. For non-AY.4.2 Delta/AY.4.2 Delta, 845 of 8644 non-AY.4.2 Delta cases were recorded as hospitalised or worse, compared to 101 of 969 AY.4.2 Delta cases. After adjustment, the cumulative odds ratio was 0.99 (95% CI: 0.76-1.27) for AY.4.2 Delta versus non-AY.4.2 Delta. For non-AY.4.2 Delta/Omicron, 30 of 1164 non-AY.4.2 Delta cases were recorded as hospitalised or worse, compared to 26 of 2694 Omicron cases. After adjustment, the median cumulative odds ratio was 0.49 (95% CI: 0.22-1.06) for Omicron versus non-AY.4.2 Delta.\n\nConclusionsThe direction of change in disease severity between successively emerging SARS-CoV-2 variants of concern was inconsistent. This heterogeneity demonstrates that severity associated with future SARS-CoV-2 variants is unpredictable.", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "David J Pascall", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Elen Vink", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Rachel Blacow", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Naomi Bulteel", - "author_inst": "NHS Fife" - }, - { - "author_name": "Alasdair Campbell", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Robyn Campbell", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Sarah Clifford", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Chris Davis", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Ana da Silva Filipe", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Noha El Sakka", - "author_inst": "NHS Grampian" - }, - { - "author_name": "Ludmila Fjodorova", - "author_inst": "NHS Greater Glasgow and Clyde" - }, - { - "author_name": "Ruth Forrest", - "author_inst": "NHS Fife" - }, - { - "author_name": "Emily Goldstein", - "author_inst": "NHS Greater Glasgow and Clyde" - }, - { - "author_name": "Rory Gunson", - "author_inst": "NHS Greater Glasgow and Clyde" - }, - { - "author_name": "John Haughney", - "author_inst": "NHS Greater Glasgow and Clyde" - }, - { - "author_name": "Matthew TG Holden", - "author_inst": "Public Health Scotland" - }, - { - "author_name": "Patrick Honour", - "author_inst": "NHS Borders" - }, - { - "author_name": "Joseph Hughes", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Edward James", - "author_inst": "NHS Borders" - }, - { - "author_name": "Tim Lewis", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Oscar MacLean", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Martin McHugh", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Guy Mollett", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Tommy Nyberg", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Yusuke Onishi", - "author_inst": "NHS Grampian" - }, - { - "author_name": "Ben Parcell", - "author_inst": "University of Dundee" - }, - { - "author_name": "Surajit Ray", - "author_inst": "University of Glasgow" - }, - { - "author_name": "David L Robertson", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Shaun R Seaman", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Sharif Shabaan", - "author_inst": "Public Health Scotland" - }, - { - "author_name": "James G Shepherd", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Katherine Smollett", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Kate Templeton", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Elizabeth Wastnedge", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Craig Wilkie", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Thomas C Williams", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium", - "author_inst": "" - }, - { - "author_name": "Emma C Thomson", - "author_inst": "University of Glasgow" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.24.485591", "rel_title": "Antiviral roles of interferon regulatory factor (IRF)-1, 3 and 7 against human coronavirus infection", @@ -348083,6 +348446,145 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.23.485509", + "rel_title": "Autoantibody discovery across monogenic, acquired, and COVID19-associated autoimmunity with scalable PhIP-Seq", + "rel_date": "2022-03-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.23.485509", + "rel_abs": "Phage Immunoprecipitation-Sequencing (PhIP-Seq) allows for unbiased, proteome-wide autoantibody discovery across a variety of disease settings, with identification of disease-specific autoantigens providing new insight into previously poorly understood forms of immune dysregulation. Despite several successful implementations of PhIP-Seq for autoantigen discovery, including our previous work (Vazquez et al. 2020), current protocols are inherently difficult to scale to accommodate large cohorts of cases and importantly, healthy controls. Here, we develop and validate a high throughput extension of PhIP-seq in various etiologies of autoimmune and inflammatory diseases, including APS1, IPEX, RAG1/2 deficiency, Kawasaki Disease (KD), Multisystem Inflammatory Syndrome in Children (MIS-C), and finally, mild and severe forms of COVID19. We demonstrate that these scaled datasets enable machine-learning approaches that result in robust prediction of disease status, as well as the ability to detect both known and novel autoantigens, such as PDYN in APS1 patients, and intestinally expressed proteins BEST4 and BTNL8 in IPEX patients. Remarkably, BEST4 antibodies were also found in 2 patients with RAG1/2 deficiency, one of whom had very early onset IBD. Scaled PhIP-Seq examination of both MIS-C and KD demonstrated rare, overlapping antigens, including CGNL1, as well as several strongly enriched putative pneumonia-associated antigens in severe COVID19, including the endosomal protein EEA1. Together, scaled PhIP-Seq provides a valuable tool for broadly assessing both rare and common autoantigen overlap between autoimmune diseases of varying origins and etiologies.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Sara E Vazquez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sabrina A Mann", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Aaron Bodansky", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Andrew F Kung", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Zoe Quandt", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Elise M N Ferr\u00e9", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Nils Landegren", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Daniel Eriksson", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Paul Bastard", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Shen-Ying Zhang", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Jamin Liu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Anthea Mitchell", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Caleigh Mandel-Brehm", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Brenda Miao", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Gavin Sowa", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kelsey Zorn", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alice Y Chan", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Chisato Shimizu", + "author_inst": "UC San Diego Health System" + }, + { + "author_name": "Adriana Tremoulet", + "author_inst": "UC San Diego Health System" + }, + { + "author_name": "Kara Lynch", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Michael R Wilson", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Olle K\u00e4mpe", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Kerry Dobbs", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Ottavia M Delmonte", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Luigi D Notarangelo", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Jane C Burns", + "author_inst": "UC San Diego Health System" + }, + { + "author_name": "Jean-Laurent Casanova", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Michail S Lionakis", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Troy R Torgerson", + "author_inst": "Allen Institute for Immunology" + }, + { + "author_name": "Mark S Anderson", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Joseph L DeRisi", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.24.485734", "rel_title": "SARS-CoV-2 harnesses host translational shutoff and autophagy to optimize virus yields: The role of the envelope (E) protein", @@ -349170,85 +349672,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.24.22272870", - "rel_title": "Prognostic factors for mortality, ICU and hospital admission due to SARS-CoV-2: A systematic review and meta-analysis of cohort studies in Europe", - "rel_date": "2022-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.24.22272870", - "rel_abs": "BackgroundAs mortality from COVID-19 is strongly age-dependent, we aimed to identify population subgroups at an elevated risk for adverse outcomes from COVID-19 using age/gender-adjusted data from European cohort studies with the aim to identify populations that could potentially benefit from booster vaccinations.\n\nMethodsWe performed a systematic literature review and meta-analysis to investigate the role of underlying medical conditions as prognostic factors for adverse outcomes due to SARS-CoV-2, including death, hospitalisation, Intensive Care Unit (ICU) admission, and mechanical ventilation within three separate settings (community, hospital and ICU). Cohort studies that reported at least age and gender-adjusted data from Europe were identified through a search of peer-reviewed articles published until 11th June 2021 in Ovid Medline and Embase. Results are presented as Odds Ratios (ORs) with 95% confidence intervals (95%C.I.) and absolute risk differences (RD) in deaths per 1,000 COVID-19 patients.\n\nFindingsWe included 88 cohort studies with age/gender adjusted data from 6,653,207 SARS-CoV-2 patients from Europe. Hospital-based mortality was associated with high and moderate certainty evidence for solid organ tumours, diabetes mellitus, renal disease, arrhythmia, ischemic heart disease, liver disease, and obesity, while a higher risk, albeit with low certainty, was noted for chronic obstructive pulmonary disease and heart failure. Community-based mortality was associated with a history of heart failure, stroke, diabetes, and end-stage renal disease. Evidence of high/moderate certainty revealed a strong association between hospitalisation for COVID-19 and solid organ transplant recipients, sleep apnoea, diabetes, stroke, and liver disease.\n\nInterpretationThe results confirmed the strong association between specific prognostic factors and mortality and hospital admission. Prioritisation of booster vaccinations and the implementation of non-pharmaceutical protective measures for these populations may contribute to a reduction in COVID-19 mortality, ICU and hospital admissions.\n\nFundingEuropean Centre for Disease Prevention and Control (ECDC) under specific contract No. 10 ECD.11843 within Framework contract ECDC/2019/001 Lot 1B.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Constantine Vardavas", - "author_inst": "School of Medicine, University of Crete, Heraklion, Crete, Greece" - }, - { - "author_name": "Alexander G Mathioudakis", - "author_inst": "Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK" - }, - { - "author_name": "Katerina Nikitara", - "author_inst": "University of Crete" - }, - { - "author_name": "Kimon Stamatelopoulos", - "author_inst": "Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece" - }, - { - "author_name": "Georgios Georgiopoulos", - "author_inst": "Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece" - }, - { - "author_name": "Revati Phalkey", - "author_inst": "Centre for Evidence Based Healthcare, Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" - }, - { - "author_name": "Jo Leonardi-Bee", - "author_inst": "Centre for Evidence Based Healthcare, Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" - }, - { - "author_name": "Esteve Fernandez", - "author_inst": "Catalan Institute of Oncology, Barcelona, Spain" - }, - { - "author_name": "Dolors Carnicer-Pont", - "author_inst": "Catalan Institute of Oncology, Barcelona, Spain" - }, - { - "author_name": "Jorgen Vestbo", - "author_inst": "Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK" - }, - { - "author_name": "Jan C Semenza", - "author_inst": "European Centre for Disease Prevention and Control (ECDC), Sweden" - }, - { - "author_name": "Charlotte Deogan", - "author_inst": "European Centre for Disease Prevention and Control (ECDC), Sweden" - }, - { - "author_name": "Jonathan E Suk", - "author_inst": "European Centre for Disease Prevention and Control (ECDC), Sweden" - }, - { - "author_name": "Piotr Kramarz", - "author_inst": "European Centre for Disease Prevention and Control (ECDC), Sweden" - }, - { - "author_name": "Favelle Lamp", - "author_inst": "European Centre for Disease Prevention and Control (ECDC), Sweden" - }, - { - "author_name": "Pasi Penttinen", - "author_inst": "European Centre for Disease Prevention and Control (ECDC), Sweden" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.24.22272891", "rel_title": "Accuracy of COVID-19 self-tests with unsupervised nasal or nasal plus oropharyngeal self-sampling in symptomatic individuals in the Omicron period", @@ -349465,6 +349888,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.24.22272835", + "rel_title": "Relative Effectiveness of Four Doses Compared to Three Dose of the BNT162b2 Vaccine in Israel", + "rel_date": "2022-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.24.22272835", + "rel_abs": "ObjectivesThe rapid spread of the Omicron variant (B.1.1.529) alongside evidence of a relatively rapid waning of the third dose prompted Israel to administer a fourth dose of the BNT162b2 vaccine on January 2022. Thus far, sufficient real-world evidence demonstrating the effectiveness of a fourth dose against infection and severe COVID-19 are lacking. This study examined the short-term effectiveness of a fourth dose compared to three doses over the span of 10 weeks.\n\nDesignA retrospective test-negative case-control study, performing both a matched analysis and an unmatched multiple-tests analysis.\n\nSettingNationally centralized database of Maccabi Healthcare Services (MHS), an Israeli national health fund that covers 2.5 million people.\n\nParticipantsThe study population included 97,499 MHS members aged 60 or older who were eligible to receive a fourth vaccine dose and performed at least one PCR test during the study period. Of them, 27,876 received the fourth dose and 69,623 received only three doses.\n\nMain outcomes and measuresAnalyses focused on the period from January 10, 2022 (7 days after the fourth dose was first administered to eligible individuals) to March 13, 2022, an Omicron-dominant period in Israel. We evaluated two SARS-CoV-2-related outcomes: (1) breakthrough infection, defined as a positive PCR test performed 7 or more days after inoculation with the BNT162b2 vaccine; and (2) breakthrough infection resulting in a severe disease, defined as COVID-19-related hospitalization or COVID-19 associated mortality.\n\nResultsA fourth dose provided considerable additional protection against both SARS-CoV-2 infection and severe disease relative to three doses of the vaccine. However, vaccine effectiveness against infection varied over time, peaking during the third week with a VE of 64% (95% CI: 62.0%-65.9%) and declining to 29.2% (95% CI: 17.7%-39.1%) by the end of the 10-week follow-up period. Unlike VE against infection, the relative effectiveness of a fourth dose against severe COVID-19 was maintained at high level (>73%) throughout the 9-week follow-up period. Importantly, severe disease was a relatively rare event, occurring in <1% of both fourth dose and third dose only recipients.\n\nConclusionsA fourth dose of the BNT162b2 vaccine provided considerable additional protection against both SARS-CoV-2 infection and severe disease relative to three doses of the vaccine. However, effectiveness of the fourth dose against infection wanes sooner than that of the third dose.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sivan Gazit", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Yaki Saciuk", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Galit Perez", + "author_inst": "Maccabi health care servises" + }, + { + "author_name": "Asaf Peretz", + "author_inst": "Maccabi Healthcare Services" + }, + { + "author_name": "Virginia E. Pitzer", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Tal Patalon", + "author_inst": "Maccabi Healthcare Services" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.03.24.22272892", "rel_title": "The modified COVID-19 Yorkshire Rehabilitation Scale (C19-YRSm) patient-reported outcome measure for Long Covid or Post-COVID syndrome", @@ -351020,53 +351482,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.22.22272775", - "rel_title": "Risk of death following SARS-CoV-2 infection or COVID-19 vaccination in young people in England: a self-controlled case series study", - "rel_date": "2022-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.22.22272775", - "rel_abs": "ObjectivesTo assess whether there is a change in the incidence of cardiac and all-cause death in young people following COVID-19 vaccination or SARS-CoV-2 infection in unvaccinated individuals.\n\nDesignSelf-controlled case series.\n\nSettingNational, linked electronic health record data in England.\n\nStudy populationIndividuals aged 12-29 who had received at least one dose of COVID-19 vaccination and died between 8 December 2020 and 2 February 2022 and registered by 16 February 2022 within 12 weeks of COVID-19 vaccination; Individuals aged 12-29 who died within 12 weeks of testing positive for SARS-CoV-2.\n\nMain outcome measuresCardiac and all-cause deaths occurring within 12 weeks of vaccination or SARS-CoV-2 infection.\n\nResultsCompared to the baseline period, there was no evidence of a change in the incidence of cardiac death in the six weeks after vaccination, whether for each of weeks 1 to 6 or the whole six-week period. There was a decrease in the risk of all-cause death in the first week after vaccination and no change in each of weeks 2 to 6 after vaccination or whole six-week period after vaccination. Subgroup analyses by sex, age, vaccine type, and last dose also showed no change in the risk of death in the first six weeks after vaccination. There was a large increase in the incidence of cardiac and all-cause death in the overall risk period after SARS-CoV-2 infection among the unvaccinated.\n\nConclusionThere is no evidence of an association between COVID-19 vaccination and an increased risk of death in young people. By contrast, SARS-CoV-2 infection was associated with substantially higher risk of cardiac related death and all-cause death.\n\nWhat is already known on this topicSeveral studies have highlighted the association between COVID-19 vaccination and the risk of myocarditis, myopericarditis, and other cardiac problems, especially in young people, but associated risk of mortality is unclear. Since younger people have lower risk of COVID-19 hospitalisation and mortality, the mortality risk associated with vaccination is potentially more important to them in balancing the risk and benefit of vaccination.\n\nWhat this study addsAlthough there is a risk of myocarditis or myopericarditis with COVID-19, there is no evidence of increased risk of cardiac or all-cause mortality following COVID-19 vaccination in young people aged 12 to 29. Given the increased risk of mortality following SARS-CoV-2 infection in this group, the risk-benefit analysis favours COVID-19 vaccination for this age group.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Vahe Nafilyan", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Charlotte Bermingham", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Isobel L Ward", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Jasper Morgan", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Francesco Zaccardi", - "author_inst": "Real World Evidence Unit, Diabetes Research Centre, University of Leicester" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "Real World Evidence Unit, Diabetes Research Centre, University of Leicester" - }, - { - "author_name": "Julie Stanborough", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Amitava Banerjee", - "author_inst": "Institute of Health Informatics, University College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.22.22272730", "rel_title": "Research on the Emotions of Uninfected People during the COVID-19 Epidemic in China", @@ -351463,6 +351878,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.23.22272804", + "rel_title": "Waning effectiveness of BNT162b2 and ChAdOx1 COVID-19 vaccines over six months since second dose: a cohort study using linked electronic health records", + "rel_date": "2022-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.23.22272804", + "rel_abs": "BackgroundThe rate at which COVID-19 vaccine effectiveness wanes over time is crucial for vaccination policies, but is incompletely understood with conflicting results from different studies.\n\nMethodsThis cohort study, using the OpenSAFELY-TPP database and approved by NHS England, included individuals without prior SARS-CoV-2 infection assigned to vaccines priority groups 2-12 defined by the UK Joint Committee on Vaccination and Immunisation. We compared individuals who had received two doses of BNT162b2 or ChAdOx1 with unvaccinated individuals during six 4-week comparison periods, separately for subgroups aged 65+ years; 16-64 years and clinically vulnerable; 40-64 years and 18-39 years. We used Cox regression, stratified by first dose eligibility and geographical region and controlled for calendar time, to estimate adjusted hazard ratios (aHRs) comparing vaccinated with unvaccinated individuals, and quantified waning vaccine effectiveness as ratios of aHRs per-4-week period. The outcomes were COVID-19 hospitalisation, COVID-19 death, positive SARS-CoV-2 test, and non-COVID-19 death.\n\nFindingsThe BNT162b2, ChAdOx1 and unvaccinated groups comprised 1,773,970, 2,961,011 and 2,433,988 individuals, respectively. Waning of vaccine effectiveness was similar across outcomes and vaccine brands: e.g. in the 65+ years subgroup ratios of aHRs versus unvaccinated for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test ranged from 1.23 (95% CI 1.15-1.32) to 1.27 (1.20-1.34) for BNT162b2 and 1.16 (0.98-1.37) to 1.20 (1.14-1.27) for ChAdOx1. Despite waning, rates of COVID-19 hospitalisation and COVID-19 death were substantially lower among vaccinated individuals compared to unvaccinated individuals up to 26 weeks after second dose, with estimated aHRs <0.20 (>80% vaccine effectiveness) for BNT162b2, and <0.26 (>74%) for ChAdOx1. By weeks 23-26, rates of SARS-CoV-2 infection in fully vaccinated individuals were similar to or higher than those in unvaccinated individuals: aHRs ranged from 0.85 (0.78-0.92) to 1.53 (1.07-2.18) for BNT162b2, and 1.21 (1.13-1.30) to 1.99 (1.94-2.05) for ChAdOx1.\n\nInterpretationThe rate at which estimated vaccine effectiveness waned was strikingly consistent for COVID-19 hospitalisation, COVID-19 death and positive SARS-CoV-2 test, and similar across subgroups defined by age and clinical vulnerability. If sustained to outcomes of infection with the Omicron variant and to booster vaccination, these findings will facilitate scheduling of booster vaccination doses.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Elsie MF Horne", + "author_inst": "University of Bristol" + }, + { + "author_name": "William J Hulme", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Ruth H Keogh", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Tom M Palmer", + "author_inst": "University of Bristol" + }, + { + "author_name": "Elizabeth J Williamson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Edward PK Parker", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Amelia Green", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Venexia Walker", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alex J Walker", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Helen Curtis", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Louis Fisher", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Brian MacKenna", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Richard Croker", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Lisa Hopcroft", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Robin Y Park", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Jon Massey", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Jessica Morely", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Amir Mehrkar", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Sebastian Bacon", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "David Evans", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Peter Inglesby", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Caroline E Morton", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "George Hickman", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Simon Davy", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Tom Ward", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Iain Dillingham", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Ben Goldacre", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Miguel A Hernan", + "author_inst": "Harvard University" + }, + { + "author_name": "Jonathan AC Sterne", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.21.22272358", "rel_title": "Undiagnosed COVID-19 in households with a child with mitochondrial disease", @@ -352898,65 +353444,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2022.03.18.484814", - "rel_title": "Immune and Clotting Dysfunction Detected in Saliva and Blood Plasma after COVID-19.", - "rel_date": "2022-03-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.18.484814", - "rel_abs": "A growing number of studies indicate that coronavirus disease 2019 (COVID-19) is associated with inflammatory sequelae, but molecular signatures governing the normal vs. pathologic convalescence process have not been well-delineated. We characterized global immune and proteome responses in matched plasma and saliva samples obtained from COVID-19 patients collected between 4-6 weeks after initial clinical symptoms resolved. Convalescent subjects showed robust IgA and IgG responses and positive antibody correlations between matched saliva and plasma samples. However, global shotgun proteomics revealed persistent inflammatory patterns in convalescent samples including dysfunction of salivary innate immune cells and clotting factors in plasma (e.g., fibrinogen and antithrombin), with positive correlations to acute COVID-19 disease severity. Saliva samples were characterized by higher concentrations of IgA, and proteomics showed altered pathways that correlated positively with IgA levels. Our study positions saliva as a viable fluid to monitor immunity beyond plasma to document COVID-19 immune, inflammatory, and coagulation-related sequelae.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Hyesun Jang", - "author_inst": "J Craig Venter Institute" - }, - { - "author_name": "Saibyasachi Choudhury", - "author_inst": "DGG-Genomics Division, Agilent, Technologies, Inc., La Jolla, CA 92037" - }, - { - "author_name": "Yanbao Yu", - "author_inst": "Department of Chemistry & Biochemistry, University of Delaware, Newark, DE, USA, 19716" - }, - { - "author_name": "Benjamin L. Sievers", - "author_inst": "Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, and Rockville, MD, USA" - }, - { - "author_name": "Terri Gelbart", - "author_inst": "Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, and Rockville, MD, USA" - }, - { - "author_name": "Harinder Singh", - "author_inst": "Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, and Rockville, MD, USA" - }, - { - "author_name": "Stephen A. Rawlings", - "author_inst": "MMP Adult Infectious Disease, Maine Medical Center, South Portland, ME, 04106" - }, - { - "author_name": "Amy Proal", - "author_inst": "PolyBio Research Foundation" - }, - { - "author_name": "Gene S. Tan", - "author_inst": "Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, and Rockville, MD, USA, Division of Infectious Diseases and Global Public Hea" - }, - { - "author_name": "Davey Smith", - "author_inst": "Division of Infectious Diseases and Global Public Health Department of Medicine, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Marcelo Freire", - "author_inst": "Genomic Medicine and Infectious Diseases, J. Craig Venter Institute, La Jolla, CA, and Rockville, MD, USA, Division of Infectious Diseases and Global Public Hea" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.03.21.485084", "rel_title": "SARS-CoV-2 Omicron spike H655Y mutation is responsible for enhancement of the endosomal entry pathway and reduction of cell surface entry pathway", @@ -353165,6 +353652,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.21.485157", + "rel_title": "Stability and expression of SARS-CoV-2 spike-protein mutations", + "rel_date": "2022-03-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.21.485157", + "rel_abs": "Protein fold stability likely plays a role in SARS-CoV-2 S-protein evolution, together with ACE2 binding and antibody evasion. While few thermodynamic stability data are available for S-protein mutants, many systematic experimental data exist for their expression. In this paper, we explore whether such expression levels relate to the thermodynamic stability of the mutants. We studied mutation-induced SARS-CoV-2 S-protein fold stability, as computed by three very distinct methods and eight different protein structures to account for method- and structure-dependencies. For all methods and structures used (24 comparisons), computed stability changes correlate significantly (99% confidence level) with experimental yeast expression from the literature, such that higher expression is associated with relatively higher fold stability. Also significant, albeit weaker, correlations were seen for ACE2 binding. The effect of thermodynamic fold stability may be direct or a correlate of amino acid or site properties, notably the solvent exposure of the site. Correlation between computed stability and experimental expression and ACE2 binding suggests that functional properties of the SARS-CoV-2 S-protein mutant space are largely determined by a few simple features, due to underlying correlations. Our study lends promise to the development of computational tools that may ideally aid in understanding and predicting SARS-CoV-2 S-protein evolution.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kristoffer T Baek", + "author_inst": "Technical University of Denmark" + }, + { + "author_name": "Rukmankesh Mehra", + "author_inst": "Indian Institute of Technology Bhilai" + }, + { + "author_name": "Kasper Planeta Kepp", + "author_inst": "Technical University of Denmark" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.03.20.485044", "rel_title": "Robust and durable prophylactic protection conferred by RNA interference in preclinical models of SARS-CoV-2", @@ -355096,69 +355610,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.03.18.484843", - "rel_title": "COVID-19 patients have increased levels of membrane-associated and soluble CD48", - "rel_date": "2022-03-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.18.484843", - "rel_abs": "COVID-19 is a respiratory-centered systemic disorder caused by SARS-CoV-2. The disease can progress into a severe form causing acute lung injury.\n\nCD48 is a co-signaling receptor, existing as both membrane-bound and soluble forms reported to be dysregulated in several inflammatory conditions. Therefore, we reasoned that CD48 could be deregulated in COVID-19 as well.\n\nHere we analyzed CD48 expression in autoptic sections and peripheral blood leukocytes and sera of COVID-19 patients by gene expression profiling (HTG(R) autoimmune panel), immunohistochemistry, flow cytometry and ELISA.\n\nLung tissue of COVID-19 patients showed increased CD48 mRNA expression and infiltration of CD48+ lymphocytes. In the peripheral blood, mCD48 was considerably increased on all evaluated cells, and additionally, sCD48 levels were significantly higher in COVID-19 patients independently of disease severity. Considering the alterations of mCD48 and sCD48, a specific role for CD48 in COVID-19 can be assumed, suggesting it as a potential target for therapy.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Hadas Pahima", - "author_inst": "The Hebrew University of Jerusalem Jerusalem, Israel" - }, - { - "author_name": "Ilan Zaffran", - "author_inst": "The Hebrew University of Jerusalem Jerusalem, Israel" - }, - { - "author_name": "Eli Ben-Chetrit", - "author_inst": "Shaare Zedek Medical Center and The Hebrew University of Jerusalem Jerusalem, Israel" - }, - { - "author_name": "Amir Jarjoui", - "author_inst": "Shaare Zedek Medical Center and The Hebrew University of Jerusalem Jerusalem, Israel" - }, - { - "author_name": "Pratibha Gaur", - "author_inst": "The Hebrew University of Jerusalem Jerusalem, Israel" - }, - { - "author_name": "Maria Laura Manca", - "author_inst": "University of Pisa" - }, - { - "author_name": "Dana Reichmann", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Efrat Orenbuch-Harroch", - "author_inst": "Hadassah-Hebrew University Medical Center, Ein Kerem Campus" - }, - { - "author_name": "Ilaria Puxeddu", - "author_inst": "University of Pisa" - }, - { - "author_name": "Carl Zinner", - "author_inst": "University Hospital Basel" - }, - { - "author_name": "Alexandar Tzankov", - "author_inst": "University Hospital Basel" - }, - { - "author_name": "Francesca Levi-Schaffer", - "author_inst": "The Hebrew University of Jerusalem Jerusalem, Israel" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.03.16.22271361", "rel_title": "Hospital length of stay in a mixed Omicron and Delta epidemic in New South Wales, Australia", @@ -355399,6 +355850,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.16.22272527", + "rel_title": "Severe Acute Respiratory Coronavirus-2 Antibody and T cell response after a third vaccine dose in hemodialysis patients compared with healthy controls", + "rel_date": "2022-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.16.22272527", + "rel_abs": "1.Hemodialysis patients (HD patients) have a high health risk from Severe Acute Respiratory Coronavirus-2 (SARS-CoV-2) infection. In this study, we assess the impact of a third vaccine dose (3D) on antibody levels and T cell response in HD patients and compare the results to those of a healthy control group.\n\nWe conducted a prospective cohort study consisting of 60 HD patients and 65 healthy controls. All of them received two doses of the Comirnaty mRNA vaccine and a third mRNA vaccine dose (Spikevax or Comirnaty). The SARS-CoV-2 S antibody response in all participants was measured 6 months after the second vaccine dose and 6 to 8 weeks after administration of the 3D. We also assessed INF-{gamma} secretion 6-8 weeks after the 3D in 24 healthy controls, 17 HD patients with a normal and 20 HD patients with a low or no antibody response after the second dose. The groups were compared using univariate quantile regressions and multiple analyses. The adverse effects of vaccines were assessed via a questionnaire.\n\nAfter the 3D, the SARS-CoV-2-specific antibody and INF-{gamma} titers of most HD patients were comparable to those of healthy controls. A subgroup of HD patients who had shown a diminished antibody response after the first two vaccine doses developed a significantly lower antibody and INF-{gamma} response compared to responder HD patients and controls, even after the 3D. A new strategy is needed to protect this patient group from severe COVID-19 infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Benedikt Simon", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Harald Rubey", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Martin Gromann", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Astrid Knop-Voelkerer", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Boris Hemedi", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Sonja Zehetmayer", + "author_inst": "MedUni Wien" + }, + { + "author_name": "Bernhard Kirsch", + "author_inst": "LK Mistelbach" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2022.03.17.22272589", "rel_title": "A multiplexed Cas13-based assay with point-of-care attributes for simultaneous COVID-19 diagnosis and variant surveillance", @@ -357034,125 +357528,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2022.03.16.22272467", - "rel_title": "Selective visuoconstructional impairment following mild COVID-19 with inflammatory and neuroimaging correlation findings.", - "rel_date": "2022-03-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.16.22272467", - "rel_abs": "People recovered from COVID-19 may still present complications including respiratory and neurological sequelae. In other viral infections, cognitive impairment occurs due to brain damage or dysfunction caused by vascular lesions and inflammatory processes. Persistent cognitive impairment compromises daily activities and psychosocial adaptation. Some level of neurological and psychiatric consequences were expected and described in severe cases of COVID-19. However, it is debatable whether neuropsychiatric complications are related to COVID-19 or to unfoldings from a severe infection. Nevertheless, the majority of cases recorded worldwide were mild to moderate self-limited illness in non-hospitalized people. Thus, it is important to understand what are the implications of mild COVID-19, which is the largest and understudied pool of COVID-19 cases. We aimed to investigate adults at least four months after recovering from mild COVID-19, which were assessed by neuropsychological, ocular and neurological tests, immune markers assay, and by structural MRI and 18FDG-PET neuroimaging to shed light on putative brain changes and clinical correlations. In approximately one-quarter of mild-COVID-19 individuals, we detected a specific visuoconstructive deficit, which was associated with changes in molecular and structural brain imaging, and correlated with upregulation of peripheral immune markers. Our findings provide evidence of neuroinflammatory burden causing cognitive deficit, in an already large and growing fraction of the world population. While living with a multitude of mild COVID-19 cases, action is required for a more comprehensive assessment and follow-up of the cognitive impairment, allowing to better understand symptom persistence and the necessity of rehabilitation of the affected individuals.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "JONAS JARDIM DE PAULA", - "author_inst": "UFMG" - }, - { - "author_name": "Rachel Elisa Rodrigues Pereira de Paiva", - "author_inst": "CTMM-Universidade Federal de Minas Gerais" - }, - { - "author_name": "Nathalia Gualberto Souza e Silva", - "author_inst": "CTMM - Universidade Federal de Minas Gerais" - }, - { - "author_name": "Daniela Valadao Freitas Rosa", - "author_inst": "Centro de Tecnologia em Medicina Molecular (CTMM), Universidade Federal de Minas Gerais (UFMG)" - }, - { - "author_name": "Fabio Luiz de Souza Duran", - "author_inst": "Departamento de Psiquiatria. Faculdade de Medicina da USP" - }, - { - "author_name": "Roney Santos Coimbra", - "author_inst": "Neurogenomica / Imunopatologia. Instituto Rene Rachou, Fiocruz" - }, - { - "author_name": "Danielle de Souza Costa", - "author_inst": "Centro de Tecnologia em Medicina Molecular (CTMM), Universidade Federal de Minas Gerais (UFMG)" - }, - { - "author_name": "Pedro Robles Dutenhefner", - "author_inst": "Centro de Tecnologia em Medicina Molecular (CTMM), Universidade Federal de Minas Gerais (UFMG)" - }, - { - "author_name": "Henrique Soares Dutra Oliveira", - "author_inst": "Universidade Federal de Minas Gerais (UFMG)" - }, - { - "author_name": "Sarah Teixeira Camargos", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Herika Martins Vasconcelos", - "author_inst": "Centro de Tecnologia em Medicina Molecular (CTMM), Universidade Federal de Minas Gerais (UFMG)" - }, - { - "author_name": "Nara de Oliveira Carvalho", - "author_inst": "Nucleo de Acoes e Pesquisa em Apoio Diagnostico (NUPAD). Faculdade de Medicina da Universidade Federal de Minas Gerais (UFMG)" - }, - { - "author_name": "Juliana Batista Silva", - "author_inst": "Centro de Desenvolvimento da Tecnologia Nuclear" - }, - { - "author_name": "Marina Bicalho Silveira", - "author_inst": "Centro de Desenvolvimento da Tecnologia Nuclear" - }, - { - "author_name": "Carlos Malamut", - "author_inst": "Centro de Desenvolvimento da Tecnologia Nuclear" - }, - { - "author_name": "Derick Matheus Oliveira", - "author_inst": "Universidade Federal de Minas Gerais (UFMG)" - }, - { - "author_name": "Luiz Carlos Molinari", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Danilo Bretas de Oliveira", - "author_inst": "Universidade Federal dos Vales do Jequitinhonha e Mucuri" - }, - { - "author_name": "Jose Nelio Januario", - "author_inst": "(NUPAD). Faculdade de Medicina da Universidade Federal de Minas Gerais (UFMG)" - }, - { - "author_name": "Luiciana Costa Silva", - "author_inst": "Instituto Hermes Pardini" - }, - { - "author_name": "Luiz Armando De Marco", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Dulciene M.M Queiroz", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Wagner Meira Jr.", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Geraldo Busatto", - "author_inst": "Departamento de Psiquiatria. Faculdade de Medicina da USP" - }, - { - "author_name": "Debora Marques de Miranda", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Marco Aurelio Romano-Silva", - "author_inst": "Universidade Federal de Minas Gerais" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2022.03.16.22272515", "rel_title": "Did national holidays accelerate COVID-19 diffusion in Bangladesh? A case study", @@ -357321,6 +357696,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.03.14.22272342", + "rel_title": "Tongue Coating in COVID-19 Patients: A Case-Control Study", + "rel_date": "2022-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272342", + "rel_abs": "It has been suggested that COVID-19 patients have distinct tongue features, which may help to monitor the development of their condition. To determine if there was any specific tongue coating feature in COVID-19, this study investigated the difference in tongue coating between COVID-19 subjects and subjects with other acute inflammatory diseases characterized by fever. Tongue images taken with smartphones from three age-matched groups, namely, COVID group (n=92), non-COVID febrile group (n=92), and normal control group (n=92), were analyzed by two blinded raters according to a tongue coating scoring scheme, which assessed the levels of thick fur, slimy or greasy fur, discolored fur and composite index of tongue coating. Compared with control, significant increases in all coating indexes were found in the COVID group (P<0.001), as well as in the non-COVID febrile group (P<0.001). However, no difference was observed between COVID and non-COVID febrile groups for all coating indexes measured. In COVID-19 subjects, their scores of coating indexes had weak but significant correlations with certain inflammatory biomarkers, including WBC and neutrophil - lymphocyte ratio. It is concluded that COVID-19 subjects have pathological tongue coating patterns that are associated with inflammatory responses, and these coating patterns can help to indicate the direction of disease development.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Zhi Chun Wang", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Xi Hong Cai", + "author_inst": "The Third Affiliated Hospital of Guangzhou University of Chinese Medicine" + }, + { + "author_name": "Jeremy Chan", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Yi Yi Chan", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Xiaotong Chen", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ching Wan Cheng", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Donghui Huang", + "author_inst": "Guangdong Provincial Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Luqi Huang", + "author_inst": "China Academy of Chinese Medical Sciences" + }, + { + "author_name": "Bei-ni Lao", + "author_inst": "Second Clinical Medical College of Guangzhou University of Chinese Medicine: The Second Affiliated Hospital of Guangzhou University of Chinese Medicine" + }, + { + "author_name": "Xu-sheng Liu", + "author_inst": "Guangdong Hospital of Traditional Chinese Medicine: Guangdong Provincial Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Aiping Lyu", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Wenliang Lv", + "author_inst": "China Academy of Chinese Medical Sciences" + }, + { + "author_name": "Huixian Wang", + "author_inst": "Guangdong Provincial Hospital of Traditional Chinese Medicine" + }, + { + "author_name": "Helen Zhang", + "author_inst": "Hong Kong Northern District Hospital" + }, + { + "author_name": "Xuebin Zhang", + "author_inst": "Hong Kong Baptist University" + }, + { + "author_name": "Shi Ping Zhang", + "author_inst": "Hong Kong Baptist University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.17.22272535", "rel_title": "Comparison of the 2021 COVID-19 'Roadmap' Projections against Public Health Data", @@ -358724,57 +359178,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.03.15.484439", - "rel_title": "Neutrophils initiate the destruction of the olfactory epithelium during SARS-CoV-2 infection in hamsters", - "rel_date": "2022-03-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.15.484439", - "rel_abs": "The loss of smell related to SARS-CoV-2 infection is one of the most prevalent symptoms of COVID-19. It is now clear that this symptom is related to the massive infection by SARS-CoV-2 of the olfactory epithelium leading to its desquamation. However, the molecular mechanism behind the destabilization of the olfactory epithelium is less clear. Using golden Syrian hamster, we show here that while apoptosis remains at a low level in damaged infected epithelium, the latter is invaded by innate immunity cells. By depleting the neutrophil population or blocking the activity of neutrophil elastase-like proteinases, we reduced the damage induced by the SARS-CoV-2 infection. Surprisingly, the impairment of neutrophil activity led to a decrease of SARS-CoV-2 infection levels in the nasal cavity. Our results indicate a counterproductive role of neutrophils leading to the release of infected cells in the lumen of the nasal cavity and thereby enhanced spreading of the virus.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Clara Bourgon", - "author_inst": "INRAe" - }, - { - "author_name": "Audrey Saint-Albin-Deliot", - "author_inst": "INRAe" - }, - { - "author_name": "Ophelie Ando-Grard", - "author_inst": "INRAe" - }, - { - "author_name": "Bruno Da-Costa", - "author_inst": "INRAe" - }, - { - "author_name": "Roxane Domain", - "author_inst": "INSERM" - }, - { - "author_name": "Brice Korkmaz", - "author_inst": "INSERM" - }, - { - "author_name": "Bernard Klonjkowski", - "author_inst": "ENVA" - }, - { - "author_name": "Sophie Lepoder", - "author_inst": "ENVA" - }, - { - "author_name": "Nicolas Meunier", - "author_inst": "INRAe" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.03.15.22272348", "rel_title": "The impact of COVID-19 on pregnant and recently pregnant women in Malawi: A national facility-based cohort", @@ -359007,6 +359410,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.14.22272368", + "rel_title": "Area-level social and structural inequalities determine mortality related to COVID-19 diagnosis in Ontario, Canada: a population-based explanatory modeling study of 11.8 million people", + "rel_date": "2022-03-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272368", + "rel_abs": "ImportanceSocial determinants of health (SDOH) play an important role in COVID-19 outcomes. More research is needed to quantify this relationship and understand the underlying mechanisms.\n\nObjectivesTo examine differential patterns in COVID-19-related mortality by area-level SDOH accounting for confounders; and to compare these patterns to those for non-COVID-19 mortality, and COVID-19 case fatality (COVID-19-related death among those diagnosed).\n\nDesign, setting, and participantsPopulation-based retrospective cohort study including all community living individuals aged 20 years or older residing in Ontario, Canada, as of March 1, 2020 who were followed through to March 2, 2021.\n\nExposureSDOH variables derived from the 2016 Canada Census at the dissemination area-level including: median household income; educational attainment; proportion of essential workers, racialized groups, recent immigrants, apartment buildings, and high-density housing; and average household size.\n\nMain outcomes and measuresCOVID-19-related death was defined as death within 30 days following, or 7 days prior to a positive SARS-CoV-2 test. Cause-specific hazard models were employed to examine the associations between SDOH and COVID-19-related mortality, treating non-COVID-19 mortality as a competing risk.\n\nResultsOf 11,810,255 individuals included, 3,880 (0.03%) died related to COVID-19 and 88,107 (0.75%) died without a positive test. After accounting for demographics, baseline health, and other SDOH, the following SDOH were associated with increased hazard of COVID-19-related death (hazard ratios [95% confidence intervals]) comparing the most to least vulnerable group): lower income (1.30[1.09-1.54]), lower educational attainment (1.27[1.10-1.47]), higher proportion essential workers (1.28[1.10-1.50]), higher proportion racialized groups (1.42[1.16-1.73]), higher proportion apartment buildings (1.25[1.11-1.41]), and larger vs. medium household size (1.30[1.13-1.48]). In comparison, areas with higher proportion racialized groups were associated with a lower hazard of non-COVID-19 mortality (0.88[0.85-0.92]). With the exception of income, SDOH were not independently associated with COVID-19 case fatality.\n\nConclusions and relevanceArea-level social and structural inequalities determine COVID-19-related mortality after accounting for individual demographic and clinical factors. COVID-19 has reversed the pattern of lower non-COVID-19 mortality by racialized groups. Pandemic responses should include prioritized and community-tailored intervention strategies to address SDOH that mechanistically underpin disproportionate acquisition and transmission risks and shape barriers to the reach of, and access to prevention interventions.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSAre area-level social determinants of health factors independently associated with coronavirus disease 2019 (COVID-19)-related mortality after accounting for demographics and clinical factors?\n\nFindingsIn this population-based cohort study including 11.8 million adults residing in Ontario, Canada and 3,880 COVID-19-related death occurred between Mar 1, 2020 and Mar 2, 2021, we found that areas characterized by lower SES (including lower income, lower educational attainment, and higher proportion essential workers), greater ethnic diversity, more apartment buildings, and larger vs. medium household size were associated with increased hazard of COVID-19-related mortality compared to their counterparts, even after accounting for individual-level demographics, baseline health, and other area-level SDOH.\n\nMeaningPandemic responses should include prioritized and community-tailored intervention strategies to address SDOH that mechanistically underpin inequalities in acquisition and transmission risks, and in the reach of, and access to prevention interventions.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Linwei Wang", + "author_inst": "Unity Health Toronto" + }, + { + "author_name": "Andrew Calzavara", + "author_inst": "ICES" + }, + { + "author_name": "Stefan Baral", + "author_inst": "JHSPH" + }, + { + "author_name": "Janet Smylie", + "author_inst": "University of Toronto" + }, + { + "author_name": "Adrienne K Chan", + "author_inst": "University of Toronto" + }, + { + "author_name": "Beate Sander", + "author_inst": "University Health Network" + }, + { + "author_name": "Peter C Austin", + "author_inst": "ICES" + }, + { + "author_name": "Jeff C Kwong", + "author_inst": "ICES" + }, + { + "author_name": "Sharmistha Mishra", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.14.22272359", "rel_title": "Biomarkers Selection for Population Normalization in SARS-CoV-2 Wastewater-based Epidemiology", @@ -360590,65 +361044,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.03.12.484088", - "rel_title": "The SARS-CoV-2 Delta variant induces an antibody response largely focused on class 1 and 2 antibody epitopes", - "rel_date": "2022-03-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.12.484088", - "rel_abs": "Exposure histories to SARS-CoV-2 variants and vaccinations will shape the specificity of antibody responses. To understand the specificity of Delta-elicited antibody immunity, we characterize the polyclonal antibody response elicited by primary or mRNA vaccine-breakthrough Delta infections. Both types of infection elicit a neutralizing antibody response focused heavily on the receptor-binding domain (RBD). We use deep mutational scanning to show that mutations to the RBDs class 1 and class 2 epitopes, including sites 417, 478, and 484-486 often reduce binding of these Delta-elicited antibodies. The anti-Delta antibody response is more similar to that elicited by early 2020 viruses than the Beta variant, with mutations to the class 1 and 2, but not class 3 epitopes, having the largest effects on polyclonal antibody binding. In addition, mutations to the class 1 epitope (e.g., K417N) tend to have larger effects on antibody binding and neutralization in the Delta spike than in the D614G spike, both for vaccine- and Delta-infection-elicited antibodies. These results help elucidate how the antigenic impacts of SARS-CoV-2 mutations depend on exposure history.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Allison J Greaney", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Rachel T Eguia", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Tyler N Starr", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Khadija Khan", - "author_inst": "African Health Research Institute" - }, - { - "author_name": "Nicholas Franko", - "author_inst": "University of Washington" - }, - { - "author_name": "Jennifer K Logue", - "author_inst": "University of Washington" - }, - { - "author_name": "Sandra M Lord", - "author_inst": "Benaroya Research Institute" - }, - { - "author_name": "Cate Speake", - "author_inst": "Benaroya Research Institute" - }, - { - "author_name": "Helen Y Chu", - "author_inst": "University of Washington" - }, - { - "author_name": "Alex Sigal", - "author_inst": "African Health Research Institute" - }, - { - "author_name": "Jesse D Bloom", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.03.10.22272222", "rel_title": "The changing impact of vaccines in the COVID-19 pandemic", @@ -360829,6 +361224,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.03.10.22272123", + "rel_title": "Polymorphism in IFNAR contributes to glucocorticoid response and outcome in ARDS and COVID-19", + "rel_date": "2022-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22272123", + "rel_abs": "The use of glucocorticoids has given contradictory results for treating acute respiratory distress syndrome (ARDS). Here we report a novel disease association of a SNP rs9984273, which is situated in the interferon alpha/beta receptor (IFNAR2) gene in an area corresponding to a binding motif of the glucocorticoid receptor (GR). The minor allele of SNP rs9984273 associates with higher IFNAR expression, lower IFN-gamma and IL-6 levels and less severe form of coronavirus diseases (COVID-19) according to the COVID-19 Host Genetics Initiative database, and better outcome in interferon (IFN) beta treated patients with ARDS. Thus, the distribution of this SNP within clinical study arms may explain the contradictory results of multiple ARDS studies and outcomes in COVID-19 concerning type I IFN signalling and glucocorticoids.\n\nOne-Sentence SummarySingle nucleotide polymorphism in interferon receptor contributes to corticosteroid response and outcome in ARDS and COVID-19", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Juho Jalkanen", + "author_inst": "Faron Pharmaceuticals" + }, + { + "author_name": "Sofia Khan", + "author_inst": "University of Turku" + }, + { + "author_name": "Kati Elima", + "author_inst": "University of Turku" + }, + { + "author_name": "Teppo Huttunen", + "author_inst": "Estimates" + }, + { + "author_name": "Ning Wang", + "author_inst": "University of Turku" + }, + { + "author_name": "Maija Hollmen", + "author_inst": "University of Turku" + }, + { + "author_name": "Laura Elo", + "author_inst": "University of Turku" + }, + { + "author_name": "Sirpa Jalkanen", + "author_inst": "University of Turku" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.03.10.22272237", "rel_title": "Long COVID in Children and Adolescents: A Systematic Review and Meta-analyses.", @@ -362408,33 +362850,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.11.483836", - "rel_title": "Crystal structures and fragment screening of SARS-CoV-2 NSP14 reveal details of exoribonuclease activation and mRNA capping and provide starting points for antiviral drug development", - "rel_date": "2022-03-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.11.483836", - "rel_abs": "The SARS-CoV-2 non-structural protein 14 (NSP14) is a dual function enzyme containing an N-terminal exonuclease domain (ExoN) and C-terminal Guanine-N7-methyltransferase (N7-MTase) domain. Both enzymatic activities appear to be essential for the viral life cycle and thus may be targeted for anti-viral therapeutics. NSP14 forms a stable complex with the SARS-CoV-2 zinc binding protein NSP10, and this interaction greatly enhances the nuclease but not the methyltransferase activity. In this study, we have determined the crystal structure of SARS-CoV-2 NSP14 in the absence of NSP10 to 1.7 [A] resolution. Comparisons of this structure with the structure of NSP14/NSP10 complexes solved to date reveal significant conformational changes that occur within the NSP14 ExoN domain upon binding of NSP10, including significant movements and helix to coil transitions that facilitate the formation of the ExoN active site and provide an explanation of the stimulation of nuclease activity by NSP10. Conformational changes are also seen in the MTase active site within a SAM/SAH interacting loop that plays a key role in viral mRNA capping. We have also determined the structure of NSP14 in complex with cap analogue 7MeGpppG, offering new insights into MTase enzymatic activity. We have used our high resolution crystals to perform X-ray fragment screening of NSP14, revealing 72 hits bound to potential sites of inhibition of the ExoN and MTase domains. These structures serve as excellent starting point tools for structure guided development and optimization of NSP14 inhibitors that may be used to treat COVID-19 and potentially other future viral threats.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Nergis Imprachim", - "author_inst": "Centre for Medicines Discovery, University of Oxford" - }, - { - "author_name": "Yuliana Yosaatmadja", - "author_inst": "University of Auckland" - }, - { - "author_name": "Joseph Newman", - "author_inst": "University Of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2022.03.11.483948", "rel_title": "Alveolar regeneration following viral infection is independent of tuft cells", @@ -362687,6 +363102,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2022.03.09.22272113", + "rel_title": "Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination", + "rel_date": "2022-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.09.22272113", + "rel_abs": "Between November 2021 and February 2022, SARS-CoV-2 Delta and Omicron variants co-circulated in the United States, allowing for co-infections and possible recombination events. We sequenced 29,719 positive samples during this period and analyzed the presence and fraction of reads supporting mutations specific to either the Delta or Omicron variant. We identified 18 co-infections, one of which displayed evidence of a low Delta-Omicron recombinant viral population. We also identified two independent cases of infection by a Delta-Omicron recombinant virus, where 100% of the viral RNA came from one clonal recombinant. In the three cases, the 5-end of the viral genome was from the Delta genome, and the 3-end from Omicron including the majority of the spike protein gene, though the breakpoints were different. Delta-Omicron recombinant viruses were rare, and there is currently no evidence that Delta-Omicron recombinant viruses are more transmissible between hosts compared to the circulating Omicron lineages.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Alexandre Bolze", + "author_inst": "Helix" + }, + { + "author_name": "Tracy Basler", + "author_inst": "Helix" + }, + { + "author_name": "Simon White", + "author_inst": "Helix" + }, + { + "author_name": "Andrew Dei Rossi", + "author_inst": "Helix" + }, + { + "author_name": "Dana Wyman", + "author_inst": "Helix" + }, + { + "author_name": "Pavitra Roychoudhury", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "University of Washington" + }, + { + "author_name": "Kathleen Hayashibara", + "author_inst": "Thermo Fisher Scientific" + }, + { + "author_name": "Eric Kil", + "author_inst": "Helix" + }, + { + "author_name": "Hang Dai", + "author_inst": "Helix" + }, + { + "author_name": "Tyler Cassens", + "author_inst": "Helix" + }, + { + "author_name": "Kevin Tsan", + "author_inst": "Helix" + }, + { + "author_name": "Jason Nguyen", + "author_inst": "Helix" + }, + { + "author_name": "Jimmy Ramirez", + "author_inst": "Helix" + }, + { + "author_name": "Scotty Carter", + "author_inst": "Helix" + }, + { + "author_name": "Elizabeth T. Cirulli", + "author_inst": "Helix" + }, + { + "author_name": "Kelly Schiabor Barrett", + "author_inst": "Helix" + }, + { + "author_name": "Nicole L Washington", + "author_inst": "Helix" + }, + { + "author_name": "Pedro Belda-Ferre", + "author_inst": "Helix" + }, + { + "author_name": "Sharoni Jacobs", + "author_inst": "Helix" + }, + { + "author_name": "Efren Sandoval", + "author_inst": "Helix" + }, + { + "author_name": "David Becker", + "author_inst": "Helix" + }, + { + "author_name": "James T Lu", + "author_inst": "Helix" + }, + { + "author_name": "Magnus Isaksson", + "author_inst": "Helix" + }, + { + "author_name": "William Lee", + "author_inst": "Helix" + }, + { + "author_name": "Shishi Luo", + "author_inst": "Helix" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.10.22272197", "rel_title": "Blood group O and post-COVID-19 syndrome", @@ -364642,41 +365176,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.01.22271693", - "rel_title": "The Acoustic Dissection of Cough: Diving into Machine Listening-based COVID-19 Analysis and Detection", - "rel_date": "2022-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.01.22271693", - "rel_abs": "PurposeThe coronavirus disease 2019 (COVID-19) has caused a crisis worldwide. Amounts of efforts have been made to prevent and control COVID-19s transmission, from early screenings to vaccinations and treatments. Recently, due to the spring up of many automatic disease recognition applications based on machine listening techniques, it would be fast and cheap to detect COVID-19 from recordings of cough, a key symptom of COVID-19. To date, knowledge on the acoustic characteristics of COVID-19 cough sounds is limited, but would be essential for structuring effective and robust machine learning models. The present study aims to explore acoustic features for distinguishing COVID-19 positive individuals from COVID-19 negative ones based on their cough sounds.\n\nMethodsWith the theory of computational paralinguistics, we analyse the acoustic correlates of COVID-19 cough sounds based on the COMPARE feature set, i. e., a standardised set of 6,373 acoustic higher-level features. Furthermore, we train automatic COVID-19 detection models with machine learning methods and explore the latent features by evaluating the contribution of all features to the COVID-19 status predictions.\n\nResultsThe experimental results demonstrate that a set of acoustic parameters of cough sounds, e. g., statistical functionals of the root mean square energy and Mel-frequency cepstral coefficients, are relevant for the differentiation between COVID-19 positive and COVID-19 negative cough samples. Our automatic COVID-19 detection model performs significantly above chance level, i. e., at an unweighted average recall (UAR) of 0.632, on a data set consisting of 1,411 cough samples (COVID-19 positive/negative: 210/1,201).\n\nConclusionsBased on the acoustic correlates analysis on the COMPARE feature set and the feature analysis in the effective COVID-19 detection model, we find that the machine learning method to a certain extent relies on acoustic features showing higher effects in conventional group difference testing.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Zhao Ren", - "author_inst": "EIHW - Chair of Embedded Intelligence for Health Care and Wellbeing, University of Augsburg, Augsburg, Germany; L3S Research Center, Hannover, Germany" - }, - { - "author_name": "Yi Chang", - "author_inst": "GLAM - Group on Language, Audio, & Music, Imperial College London, London, United Kingdom" - }, - { - "author_name": "Katrin D. Bartl-Pokorny", - "author_inst": "EIHW - Chair of Embedded Intelligence for Health Care and Wellbeing, University of Augsburg, Augsburg, Germany; Division of Phoniatrics, Medical University of G" - }, - { - "author_name": "Florian B. Pokorny", - "author_inst": "EIHW - Chair of Embedded Intelligence for Health Care and Wellbeing, University of Augsburg, Augsburg, Germany; Division of Phoniatrics, Medical University of G" - }, - { - "author_name": "Bjoern W. Schuller", - "author_inst": "EIHW - Chair of Embedded Intelligence for Health Care and Wellbeing, University of Augsburg, Augsburg, Germany; GLAM - Group on Language, Audio, & Music, Imperi" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.03.08.22271816", "rel_title": "Aerosolized Ad5-nCoV booster vaccination elicited potent immune response against the SARS-CoV-2 Omicron variant after inactivated COVID-19 vaccine priming", @@ -364945,6 +365444,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2022.03.10.483790", + "rel_title": "Evolutionary safety of death by mutagenesis", + "rel_date": "2022-03-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.10.483790", + "rel_abs": "Nucleoside analogs are a major class of antiviral drugs. Some act by increasing the viral mutation rate causing \"death by mutagenesis\" of the virus. Their mutagenic capacity, however, may lead to an evolutionary safety concern. We define evolutionary safety as a probabilistic assurance that the treatment will not generate an increased number of epidemiologically concerning mutated virus progeny. We develop a mathematical framework to estimate the total mutant load produced with and without mutagenic treatment. We predict rates of appearance of virus mutants as a function of the timing of treatment and the immune competence of patients, employing various assumptions about the vulnerability of the viral genome and its potential to generate undesired phenotypes. We focus on the case study of Molnupiravir, which is an FDA-approved treatment against COVID-19. We estimate that Molnupiravir is narrowly evolutionarily safe, subject to the current estimate of parameters. Evolutionary safety can be improved by restricting treatment to individuals with a low clearance rate and by designing treatments that lead to a greater increase in mutation rate. We report a simple rule to determine the fold-increase in mutation rate required to obtain evolutionary safety which is also applicable to other pathogen-treatment combinations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gabriela Aleksandra Lobinska", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Yitzhak Tzachi Pilpel", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Martin Andreas Nowak", + "author_inst": "Harvard" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2022.03.10.483652", "rel_title": "Open modification searching of SARS-CoV-2-human protein interaction data reveals novel viral modification sites", @@ -366708,57 +367234,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.08.22272056", - "rel_title": "Boosters protect against SARS-CoV-2 infections in young adults during an Omicron-predominant period", - "rel_date": "2022-03-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.08.22272056", - "rel_abs": "BackgroundWhile booster vaccinations clearly reduce the risk of severe COVID-19 and death, the impact of boosters on SARS-CoV-2 infection has not been fully characterized: doing so requires understanding their impact on asymptomatic and mildly symptomatic infections that often go unreported but nevertheless play an important role in spreading SARS-CoV-2. We sought to estimate the impact of COVID-19 booster doses on SARS-CoV-2 infection in a vaccinated population of young adults during an Omicron BA.1-predominant period.\n\nMethods and FindingsWe implemented a cohort study of young adults in a college environment (Cornell Universitys Ithaca campus) from a period when Omicron BA.1 was the predominant SARS-CoV-2 variant on campus (December 5 to December 31, 2021). Participants included 15,800 university students who completed an initial vaccination series with a vaccine approved by the World Health Organization for emergency use, were enrolled in mandatory at-least-weekly surveillance PCR testing, and had no positive SARS-CoV-2 PCR test within 90 days before the start of the study period. Robust multivariable Poisson regression with the main outcome of a positive SARS-CoV-2 PCR test was performed to compare those who completed their initial vaccination series and a booster dose to those without a booster dose.\n\n1,926 unique SARS-CoV-2 infections were identified in the study population. Controlling for sex, student group membership, date of completion of initial vaccination series, initial vaccine type, and temporal effect during the study period, our analysis estimates that receiving a booster dose further reduces the rate of having a PCR-detected SARS-CoV-2 infection relative to an initial vaccination series by 56% (95% confidence interval [42%, 67%], P <0.001). While most individuals had recent booster administration before or during the study period (a limitation of our study), this result is robust to the assumed delay over which a booster dose becomes effective (varied from 1 day to 14 days). The mandatory active surveillance approach used in this study, under which 86% of the person-days in the study occurred, reduces the likelihood of outcome mis-classification. Key limitations of our methodology are that we did not have an a priori protocol or statistical analysis plan because the analysis was initially done for institutional research purposes, and some analysis choices were made after observing the data.\n\nConclusionsWe observed that boosters are effective, relative to completion of initial vaccination series, in further reducing the rate of SARS-CoV-2 infections in a college student population during a period when Omicron BA.1 was predominant; booster vaccinations for this age group may play an important role in reducing incidence of COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jiayue Wan", - "author_inst": "School of Operations Research and Information Engineering, Cornell University College of Engineering, Ithaca, NY, USA" - }, - { - "author_name": "Casey L. Cazer", - "author_inst": "Department of Public and Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY, USA; Department of Population Medicine and Diagnostic " - }, - { - "author_name": "Marin E. Clarkberg", - "author_inst": "Institutional Research and Planning, Cornell University, Ithaca, NY, USA" - }, - { - "author_name": "Shane G. Henderson", - "author_inst": "School of Operations Research and Information Engineering, Cornell University College of Engineering, Ithaca, NY, USA" - }, - { - "author_name": "Scarlett E. Lee", - "author_inst": "Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, USA" - }, - { - "author_name": "Genevive Meredith", - "author_inst": "Department of Public and Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY, USA; Master of Public Health Program, Cornell Universi" - }, - { - "author_name": "Marwan Osman", - "author_inst": "Department of Public and Ecosystem Health, Cornell University College of Veterinary Medicine, Ithaca, NY, USA; Cornell Atkinson Center for Sustainability, Corne" - }, - { - "author_name": "David B. Shmoys", - "author_inst": "School of Operations Research and Information Engineering, Cornell University College of Engineering, Ithaca, NY, USA" - }, - { - "author_name": "Peter I. Frazier", - "author_inst": "School of Operations Research and Information Engineering, Cornell University College of Engineering, Ithaca, NY, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.08.22272087", "rel_title": "Sustained high prevalence of COVID-19 deaths from a systematic post-mortem study in Lusaka, Zambia: one year later", @@ -367103,6 +367578,53 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2022.03.08.483429", + "rel_title": "Geneticin shows selective antiviral activity against SARS-CoV-2 by targeting programmed -1 ribosomal frameshifting", + "rel_date": "2022-03-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.08.483429", + "rel_abs": "SARS-CoV-2 is currently causing an unprecedented pandemic. While vaccines are massively deployed, we still lack effective large-scale antiviral therapies. In the quest for antivirals targeting conserved structures, we focused on molecules able to bind viral RNA secondary structures. Aminoglycosides are a class of antibiotics known to interact with the ribosomal RNA of both prokaryotes and eukaryotes and have previously been shown to exert antiviral activities by interacting with viral RNA. Here we show that the aminoglycoside geneticin is endowed with antiviral activity against all tested variants of SARS-CoV-2, in different cell lines and in a respiratory tissue model at non-toxic concentrations. The mechanism of action is an early inhibition of RNA replication and protein expression related to a decrease in the efficiency of the -1 programmed ribosomal frameshift (PRF) signal of SARS-CoV-2. Using in silico modelling, we have identified a potential binding site of geneticin in the pseudoknot of frameshift RNA motif. Moreover, we have selected, through virtual screening, additional RNA binding compounds, interacting with the same site with increased potency.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Carmine Varricchio", + "author_inst": "Cardiff School of Pharmacy and Pharmaceutical Sciences" + }, + { + "author_name": "Gregory Mathez", + "author_inst": "University Hospital of Vaud (CHUV)" + }, + { + "author_name": "Trestan Pillonel", + "author_inst": "University Hospital of Vaud (CHUV)" + }, + { + "author_name": "Claire Bertelli", + "author_inst": "University Hospital of Vaud (CHUV)" + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Caroline Tapparel", + "author_inst": "University of Geneva" + }, + { + "author_name": "Andrea Brancale", + "author_inst": "Cardiff School of Pharmacy and Pharmaceutical Sciences" + }, + { + "author_name": "Valeria Cagno", + "author_inst": "University Hospital of Vaud (CHUV)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.03.01.22271721", "rel_title": "The relative impact of vaccination momentum on COVID-19 rates of death in the USA in 2020/2021. The forgotten role of population wellness.", @@ -368818,73 +369340,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2022.03.04.22271830", - "rel_title": "Safety and Immunogenicity of a 100 \u03bcg mRNA-1273 Vaccine Booster for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2)", - "rel_date": "2022-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.04.22271830", - "rel_abs": "ImportanceDue to the emergence of highly transmissible SARS-CoV-2 variants, evaluation of boosters is needed.\n\nObjectivesEvaluate safety and immunogenicity of 100-{micro}g of mRNA-1273 booster dose in adults.\n\nDesignOpen-label, Phase 2/3 study.\n\nSettingMulticenter study at 8 sites in the U.S.\n\nParticipantsThe mRNA-1273 100-{micro}g booster was administered to adults who previously received a two dose primary series of 100-{micro}g mRNA-1273 in the phase 3 Coronavirus Efficacy (COVE) trial, at least 6 months earlier.\n\nInterventionLipid nanoparticle containing 100-{micro}g of mRNA encoding the spike glycoprotein of SARS-CoV-2 (Wuhan-HU-1).\n\nMain Outcomes and MeasuresSolicited local and systemic adverse reactions, and unsolicited adverse events were collected after vaccination. Primary immunogenicity objectives were to demonstrate non-inferiority of the neutralizing antibody (nAb) response against SARS-CoV-2 based on the geometric mean titer (GMTs) and the seroresponse rates (SRRs) (booster dose vs. primary series in a historical control group). nAbs against SARS-CoV-2 variants were also evaluated.\n\nResultsThe 100-{micro}g booster dose had a greater incidence of local and systemic adverse reactions compared to the second dose of mRNA-1273 as well as the 50-{micro}g mRNA-1273 booster in separate studies. The geometric mean titers (GMTs; 95% CI) of SARS-CoV-2 nAbs against the ancestral SARS-CoV-2 at 28 days after the 100-{micro}g booster dose were 4039.5 (3592.7,4541.8) and 1132.0 (1046.7,1224.2) at 28 days after the second dose in the historical control group [GMT ratio=3.6 (3.1,4.2)]. SRRs (95% CI) were 100% (98.6,100) at 28 days after the booster and 98.1% (96.7,99.1) 28 days after the second dose in the historical control group [percentage difference=1.9% (0.4,3.3)]. The GMT ratio (GMR) and SRR difference for the booster as compared to the primary series met the pre-specified non-inferiority criteria. Delta-specific nAbs also increased (GMT fold-rise=233.3) after the 100-{micro}g booster of mRNA-1273.\n\nConclusions and RelevanceThe 100-{micro}g mRNA-1273 booster induced a robust neutralizing antibody response against SARS-CoV-2, and reactogenicity was higher with the 100-{micro}g booster dose compared to the authorized booster dose level in adults (50-{micro}g). mRNA-1273 100-{micro}g booster dose can be considered when eliciting an antibody response might be challenging such as in moderately or severely immunocompromised hosts.\n\nTrial Registration: NCT04927065\n\nKey PointsQuestion: What is the safety and immunogenicity of a booster dose of 100 {micro}g of mRNA-1273 in adults who previously received the primary series of mRNA-1273?\n\nFindings: In this open-label, Phase 2/3 study, the 100 {micro}g booster dose of mRNA-1273 had a greater incidence of local and systemic adverse reactions compared to a 50 {micro}g booster dose of mRNA- 1273 or after the second dose of mRNA-1273 during the primary series. The 100 {micro}g booster dose of mRNA-1273 induced a robust antibody response against the ancestral SARS-CoV-2 and variants.\n\nMeaning: mRNA-1273 100 {micro}g booster dose might be considered when eliciting an antibody response might be challenging, such as in moderately or severely immunocompromised hosts.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Spyros Chalkias", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Howard Schwartz", - "author_inst": "CMO Research Centers of America" - }, - { - "author_name": "Biliana Nestorova", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Jing Feng", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Ying Chang", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Honghong Zhou", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Frank J Dutko", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Darin K Edwards", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "David Montefiori", - "author_inst": "Duke University" - }, - { - "author_name": "Rolando Pajon", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Brett Leav", - "author_inst": "Moderna. Inc." - }, - { - "author_name": "Jacqueline M Miller", - "author_inst": "Moderna, Inc." - }, - { - "author_name": "Rituparna Das", - "author_inst": "Moderna, Inc." - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.04.22271888", "rel_title": "A systematic review about skin lesions in children affected by Coronavirus Disease 2019 (excluding multisystem inflammatory syndrome in children): study protocol.", @@ -369037,6 +369492,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.04.22271890", + "rel_title": "Protective antibodies and T cell responses to Omicron variant three months after the booster dose of BNT162b2 vaccine", + "rel_date": "2022-03-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.04.22271890", + "rel_abs": "The high number of mutations in the Omicron variant of SARS-CoV-2 cause its immune escape when compared to the earlier variants of concern (VOC). At least three vaccine doses are required for the induction of Omicron neutralizing antibodies and further reducing the risk for hospitalization. However, most of the studies have focused on the immediate response after the booster vaccination while the duration of immune response is less known. We here studied longitudinal serum samples from the vaccinated individuals up to three months after their third dose of the BNT162b2 vaccine for their capacity to produce protective antibodies and T cell responses to Wuhan and Omicron variants. After the second dose, the antibody levels to the unmutated spike protein were significantly decreased at three months, and only 4% of the individuals were able to inhibit Omicron spike interaction compared to 47%, 38%, and 14% of individuals inhibiting wild-type, delta, and beta variants spike protein. Nine months after the second vaccination, the antibody levels were similar to the levels before the first dose and none of the sera inhibited SARS-CoV-2 wild-type or any of the three VOCs. The booster dose remarkably increased antibody levels and their ability to inhibit all variants. Three months after the booster the antibody levels and the inhibition activity were trending lower but still up and not significantly different from their peak values at two weeks after the third dose. Although responsiveness towards mutated spike peptides was lost in less than 20 % of vaccinated individuals, the wild-type spike-specific CD4+ and CD8+ memory T cells were still present at three months after the booster vaccination in the majority of studied individuals. Our data show that two doses of the BNT62b2 vaccine are not sufficient to protect against the Omicron variant, however, the spike-specific antibodies and T cell responses are strongly elicited and well maintained three months after the third vaccination dose.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Paul Naaber", + "author_inst": "SYNLAB Eesti" + }, + { + "author_name": "Liina Tserel", + "author_inst": "University of Tartu" + }, + { + "author_name": "Kadri Kangro", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Epp Sepp", + "author_inst": "University of Tartu" + }, + { + "author_name": "Virge Jurjenson", + "author_inst": "SYNLAB Eesti" + }, + { + "author_name": "Jaanika Karner", + "author_inst": "University of Tartu" + }, + { + "author_name": "Liis Haljasmagi", + "author_inst": "University of Tartu" + }, + { + "author_name": "Uku Haljasorg", + "author_inst": "University of Tartu" + }, + { + "author_name": "Marilin Kuusk", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Joachim M Gerhold", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Anu Planken", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Mart Ustav", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Kai Kisand", + "author_inst": "University of Tartu" + }, + { + "author_name": "Part Peterson", + "author_inst": "University of Tartu" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.04.22271540", "rel_title": "The mutational steps of SARS-CoV-2 to become like Omicron within seven months: the story of immune escape in an immunocompromised patient.", @@ -370476,65 +371002,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2022.03.03.22271827", - "rel_title": "Immunogenicity and Safety of Booster Dose of S-268019-b or Tozinameran in Japanese Participants: An Interim Report of Phase 2/3, Randomized, Observer-Blinded, Noninferiority Study", - "rel_date": "2022-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.03.22271827", - "rel_abs": "In this randomized, observer-blinded, phase 2/3 study, S-268019-b (n=101), a recombinant spike protein vaccine, was analyzed for noninferiority versus tozinameran (n=103), when given as a booster [≥]6 months after 2-dose tozinameran regimen in Japanese adults without prior COVID-19 infection. Interim results showed noninferiority of S-268019-b versus tozinameran in co-primary endpoints for neutralizing antibodies on day 29: geometric mean titer (GMT) (124.97 versus 109.70; adjusted-GMT ratio [95% CI], 1.14 [0.94-1.39]; noninferiority P-value, <0.0001) and seroresponse rate (both 100%; noninferiority P-value, 0.0004). Both vaccines elicited anti-spike-protein immunoglobulin G antibodies, and produced T-cell response (n=29/group) and neutralizing antibodies against Delta and Omicron pseudovirus and live virus variants (n=24/group) in subgroups. Most participants reported low-grade reactogenicity on days 1-2, the most frequent being fatigue, fever, myalgia, and injection-site pain. No serious adverse events were reported. In conclusion, S-268019-b was safe and showed robust immunogenicity as a booster, supporting its use as COVID-19 booster vaccine.\n\nJRCT IDjRCT2031210470\n\nHighlightsO_LIThird COVID-19 vaccine dose (booster) enhances immune response\nC_LIO_LIInterim phase 2/3 data for booster [≥]6 months after the 2nd dose in Japan are shown\nC_LIO_LIS-268019-b was noninferior to tozinameran in inducing neutralizing antibodies\nC_LIO_LISera boosted with either vaccines neutralized Delta and Omicron virus variants\nC_LIO_LIS-268019-b was safe, and results support its use as a booster in vaccinated adults\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Masaharu Shinkai", - "author_inst": "Department of Respiratory Medicine, Tokyo Shinagawa Hospital, 6-3-22 Higashioi, Shinagawa-ku, Tokyo 140-8522, Japan" - }, - { - "author_name": "Takuhiro Sonoyama", - "author_inst": "Shionogi & Co., Ltd., Drug Development and Regulatory Science Division 8F, Nissay Yodoyabashi East Bldg., 3-3-13, Imabashi, Chuo-ku, Osaka 541-0042, Japan" - }, - { - "author_name": "Akari Kamitani", - "author_inst": "Shionogi & Co., Ltd., Drug Development and Regulatory Science Division 8F, Nissay Yodoyabashi East Bldg., 3-3-13, Imabashi, Chuo-ku, Osaka 541-0042, Japan" - }, - { - "author_name": "Risa Shibata", - "author_inst": "Shionogi & Co., Ltd., Drug Development and Regulatory Science Division 8F, Nissay Yodoyabashi East Bldg., 3-3-13, Imabashi, Chuo-ku, Osaka 541-0042, Japan" - }, - { - "author_name": "Naomi Seki", - "author_inst": "Shionogi & Co., Ltd., Pharmaceutical Research Division 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan" - }, - { - "author_name": "Shinya Omoto", - "author_inst": "Shionogi & Co., Ltd., Pharmaceutical Research Division 1-1, Futaba-cho 3-chome, Toyonaka, Osaka 561-0825, Japan" - }, - { - "author_name": "Masahiro Shinoda", - "author_inst": "Department of Respiratory Medicine, Tokyo Shinagawa Hospital, 6-3-22 Higashioi, Shinagawa-ku, Tokyo 140-8522, Japan" - }, - { - "author_name": "Takashi Sato", - "author_inst": "Department of Respiratory Medicine, Tokyo Shinagawa Hospital, 6-3-22 Higashioi, Shinagawa-ku, Tokyo 140-8522, Japan" - }, - { - "author_name": "Naoki Ishii", - "author_inst": "Department of Gastroenterology, Tokyo Shinagawa Hospital, 6-3-22 Higashioi, Shinagawa-ku, Tokyo 140-8522, Japan" - }, - { - "author_name": "Kenji Igarashi", - "author_inst": "Shionogi & Co., Ltd., Drug Development and Regulatory Science Division 8F, Nissay Yodoyabashi East Bldg., 3-3-13, Imabashi, Chuo-ku, Osaka 541-0042, Japan" - }, - { - "author_name": "Mari Ariyasu", - "author_inst": "Shionogi & Co., Ltd., Drug Development and Regulatory Science Division 8F, Nissay Yodoyabashi East Bldg., 3-3-13, Imabashi, Chuo-ku, Osaka 541-0042, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.03.22271349", "rel_title": "COVID-19 Hospitalisation in Portugal, the first year: Results from hospital discharge data", @@ -370731,6 +371198,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.03.02.22271806", + "rel_title": "Covid-19 Exposure Assessment Tool (CEAT): Easy-to-use tool to quantify exposure based on airflow, group behavior, and infection prevalence in the community", + "rel_date": "2022-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271806", + "rel_abs": "The COVID-19 Exposure Assessment Tool (CEAT) allows users to compare respiratory relative risk to SARS-CoV-2 for various scenarios, providing understanding of how combinations of protective measures affect exposure, dose, and risk. CEAT incorporates mechanistic, stochastic and epidemiological factors including the: 1) emission rate of virus, 2) viral aerosol degradation and removal, 3) duration of activity/exposure, 4) inhalation rates, 5) ventilation rates (indoors/outdoors), 6) volume of indoor space, 7) filtration, 8) mask use and effectiveness, 9) distance between people, 10) group size, 11) current infection rates by variant, 12) prevalence of infection and immunity in the community, 13) vaccination rates of the community, and 14) implementation of COVID-19 testing procedures. Demonstration of CEAT, from published studies of COVID-19 transmission events, shows the model accurately predicts transmission. We also show how health and safety professionals at NASA Ames Research Center used CEAT to manage potential risks posed by SARS-CoV-2 exposures. Given its accuracy and flexibility, the wide use of CEAT will have a long lasting beneficial impact in managing both the current COVID-19 pandemic as well as a variety of other scenarios.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Brian Schimmoller", + "author_inst": "Signature Science LLC" + }, + { + "author_name": "Nidia S Trovao", + "author_inst": "Fogarty International Center, National Institutes of Health" + }, + { + "author_name": "Molly Isbell", + "author_inst": "Signature Science LLC" + }, + { + "author_name": "Chirag Goel", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Benjamin F Heck", + "author_inst": "Bastion Technologies, NASA Ames Research Center" + }, + { + "author_name": "Tenley C Archer", + "author_inst": "Biomea Fusion, Inc." + }, + { + "author_name": "Klint D Cardinal", + "author_inst": "Leidos, Inc., NASA Ames Research Center" + }, + { + "author_name": "Neil B Naik", + "author_inst": "Leidos, Inc., NASA Ames Research Center" + }, + { + "author_name": "Som Dutta", + "author_inst": "Mechanical & Aerospace Engineering, Utah State University" + }, + { + "author_name": "Ahleah Rohr Daniel", + "author_inst": "Space Biosciences Division, NASA Ames Research Center" + }, + { + "author_name": "Afshin Beheshti", + "author_inst": "KBR, NASA Ames Research Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.03.22271836", "rel_title": "The relationship between BMI and COVID-19: exploring misclassification and selection bias in a two-sample Mendelian randomisation study", @@ -372098,81 +372624,6 @@ "type": "contradictory results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2022.03.03.482795", - "rel_title": "Soluble signal inhibitory receptor on leukocytes-1 is released from activated neutrophils by proteinase 3 cleavage", - "rel_date": "2022-03-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.03.482795", - "rel_abs": "Signal inhibitory receptor on leukocytes-1 (SIRL-1) is an immune inhibitory receptor expressed on human granulocytes and monocytes which dampens antimicrobial functions. We previously showed that sputum neutrophils from infants with severe respiratory syncytial virus (RSV) bronchiolitis have decreased SIRL-1 surface expression compared to blood neutrophils, and that SIRL-1 surface expression is rapidly lost from in vitro activated neutrophils. This led us to hypothesize that activated neutrophils lose SIRL-1 by ectodomain shedding. Here, we developed an ELISA and measured the concentration of soluble SIRL-1 (sSIRL-1) in RSV bronchiolitis and hospitalized COVID-19 patients, which are both characterized by neutrophilic inflammation. In line with our hypothesis, sSIRL-1 concentration was increased in sputum compared to plasma of RSV bronchiolitis patients, and in serum of hospitalized COVID-19 patients compared to control serum. In addition, we show that in vitro activated neutrophils release sSIRL-1 by proteolytic cleavage, which can be prevented by proteinase 3 inhibition. Finally, we found that SIRL-1 shedding is prevented by extracellular adherence protein (Eap) from S. aureus. Notably, we recently showed that SIRL-1 is activated by PSM3 from S. aureus, suggesting that S. aureus may counteract SIRL-1 shedding to benefit from preserved inhibitory function of SIRL-1. In conclusion, we are the first to report that SIRL-1 is released from activated neutrophils by proteinase 3 cleavage and that endogenous sSIRL-1 protein is present in vivo.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Helen J. von Richthofen", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Geertje H.A. Westerlaken", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Doron Gollnast", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Sjanna Besteman", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Eveline M. Delemarre", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Karlijn Rodenburg", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Petra Moerer", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Daphne A.C. Stapels", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Anand K. Andiappan", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Olaf Rotzschke", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Stefan Nierkens", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Helen L. Leavis", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Louis J. Bont", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Suzan H.M. Rooijakkers", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Linde Meyaard", - "author_inst": "University Medical Center Utrecht" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.03.03.482810", "rel_title": "Z-RNA and the flipside of the SARS Nsp13 helicase", @@ -372609,6 +373060,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.23.22271355", + "rel_title": "Genomic epidemiology offers high resolution estimates of serial intervals for COVID-19", + "rel_date": "2022-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.23.22271355", + "rel_abs": "Estimating key aspects of transmission is crucial in infectious disease control. Serial intervals - the time between symptom onset in an infector and infectee - are fundamental, and help to define rates of transmission, estimates of reproductive numbers, and vaccination levels needed to prevent transmission. However, estimating the serial interval requires knowledge of individuals contacts and exposures (who infected whom), which is typically obtained through resource-intensive contact tracing efforts. We develop an alternate framework that uses virus sequences to inform who infected whom and thereby estimate serial intervals. The advantages are many-fold: virus sequences are often routinely collected to support epidemiological investigations and to monitor viral evolution. The genomic approach offers high resolution and cluster-specific estimates of the serial interval that are comparable with those obtained from contact tracing data. Our approach does not require contact tracing data, and can be used in large populations and over a range of time periods. We apply our techniques to SARS-CoV-2 sequence data from the first two waves of COVID-19 in Victoria, Australia. We find that serial interval estimates vary between clusters, supporting the need to monitor this key parameter and use updated estimates in onward applications. Compared to an early published serial interval estimate, using cluster-specific serial intervals can cause estimates of the effective reproduction number Rt to vary by a factor of up to 2-3. We also find that serial intervals estimated in settings such as schools and meat processing/packing plants tend to be shorter than those estimated in healthcare facilities.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jessica E Stockdale", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Kurnia Susvitasari", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Paul Tupper", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Benjamin Sobkowiak", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Nicola Mulberry", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + }, + { + "author_name": "Anders Gon\u00e7alves da Silva", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Anne E Watt", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Norelle Sherry", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Corinna Minko", + "author_inst": "Victorian Department of Health, Melbourne, Victoria, Australia" + }, + { + "author_name": "Benjamin P Howden", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Courtney R Lane", + "author_inst": "Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for In" + }, + { + "author_name": "Caroline Colijn", + "author_inst": "Department of Mathematics, Simon Fraser University, Canada" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.17.22270791", "rel_title": "Vaccine effectiveness and duration of protection against symptomatic and severe Covid-19 during the first year of vaccination in France", @@ -374216,37 +374730,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.02.482662", - "rel_title": "Comparative pathogenicity of SARS-CoV-2 Omicron and Delta variants in Syrian hamsters mirrors the attenuated clinical outlook of Omicron in COVID-19 irrespective of age", - "rel_date": "2022-03-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.02.482662", - "rel_abs": "Coronavirus disease 2019 continues to batter the world with the unceasing introduction of new variants of the causative virus, SARS-CoV-2. In order to understand differences in disease caused by variants of concern and to develop variant-specific vaccines, suitable small animal models are required that mimic disease progression in humans at various stages of life. In this study, we compared the dynamics of infection with two SARS-CoV-2 variants of concern (Delta and Omicron) in aged (>1 year 3 months old) and young (<5 weeks old) Syrian hamsters (Mesocricetus auratus). We show that no weight loss occurred in Omicron infected groups regardless of age, while infection with the Delta variant caused weight loss of up to 10% by day 7 post-infection with slower and incomplete recovery in the aged group. Omicron replicated to similar levels as Delta in the lungs, trachea and nasal turbinates, with no significant differences in the tissue viral loads of aged versus young animals for either variant. In contrast to rare necrosis observed in Omicron-infected animals regardless of age, severe necrosis was observed in the olfactory epithelium in Delta-infected animals. Omicron infection also resulted in mild pulmonary disease in both young and aged animals compared to the moderate acute necrotizing bronchointerstitial pneumonia seen in Delta-infected animals. These results suggest that Omicron infection results in an attenuated clinical disease outlook in Syrian hamsters compared to infection with the Delta variant irrespective of age.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Nadia Storm", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Nicholas Crossland", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Lindsay McKay", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Anthony Griffiths", - "author_inst": "Boston University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.03.02.482639", "rel_title": "Decoding COVID-19 mRNA Vaccine Immunometabolism in Central Nervous System: human brain normal glial and glioma cells by Raman imaging", @@ -374471,6 +374954,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.02.22271385", + "rel_title": "Impact of Delta and Vaccination on SARS-CoV-2 transmission risk: Lessons for Emerging Breakthrough infections", + "rel_date": "2022-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271385", + "rel_abs": "With the continuous emergence of SARS-CoV-2 variants of concern and implementation of mass-scale interventions like vaccination, understanding factors affecting disease transmission has critical implications for control efforts. Here we used a simple adapted N95 mask sampling method to demonstrate the impact of circulating SARS-CoV-2 variants and vaccination on 92 COVID-19 patients to expel virus into the air translating to a transmission risk. Between July and September 2021, when the Delta was the dominant circulating strain in Mumbai, we noted a two-fold increase in the proportion of people expelling virus (95%), about an eighty-fold increase in median viral load and a three-fold increase in high emitter type (41%; people expelling >1000 viral copy numbers in 30 minutes) compared to initial strains of 2020. Eight percent of these patients continued to be high emitters even after eight days of symptom onset, suggesting a probable increased transmission risk for Delta strain even at this stage. There was no significant difference in expelling pattern between partial, full and un-vaccinated individuals suggesting similar transmission risk. We noted significantly more infections among vaccinated study patients and their household members than unvaccinated, probably due to increased duration from vaccination and/or increased risk behaviour upon vaccination due to lower perceived threat. This study provides biological evidence for possible continued transmission of the Delta strain even with vaccination, emphasizing the need to continue COVID-19 appropriate behaviour. The study also indicates that the mask method may be useful for screening future vaccine candidates, therapeutics or interventions for their ability to block transmission.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Kalpana Sriraman", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Ambreen Shaikh", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Smriti Vaswani", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Tejal Mestry", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Grishma Patel", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Shalini Sakthivel", + "author_inst": "The Foundation for Medical Research" + }, + { + "author_name": "Vikas Oswal", + "author_inst": "Vikas Nursing Home, Mumbai, India" + }, + { + "author_name": "Pratibha Kadam", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Kayzad Nilgiriwala", + "author_inst": "The Foundation for Medical Research, Mumbai, India" + }, + { + "author_name": "Daksha Shah", + "author_inst": "Municipal Corporation of Greater Mumbai, Mumbai, India" + }, + { + "author_name": "Mangala Gomare", + "author_inst": "Municipal Corporation of Greater Mumbai,Mumbai, India" + }, + { + "author_name": "Nerges Mistry", + "author_inst": "The Foundation for Medical Research,, Mumbai, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.01.22271735", "rel_title": "Comparison of the reactogenicity and immunogenicity of a reduced and standard booster dose of the mRNA COVID-19 vaccine in healthy adults after two doses of inactivated vaccine.", @@ -376054,37 +376600,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.25.22271516", - "rel_title": "Rapid review of government issued documents relevant to mitigation of COVID-19 in the US food manufacturing and processing industry", - "rel_date": "2022-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.25.22271516", - "rel_abs": "We surveyed publicly available records published by the United States (US) government between the start of the Coronavirus Disease 2019 (COVID-19) pandemic and September 30th, 2021, to identify documents containing resources or guidelines about COVID-19 mitigation relevant to the US food manufacturing and processing industry (hereafter referred to as \"the food processing industry\"). Among 36 documents identified and reviewed (including 35 from government agencies and one from a relevant professional association), we extracted 19 categories of mitigation strategies covering the themes of employee biosafety, surveillance, vaccination, social distancing, and worker education. We concluded that the priority of COVID-19 mitigation in the food processing industry was to protect the health and safety of industry workers while maintaining food supply chain resilience to minimize disturbance in the food market and avoid food crisis. A collated list of the identified documents and their comprehensive review will (i) aid researchers and public health workers in interpreting the potential impacts of the recommended mitigations on the epidemiology of the disease among workers in the food processing industry and (ii) help the food processing industry sort out the most essential strategies to take in face of a pandemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ziqian Chen", - "author_inst": "Cornell University" - }, - { - "author_name": "Ece Bulut", - "author_inst": "Cornell University" - }, - { - "author_name": "Aljosa Trmcic", - "author_inst": "Cornell University" - }, - { - "author_name": "Renata Ivanek", - "author_inst": "Cornell University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2022.02.28.22271645", "rel_title": "Unquantifiably low aldosterone concentrations are prevalent in hospitalised COVID-19 patients but may not be revealed by chemiluminescent immunoassay", @@ -376369,6 +376884,33 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.02.27.482153", + "rel_title": "A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2", + "rel_date": "2022-02-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.27.482153", + "rel_abs": "SARS-CoV-2 virus has caused high-priority health concerns at a global level. Vaccines have stalled the proliferation of viruses to some extent. Yet, the emergence of newer, potentially more infectious, and dangerous mutants such as delta and omicron are among the major challenges in finding a more permanent solution for this pandemic. The effectiveness of antivirals Molnupiravir and Paxlovid, authorized for emergency use by the FDA, are yet to be assessed at larger populations. Patients with a high risk of disease progression or hospitalization have received treatment with a combination of antibodies (antibody-cocktail). Most of the mutations leading to the new lineage of SARS-CoV-2 are found in the spike protein of this virus that plays a key role in facilitating host entry. The current study has investigated how to modify a promising peptide-based inhibitor of spike protein, LCB3, against common mutations in the target protein so that it retains its efficacy against the spike protein. LCB3 being a prototype for protein-based inhibitors is an ideal testing system to learn about protein-based inhibitors. Two common mutations N501Y and K417N are considered in this work. Using a structure-based approach that considers free energy decomposition of residues, distance, and the interactions between amino acids, we propose the substitutions of amino acid residues of LCB3 inhibitors. Our binding free energy calculations suggest a possible improvement in the binding affinity of existing inhibitor LCB3 to the mutant forms of the S-protein using simple substitutions at specific positions of the inhibitor. This approach, being general, can be used in different inhibitors and other mutations and help in fighting against SARS-CoV-2.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Prerna Priya", + "author_inst": "Purnea Mahila College" + }, + { + "author_name": "Abdul Basit", + "author_inst": "School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India" + }, + { + "author_name": "Pradipta Bandyopadhyay", + "author_inst": "School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.02.25.481974", "rel_title": "An immunoPET probe to SARS-CoV-2 reveals early infection of the male genital tract in rhesus macaques", @@ -378104,65 +378646,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.24.22271347", - "rel_title": "Booster protection against Omicron infection in a highly vaccinated cohort", - "rel_date": "2022-02-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.24.22271347", - "rel_abs": "BackgroundEvaluation of COVID-19 vaccine booster effectiveness is essential as new variants of SARS-CoV-2 emerge. Data support the effectiveness of boosters in preventing severe disease and hospitalization; however, the real-world impact on reducing incident SARS-CoV-2 infections across specific variants is not yet clear.\n\nObjectivesAssess the impact of COVID-19 boosters on protection against SARS-CoV-2 infection in a real-world setting from a highly vaccinated (99%) population curated from a linked database with test results, vaccination history, patient demographics, and genomic sequencing information from the National Basketball Association (NBA).\n\nMethodsIn this population, 1,613 fully vaccinated staff and players (median age 34.5 years, 88% male) who tested at least once between 1 December 2021 and 5 January 2022, were analyzed. Individuals were tested at the time of reporting any symptom, regardless of severity, after known exposure per self-report or contact tracing and/or during enhanced surveillance. Boosted individuals (n=1260) were compared to fully vaccinated and booster eligible individuals (n=162), defined as 2 months post-JNJ-78436735 or 5-months post-second dose of mRNA vaccine. Individuals not yet eligible for a booster and those who recovered from COVID-19 between 1 November and 30 November, 2021 (n=25) were examined in secondary analyses but excluded from the primary comparison. Individuals who were not fully vaccinated (n=27) or who received a booster within 14 days during or prior to the observation period (n=916) were excluded.\n\nResultsIn this closely monitored population, fully vaccinated booster-eligible individuals were 2.6 times more likely (RR = 2.6, 95% CI: 2.2 to 3.0, p<0.0001) to have a confirmed COVID-19 infection than boosted individuals. Secondary analysis including non-boosted individuals with recent vaccination or recent SARS-CoV-2 infection found that non-boosted individuals were at greater risk of infection compared with boosted individuals (RR = 2.1, 95% CI: 1.8 to 2.4, p<0.001). Results were similar when stratified by primary vaccination type with overlapping confidence intervals. No hospitalizations or deaths were observed in this cohort. Genetic sequencing confirmed 93% of infections to be Omicron (among n=330 sequenced).\n\nConclusionsThese results highlight the protective benefit of boosters against incident SARS-CoV-19 infection, not only for severe symptoms and death. Assessment of booster effectiveness remains vital for COVID-19 vaccines as new variants of SARS-CoV-2 emerge, as there is still uncertainty around performance in real-world settings. These data are needed to convince the general public that boosters remain effective at preventing in the spread of COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Caroline Tai", - "author_inst": "IQVIA" - }, - { - "author_name": "Lisa L Maragakis", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Sarah Connelly", - "author_inst": "IQVIA" - }, - { - "author_name": "John DiFiori", - "author_inst": "NBA" - }, - { - "author_name": "Leroy Sims", - "author_inst": "NBA" - }, - { - "author_name": "Eleanor Adams", - "author_inst": "NBA" - }, - { - "author_name": "Deverick Anderson", - "author_inst": "ICF for sports" - }, - { - "author_name": "Michael Merson", - "author_inst": "Duke" - }, - { - "author_name": "David Ho", - "author_inst": "Columbia" - }, - { - "author_name": "Yonatan Grad", - "author_inst": "Harvard T. H. Chan School of Public Health" - }, - { - "author_name": "Christina DeFilippo Mack", - "author_inst": "IQVIA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.25.22271494", "rel_title": "Waning Effectiveness of the Third Dose of the BNT162b2 mRNA COVID-19 Vaccine", @@ -378327,6 +378810,65 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.02.24.481684", + "rel_title": "Dictionary learning for integrative, multimodal, and scalable single-cell analysis", + "rel_date": "2022-02-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.24.481684", + "rel_abs": "Mapping single-cell sequencing profiles to comprehensive reference datasets represents a powerful alternative to unsupervised analysis. Reference datasets, however, are predominantly constructed from single-cell RNA-seq data, and cannot be used to annotate datasets that do not measure gene expression. Here we introduce bridge integration, a method to harmonize singlecell datasets across modalities by leveraging a multi-omic dataset as a molecular bridge. Each cell in the multi-omic dataset comprises an element in a dictionary, which can be used to reconstruct unimodal datasets and transform them into a shared space. We demonstrate that our procedure can accurately harmonize transcriptomic data with independent single cell measurements of chromatin accessibility, histone modifications, DNA methylation, and protein levels. Moreover, we demonstrate how dictionary learning can be combined with sketching techniques to substantially improve computational scalability, and harmonize 8.6 million human immune cell profiles from sequencing and mass cytometry experiments. Our approach aims to broaden the utility of single-cell reference datasets and facilitate comparisons across diverse molecular modalities.\n\nAvailabilityInstallation instructions, documentations, and vignettes are available at http://www.satijalab.org/seurat", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yuhan Hao", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Tim Stuart", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Madeline Kowalski", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Saket Choudhary", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Paul Hoffman", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Austin Hartman", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Avi Srivastava", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Gesmira Molla", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Shaista Madad", + "author_inst": "New York Genome Center" + }, + { + "author_name": "Carlos Fernandez-Granda", + "author_inst": "Center for Data Science, New York University" + }, + { + "author_name": "Rahul Satija", + "author_inst": "New York Genome Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2022.02.25.22271520", "rel_title": "Late-Ensemble of Convolutional Neural Networks with Test Time Augmentation for Chest XR COVID-19 Detection", @@ -379794,69 +380336,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2022.02.24.22271337", - "rel_title": "Diabetes-related excess mortality in Mexico: a comparative analysis of national death registries between 2017-2019 and 2020", - "rel_date": "2022-02-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.24.22271337", - "rel_abs": "BACKGROUNDExcess all-cause mortality rates in Mexico in 2020 during the COVID-19 pandemic were among the highest globally. Recent reports suggest that diabetes-related deaths were also higher, but the contribution of diabetes as a cause of excess mortality in Mexico during 2020 compared to prior years has not yet been characterized.\n\nMETHODSWe conducted a retrospective, state-level study using national death registries from Mexican adults [≥]20 years for the 2017-2020 period. Diabetes-related deaths were classified using ICD-10 codes that listed diabetes as the primary cause of death, excluding certificates which listed COVID-19 as a cause of death. Excess mortality was estimated as the increase in diabetes-related mortality in 2020 compared to average rates in 2017-2019. Analyses were stratified by diabetes type, diabetes-related complication, and in-hospital vs. out-of-hospital death. We evaluated the geographic distribution of diabetes-related excess mortality and its socio-demographic and epidemiologic correlates using spatial analyses and negative binomial regression models.\n\nRESULTSWe identified 148,437 diabetes-related deaths in 2020 (177/100,000 inhabitants), 41.6% higher than the average for 2017-2019, with the excess occurring after the onset of the COVID-19 pandemic. In-hospital diabetes-related deaths decreased by 17.8% in 2020 compared to 2017-2019, whereas out-of-hospital deaths increased by 89.4%. Most deaths were attributable to type 2 diabetes and type 1 diabetes (129.7 and 4.0/100,000 population). Diabetes-related emergencies as contributing causes of death also increased in 2020 compared to 2017-2019 for hyperglycemic hyperosmolar state (128%), and ketoacidosis (116%). Diabetes-related excess mortality clustered in southern Mexico and was highest in states with higher social lag, higher rates of COVID-19 hospitalization, and higher prevalence of HbA1c [≥]7.5%.\n\nINTERPRETATIONDiabetes-related mortality increased among Mexican adults by 41.6% in 2020 after the onset of the pandemic compared to 2017-2019, largely attributable to type 2 diabetes. Excess diabetes-related deaths occurred disproportionately out-of-hospital, clustered in southern Mexico, and were associated with higher state-level marginalization, rates of COVID-19 hospitalizations, and higher prevalence of suboptimal glycemic control. Urgent policies to mitigate mortality due to diabetes in Mexico are needed, particularly given the ongoing challenges in caring for people with diabetes posed by the COVID-19 pandemic.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed and Google Scholar for research articles published up to February 15, 2022, using the terms [(\"diabetes-related mortality\" OR (\"excess mortality\" AND \"diabetes\"))]. No language restriction was applied. This search revealed few international studies evaluating nationwide diabetes-related mortality in general. In Mexico, only one unpublished study evaluated diabetes-related mortality up to 2019. We identified no studies which evaluated diabetes-related excess mortality in Mexico or elsewhere during 2020 or which explored correlates of diabetes-related excess mortality in 2020.\n\nAdded value of this studyThis is the first report and characterization of an excess in diabetes-related mortality in Mexico during 2020 compared to recent years. Diabetes as a primary cause of death in Mexico was higher in 2020 compared to 2017-2019, particularly for people living with type 2 diabetes, starting in March 2020 with the onset of the COVID-19 pandemic. Compared to the 2017-2019 period, most of these excess deaths occurred out of hospital, with a concurrent decrease in in-hospital diabetes-related mortality. Hyperosmolar hyperglycemic state and ketoacidosis as primary causes of diabetes-related deaths also increased in 2020 compared to prior years. Our study also identified substantial geographic variation in diabetes-related excess mortality in Mexico, with southern, poorer States bearing a disproportionate burden. Finally, we report that diabetes-related excess mortality was associated with higher marginalization, suboptimal glycemic control, and higher rates of COVID-19 hospitalization, which were clustered in southern Mexico.\n\nImplications of the available evidenceReadily treatable, high morbidity diabetes-related conditions were likely untreated due to the constraints of the health care system during the COVID-19 pandemic, leading to diabetes-related excess mortality. This is a problem for Mexico, but it is likely to be generalizable to other countries and other conditions, as seen even in high-income countries. Given the ongoing challenges posed by the COVID-19 pandemic on healthcare systems, policies that can strengthen care for diabetes and other chronic conditions are urgently needed to mitigate the dramatic rise in diabetes-related mortality occurring in the out-of-hospital setting and its disproportionate burden on populations with high levels of marginalization.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Omar Yaxmehen Bello-Chavolla", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Neftali Eduardo Antonio-Villa", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Carlos Alberto Ferm\u00edn-Mart\u00ednez", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Luisa Fern\u00e1ndez-Chirino", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Arsenio Vargas-V\u00e1zquez", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Daniel Ram\u00edrez-Garc\u00eda", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Mart\u00edn Roberto Basile-Alvarez", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Ana Elena Hoyos-L\u00e1zaro", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Rodrigo M. Carrillo-Larco", - "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London" - }, - { - "author_name": "Deborah J. Wexler", - "author_inst": "Diabetes Unit, Massachusetts General Hospital, Harvard Medical School" - }, - { - "author_name": "Jennifer Manne-Goehler", - "author_inst": "Harvard Center for Population and Development Studies, Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Jacqueline A Seiglie", - "author_inst": "Diabetes Unit, Massachusetts General Hospital, Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2022.02.24.22271440", "rel_title": "Protection of Omicron sub-lineage infection against reinfection with another Omicron sub-lineage", @@ -380133,6 +380612,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.24.22271468", + "rel_title": "Clinical and Virologic Factors associated with Outcomes of COVID-19 before and after Vaccination among Veterans: Retrospective Analysis from Six New England States", + "rel_date": "2022-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.24.22271468", + "rel_abs": "BackgroundA region-wide analysis of COVID-19 outcomes in New England has not been done. We aimed to characterize clinical, demographic, and vaccination status affecting COVID-19 clinical outcomes and describe viral epidemiology.\n\nMethodsClinical variables of Veterans with COVID-19 in Veterans Administration healthcare systems in six New England states from April 8, 2020, to September 2, 2021 were correlated with outcomes of 30-day mortality, non-psychiatric hospitalization, intensive care unit admission (ICU-care), and post-vaccination infection. We sequenced 754 whole viral genomes and 197 partial genomes.\n\nResultsOf 4,170 Veterans with COVID-19, 81% were White, 8% women, mean age was 60.1 {+/-}17.7 years, and 2,399 became fully vaccinated. Overall, 19% Veterans needed hospitalization, 2.8% required ICU-care, and 3.7% died. Veterans with post-vaccination COVID-19 were older, with higher rates of tobacco/drug use, CKD, and malignancy, and 0.38% died. Among the unvaccinated, ICU-care and mortality correlated with age, while hospitalization correlated with age, male sex, black race, drug use, chronic heart disease, COPD, CKD, and chronic liver disease. Age, CKD, and alcohol use correlated with hospitalization in vaccinated patients.\n\nMost New England Veterans (>97%) were infected with B.1 sub-lineages with the D614G mutation in 2020 and early 2021. B.1.617.2 lineage (71%) predominated after July 2021, including the post-vaccination infections.\n\nConclusionIn New England Veterans with mean age of 60 years, age and CKD significantly correlated with hospitalization regardless of vaccination-status. Age correlated with mortality and ICU-care among the unvaccinated. The Delta variant of SARS-CoV-2 (B.1.617.2) dominated post-vaccination infections.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Megan Lee", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Danielle Cosenino", + "author_inst": "VA Connecticut Healthcare System" + }, + { + "author_name": "Tassos C Kyriakides", + "author_inst": "VA Connecticut Healthcare System" + }, + { + "author_name": "Tricia Cavallaro", + "author_inst": "VA Connecticut Healthcare System" + }, + { + "author_name": "Gary Stack", + "author_inst": "VA Connecticut Healthcare System" + }, + { + "author_name": "Shaili Gupta", + "author_inst": "Yale School of Medicine" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.21.481324", "rel_title": "A single-dose of the deactivated rabies virus vectored COVID-19 vaccine, CORAVAX, is highly efficacious and alleviates lung inflammation in the hamster model.", @@ -381520,25 +382038,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.23.22271414", - "rel_title": "Increase in SARS-CoV-2 RBD-specific IgA and IgG Antibodies in Breast Milk from Lactating Women Following the COVID-19 Booster Vaccination", - "rel_date": "2022-02-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.23.22271414", - "rel_abs": "The CDC recommended a booster dose of the Pfizer-BioNTech Comirnaty (BNT162b2) COVID-19 mRNA vaccine in September 2021 for high-risk individuals. Pregnant and high-risk lactating women were encouraged to receive the booster to obtain potential prolonged protection for themselves and their infants. This study investigated the ability of the booster vaccine to increase IgA and IgG antibodies specific to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein in human milk compared to levels pre-booster. We found a significant increase in both anti-RBD-specific IgA and IgG antibodies in human milk 1-2 weeks after the Pfizer-BioNTech booster and at the study endpoint (60 days post-booster). These results suggest the booster vaccination enhances SARS-CoV-2 specific immunity in human breast milk, which may be protective for infants.\n\nKey PointsO_LIAbs to SARS-COV-2 RBD are detected in blood [≥]60 days post-Pfizer-BioNTech booster.\nC_LIO_LIHuman milk Abs to SARS-COV-2 RBD are higher [≥]60 days post-booster vs pre-booster.\nC_LI", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Andrea M Henle", - "author_inst": "Carthage College" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.02.23.22271388", "rel_title": "Risk of Long Covid in people infected with SARS-CoV-2 after two doses of a COVID-19 vaccine: community-based, matched cohort study", @@ -381699,6 +382198,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.23.22271403", + "rel_title": "Quantifying antibody dynamics of severe and non-severe patients with COVID-19", + "rel_date": "2022-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.23.22271403", + "rel_abs": "COVID-19 pandemic is a major public health threat with unanswered questions regarding the role of the immune system in the severity level of the disease. In this paper, based on antibody kinetic data of patients with different disease severity, topological data analysis highlights clear differences in the shape of antibody dynamics between three groups of patients, which were non-severe, severe, and one intermediate case of severity. Subsequently, different mathematical models were developed to quantify the dynamics between the different severity groups. The best model was the one with the lowest media value of Akaike Information Criterion for all groups of patients. Although it has been reported high IgG level in severe patients, our findings suggest that IgG antibodies in severe patients may be less effective than non-severe patients due to early B cell production and early activation of the seroconversion process from IgM to IgG antibody.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Fernanda Ordonez-Jimenez", + "author_inst": "UNAM" + }, + { + "author_name": "Rodolfo Blanco-Rodriguez", + "author_inst": "UNAM" + }, + { + "author_name": "Alexis Erich S. Almocera", + "author_inst": "University of the Philippines Visayas" + }, + { + "author_name": "Gustavo Chinney-Herrera", + "author_inst": "UNAM" + }, + { + "author_name": "Esteban Abelardo Hernandez Vargas", + "author_inst": "UNAM" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.23.22271372", "rel_title": "Genomic surveillance of SARS-CoV-2 reveals emergence of Omicron BA.2 in Islamabad, Pakistan", @@ -383190,45 +383724,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.02.20.480711", - "rel_title": "Modular capsid decoration boosts adenovirus vaccine-induced humoral and cellular immunity against SARS-CoV-2", - "rel_date": "2022-02-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.20.480711", - "rel_abs": "Adenovirus vector vaccines have been widely and successfully deployed in response to COVID-19. However, despite inducing potent T cell immunity, improvement of vaccine-specific antibody responses upon homologous boosting is modest compared to other technologies. Here, we describe a system to enable modular decoration of adenovirus capsid surfaces with protein antigens and demonstrate induction of potent humoral immunity against these displayed antigens. Ligand attachment via a covalent isopeptide bond was achieved in a rapid and spontaneous reaction, requiring simple co-incubation of ligand and vector components. We used a recently described protein superglue, DogTag/DogCatcher, which is similar to the widely used SpyTag/SpyCatcher ligation system but performs better in loop structures. DogTag was inserted into surface-exposed loops in the adenovirus hexon protein to allow attachment of DogCatcher-fused ligands on virus particles. Efficient coverage of the capsid surface was achieved using a variety of ligands and vector infectivity was retained in each case. Capsid decoration shielded particles from anti-adenovirus neutralizing antibodies. In prime-boost regimens, proof-of-concept COVID-19 adenovirus vaccines decorated with the receptor-binding domain (RBD) of SARS-CoV-2 spike induced >10-fold higher SARS-CoV-2 neutralization titers compared to an undecorated adenovirus vector encoding spike. Importantly, decorated vectors retained robust T cell immunogenicity to encoded antigens, a key hallmark of adenovirus vector vaccines. We propose capsid decoration via protein superglue-mediated covalent ligation as a novel strategy to improve the efficacy and boostability of adenovirus-based vaccines and therapeutics.\n\nOne Sentence SummaryDecorating the capsid surface of adenovirus vaccine vectors using a spontaneous protein superglue induces potent pathogen-specific immunity", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Matthew D. J. Dicks", - "author_inst": "SpyBiotech Ltd." - }, - { - "author_name": "Louisa M. Rose", - "author_inst": "SpyBiotech Ltd." - }, - { - "author_name": "Lesley A. H. Bowman", - "author_inst": "SpyBiotech Ltd." - }, - { - "author_name": "Simon J. Draper", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mark Howarth", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sumi Biswas", - "author_inst": "SpyBiotech Ltd." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2022.02.19.481139", "rel_title": "SARS-CoV-2 Viroporins Activate The NLRP3-Inflammasome Via The Mitochondrial Permeability Transition Pore", @@ -383512,6 +384007,101 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.02.19.481107", + "rel_title": "Identification of a SARS-CoV-2 host metalloproteinase-dependent entry pathway differentially used by SARS-CoV-2 and variants of concern Alpha, Delta, and Omicron", + "rel_date": "2022-02-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.19.481107", + "rel_abs": "To infect cells, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) binds to angiotensin converting enzyme 2 (ACE2) via its spike glycoprotein (S), delivering its genome upon S-mediated membrane fusion. SARS-CoV-2 uses two distinct entry pathways: 1) a surface, serine protease-dependent or 2) an endosomal, cysteine protease-dependent pathway. In investigating serine protease-independent cell-cell fusion, we found that the matrix metalloproteinases (MMPs), MMP2/9, can activate SARS-CoV-2 S fusion activity, but not that of SARS-CoV-1. Importantly, metalloproteinase activation of SARS-CoV-2 S represents a third entry pathway in cells expressing high MMP levels. This route of entry required cleavage at the S1/S2 junction in viral producer cells and differential processing of variants of concern S dictated its usage. In addition, metalloproteinase inhibitors reduced replicative Alpha infection and abrogated syncytia formation. Finally, we found that the Omicron S exhibit reduced metalloproteinase-dependent fusion and viral entry. Taken together, we identified a MMP2/9-dependent mode of activation of SARS-CoV-2 S. As MMP2/9 are released during inflammation and severe COVID-19, they may play important roles in SARS-CoV-2 S-mediated cytopathic effects, tropism, and disease outcome.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Mehdi Benlarbi", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Genevi\u00e8ve Laroche", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Corby Fink", + "author_inst": "Western University" + }, + { + "author_name": "Kathy Fu", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Rory P Mulloy", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Alexandra Phan", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Ardeshir Ariana", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Corina M Stewart", + "author_inst": "University of Ottawa" + }, + { + "author_name": "J\u00e9r\u00e9mie Pr\u00e9vost", + "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Guillaume Beaudoin-Bussi\u00e8res", + "author_inst": "CRCHUM" + }, + { + "author_name": "Redaet Daniel", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Yuxia Bo", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Julien Yockell-Leli\u00e8vre", + "author_inst": "The Ottawa Hospital Research Institute" + }, + { + "author_name": "William L Stanford", + "author_inst": "The Ottawa Hospital Research Institute" + }, + { + "author_name": "Patrick M Gigu\u00e8re", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Samira Mubareka", + "author_inst": "Sunnybrook Research Institute and University of Toronto" + }, + { + "author_name": "Andr\u00e9s Finzi", + "author_inst": "Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Gregory A Dekaban", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Jimmy D Dikeakos", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Marceline C\u00f4t\u00e9", + "author_inst": "University of Ottawa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.19.481089", "rel_title": "Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection", @@ -385247,77 +385837,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.02.19.22271215", - "rel_title": "Four doses of the inactivated SARS-CoV-2 vaccine redistribute humoral immune responses away from the Receptor Binding Domain", - "rel_date": "2022-02-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.19.22271215", - "rel_abs": "A recent MMWR reported that the effectiveness of a 3rd dose of SARS-CoV-2 mRNA vaccine waned quickly in the Omicron-predominant period. Similarly, a substantial decline of immune responses induced by a 3rd dose of inactivated vaccines was also observed in our study. In response to the fast waning immune response and the great threat of Omicron variant of concern (VOC) to frontline healthcare workers (HCWs), 38 HCWs who were in our previous cohort investigating responses to the first three doses of inactivated vaccines participated in the current study and volunteered to receive a 4th homologous booster. Here, we demonstrated that the 4th dose is safe and capable of recalling waned immune responses 6 months after the 3rd dose. However, a greater suppression on the induction of overall Neutralizing antibodies (NAbs) and NAbs targeting the receptor-binding domain (RBD) was found in participants with stronger immune responses after the 3rd dose. As a result, a stepwise elevation of RBD-NAbs from the 1st to the 3rd vaccination achieved a \"turning point\". The peak RBD-NAbs level induced by the 4th dose was inferior to the peak of the 3rd dose. Accompanied with reduced induction of RBD-NAbs, the immune system shifted responses to the nucleocapsid protein (NP) and the N-terminal domain (NTD) of the spike protein. Although NTD directed antibodies are capable of neutralization, they only compensated the loss of RBD-NAbs to ancestral SARS-CoV-2 virus but not to the Omicron variant due to a substantial conformational change of Omicron NTD. This longitudinal clinical study monitored the immune response of the same cohort for every doses, shaping a relationship between the trajectory of immune focus and the dynamics of the neutralizing potency against the evolving virus. Our data reveal that immune responses could not be endlessly elevated, while suppression of heightened immune responses focusing on one subunit together with a shift of immune responses to other subunits would occur after repeated vaccination. Thus, an updated vaccine with more diverse epitopes capable of inducing NAbs against VOCs would be a future direction for boosters.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Ji Wang", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Caiguanxi Deng", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Ming Liu", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Yihao Liu", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Liubing Li", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Zhangping Huang", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Liru Shang", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Juan Jiang", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Yongyong Li", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Ruohui Mo", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Hui Zhang", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Min Liu", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Sui Peng", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - }, - { - "author_name": "Haipeng Xiao", - "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.20.22271237", "rel_title": "At least three doses of leading vaccines essential for neutralization of SARS-CoV-2 Omicron variant", @@ -385586,6 +386105,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2022.02.16.22270690", + "rel_title": "Narratives of the convalescent plasma donor in a Peruvian social security hospital: motivations, fears, expectations and experiences", + "rel_date": "2022-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.16.22270690", + "rel_abs": "ObjectivesTo know and explore from convalescent plasma donators voices the experience in the blood donation process at a Peruvian social security hospital.\n\nMethodsQualitative study with a phenomenological design. The investigation was carried out in 01 hospitals of the social security of Peru. Semi-structured interviews were carried out.\n\nResultsEleven donors of convalescent plasma were interviewed. The main motivations for donating were being able to contribute to national research and supporting patients affected by COVID-19. Fears focus on the possible risk of contagion within the hospital. Donors emphasised the attention and support of health personnel alongside the donation procedure. The main expectations and suggestions point towards greater dissemination of donation campaigns with special emphasis on safety. Likewise, an improvement in the time of the donation procedure (from enrolment to the extraction of convalescent plasma), and the implementation of friendly spaces to encourage future blood donation campaigns were highlighted.\n\nConclusionsThe experience of the convalescent plasma donors was positive. However, improvements must be made in terms of processes and infrastructure to ensure future successful blood donation campaigns.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Silvana M Matassini Eyzaguirre", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Christian Villanueva Yapa", + "author_inst": "Servicio de Medicina Transfusional, Hospital Nacional Egdardo Rebagliati, EsSalud, Lima, Per\u00fa" + }, + { + "author_name": "Ausberto Chunga Chunga", + "author_inst": "Servicio de Patolog\u00eda Cl\u00ednica, Hospital Nacional Egdardo Rebagliati Martins, EsSalud, Lima, Per\u00fa" + }, + { + "author_name": "Arturo Sagastegui Soto", + "author_inst": "Servicio de Medicina Transfusional, Hospital Nacional Egdardo Rebagliati, EsSalud, Lima, Per\u00fa" + }, + { + "author_name": "Ibeth Melania Neyra Vera", + "author_inst": "Servicio de Patolog\u00eda Cl\u00ednica, Hospital Nacional Egdardo Rebagliati Martins, EsSalud, Lima, Per\u00fa" + }, + { + "author_name": "Suly Soto-Ordo\u00f1ez", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Martina Guillermo Roman", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Martin Oyanguren Miranda", + "author_inst": "Servicio de Cuidados Intensivos, Hospital Nacional Egdardo Rebagliati Martins, EsSalud, Lima, Peru" + }, + { + "author_name": "Percy Soto-Becerra", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Yamilee Hurtado-Roca", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Jorge L Magui\u00f1a", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + }, + { + "author_name": "Roger Vladimir Araujo-Castillo", + "author_inst": "Instituto de Evaluaci\u00f3n de Tecnolog\u00edas en Salud e Investigaci\u00f3n - IETSI, EsSalud, Lima, Per\u00fa." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2022.02.17.22271142", "rel_title": "Performance of three rapid antigen tests against the SARS-CoV-2 Omicron variant", @@ -387117,29 +387699,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2022.02.18.481028", - "rel_title": "Furin-cleavage site is present in an antiparallel \u03b2-strand in SARS-CoV2 Spike protein", - "rel_date": "2022-02-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.18.481028", - "rel_abs": "Furin cleavage-site (CS) present between the S1/S2 junction in SARS-CoV2 spike (S) protein is critical to drive the fusion of SARS-CoV2 with the host cell. SARS-CoV2 falls in the sarbecovirus lineage that doesnt comprise of furin CS and therefore makes its origin enigmatic. The available wild-type (Wt) SARS-CoV2 S protein with PDB ID: 6yvb lacks a stretch of amino acid including furin CS as well. All investigators till date have shown this stretch existing in the form of a loop. We are for the first time reporting that this stretch comprises of 14 amino acid residues (677QTNSPRRARSVASQ689), forming an antiparallel {beta}-sheet comprising of PRRAR furin CS. We observed the presence of this antiparallel {beta}-sheet in MERS spike protein as well. While switching over from Wt. SARS-CoV2 with PRRAR furin CS to B.1.1.7 variant with HRRAR furin CS, we found 3% increase in the percentage content of {beta} stands. Interestingly, we found that the change of B.1.1.7 to B.1.617 variant comprising of RRRAR furin CS shifted the percentage secondary structure back to that found in Wt. SARS-CoV2. We anticipate that this {beta}-sheet is used as a docking site by host cell proteases to act on furin-CS. Additionally, we studied the interaction of modeled SARS-CoV2 S protein with transmembrane protease, serine 2 (TMPRSS2), and furin proteases, which clearly highlighted that these proteases exclusively uses furin CS located in {beta}-sheet to cleave the SARS-CoV2 S protein at its S1/S2 junction.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Arif Bashir Sr.", - "author_inst": "Higher Education Department, Civil-Secretariat, J&K, India-190001" - }, - { - "author_name": "Naveed Nazir Shah", - "author_inst": "Government Medical College, Srinagar" - } - ], - "version": "1", - "license": "cc_no", - "type": "contradictory results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.02.18.481058", "rel_title": "Potent Neutralization of Omicron and other SARS-CoV-2 Variants of Concern by Biparatopic Human VH Domains", @@ -387580,6 +388139,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.16.22271096", + "rel_title": "Analytical Sensitivity of the SalivaDirect\u2122 Assay on the Liberty16 for detecting SARS-CoV-2 B.1.1.529 Omicron", + "rel_date": "2022-02-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.16.22271096", + "rel_abs": "The newly emerged Omicron variant of SARS-CoV-2 has numerous mutations that are not found in other variants of concern (VOCs). Despite acquiring extended functions in adapting to the host-cell environment, the viral genetic variation exerts a potential negative impact on a molecular test, which in turn, compromises public health and safety. The Liberty16 has been clinically validated as a flexible and accessible device system for running the affordable SalivaDirect real time PCR detection assay for SARS-CoV-2 especially in low resource settings. Preliminary, based on in-silico sequence analysis, we found that Omicrons mutation at position 28,311 overlaps with the CDC 2019-nCoV_N1 probe binding region. In order to verify the performance of CDC 2019-nCoV-N1 primers-probe set in detecting the Omicron variant of SARS-CoV-2, plasmids containing Wuhan/WH01/2019 (wild-type) and B.1.1.529 (Omicron) sequences were serially diluted and subsequently directed for SalivaDirect RT-qPCR detection on Liberty16 using commercially procured reagents. Our findings provide analytical support for reports that the mutations in the Omicron variant have little or no impact on SalivaDirect assay in terms of amplification efficiency and detection sensitivity using either standard and the recently reported fast Liberty16 SalivaDirect thermal cycling protocols.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yen Pei Tan", + "author_inst": "Ubiquitome Limited" + }, + { + "author_name": "Mila Al-Halbouni", + "author_inst": "Ubiquitome Limited" + }, + { + "author_name": "Ching-Huan Chen", + "author_inst": "Ubiquitome Limited" + }, + { + "author_name": "David B. Hirst", + "author_inst": "Ubiquitome Limited" + }, + { + "author_name": "Paul J. Pickering", + "author_inst": "Ubiquitome Limited" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.16.22271093", "rel_title": "A novel SEIR-e model for disease transmission and pathogen exposure", @@ -389055,41 +389649,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.10.22270817", - "rel_title": "Role of COVID-19 vaccinal status in admitted children during OMICRON variant circulation in Rio de Janeiro, city- Preliminary report", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.10.22270817", - "rel_abs": "ObjectiveTo evaluate COVID-19 vaccination status in admitted children during the OMICRON variant circulation.\n\nDesignObservational retrospective study. Patients with confirmed COVID-19 were compared in two different periods: 2020-2021 when full COVID-19 vaccine were not completed for adolescents between 12 and 18 years and 2022, when Pfizer-BioNTech vaccine full scheme were completed for children older 12 years\n\nSettingTwo paediatric hospitals in Rio de Janeiro, city\n\nPatientsChildren aged <18 years with confirmed COVID-19.\n\nInterventionNone\n\nMain outcomeVaccination status for COVID-19 at the admission.\n\nResultsThree-hundred patients were admitted with confirmed COVID-19, being 240 in 2020-2021, and 60 in 2022. The distribution of patients according to the age-groups were: 0-2 years (33.3% in 2020-2021 and 53.4% in 2022), 2-5 years (21.7% in 2020-2021 and 10% in 2022), 5-11 years (29.2% in 2020-2021 and 28.3% in 2022) and 12-18 years (15.8% in 2020-2021 and 8.3% in 2022) (p= 0.015). The median of lenght of stay was 6 days in 2020-2021 and 5 days in 2022 (p=0.036). We verified 6 deaths and in the first period of analysis and 1 death in the second one (p=0.777). Of 60 children admitted in 2022, fifty-eigth (96.7%) not received the full scheme of COVID-19 vaccine available\n\nConclusionsWe verified in a \"real world condition\" ability of Pfizer-BioNTech vaccine in avoid hospitalization in children older than 12 years", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Andre Ricardo Araujo da Silva", - "author_inst": "Federal Fluminense University" - }, - { - "author_name": "Bernardo Rodrigues Rosa de Carvalho", - "author_inst": "Federal Fluminense University" - }, - { - "author_name": "Monica del Monaco Esteves", - "author_inst": "Federal Fluminense University" - }, - { - "author_name": "Cristiane Henriques Teixeira", - "author_inst": "Prontobaby Group" - }, - { - "author_name": "Cristina Vieira Souza", - "author_inst": "Prontobaby Group" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2022.02.10.22270772", "rel_title": "SARS-CoV-2 seroprevalence in a rural and urban community household cohort in South Africa, after the third wave, April-November 2021", @@ -389354,6 +389913,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.11.22270843", + "rel_title": "Evaluation of test-to-return after COVID-19 diagnosis in a Massachusetts public school district", + "rel_date": "2022-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270843", + "rel_abs": "The Centers for Disease Control allows rapid antigen testing (RAT) towards the end of a 5-day isolation for COVID-19 infection to determine eligibility to leave isolation. The impact of a test-to-return (TTR) program in schools is unknown. In January 2022 a Massachusetts school district initiated a TTR program utilizing a single school-administered RAT on days 5-9 after symptom onset or positive test, whichever was first. Of 636 students with COVID-19 infection, 408 (64.2%) participated in TTR; of these, 128 (31.4%) had a positive TTR rapid antigen test. Students who were symptomatic at any time during their infection were more likely to have a positive TTR than those who were never symptomatic (43.1% vs. 17.3%); positivity rates were lower when TTR was performed later during days 6-9. TTR may identify students who carry higher viral loads after recovery from COVID-19 infection thereby extending their isolation, while facilitating earlier return of those with negative results.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sandra B. Nelson", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Isaac Ravi Brenner", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Elizabeth Homan", + "author_inst": "Arlington Public Schools" + }, + { + "author_name": "Sarah Bott Lee", + "author_inst": "Arlington Public Schools" + }, + { + "author_name": "Christine Bongiorno", + "author_inst": "Town of Arlington, Massachusetts" + }, + { + "author_name": "Nira Pollock", + "author_inst": "Boston Children's Hospital" + }, + { + "author_name": "Andrea L Ciaranello", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.10.22270733", "rel_title": "Differential durability of humoral and T cell immunity after two and three BNT162b2 vaccinations in adults aged >80 years", @@ -391333,49 +391935,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.02.15.480546", - "rel_title": "Reduced antigenicity of Omicron lowers host serologic response", - "rel_date": "2022-02-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.15.480546", - "rel_abs": "SARS-CoV-2 Omicron variant of concern (VOC) contains fifteen mutations on the receptor binding domain (RBD), evading most neutralizing antibodies from vaccinated sera. Emerging evidence suggests that Omicron breakthrough cases are associated with substantially lower antibody titers than other VOC cases. However, the mechanism remains unclear. Here, using a novel geometric deep-learning model, we discovered that the antigenic profile of Omicron RBD is distinct from the prior VOCs, featuring reduced antigenicity in its remodeled receptor binding sites (RBS). To substantiate our deep-learning prediction, we immunized mice with different recombinant RBD variants and found that the Omicrons extensive mutations can lead to a drastically attenuated serologic response with limited neutralizing activity in vivo, while the T cell response remains potent. Analyses of serum cross-reactivity and competitive ELISA with epitope-specific nanobodies revealed that the antibody response to Omicron was reduced across RBD epitopes, including both the variable RBS and epitopes without any known VOC mutations. Moreover, computational modeling confirmed that the RBS is highly versatile with a capacity to further decrease antigenicity while retaining efficient receptor binding. Longitudinal analysis showed that this evolutionary trend of decrease in antigenicity was also found in hCoV229E, a common cold coronavirus that has been circulating in humans for decades. Thus, our study provided unprecedented insights into the reduced antibody titers associated with Omicron infection, revealed a possible trajectory of future viral evolution and may inform the vaccine development against future outbreaks.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "J\u00e9r\u00f4me Tubiana", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Yufei Xiang", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Li Fan", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Haim J. Wolfson", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Kong Chen", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Dina Schneidman-Duhovny", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Yi Shi", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.02.14.480298", "rel_title": "Milk of cow and goat, immunized by recombinant protein vaccine ZF-UZ-VAC2001(Zifivax), contains neutralizing antibodies against SARS-CoV-2 and remains active after standard milk pasteurization", @@ -391632,6 +392191,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2022.02.14.22270958", + "rel_title": "COVID-19 mortality and excess mortality among working-age Californians, by occupational sector: March 2020 through November 2021", + "rel_date": "2022-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.14.22270958", + "rel_abs": "BackgroundDuring the first year of the pandemic, essential workers faced higher rates of SARS-CoV-2 infection and COVID-19 mortality than non-essential workers. It is unknown whether disparities in pandemic-related mortality across occupational sectors have continued to occur, amidst SARS-CoV-2 variants and vaccine availability.\n\nMethodsWe obtained data on all deaths occurring in the state of California from 2016 through 2021. We restricted our analysis to California residents who were working age (18-65 years at time of death) and died of natural causes. Occupational sector was classified into 9 essential sectors; non-essential; or not in the labor market. We calculated the number of COVID-19 deaths in total and per capita that occurred in each occupational sector. Separately, using autoregressive integrated moving average models, we estimated total, per-capita, and relative excess natural-cause mortality by week between March 1, 2020, and November 30, 2021, stratifying by occupational sector. We additionally stratified analyses of occupational risk into regions with high versus low vaccine uptake, categorizing high-uptake regions as counties where at least 50% of the population completed a vaccination series by August 1, 2021.\n\nFindingsFrom March 2020 through November 2021, essential work was associated with higher COVID-19 and excess mortality compared with non-essential work, with the highest per-capita COVID-19 mortality in agriculture (131.8 per 100,000), transportation/logistics (107.1), manufacturing (103.3), and facilities (101.1). Essential workers continued to face higher COVID-19 and excess mortality during the period of widely available vaccines (March through November 2021). Between July and November 2021, emergency workers experienced higher per-capita COVID-19 mortality (113.7) than workers from any other sector. Essential workers faced the highest COVID-19 mortality in counties with low vaccination rates, a difference that was more pronounced during the period of the Delta surge in Summer 2021.\n\nInterpretationEssential workers have continued to bear the brunt of high COVID-19 and excess mortality throughout the pandemic, particularly in the agriculture, emergency, manufacturing, facilities, and transportation/logistics sectors. This high death toll has continued during periods of vaccine availability and the delta surge. In an ongoing pandemic without widespread vaccine coverage and anticipated threats of new variants, the US must actively adopt policies to more adequately protect essential workers.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yea-Hung Chen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alicia R Riley", + "author_inst": "University of California, Santa Cruz" + }, + { + "author_name": "Kate A Duchowny", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Helene E Aschmann", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Ruijia Chen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Mathew V Kiang", + "author_inst": "Stanford University" + }, + { + "author_name": "Alyssa Mooney", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Andrew C Stokes", + "author_inst": "Boston University" + }, + { + "author_name": "M Maria Glymour", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kirsten Bibbins-Domingo", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2022.02.11.22270859", "rel_title": "Clinical and economic benefits of lenzilumab plus standard of care compared with standard of care alone for the treatment of hospitalized patients with Coronavirus Disease 19 (COVID-19) from the perspective of National Health Service England", @@ -393295,37 +393909,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.14.480347", - "rel_title": "Molecular dynamics simulations of the Spike trimeric ectodomain of the SARS-CoV-2 Omicron variant: structural relationships with infectivity, evasion to immune system and transmissibility", - "rel_date": "2022-02-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.14.480347", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is replacing Delta, the most prevalent variant worldwide from the beginning of 2021 until early 2022. The Omicron variant is highly transmissible and responsible for a new worldwide COVID-19 wave. Herein, we calculated molecular dynamics simulations of the SARS-CoV-2 trimeric spike protein of Wuhan-Hu-1 strain (wild type, WT) and the Omicron variant of concern. Structural analyses reveal that the SpikeOmicron presents more conformational flexibility than SpikeWT, mainly in the N-terminal domain (NTD) and receptor-binding domain (RBD). Such flexibility results in a broader spectrum of different conformations for SpikeOmicron, whereby the RBD can more easily visit an up-conformational state. We reported how the mutations in this variant may influence the intra- and inter-protomer contacts caused by conformational flexibility of the NTD. Based on our analysis, we suggest that the differences in conformational flexibility between SpikeOmicron and SpikeWT may explain the observed gains in infectivity, immune system evasion and transmissibility in this novel variant.\n\nGraphical abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Vitor Martins de Freitas Amorim", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Robson F de Souza", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Anacleto Silva de Souza", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Cristiane Rodrigues Guzzo", - "author_inst": "Universidade de Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.02.12.480218", "rel_title": "Distinct upper airway epithelium interferon-stimulated and profibrotic gene expression between adult and infant rhesus macaques infected with SARS-CoV-2", @@ -393554,6 +394137,45 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.02.10.22270744", + "rel_title": "Coronavirus Disease 2019 (COVID-19) Vaccine Boosting in Persons Already Protected by Natural or Vaccine-Induced Immunity", + "rel_date": "2022-02-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.10.22270744", + "rel_abs": "BackgroundThe purpose of this study was to evaluate whether boosting healthcare personnel, already reasonably protected by prior infection or vaccination, with a vaccine developed for an earlier variant of COVID-19 protects against the Omicron variant.\n\nMethodsEmployees of Cleveland Clinic who were previously infected with or vaccinated against COVID-19, and were working in Ohio the day the Omicron variant was declared a variant of concern, were included. The cumulative incidence of COVID-19 was examined over two months during an Omicron variant surge. Protection provided by boosting (analyzed as a time-dependent covariate) was evaluated using Cox proportional hazards regression. Analyses were adjusted for time since proximate overt immunologic challenge (POIC) as a time-dependent covariate.\n\nResultsAmong 39 766 employees, 8037 (20%) previously infected and the remaining previously vaccinated, COVID-19 occurred in 6230 (16%) during the study. Risk of COVID-19 increased with time since POIC. In multivariable analysis, boosting was independently associated with lower risk of COVID-19 among those with vaccine-induced immunity (HR, .43; 95% CI, .41-.46) as well as those with natural immunity (HR, .66; 95% CI, .58-.76). Among those with natural immunity, receiving 2 compared to 1 dose of vaccine was associated with higher risk of COVID-19 (HR, 1.54; 95% CI, 1.21-1.97).\n\nConclusionsAdministering a COVID-19 vaccine not designed for the Omicron variant, 6 months or more after prior infection or vaccination, protects against Omicron variant infection in both previously infected and previously vaccinated individuals. There is no evidence of an advantage to administering more than 1 dose of vaccine to previously infected persons.\n\nSummaryAmong 39 766 Cleveland Clinic employees already protected by prior infection or vaccination, vaccine boosting after 6 months was associated with significantly lower risk of COVID-19. After COVID-19 infection, there was no advantage to more than one dose of vaccine.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nabin K Shrestha", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Priyanka Shrestha", + "author_inst": "Stanford University" + }, + { + "author_name": "Patrick C Burke", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Amy S Nowacki", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Paul Terpeluk", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Steven M Gordon", + "author_inst": "Cleveland Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.11.22270667", "rel_title": "Correlation between post-vaccination titres of combined IgG, IgA, and IgM anti-Spike antibodies and protection against breakthrough SARS-CoV-2 infection: a population-based longitudinal study (COVIDENCE UK)", @@ -395004,53 +395626,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.02.10.479714", - "rel_title": "Profiling of the most reliable mutations from sequenced SARS-CoV-2 genomes scattered in Uzbekistan", - "rel_date": "2022-02-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.10.479714", - "rel_abs": "Due to rapid mutations in the coronavirus genome over time and re-emergence of multiple novel variants of concerns (VOC), there is a continuous need for a periodic genome sequencing of SARS-CoV-2 genotypes of particular region. This is for on-time development of diagnostics, monitoring and therapeutic tools against virus in the global pandemics condition. Toward this goal, we have generated 18 high-quality whole-genome sequence data from 32 SARS-CoV-2 genotypes of PCR-positive COVID-19 patients, sampled from the Tashkent region of Uzbekistan. The nucleotide polymorphisms in the sequenced sample genomes were determined, including nonsynonymous (missense) and synonymous mutations in coding regions of coronavirus genome. Phylogenetic analysis grouped fourteen whole genome sample sequences (1, 2, 4, 5, 8, 10-15, 17, 32) into the G clade (or GR sub-clade) and four whole genome sample sequences (3, 6, 25, 27) into the S clade. A total of 128 mutations were identified, consisting of 45 shared and 83 unique mutations. Collectively, nucleotide changes represented one unique frameshift mutation, four upstream region mutations, six downstream region mutations, 50 synonymous mutations, and 67 missense mutations. The sequence data, presented herein, is the first coronavirus genomic sequence data from the Republic of Uzbekistan, which should contribute to enrich the global coronavirus sequence database, helping in future comparative studies. More importantly, the sequenced genomic data of coronavirus genotypes of this study should be useful for comparisons, diagnostics, monitoring, and therapeutics of COVID-19 disease in local and regional levels.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Mirzakamol S Ayubov", - "author_inst": "Center ofGenomics and Bioinformatics, Acacdemy of Sciences of Uzbekistan" - }, - { - "author_name": "Zabardast T. Buriev", - "author_inst": "Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan" - }, - { - "author_name": "Mukhammadjon K. Mirzakhmedov", - "author_inst": "Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan" - }, - { - "author_name": "Abdurakhmon N. Yusupov", - "author_inst": "Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan" - }, - { - "author_name": "Dilshod E. Usmanov", - "author_inst": "enter of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan" - }, - { - "author_name": "Shukhrat E. Shermatov", - "author_inst": "enter of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan" - }, - { - "author_name": "Khurshida A. Ubaydullaeva", - "author_inst": "Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan" - }, - { - "author_name": "Ibrokhim Abdurakhmonov", - "author_inst": "Center of Genomics and bioinformatics, Academy of Sciences of Uzbekistan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2022.02.08.22270649", "rel_title": "Innovative Randomized Phase 1 Study and Dosing Regimen Selection to Accelerate and Inform Pivotal COVID-19 Trial of Nirmatrelvir", @@ -395367,6 +395942,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.09.22270747", + "rel_title": "Immune responses after twofold SARS-CoV-2 immunisation in elderly residents and Health Care Workers in nursing homes and homes with assisted living support - Proposal for a correlate of protection", + "rel_date": "2022-02-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.09.22270747", + "rel_abs": "In the present study, we were interested in the decline over time of anti SARS-CoV-2 antibodies and SARS-CoV-2 specific T-cell responses after two doses of mRNA vaccines in total and by age group and comorbidity. The second goal was to suggest an immunological correlate for protection on an individual basis and to describe the probability of protection over time after second vaccination.\n\nWe analysed blood samples from 228 residents (median age 83.8 years) and from 273 Health Care Workers (HCW; median age 49.7 years) of five nursing homes and one home for the elderly with assisted living support. Participants had received two vaccinations. The blood samples were analysed for SARS-CoV-2 specific antibody and T-cell responses. We compared outcomes in the HCW and residents in the respective institutions. No breakthrough infections occurred during the study period. The initial immune responses in the younger participants were about 30 % higher than in the older ones. Over time, all parameters dropped continuously in all groups within the maximum observation period of 232 days. Comorbidities such as coronary heart disease or diabetes mellitus reduced the initial immune responses, regardless of age. In contrast to an almost linear decline in antibody levels, we observed that the interferon-gamma response remained at a constant level between about day 120 and 180, only to decline further thereafter.\n\nBased on our data, we propose on an individual level a correlate of protection: Persons who have a neutralizing capacity of 75 % (which would correspond to approx. 200 BAU/ml) and an interferon-gamma response above 200 mIU/ml should be considered to be protected resp. sufficiently immunized.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Julia Schiffner", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Nora Eisemann", + "author_inst": "Institute of Social Medicine and Epidemiology, University of Luebeck, Germany" + }, + { + "author_name": "Hannah Baltus", + "author_inst": "Institute of Social Medicine and Epidemiology, University of Luebeck, Germany" + }, + { + "author_name": "Sina Jensen", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Katharina Wunderlich", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Stefan Schuesseler", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Charlotte Eicker", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Bianca Teegen", + "author_inst": "Klinisch-Immunologisches Labor Stoecker, Luebeck, Germany" + }, + { + "author_name": "Doreen Boniakowsky", + "author_inst": "Vorwerker Diakonie gemeinnuetzige GmbH, Luebeck, Germany" + }, + { + "author_name": "Werner Solbach", + "author_inst": "Center for Infection and Inflammation Research, University of Luebeck, Luebeck, Germany, German Center for Infection Research (DZIF), Luebeck, Germany" + }, + { + "author_name": "Alexander Mischnik", + "author_inst": "Health Protection Authority, Luebeck, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.02.10.22270783", "rel_title": "Implementation and economic effects of local non-pharmaceutical interventions", @@ -396882,45 +397516,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2022.02.08.22270591", - "rel_title": "Bacterial Pneumonia and Respiratory Culture Utilization among Hospitalized Patients with and without COVID-19 in New York City", - "rel_date": "2022-02-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.08.22270591", - "rel_abs": "COVID-19 is associated with prolonged hospitalization and a high risk of intubation, which raises concern for bacterial co-infection and antimicrobial resistance. Previous research has shown a wide range of bacterial pneumonia rates for COVID-19 patients in a variety of clinical and demographic settings, but none have compared hospitalized COVID-19 patients to patients testing negative for SARS-CoV-2 in similar care settings. We performed a retrospective cohort study on hospitalized patients with COVID-19 testing from 10 March 2020 to 31 December 2020. A total of 19,219 patients were included, of which 3,796 tested positive for SARS-CoV-2. We found a 2.6-fold increase (p < 0.001) in respiratory culture ordering in COVID-19 patients. On a per-patient basis, COVID-19 patients were 1.5-fold more likely than non-COVID patients to have abnormal respiratory cultures (46.8% vs. 30.9%, p < 0.001), which was primarily driven by patients requiring intubation. Among patients with pneumonia, a significantly higher proportion of COVID-19 patients had ventilator-associated pneumonia (VAP) relative to non-COVID patients (85.7% vs 55.1%, p <0.001), but a lower proportion had community-acquired (12.2% vs 22.1%, p < 0.01) or hospital-acquired pneumonia (2.1% vs. 22.8%, p < 0.001). There was also a significantly higher proportion of respiratory cultures positive for MRSA, K. pneumoniae, and antibiotic-resistant organisms in COVID-19 patients. Increased rates of respiratory culture ordering for COVID-19 patients therefore appear to be clinically justified for patients requiring intubation, but further research is needed to understand how SARS-CoV-2 increases the risk of VAP.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Maxwell Drach Weidmann", - "author_inst": "Columbia University Medical Center" - }, - { - "author_name": "Gregory J Berry", - "author_inst": "Columbia University Medical Center" - }, - { - "author_name": "Jason E. Zucker", - "author_inst": "Columbia University Medical Center" - }, - { - "author_name": "Simian Huang", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Magdalena E Sobieszczyk", - "author_inst": "Columbia University Medical Center" - }, - { - "author_name": "Daniel A. Green", - "author_inst": "Columbia University Irving Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.07.479468", "rel_title": "Distinct sensitivities to SARS-CoV-2 variants in vaccinated humans and mice", @@ -397233,6 +397828,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.07.479477", + "rel_title": "The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature", + "rel_date": "2022-02-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.07.479477", + "rel_abs": "The NSP3 macrodomain of SARS CoV 2 (Mac1) removes ADP-ribosylation post-translational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the COVID-19 pandemic. Here, we determined neutron and X-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site, and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a re-evaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Galen J Correy", + "author_inst": "Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Daniel W Kneller", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Gwyndalyn Phillips", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Swati Pant", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Silvia Russi", + "author_inst": "Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA" + }, + { + "author_name": "Aina E Cohen", + "author_inst": "Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA" + }, + { + "author_name": "George Meigs", + "author_inst": "Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA" + }, + { + "author_name": "James M Holton", + "author_inst": "Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA" + }, + { + "author_name": "Stefan Gahbauer", + "author_inst": "Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA" + }, + { + "author_name": "Michael C Thompson", + "author_inst": "Department of Chemistry and Chemical Biology, University of California Merced, CA 95343, USA" + }, + { + "author_name": "Alan Ashworth", + "author_inst": "Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA 94158, USA" + }, + { + "author_name": "Leighton Coates", + "author_inst": "Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Andrey Kovalevsky", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "Flora Meilleur", + "author_inst": "Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA" + }, + { + "author_name": "James S Fraser", + "author_inst": "Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.02.07.479471", "rel_title": "The mechanism of RNA capping by SARS-CoV-2", @@ -398980,37 +399650,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.06.22270562", - "rel_title": "Circulating polyunsaturated fatty acids and COVID-19: a prospective cohort study and Mendelian randomization analysis", - "rel_date": "2022-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.06.22270562", - "rel_abs": "BackgroundHigher circulating polyunsaturated fatty acids (PUFAs), especially omega-3 ones, have been linked to a better prognosis in patients of coronavirus disease 2019 (COVID-19). However, the effects and causality of pre-infection PUFA levels remain unclear.\n\nObjectiveTo investigate the observational and causal associations of circulating PUFAs with COVID-19 susceptibility and severity.\n\nDesignWe first performed a prospective cohort study in UK Biobank, with 20,626 controls who were tested negative and 4,101 COVID-19 patients, including 970 hospitalized ones. Plasma PUFAs at baseline were measured by nuclear magnetic resonance, including total PUFAs, omega-3 PUFAs, omega-6 PUFAs, docosahexaenoic acid (DHA), linoleic acid (LA), and the omega-6/omega-3 ratio. Moreover, bidirectional two-sample Mendelian randomization (MR) analyses were performed to examine the causal associations of eight individual PUFAs, measured in either plasma or red blood cells, with COVID-19 susceptibility and severity using summary statistics from existing genome-wide association studies.\n\nResultsIn the observational association analysis, total PUFAs, omega-3 PUFAs, omega-6 PUFAs, DHA, and LA were associated with a lower risk of severe COVID-19. Omega-3 PUFAs and DHA were also associated with a lower risk of testing positive for COVID-19. The omega-6/omega-3 ratio was positively associated with risks of both susceptibility and severity. The forward MR analysis indicated that arachidonic acid (AA) and docosapentaenoic acid (DPA-n3) might be causally associated with a lower risk of severe COVID-19, with OR (95% CI) per one SD increase in the plasma level as 0.96 (0.94, 0.99) and 0.89 (0.81, 0.99), respectively. The reverse MR analysis did not support any causal effect of COVID-19 on PUFAs.\n\nConclusionsOur observational analysis supported that higher circulating PUFAs, either omega-3 or omega-6, are protective against severe COVID-19, while omega-3 PUFAs, especially DHA, were also associated with reducing COVID-19 susceptibility. Our MR analysis further supported causal associations of AA and DPA-n3 with a lower risk of severe COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Yitang Sun", - "author_inst": "Department of Genetics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA" - }, - { - "author_name": "Radhika Chatterjee", - "author_inst": "Department of Genetics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA" - }, - { - "author_name": "Akash Ronanki", - "author_inst": "Department of Genetics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA" - }, - { - "author_name": "Kaixiong Ye", - "author_inst": "Department of Genetics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, University of Georgia, Athen" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.07.22270437", "rel_title": "Increased household transmission and immune escape of the SARS-CoV-2 Omicron variant compared to the Delta variant: evidence from Norwegian contact tracing and vaccination data", @@ -399311,6 +399950,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.02.07.22270555", + "rel_title": "Clinical outcomes in hospitalized vaccine-breakthrough COVID-19 cases compared with contemporary unvaccinated hospitalized adults", + "rel_date": "2022-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270555", + "rel_abs": "SummaryThe inactivated SARS-CoV-2 vaccine (CoronaVac(R)) has been the principal vaccine used in Chiles pre-booster immunization campaign. We compared major outcomes in 260 hospitalized vaccinated vs 507 unvaccinated adults with COVID-19 (mid-2021). The vaccinated group was much older, required less critical care, had lower hospital mortality (adjusted by age), and had shorter hospitalization than the unvaccinated. Benefits were most pronounced in those older than 59 years\n\nObjectiveTo compare major outcomes in fully vaccinated and unvaccinated adult persons hospitalized for COVID-19 in a general private hospital in Santiago, Chile during mid2021.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Marcelo J Wolff Sr.", + "author_inst": "Clinica Santa Maria; U. of Chile School of Medicine;" + }, + { + "author_name": "Margarita Gilabert", + "author_inst": "Clinica Santa Maria, Santiago, Chile" + }, + { + "author_name": "Rodrigo Hernandez", + "author_inst": "Clinica Santa maria, Santiago, Chile" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.07.22270613", "rel_title": "Time to reinfection and vaccine breakthrough SARS-CoV-2 infections: a retrospective cohort study", @@ -401026,37 +401692,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.02.04.479136", - "rel_title": "Mutations of Omicron variant at the interface of the receptor domain motif and human angiotensin-converting enzyme-2", - "rel_date": "2022-02-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.04.479136", - "rel_abs": "The most recent Omicron variant of SARS-CoV-2 has caused global concern and anxiety. The only thing certain about this strain, with large number of mutations in the spike protein, is that it spreads quickly, seems to evade immune defense and mitigates the benefits of existing vaccines. Based on the ultra-large-scale ab initio computational modeling of the receptor binding motif (RBM) and human angiotensin-converting enzyme-2 (ACE2) interface we provide the details of the effect of Omicron mutations at the fundamental atomic scale level. In-depth analysis anchored in the novel concept of amino acid-amino acid bond pair units (AABPU), indicates that mutations in the Omicron variant are connected with (i) significant changes in the shape and structure of AABPU components, together with (ii) significant increase in the positive partial charge which facilitates the interaction with ACE2. The calculated bond order, based on AABPU, reveals that the Omicron mutations increase the binding strength of RBM to ACE2. Our findings correlate with and are instrumental to explain the current observations and can contribute to the prediction of next potential new variant of concern.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Puja Adhikari", - "author_inst": "University of Missouri-Kansas City" - }, - { - "author_name": "Bahaa Jawad", - "author_inst": "University of Missouri-Kansas City" - }, - { - "author_name": "Rudolf Podgornik", - "author_inst": "University of Chinese Academy of Sciences" - }, - { - "author_name": "Wai-Yim Ching", - "author_inst": "University of Missouri-Kansas City" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.02.04.479189", "rel_title": "Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer", @@ -401313,6 +401948,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.06.479332", + "rel_title": "A potent SARS-CoV-2 neutralizing antibody recognizing a conserved epitope with broad mutant variant and SARS-CoV activity.", + "rel_date": "2022-02-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.06.479332", + "rel_abs": "COVID-19 is the deadliest respiratory virus pandemic since 1918 and the latest of several coronavirus epidemics and pandemics in recent years. Despite the unprecedented response by both the government and private sectors to develop vaccines and therapies, the evolution of SARS-CoV-2 variants resistant to these interventions reveals a crucial need for therapeutics that maintain their efficacy against current and future mutant variants. Here we describe a SARS-CoV-2 neutralizing antibody, ABP-310, with potent activity against all variants tested including the Omicron variant. ABP-310 also displays potent neutralizing activity against SARS-CoV, highlighting the conserved nature of the ABP-310 epitope. By targeting a conserved epitope, we believe that ABP-310 has therapeutic promise not only against the current SARS-CoV-2 variants but would be expected to maintain efficacy against future variants and possibly even novel coronaviruses.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Adam J Pelzek", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Sanam Ebtehaj", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "James Lulo", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Lucy Zhang", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Olivia Balduf", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Lindsay Dolan", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Chaohua Zhang", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Shengqin Wan", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Gang An", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Awo Kankam", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Eugene Chan", + "author_inst": "Abpro Corporation" + }, + { + "author_name": "Shaun P Murphy", + "author_inst": "Abpro Corporation" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.06.479285", "rel_title": "Vaccine Protection Against the SARS-CoV-2 Omicron Variant in Macaques", @@ -403284,249 +403982,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.04.22270304", - "rel_title": "Effective high-throughput RT-qPCR screening for SARS-CoV-2 infections in children", - "rel_date": "2022-02-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.04.22270304", - "rel_abs": "Systematic SARS-CoV-2 testing is a valuable tool for infection control and surveillance. However, broad application of high sensitive RT-qPCR testing in children is often hampered due to unpleasant sample collection, limited RT-qPCR capacities and high costs. Here, we developed a high-throughput approach ( Lolli-Method) for SARS-CoV-2 detection in children, combining non-invasive sample collection with an RT-qPCR-pool testing strategy. SARS-CoV-2 infections were diagnosed with sensitivities of 100% and 93.9% when viral loads were >106 copies/ml and >103 copies/ml in corresponding Naso-/Oropharyngeal-swabs, respectively. For effective application of the Lolli-Method in schools and daycare facilities, SEIR-modeling indicated a preferred frequency of two tests per week. The developed test strategy was implemented in 3,700 schools and 698 daycare facilities in Germany, screening over 800,000 individuals twice per week. In a period of 3 months, 6,364 pool-RT-qPCRs tested positive (0.64%), ranging from 0.05% to 2.61% per week. Notably, infections correlated with local SARS-CoV-2 incidences and with a school social deprivation index. Moreover, in comparison with the alpha variant, statistical modeling revealed a 36.8% increase for multiple ([≥]2 children) infections per class following infections with the delta variant. We conclude that the Lolli-Method is a powerful tool for SARS-CoV-2 surveillance and infection control in schools and daycare.", - "rel_num_authors": 57, - "rel_authors": [ - { - "author_name": "Felix Dewald", - "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Isabelle Suarez", - "author_inst": "Department I of Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Ronja Johnen", - "author_inst": "CECAD Research center, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Jan Grossbach", - "author_inst": "CECAD Research center, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Roberto Tovar", - "author_inst": "Institute for Biological Physics, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Gertrud Steger", - "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Alexander Joachim", - "author_inst": "Department of Pediatrics, Childrens and Adolescents Hospital, University Hospital Cologne, Faculty of Medicine, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Gibran Rubio", - "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Mira Fries", - "author_inst": "Health department of Cologne, Cologne, Germany" - }, - { - "author_name": "Florian Behr", - "author_inst": "Health department of Cologne, Cologne, Germany" - }, - { - "author_name": "Joao Kley", - "author_inst": "Department I of Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Andreas Lingnau", - "author_inst": "Ministry of Schools and Education of North Rhine-Westphalia, Duesseldorf, Germany" - }, - { - "author_name": "Alina Kretschmer", - "author_inst": "Department I of Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Carina Gude", - "author_inst": "CECAD Research center, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Guadelupe Flores", - "author_inst": "Centro de Investigacion en Enfermedades Tropicales y Emergentes, Hospital Regional de Alta Especialidad, Dr. Juan Graham Casasus, Villahermosa, Mexico" - }, - { - "author_name": "David del Valle", - "author_inst": "Centro de Investigacion en Enfermedades Tropicales y Emergentes, Hospital Regional de Alta Especialidad, Dr. Juan Graham Casasus, Villahermosa, Mexico" - }, - { - "author_name": "Alberto Hernandez", - "author_inst": "Centro de Investigacion en Enfermedades Tropicales y Emergentes, Hospital Regional de Alta Especialidad, Dr. Juan Graham Casasus, Villahermosa, Mexico" - }, - { - "author_name": "Jesus Cerino", - "author_inst": "Centro de Investigacion en Enfermedades Tropicales y Emergentes, Hospital Regional de Alta Especialidad, Dr. Juan Graham Casasus, Villahermosa, Mexico" - }, - { - "author_name": "Adriana Hernandez", - "author_inst": "Bioclilab SA de CV, Villahermosa, Mexico" - }, - { - "author_name": "Jesus Quinones", - "author_inst": "Centro de Investigacion en Enfermedades Tropicales y Emergentes, Hospital Regional de Alta Especialidad, Dr. Juan Graham Casasus, Villahermosa, Mexico" - }, - { - "author_name": "Konstantin Schega", - "author_inst": "Health department of Cologne, Cologne, Germany" - }, - { - "author_name": "Viktoria Linne", - "author_inst": "Department I of Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Lena Junker", - "author_inst": "Department I of Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Marie Wunsch", - "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Eva Heger", - "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Elena Knops", - "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Veronica Di Cristanziano", - "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Meike Meyer", - "author_inst": "Department of Pediatrics, Childrens and Adolescents Hospital, University Hospital Cologne, Faculty of Medicine, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Christoph Huenseler", - "author_inst": "Department of Pediatrics, Childrens and Adolescents Hospital, University Hospital Cologne, Faculty of Medicine, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Lutz T. Weber", - "author_inst": "Department of Pediatrics, Childrens and Adolescents Hospital, University Hospital Cologne, Faculty of Medicine, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Jan Lueers", - "author_inst": "Department of Otorhinolaryngology, Head and Neck Surgery, University of Cologne, Cologne" - }, - { - "author_name": "Gustav Quade", - "author_inst": "MVZ Labor Dr. Quade und Kollegen GmbH, Cologne, Germany" - }, - { - "author_name": "Hilmar Wisplinghoff", - "author_inst": "Labor Dr. Wisplinghoff, Cologne, Germany" - }, - { - "author_name": "Carsten Tiemann", - "author_inst": "Labor Krone, Bad Salzuflen, Germany" - }, - { - "author_name": "Rainer Zotz", - "author_inst": "Labor ZotzKlimas, Duesseldorf, Germany" - }, - { - "author_name": "Hassan Jomaa", - "author_inst": "Synlab, Leverkusen, Germany" - }, - { - "author_name": "Arthur Pranada", - "author_inst": "Medizinisches Versorgungszentrum Dr. Eberhard und Partner, Dortmund, Germany" - }, - { - "author_name": "Ileana Herzum", - "author_inst": "Medizinische Laboratorien Duesseldorf, Duesseldorf, Germany" - }, - { - "author_name": "Paul Cullen", - "author_inst": "MVZ Labor Muenster, Muenster, Germany" - }, - { - "author_name": "Franz Schmitz", - "author_inst": "Muehlenkreiskliniken, Minden, Germany" - }, - { - "author_name": "Paul Philipsen", - "author_inst": "Labor Moenchengladbach MVZ Dr. Stein und Kollegen, Moenchengladbach, Germany" - }, - { - "author_name": "Georg Kirchner", - "author_inst": "Eurofins Laborbetriebsgesellschaft Gelsenkirchen GmbH und Eurofins MVZ Medizinisches Labor Gelsenkirchen GmbH, Gelsenkirchen, Germany" - }, - { - "author_name": "Cornelius Knabbe", - "author_inst": "Heart and Diabetes Center NRW, Medical Faculty, Ruhr University Bochum, Institute for Laboratory and Transfusion Medicine, Bochum, Germany" - }, - { - "author_name": "Martin Hellmich", - "author_inst": "Institute of Medical Statistics and Computational Biology, Faculty of Medicine and University Hospital Cologne, University of Cologne" - }, - { - "author_name": "Michael Buess", - "author_inst": "Health department of Cologne, Cologne, Germany" - }, - { - "author_name": "Anna Wolf", - "author_inst": "Health department of Cologne, Cologne, Germany" - }, - { - "author_name": "Annelene Kossow", - "author_inst": "Health department of Cologne, Cologne, Germany" - }, - { - "author_name": "Johannes Niessen", - "author_inst": "Health department of Cologne, Cologne, Germany" - }, - { - "author_name": "Sebastian Jeworutzki", - "author_inst": "Faculty of Social Science, Ruhr-University Bochum, Bochum, Germany" - }, - { - "author_name": "Joerg Schraepler", - "author_inst": "Faculty of Social Science, Ruhr-University Bochum, Bochum, Germany" - }, - { - "author_name": "Michael Laessig", - "author_inst": "Institute for Biological Physics, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Joerg Doetsch", - "author_inst": "Department of Pediatrics, Childrens and Adolescents Hospital, University Hospital Cologne, Faculty of Medicine, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Gerd Faetkenheuer", - "author_inst": "Department I of Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Rolf Kaiser", - "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Andreas Beyer", - "author_inst": "CECAD Research center, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Jan Rybniker", - "author_inst": "Department I of Internal Medicine, Division of Infectious Diseases, University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Florian Klein", - "author_inst": "Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.03.22270365", "rel_title": "Post-peak dynamics of a national Omicron SARS-CoV-2 epidemic during January 2022", @@ -403891,6 +404346,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.04.22270433", + "rel_title": "The usefulness of D-dimer as a predictive marker for mortality in patients with COVID-19 hospitalized during the first wave in Italy.", + "rel_date": "2022-02-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.04.22270433", + "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) presents an urgent threat to global health. Identification of predictors of poor outcomes will assist medical staff in treatment and allocating limited healthcare resources.\n\nAimsThe primary aim was to study the value of D-dimer as a predictive marker for in-hospital mortality.\n\nMethodsThis was a cohort study. The study population consisted of hospitalized patients (age >18 years), who were diagnosed with COVID-19 based on real-time PCR at 9 hospitals during the first COVID-19 wave in Lombardy, Italy (Feb-May 2020). The primary endpoint was in-hospital mortality. Information was obtained from patient records. Statistical analyses were performed using a Fine-Gray competing risk survival model. Model discrimination was assessed using Harrells C-index and model calibration was assessed using a calibration plot.\n\nResultsOut of 1049 patients, 501 patients had evaluable data. Of these 501 patients, 96 died. The cumulative incidence of in-hospital mortality within 30 days was 20% (95CI: 16%-23%), and the majority of deaths occurred within the first 10 days. A prediction model containing D-dimer as the only predictor had a C-index of 0.66 (95%CI: 0.61-0.71). Overall calibration of the model was very poor. The addition of D-dimer to a model containing age, sex and co-morbidities as predictors did not lead to any meaningful improvement in either the C-index or the calibration plot.\n\nConclusionThe predictive value of D-dimer alone was moderate, and the addition of D-dimer to a simple model containing basic clinical characteristics did not lead to any improvement in model performance.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Shermarke Hassan", + "author_inst": "University of Milan" + }, + { + "author_name": "Barbara Ferrari", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Raffaella Rossio", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Vincenzo la Mura", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Andrea Artoni", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Roberta Gualtierotti", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Ida Martinelli", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Alessandro Nobili", + "author_inst": "Mario Negri Institute for Pharmacological Research Branch of Milan: Istituto di Ricerche Farmacologiche Mario Negri" + }, + { + "author_name": "Alessandra Bandera", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Andrea Gori", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Francesco Blasi", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Valter Monzani", + "author_inst": "Policlinico di Milano: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Giorgio Costantino", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Sergio Harari", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "Frits Richard Rosendaal", + "author_inst": "Leiden Universitair Medisch Centrum: Leids Universitair Medisch Centrum" + }, + { + "author_name": "Flora Peyvandi", + "author_inst": "Universit\u00e0 degli Studi di Milano: Universita degli Studi di Milano" + }, + { + "author_name": "the COVID-19 Network working group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.05.22270499", "rel_title": "Comparative study of immunogenicity and safety of Gam-COVID-Vac and Sinopharm BBIBP-CorV vaccines in Belarus", @@ -405510,41 +406048,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2022.02.03.479081", - "rel_title": "Circulatory exosomes from COVID-19 patients trigger NLRP3 inflammasome in endothelial cells", - "rel_date": "2022-02-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.03.479081", - "rel_abs": "SARS-CoV-2 infection induces inflammatory response, cytokine storm, venous thromboembolism, coagulopathy, and multiple organ damage. Resting endothelial cells prevent coagulation, control blood flow and inhibit inflammation. However, it remains unknown how SARS-CoV-2 induces strong molecular signals in distant cells for immunopathogenesis. In this study, we examined the consequence of human endothelial cells (microvascular endothelial cells (HMEC-1) and liver endothelial cells (TMNK-1)) to exosomes from plasma of severe COVID-19 patients. We observed a significant induction of NLRP3, caspase-1 and IL-1{beta} mRNA expression in the endothelial cells following exposure to exosomes from plasma of COVID-19 patients as compared to that of healthy donors. Activation of caspase-1 was noted in the endothelial cell culture medium following exposure to the COVID-19 exosomes. Further, COVID-19 exosomes significantly induced mature IL-1{beta} secretion in the endothelial cell culture medium. Thus, our results demonstrated for the first time that exosomes from COVID-19 plasma trigger NLRP3 inflammasome in endothelial cells of distant organs.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Subhayan Sur", - "author_inst": "Saint Louis University" - }, - { - "author_name": "robert steele", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Scott Isbell", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Ranjit Ray", - "author_inst": "St. Louis University" - }, - { - "author_name": "Ratna B Ray", - "author_inst": "Saint Louis University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.02.03.479007", "rel_title": "VE607 Stabilizes SARS-CoV-2 Spike In the \"RBD-up\" Conformation and Inhibits Viral Entry", @@ -405977,6 +406480,53 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.02.03.22270401", + "rel_title": "RISK STRATIFICATION OF PATIENTS WITH COVID-19 DISEASE THROUGH THE USE OF CLINICAL SCORES IN AN EMERGENCY DEPARTMENT. A review of the literature", + "rel_date": "2022-02-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22270401", + "rel_abs": "DISCLAIMER STATEMENTThe authors have withdrawn the manuscript because there are some errors in the Area Under the Curve values regarding to intensive care unit admission and mortality for some scores analyzed. The article must be revised in its conclusions in order to affirm that NEWS and NEWS2 are the best clinical scores to be used in Emergency to evaluate patients with Covid-19 disease.\n\nTherefore, the authors do not wish this work to be cited as reference for one project. If you have any questions, please contact the corresponding author.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Simone Zanella", + "author_inst": "APSS Trento" + }, + { + "author_name": "Francesco Zanella", + "author_inst": "APSS Trento" + }, + { + "author_name": "Alena Mancosu", + "author_inst": "University of Verona" + }, + { + "author_name": "Anna Brugnolli", + "author_inst": "Nursing School of Trento, University of Verona" + }, + { + "author_name": "Alessandro Carrara", + "author_inst": "APSS Trento" + }, + { + "author_name": "Anita Bevilacqua", + "author_inst": "Nursing School of Trento, University of Verona" + }, + { + "author_name": "Elisa Marinelli", + "author_inst": "Nursing School of Trento, University of Verona" + }, + { + "author_name": "Nicola Ricci", + "author_inst": "APSS Trento" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2022.02.03.22270417", "rel_title": "Fatality assessment and variant risk monitoring for COVID-19 using three new hospital occupancy related metrics", @@ -407424,77 +407974,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.02.22269258", - "rel_title": "At-Home Testing Study to Assess Risk Factors for Acquisition of SARS-CoV-2 Infection in a Major US Metropolitan Area", - "rel_date": "2022-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22269258", - "rel_abs": "ImportanceUnbiased assessment of risks associated with acquisition of SARS-CoV-2 is critical to informing mitigation efforts during pandemics.\n\nObjectiveUnderstand risk factors for acquiring COVID-19 in a large, prospective cohort of adult residents recruited to be representative of a large US metropolitan area.\n\nDesignFully remote longitudinal cohort study launched in October 2020 and ongoing; Study data reported through June 15, 2021.\n\nSettingBrigham and Womens Hospital, Boston MA.\n\nParticipantsAdults within 45 miles of Boston, MA.\n\nInterventionMonthly at-home SARS-CoV-2 viral and antibody testing.\n\nMain OutcomesBetween October 2020 and January 2021, we enrolled 10,289 adults reflective of Massachusetts census data. At study entry, 567 (5.5%) participants had evidence of current or prior SARS-CoV-2 infection. This increased to 13.4% by June 15, 2021. Compared to whites, Black non-Hispanic participants had a 2.2 fold greater risk of acquiring COVID-19 (HR 2.19, 95% CI 1.91-2.50; p=<0.001) and Hispanics had a 1.5 fold greater risk (HR 1.52, 95% CI 1.32-1.71; p=<0.016). Individuals aged 18-29, those who worked outside the home, and those living with other adults and children were at an increased risk. Individuals in the second and third lowest disadvantaged neighborhood communities, as measured by the area deprivation index as a marker for socioeconomic status by census block group, were associated with an increased risk in developing COVID-19. Individuals with medical risk factors for severe COVID-19 disease were at a decreased risk of SARS-CoV-2 acquisition.\n\nConclusionsThese results demonstrate that race/ethnicity and socioeconomic status are not only risk factors for severity of disease but are also the biggest determinants of acquisition of infection. Importantly, this disparity is significantly underestimated if based on PCR data alone as noted by the discrepancy in serology vs. PCR detection for non-white participants, and points to persistent disparity in access to testing. Meanwhile, medical conditions and advanced age that increase the risk for severity of SARS-CoV-2 disease were associated with a lower risk of acquisition of COVID-19 suggesting the importance of behavior modifications. These findings highlight the need for mitigation programs that overcome challenges of structural racism in current and future pandemics.\n\nTrial RegistrationN/A\n\nKEY POINTS\n\nQuestionWhat population and occupational groups in the United States are at increased risk for acquiring COVID-19?\n\nFindingsIn this remote, longitudinal cohort study involving monthly PCR and serology self-testing of 10,289 adult residents of the Boston metropolitan area, 9257 (90.0%) of TestBoston participants acquired evidence of immunity to SARS-CoV-2 through vaccination, infection, or both as of June 15, 2021. Residents identifying as Black, Hispanic/Latinx had an increased risk of acquisition of COVID-19. Healthcare workers were not at increased risk of SARS-CoV-2 acquisition. Individuals with medical risk factors for severe COVID-19 disease were at a decreased risk of SARS-CoV-2 acquisition.\n\nMeaningThese results demonstrate that race/ethnicity and socioeconomic status are not only risk factors for severity of disease but also are the biggest determinants of acquisition of infection. These findings highlight the need to address the consequences of structural racism during the development of mitigation programs for current and future pandemics.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Ann E Woolley", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Scott Dryden-Peterson", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Andy Kim", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Sarah Naz-McLean", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Christina Kelly", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Hannah H Laibinis", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Josephine Bagnall", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Jonathan Livny", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Peijun Ma", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Marek Orzechowski", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Noam Shoresh", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Stacey Gabriel", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Deborah T Hung", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Lisa A Cosimi", - "author_inst": "Brigham and Women's Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.03.22270393", "rel_title": "Concordance of B and T cell responses to SARS-CoV-2 infection, irrespective of symptoms suggestive of COVID-19.", @@ -407719,6 +408198,201 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.02.03.22270391", + "rel_title": "Device-assessed sleep and physical activity in individuals recovering from a hospital admission for COVID-19: a prospective, multicentre study", + "rel_date": "2022-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22270391", + "rel_abs": "ObjectivesTo describe physical behaviours following hospital admission for COVID-19 including associations with acute illness severity and ongoing symptoms.\n\nMethods1077 patients with COVID-19 discharged from hospital between March and November 2020 were recruited. Using a 14-day wear protocol, wrist-worn accelerometers were sent to participants after a five-month follow-up assessment. Acute illness severity was assessed by the WHO clinical progression scale, and the severity of ongoing symptoms was assessed using four previously reported data-driven clinical recovery clusters. Two existing control populations of office workers and type 2 diabetes were comparators.\n\nResultsValid accelerometer data from 253 women and 462 men were included. Women engaged in a mean{+/-}SD of 14.9{+/-}14.7 minutes/day of moderate-to-vigorous physical activity (MVPA), with 725.6{+/-}104.9 minutes/day spent inactive and 7.22{+/-}1.08 hours/day asleep. The values for men were 21.0{+/-}22.3 and 755.5{+/-}102.8 minutes/day and 6.94{+/-}1.14 hours/day, respectively. Over 60% of women and men did not have any days containing a 30-minute bout of MVPA. Variability in sleep timing was approximately 2 hours in men and women. More severe acute illness was associated with lower total activity and MVPA in recovery. The very severe recovery cluster was associated with fewer days/week containing continuous bouts of MVPA, longer sleep duration, and higher variability in sleep timing. Patients post-hospitalisation with COVID-19 had lower levels of physical activity, greater sleep variability, and lower sleep efficiency than a similarly aged cohort of office workers or those with type 2 diabetes.\n\nConclusionsPhysical activity and regulating sleep patterns are potential treatable traits for COVID-19 recovery programmes.", + "rel_num_authors": 45, + "rel_authors": [ + { + "author_name": "Tatiana Plekhanova", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Alex V Rowlands", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Rachael A Evans", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Charlotte L Edwardson", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Nicolette C Bishop", + "author_inst": "School of Sport, Exercise and Health Sciences, Loughborough University, Loughborough, UK" + }, + { + "author_name": "Charlotte E Bolton", + "author_inst": "University of Nottingham, Nottingham, UK" + }, + { + "author_name": "James D Chalmers", + "author_inst": "University of Dundee, Ninewells Hospital and Medical School, Dundee, UK" + }, + { + "author_name": "Melanie J Davies", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Enya Daynes", + "author_inst": "NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Annemarie B Docherty", + "author_inst": "Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Omer Elneima", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Neil J Greening", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Sharlene A Greenwood", + "author_inst": "King's College Hospital, Department of Physiotherapy and Renal Medicine, London, UK" + }, + { + "author_name": "Andrew P Hall", + "author_inst": "University Hospitals of Leicester NHS Trust, Leicester, UK" + }, + { + "author_name": "Victoria C Harris", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Ewen M Harrison", + "author_inst": "Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Joseph Henson", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Ling-Pei Ho", + "author_inst": "MRC Human Immunology Unit, University of Oxford, Oxford, UK" + }, + { + "author_name": "Alex Horsley", + "author_inst": "Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK" + }, + { + "author_name": "Linzy Houchen-Wolloff", + "author_inst": "Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Olivia C Leavy", + "author_inst": "Department of Health Sciences, University of Leicester, Leicester, UK" + }, + { + "author_name": "Nazir I Lone", + "author_inst": "Usher Institute, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Michael Marks", + "author_inst": "Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK" + }, + { + "author_name": "Ben Maylor", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Hamish J C McAuley", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Claire M Nolan", + "author_inst": "Harefield Respiratory Research Group, Royal Brompton and Harefield Clinical Group, Guys and St. Thomas NHS Foundation Trust, London, UK" + }, + { + "author_name": "Krisnah Poinasamy", + "author_inst": "Asthma UK and British Lung Foundation, London, UK" + }, + { + "author_name": "Jennifer K Quint", + "author_inst": "NHLI, Imperial College London, London, UK" + }, + { + "author_name": "Betty Raman", + "author_inst": "Radcliffe Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "Matthew Richardson", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Jack A Sargeant", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Ruth M Saunders", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Marco Sereno", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Aarti Shikotra", + "author_inst": "NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Amisha Singapuri", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Michael Steiner", + "author_inst": "Department of Respiratory Sciences, University of Leicester, Leicester, UK" + }, + { + "author_name": "David J Stensel", + "author_inst": "NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Louise V Wain", + "author_inst": "Department of Health Sciences, University of Leicester, Leicester, UK" + }, + { + "author_name": "Julie Whitney", + "author_inst": "School of Life Course & Population Sciences, Kings College London, London, UK" + }, + { + "author_name": "Dan G Wootton", + "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK" + }, + { + "author_name": "Christopher E Brightling", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "William D-C Man", + "author_inst": "Royal Brompton and Harefield Clinical Group, Guys and St. Thomas NHS Foundation Trust, London, UK" + }, + { + "author_name": "Sally J Singh", + "author_inst": "The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK" + }, + { + "author_name": "Tom Yates", + "author_inst": "Diabetes Research Centre, University of Leicester, Leicester, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.03.22270396", "rel_title": "COVID-19 Vaccination is Associated with Decreasing Cases, Hospitalizations, and Deaths Across Age Groups and Variants over 9 months in Switzerland", @@ -409298,29 +409972,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.01.22270288", - "rel_title": "Understanding of and Trust in the Centers for Disease Control and Prevention's Revised COVID-19 Isolation and Quarantine Guidance Among US Adults", - "rel_date": "2022-02-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.01.22270288", - "rel_abs": "On December 27, 2021 the Centers for Disease Control and Prevention (CDC) announced changes to their guidance for individuals who are exposed to or test positive for COVID-19. The revised recommendations have prompted widespread discussion of both the scientific rationale and communication strategy, including criticism from the American Medical Association.1,2 In this survey study, we assessed understanding of and trust in the CDCs initial public statement about the new guidance among US adults.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Vishala Mishra", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Joseph P. Dexter", - "author_inst": "Harvard University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.02.01.22270235", "rel_title": "Hospitalisation for COVID-19 predicts long lasting cerebrovascular impairment: A prospective observational cohort study", @@ -409557,6 +410208,33 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.02.01.478632", + "rel_title": "Design and development of potent h-ACE2 derived peptide mimetics in SARS-CoV-2 Omicron variant therapeutics", + "rel_date": "2022-02-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.01.478632", + "rel_abs": "The pandemic of COVID-19 has become the global health challenge due to the emergence of new variants. The Receptor binding domain (RBD) of spike protein that makes direct interaction with ACE-2 has shown unique mutated residues in most of the variants of concern (VOC). Recently WHO declared the Omicron (B.1.1.529) as VOC considering it as a highly mutated variant which includes a total of 60 mutations out of which 15 mutations occurred in RBD region of SARS-CoV-2. Inhibition of Protein-protein (Omicron RBD-h-ACE2) interaction was already proved to inhibit the viral infection. In this study, by using molecular dynamic simulations efforts are made to explore the atomistic details of Omicron RBD-h-ACE2 interaction. Based on MD simulations, h-ACE2 motif is found to be interacting with omicron RBD domain. Interaction analysis had provided key residues interacting with Omicron-RBD that helped to extract h-ACE2 peptide. Here, rational design of the peptides that have resemblance with h-ACE2 is done and the peptide library is subjected for inhibition studies against Omicron-RBD. The current study helped to identify the significant peptides that can inhibit Omicron-RBD. Altogether the performed studies will provide an opportunity to develop potential therapeutic peptidomimetics effective against Omicron variant of SARS-CoV-2.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Stanly M L Paul", + "author_inst": "University of Szeged" + }, + { + "author_name": "Swathi Nadendla", + "author_inst": "National Institute of Pharmaceutical Education and Research (NIPER) S.A.S. Nagar" + }, + { + "author_name": "Elizabeth M Sobhia", + "author_inst": "National Institute of Pharmaceutical Education and Research (NIPER) S.A.S. Nagar" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.02.01.478697", "rel_title": "Patterns of Volatility Across the Spike Protein Accurately Predict the Emergence of Mutations within SARS-CoV-2 Lineages", @@ -410944,53 +411622,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.01.22270247", - "rel_title": "Ethiopian Healthcare Workers' Experiences During the COVID-19 Pandemic", - "rel_date": "2022-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.01.22270247", - "rel_abs": "BackgroundThe COVID-19 pandemic has caused widespread health and socioeconomic disruptions around the world. Understanding the impact that this crisis has had on health workers and the delivery of routine health care services within countries provides evidence on pandemic preparedness and response. Here, we conduct an investigation into these factors for the Ethiopian context.\n\nMethods and findingsWe conducted an online cross-sectional survey with Ethiopian health care professionals between August 27 and October 10, 2020 via existing research networks. The variables of interest were confidence in COVID-19 related knowledge, training and experience, the adoption of precautionary health practices, risk perceptions, and respondent concerns. The majority of surveyed health care professionals in Ethiopia reported seeing fewer patients than usual during the COVID-19 crisis, gaps in pandemic training, inadequate access to personal protective equipment (PPE) and barriers to accessing COVID-19 testing. Most health care professionals were also deeply concerned and worried about their own COVID-19 risks and the likelihood that they would transmit the disease to others.\n\nConclusionsOur study findings point to a possible reduction in routine health care services during the COVID-19 pandemic and gaps in pandemic preparedness in Ethiopia. The ministry of health and other stakeholders should work towards improving access to PPE and testing, and identify approaches to ensure that essential healthcare provision (such as immunizations) is not disrupted during crises akin to the COVID-19 outbreak.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Solomon Tessema Memirie", - "author_inst": "Addis Ababa University" - }, - { - "author_name": "Averi Chakrabarti", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Delayehu Bekele", - "author_inst": "Saint Paul's Hospital Millennium Medical College" - }, - { - "author_name": "Mizan Kiros", - "author_inst": "Federal Ministry of Health of Ethiopia" - }, - { - "author_name": "Christina Meyer", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Phuong Pham", - "author_inst": "Harvard T. H. Chan School of Public Health" - }, - { - "author_name": "Patrick Vinck", - "author_inst": "Harvard University" - }, - { - "author_name": "Stephane Verguet", - "author_inst": "Harvard T. H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.01.478677", "rel_title": "Assessing functional connectivity differences and work-related fatigue in surviving COVID-negative patients.", @@ -411379,6 +412010,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.29.22270074", + "rel_title": "Partnering with Athletes to Assess Risk of COVID-Related Myocarditis", + "rel_date": "2022-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.29.22270074", + "rel_abs": "BackgroundMyocarditis in athletes is a feared complication of SARS-CoV-2, yet guidelines for screening with cardiac magnetic resonance imaging are lacking. Further, stakeholder involvement in the research is rare.\n\nHypothesisWe sought to determine the rates of cardiac magnetic resonance imaging evidence of SARS-CoV-2 related myocarditis in student athletes. We hypothesized that rates of myocarditis were lower than initially reported and that including athletes on the research team would enhance participant satisfaction and scientific integrity.\n\nMethodsAccordingly, when members of a hockey team were infected with SARS-CoV-2, we invited them and their team physicians to be part of the design of a study assessing the incidence of myocarditis. We performed cardiac magnetic resonance imaging on participating hockey players infected with SARS-CoV-2 and compared them to a healthy lacrosse cohort. Participants were given an optional survey to complete at the end of the study to assess their satisfaction with it.\n\nResultsFour hockey players and two team physicians joined the study team; eight hockey players and four lacrosse players participated in the study. Zero athletes met imaging criteria for myocarditis; delayed enhancement was observed in seven cases and three controls. Athletes supported sharing the findings with the participants. No athletes reported feeling uncomfortable participating, knowing other athletes participated on the research team.\n\nConclusionRates of SARS-CoV-2 myocarditis in young athletes appears to be lower than initially reported. Partnered research is important, especially in populations with more to lose, such as collegiate athletes; future studies should include stakeholders in the study design and execution.\n\nKey pointsCardiac MRI findings of myocarditis after COVID infection in young athletes is rare. Subjects of research studies appreciate involvement in the development of the study, and this also builds trust with the research team.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Bradley William Kay", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Attila Feher", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Samuel Reinhardt", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Jason Cuomo", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Stephanie Arlis-Mayor", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Matthew Lynch", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Kyle Johnson", + "author_inst": "Yale University" + }, + { + "author_name": "Phil Kemp", + "author_inst": "Yale University" + }, + { + "author_name": "Henry Wagner", + "author_inst": "Yale University" + }, + { + "author_name": "Tyler Welsh", + "author_inst": "Yale University" + }, + { + "author_name": "Jerome Lamy", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Dana Peters", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Hamid Mojibian", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Lawrence Young", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Rachel Lampert", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Robert McNamara", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Lauren Baldassarre", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Edward J Miller", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Erica S Spatz", + "author_inst": "Yale School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2022.02.01.22270170", "rel_title": "Detection of prevalent SARS-CoV-2 variant lineages in wastewater and clinical sequences from cities in Quebec, Canada", @@ -412778,117 +413500,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.28.22270035", - "rel_title": "A Phase 2 Randomized, Double-Blind, Placebo-controlled Trial of Oral Camostat Mesylate for Early Treatment of COVID-19 Outpatients Showed Shorter Illness Course and Attenuation of Loss of Smell and Taste", - "rel_date": "2022-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.28.22270035", - "rel_abs": "ImportanceEarly treatment of mild SARS-CoV-2 infection might lower the risk of clinical deterioration in COVID-19.\n\nObjectiveTo determine whether oral camostat mesylate would reduce upper respiratory SARS-CoV-2 viral load in newly diagnosed outpatients with mild COVID-19, and would lead to improvement in COVID-19 symptoms.\n\nDesignFrom June, 2020 to April, 2021, we conducted a randomized, double-blind, placebo-controlled phase 2 trial.\n\nSettingSingle site, academic medical center, outpatient setting in Connecticut, USA.\n\nParticipantsOf 568 COVID-19 positive potential adult participants diagnosed within 3 days of study entry and assessed for eligibility, 70 were randomized and 498 were excluded (198 did not meet eligibility criteria, 37 were not interested, 265 were excluded for unknown or other reasons). The primary inclusion criteria were a positive SARS-CoV-2 nucleic acid amplification result in adults within 3 days of screening regardless of COVID-19 symptoms.\n\nInterventionTreatment was 7 days of oral camostat mesylate, 200 mg po four times a day, or placebo.\n\nMain Outcomes and MeasuresThe primary outcome was reduction of 4-day log10 nasopharyngeal swab viral load by 0.5 log10 compared to placebo. The main prespecified secondary outcome was reduction in symptom scores as measured by a quantitative Likert scale instrument, Flu-PRO-Plus modified to measure changes in smell/taste measured using FLU-PRO-Plus.\n\nResultsParticipants receiving camostat had statistically significant lower quantitative symptom scores (FLU-Pro-Plus) at day 6, accelerated overall symptom resolution and notably improved taste/smell, and fatigue beginning at onset of intervention in the camostat mesylate group compared to placebo. Intention-to-treat analysis demonstrated that camostat mesylate was not associated with a reduction in 4-day log10 NP viral load compared to placebo.\n\nConclusions and relevanceThe camostat group had more rapid resolution of COVID-19 symptoms and amelioration of the loss of taste and smell. Camostat compared to placebo was not associated with reduction in nasopharyngeal SARS-COV-2 viral load. Additional clinical trials are warranted to validate the role of camostat mesylate on SARS-CoV-2 infection in the treatment of mild COVID-19.\n\nTrial registration: Clinicaltrials.gov, NCT04353284 (04/20/20)(https://clinicaltrials.gov/ct2/show/NCT04353284?term=camostat+%2C+yale&draw=2&rank=1)\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWill early treatment of COVID-19 with a repurposed medication, camostat mesylate, improve clinical outcomes?\n\nFindingsIn this phase 2 randomized, double-blind placebo-controlled clinical trial that included 70 adults with early COVID-19, the oral administration of camostat mesylate treatment within 3 days of diagnosis prevented the loss of smell/taste and reduced the duration of illness.\n\nMeaningIn the current COVID-19 pandemic, phase III testing of an inexpensive, repurposed drug for early COVID-19 is warranted.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Geoffrey Chupp", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Anne Spichler-Moffarah", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Ole S Sogaard", - "author_inst": "Aarhus University, Aarhus, Denmark" - }, - { - "author_name": "Denise Esserman", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "James Dziura", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Lisa Danzig", - "author_inst": "Amicitiam Partners, San Francisco, CA" - }, - { - "author_name": "Reetika Chaurasia", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Kailash P. Patra", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Aryeh Salovey", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Angela Nunez", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Jeanine May", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Lauren Astorino", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Amisha Patel", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Stephanie Halene", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Jianhui Wang", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Pei Hui", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Prashant Patel", - "author_inst": "Yale New Haven Hospital" - }, - { - "author_name": "Jing Lu", - "author_inst": "Yale New Haven Hospital" - }, - { - "author_name": "Fangyong Li", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Geliang Gan", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Stephen Parziale", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Lily Katsovich", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Gary Desir", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Joseph M Vinetz", - "author_inst": "Yale School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.29.477140", "rel_title": "Significant Broad Spectrum Antiviral activity of Bi121 Against Different Variants of SARS-CoV-2", @@ -413041,6 +413652,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.01.30.22269980", + "rel_title": "Quantitative risk assessment of COVID-19 and serious illness among spectators at mass gathering events with vaccine-testing package implementation", + "rel_date": "2022-01-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.30.22269980", + "rel_abs": "While mass gathering events have resumed in conjunction with vaccine-testing (VT) packages, their effects on reducing COVID-19 risk remain unclear. Here, we used an environmental exposure model to analyze the effects of vaccinations and proof of negative test results on reducing infection risk and serious illness among spectators at mass gathering events. We then analyzed the difference in risk with and without VT and regular seat zoning. Risk of infection and serious illness were quantified using a model incorporating parameters such as vaccination coverage, vaccine prevention effectiveness, and sensitivity of polymerase chain reaction (PCR) or qualitative antigen tests. When vaccine prevention effectiveness was 50% (corresponding to 4 months for the delta variant and 1-2 months for the omicron variant after the second vaccine dose), the risk of infection and serious illness among vaccinated spectators were 0.32-0.40 and 0.13-0.16 times of those who tested negative, respectively. In contrast, the risks of infection and serious illness among vaccinated spectators without measures such as mask wearing were 4.0 and 1.6 times higher than those among unvaccinated spectators with such measures, respectively. The risk of infection with an 80% vaccination coverage and a vaccine prevention effectiveness of 20% (corresponding to 5-6 months for the delta variant or 3-4 months for the omicron variant after the second vaccine dose) was comparable to that of a 20% vaccine coverage and a vaccine prevention effectiveness of 80% (corresponding to 1-3 months for delta variant after the second vaccine dose). Regarding zoning, there was little difference in risk with a vaccination coverage of [≥]80%. Adherence to individual measures after vaccination and maintenance of high vaccine effectiveness among spectators at stadiums are important for reducing risk of infection and serious illness. Furthermore, seat zoning did not affect overall infection risk reduction.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Michio Murakami", + "author_inst": "Osaka University; National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Tsukasa Fujita", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Yuichi Iwasaki", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Masaki Onishi", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Wataru Naito", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + }, + { + "author_name": "Seiya Imoto", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Tetsuo Yasutaka", + "author_inst": "National Institute of Advanced Industrial Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.29.22270094", "rel_title": "Polygenic predisposition to venous thromboembolism is associated with increased COVID-19 positive testing rates", @@ -414740,57 +415394,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.01.28.22270013", - "rel_title": "Agility and sustainability: A qualitative evaluation of COVID-19 Non-pharmaceutical Interventions (NPIs) in the UK logistics sector", - "rel_date": "2022-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.28.22270013", - "rel_abs": "BackgroundThe emergence of SARS-CoV-2 triggered a chain of public health responses that radically changed our way of living and working. Non-healthcare sectors, such as the logistics sector, play a key role in such responses. This research aims to qualitatively evaluate the non-pharmaceutical interventions (NPIs) implemented in the UK logistics sector during the COVID-19 pandemic.\n\nMethodsWe conducted nine semi-structured interviews in July-August 2020 and May-June 2021. In total 11 interviewees represented six companies occupying a range of positions in the UKs logistics sector, including takeaway food delivery, large and small goods delivery and home appliance installation, and logistics technology providers. Inductive thematic analysis was completed using NVivo12 to generate emerging themes and subthemes. Themes/subthemes relevant to interventions were mapped deductively onto an adapted Hierarchy of Control (HoC) framework, focusing on delivery workers. Themes/subthemes relevant to the process of implementation were analyzed to understand the barriers and facilitators of rapid responses.\n\nResultsHoC analysis suggests the sector has implemented a wide range of risk mitigation measures, with each company developing their own portfolio of measures. Contact-free delivery was the most commonly implemented measure and perceived effective. In addition, a broad range of measures were implemented, including social distancing, internal contact tracing, communication and collaboration with other key stakeholders of the sector. Process evaluation identified facilitators of rapid responses including capacity to develop interventions internally, localized government support, overwhelming external mandates, effective communication, leadership support and financial support for self-isolation, while barriers included unclear government guidance, shortage of testing capacity and supply, high costs and diversified language and cultural backgrounds. Main sustainability issues included compliance fatigue, and the possible mental health impacts of a prolonged rapid response.\n\nConclusionsThis research identified drivers and obstacles of rapid implementation of NPIs in response to a respiratory infection pandemic. Existing implementation process models do not consider speed to respond and the absence or lack of guidance in emergency situations such as the COVID-19. We recommend the development of a rapid response model to inform the design of effective and sustainable infection prevention and control policies and to focus future research priorities.\n\nContributions to the fieldO_LIThe study offered important insights into the process of the UK logistics sectors response to the COVID-19 pandemic.\nC_LIO_LIThe Hierarchy of Control (HoC) framework was adapted for the evaluation of a collection of non-pharmaceutical interventions (NPIs) implemented in a non-healthcare sector.\nC_LIO_LIThematic analysis of qualitative data generated themes that were relevant to the process of rapid implementation of NPIs during a public health emergency.\nC_LIO_LIBarriers, facilitators and sustainability issues of the sectors rapid response to the COVID-19 pandemic have been highlighted to inform future research on implementation strategies.\nC_LI", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hua Wei", - "author_inst": "The University of Manchester" - }, - { - "author_name": "Sarah A Daniels", - "author_inst": "The University of Manchester" - }, - { - "author_name": "Carl A Whitfield", - "author_inst": "University of Manchester" - }, - { - "author_name": "Yang Han", - "author_inst": "University of Manchester" - }, - { - "author_name": "David W Denning", - "author_inst": "University of Manchester" - }, - { - "author_name": "Ian Hall", - "author_inst": "University of Manchester" - }, - { - "author_name": "Martyn Regan", - "author_inst": "University of Manchester" - }, - { - "author_name": "Arpana Verma", - "author_inst": "University of Manchester" - }, - { - "author_name": "Martie J van Tongeren", - "author_inst": "University of Manchester" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2022.01.28.22270001", "rel_title": "Calprotectin and inflammation-associated serum biomarkers determine critical illness in COVID-19", @@ -415039,6 +415642,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.27.22269949", + "rel_title": "Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 - January 2022", + "rel_date": "2022-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.27.22269949", + "rel_abs": "The SARS-CoV-2 variant of concern Omicron was first detected in Italy in November 2021. Data from three genomic surveys conducted in Italy between December 2021 and January 2022 suggest that Omicron became dominant in less than one month (prevalence on January 3: 78.6%-83.8%) with a doubling time of 2.7-3.1 days. The mean net reproduction number rose from about 1.15 in absence of Omicron to a peak of 1.83 for symptomatic cases and 1.33 for hospitalized cases, while it remained stable for critical cases.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Paola Stefanelli", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Filippo Trentini", + "author_inst": "Dondena Centre for Research on Social Dynamics and Public Policy, Bocconi University, Milan, Italy" + }, + { + "author_name": "Daniele Petrone", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Alessia Mammone", + "author_inst": "Ministero della Salute" + }, + { + "author_name": "Luigina Ambrosio", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Mattia Manica", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Giorgio Guzzetta", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Valeria D Andrea", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Valentina Marziano", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Agnese Zardini", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Carla Molina Grane", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA" + }, + { + "author_name": "Angela Di Martino", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Flavia Riccardo", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Antonino Bella", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Monica Sane Schepisi", + "author_inst": "Ministero della Salute" + }, + { + "author_name": "Francesco Maraglino", + "author_inst": "Ministero della Salute" + }, + { + "author_name": "Piero Poletti", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Anna Teresa Palamara", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Silvio Brusaferro", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Giovanni Rezza", + "author_inst": "Ministero della Salute" + }, + { + "author_name": "Patrizio Pezzotti", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Stefano Merler", + "author_inst": "Center for Health Emergencies, Bruno Kessler Foundation, Trento, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.28.22270022", "rel_title": "Continuing inequalities in COVID-19 mortality in England and Wales, and the changing importance of regional, over local, deprivation", @@ -416602,37 +417312,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.01.26.22269886", - "rel_title": "Questioning the Seasonality of SARS-COV-2: A Fourier Spectral Analysis", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269886", - "rel_abs": "ObjectivesCOVID-19 recurrent waves have ignited a debate on the role of seasonality in the contagion resurgence. Two opposite positions emerged. Those convinced of a sinusoidal seasonality recurring over one-year period driven by climate. Those believing that a fluctuation of the outbreaks repeats without limits, in the absence of control measures. We studied the series of daily confirmed SARS-CoV-2 cases in 30 different countries (February 2020 - December 2021), investigating the hypothesis of whether seasonal and geographic variations may guide the pandemic trajectory.\n\nMethodsWe chose 30 countries from different geographies and climates. With a discrete Fourier transform, we performed a spectral analysis of the series of the daily SARS-CoV-2 infections, looking for peaks in the frequency spectrum that could correspond to a recurrent cycle of a given length. This analysis allows to question whether COVID-19 outbreaks have an observable seasonal periodicity.\n\nResultsAll the 30 investigated countries see the recurrence of at least one COVID-19 wave, repeating over a period in the range 3 - 9 months, with a peak of magnitude at least half as large as that of the highest peak ever experienced since the beginning of the pandemic until December 2021. We also computed the distance in days between the two higher peaks in each country, and then we averaged those values over the 30 countries, yielding a mean of 190 days (SD 100). This suggests that outbreaks may repeat with cycles of different lengths, without a precisely predictable seasonality of one year.\n\nConclusionOur findings suggest that COVID-19 outbreaks are likely to occur worldwide, with cycles of repetition of variable lengths. Our Fourier analysis with 30 different countries has not found evidence in favor of a seasonality that recurs over one-year period, solely or with a precisely fixed periodicity.\n\nDesignNot Applicable\n\nSettingNot Applicable\n\nParticipantsNot Applicable\n\nInterventionsNot Applicable\n\nPrimary and Secondary Outcome MeasuresNot Applicable\n\nArticle SummaryO_ST_ABSStrengths and Limitations of this StudyC_ST_ABSO_LIThe use of a discrete Fourier transform offers the advantage of a temporal decomposition of the time series of the daily SARS-COV-2 cases, allowing to explore the temporal relationships among recurrent outbreaks.\nC_LIO_LIAnalyzing for each country the various repetition cycles of the outbreaks, along with their magnitudes, represents an appropriate method to question the assumption of a seasonal \"rise and fall\" structure of COVID-19 assumed to recur, almost exclusively, based on a one-year long period.\nC_LIO_LIWe have made inferences about the seasonality of COVID-19 from a purely observational study. The problem has been avoided to quantify, precisely, the role attributable to various climatic factors or control measures, like temperatures or vaccination.\nC_LIO_LITo take advantage of a natural experiment, the time series of the number of daily SARS-CoV-2 cases were subjected to a discrete Fourier transform without resorting to any form of correction/normalization. The SARS-CoV-2 outbreak (started in December 2021) has not been included in this study as the progression of this wave is still ongoing.\nC_LIO_LIThis analysis presents a natural limitation in time as the pandemic has been in progress so far, for only two years. The Fourier uncertainty principle may render the results at low frequencies somewhat uncertain given this extremely short time domain.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Riccardo Cappi", - "author_inst": "University of Insubria" - }, - { - "author_name": "Luca Casini", - "author_inst": "University of Bologna" - }, - { - "author_name": "Davide Tosi", - "author_inst": "University of Insubria" - }, - { - "author_name": "Marco Roccetti", - "author_inst": "University of Bologna" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.26.477612", "rel_title": "Endogenous pancreatic microRNAs differentially target the Delta, Omicron, and Wuhan SARS-CoV-2 genomes to upregulate the Diabetes-associated genes", @@ -416841,6 +417520,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.01.26.22269874", + "rel_title": "General practitioner wellbeing during the COVID-19 pandemic: a qualitative interview study", + "rel_date": "2022-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269874", + "rel_abs": "BackgroundWorkload pressures and poor job satisfaction have been reported by UK general practitioners (GPs) for some time. The COVID-19 pandemic presented new challenges, with growing international evidence of its negative impact on GPs mental health and wellbeing. While there has been wide commentary on this topic, UK research evidence is lacking. Developing greater understanding of these lived experiences and subgroup differences is important as doctor wellbeing may affect the sustainability of health care systems and quality of patient care.\n\nObjectivesTo explore the lived experience of UK GPs during COVID-19, and the pandemics impact on their psychological wellbeing.\n\nDesign and SettingIn-depth qualitative interviews, conducted remotely by telephone or video call, with NHS GPs.\n\nParticipantsGPs were sampled purposively across three career stages (early career, established and late career or retired GPs) with variation in other key demographics. A comprehensive recruitment strategy used multiple channels. Data were analysed thematically using Framework Analysis.\n\nResultsWe interviewed 40 GPs; most described generally negative sentiment and many displayed signs of psychological distress and burnout. Causes of stress and anxiety related to personal risk, workload, practice changes, public perceptions and leadership, teamworking and wider collaboration and personal challenges. GPs described facilitators of their wellbeing, including sources of support and plans to reduce clinical hours or change career path.\n\nConclusionsA range of factors detrimentally affected the wellbeing of GPs during the pandemic and we highlight the potential impact of this on workforce retention and quality of care. As the pandemic progresses and general practice faces continued challenges, urgent policy measures are now needed.\n\nStrengths and limitations of this studyO_LIWhile there is growing international evidence base demonstrating the impact of the COVID-19 pandemic on GPs wellbeing and much UK media coverage, this qualitative interview study provides much-needed research evidence of UK GPs lived experiences and wellbeing during COVID-19.\nC_LIO_LI40 GPs were sampled purposively to include GPs with different demographic and practice characteristics.\nC_LIO_LIWhile there are no easy solutions to the problems highlighted, this research provides increased contextualised understanding of how these experiences may impact future workforce retention and the sustainability of health systems longer-term.\nC_LIO_LISub-group differences by gender and age are reported; highlighting a potential need for further research and support targeted at specific groups.\nC_LIO_LIFindings are necessarily limited to the time of data collection (Spring/Summer 2021); further tensions in general practice have since arisen, particularly regarding negative and misleading media portrayal.\nC_LI", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Laura A Jefferson", + "author_inst": "University of York" + }, + { + "author_name": "Claire Heathcote", + "author_inst": "University of York" + }, + { + "author_name": "Karen Bloor", + "author_inst": "University of York" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2022.01.26.22269856", "rel_title": "Antibody and T cell responses to SARS-CoV-2 mRNA vaccines during maintenance therapy for immune-mediated inflammatory diseases", @@ -418664,49 +419370,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.01.26.477790", - "rel_title": "Serum proteomics identifies immune pathways and candidate biomarkers of coronavirus infection in wild vampire bats", - "rel_date": "2022-01-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.26.477790", - "rel_abs": "The apparent ability of bats to harbor many virulent viruses without showing disease is likely driven by distinct immune responses that coevolved with mammalian flight and the exceptional longevity of this order. Yet our understanding of the immune mechanisms of viral tolerance is restricted to a small number of bat-virus relationships and remains poor for coronaviruses (CoVs), despite their relevance to human health. Proteomics holds particular promise for illuminating the immune factors involved in bat responses to infection, because it can accommodate especially low sample volumes (e.g., sera) and thus can be applied to both large and small bat species as well as in longitudinal studies where lethal sampling is necessarily limited. Further, as the serum proteome includes proteins secreted from not only blood cells but also proximal organs, it provides a more general characterization of immune proteins. Here, we expand our recent work on the serum proteome of wild vampire bats (Desmodus rotundus) to better understand CoV pathogenesis. Across 19 bats sampled in 2019 in northern Belize with available sera, we detected CoVs in oral or rectal swabs from four individuals (21.1% positivity). Phylogenetic analyses identified all vampire bat sequences as novel -CoVs most closely related to known human CoVs. Across 586 identified serum proteins, we found no strong differences in protein composition nor abundance between uninfected and infected bats. However, receiver operating characteristic curve analyses identified seven to 32 candidate biomarkers of CoV infection, including AHSG, C4A, F12, GPI, DSG2, GSTO1, and RNH1. Enrichment analyses using these protein classifiers identified downregulation of complement, regulation of proteolysis, immune effector processes, and humoral immunity in CoV-infected bats alongside upregulation of neutrophil immunity, overall granulocyte activation, myeloid cell responses, and glutathione processes. Such results denote a mostly cellular immune response of vampire bats to CoV infection and identify putative biomarkers that could provide new insights into CoV pathogenesis in wild and experimental populations. More broadly, applying a similar proteomic approach across diverse bat species and to distinct life history stages in target species could improve our understanding of the immune mechanisms by which wild bats tolerate viruses.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Daniel Becker", - "author_inst": "University of Oklahoma" - }, - { - "author_name": "Guang-Sheng Lei", - "author_inst": "Indiana Univ. School of Medicine" - }, - { - "author_name": "Michael G Janech", - "author_inst": "College of Charleston" - }, - { - "author_name": "Alison M. Brand", - "author_inst": "Hollings Marine Laboratory" - }, - { - "author_name": "Brock Fenton", - "author_inst": "University of Western Ontario" - }, - { - "author_name": "Nancy B Simmons", - "author_inst": "American Museum of Natural History;" - }, - { - "author_name": "Benjamin A. Neely", - "author_inst": "National Institute of Standards and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2022.01.26.477937", "rel_title": "Germinal center-derived broadly neutralizing antibodies adapt to SARS-CoV-2 antigenic drift", @@ -419003,6 +419666,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.18.22269420", + "rel_title": "Immune response to third SARS-CoV-2 vaccination in seronegative kidney transplant recipients: possible improvement by mycophenolate mofetil reduction", + "rel_date": "2022-01-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22269420", + "rel_abs": "BackgroundModification of vaccination strategies is needed to improve the immune response to SARS-CoV-2 vaccination in kidney transplant recipients (KTRs).\n\nMethodsThis multicenter observational study aimed to determine antibody kinetics among 60 seropositive KTRs and analyzed the effects of the third vaccination against SARS-CoV-2 in 174 previously seronegative KTRs. We investigated whether mycophenolate mofetil (MMF) dose reduction by 25-50% prior the third vaccination influences vaccination success.\n\nResults18 of 60 (30%) seropositive KTRs became seronegative in the serological assay within six months. Loss of antibodies was predicted by low initial antibody levels ([≤]206.8 BAU/ml), older age, and impaired graft function. A third vaccination in previously seronegative KTRs induced seroconversion in 56 of 174 (32.1%) KTRs with median antibody levels 119 (76-353) BAU/ml and median neutralizing capacity titer of 1:10 (0- 1:40). Multivariate logistic regression revealed that initial antibody levels (OR 1.39, 95% CI 1.09-1.76), graft function (OR 0.05, 95% CI 0.01-0.39), time after transplantation (OR 1.04, 95% CI 1.02-1.07) and MMF trough levels (OR 0.43, 95% CI 0.21-0.88) correlated with seroconversion, p<0.05. After controlling for these confounders, the effect of MMF dose reduction was calculated using propensity score matching. KTRs in the MMF reduction group had significantly lower MMF serum concentrations prior to the third vaccination and were more likely to develop antibody levels [≥]35.2 BAU/ml than their matched KTRs (p=0.02).\n\nConclusionsTemporary reduction in MMF dose might be a promising approach to improve the immune response in KTRs.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Marta Kantauskaite", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Lias Mueller", + "author_inst": "University Hospital Duesseldorf" + }, + { + "author_name": "Jonas Hillebrandt", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Joshua Leon Lamberti", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Svenja Fischer", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Thilo Kolb", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Katrin Ivens", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Michael Koch", + "author_inst": "Nephrocare Mettmann" + }, + { + "author_name": "Marcel Andree", + "author_inst": "University Hospital Duesseldorf" + }, + { + "author_name": "Nadine Luebke", + "author_inst": "University Hospital Duesseldorf" + }, + { + "author_name": "Michael Schmitz", + "author_inst": "Klinikum Solingen" + }, + { + "author_name": "Tom Luedde", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Hans Martin Orth", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Torsten Feldt", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Heiner Schaal", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Ortwin Adams", + "author_inst": "University Hospital Duesseldorf" + }, + { + "author_name": "Claudia Schmidt", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Margarethe Kittel", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Eva Koenigshausen", + "author_inst": "Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Lars Christian Rump", + "author_inst": "Heinrich-Heine University-Duesseldorf" + }, + { + "author_name": "Joerg Timm", + "author_inst": "University hospital Duesseldorf" + }, + { + "author_name": "Johannes Stegbauer", + "author_inst": "Heinrich-Heine-University Duesseldorf" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2022.01.20.21267627", "rel_title": "\"It affects every aspect of your life\": A qualitative study of the impact of delaying surgery during COVID-19", @@ -420978,57 +421744,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.01.21.475953", - "rel_title": "SARS-CoV-2 Omicron Variant AI-based Primers", - "rel_date": "2022-01-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.21.475953", - "rel_abs": "As the COVID-19 pandemic continues to affect the world, a new variant of concern, B.1.1.529 (Omicron), has been recently identified by the World Health Organization. At the time of writing, there are still no available primer sets specific to the Omicron variant, and its identification is only possible by using multiple targets, checking for specific failures, amplifying the suspect samples, and sequencing the results. This procedure is considerably time-consuming, in a situation where time might be of the essence. In this paper we use an Artificial Intelligence (AI) technique to identify a candidate primer set for the Omicron variant. The technique, based on Evolutionary Algorithms (EAs), has been already exploited in the recent past to develop primers for the B.1.1.7/Alpha variant, that have later been successfully tested in the lab. Starting from available virus samples, the technique explores the space of all possible subsequences of viral RNA, evaluating them as candidate primers. The criteria used to establish the suitability of a sequence as primer includes its frequency of appearance in samples labeled as Omicron, its absence from samples labeled as other variants, a specific range of melting temperature, and its CG content. The resulting primer set has been validated in silico and proves successful in preliminary laboratory tests. Thus, these results prove further that our technique could be established as a working template for a quick response to the appearance of new SARS-CoV-2 variants.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Carmina Angelica Perez-Romero", - "author_inst": "Universidad Central de Queretaro Santiago de Queretaro, Queretaro, MX" - }, - { - "author_name": "Alberto Tonda", - "author_inst": "INRAE" - }, - { - "author_name": "Lucero Mendoza-Maldonado", - "author_inst": "Hospital Civil de Guadalajara" - }, - { - "author_name": "John MacSharry", - "author_inst": "School of Microbiology and School of Medicine, University College Cork" - }, - { - "author_name": "Joanna Szafran", - "author_inst": "School of Microbiology and School of Medicine, University College Cork" - }, - { - "author_name": "Eric Claassen", - "author_inst": "Vrije Universiteit Amsterdam" - }, - { - "author_name": "Johan Garssen", - "author_inst": "Universiteit Utrecht Utrecht, Utrecht, NL" - }, - { - "author_name": "Aletta D. Kraneveld", - "author_inst": "Universiteit Utrecht Utrecht, Utrecht, NL" - }, - { - "author_name": "Alejandro Lopez-Rincon", - "author_inst": "Centrum Wiskunde en Informatica" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.01.26.477860", "rel_title": "Comprehensive fitness landscape of SARS-CoV-2 Mpro reveals insights into viral resistance mechanisms", @@ -421245,6 +421960,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.23.22269669", + "rel_title": "Effects of 12 weeks of Multi-nutrient supplementation on the Immune and Musculoskeletal systems of Older Adults in Aged-Care (The Pomerium Study): Protocol for a Randomised Controlled Trial", + "rel_date": "2022-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.23.22269669", + "rel_abs": "IntroductionImmunosenescence leads to increased morbidity and mortality associated with viral infections and weaker vaccine responses. This has been well documented for seasonal influenza and the current pandemic with Sars-Cov2, which disproportionately impact older adults, particularly those in residential aged care facilities. Inadequate nutrient intake associated with impaired immunity, respiratory and muscle function are likely to augment the effects of immunosenescence. In this study, we test whether the effects of inadequate nutrition can be reversed by multi-nutrient supplementation, consequently enhancing vaccine responses, reducing the risk of viral infections, and improving respiratory and muscle function.\n\nMethods and analysisThe Pomerium Study is a 12-week, single-blinded, randomised, placebo-controlled trial testing the effects of two daily servings of an oral multi-nutrient supplement (330 kcal, 20g protein, 1.2g CaHMB, 449mg calcium, 520IU vitamin D3, and 25 vitamins and minerals) on the immune system and muscle and respiratory function of older adults in aged-care in Melbourne, Australia. 160 older adults ([≥]75 years old) will be recruited from aged-care facilities and randomised to treatment (multi-nutrient supplement) or control (usual care). Primary outcome is the change in T-cell subsets CD8+ and CD28null counts at 4 and 12 weeks post-intervention. Secondary outcomes measured at baseline and after 12 weeks post-intervention are multiple markers of immunosenescence, body composition (bioimpedance), handgrip strength (dynamometer), physical function (short physical performance battery), respiratory function (spirometry), and quality of life (EQ-5D-3L). Incidence and complications of COVID-19 and/or viral infections (i.e., hospitalisation, complications, or death) will be recorded throughout the trial.\n\nDiscussionIf the Pomerium Study demonstrates efficacy and safety of a multi-nutrient supplement on immune, muscle and respiratory function, it may be suitable as a strategy to reduce the adverse outcomes from seasonal influenza and viral infections such as COVID-19 in older adults in aged-care.\n\nFunding, Ethics, Registration and DisseminationThe study is funded by the Australian Medical Research Future Fund. It is approved by Melbourne Health Human Research Ethics Committee (Ref No. HREC/73985/MH-2021, ERM Ref No. RMH73985, Melbourne Health Site Ref No. 2021.115), and registered at ANZCTR (12621000420842). Results will be published in peer-reviewed journals and made available to aged-care stakeholders, including providers, residents, and government bodies.\n\nArticle Summary Strengths and LimitationsO_LIThis is the first study performing a comprehensive immune, respiratory and functional assessment in aged care residents after receiving a multi-nutrient solution that is commercially available.\nC_LIO_LIOur design and tested intervention assure that the results of the study will be rapidly translated into practice.\nC_LIO_LIThe main limitation is that any biological effect observed cannot be attributed to one component of the multi-nutrient supplement.\nC_LIO_LIAnother limitation is that the potential effect of group differences in energy intake on outcomes can only be monitored by assessing regular dietary intake and weight changes during the study period.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Ahmed Al Saedi", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Ben Kirk", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Sandra Iuliano", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Jesse Zanker", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Sara Vogrin", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Lata Jayaram", + "author_inst": "Western Health" + }, + { + "author_name": "Shane Thomas", + "author_inst": "Australian Institute for Musculoskeletal Science (AIMSS)" + }, + { + "author_name": "Christine Golding", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Diana Navarro-Perez", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Petra Marusic", + "author_inst": "Australian Institute for Musculoskeletal Science (AIMSS)" + }, + { + "author_name": "Sean Leng", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Ralph Nanan", + "author_inst": "University of Sydney" + }, + { + "author_name": "Gustavo Duque", + "author_inst": "The University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2022.01.23.22269626", "rel_title": "Death review caused by Covid 19 in Bangladesh", @@ -422424,89 +423206,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2022.01.14.22269235", - "rel_title": "Dynamics of infection-elicited SARS-CoV-2 antibodies in children over time", - "rel_date": "2022-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.14.22269235", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection elicits an antibody response that targets several viral proteins including spike (S) and nucleocapsid (N); S is the major target of neutralizing antibodies. Here, we assess levels of anti-N binding antibodies and anti-S neutralizing antibodies in unvaccinated children compared with unvaccinated older adults following infection. Specifically, we examine neutralization and anti-N binding by sera collected up to 52 weeks following SARS-CoV-2 infection in children and compare these to a cohort of adults, including older adults, most of whom had mild infections that did not require hospitalization. Neutralizing antibody titers were lower in children than adults early after infection, but by 6 months titers were similar between age groups. The neutralizing activity of the childrens sera decreased modestly from one to six months; a pattern that was not significantly different from that observed in adults. However, infection of children induced much lower levels of anti-N antibodies than in adults, and levels of these anti-N antibodies decreased more rapidly in children than in adults, including older adults. These results highlight age-related differences in the antibody responses to SARS-CoV-2 proteins and, as vaccines for children are introduced, may provide comparator data for the longevity of infection-elicited and vaccination-induced neutralizing antibody responses.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Lauren E Gentles", - "author_inst": "University of Washington" - }, - { - "author_name": "Leanne Kehoe", - "author_inst": "Seattle Children's Hospital" - }, - { - "author_name": "Katharine HD Crawford", - "author_inst": "University of Washington" - }, - { - "author_name": "Kirsten Lacombe", - "author_inst": "Seattle Children's Hospital" - }, - { - "author_name": "Jane Dickerson", - "author_inst": "Seattle Children's Hospital" - }, - { - "author_name": "Caitlin Wolf", - "author_inst": "Seattle Children's Hospital" - }, - { - "author_name": "Joanna Yuan", - "author_inst": "Seattle Children's Hospital" - }, - { - "author_name": "Susanna Schuler", - "author_inst": "Seattle Children's Hospital" - }, - { - "author_name": "John T Watson", - "author_inst": "CDC" - }, - { - "author_name": "Sankan Nyanseor", - "author_inst": "CDC" - }, - { - "author_name": "Melissa Briggs-Hagen", - "author_inst": "CDC" - }, - { - "author_name": "Sharon Saydah", - "author_inst": "CDC" - }, - { - "author_name": "Claire M Midgley", - "author_inst": "CDC" - }, - { - "author_name": "Kimberly Pringle", - "author_inst": "CDC" - }, - { - "author_name": "Helen Y Chu", - "author_inst": "University of Washington" - }, - { - "author_name": "Jesse D Bloom", - "author_inst": "FRED HUTCHINSON CANCER RESEARCH CENTER" - }, - { - "author_name": "Janet E Englund", - "author_inst": "Seattle Children's Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.24.22269773", "rel_title": "Establishment of human post-vaccination SARS-CoV-2 standard reference sera", @@ -422795,6 +423494,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.25.22269735", + "rel_title": "Acquired neutralizing breadth against SARS-CoV-2 variants including Omicron after three doses of mRNA COVID-19 vaccination and the vaccine efficacy", + "rel_date": "2022-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.25.22269735", + "rel_abs": "To investigate the induction of neutralizing antibodies against Omicron after two and three vaccine doses in recipients of different ages. Physicians at Kobe University Hospital who had received the second dose of the BNT162b2 mRNA vaccine. At 2 months after the second vaccinations, the positive rate of neutralizing antibody against Omicron was 28%, and the titer was significantly lower than those against other variants, 11.8-fold and 3.6-fold lower than those against D614G and Delta, respectively. Unlike Delta, that positive rates of neutralizing antibody against Omicron were low in all age groups, and there was no significant difference in titers among age groups. Seven months after the 2nd dose, the positive rate of neutralizing antibody against Omicron decreased to 6%, but after the booster,3rd vaccination, it increased to 100%, and the titer was much higher than those at 2 and 7 months post-vaccination, 32-fold and 39-fold respectively. The booster vaccination effect was also observed in the younger at 41-fold, middle-aged at 43-fold, and older at 27-fold groups compared to the 7-month titers. Surprisingly, higher-than-predicted titers of the neutralizing antibodies against Omicron were induced after the booster vaccination regardless of recipient age, while this effect was not observed after two doses, indicating the induction of antibodies against common epitopes by the booster vaccination. Three doses can be confidently recommended to suppress the pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Koichi Furukawa", + "author_inst": "Kobe Unibersity" + }, + { + "author_name": "Lidya Handayani Tjan", + "author_inst": "Kobe University" + }, + { + "author_name": "Yukiya Kurahashi", + "author_inst": "Kobe University" + }, + { + "author_name": "Silvia Sutandhio", + "author_inst": "Kobe University" + }, + { + "author_name": "Mitsuhiro Nishimura", + "author_inst": "Kobe University" + }, + { + "author_name": "Jun Arii", + "author_inst": "Kobe University" + }, + { + "author_name": "Yasuko Mori", + "author_inst": "Kobe University Graduate School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.24.22269781", "rel_title": "Effects of vaccination against COVID-19 on the emotional health of Peruvian older adults", @@ -424226,41 +424968,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.22.22269694", - "rel_title": "A NOVEL METHOD FOR HANDLING PRE-EXISTING CONDITIONS IN PREDICTION MODELS FOR COVID-19 DEATH", - "rel_date": "2022-01-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.22.22269694", - "rel_abs": "ObjectiveTo derive a predicted probability of death (PDeathDx) based upon complete sets of ICD-10 codes assigned to patients prior to their diagnosis of COVID-19. PDeathDx is intended for use as a summary metric for pre-existing conditions in multivariate models for COVID-19 death.\n\nMethodsCases were identified through the COVID-19 Shared Data Resource (CSDR) of the Department of Veterans Affairs. The diagnosis required at least one positive nucleic acid amplification test (NAAT). The primary outcome was death within 60 days of the first positive test. We retrieved all diagnoses entered into the electronic medical record for visits, on problem lists, and at the time of hospital discharge if they were at least 14 days prior to the NAAT. ICD-9 codes were converted to ICD-10 equivalents using a crosswalk provided by the Centers for Medicare/Medicaid Services. ICD-10 codes were converted to their category diagnoses defined as all columns to the left of the decimal point. Each patient was considered to have or not have each category diagnosis prior to the NAAT. A computer program calculated the number of cases for each category diagnosis, the relative risk (RR) of death, and its confidence interval (CI) using a Bonferroni adjustment for multiple comparisons. RRs were re-centered by subtracting 1 so that high-risk conditions had a positive value while protective conditions had a negative one. Diagnoses found to be significant were entered into a logistic model for death in a stepwise fashion. Each patient was assigned (RR-1) to each category diagnosis if they had the condition or 0 otherwise. The resulting model was used to derive PDeathDx for each patient and the area under its receiver operating characteristic (ROC) curve calculated. Single variable logistic models were also derived for age at diagnosis, the Charlson 2-year (Charl2Yr) and lifetime (CharlEver) scores, and the Elixhauser 2-year (Elix2Yrs) and lifetime (ElixEver) scores. Stata was used to compare the ROCs for PDeathDx and each of the other metrics.\n\nResultsOn September 30, 2021 there were 347,220 COVID-19 patients in the CSDR. 18,120 patients (5.33%) died within 60 days of their diagnosis. After consolidating ICD-9 and ICD-10 codes, 29,162,710 separate diagnoses were given to the subjects representing 41,341 ICD-10 codes. This set was reduced to 1,890 category diagnoses assigned to the group for the first time on 19,184,437 occasions. Of the 1,890 category diagnoses, 425 involved >= 100 subjects and had a lower boundary for the CI >= 1.50 (a high-risk condition) or upper boundary <= 0.80 (a protective condition). Stepwise logistic regression showed that 153 were statistically significant, independent predictors of death. PDeathDx was slightly less powerful than age as a discriminator (ROC = 0.811 +/- 0.002 vs 0.812 +/- 0.001, respectively; P < 0.001) but was superior to the Charl2Yr (ROC = 0.727 +/- 0.002; P < 0.001), CharlEver (ROC = 0.753 +/- 0.002; P <= 0.001), Elix2Yr (ROC = 0.694 +/- 0.002; P < 0.001); and ElixEver (ROC = 0.731 +/- 0.002; P < 0.001). Univariate analysis and multivariate modeling showed that many of the most high-risk conditions are under-represented or not included in the Charlson Index. These include hypertension, dementia, degenerative neurologic disease, or diagnoses associated with severe physical disability.\n\nConclusionsOur method for handling pre-existing conditions in multivariate analysis has many advantages over conventional comorbidity indices. The approach can be applied to any condition or outcome, can use any categorical predictors including medications, creates its own condition weights, handles rare as well as protective conditions, and returns actionable information to providers. The latter include the specific ICD-10 groups, their contribution to the risk, and their rank order of importance. Finally, PDeathDx is equivalent to age as a discriminator of outcomes and outperforms 4 other comorbidity scores. If validated by others, this approach provides an alternative and more robust approach to handling comorbidities in multivariate models.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Glen H Murata", - "author_inst": "New Mexico VA Health Care System" - }, - { - "author_name": "Allison E Murata", - "author_inst": "VA Cooperative Studies Program - Clinical Research Pharmacy Coordinating Center" - }, - { - "author_name": "Heather M Campbell", - "author_inst": "VA Cooperative Studies Program - Clinical Research Pharmacy Coordinating Center" - }, - { - "author_name": "Benjamin H Mcmahon", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Jenny T Mao", - "author_inst": "New Mexico VA Health Care System" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.23.22269711", "rel_title": "Detection of SARS-CoV-2 in Different Human Biofluids Using the Loop-Mediated Isothermal Amplification Assay: A Prospective Diagnostic Study in Fortaleza, Brazil", @@ -424437,6 +425144,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.23.22269716", + "rel_title": "Evidence on the role of journal editors in the COVID19 infodemic: metascientific study analyzing COVID19 publication rates and patterns", + "rel_date": "2022-01-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.23.22269716", + "rel_abs": "ObjectiveInfodemic, a neologism characterizing an excess of fast-tracked low quality publications, has been employed to depict the scientific research response to the COVID19 crisis. The concept relies on the presumed exponential growth of research output. This study aimed to test the COVID19 infodemic claim by assessing publication rates and patterns of COVID19-related research and a control, a year prior.\n\nDesignA Reproduction Number of Publications (Rp) was conceived. It was conceptualized as a division of a week incidence of publications by the average of publications of the previous week. The publication growth rates of preprint and MEDLINE-indexed peer-reviewed literature on COVID19 were compared using the correspondent Influenza output, a year prior, as control. Rp for COVID19 and Influenza papers and preprints were generated and compared and then analyzed in light of the respective growth patterns of their papers and preprints.\n\nMain outcomesOutput growth rates and Reproduction Number of Publications (Rp).\n\nResultsCOVID19 peer-reviewed papers showed a fourteen fold increase compared to Influenza papers. COVID19 papers and preprints displayed an exponential growth curve until the 20th week. COVID19 papers displayed Rp=3.17{+/-}0.72, while the control group presented Rp=0.97{+/-}0.12. Their preprints exhibited Rp=2.18{+/-}0.54 and Rp=0.97{+/-}0.27 respectively, with no evidence of exponential growth in the control group, as its Rp remained approximately one.\n\nConclusionsCOVID19 publications displayed an epidemic pattern. As the growth patterns of COVID19 peer-reviewed articles and preprints were similar, and the majority of the COVID19 output came from indexed journals, not only authors but also editors appear to had played a significant part on the infodemic.\n\nReview protocolhttps://osf.io/q3zkw/?view_only=ff540dc4630b4c6e9a2639d732047324\n\nEthical aspectsNo ethical clarence was required as all analyzed data were publicly available.\n\nO_TEXTBOXSUMMARY BOX\n\n1. What is already known about this subject?\n\nMuch has been commented on 2020s excess of publications on COVID19. Independent studies found evidence of increased volume and speed of publication, decreased methodological quality, and qualitative variations in peer review of COVID19 papers, when compared to the scholarly output from before the pandemic. This phenomenon has been branded an infodemic, a neologism implying an epidemic of low-quality information on COVID19 when high quality scientific reports to inform health policies would have been needed the most.\n\n2. What are the new findings?\n\nNo study pushed the infodemic metaphor forward to analyze not only volume of publication but also publication rates comparing them to a control group as to clearly pinpoint an exponential phase of contagion in the infodemic (as it would take place in a real epidemic) through a mathematical analysis of the growth patterns and rates of those publications. In this paper, we were able to demonstrate that there has been an infodemic indeed and that the editor population was as susceptible to the infodemic bug as the author population because the exponential phase was shaped not only by authors but mainly by editors from PubMed-indexed journals.\n\n3.How might it impact clinical practice in the foreseeable future?\n\nThese results and conclusions are consequential to subsequent studies on rigor and depth of post publication peer review and on editorial practices within the life and health sciences research community.\n\nC_TEXTBOX", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Gabriel Grisi", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Joao de Deus Barreto Segundo", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Camila Veronica Freire", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Denise Matias", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Mariana Cruz", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Larrie Rabelo Laporte", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Daniel Medina", + "author_inst": "Universidade Federal do Reconcavo da Bahia" + }, + { + "author_name": "Thiago Masashi Taniguchi", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Leticia Requiao", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Bruno Goes", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + }, + { + "author_name": "Luis Claudio Lemos Correia", + "author_inst": "Escola Bahiana de Medicina e Saude Publica" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.01.24.22269734", "rel_title": "SARS-CoV-2 viremia precedes an IL6 response in severe COVID-19 patients: results of a longitudinal prospective cohort", @@ -426116,45 +426882,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.22.22269655", - "rel_title": "Impact of accelerating booster vaccination amidst Omicron surge in the United States", - "rel_date": "2022-01-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.22.22269655", - "rel_abs": "COVID-19 infections driven by the Omicron variant are sweeping across the United States. Although early evidence suggests that the Omicron variant may cause less severe disease than previous variants, the explosive spread of infections threatens to drive hospitalizations and deaths to unprecedented high levels, swamping already overburdened hospitals. Booster vaccination appears to be effective at preventing severe illness and hospitalization. However, the pace of booster vaccination in the US has been slow despite the available infrastructure to administer doses at a much higher rate.\n\nWe used an age-stratified, multi-variant agent-based model to project the reduction in COVID-related deaths and hospitalizations that could be achieved by accelerating the current daily pace of booster vaccination in the US. We found that doubling the rate of booster vaccination would prevent over 400,000 hospitalizations and 48,000 deaths. Tripling the booster vaccination rate would avert over 600,000 hospitalizations and save 70,000 lives during the first four months of 2022.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Pratha Sah", - "author_inst": "Yale University" - }, - { - "author_name": "Thomas Nogueira Vilches", - "author_inst": "York University" - }, - { - "author_name": "Seyed M Moghadas", - "author_inst": "York University" - }, - { - "author_name": "Meagan C Fitzpatrick", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Eric C Schneider", - "author_inst": "The Commonwealth Fund" - }, - { - "author_name": "Alison P Galvani", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.20.477147", "rel_title": "SARS-CoV-2 Viral Genes Compromise Survival and Functions of Human Pluripotent Stem Cell-derived Cardiomyocytes via Reducing Cellular ATP Level", @@ -426551,6 +427278,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.17.475291", + "rel_title": "Comprehensive Evaluation of ACE2-Fc Combination with Neutralization Antibody on Broad Protection against SARS-CoV-2 and Its Variants", + "rel_date": "2022-01-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.17.475291", + "rel_abs": "Emerging SARS-CoV-2 variants are threatening the efficacy of antibody therapies. Combination treatments including ACE2-Fc have been developed to overcome the evasion of neutralizing antibodies (NAbs) in individual cases. Here we conducted a comprehensive evaluation of this strategy by combining ACE2-Fc with NAbs of diverse epitopes on the RBD. NAb+ACE2-Fc combinations efficiently neutralized HIV-based pseudovirus carrying the spike protein of the Delta or Omicron variants, achieving a balance between efficacy and breadth. In an antibody escape assay using replication-competent VSV-SARS-CoV-2-S, all the combinations had no escape after fifteen passages. By comparison, all the NAbs without combo with ACE2-Fc had escaped within six passages. Further, the VSV-S variants escaped from NAbs were neutralized by ACE2-Fc, revealing the mechanism of NAb+ACE2-Fc combinations survived after fifteen passages. We finally examined ACE2-Fc neutralization against pseudovirus variants that were resistant to the therapeutic antibodies currently in clinic. Our results suggest ACE2-Fc is a universal combination partner to combat SARS-CoV-2 variants including Delta and Omicron.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Haoneng Tang", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yong Ke", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Hang Ma", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Lei Han", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China; Jecho Institu" + }, + { + "author_name": "Lei Wang", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Huifang Zong", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yunsheng Yuan", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Zhenyu Wang", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China" + }, + { + "author_name": "Yang He", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China" + }, + { + "author_name": "Yunsong Chang", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China" + }, + { + "author_name": "Shusheng Wang", + "author_inst": "Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "Junjun Liu", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yali Yue", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Wenbo Xu", + "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, China" + }, + { + "author_name": "Xiaoju Zhang", + "author_inst": "Zhengzhou University Peoples Hospital; Henan Provincial Peoples Hospital, Department of Respiratory and Critical Care Medicine, Zhengzhou 450003, Henan, China" + }, + { + "author_name": "Ziqi Wang", + "author_inst": "Zhengzhou University Peoples Hospital; Henan Provincial Peoples Hospital, Department of Respiratory and Critical Care Medicine, Zhengzhou 450003, Henan, China" + }, + { + "author_name": "Li Yang", + "author_inst": "Zhengzhou University Peoples Hospital; Henan Provincial Peoples Hospital, Department of Respiratory and Critical Care Medicine, Zhengzhou 450003, Henan, China" + }, + { + "author_name": "Hua Chen", + "author_inst": "Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "Yanlin Bian", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Baohong Zhang", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yunji Liao", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Haiyang Yin", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Yi Chen", + "author_inst": "Zhengzhou University Peoples Hospital; Henan Provincial Peoples Hospital, Clinical Research Service Center, Zhengzhou 450003, Henan, China" + }, + { + "author_name": "En Zhang", + "author_inst": "School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Municipal Veterinary Key Laboratory, Shanghai 200240, China" + }, + { + "author_name": "Xiaoxiao Zhang", + "author_inst": "School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Municipal Veterinary Key Laboratory, Shanghai 200240, China" + }, + { + "author_name": "Hua Jiang", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China; Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "Yueqing Xie", + "author_inst": "Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "John Gilly", + "author_inst": "Jecho Biopharmaceuticals Co., Ltd. Tianjin 300467, China; Jecho Laboratories, Inc. Frederick, MD 21704, USA" + }, + { + "author_name": "Mingyuan Wu", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China" + }, + { + "author_name": "Tao Sun", + "author_inst": "School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Municipal Veterinary Key Laboratory, Shanghai 200240, China" + }, + { + "author_name": "Jianwei Zhu", + "author_inst": "Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, China; Shanghai Jiao Tong University, Shanghai 200240, China; Jecho Biophar" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2022.01.20.477105", "rel_title": "In Silico Analysis Of The Effects Of Omicron Spike Amino Acid Changes On The Interactions With Human ACE2 Receptor And Structurally Characterized Complexes With Human Antibodies", @@ -428106,37 +428972,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.18.22268929", - "rel_title": "The Impact of Frequent SARS-CoV-2 Testing on Weekly Case Rates Among Long-Term Care Facilities in Florida", - "rel_date": "2022-01-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22268929", - "rel_abs": "SARS-CoV-2 testing frequency may be as important as test performance for disease control. We analyzed 1,292,165 SARS-CoV-2 test results among 361 long-term care facilities across Florida after implementing twice monthly testing (June 2020-April 2021). Our findings demonstrate that an increase in testing frequency reduced weekly case rates.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Lao Allan-Blitz", - "author_inst": "Brigham and Women's Hospital Department of Medicine" - }, - { - "author_name": "Belal Aboabdo", - "author_inst": "Curative Inc." - }, - { - "author_name": "Isaac Turner", - "author_inst": "Curative Inc" - }, - { - "author_name": "Jeffrey D. Klausner", - "author_inst": "Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.18.22269408", "rel_title": "The impact of recurrent rapid test strategies on the effectiveness of at-home antiviral treatments for SARS-CoV-2", @@ -428305,6 +429140,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.01.20.22269321", + "rel_title": "Extreme \u03b3' fibrinogen levels in COVID-19 patients", + "rel_date": "2022-01-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.20.22269321", + "rel_abs": "BackgroundCOVID-19 progression can be accompanied by a \"cytokine storm\" that leads to secondary sequelae such as thrombosis and acute respiratory distress syndrome. Several inflammatory cytokines have been associated with COVID-19 progression, but have far too much daily intra-individual variability to be useful in tracking the course of the disease. In contrast, we have shown that the inflammatory biomarker {gamma} fibrinogen ({gamma} Fbg) has a 6-fold lower coefficient of variability compared to other inflammatory markers such as hs-CRP. Objectives: The aims of the study were to measure {gamma} Fbg in serial blood samples from COVID-19 patients at a tertiary care medical center in order to investigate its association with clinical measures of disease progression.\n\nMethodsCOVID-19 patients at a tertiary care medical center were retrospectively enrolled between 3/16/2020 and 8/1/2020. {gamma} Fbg was measured using a commercial ELISA. Results: Our results showed that nine out of the seventeen patients with COVID-19 had extremely high levels of {gamma} Fbg. {gamma} Fbg levels were significantly associated with the need for ECMO and with mortality.\n\nConclusionsWe found that COVID-19 patients can develop extraordinarily high levels of {gamma} Fbg. The previous highest {gamma} Fbg level that we are aware of was 80.3 mg/dL found in a study of 10,601 participants in the ARIC study. These results have several important clinical implications. {gamma} Fbg contains a high affinity binding site for thrombin that binds to anion-binding exosite II on thrombin and protects it from inactivation by heparin. High levels of {gamma} Fbg therefore provide a reservoir of heparin-resistant clot-bound thrombin when the {gamma} Fbg is clotted. These findings have potential implications regarding prophylactic anticoagulation of COVID-19 patients and suggest that heparin prophylaxis may be less effective than using other anticoagulants, particularly direct thrombin inhibitors.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "David Henry Farrell", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Matthew Hudkins", + "author_inst": "OHSU" + }, + { + "author_name": "Heather Hamilton", + "author_inst": "OHSU" + }, + { + "author_name": "Samantha J Underwood", + "author_inst": "OHSU" + }, + { + "author_name": "Elizabeth N Dewey", + "author_inst": "OHSU" + }, + { + "author_name": "Diana E Kazmierczak", + "author_inst": "OHSU" + }, + { + "author_name": "Steven C Kazmierczak", + "author_inst": "OHSU" + }, + { + "author_name": "William B Messer", + "author_inst": "OHSU" + }, + { + "author_name": "Akram Khan", + "author_inst": "OHSU" + }, + { + "author_name": "Martin A Schreiber", + "author_inst": "OHSU" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.20.22269618", "rel_title": "Molecular diagnosis of SARS-CoV-2: a validation of saliva samples", @@ -429956,49 +430846,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.01.20.476754", - "rel_title": "Omicron variant of SARS-CoV-2 exhibits an increased resilience to the antiviral type I interferon response", - "rel_date": "2022-01-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.20.476754", - "rel_abs": "The new variant of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Omicron (B.1.1.529), is genetically very different from other VOCs. We compared Omicron with the preceding VOC Delta (B.1.617.2) and the wildtype strain (B.1) with respect to their interactions with the antiviral type I interferon (IFN-alpha/beta) response in infected cells. Our data indicate that Omicron has gained an elevated capability to suppress IFN-beta induction upon infection and to better withstand the antiviral state imposed by exogenously added IFN-alpha.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Lyudmila Shalamova", - "author_inst": "Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University; D-35392 Giessen, Germany" - }, - { - "author_name": "Ulrike Felgenhauer", - "author_inst": "Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University; D-35392 Giessen, Germany" - }, - { - "author_name": "Andreas R. Schaubmar", - "author_inst": "Unit for Biomathematics and Data processing, FB10-Veterinary Medicine, Justus-Liebig University; D-35392 Giessen, Germany" - }, - { - "author_name": "Kathrin Buettner", - "author_inst": "Unit for Biomathematics and Data processing, FB10-Veterinary Medicine, Justus-Liebig University; D-35392 Giessen, Germany" - }, - { - "author_name": "Marek Widera", - "author_inst": "University Hospital, Goethe University Frankfurt am Main" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "University Hospital, Goethe University; Frankfurt am Main, Germany" - }, - { - "author_name": "Friedemann Weber", - "author_inst": "Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University; D-35392 Giessen, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.19.476940", "rel_title": "Targeting SARS-CoV-2 infection through CAR T cells and bispecific T cell engagers", @@ -430283,6 +431130,69 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.01.17.476644", + "rel_title": "Nirmatrelvir, an orally active Mpro inhibitor, is a potent inhibitor of SARS-CoV-2 Variants of Concern", + "rel_date": "2022-01-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.17.476644", + "rel_abs": "New variants of SARS-CoV-2 with potential for enhanced transmission, replication, and immune evasion capabilities continue to emerge causing reduced vaccine efficacy and/or treatment failure. As of January 2021, the WHO has defined five variants of concern (VOC): B.1.1.7 (Alpha, ), B.1.351 (Beta, {beta}), P.1 (Gamma, {gamma}), B.1.617.2 (Delta, {delta}), and B.1.1.529 (Omicron, o). To provide a therapeutic option for the treatment of COVID-19 and variants, Nirmatrelvir, the antiviral component of PAXLOVID, an oral outpatient treatment recently authorized for conditional or emergency use treatment of COVID-19, was developed to inhibit SARS-CoV-2 replication. Nirmatrelvir (PF-07321332) is a specific inhibitor of coronavirus main protease (Mpro, also referred to as 3CLpro), with potent antiviral activity against several human coronaviruses, including SARS-CoV-2, SARS-CoV, and MERS (Owen et al, Science 2021. doi: 10.1126/science.abl4784). Here, we evaluated PF-07321332 against the five SARS-CoV-2 VOC (, {beta}, {gamma}, {delta},, o) and two Variants of Interest or VOI, C.37 ({lambda}) and B.1.621 (), using qRT-PCR in VeroE6 cells lacking the P-glycoprotein (Pgp) multidrug transporter gene (VeroE6 P-gp knockout cells). Nirmatrelvir potently inhibited USA-WA1/2020 strain, and , {beta}, {gamma}, {lambda}, {delta}, , and o variants in VeroE6 P-gp knockout cells with mean EC50 values 38.0 nM, 41.0 nM, 127.2 nM, 24.9 nM, 21.2 nM, 15.9 nM, 25.7 nM and 16.2 nM, respectively. Sequence analysis of the Mpro encoded by the variants showed ~100% identity of active site amino acid sequences, reflecting the essential role of Mpro during viral replication leading to ability of Nirmatrelvir to exhibit potent activity across all the variants.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Devendra K. Rai", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Irina Yurgelonis", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Patricia McMonagle", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Hussin A. Rothan", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA." + }, + { + "author_name": "Li Hao", + "author_inst": "Pfizer Worldwide Researhc, Development & Medical, Pearl River, NY 10965, USA." + }, + { + "author_name": "Alexey Gribenko", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA." + }, + { + "author_name": "Elizabeth Titova", + "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA" + }, + { + "author_name": "Barry Kreiswirth", + "author_inst": "Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA" + }, + { + "author_name": "Kris M. White", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, USA, and Global Health Emerging Pathogens Institute, Icahn School of Med" + }, + { + "author_name": "Yuao Zhu", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Annaliesa S. Anderson", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + }, + { + "author_name": "Rhonda D. Cardin", + "author_inst": "Pfizer Worldwide Research, Development & Medical, Pearl River, NY 10965, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.17.22269283", "rel_title": "ELF5 is a respiratory epithelial cell-specific risk gene for severe COVID-19", @@ -431974,20 +432884,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.16.22269210", - "rel_title": "Understanding Evolution of COVID-19 Driven Mortality Rate", - "rel_date": "2022-01-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.16.22269210", - "rel_abs": "ObjectiveCOVID-19 has resulted in the death of almost 4 million people till date1. However, the mortality rate across countries seems to be vastly different irrespective of their respective socio-economic backgrounds. It is well known now that COVID-19 is an acute inflammatory infectious disease that gets complicated by type-I interferon response2,3. However, the precise reason for variations in COVID-19 related mortality rates is unknown. A detailed understanding behind the evolution of mortality rate around the globe is needed.\n\nMethodsIn this article, we show that a biological science guided machine learning-based approach can predict the evolution of mortality rates across countries. We collected the publicly available data of all the countries in the world with regard to the mortality rate and the relevant biological and socio-economical causes. The data was analyzed using a novel FFT driven machine learning algorithm.\n\nResultsOur results demonstrate how COVID-19 related mortality rate is closely dependent on a multitude of socio-economic factors (population density, GDP per capita, global health index and population above 65 years of age), environmental (PM2.5 air pollution) and lifestyle aka food habits (meat consumption per capita, alcohol consumption per capita, dairy product consumption per capita and sugar consumption per capita). Interestingly, we found that individually these parameters show no visible trend that can be generalized with mortality.\n\nConclusionsWe anticipate that our work will initiate conversations between health officials, policymakers and world leaders towards providing preventative measures against COVID-19 and future coronavirus-based diseases and endemics/ pandemics by taking a holistic view.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.17.22269439", "rel_title": "Detection of SARS-CoV-2 variant Mu, Beta, Gamma, Lambda, Delta, Alpha, and Omicron in wastewater settled solids using mutation-specific assays is associated with regional detection of variants in clinical samples", @@ -432200,6 +433096,81 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2022.01.14.22269074", + "rel_title": "Evaluation of an emergency safe supply drug and managed alcohol program in COVID-19 isolation hotel shelters for people experiencing homelessness", + "rel_date": "2022-01-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.14.22269074", + "rel_abs": "BackgroundDuring a COVID-19 outbreak in the congregate shelter system in Halifax, Nova Scotia, Canada, a multidisciplinary health care team provided an emergency \"safe supply\" of pharmaceutical-grade medications and beverage-grade alcohol to facilitate isolation in COVID-19 hotel shelters for residents who are dependent on these substances. We aimed to evaluate (a) substances and dosages provided, and (b) effectiveness and safety of the program.\n\nMethodsWe retrospectively reviewed medical records of all COVID-19 isolation hotel shelter residents during May 2021. We extracted data on medication and alcohol dosages provided each day. The primary outcome was residents prematurely leaving isolation against public health orders. Adverse events included (a) overdose; (b) intoxication; and (c) diversion, selling, or sharing of medications or alcohol.\n\nResultsOver 25 days, 77 isolation hotel residents were assessed (mean age 42 {+/-} 14 years; 24% women). Sixty-two (81%) residents were provided medications, alcohol, or cigarettes. Seventeen residents (22%) received opioid agonist treatment medications (methadone, buprenorphine, or slow-release oral morphine) and 27 (35%) received hydromorphone tablets. Thirty-one (40%) residents received stimulant tablets with methylphenidate (27; 35%), dextroamphetamine (8; 10%), or lisdexamfetamine (2; 3%). Six residents (8%) received benzodiazepines. Forty-two (55%) residents received alcohol, including 41 (53%) with strong beer, three (3%) with wine, and one (1%) with hard liquor. Over 14 days in isolation, mean daily dosages increased of hydromorphone (45 {+/-} 32 to 57 {+/-} 42mg), methylphenidate (51 {+/-} 28 to 77 {+/-} 37mg), dextroamphetamine (33 {+/-} 16 to 46 {+/-} 13mg), and alcohol (12.3 {+/-} 7.6 to 13.0 {+/-} 6.9 standard drinks). Six residents (8%) left isolation prematurely, but four of those residents returned. Over 1,059 person-days in isolation, there were zero overdoses. Documented concerns regarding intoxication occurred six times (0.005 events/person-day) and medication diversion or sharing three times (0.003 events/person-day).\n\nConclusionsAn emergency safe supply and managed alcohol program, paired with housing, was associated with low rates of adverse events and high rates of successful completion of the 14-day isolation period in COVID-19 isolation hotel shelters. This supports the effectiveness and safety of emergency safe supply prescribing and managed alcohol in this setting.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Thomas D Brothers", + "author_inst": "Dalhousie University; University College London" + }, + { + "author_name": "Malcolm Leaman", + "author_inst": "North End Community Health Centre" + }, + { + "author_name": "Matthew Bonn", + "author_inst": "Canadian Association of People who Use Drugs (CAPUD)" + }, + { + "author_name": "Dan Lewer", + "author_inst": "University College London" + }, + { + "author_name": "Jacqueline Atkinson", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre" + }, + { + "author_name": "John Fraser", + "author_inst": "North End Community Health Centre" + }, + { + "author_name": "Amy Gillis", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Michael Gniewek", + "author_inst": "Dalhousie University; Direction 180" + }, + { + "author_name": "Leisha Hawker", + "author_inst": "North End Community Health Centre; Dalhousie University" + }, + { + "author_name": "Heather Hayman", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre" + }, + { + "author_name": "Peter Jorna", + "author_inst": "Nova Pharmacy" + }, + { + "author_name": "David Martell", + "author_inst": "Dalhousie University; Direction 180" + }, + { + "author_name": "Tiffany O'Donnell", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre; Dalhousie University" + }, + { + "author_name": "Helen Rivers-Bowerman", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre" + }, + { + "author_name": "Leah Genge", + "author_inst": "Mobile Outreach Street Health (MOSH), North End Community Health Centre; Dalhousie University; Direction 180" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "addiction medicine" + }, { "rel_doi": "10.1101/2022.01.16.22269377", "rel_title": "The Impact of State Paid Sick Leave Policies on Longitudinal Weekday Workplace Mobility During the COVID-19 Pandemic", @@ -433587,81 +434558,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.12.22269095", - "rel_title": "COVID MED - An Early Pandemic Trial of Losartan for Hospitalized COVID-19 Patients", - "rel_date": "2022-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.12.22269095", - "rel_abs": "BackgroundACEi/ARB medications have been hypothesized to have potential benefit in COVID-19. Despite concern for increased ACE-2 expression in some animal models, preclinical and observational-retrospective and uncontrolled trials suggested possible benefit. Two RCTs of the ARB losartan from University of Minnesota showed no benefit yet safety signals for losartan in outpatient and hospitalized COVID-19 patients. COVID MED, started early in the pandemic, also assessed losartan in a RCT in hospitalized patients with COVID-19.\n\nMethodsCOVID MED was a double-blinded, placebo-controlled, multicenter, platform randomized clinical trial (RCT). Hospitalized COVID-19 patients were randomized to receive standard care and hydroxychloroquine, lopinavir/ritonavir, losartan, or placebo. Hydroxychloroquine and lopinavir/ritonavir arms were discontinued after RCTs showed no benefit. We report data from the losartan arm compared to combined (lopinavir-ritonavir and placebo) and prespecified placebo-only controls. The primary endpoint, the mean COVID-19 Ordinal Severity Score (COSS) slope of change, was compared with the Students t-test. Slow enrollment prompted early termination.\n\nResultsOf 448 screened patients, 15 (3.5%) were randomized/enrolled, 9 to receive losartan and 6 to receive control (lopinavir/ritonavir [N=2], placebo [N=4]); 1 patient who withdrew prior to study drug was excluded yielding 14 patients for analysis (losartan [N=9] vs. control [N=5] [lopinavir/ritonavir [N=2], placebo [N=3]]). Most baseline parameters were balanced. Treatment with losartan was not associated with a difference in mean COSS slope of change in comparison with combined control (p=0.4) or placebo-only control (p=0.05) (trend favoring placebo). 60-day mortality and overall AE and SAE rates were numerically but not significantly higher with losartan.\n\nConclusionsIn this small blinded RCT in hospitalized COVID-19 patients, losartan did not improve outcome vs. control comparisons and was associated with adverse safety signals.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Daniel Freilich", - "author_inst": "Bassett Medical Center" - }, - { - "author_name": "Jennifer Victory", - "author_inst": "Bassett Research Institute" - }, - { - "author_name": "Paul Jenkins", - "author_inst": "Bassett Research Institute" - }, - { - "author_name": "James Wheeler", - "author_inst": "Goshen Health" - }, - { - "author_name": "G Matthew Vail", - "author_inst": "Reid Health" - }, - { - "author_name": "Erik Riesenfeld", - "author_inst": "Bassett Medical Center" - }, - { - "author_name": "Peggy Cross", - "author_inst": "Bassett Research Institute" - }, - { - "author_name": "Catherine Gilmore", - "author_inst": "Bassett Research Institute" - }, - { - "author_name": "Melissa Huckabone", - "author_inst": "Bassett Research Institute" - }, - { - "author_name": "Anna Schworm", - "author_inst": "Bassett Research Institute" - }, - { - "author_name": "Umesha Boregowda", - "author_inst": "Bassett Medical Center" - }, - { - "author_name": "Farah Deshmukh", - "author_inst": "Bassett Medical Center" - }, - { - "author_name": "Yuri Choi", - "author_inst": "Bassett Medical Center" - }, - { - "author_name": "Azkia Kahn", - "author_inst": "Bassett Medical Center" - }, - { - "author_name": "Anne Gadomski", - "author_inst": "Bassett Research Institute" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.14.22269324", "rel_title": "Improved prediction of new COVID-19 cases using a simple vector autoregressive model: Evidence from seven New York State counties", @@ -433882,6 +434778,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.11.22269069", + "rel_title": "Hydroxychloroquine/Chloroquine in COVID-19 With Focus on Hospitalized Patients - A Systematic Review", + "rel_date": "2022-01-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.11.22269069", + "rel_abs": "BackgroundIn the beginning of the COVID-19 pandemic, many hospitalized patients received empiric hydroxychloroquine/chloroquine (HC/CQ). Although some retrospective-observational trials suggested potential benefit, all subsequent randomized clinical trials (RCTs) failed to show benefit and use generally ceased. Herein, we summarize key studies that clinicians advising patients on HC/CQs efficacy:safety calculus in hospitalized COVID-19 patients would want to know about in a practical one-stop-shopping source.\n\nMethodsPubmed and Google were searched on November 4, 2021. Search words included: COVID-19, hydroxychloroquine, chloroquine, in vitro, animal studies, clinical trials, and meta-analyses. Studies were assessed for import and included if considered impactful for benefit:risk assessment.\n\nResultsThese searches led to inclusion of 12 in vitro and animal reports; 12 retrospective-observational trials, 19 interventional clinical trials (17 RCTs, 1 single-arm, 1 controlled but unblinded), and 51 meta-analyses in hospitalized patients.\n\nInconsistent efficacy was seen in vitro and in animal studies for coronaviruses and nil in SARS-CoV-2 animal models specifically. Most retrospective-observational studies in hospitalized COVID-19 patients found no efficacy; QT prolongation and increased adverse events and mortality were reported in some. All RCTs and almost all meta-analyses provided robust data showing no benefit in overall populations and subgroups, yet concerning safety issues in many.\n\nConclusionsHC/CQ have inconsistent anti-coronavirus efficacy in vitro and in animal models, and no convincing efficacy yet substantial safety issues in the overwhelming majority of retrospective-observational trials, RCTs, and meta-analyses in hospitalized COVID-19 patients. HC/CQ should not be prescribed for hospitalized COVID-19 patients outside of clinical trials.\n\nKey Summary PointsPreclinical hydroxychloroquine/chloroquine in vitro studies found inconsistent activity against coronaviruses including SARS-CoV-2.\n\nPreclinical hydroxychloroquine/chloroquine animals studies found inconsistent efficacy for coronaviruses in general and none for SARS-CoV-2.\n\nThe overhwelming majority of RCTs and retrospective-observational trials found no benefit for hydroxychloroquine/chloroquine in hospitalized COVID-19 patients, and many found concerning safety signals.\n\nThe majority of RCTs and retrospective-observational trials found no benefit for hydroxychloroquine/chloroquine in COVID-19 outpatients or for pre- or post-exposure prophylaxis, and some found concerning safety signals.\n\nThe overwhelming majority of meta-analyses found no benefit for hydroxychloroquine/chloroquine in COVID-19 inpatients, outpatients, or for prophylaxis, and many found concerning safety signals.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Daniel Freilich", + "author_inst": "Bassett Medical Center" + }, + { + "author_name": "Jennifer Victory", + "author_inst": "Bassett Research Institute" + }, + { + "author_name": "Anne Gadomski", + "author_inst": "Bassett Research Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.13.476204", "rel_title": "Covariance predicts conserved protein residue interactions important to the emergence and continued evolution of SARS-CoV-2 as a human pathogen", @@ -435413,161 +436336,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.13.22269205", - "rel_title": "Assessing and improving the validity of COVID-19 autopsy studies - a multi center approach to establish essential standards for immunohistochemical and ultrastructural analyses", - "rel_date": "2022-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.13.22269205", - "rel_abs": "BackgroundAutopsy studies have provided valuable insights into the pathophysiology of COVID-19. Controversies remain whether the clinical presentation is due to direct organ damage by SARS-CoV-2 or secondary effects, e.g. by an overshooting immune response. SARS-CoV-2 detection in tissues by RT-qPCR and immunohistochemistry (IHC) or electron microscopy (EM) can help answer these questions, but a comprehensive evaluation of these applications is missing.\n\nMethodsWe assessed publications using IHC and EM for SARS-CoV-2 detection in autopsy tissues. We systematically evaluated commercially available antibodies against the SARS-CoV-2 spike protein and nucleocapsid, dsRNA, and non-structural protein Nsp3 in cultured cell lines and COVID-19 autopsy tissues. In a multicenter study, we evaluated specificity, reproducibility, and inter-observer variability of SARS-CoV-2 nucleocapsid staining. We correlated RT-qPCR viral tissue loads with semiquantitative IHC scoring. We used qualitative and quantitative EM analyses to refine criteria for ultrastructural identification of SARS-CoV-2.\n\nFindingsPublications show high variability in the detection and interpretation of SARS-CoV-2 abundance in autopsy tissues by IHC or EM. In our study, we show that IHC using antibodies against SARS-CoV-2 nucleocapsid yields the highest sensitivity and specificity. We found a positive correlation between presence of viral proteins by IHC and RT-qPCR-determined SARS-CoV-2 viral RNA load (r=-0.83, p-value <0.0001). For EM, we refined criteria for virus identification and also provide recommendations for optimized sampling and analysis. 116 of 122 publications misinterpret cellular structures as virus using EM or show only insufficient data. We provide publicly accessible digitized EM and IHC sections as a reference and for training purposes.\n\nInterpretationSince detection of SARS-CoV-2 in human autopsy tissues by IHC and EM is difficult and frequently incorrect, we propose criteria for a re-evaluation of available data and guidance for further investigations of direct organ effects by SARS-CoV-2.\n\nKey messagesO_LIDetection of SARS-CoV-2 proteins by IHC in autopsy tissues is less sensitive in comparison to SARS-CoV-2 RNA detection by RT-qPCR.\nC_LIO_LIFor determination of SARS-CoV-2 protein positive cells by IHC in autopsy tissues, detection of spike protein is less sensitive than nucleocapsid protein.\nC_LIO_LICorrect identification of SARS-CoV-2 particles in human samples by EM is limited to the respiratory system.\nC_LIO_LIInterpretation of IHC and EM should follow substantiated consensus criteria to enhance accuracy.\nC_LIO_LIExisting datasets describing SARS-CoV-2 presence in human autopsy tissues need to be critically re-evaluated.\nC_LI\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC=\"FIGDIR/small/22269205v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (44K):\norg.highwire.dtl.DTLVardef@eafd97org.highwire.dtl.DTLVardef@1aed770org.highwire.dtl.DTLVardef@1c21ab9org.highwire.dtl.DTLVardef@68a101_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Susanne Krasemann", - "author_inst": "Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany" - }, - { - "author_name": "Carsten Dittmayer", - "author_inst": "Department of Neuropathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Saskia v. Stillfried", - "author_inst": "Institute of Pathology and Electron Microscopy Facility, RWTH University of Aachen, Germany" - }, - { - "author_name": "Jenny Meinhardt", - "author_inst": "Department of Neuropathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Fabian Heinrich", - "author_inst": "Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany" - }, - { - "author_name": "Kristin Hartmann", - "author_inst": "Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany" - }, - { - "author_name": "Susanne Pfefferle", - "author_inst": "Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany" - }, - { - "author_name": "Edda Thies", - "author_inst": "Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany" - }, - { - "author_name": "Regina v. Manitius", - "author_inst": "Department of Neuropathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Tom Aschman", - "author_inst": "Department of Neuropathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Josefine Radke", - "author_inst": "Department of Pathology, Universitatsmedizin Greifswald, Greifswald, Germany" - }, - { - "author_name": "Anja Osterloh", - "author_inst": "Department of Neuropathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Simone Schmid", - "author_inst": "Department of Neuropathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Eva M Buhl", - "author_inst": "Institute of Pathology and Electron Microscopy Facility, RWTH University of Aachen, Germany" - }, - { - "author_name": "Jana Ihlow", - "author_inst": "Institute for Pathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Sefer Elezkurtaj", - "author_inst": "Institute for Pathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "David Horst", - "author_inst": "Institute for Pathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Andreas C Hocke", - "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charite- Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Sara Timm", - "author_inst": "Core Facility Electron Microscopy, Charite - Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Sebastian Bachmann", - "author_inst": "Institute of Functional Anatomy, Charite Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Victor Corman", - "author_inst": "Institute of Virology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Hans-Hilmar Goebel", - "author_inst": "Department of Neuropathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Jakob Matschke", - "author_inst": "Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany" - }, - { - "author_name": "Stephanie Stanelle-Bertram", - "author_inst": "Department for Viral Zoonoses-One Health, Leibniz Institute for Experimental Virology, Hamburg, Germany" - }, - { - "author_name": "Guelsah Gabriel", - "author_inst": "Department for Viral Zoonoses-One Health, Leibniz Institute for Experimental Virology, Hamburg, Germany" - }, - { - "author_name": "Danielle Seilhean", - "author_inst": "Raymond Escourolle Department of Neuropathology, APHP, Sorbonne University, Paris, France" - }, - { - "author_name": "Homa Adle-Biassette", - "author_inst": "Hopital Bichat-Claude Bernard, Service d'Anatomie Pathologie, Universite Paris, Paris, France" - }, - { - "author_name": "Benjamin Ondruschka", - "author_inst": "Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany" - }, - { - "author_name": "Matthias Ochs", - "author_inst": "Core Facility Electron Microscopy, Charite - Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Werner Stenzel", - "author_inst": "Department of Neuropathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Frank Heppner", - "author_inst": "Department of Neuropathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Peter Boor", - "author_inst": "Institute of Pathology and Electron Microscopy Facility, RWTH University of Aachen, Germany" - }, - { - "author_name": "Helena Radbruch", - "author_inst": "Department of Neuropathology, Charite-Universitatsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Michael Laue", - "author_inst": "National Consultant Laboratory for Electron Microscopy of Infectious Pathogens, Centre for Biological Threats and Special Pathogens 4 (ZBS 4), Robert Koch Insti" - }, - { - "author_name": "Markus Glatzel", - "author_inst": "Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.12.22269134", "rel_title": "Incidence and Risk Factors of Immediate Hypersensitivity Reactions and Immunisation Stress-related Responses with COVID-19 mRNA Vaccine", @@ -436024,6 +436792,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.12.22269048", + "rel_title": "A unique dexamethasone-dependent gene expression profile in the lungs of COVID-19 patients", + "rel_date": "2022-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.12.22269048", + "rel_abs": "Local immunopathogenesis of COVID-19 acute respiratory distress syndrome (CARDS) and the effects of systemic dexamethasone (DXM) treatment on pulmonary immunity in COVID-19 remain insufficiently understood. To provide further insight into insight into immune regulatory mechanisms in the lungs of CARDS (with and without DXM treatment) and critically ill non-COVID-19 patients (without DXM treatment), transcriptomic RNA-seq analysis of bronchoalveolar lavage fluid (BALF) was performed in these patients. Functional analysis was performed using gene ontology and a blood transcription module, and gene expression of select pro-inflammatory cytokines, interferon-stimulated genes (ISGs) and auto-IFN antibodies were assessed. We found 550 and 2173 differentially expressed genes in patients with non-DXM-CARDS and DXM-CARDS, respectively. DXM-CARDS was characterized by upregulation of genes related to pulmonary innate and adaptive immunity, notably B-cell and complement pathway activation, antigen presentation, phagocytosis and FC-gamma receptor signalling. Pro-inflammatory genes were not differentially expressed in CARDS vs. non-COVID-19, nor did they differ according to DXM. Most ISGs were specifically upregulated in CARDS, particularly in non-DXM-CARDS. Auto-IFN autoantibodies were detectable in BALF of some CARDS patients. In conclusion, DXM treatment was not associated with regulation of pro-inflammatory pathways in CARDS but with regulation of other specific local innate and adaptive immune responses.\n\nsummaryThis study identifies differentially expressed genes in bronchoalveolar fluid of COVID-19 acute respiratory distress patients with a distinct RNA expression profile of those treated with dexamethasone. These results challenge the concept of a COVID-19 specific cytokine storm.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ulrik Fahnoe", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre; Copenhagen University" + }, + { + "author_name": "Andreas Ronit", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre" + }, + { + "author_name": "Ronan M.G. Berg", + "author_inst": "Copenhagen University Hospital - Rigshospitalet; Copenhagen University" + }, + { + "author_name": "Sofie E.G. Joergensen", + "author_inst": "Aarhus University Hospital; Aarhus University" + }, + { + "author_name": "Trine H. Mogensen", + "author_inst": "Aarhus University Hospital; Aarhus University" + }, + { + "author_name": "Alexander P. Underwood", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre" + }, + { + "author_name": "Troels K.H. Scheel", + "author_inst": "The Rockefeller University; University of Copenahagen" + }, + { + "author_name": "Jens Bukh", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre; Copenhagen University" + }, + { + "author_name": "Ronni R. Plovsing", + "author_inst": "Copenhagen University Hospital - Amager and Hvidovre; Copenhagen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.01.13.22269236", "rel_title": "Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples", @@ -437571,161 +438390,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.11.475918", - "rel_title": "Shift of lung macrophage composition is associated with COVID-19 disease severity and recovery", - "rel_date": "2022-01-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.11.475918", - "rel_abs": "Though it has been 2 years since the start of the Coronavirus Disease 19 (COVID-19) pandemic, COVID-19 continues to be a worldwide health crisis. Despite the development of preventive vaccines, very little progress has been made to identify curative therapies to treat COVID-19 and other inflammatory diseases which remain a major unmet need in medicine. Our study sought to identify drivers of disease severity and death to develop tailored immunotherapy strategies to halt disease progression. Here we assembled the Mount Sinai COVID-19 Biobank which was comprised of ~600 hospitalized patients followed longitudinally during the peak of the pandemic. Moderate disease and survival were associated with a stronger antigen (Ag) presentation and effector T cell signature, while severe disease and death were associated with an altered Ag presentation signature, increased numbers of circulating inflammatory, immature myeloid cells, and extrafollicular activated B cells associated with autoantibody formation. Strikingly, we found that in severe COVID-19 patients, lung tissue resident alveolar macrophages (AM) were not only severely depleted, but also had an altered Ag presentation signature, and were replaced by inflammatory monocytes and monocyte-derived macrophages (MoM{Phi}). Notably, the size of the AM pool correlated with recovery or death, while AM loss and functionality were restored in patients that recovered. These data therefore suggest that local and systemic myeloid cell dysregulation is a driver of COVID-19 severity and that modulation of AM numbers and functionality in the lung may be a viable therapeutic strategy for the treatment of critical lung inflammatory illnesses.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Steven Tiwen Chen", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Matthew D Park", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Diane Marie Del Valle", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Mark Buckup", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Alexandra Tabachnikova", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Nicole W Simons", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Konstantinos Mouskas", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Brian Lee", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Daniel Geanon", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Travis Dawson", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Robert Marvin", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Kai Nie", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ryan Thompson", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Zhen Zhao", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jessica LeBerichel", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Christie Chang", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Hajra Jamal", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Udit Chaddha", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Kusum Mathews", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Samuel Acquah", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Stacey-Ann Brown", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Michelle Reiss", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Timothy Harkin", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Marc Feldmann", - "author_inst": "University of Oxford" - }, - { - "author_name": "Charles A Powell", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jaime Hook", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Seunghee Kim-Schulze", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Adeeb H Rahman", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Brian Brown", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "- The COVID-19 Biobank Team", - "author_inst": "-" - }, - { - "author_name": "Noam D Beckmann", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Sacha Gnjatic", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ephraim Kenigsberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Alexander Charney", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Miriam Merad", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.01.12.22269139", "rel_title": "Comparison of Anterior Nares Viral Loads in Asymptomatic and Symptomatic Individuals Diagnosed with SARS-CoV-2 in a University Screening Program", @@ -438070,6 +438734,137 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.11.475947", + "rel_title": "SARS-CoV-2 drives NLRP3 inflammasome activation in human microglia through spike-ACE2 receptor interaction", + "rel_date": "2022-01-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.11.475947", + "rel_abs": "Coronavirus disease-2019 (COVID-19) is primarily a respiratory disease, however, an increasing number of reports indicate that SARS-CoV-2 infection can also cause severe neurological manifestations, including precipitating cases of probable Parkinsons disease. As microglial NLRP3 inflammasome activation is a major driver of neurodegeneration, here we interrogated whether SARS-CoV-2 can promote microglial NLRP3 inflammasome activation utilising a model of human monocyte-derived microglia. We identified that SARS-CoV-2 isolates can bind and enter microglia, triggering inflammasome activation in the absence of viral replication. Mechanistically, microglial NLRP3 could be both primed and activated with SARS-CoV-2 spike glycoprotein in a NF-{kappa}B and ACE2-dependent manner. Notably, virus- and spike protein-mediated inflammasome activation in microglia was significantly enhanced in the presence of -synuclein fibrils, which was entirely ablated by NLRP3-inhibition. These results support a possible mechanism of microglia activation by SARS-CoV-2, which could explain the increased vulnerability to developing neurological symptoms akin to Parkinsons disease in certain COVID-19 infected individuals, and a potential therapeutic avenue for intervention.\n\nSIGNIFICANCE STATEMENTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) principally affects the lungs, however there is evidence that the virus can also reach the brain and lead to chronic neurological symptoms. In this study, we examined the interaction SARS-CoV-2 with brain immune cells, by using an ex-vivo model of human monocyte-derived microglia. We identified robust activation of the innate immune sensor complex, NLRP3 inflammasome, in cells exposed to SARS-CoV-2. This was dependent on spike protein-ACE2 receptor interaction and was potentiated in the presence of -synuclein. We therefore identify a possible mechanism for SARS-CoV-2 and increased vulnerability to developing neurological dysfunction. These findings support a potential therapeutic avenue for treatment of SARS-CoV-2 driven neurological manifestations, through use of NLRP3 inflammasome or ACE2 inhibitors.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Eduardo A Albornoz", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Alberto A Amarilla", + "author_inst": "School of Chemistry and molecular Biosciences, University of Queensland" + }, + { + "author_name": "Naphak Modhiran", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Sandra Parker", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Xaria X Li", + "author_inst": "School of biomedical sciences, University of Queensland" + }, + { + "author_name": "Danushka K Wijesundara", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Adriana Pliego Zamora", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Christopher LD McMillan", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Benjamin Liang", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Nias Y.G Peng", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Julian D.J Sng", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Fatema Tuj Saima", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Devina Paramitha", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Rhys Parry", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Michael S Avumegah", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Ariel Isaacs", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Martin Lo", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Zaray Miranda-Chacon", + "author_inst": "Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile" + }, + { + "author_name": "Daniella Bradshaw", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Constanza Salinas-Rebolledo", + "author_inst": "Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile" + }, + { + "author_name": "Niwanthi W Rajapakse", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + }, + { + "author_name": "Trent Munro", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Alejandro Rojas-Fernandez", + "author_inst": "Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile" + }, + { + "author_name": "Paul R Young", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Katryn J Stacey", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Alexander A Khromykh", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Keith J Chappell", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Daniel Watterson", + "author_inst": "School of Chemistry and Molecular Biosciences, University of Queensland" + }, + { + "author_name": "Trent M Woodruff", + "author_inst": "School of Biomedical Sciences, Faculty of Medicine, University of Queensland" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2022.01.11.475327", "rel_title": "Systemic infection of SARS-CoV-2 in free ranging Leopard (Panthera pardus fusca) in India", @@ -439485,49 +440280,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.01.09.22268977", - "rel_title": "COVID-19 Time of Intubation Mortality Evaluation (C-TIME): A System for Predicting Mortality of Patients with COVID-19 Pneumonia at the Time They Require Mechanical Ventilation.", - "rel_date": "2022-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.09.22268977", - "rel_abs": "BackgroundAn accurate system to predict mortality in patients requiring intubation for COVID-19 could help to inform consent, frame family expectations and assist end-of-life decisions.\n\nResearch objectiveTo develop and validate a mortality prediction system called C-TIME (COVID-19 Time of Intubation Mortality Evaluation) using variables available before intubation, determine its discriminant accuracy, and compare it to APACHE IVa and SOFA.\n\nMethodsA retrospective cohort was set in 18 medical-surgical ICUs, enrolling consecutive adults, positive by SARS-CoV 2 RNA by reverse transcriptase polymerase chain reaction or positive rapid antigen test, and undergoing endotracheal intubation. All were followed until hospital discharge or death. The combined outcome was hospital mortality or terminal extubation with hospice discharge. Twenty-five clinical and laboratory variables available 48 hours prior to intubation were entered into multiple logistic regression (MLR) and the resulting model was used to predict mortality of validation cohort patients. AUROC was calculated for C-TIME, APACHE IVa and SOFA.\n\nResultsThe median age of the 2,440 study patients was 66 years; 61.6 percent were men, and 50.5 percent were Hispanic, Native American or African American. Age, gender, COPD, minimum mean arterial pressure, Glasgow Coma scale score, and PaO2/FiO2 ratio, maximum creatinine and bilirubin, receiving factor Xa inhibitors, days receiving non-invasive respiratory support and days receiving corticosteroids prior to intubation were significantly associated with the outcome variable. The validation cohort comprised 1,179 patients. C-TIME had the highest AUROC of 0.75 (95%CI 0.72-0.79), vs 0.67 (0.64-0.71) and 0.59 (0.55-0.62) for APACHE and SOFA, respectively (Chi2 P<0.0001).\n\nConclusionsC-TIME is the only mortality prediction score specifically developed and validated for COVID-19 patients who require mechanical ventilation. It has acceptable discriminant accuracy and goodness-of-fit to assist decision-making just prior to intubation. The C-TIME mortality prediction calculator can be freely accessed on-line at https://phoenixmed.arizona.edu/ctime.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Robert A Raschke", - "author_inst": "University of Arizona College of Medicine- Phoenix" - }, - { - "author_name": "Pooja Rangan", - "author_inst": "University of Arizona College of Medicine-Phoenix" - }, - { - "author_name": "Sumit Agarwal", - "author_inst": "University of Arizona College of Medicine-Phoenix" - }, - { - "author_name": "Suresh Uppalapu", - "author_inst": "University of Arizona College of Medicine-Phoenix" - }, - { - "author_name": "Nehan Sher", - "author_inst": "University of Arizona College of Medicine-Phoenix" - }, - { - "author_name": "Steven c Curry", - "author_inst": "University of Arizona College of Medicine-Phoenix" - }, - { - "author_name": "C Williiam Hesie", - "author_inst": "University of Arizona College of Medicine-Phoenix" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2022.01.11.22268908", "rel_title": "Longitudinal symptom and clinical outcome analysis of hospitalized COVID-19 patients", @@ -439808,6 +440560,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.07.22268883", + "rel_title": "Safety and immunogenicity of the BBIBP-CorV vaccine in adolescents aged 12-17 years in Thai population, prospective cohort study.", + "rel_date": "2022-01-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.07.22268883", + "rel_abs": "IntroductionCOVID-19 pandemic affects all populations worldwide, including adolescents. Adolescents can develop a severe form of COVID-19, especially with comorbidity underlying. The prior studies of the mRNA COVID-19 vaccine showed excellent effectiveness in adolescents. Therefore, this study aimed to evaluate the safety and effectiveness of the BBIBP-CorV vaccine with the immunobridging approach in Thai adolescents.\n\nMethodsThis single-center, prospective cohort study compared the immunogenicity after 2 doses of the BBIBO-CorV vaccine with 21 days interval of participants aged 12-17 years with 18-30 years at Chulabhorn Hospital, Chulabhorn Royal Academy, Bangkok, Thailand. The key eligible criteria were healthy or had stable pre-existing comorbidity participants, aged 12-17 years. The primary endpoint was the anti-receptor binding domain antibody concentration at 4 weeks after dose 2 of the vaccine. In addition, safety profiles were solicited adverse events within 7 days after each dose of vaccine and any adverse events through 1 month after dose 2 of the vaccine.\n\nResultsFour weeks after the second vaccination, the GMC of anti-RBD antibody in the adolescent cohort was 102.9 BAU/mL (95%CI; 91.0-116.4) and 36.9 BAU/mL (95%CI; 30.9-44.0) in the adult cohort. The GMR of the adolescent cohort was 2.79 (95%CI; 2.25-3.46, p-value; <0.0001) compared with the adult cohort which met non-inferiority criteria. The reactogenicity was slightly less reported in the adolescent cohort compared with the adult cohort. No serious adverse events were reported in both cohorts.\n\nConclusionVaccination with the BBIBP-CorV vaccine in the adolescent participants was safe and effective.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Kriangkrai Tawinprai", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Taweegrit Siripongboonsitti", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Thachanun Porntharukchareon", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Preeda Vanichsetakul", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Saraiorn Thonginnetra", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Krongkwan Niemsorn", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Pathariya Promsena", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Manunya Tandhansakul", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Naruporn Kasemlawan", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Natthanan Ruangkijpaisal", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Narin Banomyong", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Nanthida Phattraprayoon", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Teerapat Ungtrakul", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Kasiruck Wittayasak", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Nawarat Thonwirak", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Kamonwan Soonklang", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Gaidganok Sornsamdang", + "author_inst": "Chulabhorn Royal Academy" + }, + { + "author_name": "Nithi Mahanonda", + "author_inst": "Chulabhorn Royal Academy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.08.22268953", "rel_title": "Anti-PEG antibodies boosted in humans by SARS-CoV-2 lipid nanoparticle mRNA vaccine", @@ -441282,57 +442121,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.01.07.475443", - "rel_title": "Evaluation of an optimized protocol and Illumina ARTIC V4 primer pool for sequencing of SARS-CoV-2 using COVIDSeq\u2122 and DRAGEN\u2122 COVID Lineage App workflow", - "rel_date": "2022-01-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.07.475443", - "rel_abs": "Next-Generation Sequencing based genomic surveillance has been widely implemented for identification and tracking of emerging SARS-CoV-2 variants to guide the Public Health response to the COVID-19 pandemic. Amplicon-based assays, such as the Illumina(R) COVIDSeq Test (RUO) and COVIDSeq Assay (RUO), enable scalable sequencing of SARS-CoV-2, leveraging V3 and V4 primer designs from the ARTIC community and DRAGEN COVID Lineage App analysis available on Illumina BaseSpace. We report here a comparison of COVIDSeq performance for SARS-CoV-2 genome reporting using the ARTIC V3 based primer pool (including primers for human control genes) that is provided with the COVIDSeq kit versus the ARTIC V4 based Illumina COVIDSeq V4 primer pool, using an optimized protocol and DRAGEN COVID Lineage App analysis. The data indicates that both primer pools enable robust reporting of SARS-CoV-2 variants. The Illumina COVIDSeq V4 primer pool has superior performance for SARS-CoV-2 genome reporting, particularly in samples with low virus load, and is therefore the recommended primer pool for genomic surveillance of SARS-CoV-2 for research use using COVIDSeq.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Cyndi R Clark", - "author_inst": "Aegis Labs, 515 Great Circle Road Nashville, TN 37228" - }, - { - "author_name": "Matthew T Hardison", - "author_inst": "Aegis Labs, 515 Great Circle Road Nashville, TN 37228" - }, - { - "author_name": "Holly N Houdeshell", - "author_inst": "Aegis Labs, 515 Great Circle Road Nashville, TN 37228" - }, - { - "author_name": "Alec C Vest", - "author_inst": "Aegis Labs, 515 Great Circle Road Nashville, TN 37228" - }, - { - "author_name": "Darcy A Whitlock", - "author_inst": "Illumina Inc., 5200 Illumina Way, San Diego, CA 92122" - }, - { - "author_name": "Dylan D Skola", - "author_inst": "Illumina Inc., 5200 Illumina Way, San Diego, CA 92122" - }, - { - "author_name": "Jeffrey S Koble", - "author_inst": "Illumina Inc., 5200 Illumina Way, San Diego, CA 92122" - }, - { - "author_name": "Michael Oberholzer", - "author_inst": "Illumina Inc., 5200 Illumina Way, San Diego, CA 92122" - }, - { - "author_name": "Gary P Schroth", - "author_inst": "Illumina Inc., 5200 Illumina Way, San Diego, CA 92122" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2022.01.04.474799", "rel_title": "Putative host-derived insertions in the genome of circulating SARS-CoV-2 variants", @@ -441565,6 +442353,117 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.07.475248", + "rel_title": "Fusogenicity and neutralization sensitivity of the SARS-CoV-2 Delta sublineage AY.4.2", + "rel_date": "2022-01-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.07.475248", + "rel_abs": "SARS-CoV-2 lineages are continuously evolving. As of December 2021, the AY.4.2 Delta sub-lineage represented 20 % of sequenced strains in UK and has been detected in dozens of countries. It has since then been supplanted by the Omicron variant. AY.4.2 displays three additional mutations (T95I, Y145H and A222V) in the N-terminal domain (NTD) of the spike when compared to the original Delta variant (B.1.617.2) and remains poorly characterized. Here, we analyzed the fusogenicity of the AY.4.2 spike and the sensitivity of an authentic AY.4.2 isolate to neutralizing antibodies. The AY.4.2 spike exhibited similar fusogenicity and binding to ACE2 than Delta. The sensitivity of infectious AY.4.2 to a panel of monoclonal neutralizing antibodies was similar to Delta, except for the anti-RBD Imdevimab, which showed incomplete neutralization. Sensitivity of AY.4.2 to sera from individuals having received two or three doses of Pfizer or two doses of AstraZeneca vaccines was reduced by 1.7 to 2.1 fold, when compared to Delta. Our results suggest that mutations in the NTD remotely impair the efficacy of anti-RBD antibodies. The temporary spread of AY.4.2 was not associated with major changes in spike function but rather to a partially reduced neutralization sensitivity.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Nell Saunders", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Delphine Planas", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "William Henry Bolland", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Christophe Rodriguez", + "author_inst": "AP-HP" + }, + { + "author_name": "Slim Fourati", + "author_inst": "AP-HP" + }, + { + "author_name": "Julian Buchrieser", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Cyril Planchais", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Matthieu Prot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Isabelle Staropoli", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Florence Guivel-Benhassine", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Francoise Porrot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "David Veyer", + "author_inst": "AP-HP" + }, + { + "author_name": "Helene Pere", + "author_inst": "AP-HP" + }, + { + "author_name": "Nicolas Robillard", + "author_inst": "AP-HP" + }, + { + "author_name": "Madelina Saliba", + "author_inst": "AP-HP" + }, + { + "author_name": "Artem Baidaliuk", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Aymeric Seve", + "author_inst": "CHR Orleans" + }, + { + "author_name": "Laurent Hocqueloux", + "author_inst": "CHR Orleans" + }, + { + "author_name": "Thierry Prazuck", + "author_inst": "CHR Orleans" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Etienne Simon-Loriere", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Timothee Bruel", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Jean-Michel Pawlotsky", + "author_inst": "AP-HP" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.10.475620", "rel_title": "Strong SARS-CoV-2 N-specific CD8+ T immunity induced by engineered extracellular vesicles associates with protection from lethal infection in mice.", @@ -443304,57 +444203,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.07.22268889", - "rel_title": "COVID-19 vaccine effectiveness among healthcare workers in Portugal: results from a hospital-based cohort study, December 2020 to November 2021", - "rel_date": "2022-01-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.07.22268889", - "rel_abs": "IntroductionHealthcare workers (HCW) were amongst the first prioritized for COVID-19 vaccination but data on COVID-19 vaccine effectiveness among HCW is still limited. This study aims to estimate the COVID-19 vaccine effectiveness (VE) against SARS-CoV-2 symptomatic infection among HCW from Portuguese hospitals.\n\nMethodsIn this prospective cohort study, we analysed data from HCW (all professional categories) from two central hospitals in the Lisbon and Tagus Valley and Centre regions of mainland Portugal between December 2020 and November 2021. VE against symptomatic SARS-CoV-2 infection was estimated as one minus the confounder adjusted hazard ratios by Cox models considering age group, sex, presence of chronic disease and occupational exposure to patients diagnosed with COVID-19 as adjustment variables.\n\nResultsDuring the 11 months of follow up, the 2213 HCW contributed a total of 1950 person-years at risk and 171 SARS-CoV-2 events occurred. The COVID-19 incidence rate for unvaccinated HCW was 348.7 per 1000 person-years while for fully vaccinated HCW was 43.0 per 1000 person-years. We observed a VE against symptomatic SARS-CoV-2 infection of 73.9% (95% CI: 26.2-90.8%) for complete vaccination status.\n\nConclusionThis cohort study found a high COVID-19 VE against symptomatic SARS-CoV-2 infection in Portuguese HCW, which is in concordance with previous studies from other countries. Monitoring of VE in this HCW cohort continues during the winter 2021/2022 to evaluate potential VE decay and booster vaccine effect.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "V\u00e2nia Gaio", - "author_inst": "Department of Epidemiology, Instituto Nacional de Saude Doutor Ricardo Jorge IP (INSA, IP), Lisboa, Portugal" - }, - { - "author_name": "Adriana Silva", - "author_inst": "Department of Epidemiology, Instituto Nacional de Saude Doutor Ricardo Jorge IP (INSA, IP), Lisboa, Portugal" - }, - { - "author_name": "Palmira Amaral", - "author_inst": "Centro Hospitalar Tondela-Viseu, Viseu, Portugal" - }, - { - "author_name": "Jo\u00e3o Faro Viana", - "author_inst": "Centro Hospitalar Lisboa Ocidental, Lisboa, Portugal" - }, - { - "author_name": "Pedro Pinto Leite", - "author_inst": "Directorate of Information and Analysis, Direcao-Geral da Saude, Lisboa, Portugal" - }, - { - "author_name": "Carlos Matias Dias", - "author_inst": "Department of Epidemiology, Instituto Nacional de Saude Doutor Ricardo Jorge IP (INSA, IP), Lisboa, Portugal" - }, - { - "author_name": "Irina Kislaya", - "author_inst": "Department of Epidemiology, Instituto Nacional de Saude Doutor Ricardo Jorge IP (INSA, IP), Lisboa, Portugal;" - }, - { - "author_name": "Baltazar Nunes", - "author_inst": "Department of Epidemiology, Instituto Nacional de Saude Doutor Ricardo Jorge IP (INSA, IP), Lisboa, Portugal;" - }, - { - "author_name": "Ausenda Machado", - "author_inst": "Department of Epidemiology, Instituto Nacional de Saude Doutor Ricardo Jorge IP (INSA, IP), Lisboa, Portugal;" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.07.21268513", "rel_title": "Epidemiological waves - types, drivers and modulators in the COVID-19 pandemic", @@ -443559,6 +444407,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2022.01.06.475246", + "rel_title": "Climate Surveys of Biomedical PhD Students and Training Faculty Members in the Time of Covid", + "rel_date": "2022-01-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.06.475246", + "rel_abs": "In July 2020, four months into the disruption of normal life caused by the Covid-19 pandemic, we assessed the institutional climate within the School of Medicine. Voluntary surveys were completed by 135 graduate students in 11 PhD-granting programs and by 83 members of the graduate training faculty. Several themes emerged. PhD students work hard, but the number of hours spent on research-related activities has declined during the pandemic. The students are worried about the pandemics impact on their research productivity, consequent delays in their graduation, and diminished future job prospects. Many late stage PhD students feel they do not have adequate time or resources to plan for their future careers. Symptoms of anxiety and/or depression are prevalent in 51% of the students, based on answers to standardized questions. Most students report they have strong mentoring relationships with their faculty advisors and like their programs, but they identify to a lesser extent with the medical school as a whole. Faculty think highly of their graduate students and are also worried about the pandemics impact upon productivity and the welfare of students. Students are interested in access to an Ombuds office, which is currently being organized by the medical school. Moving forward, the school needs to address issues of bias, faculty diversity, support for mentor training, professional development, and the imposter syndrome. We must also work to create a climate in which many more graduate students feel that they are valued members of the academic medicine community.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Deepti Ramadoss", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Meghan Campbell McCord", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Johm P Horn", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2022.01.05.21268323", "rel_title": "Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey", @@ -445153,41 +446028,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.01.03.22268669", - "rel_title": "Full title: COVID-19 disease progression according to initial symptoms. A telemedicine cohort study.", - "rel_date": "2022-01-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.03.22268669", - "rel_abs": "ObjectiveCOVID-19 progression to severe or critical illness may be related to initial clinical presentation. Main objective was to identify initial symptoms related to highest risk of disease progression, in mild or moderate suspected or confirmed COVID-19 patients or in asymptomatic subjects in contact with a recently diagnosed patient.\n\nDesign and methodsHistoric cohort study of Mexican patients with suspected or confirmed mild or moderate COVID-19 or asymptomatic subjects in recent contact with positive patients. They sought medical attention in \"Centro Medico ABC\" or claimed for remote attention, and daily telemedicine follow up until recovery or illness progression, from April 17th to October 08th 2020. Data excerpted for analysis were sex, age, body mass index, comorbidities, and signs, and symptoms presented in first day of disease manifestations and during follow up. We used logistic regression to identify initial symptoms associated with progression disease and through a conjunctive consolidation analysis a symptom index was created.\n\nResults120 of 1635 patients (7.2%) had clinical progression disease. By logistic regression we found as initial symptoms related to progression: fever OR 3 (1.89-4.77, p<0.001), cough OR 2.34 (1.56-3.52, p<0.001), myalgias or arthralgias OR 1.69 (1.09-2.63, p=0.018), and fatigue OR 1.65 (1.08-2.53, p=0.019). Conjunctive consolidation was processed with the previous symptoms, and a 3 groups score resulted C-19PAIS Index: 1) Fever with cough or fever with fatigue, with a probability of progression disease of 29% (31/106 patients), 2) Fever or cough or fatigue or cough with fatigue, 10.7% (66/615 patients) and 3) No fever, no cough, no fatigue, 2% (23/914).\n\nConclusionsInitial symptoms predict clinical progression in COVID-19 patients.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Karla Murillo-Villanueva", - "author_inst": "Department of Medical Education and Research, ABC Medical Center, Mexico City, CDMX, Mexico.Centro de Investigacion en Ciencias de la Salud Anahuac (CICSA), Fac" - }, - { - "author_name": "Blanca Velazquez-Hernandez", - "author_inst": "Department of Inclusive health and education, ABC Medical Center, Mexico City, CDMX, Mexico" - }, - { - "author_name": "Jose A Jacome-Mondragon", - "author_inst": "Department of Inclusive health and education, ABC Medical Center, Mexico City, CDMX, Mexico" - }, - { - "author_name": "Judit J Cervantes-Llamas", - "author_inst": "Department of Inclusive health and education, ABC Medical Center, Mexico City, CDMX, Mexico" - }, - { - "author_name": "Juan O Talavera", - "author_inst": "Department of Medical Education and Research, ABC Medical Center, Mexico City, CDMX, Mexico" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2022.01.03.22268676", "rel_title": "The French domestic \"sanitary pass\" did not solve Covid-19 vaccination inequities in France", @@ -445376,6 +446216,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.03.22268704", + "rel_title": "Immune responses to inactivated and vector-based vaccines in individuals previously infected with SARS-CoV-2", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.03.22268704", + "rel_abs": "Immunity wanes in individuals previously infected with SARS-CoV-2, and vaccinating those individuals may help reduce reinfection. Herein, reactogenicity and immunogenicity following vaccination with inactivated (CoronaVac) and vector-based (ChAdOx1-S, AZD1222) vaccines were examined in previously infected individuals. Immune response was also compared between short and long intervals between first date of detection and vaccination. Adverse events were mild but were higher with AZD1222 than with CoronaVac. Baseline IgG-specific antibodies and neutralizing activity were significantly higher with shorter than longer intervals. With a single-dose vaccine, IgG and IgA-specific binding antibodies, neutralizing activity, and total interferon-gamma response peaked at 14 days. Immune response was significantly higher in recovered individuals than in infection-naive individuals. Antibody response was greater with longer than shorter intervals. AZD1222 induced higher antibody and T cell responses than those of CoronaVac. Thus, to achieve immunity, individuals with prior SARS-CoV-2 exposure may require only a single dose of AZD1222 or two doses of CoronaVac to achieve the immune response. These findings supported vaccine strategies in previously infected individuals.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Nungruthai Suntronwong", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Ritthideach Yorsaeng", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Chompoonut Auphimai", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Thanunrat Thongmee", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Preeyaporn Vichaiwattana", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Sitthichai Kanokudom", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Suvichada Assawakosri", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Pornjarim Nilyanimit", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Donchida Srimuan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Thaksaporn Thatsanatorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Natthinee Sudhinaraset", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Nasamon Wanlapakorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Yong Poovorawan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.01.03.22268681", "rel_title": "Reported Cases of Multisystem Inflammatory Syndrome in Children Aged 12 to 20 Years in the United States Who Received COVID-19 Vaccine, December 2020 through August 2021", @@ -446911,45 +447818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.01.05.22268779", - "rel_title": "Heart Block in patients with COVID-19", - "rel_date": "2022-01-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268779", - "rel_abs": "BackgroundSince the emergence of the SARS COV-19 pandemic, multiple extrapulmonary manifestations of the virus have been reported from around the world. Cardiovascular complications including arrhythmias in patients with COVID-19 have been described in multiple studies. Our aim was to review various case reports detailing the new onset of heart block in COVID-19 patients and to summarise the clinical course of these patients.\n\nMethodsWe systematically reviewed all reports published and indexed in PubMed, Scopus, and Embase between March 2020 to May 2021, analyzing the relation between the demographics of the patients, pre-existing comorbidities, and the progression of heart block in patients infected with COVID-19.\n\nResultsWe identified and included in this study 30 relevant articles describing 49 COVID-19 patients with heart block. Among them, 69.3% (n=34) of patients suffered from at least one comorbidity. 36.73% (n=18) of the patients showed spontaneous resolution of the heart block. Conversely, 63.26% (n=31) of the patients had persistent heart block, out of which 16.33% (n=8) and 42.86% (n=21) were implanted with a temporary and permanent pacemaker respectively. The reported mortality rate was 22.45% (n=11) during hospitalization. We noted that 45.45% (n=5) of the patients who died had complete heart block. 24.49% (n=12) of the patients in the studies we reviewed were suspected of having myocarditis. However, none were confirmed with MRI or cardiac biopsy.\n\nConclusionsAdditional research is necessary to unearth the mechanism of development of heart block in COVID-19 patients as well as its implications on the clinical course and prognosis. Physicians must be aware of the importance of monitoring patients hospitalized for COVID-19 for arrhythmias including heart blocks, especially in the presence of comorbidities. Early detection can improve the prognosis of the patient.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Md Ripon Ahammed", - "author_inst": "Larkin Community Hospital" - }, - { - "author_name": "Medha Sharath", - "author_inst": "Larkin Community Hospital" - }, - { - "author_name": "Mehul Sinha", - "author_inst": "Larkin Community Hospital" - }, - { - "author_name": "Cristina Sestacovschi", - "author_inst": "Larkin Community Hospital" - }, - { - "author_name": "Varadha Retnakumar", - "author_inst": "Larkin Community Hospital" - }, - { - "author_name": "Naisargee Solanki", - "author_inst": "Larkin Community Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2022.01.04.22268776", "rel_title": "Waning Effectiveness of the BNT162b2 Vaccine Against Infection in Adolescents", @@ -447134,6 +448002,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.05.22268637", + "rel_title": "Personal Resilience, Social Support, and Organizational Support Impact Burnout among Nurses During COVID-19", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268637", + "rel_abs": "BackgroundNurses have been under heavy workloads since the outbreak of COVID-19 and are at a high risk of infection, leading to a high level of psychosocial risk. This can adversely affect nurses both psychologically and physically. Burnout is caused by prolonged stress during work. In the nursing profession, burnout is common, potentially affecting the well-being of nurses and their productivity. The identification of factors that may contribute to maintaining mental health and reducing burnout among frontline nurses during a pandemic is essential.\n\nPurposeThe purpose of this study was to explore how personal resilience, social support, and organizational support impact burnout among frontline staff nurses.\n\nMethodsThis study involved 129 registered nurses from a COVID-19 designated hospital using four standardized scales.\n\nResultsThe mean age of the respondents was 29.46 years (standard deviation = 4.89). The mean number of years respondents worked in this organization was 5.60 years and the nursing profession was 4.16 years. Most of the respondents were female and held a bachelors degree in nursing. Multiple regression analysis was performed to predict burnout. Burnout was statistically significantly predicted by the multiple regression model (R2 = .420, F (3, 125) = 10.941, p < .0001; adjusted R2 = .406). Personal resilience, social support, and organizational support added statistically significantly to the prediction of burnout (p < .05).\n\nConclusionFindings from multiple regression analysis showed that nurses with low resilience and those who perceived inadequate social and organizational support had a higher risk of reporting more burnout. As a result of a bivariate analysis, there was no significant correlation between nurse variables and burnout level, except for age, which was negatively correlated with burnout level. Accordingly, young nurses tend to experience burnout, and nurse directors and managers must address this problem.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hanan Daghash", + "author_inst": "Al-Ghad International Colleges for Health Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2022.01.05.22268646", "rel_title": "SARS-CoV-2 Genetic diversity and lineage dynamics of in Egypt", @@ -448733,129 +449620,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2022.01.03.21268582", - "rel_title": "Mapping the antigenic diversification of SARS-CoV-2", - "rel_date": "2022-01-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.03.21268582", - "rel_abs": "Large-scale vaccination campaigns have prevented countless hospitalizations and deaths due to COVID-19. However, the emergence of SARS-CoV-2 variants that escape from immunity challenges the effectiveness of current vaccines. Given this continuing evolution, an important question is when and how to update SARS-CoV-2 vaccines to antigenically match circulating variants, similar to seasonal influenza viruses where antigenic drift necessitates periodic vaccine updates. Here, we studied SARS-CoV-2 antigenic drift by assessing neutralizing activity against variants-of-concern (VOCs) of a unique set of sera from patients infected with a range of VOCs. Infections with D614G or Alpha strains induced the broadest immunity, while individuals infected with other VOCs had more strain-specific responses. Omicron BA.1 and BA.2 were substantially resistant to neutralization by sera elicited by all other variants. Antigenic cartography revealed that Omicron BA.1 and BA.2 are antigenically most distinct from D614G, associated with immune escape and likely requiring vaccine updates to ensure vaccine effectiveness.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Karlijn van der Straten", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Denise Guerra", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Marit van Gils", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Ilja Bontjer", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Tom G Caniels", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Hugo D van Willigen", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Elke Wynberg", - "author_inst": "Public Health Service of Amsterdam" - }, - { - "author_name": "Meliawati Poniman", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Judith A Burger", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Joey H Bouhuijs", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Jacqueline van Rijswijk", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Wouter Olijhoek", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Marinus H Liesdek", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "A H Ayesha Lavell", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Brent Appelman", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Jonne J Sikkens", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Marije K Bomers", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Alvin X Han", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Brooke E Nichols", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Maria Prins", - "author_inst": "Public Health Service of Amsterdam" - }, - { - "author_name": "Harry Vennema", - "author_inst": "National Institute for Public Health and The Environment (RIVM)" - }, - { - "author_name": "Chantal Reusken", - "author_inst": "RIVM" - }, - { - "author_name": "Menno de Jong", - "author_inst": "Amsterdam UMC, University of Amsterdam" - }, - { - "author_name": "Godelieve J de Bree", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Colin A Russell", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Dirk Eggink", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Rogier Willem Sanders", - "author_inst": "Amsterdam UMC & Weill Medical College of Cornell University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.03.21268111", "rel_title": "The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism", @@ -449256,6 +450020,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.02.22268629", + "rel_title": "Cognitive predictors of vaccine hesitancy and COVID-19 mitigation behaviors in a population representative sample", + "rel_date": "2022-01-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.02.22268629", + "rel_abs": "With the continued threat of COVID-19, predictors of vaccination hesitancy and mitigation behaviors are critical to identify. Prior studies have found that cognitive factors are associated with some COVID-19 mitigation behaviors, but few studies employ representative samples and to our knowledge no prior studies have examined cognitive predictors of vaccine hesitancy. The purpose of the present study, conducted among a large national sample of Canadian adults, was to examine associations between cognitive variables (executive function, delay discounting, and temporal orientation) and COVID-19 mitigation behaviors (vaccination, mask wearing, social distancing, and hand hygiene). Findings revealed that individuals with few executive function deficits, limited delay discounting and who adopted a generally future-orientation mindset were more likely to be double-vaccinated and to report performing COVID-19 mitigation behaviors with high consistency. The most reliable findings were for delay discounting and future orientation, with executive function deficits predicting mask wearing and hand hygiene behaviors but not distancing and vaccination. These findings identify candidate mediators and moderators for health communication messages targeting COVID-19 mitigation behaviors and vaccine hesitancy.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anna Hudson", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Peter A Hall", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Sara Hitchman", + "author_inst": "University of Zurich" + }, + { + "author_name": "Gang Meng", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Geoffrey T Fong", + "author_inst": "University of Waterloo" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.30.21268571", "rel_title": "Estimation the state of the Covid-19 epidemic curve in Mayotte", @@ -450847,53 +451646,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.12.30.21266217", - "rel_title": "Increased Risk of Poor Clinical Outcome in COVID-19 Patients with Diabetes Mellitus and in-hospital Mortality Predictors: A Retrospective Cohort from a Tertiary Hospital in Indonesia", - "rel_date": "2022-01-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21266217", - "rel_abs": "AimTo determine association between diabetes in confirmed cases of COVID-19 and intensive care admission and in-hospital mortality, evaluate several laboratory parameters as mortality predictor, and develop predictors of in-hospital mortality among diabetics with COVID-19.\n\nMethodsThis retrospective cohort recruited all cases of COVID-19 hospitalized in Fatmawati General Hospital during March to October 2020. Inclusion criteria was RT-PCR confirmed cases of COVID-19 who aged 18 years and older while exclusion criteria were incomplete medical record or cannot be found and pregnant women.\n\nResultsWe enrolled 506 participants to this study with median age of 51 years (IQR:22), female (56.32%), and diabetes (28.46%). Diabetes increased intensive care admission (adjusted OR:6.07;95%CI:3.52-10,43) and in-hospital mortality (adjusted OR:50;95%CI:1.61-3.89). In predicting in-hospital mortality, ferritin and lactate dehydrogenase offered an acceptable discrimination, AUC:0.71 (95%CI: 0.62-0.79) and AUC:0.70 (95%CI: 0.61-0.78), respectively. The optimal cut-off of predicting mortality for ferritin was 786 g/mL and for LDH was 514.94 u/L. Factors include age above 70 years old, RBGs level on admission above 250 mg/dL or below 140 mg/dL, ferritin level above 786 ng/mL, and presence of ARDS increased the odds of mortality among individuals with diabetes.\n\nConclusionsDiabetes increases risk of intensive care admission and in hospital mortality in COVID-19. Multivariate analysis showed that older age, RBG on admission, high ferritin level, presence of ARDS increased the odds of mortality among individuals with diabetes.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Md Ikhsan Mokoagow", - "author_inst": "Division of Endocrinology, Metabolism, and Diabetes, Department of Internal Medicine, Fatmawati General Hospital" - }, - { - "author_name": "Dante Saksono Harbuwono", - "author_inst": "Division of Endocrinology and Metabolism, Department of Internal Medicine, Dr. Cipto Mangunkusumo National Referral Hospital, Faculty of Medicine Universitas In" - }, - { - "author_name": "Ida Ayu Kshanti", - "author_inst": "Division of Endocrinology, Metabolism, and Diabetes, Department of Internal Medicine, Fatmawati General Hospital" - }, - { - "author_name": "Cleopas Martin Rumende", - "author_inst": "Clinical Epidemiology Unit, Department of Internal Medicine, Dr. Cipto Mangunkusumo National Referral Hospital, Faculty of Medicine Universitas Indonesia" - }, - { - "author_name": "Imam Subekti", - "author_inst": "Division of Endocrinology and Metabolism, Department of Internal Medicine, Dr. Cipto Mangunkusumo National Referral Hospital, Faculty of Medicine Universitas In" - }, - { - "author_name": "Kuntjoro Harimurti", - "author_inst": "Clinical Epidemiology Unit, Department of Internal Medicine, Dr. Cipto Mangunkusumo National Referral Hospital, Faculty of Medicine Universitas Indonesia" - }, - { - "author_name": "Khie Chen Lie", - "author_inst": "Departement of Internal Medicine, Faculty of Medicine, Universitas Indonesia" - }, - { - "author_name": "Hamzah Shatri", - "author_inst": "Departement of Internal Medicine, Faculty of Medicine, Universitas Indonesia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2021.12.31.21268591", "rel_title": "Inferring effects of mutations on SARS-CoV-2 transmission from genomic surveillance data", @@ -451134,6 +451886,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2021.12.29.21268529", + "rel_title": "Humoral immune responses against SARS-CoV-2 variants including omicron in solid organ transplant recipients after three doses of a COVID-19 mRNA vaccine", + "rel_date": "2022-01-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.29.21268529", + "rel_abs": "BackgroundSolid organ transplant recipients (SOTR), who typically receive post-transplant immunosuppression, show increased COVID-19-related mortality. It is unclear whether an additional dose of COVID-19 vaccines in SOTR can overcome the reduced immune responsiveness against Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants.\n\nMethodsWe performed a prospective cohort study of 53 SOTR receiving SARS-CoV-2 vaccination into a prospective cohort study performing detailed immunoprofiling of humoral immune responses against SARS-CoV-2 and its variants.\n\nResultsPrior to the additional vaccine dose, 60.3% of SOTR showed no measurable neutralization and only 18.9% demonstrated neutralizing activity of >90% following two vaccine doses. More intensive immunosuppression, antimetabolites in particular, negatively impacted antiviral immunity. While absolute IgG levels were lower in SOTR than controls, antibody titers against microbial recall antigens were in fact higher. In contrast, SOTR showed reduced vaccine-induced IgG/IgA antibody titers against SARS-CoV-2 and its delta variants. Vaccinated SOTR showed a markedly fewer linear B cell epitopes, indicating reduced B cell diversity. Importantly, a third vaccine dose led to an increase in anti-SARS-CoV-2 antibody titers and neutralizing activity across alpha, beta and delta variants. However, we observed a significant decrease in anti-spike antibody titers with the omicron variant.\n\nConclusionsOnly a small subgroup of SOTR generated functionally relevant antibodies after completing the initial vaccine series based on dysfunctional priming of immune responses against novel antigens. An additional dose of the vaccine results in dramatically improved antibody responses against all SARS-CoV-2 variants except omicron.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Kapil K. Saharia", + "author_inst": "Institute of Human Virology, University of Maryland School of Medicine" + }, + { + "author_name": "Jennifer S. Husson", + "author_inst": "Institute of Human Virology, University of Maryland School of Medicine" + }, + { + "author_name": "Silke V. Niederhaus", + "author_inst": "Department of Surgery, University of Maryland School of Medicine" + }, + { + "author_name": "Thierry Iraguha", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Stephanie V. Avila", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Youngchae J. Yoo", + "author_inst": "Institute of Human Virology, University of Maryland School of Medicine" + }, + { + "author_name": "Nancy M. Hardy", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Xiaoxuan Fan", + "author_inst": "University of Maryland Greenebaum Comprehensive Cancer Center" + }, + { + "author_name": "Destiny Omili", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Alice Crane", + "author_inst": "Department of Surgery, University of Maryland School of Medicine" + }, + { + "author_name": "Amber Carrier", + "author_inst": "Department of Surgery, University of Maryland School of Medicine" + }, + { + "author_name": "Wen Y. Xie", + "author_inst": "Department of Surgery, University of Florida College of Medicine" + }, + { + "author_name": "Erica Vander Mause", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Kim Hankey", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Sheri Bauman", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Patricia Lesho", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Heather D. Mannuel", + "author_inst": "University of Maryland Greenebaum Comprehensive Cancer Center" + }, + { + "author_name": "Ashish Ahuja", + "author_inst": "Department of Medicine, University of Maryland Medical Center" + }, + { + "author_name": "Minu Mathew", + "author_inst": "Divison of Infectious Diseases, University of Maryland School of Medicine" + }, + { + "author_name": "James Avruch", + "author_inst": "Department of Surgery, University of Maryland School of Medicine" + }, + { + "author_name": "John Baddley", + "author_inst": "Institute of Human Virology, University of Maryland School of Medicine" + }, + { + "author_name": "Olga Goloubeva", + "author_inst": "Department of Epidemiology and Public Health, University of Maryland Greenebaum Comprehensive Cancer Center" + }, + { + "author_name": "Kirti Shetty", + "author_inst": "Division of Hepatology/Liver Transplantation, University of Maryland School of Medicine," + }, + { + "author_name": "Saurabh Dahiya", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Aaron P. Rapoport", + "author_inst": "Transplant and Cellular Therapy Program, Department of Medicine, University of Maryland" + }, + { + "author_name": "Tim Luetkens", + "author_inst": "Department of Microbiology and Immunology, University of Maryland" + }, + { + "author_name": "Djordje Atanackovic", + "author_inst": "University of Maryland Greenebaum Comprehensive Cancer Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2021.12.30.21268565", "rel_title": "Effectiveness of COVID-19 vaccines against Omicron or Delta infection", @@ -452881,105 +453756,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.29.21268469", - "rel_title": "Long-lasting cellular immunity to SARS-CoV-2 following infection or vaccination and implications for booster strategies", - "rel_date": "2021-12-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.29.21268469", - "rel_abs": "Immunization against SARS-CoV-2, the causative agent of coronavirus disease-19 (COVID-19) occurs via natural infection or vaccination. However, it is currently unknown how long infection- or vaccination-induced immunological memory will last. We performed a longitudinal evaluation of immunological memory to SARS-CoV-2 following mRNA vaccination in naive and COVID-19 recovered individuals. We found that cellular immunity is still detectable 8 months after vaccination, while antibody levels decline significantly especially in naive subjects. We also found that a booster injection is more efficacious in reactivating immunological memory to spike protein in naive than in previously SARS-CoV-2 infected subjects. Finally, we observed a similar kinetics of decay of humoral and cellular immunity to SARS-CoV-2 up to one year following natural infection in a cohort of unvaccinated individuals. Short-term persistence of humoral immunity may account for reinfections and breakthrough infections, although long-lived memory B and CD4+ T cells may protect from severe disease. A booster dose restores optimal anti-spike immunity in naive subjects, while the need for vaccinated COVID-19 recovered subjects has yet to be defined.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Alessio Mazzoni", - "author_inst": "University of Florence" - }, - { - "author_name": "Anna Vanni", - "author_inst": "University of Florence" - }, - { - "author_name": "Michele Spinicci", - "author_inst": "University of Florence" - }, - { - "author_name": "Giulia Lamacchia", - "author_inst": "University of Florence" - }, - { - "author_name": "Seble Tekle Kiros", - "author_inst": "University of Florence" - }, - { - "author_name": "Arianna Rocca", - "author_inst": "University of Florence" - }, - { - "author_name": "Manuela Capone", - "author_inst": "University of Florence" - }, - { - "author_name": "Nicoletta Di Lauria", - "author_inst": "Azienda Ospedaliero Universitaria Careggi" - }, - { - "author_name": "Lorenzo Salvati", - "author_inst": "University of Florence" - }, - { - "author_name": "Alberto Carnasciali", - "author_inst": "University of Florence" - }, - { - "author_name": "Elisabetta Mantengoli", - "author_inst": "Azienda Ospedaliero Universitaria Careggi" - }, - { - "author_name": "Parham Farahvachi", - "author_inst": "University of Florence" - }, - { - "author_name": "Lorenzo Zammarchi", - "author_inst": "University of Florence" - }, - { - "author_name": "Filippo Lagi", - "author_inst": "Azienda Ospedaliero Universitaria Careggi" - }, - { - "author_name": "Maria Grazia Colao", - "author_inst": "Azienda Ospedaliero Universitaria Careggi" - }, - { - "author_name": "Francesco Liotta", - "author_inst": "University of Florence" - }, - { - "author_name": "Lorenzo Cosmi", - "author_inst": "University of Florence" - }, - { - "author_name": "Laura Maggi", - "author_inst": "University of Florence" - }, - { - "author_name": "Alessandro Bartoloni", - "author_inst": "University of Florence" - }, - { - "author_name": "Gian Maria Rossolini", - "author_inst": "University of Florence" - }, - { - "author_name": "Francesco Annunziato", - "author_inst": "University of Florence" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.28.21268435", "rel_title": "Transition of antibody titers after the SARS-CoV-2 mRNA vaccine in Japanese healthcare workers", @@ -453368,6 +454144,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.24.474110", + "rel_title": "Reduced infectivity but increased immune escape of the new SARS-CoV-2 variant of concern Omicron", + "rel_date": "2021-12-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.24.474110", + "rel_abs": "A new detected SARS-CoV-2 variant Omicron (B.1.1.529) had reported from more than 80 countries. In the past few weeks, a new wave of infection driven by Omicron is in progress. Omicron Spike (S) protein pseudotyped virus was used to determine the effect of S mutations on its capacity of infectivity and immune evasion. Our results showed the lower entry efficiency and less cleavage ability of Omicron than D614G variant. Pseudotype-based neutralizing assay was performed to analyze neutralizing antibodies elicited by previously infection or the RBD-based protein subunit vaccine ZF2001 against the Omicron variant. Sera sampled at around one month after symptom onset from 12 convalescents who were previously infected by SARS-CoV-2 original strain shows a more than 20-fold decrease of neutralizing activity against Omicron variant, when compared to D614G variant. Among 12 individuals vaccinated by RBD subunit vaccine, 58.3% (7/12) sera sampled at 15-60 days after 3rd-dose vaccination did not neutralize Omicron. Geometric mean titers (GMTs, 50% inhibitory dose [ID50]) of these sera against Omicron were 9.4-fold lower than against D614G. These results suggested a higher risk of Omicron breakthrough infections and reduced efficiency of the protective immunity elicited by existing vaccines. There are important implications about the modification and optimization of the current epidemic prevention and control including vaccine strategies and therapeutic antibodies against Omicron variant.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jie Hu", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Pai Peng", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Kang Wu", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Quan-xin Long", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Juan Chen", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Kai Wang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Ni Tang", + "author_inst": "Chongqing Medical University" + }, + { + "author_name": "Ailong Huang", + "author_inst": "Chongqing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.30.21268537", "rel_title": "The rich-to-poor vaccine donation game: When will self-interested countries donate their surplus vaccines during pandemics?", @@ -454963,69 +455786,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.29.474427", - "rel_title": "Dynamic Expedition of Leading Mutations in SARS-CoV-2 Spike Glycoproteins", - "rel_date": "2021-12-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.29.474427", - "rel_abs": "Throughout the coronavirus disease 2019 (COVID-19) pandemic, the continuous genomic evolution of its etiological agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has generated many new variants with enhanced transmissibility and immune escape capabilities. Being an essential mediator of infections and a key target of antibodies, mutations of its spike glycoprotein play a vital role in modulating its evolutionary trajectory. Here, we present a time-resolved statistical method, Dynamic Expedition of Leading Mutations (deLemus), to analyze the evolutionary dynamics of the SARS-CoV-2 spike. Together with analysis of its single amino acid polymorphism (SAP), we propose the use of L-index in quantifying the mutation strength of each amino acid site, such that the evolutionary mutation pattern of the spike glycoprotein can be unravelled.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Muhammad Hasan", - "author_inst": "Hongkong University of Science and Technology" - }, - { - "author_name": "Zhouyi He", - "author_inst": "Hongkong University of Science and Technology" - }, - { - "author_name": "Mengqi Jia", - "author_inst": "Hongkong University of Science and Technology" - }, - { - "author_name": "Alvin C.F. Leung", - "author_inst": "Hongkong University of Science and Technology" - }, - { - "author_name": "Kathiresan Natarajan", - "author_inst": "Rajiv Gandhi Centre for Biotechnology" - }, - { - "author_name": "Wentao Xu", - "author_inst": "Hongkong University of Science and Technology" - }, - { - "author_name": "Shan Qi Yap", - "author_inst": "Hongkong University of Science and Technology" - }, - { - "author_name": "Feng Zhou", - "author_inst": "Hongkong University of Science and Technology" - }, - { - "author_name": "Shihong Chen", - "author_inst": "Hongkong University of Science and Technology" - }, - { - "author_name": "Hailei Su", - "author_inst": "Bengbu Hospital of Traditional Chinese Medicine" - }, - { - "author_name": "Kaicheng Zhu", - "author_inst": "Hongkong University of Science and Technology" - }, - { - "author_name": "Haibin Su", - "author_inst": "The Hong Kong University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2021.12.28.21268436", "rel_title": "Vaccine effectiveness against hospital admission in South African health care workers who received a homologous booster of Ad26.COV2 during an Omicron COVID19 wave: Preliminary Results of the Sisonke 2 Study.", @@ -455362,6 +456122,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2021.12.27.21268459", + "rel_title": "Immunogenicity of heterologous BNT162b2 booster in fully vaccinated individuals with CoronaVac against SARS-CoV-2 variants Delta and Omicron: the Dominican Republic Experience", + "rel_date": "2021-12-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268459", + "rel_abs": "The recent emergence of the SARS-CoV-2 Omicron variant is raising concerns because of its increased transmissibility and by its numerous spike mutations with potential to evade neutralizing antibodies elicited by COVID-19 vaccines. The Dominican Republic was among the first countries in recommending the administration of a third dose COVID-19 vaccine to address potential waning immunity and reduced effectiveness against variants. Here, we evaluated the effects of a heterologous BNT162b2 mRNA vaccine booster on the humoral immunity of participants that had received a two-dose regimen of CoronaVac, an inactivated vaccine used globally. We found that heterologous CoronaVac prime followed by BNT162b2 booster regimen induces elevated virus-specific antibody levels and potent neutralization activity against the ancestral virus and Delta variant, resembling the titers obtained after two doses of mRNA vaccines. While neutralization of Omicron was undetectable in participants that had received a two-dose regimen of CoronaVac vaccine, BNT162b2 booster resulted in a 1.4-fold increase in neutralization activity against Omicron, compared to two-dose mRNA vaccine. Despite this increase, neutralizing antibody titers were reduced by 6.3-fold and 2.7-fold for Omicron compared to ancestral and Delta variant, respectively. Surprisingly, previous SARS-CoV-2 infection did not affect the neutralizing titers for Omicron in participants that received the heterologous regimen. Our findings have immediate implications for multiples countries that previously used a two-dose regimen of CoronaVac and reinforce the notion that the Omicron variant is associated with immune escape from vaccines or infection-induced immunity, highlighting the global need for vaccine boosters to combat the impact of emerging variants.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Eddy Perez-Then", + "author_inst": "Ministry of Health, Santo Domingo, Dominican Republic." + }, + { + "author_name": "Carolina Lucas", + "author_inst": "Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA." + }, + { + "author_name": "Valter Silva Monteiro", + "author_inst": "Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA." + }, + { + "author_name": "Marija Miric", + "author_inst": "Two Oceans in Health, Santo Domingo, Dominican Republic." + }, + { + "author_name": "Vivian Brache", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Leila Cochon", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Chantal B.F. Vogels", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Elena De la Cruz", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Aidelis Jorge", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Margarita De los Santos", + "author_inst": "Departamento de Investigaciones Biomedicas, Clinica Evangelina Rodriguez, PROFAMILIA. Santo Domingo, Dominican Republic." + }, + { + "author_name": "Patricia Leon", + "author_inst": "Laboratorio de Referencia, Dominican Republic." + }, + { + "author_name": "Mallery I. Breban", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Kendall Billig", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Inci Yildirim", + "author_inst": "Department of Pediatric, Section of Infectious Diseases and Global Health; Yale University School of Medicine, New Haven, CT, USA." + }, + { + "author_name": "Claire Pearson", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Randy Downing", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Emily Gagnon", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Anthony Muyombwe", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Jafar Razeq", + "author_inst": "Connecticut State Department of Public Health, Rocky Hill, USA" + }, + { + "author_name": "Melissa Campbell", + "author_inst": "Department of Pediatric, Section of Infectious Diseases and Global Health; Yale University School of Medicine, New Haven, CT, USA." + }, + { + "author_name": "Albert Ko", + "author_inst": "Yale University School of Public Health" + }, + { + "author_name": "Saad B. Omer", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Nathan D Grubaugh", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Sten H. Vermund", + "author_inst": "Yale School of Public Health, New Haven, CT, USA." + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.27.21268416", "rel_title": "Divergent SARS CoV-2 Omicron-specific T- and B-cell responses in COVID-19 vaccine recipients", @@ -457065,89 +457940,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.28.474333", - "rel_title": "SARS-CoV-2 vaccination induces immunological memory able to cross-recognize variants from Alpha to Omicron", - "rel_date": "2021-12-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.28.474333", - "rel_abs": "We address whether T cell responses induced by different vaccine platforms (mRNA-1273, BNT162b2, Ad26.COV2.S, NVX-CoV2373) cross-recognize SARS-CoV-2 variants. Preservation of at least 83% and 85% for CD4+ and CD8+ T cell responses was found, respectively, regardless of vaccine platform or variants analyzed. By contrast, highly significant decreases were observed for memory B cell and neutralizing antibody recognition of variants. Bioinformatic analyses showed full conservation of 91% and 94% of class II and class I spike epitopes. For Omicron, 72% of class II and 86% of class I epitopes were fully conserved, and 84% and 85% of CD4+ and CD8+ T cell responses were preserved. In-depth epitope repertoire analysis showed a median of 11 and 10 spike epitopes recognized by CD4+ and CD8+ T cells from vaccinees. Functional preservation of the majority of the T cell responses may play an important role as a second-level defense against diverse variants.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Alison Tarke", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Camila H. Coelho", - "author_inst": "La Jolla institute for immunology" - }, - { - "author_name": "Zeli Zhang", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Jennifer M. Dan", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Esther Dawen Yu", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Nils Methot", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Nathaniel I Bloom", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Benjamin Goodwin", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Elizabeth Phillips", - "author_inst": "Institute for Immunology and Infectious Diseases, Murdoch University," - }, - { - "author_name": "Simon Mallal", - "author_inst": "Institute for Immunology and Infectious Diseases, Murdoch University," - }, - { - "author_name": "John Sidney", - "author_inst": "La Jolla Institute For Immunology" - }, - { - "author_name": "Gilberto Filaci", - "author_inst": "Bioterapy Unit, IRCCS Ospedale Policlinico San Martino" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute For Immunology" - }, - { - "author_name": "Ricardo da Silva Antunes", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Shane Crotty", - "author_inst": "La Jolla Institute For Immunology (LJI)" - }, - { - "author_name": "Alba Grifoni", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Immunology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.28.474325", "rel_title": "Deciphering the quality of SARS-CoV-2 specific T-cell response associated with disease severity, immune memory and heterologous response", @@ -457488,6 +458280,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.27.474218", + "rel_title": "Vaccine-breakthrough infection by the SARS-CoV-2 Omicron variant elicits broadly cross-reactive immune responses", + "rel_date": "2021-12-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.27.474218", + "rel_abs": "Highly transmissible SARS-CoV-2 Omicron variant has posted a new crisis for COVID-19 pandemic control. Within a month, Omicron is dominating over Delta variant in several countries probably due to immune evasion. It remains unclear whether vaccine-induced memory responses can be recalled by Omicron infection. Here, we investigated host immune responses in the first vaccine-breakthrough case of Omicron infection in Hong Kong. We found that the breakthrough infection rapidly recruited potent cross-reactive broad neutralizing antibodies (bNAbs) against current VOCs, including Alpha, Beta, Gamma, Delta and Omicron, from unmeasurable IC50 values to mean 1:2929 at around 9-12 days, which were higher than the mean peak IC50 values of BioNTech-vaccinees. Cross-reactive spike- and nucleocapsid-specific CD4 and CD8 T cell responses were detected. Similar results were also obtained in the second vaccine-breakthrough case of Omicron infection. Our preliminary findings may have timely implications to booster vaccine optimization and preventive strategies of pandemic control.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Runhong Zhou", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Kelvin Kai-Wang To", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Qiaoli Peng", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Jacky Man-Chun Chan", + "author_inst": "Princess Margaret Hospital" + }, + { + "author_name": "Haode Huang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Dawei Yang", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Bosco Hoi-Shiu Lam", + "author_inst": "Princess Margaret Hospital" + }, + { + "author_name": "Vivien Wai-Man Chuang", + "author_inst": "Quality & Safety Division, Hospital Authority" + }, + { + "author_name": "Jian-Piao Cai", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Na Liu", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ka-Kit Au", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Owen Tak-Yin Tsang", + "author_inst": "Princess Margaret Hospital" + }, + { + "author_name": "Kwok-Yung Yuen", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Zhiwei Chen", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.26.472655", "rel_title": "Evaluation of maternal-infant dyad inflammatory cytokines in pregnancies affected by maternal SARS-CoV-2 infection in early and late gestation.", @@ -459275,129 +460138,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.25.21268392", - "rel_title": "BNT162b2 boosted immune responses six months after heterologous or homologous ChAdOx1nCoV-19/BNT162b2 vaccination against COVID-19", - "rel_date": "2021-12-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.25.21268392", - "rel_abs": "Reports suggest that COVID-19 vaccine effectiveness is decreasing, either due to waning immune protection, emergence of new variants of concern, or both. Heterologous prime/boost vaccination with a vector-based approach (ChAdOx-1nCov-19, ChAd) followed by an mRNA vaccine (e.g. BNT162b2, BNT) appeared to be superior in inducing protective immunity, and large scale second booster vaccination is ongoing. However, data comparing declining immunity after homologous and heterologous vaccination as well as effects of a third vaccine application after heterologous ChAd/BNT vaccination are lacking. We longitudinally monitored immunity in ChAd/ChAd (n=41) and ChAd/BNT (n=88) vaccinated individuals and assessed the impact of a second booster with BNT in both groups. The second booster greatly augmented waning anti-spike IgG but only moderately increased spike-specific CD4+ and CD8+ T cells in both groups to cell frequencies already present after the boost. More importantly, the second booster efficiently restored neutralizing antibody responses against Alpha, Beta, Gamma, and Delta, but neutralizing activity against B.1.1.529 (Omicron) stayed severely impaired. Our data suggest that inferior SARS-CoV-2 specific immune responses after homologous ChAd/ChAd vaccination can be cured by a heterologous BNT vaccination. However, prior heterologous ChAd/BNT vaccination provides no additional benefit for spike-specific T cell immunity or neutralizing Omicron after the second boost.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Georg MN Behrens", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Joana Barros-Martins", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Anne Cossmann", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Gema Morillas Ramos", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Metodi V Stankov", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Ivan Odak", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Alexandra Dopfer-Jablonka", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Laura Hetzel", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Miriam Koehler", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Gwendolyn Patzer", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Chritoph Binz", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Christiane Ritter", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Michaela Friedrichsen", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Christian R Schultze-Florey", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Ravens Inga", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Stefanie Willenzon", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Anja Bubke", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Jasmin Rispenpart", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Anika Janssen", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "George Ssebyatika", - "author_inst": "Luebeck University" - }, - { - "author_name": "Guenter Bernhardt", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Markus R Hoffmann", - "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" - }, - { - "author_name": "Stefan Poehlmann", - "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" - }, - { - "author_name": "Thomas Krey", - "author_inst": "Luebeck University" - }, - { - "author_name": "Berislav Bosnjak", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Swantje I Hammerschmidt", - "author_inst": "Hannover Medical School" - }, - { - "author_name": "Reinhold Foerster", - "author_inst": "Hannover Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.25.21268336", "rel_title": "Durability of Response to a Third BNT162b2 Vaccine in Adults >=60 Years", @@ -459674,6 +460414,85 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.12.26.473325", + "rel_title": "Comparative analysis of single cell lung atlas of bat, cat, tiger and pangolin", + "rel_date": "2021-12-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.26.473325", + "rel_abs": "Horseshoe bats (Rhinolophus sinicus) might help maintain coronaviruses severely affecting human health, such as SARS-CoV and SARS-CoV-2. It has long been suggested that bats may be more tolerant of viral infection than other mammals due to their unique immune system, but the exact mechanism remains to be fully explored. During the COVID-19 pandemic, multiple animal species were diseased by SARS-CoV-2 infection, especially in the respiratory system. Herein, single-cell transcriptomic data of the lungs of a horseshoe bat, a cat, a tiger, and a pangolin were generated. The receptor distribution of twenty-eight respiratory viruses belonging to fourteen viral families were characterized for the four species. Comparison on the immune-related transcripts further revealed limited cytokine activations in bats, which might explain the reason why bats experienced only mild diseases or even no symptoms upon virus infection. Our findings might increase our understanding of the immune background of horseshoe bats and their insensitivity to virus infections.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Xiran Wang", + "author_inst": "National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong L" + }, + { + "author_name": "Zhihua Ou", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China." + }, + { + "author_name": "Peiwen Ding", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Chengcheng Sun", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; School of Basic Medicine, Qing" + }, + { + "author_name": "Daxi Wang", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China." + }, + { + "author_name": "Jiacheng Zhu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Wendi Wu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; School of Basic Medicine, Qing" + }, + { + "author_name": "Yanan Wei", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; School of Basic Medicine, Qing" + }, + { + "author_name": "Xiangning Ding", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Lihua Luo", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Meiling Li", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Wensheng Zhang", + "author_inst": "School of Basic Medical Sciences, Binzhou Medical University, No. 346, Guanhai Road, Laishan District, Yantai City, Shandong, China" + }, + { + "author_name": "Xin Jin", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + }, + { + "author_name": "Jian Sun", + "author_inst": "National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, South China Agricultural University, Guangzhou, China; Guangdong L" + }, + { + "author_name": "Huan Liu", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China" + }, + { + "author_name": "Dongsheng Chen", + "author_inst": "BGI-Shenzhen, Shenzhen 518083, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.21.21268143", "rel_title": "Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission", @@ -461477,97 +462296,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.12.24.474091", - "rel_title": "Two doses of mRNA vaccine elicit cross-neutralizing memory B-cells against SARS-CoV-2 Omicron variant", - "rel_date": "2021-12-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.24.474091", - "rel_abs": "SARS-CoV-2 Beta and Omicron variants have multiple mutations in the receptor-binding domain (RBD) allowing antibody evasion. Despite the resistance to circulating antibodies in those who received two doses of mRNA vaccine, the third dose prominently recalls cross-neutralizing antibodies with expanded breadth to these variants. Herein, we longitudinally profiled the cellular composition of persistent memory B-cell subsets and their antibody reactivity against these variants following the second vaccine dose. The vaccination elicited a memory B-cell subset with resting phenotype that dominated the other subsets at 4.9 months. Notably, most of the resting memory subset retained the ability to bind the Beta variant, and the memory-derived antibodies cross-neutralized the Beta and Omicron variants at frequencies of 59% and 29%, respectively. The preservation of cross-neutralizing antibody repertoires in the durable memory B-cell subset likely contributes to the prominent recall of cross-neutralizing antibodies following the third dose of the vaccine.\n\nOne Sentence SummaryFully vaccinated individuals preserve cross-neutralizing memory B-cells against the SARS-CoV-2 Omicron variant.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Ryutaro Kotaki", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Yu Adachi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Saya Moriyama", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Taishi Onodera", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Shuetsu Fukushi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Takaki Nagakura", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Keisuke Tonouchi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Kazutaka Terahara", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Lin Sun", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Tomohiro Takano", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Ayae Nishiyama", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Masaharu Shinkai", - "author_inst": "Tokyo Shinagawa Hospital" - }, - { - "author_name": "Kunihiro Oba", - "author_inst": "Showa General Hospital" - }, - { - "author_name": "Fukumi Nakamura-Uchiyama", - "author_inst": "Tokyo Metropolitan Bokutoh Hospital" - }, - { - "author_name": "Hidefumi Shimizu", - "author_inst": "JCHO Tokyo Shinjuku Medical Center" - }, - { - "author_name": "Tadaki Suzuki", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Takayuki Matsumura", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Masanori Isogawa", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Yoshimasa Takahashi", - "author_inst": "National Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.24.474081", "rel_title": "Convalescence from prototype SARS-CoV-2 protects Syrian hamsters from disease caused by the Omicron variant", @@ -462008,6 +462736,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.23.21267374", + "rel_title": "Immunogenicity and Safety Following a Homologous Booster Dose of a SARS-CoV-2 recombinant spike protein vaccine (NVX-CoV2373): A Phase 2 Randomized Placebo-Controlled Trial", + "rel_date": "2021-12-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21267374", + "rel_abs": "BackgroundEmerging SARS-CoV-2 variants and evidence of waning vaccine efficacy present significant obstacles toward controlling the COVID-19 pandemic. Booster doses of SARS-CoV-2 vaccines may address these concerns by both amplifying and broadening the immune responses seen with initial vaccination regimens.\n\nMethodsIn a phase 2 study, a single booster dose of a SARS-CoV-2 recombinant spike protein vaccine with Matrix-M adjuvant (NVX-CoV2373) was administered to healthy adult participants 18 to 84 years of age approximately 6 months following their primary two-dose vaccination series. Safety and immunogenicity parameters were assessed, including assays for IgG, MN50, and hACE2 receptor binding inhibition against the ancestral SARS-CoV-2 strain and select variants (B.1.351 [Beta], B.1.1.7 [Alpha], B.1.617.2 [Delta], and B.1.1.529 [Omicron]). This trial is registered with ClinicalTrials.gov, NCT04368988.\n\nFindingsAn incremental increase in the incidence of solicited local and systemic reactogenicity events was observed with subsequent vaccinations. Following the booster, incidence rates of local and systemic reactions were 82.5% (13.4% [≥] Grade 3) and 76.5% (15.3% [≥] Grade 3), respectively, compared to 70.0% (5.2% [≥] Grade 3) and 52.8% (5.6% [≥] Grade 3), respectively, following the primary vaccination series. Events were primarily mild or moderate in severity and transient in nature, with a median duration of 1.0 to 2.5 days. Immune responses seen 14 days following the primary vaccination series were compared with those observed 28 days following the booster (Day 35 and Day 217, respectively). For the ancestral SARS-CoV-2 strain, serum IgG geometric mean titers (GMTs) increased [~]4.7-fold from 43,905 ELISA units (EU) at day 35 to 204,367 EU at Day 217. Neutralization (MN50) assay GMTs showed a similar increase of [~]4.1-fold from 1,470 at day 35 to 6,023 at Day 217. A functional hACE2 receptor binding inhibition assay analyzing activity against ancestral and variant strains of SARS-CoV-2 at Day 189 vs Day 217 found 54.4-fold (Ancestral), 21.9-fold (Alpha), 24.5-fold (Beta), 24.4-fold (Delta), and 20.1-fold (Omicron) increases in titers. An anti-rS IgG activity assay comparing the same time points across the same SARS-CoV-2 strains found titers improved 61.2-fold, 85.9-fold, 65.0-fold, 92.5-fold, and 73.5-fold, respectively.\n\nInterpretationAdministration of a booster dose of NVX-CoV2373 approximately 6 months following the primary vaccination series resulted in an incremental increase in reactogenicity along with enhanced immune responses. For both the prototype strain and all variants evaluated, immune responses following the booster were notably higher than those associated with high levels of efficacy in phase 3 studies of the vaccine.\n\nFundingNovavax(R) and the Coalition for Epidemic Preparedness Innovations (CEPI(R)).", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Raburn Mallory", + "author_inst": "Novavax" + }, + { + "author_name": "Neil Formica", + "author_inst": "Novavax" + }, + { + "author_name": "Susan Pfeiffer", + "author_inst": "Novavax" + }, + { + "author_name": "Bethanie Wilkinson", + "author_inst": "Novavax" + }, + { + "author_name": "Alex Marcheschi", + "author_inst": "Novavax" + }, + { + "author_name": "Gary Albert", + "author_inst": "Novavax" + }, + { + "author_name": "Heather McFall", + "author_inst": "Novavax" + }, + { + "author_name": "Michelle Robinson", + "author_inst": "Novavax" + }, + { + "author_name": "Joyce Plested", + "author_inst": "Novavax" + }, + { + "author_name": "MingZhu Zhu", + "author_inst": "Novavax" + }, + { + "author_name": "Shane Cloney-Clark", + "author_inst": "Novavax" + }, + { + "author_name": "Bin Zhou", + "author_inst": "Novavax" + }, + { + "author_name": "Gordon Chau", + "author_inst": "Novavax" + }, + { + "author_name": "Andreana Robertson", + "author_inst": "Novavax" + }, + { + "author_name": "Sonia Maciejewski", + "author_inst": "Novavax" + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax" + }, + { + "author_name": "Nita Patel", + "author_inst": "Novavax" + }, + { + "author_name": "Gregory M Glenn", + "author_inst": "Novavax" + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.23.21268332", "rel_title": "Extending upon: What effect might border screening have on preventing importation of COVID-19 compared with other infections? - Considering the additional effect of post-arrival isolation", @@ -463503,57 +464322,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.23.21268325", - "rel_title": "Exploration of attitudes regarding uptake of COVID-19 vaccines among vaccine hesitant adults in the UK: A qualitative analysis.", - "rel_date": "2021-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268325", - "rel_abs": "BackgroundThe aim of this work was to explore barriers and facilitators to uptake of COVID-19 vaccines and to explore views and reactions to efforts to improve vaccine uptake among those who were vaccine hesitant.\n\nMethodsSemi-structured interviews were conducted with people between the age of 18-29 years who had not had a COVID-19 vaccine, and those between 30-49 years who had not received a second dose of a COVID-19 vaccine (more than 12 weeks after receiving a first).\n\nResultsA total of 70 participants took part in the study, 35 participants had received one dose of the vaccine, and 35 had not received any vaccine.\n\nParticipants described a possible willingness to be vaccinated to keep themselves and those around them safe, and to avoid restrictions and return to normal. Barriers to uptake included: 1) perceived lack of need for COVID-19 vaccinations, 2) concerns about the efficacy of vaccinations, 3) concerns about safety, and 4) access issues. Uptake appeared to be influenced by the age and health status of the individual, trust in government and knowledge and understanding of science. Introduction of vaccine passes may provide a motive for having a vaccine but may also be viewed as coercive.\n\nConclusionParticipants were hesitant, rather than opposed, and had questions about their need for, and the safety and efficacy of the vaccine. Young people did not consider themselves to be at risk of becoming ill from COVID-19, did not think the vaccination was effective in preventing infection and transmission, and did not think sufficient research had been conducted with regard to the possible long-term side-effects. These concerns were exacerbated by a lack of trust in the government, and misunderstanding of science. In order to promote uptake, public health campaigns should focus on the provision of information from trusted sources that carefully explains the benefits of vaccination and addresses safety concerns more effectively. To overcome inertia in people with low levels of motivation to be vaccinated, appointments must be easily accessible.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sarah Denford", - "author_inst": "University of Bristol" - }, - { - "author_name": "Fiona Mowbray", - "author_inst": "King's College London" - }, - { - "author_name": "Lauren Towler", - "author_inst": "University of Southampton" - }, - { - "author_name": "Helena Wehling", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Gemma Lasseter", - "author_inst": "University of Bristol" - }, - { - "author_name": "Richard Amlot", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Isabel Oliver", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Lucy Yardley", - "author_inst": "University of Bristol" - }, - { - "author_name": "Matthew Hickman", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.22.21268296", "rel_title": "Diversity in antibody titer at an average of 87 days after the second dose of BNT162b2 mRNA coronavirus disease 2019 vaccine: data from a predominantly elderly population in a practice in Tokyo", @@ -463758,6 +464526,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.22.21268265", + "rel_title": "Infrared spectroscopy enables rapid, robust, portable COVID-19 saliva screening based on pathophysiological response to SARS-CoV-2", + "rel_date": "2021-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268265", + "rel_abs": "Fourier-transform infrared (FTIR) spectroscopy provides a (bio)chemical snapshot of the sample, and was recently proposed for COVID-19 saliva screening in proof-of-concept cohort studies. As a step towards translation of this technology, we conducted controlled validation experiments in multiple biological systems. SARS-CoV-2 or UV-inactivated SARS-CoV-2 were used to infect Vero E6 cells in vitro, and K18-hACE2 mice in vivo. Potentially infectious culture supernatant or mouse oral lavage samples were treated with ethanol or Trizol to 75% (v/v) for attenuated total reflectance (ATR)-FTIR spectroscopy, or RT-PCR, respectively. The control condition, UV-inactivated SARS-CoV-2 elicited strong biochemical changes in culture supernatant/oral lavage despite lack of replication determined by RT-PCR or cell culture infectious dose 50%. Crucially, we show that active SARS-CoV-2 infection induced additional FTIR signals over the UV-inactivated SARS-CoV-2 infection, which correspond to innate immune response, aggregated proteins, and RNA. For human patient cohort prediction, we achieved high sensitivity of 93.48% on leave-on-out cross validation (n=104 participants) for predicting COVID-19 positivity using a partial least squares discriminant analysis model, in agreement with recent studies. However, COVID-19 patients negative on follow-up (RT-PCR on day of saliva sampling) were poorly predicted in this model. Importantly, COVID-19 vaccination did not lead to mis-classification of COVID-19 negatives. Meta-analysis revealed SARS-CoV-2 induced increase in Amide II band in all arms of this study and recent studies, indicative of altered {beta}-sheet structures in secreted proteins. In conclusion, ATR-FTIR is a robust, simple, portable method for COVID-19 saliva screening based on detection of pathophysiological responses to SARS-CoV-2.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Seth Kazmer", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Gunter Hartel", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Harley Robinson", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Renee S Richards", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Kexin Yan", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Sebastiaan J. Van Hal", + "author_inst": "NSW Health Pathology: New South Wales Health Pathology" + }, + { + "author_name": "Raymond Chan", + "author_inst": "NSW Health Pathology: New South Wales Health Pathology" + }, + { + "author_name": "Andrew Hind", + "author_inst": "Agilent Technologies Australia" + }, + { + "author_name": "David Bradley", + "author_inst": "Agilent Technologies Australia" + }, + { + "author_name": "Fabian Zieschang", + "author_inst": "Agilent Technologies Australia" + }, + { + "author_name": "Daniel J Rawle", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Thuy T Le", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "David W Reid", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Andreas Suhrbier", + "author_inst": "QIMR Berghofer Medical Research Institute" + }, + { + "author_name": "Michelle M Hill", + "author_inst": "QIMR Berghofer Medical Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.23.21267893", "rel_title": "Echinacea as a Potential Force against Coronavirus Infections? A Mini-Review of Randomized Controlled Trials in Adults and Children", @@ -465464,25 +466307,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.12.22.473887", - "rel_title": "Allosteric Determinants of the SARS-CoV-2 Spike Protein Binding with Nanobodies: Examining Mechanisms of Mutational Escape and Sensitivity of the Omicron Variant", - "rel_date": "2021-12-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.22.473887", - "rel_abs": "Structural and biochemical studies have recently revealed a range of rationally engineered nanobodies with efficient neutralizing capacity against SARS-CoV-2 virus and resilience against mutational escape. In this study, we performed a comprehensive computational analysis of the SARS-CoV-2 spike trimer complexes with Nb6, VHH E and bi-paratopic VHH VE nanobodies. We combined atomistic dynamics and collective motions analysis with binding free energy scanning, perturbation-response scanning and network centrality analysis to examine mechanisms of nanobody-induced allosteric modulation and cooperativity in the SARS-CoV-2 spike trimer complexes with these nanobodies. By quantifying energetic and allosteric determinants of the SARS-CoV-2 spike protein binding with nanobodies, we also examined nanobody-induced modulation of escaping mutations and the effect of the Omicron variant on nanobody binding. The mutational scanning analysis supported the notion that E484A mutation can have a significant detrimental effect on nanobody binding and result in Omicron-induced escape from nanobody neutralization. Our findings showed that SARS-CoV-2 spike protein may exploit plasticity of specific allosteric hotspots to generate escape mutants that alter response to binding without compromising activity. The network analysis supported these findings showing that VHH VE nanobody binding can induce long-range couplings between the cryptic binding epitope and ACE2-binding site through a broader ensemble of communication paths that is less dependent on specific mediating centers and therefore may be less sensitive to mutational perturbations of functional residues. The results suggest that binding affinity and long-range communications of the SARS-CoV-2 complexes with nanobodies can be determined by structurally stable regulatory centers and conformationally adaptable hotspots that are allosterically coupled and collectively control resilience to mutational escape.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Gennady Verkhivker", - "author_inst": "Chapman University School of Pharmacy" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.12.22.473902", "rel_title": "Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization", @@ -465755,6 +466579,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.22.21268021", + "rel_title": "Omicron outbreak at a private gathering in the Faroe Islands, infecting 21 of 33 triple-vaccinated healthcare workers", + "rel_date": "2021-12-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268021", + "rel_abs": "There are concerns that the SARS-CoV-2 Omicron variant evades immune responses due to unusually high numbers of mutations on the spike protein. Here we report a super-spreading event of Omicron infections amongst triple-vaccinated healthcare workers, infecting 21 of 33 attending a private gathering in the Faroe Islands.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Gunnhild Helmsdal", + "author_inst": "General Practitioner Service, Vestmanna, Faroe Islands" + }, + { + "author_name": "Olga Kristina Hansen", + "author_inst": "Office of the Chief Medical Officer, Torshavn, Faroe Islands" + }, + { + "author_name": "Lars Fodgaard Moller", + "author_inst": "Office of the Chief Medical Officer, Torshavn, Faroe Islands" + }, + { + "author_name": "Debes Hammershaimb Christiansen", + "author_inst": "Faroese Food and Veterinary Authority, Torshavn, Faroe Islands" + }, + { + "author_name": "Maria Skaalum Petersen", + "author_inst": "The Faroese Hospital System, Torshavn, Faroe Islands" + }, + { + "author_name": "Marnar Fridheim Kristiansen", + "author_inst": "University of the Faroe Islands, Torshavn, Faroe Islands" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.22.21268274", "rel_title": "SARS-CoV-2 Antigen Tests Predict Infectivity Based on Viral Culture: Comparison of Antigen, PCR Viral Load, and Viral Culture Testing on a Large Sample Cohort", @@ -467546,121 +468409,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.20.473523", - "rel_title": "Conjunctival epithelial cells resist productive SARS-CoV-2 infection", - "rel_date": "2021-12-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.20.473523", - "rel_abs": "Although tropism of SARS-CoV-2 for respiratory tract epithelial cells is well established, an open question is whether the conjunctival epithelium is also a target for SARS-CoV-2. Conjunctival epithelial cells, which express viral entry receptors ACE2 and TMPRSS2, constitute the largest exposed epithelium of the ocular surface tissue, and may represent a relevant viral entry route. To address this question, we generated an organotypic air-liquid-interface model of conjunctival epithelium, composed of progenitor, basal and superficial epithelial cells and fibroblasts, which could be maintained successfully up to day 75 of differentiation. Using single-cell RNA Seq, with complementary imaging and virological assays, we observed that while all conjunctival cell types were permissive to SARS-CoV-2 genome expression, a productive infection did not ensue. The early innate immune response to SARS-CoV-2 infection in conjunctival cells was characterised by a robust autocrine and paracrine NF-K{beta} activity, without activation of antiviral interferon signalling. Collectively, these data enrich our understanding of SARS-CoV-2 infection at the human ocular surface, with potential implications for the design of preventive strategies and conjunctival transplants.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Majlinda Lako", - "author_inst": "Newcastle University" - }, - { - "author_name": "Robert M Jackson", - "author_inst": "Newcastle University" - }, - { - "author_name": "Catherine F Hatton", - "author_inst": "Newcastle University" - }, - { - "author_name": "Jarmila S Spegarova", - "author_inst": "Newcastle University" - }, - { - "author_name": "Maria Georgiou", - "author_inst": "Newcastle University" - }, - { - "author_name": "Joseph Collin", - "author_inst": "Newcastle University" - }, - { - "author_name": "Emily Stephenson", - "author_inst": "Newcastle University" - }, - { - "author_name": "Bernard Vernon", - "author_inst": "Newcastle University" - }, - { - "author_name": "Iram J Haq", - "author_inst": "Newcastle University" - }, - { - "author_name": "Rafiqul Hussain", - "author_inst": "Newcastle University" - }, - { - "author_name": "Jonathan M Coxhead", - "author_inst": "Newcastle University" - }, - { - "author_name": "Hardeep S Mudhar", - "author_inst": "Royal Hallamshire Hospital" - }, - { - "author_name": "Bart Wagner", - "author_inst": "Royal Hallamshire Hospital" - }, - { - "author_name": "Megan Hasoon", - "author_inst": "Newcastle University" - }, - { - "author_name": "Tracey Davie", - "author_inst": "Newcastle University" - }, - { - "author_name": "Paul Rooney", - "author_inst": "NHS Blood and Transplant Tissue and Eye Services" - }, - { - "author_name": "C.M. Anjam Khan", - "author_inst": "Newcastle University" - }, - { - "author_name": "Christopher Ward", - "author_inst": "Newcastle University" - }, - { - "author_name": "Malcolm Brodlie", - "author_inst": "Newcastle University" - }, - { - "author_name": "Muzlifah Haniffa", - "author_inst": "Newcastle University" - }, - { - "author_name": "Sophie Hambleton", - "author_inst": "Newcastle University" - }, - { - "author_name": "Lyle Armstrong", - "author_inst": "University of Newcastle" - }, - { - "author_name": "Francisco Figueiredo", - "author_inst": "Newcastle University" - }, - { - "author_name": "Rachel Queen", - "author_inst": "Newcastle University" - }, - { - "author_name": "Christopher JA Duncan", - "author_inst": "Newcastle University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.12.20.473613", "rel_title": "The Geometry of ATG-Walks of the Omicron SARS CoV-2 Virus RNAs", @@ -467829,6 +468577,237 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.17.473248", + "rel_title": "SARS-CoV-2 Omicron spike mediated immune escape, infectivity and cell-cell fusion", + "rel_date": "2021-12-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.17.473248", + "rel_abs": "The SARS-CoV-2 Omicron BA.1 variant emerged in late 2021 and is characterised by multiple spike mutations across all spike domains. Here we show that Omicron BA.1 has higher affinity for ACE2 compared to Delta, and confers very significant evasion of therapeutic monoclonal and vaccine-elicited polyclonal neutralising antibodies after two doses. mRNA vaccination as a third vaccine dose rescues and broadens neutralisation. Importantly, antiviral drugs remdesevir and molnupiravir retain efficacy against Omicron BA.1. We found that in human nasal epithelial 3D cultures replication was similar for both Omicron and Delta. However, in lower airway organoids, Calu-3 lung cells and gut adenocarcinoma cell lines live Omicron virus demonstrated significantly lower replication in comparison to Delta. We noted that despite presence of mutations predicted to favour spike S1/S2 cleavage, the spike protein is less efficiently cleaved in live Omicron virions compared to Delta virions. We mapped the replication differences between the variants to entry efficiency using spike pseudotyped virus (PV) entry assays. The defect for Omicron PV in specific cell types correlated with higher cellular RNA expression of TMPRSS2, and accordingly knock down of TMPRSS2 impacted Delta entry to a greater extent as compared to Omicron. Furthermore, drug inhibitors targeting specific entry pathways demonstrated that the Omicron spike inefficiently utilises the cellular protease TMPRSS2 that mediates cell entry via plasma membrane fusion. Instead, we demonstrate that Omicron spike has greater dependency on cell entry via the endocytic pathway requiring the activity of endosomal cathepsins to cleave spike. Consistent with suboptimal S1/S2 cleavage and inability to utilise TMPRSS2, syncytium formation by the Omicron spike was dramatically impaired compared to the Delta spike. Overall, Omicron appears to have gained significant evasion from neutralising antibodies whilst maintaining sensitivity to antiviral drugs targeting the polymerase. Omicron has shifted cellular tropism away from TMPRSS2 expressing cells that are enriched in cells found in the lower respiratory and GI tracts, with implications for altered pathogenesis.", + "rel_num_authors": 54, + "rel_authors": [ + { + "author_name": "Bo Meng", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Isabella Ferreira", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Adam Abdullahi", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Niluka Goonawardane", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Akatsuki Saito", + "author_inst": "University of Miyazaki" + }, + { + "author_name": "Izumi Kimura", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Daichi Yamasoba", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Steven A Kemp", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Guido Papa", + "author_inst": "LMB Cambridge" + }, + { + "author_name": "Saman Fatihi", + "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" + }, + { + "author_name": "Surabhi Rathore", + "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" + }, + { + "author_name": "Pehuen Perera Gerba", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Terumasa Ikeda", + "author_inst": "Kumamoto Univ" + }, + { + "author_name": "Mako Toyoda", + "author_inst": "Kumamoto University, Kumamoto" + }, + { + "author_name": "Toong Seng Tan", + "author_inst": "Kuramochi Clinic Interpark" + }, + { + "author_name": "Jin Kuramochi", + "author_inst": "Kuramochi Clinic Interpark" + }, + { + "author_name": "Shigeki Mitsunaga", + "author_inst": "National Institute of Genetics, Mishima, Shizuoka" + }, + { + "author_name": "Takamasa Ueno", + "author_inst": "Kumamoto University, Kumamoto" + }, + { + "author_name": "Oscar Charles", + "author_inst": "University College London" + }, + { + "author_name": "Dami Collier", + "author_inst": "University of Cambridge" + }, + { + "author_name": "- CITIID-NIHR BioResource COVID-19 Collaboration", + "author_inst": "-" + }, + { + "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) Consortium", + "author_inst": "-" + }, + { + "author_name": "- Ecuador-COVID19 Consortium", + "author_inst": "-" + }, + { + "author_name": "John Bradley", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Jinwook Choi", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Kenneth Smith", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Elo Madissoon", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Kerstin Meyer", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Petra Mlcochova", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Rainer Doffinger", + "author_inst": "Cambridge University Hospitals NHS Trust" + }, + { + "author_name": "Sarah A Teichmann", + "author_inst": "Cambridge University" + }, + { + "author_name": "Leo James", + "author_inst": "MRC LMB" + }, + { + "author_name": "Joo Hyeon Lee", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Teresa Brevini", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Matteo Pizzuto", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Myra Hosmillo", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Donna Mallery", + "author_inst": "MRC LMB Cambridge" + }, + { + "author_name": "Samantha Zepeda", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexandra Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "Anshu Joshi", + "author_inst": "University of Washington" + }, + { + "author_name": "John Bowen", + "author_inst": "University of Washington" + }, + { + "author_name": "John Briggs", + "author_inst": "University of Heidelberg" + }, + { + "author_name": "Alex Sigal", + "author_inst": "Africa Health Research Institute, Durban, South Africa" + }, + { + "author_name": "Laurelle Jackson", + "author_inst": "Africa Health Research Institute, Durban, South Africa" + }, + { + "author_name": "Sandile Cele", + "author_inst": "Africa Health Research Institute, Durban, South Africa" + }, + { + "author_name": "Anna De Marco", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Fotios Sampaziotis", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + }, + { + "author_name": "Nicholas Matheson", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ian Goodfellow", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Lipi Thukral", + "author_inst": "CSIR Institute of Genomics and Integrative Biology, Delhi, India" + }, + { + "author_name": "Kei Sato", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Ravindra K Gupta", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.17.473140", "rel_title": "Human genetic variants associated with COVID-19 severity are enriched in immune and epithelium regulatory networks", @@ -469736,85 +470715,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.19.21268037", - "rel_title": "Superior immunogenicity and effectiveness of the 3rd BNT162b2 vaccine dose", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.19.21268037", - "rel_abs": "In a prospective cohort study involving 12,413 Health Care Workers (HCW), we assessed immunogenicity, vaccine-effectiveness (VE) and safety of the third BNT162b2 vaccine dose. One month after third dose, anti-RBD-IgG were induced 1.7-folds compared to one month after the second. A significant increase in avidity from 61.1% (95%CI:56.1-66.7) to 96.3% (95%CI:94.2-98.5) resulted in a 6.1-folds neutralizing antibodies induction. Linear mixed model demonstrated that the third dose elicited a greater response among HCW[≥]60 or those with [≥]two comorbidities who had a lower response following the second dose. VE of the third dose relative to two doses was 85.6% (95% CI, 79.2-90.1%). No serious adverse effects were reported. These results suggest that the third dose is superior to the second dose in both quantity and quality of IgG-antibodies and safely boosts protection from SARS-CoV-2 infection by generating high avidity antibodies to levels that are not significantly different between healthy and vulnerable populations.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Yaniv Lustig", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Tal Gonen", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Lilac Meltzer", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Mayan Gilboa", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Victoria Indenbaum", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Carmit Cohen", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Sharon Amit", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Hanaa Jaber", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Ram Doolman", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Keren Asraf", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Carmit Rubin", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Ronen Fluss", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Ella Mendelson", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Laurence Freedman", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Gili Regev-Yochay", - "author_inst": "Sheba Medical Center" - }, - { - "author_name": "Yitshak Kreiss", - "author_inst": "Sheba Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.18.473330", "rel_title": "The N-Terminal Carbamate is Key to High Cellular and Antiviral Potency for Boceprevir-Based SARS-CoV-2 Main Protease Inhibitors", @@ -470074,6 +470974,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.20.21268134", + "rel_title": "Activity of convalescent and vaccine serum against a B.1.1.529 variant SARS-CoV-2 isolate", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21268134", + "rel_abs": "The B.1.1.529 (Omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was identified in November of 2021 in South Africa and Botswana as well as in a sample of a traveler from South Africa in Hong Kong.1,2 Since then, B.1.1.529 has been detected in many countries globally. This variant seems to be more infectious than B.1.617.2 (Delta), has already caused super spreader events3 and has outcompeted Delta within weeks in several countries and metropolitan areas. B.1.1.529 hosts an unprecedented number of mutations in its spike gene and early reports have provided evidence for extensive immune escape and reduced vaccine effectiveness.2,4-6 Here, we investigated the neutralizing and binding activity of sera from convalescent, mRNA double vaccinated, mRNA boosted as well as convalescent double vaccinated and convalescent boosted individuals against wild type, B.1.351 and B.1.1.529 SARS-CoV-2 isolates. Neutralizing activity of sera from convalescent and double vaccinated participants was undetectable to very low against B.1.1.529 while neutralizing activity of sera from individuals who had been exposed to spike three or four times was maintained, albeit at strongly reduced levels. Binding to the B.1.1.529 receptor binding domain (RBD) and N-terminal domain (NTD) was reduced in convalescent not vaccinated but was mostly retained in vaccinated individuals.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Juan Manuel Carreno", + "author_inst": "ISMMS" + }, + { + "author_name": "Hala Alshammary", + "author_inst": "ISMMS" + }, + { + "author_name": "Johnstone Tcheou", + "author_inst": "ISMMS" + }, + { + "author_name": "Gagandeep Singh", + "author_inst": "ISMMS" + }, + { + "author_name": "Ariel Raskin", + "author_inst": "ISMMS" + }, + { + "author_name": "Hisaaki Kawabata", + "author_inst": "ISMMS" + }, + { + "author_name": "Levy Sominsky", + "author_inst": "ISMMS" + }, + { + "author_name": "Jordan Clark", + "author_inst": "ISMMS" + }, + { + "author_name": "Daniel C. Adelsberg", + "author_inst": "ISMMS" + }, + { + "author_name": "Dominika Bielak", + "author_inst": "ISMMS" + }, + { + "author_name": "Ana Silvia Gonzalez-Reiche", + "author_inst": "ISMMS" + }, + { + "author_name": "PSP/PARIS Study Group", + "author_inst": "ISMMS" + }, + { + "author_name": "Komal Srivastava", + "author_inst": "ISMMS" + }, + { + "author_name": "Emilia M Sordillo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Goran Bajic", + "author_inst": "ISMMS" + }, + { + "author_name": "Harm van Bakel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Viviana Simon", + "author_inst": "Icahn School of Medicine" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.20.21268124", "rel_title": "SARS-CoV-2 vaccine effectiveness and breakthrough infections in maintenance dialysis patients", @@ -471601,129 +472588,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.12.21.21267898", - "rel_title": "Diminished neutralization responses towards SARS-CoV-2 Omicron VoC after mRNA or vector-based COVID-19 vaccinations", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21267898", - "rel_abs": "SARS-CoV-2 variants accumulating immune escape mutations provide a significant risk to vaccine-induced protection. The novel variant of concern (VoC) Omicron (B.1.1.529) has the largest number of amino acid alterations in its Spike protein to date. Thus, it may efficiently escape recognition by neutralizing antibodies, allowing breakthrough infections in convalescent and vaccinated individuals. We analyzed neutralization activity of sera from individuals after vaccination with all mRNA-, vector- or heterologous immunization schemes currently available in Europe by in vitro neutralization assay at peak response towards SARS-CoV-2 B.1, Omicron, Beta and Delta pseudotypes and also provide longitudinal follow-up data from BNT162b2 vaccinees. All vaccines apart from Ad26.CoV2.S showed high levels of responder rates (93-100%) towards SARS-CoV-2 wild-type, but some reductions in neutralizing Beta and Delta VoC pseudotypes. The novel Omicron variant had the biggest impact, both in terms of response rates and neutralization titers. Only mRNA-1273 showed a 100% response rate to Omicron and induced the highest level of neutralizing antibody titers, followed by heterologous prime-boost approaches. Homologous BNT162b2 vaccination or vector-based AZD1222 or Ad26.CoV2.S performed less well with peak responder rates of 33%, 50% and 9%, respectively. However, Omicron responder rates in BNT162b2 recipients were maintained in our six month longitudinal follow-up indicating that individuals with cross-protection against Omicron maintain it over time. Overall, our data strongly argues for urgent booster doses in individuals who were previously vaccinated with BNT162b2, or a vector-based immunization scheme.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Henning Jacobsen", - "author_inst": "Helmholtz Centre for Infection Research, Department of Viral Immunology, Braunschweig, Germany" - }, - { - "author_name": "Monika Strengert", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Henrike Maass", - "author_inst": "Helmholtz Centre for Infection Research, Department of Viral Immunology, Braunschweig, Germany" - }, - { - "author_name": "Mario Alberto Ynga Durand", - "author_inst": "Helmholtz Centre for Infection Research, Department of Viral Immunology, Braunschweig, Germany" - }, - { - "author_name": "Barbora Kessel", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Manuela Harries", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Ulfert Rand", - "author_inst": "Helmholtz Centre for Infection Research, Department of Viral Immunology, Braunschweig, Germany" - }, - { - "author_name": "Leila Abassi", - "author_inst": "Helmholtz Centre for Infection Research, Department of Viral Immunology, Braunschweig, Germany" - }, - { - "author_name": "Yeonsu Kim", - "author_inst": "Helmholtz Centre for Infection Research, Department of Viral Immunology, Braunschweig, Germany" - }, - { - "author_name": "Tatjana Lueddecke", - "author_inst": "Helmholtz Centre for Infection Research, Department of Viral Immunology, Braunschweig, Germany" - }, - { - "author_name": "Pilar Hernandez", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Julia Ortmann", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Jana-Kristin Heise", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Stefanie Castell", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Daniela Gornyk", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Stephan Gloeckner", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Vanessa Melhorn", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Yvonne Kemmling", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Berit Lange", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Alex Dulovic", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Department for Multiplex Immunosassays, Reutlingen, Germany" - }, - { - "author_name": "Julia Haering", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Department for Multiplex Immunosassays, Reutlingen, Germany" - }, - { - "author_name": "Daniel Junker", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Department for Multiplex Immunosassays, Reutlingen, Germany" - }, - { - "author_name": "Nicole Schneiderhan-Marra", - "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Department for Multiplex Immunosassays, Reutlingen, Germany" - }, - { - "author_name": "Stefan Poehlmann", - "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" - }, - { - "author_name": "Markus Hoffmann", - "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" - }, - { - "author_name": "Gerard Krause", - "author_inst": "Helmholtz Centre for Infection Research, Department of Epidemiology Braunschweig, Germany" - }, - { - "author_name": "Luka Cicin-Sain", - "author_inst": "Helmholtz Centre for Infection Research, Department of Viral Immunology, Braunschweig, Germany" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.12.20.21268113", "rel_title": "A nationwide deep learning pipeline to predict stroke and COVID-19 death in atrial fibrillation", @@ -471888,6 +472752,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.21.21267983", + "rel_title": "GB0139, an inhaled small molecule inhibitor of galectin-3, in COVID-19 pneumonitis: a randomised, controlled, open-label, phase 2a experimental medicine trial of the safety, pharmacokinetics, and potential therapeutic value", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21267983", + "rel_abs": "RationaleHigh galectin-3 levels predict poor outcomes in patients with COVID-19. Galectin-3 activates monocytes and macrophages which are directly implicated in COVID-19 immunopathology and the cytokine storm. GB0139 is a potent thiodigalactoside galectin-3 inhibitor and may reduce the severe effects of the disease. We report safety and pharmacokinetics and pharmacodynamics of the inhaled galectin-3 inhibitor, GB0139, and assess clinical outcomes and key systemic inflammatory biomarkers in hospitalised patients with COVID-19 (ClinicalTrials.gov/EudraCT identifier: NCT04473053/2020-002230-32).\n\nMethodsAdults with COVID-19 requiring oxygen, and with pneumonitis on x-ray, were randomised to receive standard of care (SOC; including dexamethasone; n=21) or SOC plus 10 mg GB0139 twice daily for 48 hours, then once daily for [≤]14 days (n=20).\n\nResultsPatients aged 27-87 years were enrolled from July 2020; the final patient completed the 90-day follow-up in April 2021. GB0139+SOC was well tolerated with no treatment-related serious adverse events reported. Incidences of adverse events were similar between treatment arms (40 with GB0139+SOC vs 35 with SOC). Plasma GB0139 was measurable in all patients after inhaled exposure, with moderate interpatient variability, and demonstrated target engagement with decreased circulating galectin (overall treatment effect post-hoc over days 2-7: p=0{middle dot}0099 vs SOC). Rate of decline in fraction of inspired oxygen (%) requirement was significantly greater in the GB0139+SOC arm with a posterior mean difference of -1{middle dot}51 (95% highest posterior density: -2{middle dot}90, -0{middle dot}189) versus SOC. Plasma levels of biomarkers associated with inflammation, coagulopathy, major organ function and fibrosis showed a downward trend versus SOC.\n\nConclusionsGB0139+SOC was well tolerated and achieved clinically relevant plasma concentrations and target engagement. This, and the reduction in markers associated with inflammatory, coagulation, fibrosis, and reduction in inspired oxygen (%) over SOC alone, indicates the therapeutic potential for inhaled GB0139 in hospitalised patients with COVID-19.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Erin Gaughan", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Tariq Sethi", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Tom Quinn", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Nikhil Hirani", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Andrew Mills", + "author_inst": "Exploristics" + }, + { + "author_name": "Annya M. Bruce", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Alison MacKinnon", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Vassilios Aslanis", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Feng Li", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Richard O'Connor", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Richard A. Parker", + "author_inst": "Edinburgh Clinical Trials Unit, Usher Institute, University of Edinburgh" + }, + { + "author_name": "John Norrie", + "author_inst": "Edinburgh Clinical Trials Unit, Usher Institute, University of Edinburgh" + }, + { + "author_name": "James Dear", + "author_inst": "Centre for Cardiovascular Science, University of Edinburgh" + }, + { + "author_name": "Ahsan R. Akram", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + }, + { + "author_name": "Oliver Koch", + "author_inst": "Infectious Diseases Department, NHS Lothian" + }, + { + "author_name": "Jie Wang-Jairaj", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Robert J. Slack", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Lise Gravelle", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Bertil Lindmark", + "author_inst": "Galecto Inc." + }, + { + "author_name": "Kevin Dhaliwal", + "author_inst": "Centre for Inflammation Research, Edinburgh BioQuarter, University of Edinburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.12.19.21268028", "rel_title": "Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa", @@ -473719,161 +474678,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.18.21268003", - "rel_title": "Evaluation of the Implementation of the 4C Mortality Score in United Kingdom hospitals during the second pandemic wave", - "rel_date": "2021-12-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.18.21268003", - "rel_abs": "The 4C Mortality Score (4C Score) was designed to risk stratify hospitalised patients with COVID-19. We assessed inclusion of 4C Score in COVID-19 management guidance and its documentation in patients case notes in January 2021 in UK hospitals. 4C Score was included within guidance by 50% of sites, though score documentation in case notes was highly variable. Higher documentation of 4C Score was associated with score integration within admissions proformas, inclusion of 4C Score variables or link to online calculator, and management decisions. Integration of 4C Score within clinical pathways may encourage more widespread use.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Andrew E Blunsum", - "author_inst": "Queen Elizabeth University Hospital, Glasgow" - }, - { - "author_name": "Jonathan S. Perkins", - "author_inst": "Queen Elizabeth University Hospital, Glasgow; Glasgow Royal Infirmary, Glasgow" - }, - { - "author_name": "Areeb Arshad", - "author_inst": "Forth Valley Royal Hospital, Larbert" - }, - { - "author_name": "Sukrit Bajpai", - "author_inst": "Queen Elizabeth University Hospital, Birmingham" - }, - { - "author_name": "Karen Barclay-Elliott", - "author_inst": "University Hospital Coventry, Coventry" - }, - { - "author_name": "Sanjita Brito-Mutunayagam", - "author_inst": "St. John's Hospital, Livingston" - }, - { - "author_name": "Rebecca Brooks", - "author_inst": "Addenbrooke's Hospital, Cambridge" - }, - { - "author_name": "Terrence Chan", - "author_inst": "Kingston Hospital, Kingston upon Thames" - }, - { - "author_name": "Dominic Coates", - "author_inst": "University Hospital Wishaw, Wishaw" - }, - { - "author_name": "Alina Corobana", - "author_inst": "St. George's Hospital, London" - }, - { - "author_name": "Tim Crocker-Buque", - "author_inst": "Royal Free Hospital, London" - }, - { - "author_name": "Terry John Evans", - "author_inst": "St. George's Hospital, London" - }, - { - "author_name": "Jasmine Gordon-Brown", - "author_inst": "University Hospital Hairmyres, East Kilbride" - }, - { - "author_name": "Berkin Hack", - "author_inst": "Newham University Hospital, London" - }, - { - "author_name": "Heather Hiles", - "author_inst": "Royal Hallamshire Hospital, Sheffield" - }, - { - "author_name": "Aakash Khanijau", - "author_inst": "Warrington Hospital, Warrington" - }, - { - "author_name": "Salina Lalwani", - "author_inst": "St. John's Hospital, Livingston; Edinburgh Royal Infirmary, Edinburgh" - }, - { - "author_name": "Clare Leong", - "author_inst": "Addenbrooke's Hospital, Cambridge" - }, - { - "author_name": "Kirsty MacKay", - "author_inst": "Lady Margaret Hospital, Millport; University Hospital Crosshouse, Kilmarnock; Arran War Memorial Hospital, Lamlash; University Hospital Ayr, Ayr" - }, - { - "author_name": "Catriona Macrae", - "author_inst": "University Hospital Monklands, Airdrie" - }, - { - "author_name": "Bryony Martin", - "author_inst": "Royal Alexandra Hospital, Paisley" - }, - { - "author_name": "Christopher A Martin", - "author_inst": "Leicester General Hospital, Leicester; Glenfield Hospital, Leicester; University of Leicester" - }, - { - "author_name": "Emily McKemey", - "author_inst": "Queen Elizabeth Hospital, Birmingham" - }, - { - "author_name": "Joshua Nazareth", - "author_inst": "Leicester General Hospital, Leicester; Glenfield Hospital, Leicester; Department of Respiratory Sciences University of Leicester" - }, - { - "author_name": "Daniel Pan", - "author_inst": "Glenfield Hospital, Leicester; Leicester Royal Infirmary, Leicester; Department of Respiratory Sciences, University of Leicester" - }, - { - "author_name": "Marcello Scopazzini", - "author_inst": "Victoria Hospital, Kirkcaldy" - }, - { - "author_name": "David Simons", - "author_inst": "University College Hospital, London" - }, - { - "author_name": "Sophie Swinhoe", - "author_inst": "Warrington Hospital, Warrington" - }, - { - "author_name": "Julia Thomas", - "author_inst": "Dumfries and Galloway Royal Infirmary, Dumfries; Galloway Community Hospital, Stranraer" - }, - { - "author_name": "Fiona Thorburn", - "author_inst": "Queen Elizabeth University Hospital, Glasgow" - }, - { - "author_name": "Sarah Walpole", - "author_inst": "Royal Victoria Infirmary, Newcastle" - }, - { - "author_name": "Esmie Warne", - "author_inst": "John Radcliffe Hospital, Oxford" - }, - { - "author_name": "Rory Wilson", - "author_inst": "Ninewells Hospital, Dundee" - }, - { - "author_name": "Alisdair MacConnachie", - "author_inst": "Queen Elizabeth University Hospital, Glasgow" - }, - { - "author_name": "Antonia Ho", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.18.21268032", "rel_title": "SARS-CoV-2 transmission potential and rural-urban disease burden disparities across Alabama, Louisiana, and Mississippi, March 2020 -- May 2021", @@ -474042,6 +474846,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.18.21267819", + "rel_title": "Knowledge, Attitude and Practices towards COVID 19 pandemic among homeless street young adults in Lusaka, Zambia: A Mixed Methods Approach", + "rel_date": "2021-12-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.18.21267819", + "rel_abs": "ObjectiveTo determine the knowledge, attitude and practices towards COVID-19 among homeless street young adults in Lusaka district, Zambia.\n\nMethodsA total of 89 young street adults aged between 16-35 years were sampled. A concurrent mixed methods approach was used, Structured questionnaires and focused group discussion, to achieve the objectives. STATA 13 was used to produce Descriptive statistics while thematic analysis was used to analyze the qualitative data.\n\nResultsMajority of the survey participants were male 67(78%), 55(62%) were single while 53(59%) had attained a Primary School Education. The majority of the participants received the COVID-19 information through the radio (61%). Only 44 (49%)% had adequate knowledge on Covid-19 of whom 70 (78.6%) had a positive attitude towards COVID-19. However, the 65(73%) had a low risk perception of contracting the disease. Further, 66 (74.2%) had a positive attitude towards the effectiveness of precautionary behaviors and measures. The finding also revealed that only 3(3.3%) had good practice towards the Covid-19 preventative measures overall with (SD:0).\n\nConclusionKnowledge and attitudes towards COVID-19 were quite high among homeless street adults. However, their good practices were alarmingly low. Specific strategies for them being a vulnerable group are required.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kahilu Samuyachi", + "author_inst": "Keeping Girls in School Project-Ministry of Education, Lusaka, Zambia" + }, + { + "author_name": "Mowa Zambwe", + "author_inst": "Workers Compensation Fund Control Board" + }, + { + "author_name": "Mutale Sampa", + "author_inst": "University of Zambia" + }, + { + "author_name": "Peter J. Chipimo", + "author_inst": "Zambia National Public Health Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.18.21268026", "rel_title": "Measurement of the extent of Anxiety and Depression that has occurred in college students due to the COVID 19 pandemic: An Survey based cross-sectional study.", @@ -475165,85 +476000,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sports medicine" }, - { - "rel_doi": "10.1101/2021.12.15.472450", - "rel_title": "QTQTN motif upstream of the furin-cleavage site plays key role in SARS-CoV-2 infection and pathogenesis.", - "rel_date": "2021-12-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.15.472450", - "rel_abs": "The furin cleavage site (FCS), an unusual feature in the SARS-CoV-2 spike protein, has been spotlighted as a factor key to facilitating infection and pathogenesis by increasing spike processing 1,2. Similarly, the QTQTN motif directly upstream of the FCS is also an unusual feature for group 2B coronaviruses (CoVs). The QTQTN deletion has consistently been observed in in vitro cultured virus stocks and some clinical isolates 3. To determine whether the QTQTN motif is critical to SARS-CoV-2 replication and pathogenesis, we generated a mutant deleting the QTQTN motif ({Delta}QTQTN). Here we report that the QTQTN deletion attenuates viral replication in respiratory cells in vitro and attenuates disease in vivo. The deletion results in a shortened, more rigid peptide loop that contains the FCS, and is less accessible to host proteases, such as TMPRSS2. Thus, the deletion reduced the efficiency of spike processing and attenuates SARS-CoV-2 infection. Importantly, the QTQTN motif also contains residues that are glycosylated4, and disruption its glycosylation also attenuates virus replication in a TMPRSS2-dependent manner. Together, our results reveal that three aspects of the S1/S2 cleavage site - the FCS, loop length, and glycosylation - are required for efficient SARS-CoV-2 replication and pathogenesis.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Michelle N Vu", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Kumari Lokugamage", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Jessica A Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Dionna Scharton", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Bryan A Johnson", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Stephanea Sotcheff", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Daniele Swetnam", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Craig Schindewolf", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "R Elias Alvarado", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Patricia A Crocquet-Valdes", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Kari Debbink", - "author_inst": "Bowie State University" - }, - { - "author_name": "Scott Weaver", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "David H Walker", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Andrew Laurence Routh", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "Kenneth S Plante", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Vineet D Menachery", - "author_inst": "University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.16.21266656", "rel_title": "White Matter Beta-Amyloid Precursor Protein Immunoreactivity in Autopsied Subjects With and Without COVID-19", @@ -475968,6 +476724,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.12.17.21267968", + "rel_title": "Patients' and carers' experiences of, and engagement with remote home monitoring services for COVID-19 patients: a rapid mixed-methods study", + "rel_date": "2021-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.17.21267968", + "rel_abs": "IntroductionRemote home monitoring models were implemented during the COVID-19 pandemic to shorten hospital length of stay, reduce unnecessary hospital admission, readmission and infection, and appropriately escalate care. Within these models, patients are asked to take and record readings and escalate care if advised. There is limited evidence on how patients and carers experience these services. This study aimed to evaluate patient experiences of, and engagement with, remote home monitoring models for COVID-19.\n\nMethodsA rapid mixed-methods study in England. We conducted a cross-sectional survey and interviews with patients and carers. Interview findings were summarised using rapid assessment procedures sheets and grouping data into themes (using thematic analysis). Survey data were analysed using descriptive statistics.\n\nResultsWe received 1069 surveys (18% response rate) and conducted interviews with patients (n=59) and carers (n=3). Care relied on support from staff members, and family/friends. Patients and carers reported positive experiences and felt that the service and human contact reassured them and was easy to engage with. Yet, some patients and carers identified problems with engagement. Engagement was influenced by: patient factors such as health and knowledge, support from family/friends and staff, availability and ease-of-use of informational and material resources (e.g. equipment), and service factors.\n\nConclusionRemote home monitoring models place responsibility on patients to self-manage symptoms in partnership with staff; yet many patients required support and preferred human contact (especially for identifying problems). Caring burden and experiences of those living alone, and barriers to engagement should be considered when designing and implementing remote home monitoring services.\n\nPatient or public contributionFor this evaluation, members of the study team met with service user and public members of the BRACE PPI group and Health and Care Panel and patient representatives from RSET in a series of workshops. These workshops informed study design, data collection tools, data interpretation and to discuss study dissemination for Phase 2. For example, patient facing documents, such as the consent form, topic guides, patient survey and patient information sheet were reviewed by this group. Additionally, PPI members helped to pilot patient surveys and interview guides with the research team. We also asked some members of the public to pilot the patient survey. Members of the PPI group were given the opportunity to comment on the manuscript. One PPI member commented on the manuscript and the manuscript was amended accordingly.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Holly Walton", + "author_inst": "University College London" + }, + { + "author_name": "Cecilia Vindrola-Padros", + "author_inst": "University College London" + }, + { + "author_name": "Nadia Crellin", + "author_inst": "Nuffield Trust" + }, + { + "author_name": "Manbinder S Sidhu", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Lauren Herlitz", + "author_inst": "University College London" + }, + { + "author_name": "Ian Litchfield", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Jo Ellins", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Pei Li Ng", + "author_inst": "University College London" + }, + { + "author_name": "Efthalia Massou", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Sonila M Tomini", + "author_inst": "University College London" + }, + { + "author_name": "Naomi J Fulop", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.12.16.21267932", "rel_title": "A Single Dose of COVID-19 mRNA Vaccine Induces Airway Immunity in COVID-19 Convalescent Patients", @@ -477435,61 +478250,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.14.21267764", - "rel_title": "Machine learning identified distinct serum lipidomic signatures in hospitalized COVID-19-positive and COVID-19-negative patients", - "rel_date": "2021-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267764", - "rel_abs": "BackgroundLipids are involved in the interaction between viral infection and the host metabolic and immunological response. Several studies comparing the lipidome of COVID-19-positive hospitalized patients vs. healthy subjects have already been reported. It is largely unknown, however, whether these differences are specific to this disease. The present study compared the lipidomic signature of hospitalized COVID-19-positive patients with that of healthy subjects, and with COVID-19-negative patients hospitalized for other infectious/inflammatory diseases. Potential COVID-19 biomarkers were identified.\n\nMethodsWe analyzed the lipidomic signature of 126 COVID-19-positive patients, 45 COVID-19-negative patients hospitalized with other infectious/inflammatory diseases and 50 healthy volunteers. Results were interpreted by machine learning.\n\nResultsWe identified acylcarnitines, lysophosphatidylethanolamines, arachidonic acid and oxylipins as the most altered species in COVID-19-positive patients compared to healthy volunteers. However, we found similar alterations in COVID-19-negative patients. By contrast, we identified lysophosphatidylcholine 22:6-sn2, phosphatidylcholine 36:1 and secondary bile acids as the parameters that had the greatest capacity to discriminate between COVID-19-positive and COVID-19-negative patients.\n\nConclusionThis study shows that COVID-19 infection shares many lipid alterations with other infectious/inflammatory diseases, but differentiating them from the healthy population. Also, we identified some lipid species the alterations of which distinguish COVID-19-positive from Covid-19-negative patients. Our results highlight the value of integrating lipidomics with machine learning algorithms to explore the pathophysiology of COVID-19 and, consequently, improve clinical decision making.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Helena Castane", - "author_inst": "Universitat Rovira i Virgili" - }, - { - "author_name": "Simona Iftimie", - "author_inst": "Universitat Rovira i Virgili" - }, - { - "author_name": "Gerard Baiges-Gaya", - "author_inst": "Universitat Rovira i Virgili" - }, - { - "author_name": "Elisabet Rodriguez-Tomas", - "author_inst": "Universitat Rovira i Virgili" - }, - { - "author_name": "Andrea Jimenez-Franco", - "author_inst": "Universitat Rovira i Virgili" - }, - { - "author_name": "Ana Felisa Lopez-Azcona", - "author_inst": "Universitat Rovira i Virgili" - }, - { - "author_name": "Pedro Garrido", - "author_inst": "Universitat Rovira i Virgili" - }, - { - "author_name": "Antoni Castro", - "author_inst": "Universitat Rovira i Virgili" - }, - { - "author_name": "Jordi Camps", - "author_inst": "Hospital Universitari Sant Joan de Reus" - }, - { - "author_name": "Jorge Joven", - "author_inst": "Universitat Rovira i Virgili" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.14.21267750", "rel_title": "The role of sub-genomic RNA in discordant results from RT-PCR tests for COVID-19.", @@ -477646,6 +478406,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2021.12.16.21267902", + "rel_title": "Waning of mRNA-1273 vaccine effectiveness against SARS-CoV-2 infection in Qatar", + "rel_date": "2021-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.16.21267902", + "rel_abs": "BACKGROUNDIn early 2021, Qatar launched a mass immunization campaign with Modernas mRNA-1273 COVID-19 vaccine. We assessed persistence of real-world mRNA-1273 effectiveness against SARS-CoV-2 infection and against COVID-19 hospitalization and death.\n\nMETHODSEffectiveness was estimated using test-negative, case-control study design, between January 1 and December 5, 2021. Effectiveness was estimated against documented infection (a PCR-positive swab, regardless symptoms), and against any severe (acute-care hospitalization), critical (ICU hospitalization), or fatal COVID-19.\n\nRESULTSBy December 5, 2021, 2,962 breakthrough infections had been recorded among those who received two mRNA-1273 doses. Of these infections, 19 progressed to severe COVID-19 and 4 to critical, but none to fatal disease. mRNA-1273 effectiveness against infection was negligible for the first two weeks after the first dose, increased to 65.5% (95% CI: 62.7-68.0%) 14 or more days after the first dose, and reached its peak at about 90% in the first three months after the second dose. Effectiveness declined gradually starting from the fourth month after the second dose and was below 50% by the 7th month after the second dose. Effectiveness against severe, critical, or fatal COVID-19 reached its peak at essentially 100% right after the second dose, and there was no evidence for declining effectiveness over time. Effectiveness against symptomatic versus asymptomatic infection demonstrated the same pattern of waning, but effectiveness against symptomatic infection was consistently higher than that against asymptomatic infection and waned more slowly.\n\nCONCLUSIONSmRNA-1273-induced protection against infection appears to wane month by month after the second dose. Meanwhile, protection against hospitalization and death appears robust with no evidence for waning for several months after the second dose.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Houssein H. Ayoub", + "author_inst": "Qatar University" + }, + { + "author_name": "HADI M. YASSINE", + "author_inst": "Qatar University" + }, + { + "author_name": "Fatiha Benslimane", + "author_inst": "Qatar University" + }, + { + "author_name": "Heba A. Al Khatib", + "author_inst": "Qatar University" + }, + { + "author_name": "Patrick Tang", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Mohammad Rubayet Hasan", + "author_inst": "Sidra Medicine" + }, + { + "author_name": "Peter Coyle", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Zaina Al Kanaani", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Einas Al Kuwari", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hanan F. Abdul Rahim", + "author_inst": "Qatar University" + }, + { + "author_name": "Gheyath Nasrallah", + "author_inst": "Qatar University" + }, + { + "author_name": "Mohamed Ghaith Al Kuwari", + "author_inst": "Primary Health Care Corporation" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Hamad Eid Al Romaihi", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health" + }, + { + "author_name": "Abdullatif Al Khal", + "author_inst": "Hamad Medical Corporation" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.16.21267703", "rel_title": "Evaluation of SARS-CoV-2 Antibody Point of Care Devices in the Laboratory and Clinical Setting", @@ -479560,61 +480427,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.12.14.472657", - "rel_title": "Development and Characterization of Recombinant Vesicular Stomatitis Virus (rVSV)-based Bivalent Vaccine Against COVID-19 Delta Variant and Influenza Virus", - "rel_date": "2021-12-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.14.472657", - "rel_abs": "COVID-19 and influenza are both highly contagious respiratory diseases with a wide range of severe symptoms and cause great disease burdens globally. It has become very urgent and important to develop a bivalent vaccine that is able to target these two infectious diseases simultaneously. In this study, we generated three attenuated replicating recombinant VSV (rVSV) vaccine candidates. These rVSV-based vaccines co-express SARS-CoV-2 Delta variant spike protein (SP) or the receptor binding domain (RBD) and four copies of the highly conserved M2 ectodomain (M2e) of influenza A fused with the Ebola glycoprotein DC-targeting/activation domain. Animal studies have shown that immunization with these bivalent rVSV vaccines induced efficient but variable levels of humoral and cell-mediated immune responses against both SARS-CoV-2 and influenza M2e protein. Significantly, our vaccine candidates induced production of high levels of neutralizing antibodies that protected cells against SARS-CoV-2 Delta and other SP-pseudovirus infections in culture. Furthermore, vaccination with the bivalent VSV vaccine via either intramuscular or intranasal route efficiently protected mice from the lethal challenge of H1N1 and H3N2 influenza viruses and significantly reduced viral load in the lungs. These studies provide convincing evidence for the high efficacy of this bivalent vaccine to prevent influenza replication and initiate robust immune responses against SARS-CoV-2 Delta variants. Further investigation of its efficacy to protect against SARS-CoV-2 Delta variants will provide substantial evidence for new avenues to control two contagious respiratory infections, COVID-19 and influenza.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Zhujun Ao", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Maggie Jing Ouyang", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Titus Abiola Olukitibi", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Bryce Warner", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Robert Vendramelli", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Thang Truong", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Manli Zhang", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Keith R Fowke", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Darwyn Kobasa", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Xiaojian Yao", - "author_inst": "University of Manitoba" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.14.472585", "rel_title": "Compared with SARS-CoV2 wild type's spike protein, the SARS-CoV2 omicron's receptor binding motif has adopted a more SARS-CoV1 and/or bat/civet-like structure.", @@ -479779,6 +480591,217 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.13.21267368", + "rel_title": "Acute COVID-19 severity and 16-month mental morbidity trajectories in patient populations of six nations", + "rel_date": "2021-12-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267368", + "rel_abs": "BACKGROUNDThe aim of this multinational study was to assess the development of adverse mental health symptoms among individuals diagnosed with COVID-19 in the general population by acute infection severity up to 16 months after diagnosis.\n\nMETHODSParticipants consisted of 247 249 individuals from seven cohorts across six countries (Denmark, Estonia, Iceland, Norway, Scotland, and Sweden) recruited from April 2020 through August 2021. We used multivariable Poisson regression to contrast symptom-prevalence of depression, anxiety, COVID-19 related distress, and poor sleep quality among individuals with and without a diagnosis of COVID-19 at entry to respective cohorts by time (0-16 months) from diagnosis. We also applied generalised estimating equations (GEE) analysis to test differences in repeated measures of mental health symptoms before and after COVID-19 diagnosis among individuals ever diagnosed with COVID-19 over time.\n\nFINDINGSA total of 9979 individuals (4%) were diagnosed with COVID-19 during the study period and presented overall with a higher symptom burden of depression (prevalence ratio [PR] 1{middle dot}18, 95% confidence interval [95% CI] 1{middle dot}03-1{middle dot}36) and poorer sleep quality (1{middle dot}13, 1{middle dot}03-1{middle dot}24) but not with higher levels of symptoms of anxiety or COVID-19 related distress compared with individuals without a COVID-19 diagnosis. While the prevalence of depression and COVID-19 related distress attenuated with time, the trajectories varied significantly by COVID-19 acute infection severity. Individuals diagnosed with COVID-19 but never bedridden due to their illness were consistently at lower risks of depression and anxiety (PR 0{middle dot}83, 95% CI 0{middle dot}75-0{middle dot}91 and 0{middle dot}77, 0{middle dot}63-0{middle dot}94, respectively), while patients bedridden for more than 7 days were persistently at higher risks of symptoms of depression and anxiety (PR 1{middle dot}61, 95% CI 1{middle dot}27-2{middle dot}05 and 1{middle dot}43, 1{middle dot}26-1{middle dot}63, respectively) throughout the 16-month study period.\n\nCONCLUSIONAcute infection severity is a key determinant of long-term mental morbidity among COVID-19 patients.", + "rel_num_authors": 49, + "rel_authors": [ + { + "author_name": "Ingibjorg Magnusdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Aniko Lovik", + "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Anna Bara Unnarsdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Daniel L. McCartney", + "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK" + }, + { + "author_name": "Helga Ask", + "author_inst": "Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway" + }, + { + "author_name": "Kadri Koiv", + "author_inst": "Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia" + }, + { + "author_name": "Lea Arregui Nordahl Christoffersen", + "author_inst": "Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Sverre Urnes Johnson", + "author_inst": "Department of Psychology, University of Oslo, Oslo, Norway" + }, + { + "author_name": "Andrew M McIntosh", + "author_inst": "Division of Psychiatry, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Anna K. Kahler", + "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Archie Campbell", + "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK" + }, + { + "author_name": "Arna Hauksdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Chloe Fawns-Ritchie", + "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK" + }, + { + "author_name": "Christian Erikstrup", + "author_inst": "Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark" + }, + { + "author_name": "Dorte Helenius", + "author_inst": "Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Drew Altschul", + "author_inst": "Department of Psychology, University of Edinburgh, Edinburgh, UK" + }, + { + "author_name": "Edda Bjork Thordardottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Elias Eythorsson", + "author_inst": "Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Emma M. Frans", + "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Gunnar Tomasson", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Harpa Lind Jonsdottir", + "author_inst": "Faculty of Psychology, University of Iceland School of Health Sciences, Reykjavik, Iceland" + }, + { + "author_name": "Harpa Runarsdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Henrik Hjalgrim", + "author_inst": "Danish Cancer Society Research Center, Copenhagen, Denmark" + }, + { + "author_name": "Hronn Hardardottir", + "author_inst": "Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Juan Gonzalez-Hijon", + "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Karina Banasik", + "author_inst": "Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark" + }, + { + "author_name": "Khoa Manh Dinh", + "author_inst": "Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark" + }, + { + "author_name": "Li Lu", + "author_inst": "Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway" + }, + { + "author_name": "Lili Milani", + "author_inst": "Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia" + }, + { + "author_name": "Lill Trogstad", + "author_inst": "Division of Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway" + }, + { + "author_name": "Maria Didriksen", + "author_inst": "Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Omid V. Ebrahimi", + "author_inst": "Department of Psychology, University of Oslo, Oslo, Norway" + }, + { + "author_name": "Patrick F. Sullivan", + "author_inst": "Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, North Carolina, USA" + }, + { + "author_name": "Per Minor Magnus", + "author_inst": "Centre of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway" + }, + { + "author_name": "Qing Shen", + "author_inst": "Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Ragnar Nesvag", + "author_inst": "Department of Mental Disorders, Norwegian Institute of Public Health, Oslo, Norway." + }, + { + "author_name": "Reedik Magi", + "author_inst": "Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia" + }, + { + "author_name": "Runolfur Palsson", + "author_inst": "Landspitali - The National University Hospital of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Sisse Rye Ostrowski", + "author_inst": "Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Thomas Werge", + "author_inst": "Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Asle Hoffart", + "author_inst": "Department of Psychology, University of Oslo, Oslo, Norway" + }, + { + "author_name": "David J. Porteous", + "author_inst": "Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, UK" + }, + { + "author_name": "Fang Fang", + "author_inst": "Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Johanna Jakobsdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Kelli Lehto", + "author_inst": "Estonian Genome Centre, Institute of Genomics, University of Tartu, Estonia" + }, + { + "author_name": "Ole A. Andreassen", + "author_inst": "NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway" + }, + { + "author_name": "Ole B.V. Pedersen", + "author_inst": "Department of Clinical Immunology, Zealand University Hospital, Denmark" + }, + { + "author_name": "Thor Aspelund", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + }, + { + "author_name": "Unnur Anna Valdimarsdottir", + "author_inst": "Centre of Public Health Sciences, Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.14.21267418", "rel_title": "COVID-19 vaccination and Guillain-Barre syndrome: analyses using the National Immunoglobulin Database", @@ -481726,33 +482749,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.12.12.21267672", - "rel_title": "Vaccination is reasonably effective in limiting the spread of COVID-19 infections, hospitalizations and deaths with COVID-19", - "rel_date": "2021-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.12.21267672", - "rel_abs": "This paper uses large cross-country data for 110 countries to examine the effectiveness of COVID vaccination coverage. Our results confirm that vaccines are reasonably effective in both limiting the spread of infections and containing more severe disease progression in symptomatic patients. First, the results show that full vaccination rate is consistently negatively correlated with the number of new COVID cases, whereby a 10 percent increase in vaccination rate is associated with a 1.3 to 1.7 percent decrease in new COVID cases. Second, the magnitude of vaccination is shown to contribute significantly to moderating severe disease progression. On average, a 10 percent increase in the rate of vaccination leads to a reduction of about 5 percent in the number of new hospitalizations, 12 percent decrease in the number of new intensive care patients and 2 percent reduction in the number of new deaths. Finally, by comparing the data for the same period between 2020 and 2021, we also check how good is vaccination as a substitute for lockdowns or other stringent government protection measures. Results suggest that vaccination does not appear to be an effective substitute for more stringent government safety measures to contain the spread of COVID infections until a high vaccination coverage threshold (more than 70 percent) has been achieved. On the other hand, vaccination is shown to be quite effective in limiting the more severe course of the disease in symptomatic patients already at moderate vaccination coverage (between 40 and 70 percent). This suggests that vaccination can also help to reduce pressure on the health system and thus benefit the overall public health of society.\n\nSummaryO_ST_ABSBackgroundC_ST_ABSUsing a simple descriptive analysis, in a recent paper Subramanian and Kumar (2021) claim that the increase in COVID-19 cases is not related to levels of vaccination across 68 countries and US counties. We demonstrate that this type of analysis, based on only one data point per country and without rigorous analysis of the dynamics of the pandemic and vaccination, is far too simplistic and inevitably leads to false conclusions that are not justified by the data. Using large cross-country data for 110 countries, we estimate two complex models to examine the impact of vaccination coverage on the spread of COVID infections and on the course of severe COVID disease.\n\nMethodsWe use daily COVID-related data for 110 countries (from Our World in Data) for the period from August 1, 2021 onwards to estimate two comprehensive models - one for the impact on the spread of COVID infections (in terms of number of new confirmed cases) and another one for the impact on severe COVID disease progression (in terms of number of new hospitalizations, admissions to intensive care and deaths). In estimating the vaccines effectiveness, the models capture the differences across countries regarding the state of epidemics and its dynamics, the timing of full vaccination, and country-specific factors. The latter account for differences between countries that determine countries specific vulnerabilities or strengths in response to the pandemic.\n\nOur data are structured as panel data with a cross-sectional (country) and time (week) dimension. Both models are estimated using a pooled ordinary least squares (OLS) estimator. We first estimate our baseline models and then proceed with two alternative model specifications to examine to what extent vaccination can serve as a substitute for more stringent government protective measures.\n\nFindingsOur results confirm that vaccines are reasonably effective in both limiting the spread of infections and containing more severe disease progression in symptomatic patients. First, we show that full vaccination rate is consistently negatively correlated with the number of new COVID cases, whereby a 10 percent increase in vaccination rate is associated with a 1.3 to 1.7 percent decrease in new COVID cases. Second, the estimations show that the magnitude of vaccination contributes significantly to moderating severe disease progression. On average, a 10 percent increase in the rate of vaccination leads to about a 5 percent reduction in the number of new hospitalizations, 12 percent decrease in the number of new intensive care patients and 2 percent reduction in the number of new deaths associated with COVID. Third, the estimations confirm that the moderating effect of vaccines on the number of cases and deaths occurs when the vaccination rate is sufficiently high. Finally, by comparing the data for the same period between 2020 and 2021, we also check how good a substitute vaccination is for lockdowns or less stringent government protection measures. Our results suggest that vaccination does not appear to be an effective substitute for more stringent government safety measures to contain the spread of COVID infections until a high vaccination coverage threshold (more than 70 percent) has been achieved. On the other hand, vaccination is shown to be quite effective in limiting the more severe course of the disease in symptomatic patients already at moderate vaccination coverage (between 40 and 70 percent).\n\nInterpretationOur results show that vaccines are effective in both limiting the spread of infection and containing a more severe course of disease in symptomatic patients. High vaccination coverage has been shown to be a reasonably effective tool and may serve in part as a substitute for more stringent government protective measures. In this way, it can also help to reduce pressure on the health system and thus benefit the overall public health of society during such severe pandemics.\n\nFundingEuropean Union Horizon 2020 grant (GROWINPRO, Grant Agreement No. 822781)", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Joze P. Damijan", - "author_inst": "University of Ljubljana" - }, - { - "author_name": "Sandra Damijan", - "author_inst": "University of Ljubljana" - }, - { - "author_name": "Crt Kostevc", - "author_inst": "University of Ljubljana" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.13.21267725", "rel_title": "Vaccine breakthrough and the invasion dynamics of SARS-CoV-2 variants", @@ -481881,6 +482877,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.10.21267574", + "rel_title": "Safety and immunogenicity of a heterologous booster of protein subunit vaccine MVC-COV1901 after two doses of adenoviral vector vaccine AZD1222", + "rel_date": "2021-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267574", + "rel_abs": "We report the interim safety and immunogenicity results in participants administrated with a booster dose of protein subunit vaccine MVC-COV1901 at 12 or 24 weeks after two doses of AZD1222 (ChAdOx1 nCoV-19). In subjects fully vaccinated with two doses of AZD1222, waning antibody immunity was apparent within six months of the second dose of AZD1222. At one month after the MVC-COV1901 booster dose, anti-SARS-CoV-2 spike IgG antibody titers and neutralizing antibody titers were 14- and 8.6-fold increased, respectively, when compared to the titer levels on the day of the booster dose. We also observed 5.2- and 5.6-fold increases in neutralizing titer levels against wildtype and Omicron variant pseudovirus after the booster dose, respectively. These interim results support the use of MVC-COV1901 as a heterologous booster for individuals vaccinated with AZD1222.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shu-Hsing Cheng", + "author_inst": "Taoyuan General Hospital" + }, + { + "author_name": "Yi-Chun Lin", + "author_inst": "Taoyuan General Hospital" + }, + { + "author_name": "Cheng-Pin Chen", + "author_inst": "Taoyuan General Hospital" + }, + { + "author_name": "Chien-Yu Cheng", + "author_inst": "Taoyuan General Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.10.21267582", "rel_title": "Echinacea purpurea for the Long-term Prevention of Viral Respiratory Tract Infections during COVID-19 Pandemic: A Randomized, Open, Controlled, Exploratory Clinical Study", @@ -483600,89 +484627,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.14.21267755", - "rel_title": "mRNA-based COVID-19 vaccine boosters induce neutralizing immunity against SARS-CoV-2 Omicron variant", - "rel_date": "2021-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267755", - "rel_abs": "Recent surveillance has revealed the emergence of the SARS-CoV-2 Omicron variant (BA.1/B.1.1.529) harboring up to 36 mutations in spike protein, the target of vaccine-induced neutralizing antibodies. Given its potential to escape vaccine-induced humoral immunity, we measured neutralization potency of sera from 88 mRNA-1273, 111 BNT162b, and 40 Ad26.COV2.S vaccine recipients against wild type, Delta, and Omicron SARS-CoV-2 pseudoviruses. We included individuals that were vaccinated recently (<3 months), distantly (6-12 months), or recently boosted, and accounted for prior SARS-CoV-2 infection. Remarkably, neutralization of Omicron was undetectable in most vaccinated individuals. However, individuals boosted with mRNA vaccines exhibited potent neutralization of Omicron only 4-6-fold lower than wild type, suggesting that boosters enhance the cross-reactivity of neutralizing antibody responses. In addition, we find Omicron pseudovirus is more infectious than any other variant tested. Overall, this study highlights the importance of boosters to broaden neutralizing antibody responses against highly divergent SARS-CoV-2 variants.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Wilfredo F Garcia-Beltran", - "author_inst": "The Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "Kerri J. St Denis", - "author_inst": "The Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Angelique Hoelzemer", - "author_inst": "First Department of Internal Medicine, Division of Infectious Diseases, University Medical Centre Eppendorf, Hamburg, Germany" - }, - { - "author_name": "Evan C. Lam", - "author_inst": "The Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Adam D. Nitido", - "author_inst": "The Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Maegan L. Sheehan", - "author_inst": "The Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Cristhian Berrios", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Onosereme Ofoman", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Christina C. Chang", - "author_inst": "Center for the AIDS Programme of Research in South Africa, Durban" - }, - { - "author_name": "Blake M. Hauser", - "author_inst": "The Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Jared Feldman", - "author_inst": "The Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "David J. Gregory", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Mark C. Poznansky", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Aaron G. Schmidt", - "author_inst": "The Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "A. John Iafrate", - "author_inst": "Massassachusetts General Hospital" - }, - { - "author_name": "Vivek Naranbhai", - "author_inst": "Massachusetts General Hospital/ Dana Farber Cancer Institute" - }, - { - "author_name": "Alejandro B. Balazs", - "author_inst": "The Ragon Institute of MGH, MIT and Harvard" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.14.21267769", "rel_title": "mRNA booster immunization elicits potent neutralizing serum activity against the SARS-CoV-2 Omicron variant", @@ -483983,6 +484927,141 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.11.472236", + "rel_title": "Isolation and comparative analysis of antibodies that broadly neutralize sarbecoviruses", + "rel_date": "2021-12-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.11.472236", + "rel_abs": "The devastation caused by SARS-CoV-2 has made clear the importance of pandemic preparedness. To address future zoonotic outbreaks due to related viruses in the sarbecovirus subgenus, we identified a human monoclonal antibody, 10-40, that neutralized or bound all sarbecoviruses tested in vitro and protected against SARS-CoV-2 and SARS-CoV in vivo. Comparative studies with other receptor-binding domain (RBD)-directed antibodies showed 10-40 to have the greatest breadth against sarbecoviruses and thus its promise as an agent for pandemic preparedness. Moreover, structural analyses on 10-40 and similar antibodies not only defined an epitope cluster in the inner face of the RBD that is well conserved among sarbecoviruses, but also uncovered a new antibody class with a common CDRH3 motif. Our analyses also suggested that elicitation of this class of antibodies may not be overly difficult, an observation that bodes well for the development of a pan-sarbecovirus vaccine.\n\nOne sentence summaryA monoclonal antibody that neutralizes or binds all sarbecoviruses tested and represents a reproducible antibody class.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Lihong Liu", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Sho Iketani", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Yicheng Guo", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Ryan Casner", + "author_inst": "Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA" + }, + { + "author_name": "Eswar Reddem", + "author_inst": "Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA" + }, + { + "author_name": "Manoj S. Nair", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Jian Yu", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Jasper Chan", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Maple Wang", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Gabriele Cerutti", + "author_inst": "Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA" + }, + { + "author_name": "Zhiteng Li", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Candace Castagna", + "author_inst": "Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA" + }, + { + "author_name": "Laura Corredor", + "author_inst": "Institute of Comparative Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA" + }, + { + "author_name": "Hin Chu", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Shuofeng Yuan", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Vincent Poon", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Chris Chan", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Zhiwei Chen", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Yang Luo", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Marcus Cunningham", + "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA" + }, + { + "author_name": "Alejandro Chavez", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA" + }, + { + "author_name": "Michael Yin", + "author_inst": "Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA" + }, + { + "author_name": "David Perlin", + "author_inst": "Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA" + }, + { + "author_name": "Moriya Tsuji", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Kwok-Yung Yuen", + "author_inst": "State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University" + }, + { + "author_name": "Peter Kwong", + "author_inst": "Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA" + }, + { + "author_name": "Zizhang Sheng", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Yaoxing Huang", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + }, + { + "author_name": "Lawrence Shapiro", + "author_inst": "Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA" + }, + { + "author_name": "David D. Ho", + "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.13.21267761", "rel_title": "SARS-CoV-2 Omicron variant escapes neutralization by vaccinated and convalescent sera and therapeutic monoclonal antibodies", @@ -485334,93 +486413,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.12.472252", - "rel_title": "Improved neutralization of the SARS-CoV-2 Omicron variant after Pfizer-BioNTech BNT162b2 COVID-19 vaccine boosting", - "rel_date": "2021-12-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.12.472252", - "rel_abs": "In late November 2021, the World Health Organization declared the SARS-CoV-2 lineage B.1.1.529 the fifth variant of concern, Omicron. This variant has acquired 15 mutations in the receptor binding domain of the spike protein, raising concerns that Omicron could evade naturally acquired and vaccine-derived immunity. We utilized an authentic virus, multicycle neutralisation assay to demonstrate that sera collected one, three and six months post-two doses of Pfizer-BioNTech BNT162b2 has a limited ability to neutralise SARS-CoV-2. However, four weeks after a third dose, neutralising antibody titres are boosted. Despite this increase, neutralising antibody titres are reduced four-fold for Omicron compared to lineage A.2.2 SARS-CoV-2.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Kerri Basile", - "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospi" - }, - { - "author_name": "Rebecca J Rockett", - "author_inst": "Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead New South Wales 2145, Australia" - }, - { - "author_name": "Kenneth McPhie", - "author_inst": "Westmead Institute for Medical Research, Westmead, New South Wales 2145, Australia" - }, - { - "author_name": "Michael Fennell", - "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospi" - }, - { - "author_name": "Jessica Johnson-Mackinnon", - "author_inst": "Sydney Institute for Infectious Diseases, The University of Sydney New South Wales 2006, Australia" - }, - { - "author_name": "Jessica Agius", - "author_inst": "Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead New South Wales 2145, Australia" - }, - { - "author_name": "Winkie Fong", - "author_inst": "Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead New South Wales 2145, Australia" - }, - { - "author_name": "Hossinur Rahman", - "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospi" - }, - { - "author_name": "Danny Ko", - "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospi" - }, - { - "author_name": "Linda Donavan", - "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospi" - }, - { - "author_name": "Linda Hueston", - "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospi" - }, - { - "author_name": "Connie Lam", - "author_inst": "Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead New South Wales 2145, Australia" - }, - { - "author_name": "Alicia Arnott", - "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospi" - }, - { - "author_name": "Sharon Chen", - "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospi" - }, - { - "author_name": "Susan Maddocks", - "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospi" - }, - { - "author_name": "Dominic E Dwyer", - "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospi" - }, - { - "author_name": "Vitali Sintchenko", - "author_inst": "Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Westmead New South Wales 2145, Australia" - }, - { - "author_name": "Jen Kok", - "author_inst": "Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead Hospi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.11.472202", "rel_title": "Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes", @@ -485597,6 +486589,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.12.472286", + "rel_title": "The Omicron variant is highly resistant against antibody-mediated neutralization - implications for control of the COVID-19 pandemic", + "rel_date": "2021-12-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.12.472286", + "rel_abs": "The rapid spread of the SARS-CoV-2 Omicron variant suggests that the virus might become globally dominant. Further, the high number of mutations in the viral spike-protein raised concerns that the virus might evade antibodies induced by infection or vaccination. Here, we report that the Omicron spike was resistant against most therapeutic antibodies but remained susceptible to inhibition by Sotrovimab. Similarly, the Omicron spike evaded neutralization by antibodies from convalescent or BNT162b2-vaccinated individuals with 10- to 44-fold higher efficiency than the spike of the Delta variant. Neutralization of the Omicron spike by antibodies induced upon heterologous ChAdOx1/BNT162b2-vaccination or vaccination with three doses of BNT162b2 was more efficient, but the Omicron spike still evaded neutralization more efficiently than the Delta spike. These findings indicate that most therapeutic antibodies will be ineffective against the Omicron variant and that double immunization with BNT162b2 might not adequately protect against severe disease induced by this variant.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Markus Hoffmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Nadine Kr\u00fcger", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Sebastian Schulz", + "author_inst": "Friedrich-Alexander-Universit\u00e4 Erlangen-N\u00fcrnberg" + }, + { + "author_name": "Anne Cossmann", + "author_inst": "Medizinische Hochschule Hannover" + }, + { + "author_name": "Cheila Rocha", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fc Primatenforschung" + }, + { + "author_name": "Amy Kempf", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Inga Nehlmeier", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Luise Graichen", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Anna-Sophie Moldenhauer", + "author_inst": "Deutsches Primatenzentrum - Leibniz Institut f\u00fcr Primatenforschung" + }, + { + "author_name": "Martin Sebastian Winkler", + "author_inst": "Universit\u00e4tsmedizin G\u00f6ttingen" + }, + { + "author_name": "Martin Lier", + "author_inst": "Universit\u00e4tsmedizin G\u00f6ttingen" + }, + { + "author_name": "Alexandra Dopfer-Jablonka", + "author_inst": "Medizinische Hochschule Hannover" + }, + { + "author_name": "Hans-Martin J\u00e4ck", + "author_inst": "Friedrich-Alexander-Universit\u00e4t Erlangen-N\u00fcrnberg" + }, + { + "author_name": "Georg Behrens", + "author_inst": "Medizinische Hochschule Hannover" + }, + { + "author_name": "Stefan P\u00f6hlmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut f\u00fcr Primatenforschung" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.09.471735", "rel_title": "The T cell receptor repertoire reflects the dynamics of the immune response to vaccination", @@ -487584,65 +488651,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.09.21267537", - "rel_title": "SARS-CoV-2 and endemic coronaviruses: Comparing symptom presentation and severity of symptomatic illness among Nicaraguan children", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267537", - "rel_abs": "It has been proposed that as SARS-CoV-2 transitions to endemicity, children will represent the greatest proportion of SARS-Co-V-2 infections as they currently do with endemic coronavirus infections. While SARS-CoV-2 infection severity is low for children, it is unclear if SARS-CoV-2 infections are distinct in symptom presentation, duration, and severity from endemic coronavirus infections in children. We compared symptom risk and duration of endemic human coronavirus (HCoV) infections from 2011-2016 with SARS-CoV-2 infections from March 2020-September 2021 in a Nicaraguan pediatric cohort. Blood samples were collected from study participants annually in February-April. Respiratory samples were collected from participants that met testing criteria. Blood samples collected in were tested for SARS-CoV-2 antibodies and a subset of 2011-2016 blood samples from four-year-old children were tested for endemic HCoV antibodies. Respiratory samples were tested for each of the endemic HCoVs from 2011-2016 and for SARS-CoV-2 from 2020-2021 via rt-PCR. By April 2021, 854 (49%) cohort participants were ELISA positive for SARS-CoV-2 antibodies. Most participants had antibodies against one alpha and one beta coronavirus by age four. We observed 595 symptomatic endemic HCoV infections from 2011-2016 and 121 symptomatic with SARS-CoV-2 infections from March 2020-September 2021. Symptom presentation of SARS-CoV-2 infection and endemic coronavirus infections were very similar, and SARS-CoV-2 symptomatic infections were as or less severe on average than endemic HCoV infections. This suggests that, for children, SARS-CoV-2 may be just another endemic coronavirus. However, questions about the impact of variants and the long-term effects of SARS-CoV-2 remain.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Aaron M Frutos", - "author_inst": "Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA" - }, - { - "author_name": "John Kubale", - "author_inst": "Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA" - }, - { - "author_name": "Guillermina Kuan", - "author_inst": "Health Center Socrates Flores Vivas, Ministry of Health, Managua, Nicaragua" - }, - { - "author_name": "Sergio Ojeda", - "author_inst": "Laboratorio Nacional de Virologia, Centro Nacional de Diagnostico y Referencia, Ministry of Health, Managua, Nicaragua" - }, - { - "author_name": "Nivea Vydiswaran", - "author_inst": "Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA" - }, - { - "author_name": "Nery Sanchez", - "author_inst": "Laboratorio Nacional de Virologia, Centro Nacional de Diagnostico y Referencia, Ministry of Health, Managua, Nicaragua" - }, - { - "author_name": "Miguel Plazaola", - "author_inst": "Laboratorio Nacional de Virologia, Centro Nacional de Diagnostico y Referencia, Ministry of Health, Managua, Nicaragua" - }, - { - "author_name": "May Patel", - "author_inst": "Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA" - }, - { - "author_name": "Roger Lopez", - "author_inst": "Laboratorio Nacional de Virologia, Centro Nacional de Diagnostico y Referencia, Ministry of Health, Managua, Nicaragua & Sustainable Sciences Institute, Managua" - }, - { - "author_name": "Angel Balmaseda", - "author_inst": "Laboratorio Nacional de Virologia, Centro Nacional de Diagnostico y Referencia, Ministry of Health, Managua, Nicaragua & Sustainable Sciences Institute, Managua" - }, - { - "author_name": "Aubree Gordon", - "author_inst": "Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.06.21267352", "rel_title": "Efficient mucosal antibody response to SARS-CoV-2 vaccination is induced in previously infected individuals", @@ -487843,6 +488851,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.10.21267338", + "rel_title": "Mental health indicators in Sweden over a 12-month period during the COVID-19 pandemic", + "rel_date": "2021-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267338", + "rel_abs": "BackgroundThe ongoing COVID-19 pandemic has had an unprecedented impact on the lives of people globally and is expected to have profound effects on mental health. Yet, self-reported large-scale online surveys on mental health are still relatively uncommon. Here we aim to describe the mental health burden experienced in Sweden using baseline data of the Omtanke2020 Study.\n\nMethodSelf-reported baseline data collected over a 12-month period (June 9, 2020-June 8, 2021) from the longitudinal online survey of the Omtanke2020 Study including 27,950 adults in Sweden. Participants were volunteers or actively recruited through existing cohorts and after providing informed consent responded to monthly online questionnaires on socio-demographics, mental and physical health, COVID-19 infection, and impact. Poisson regression was fitted to assess the relative risk of high mental health burden (depression, anxiety, and COVID-19 specific PTSD).\n\nResultThe overall proportion of persons with high level of symptoms was 15.6%, 9.5% and 24.5% for depression, anxiety, and COVID-19 specific PTSD, respectively. Overall, 43.4% of the participants had significant, clinically relevant symptoms for at least one mental health outcome and 7.3% had significant symptoms for all three outcomes. We also observed differences in the prevalence of these symptoms across strata of sex, age, recruitment type, COVID-19 status, region, and seasonality.\n\nConclusionWhile the proportion of persons with high mental health burden remains higher than in pre-pandemic publications, our estimates are lower than previously reported levels of depression, anxiety, and PTSD during the pandemic in Sweden and elsewhere.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Anik\u00f3 Lovik", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Juan Gonz\u00e1lez-Hij\u00f3n", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Anna K. K\u00e4hler", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Unnur A. Valdimarsd\u00f3ttir", + "author_inst": "University of Iceland, Karolinska Institutet" + }, + { + "author_name": "Emma M. Frans", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Nancy L. Pedersen", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Per Hall", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Kamila Czene", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Patrick F. Sullivan", + "author_inst": "University of North Carolina, Karolinska Institutet" + }, + { + "author_name": "Fang Fang", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.12.09.21267349", "rel_title": "Down-regulation of SARS-CoV-2 neutralizing antibodies in vaccinated smokers", @@ -489402,33 +490465,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.12.08.471777", - "rel_title": "Structural Insights of SARS-CoV-2 Spike Protein from Delta and Omicron Variants", - "rel_date": "2021-12-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.08.471777", - "rel_abs": "Given the continuing heavy toll of the COVID-19 pandemic and the emergence of the Delta (B.1.617.2) and Omicron (B.1.1.529) variants, the WHO declared both as variants of concern (VOC). There are valid concerns that the latest Omicron variant might have increased infectivity and pathogenicity. In addition, the sheer number of S protein mutations in the Omicron variant raise concerns of potential immune evasion and resistance to therapeutics such as monoclonal antibodies. However, structural insights that underpin the potential increased pathogenicity are unknown. Here we adopted an artificial intelligence (AI)-based approach to predict the structural changes induced by mutations of the Delta and Omicron variants in the spike (S) protein using Alphafold. This was followed by docking the human angiotensin-converting enzyme 2 (ACE2) with the predicted S proteins for Wuhan-Hu-1, Delta, and Omicron variants. Our in-silico structural analysis indicates that S protein for Omicron variant has a higher binding affinity to ACE-2 receptor, compared to Wuhan-Hu-1 and Delta variants. In addition, the recognition sites of the receptor binding domains for Delta and Omicron variants showed lower electronegativity compared to Wuhan-Hu-1. Importantly, further molecular insights revealed significant changes induced at fusion protein (FP) site, which may mediate enhanced viral entry. These results represent the first computational analysis of structural changes associated with Omicron variant using Alphafold, Collectively, our results highlight potential structural basis for enhanced pathogenicity of the Omicron variant, however further validation using X-ray crystallography and cryo-EM are warranted.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ali Sadek", - "author_inst": "Biology Program, Trinity School of Arts and Sciences, Duke University" - }, - { - "author_name": "David Zaha", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Mahmoud Salama Ahmed", - "author_inst": "UTSW: The University of Texas Southwestern Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.12.09.21267520", "rel_title": "First and Second Wave Dynamics of Emergency Department Utilization during the COVID-19 Pandemic: a retrospective study", @@ -489649,6 +490685,89 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.07.471590", + "rel_title": "A novel bacterial protease inhibitor adjuvant in RBD-based COVID-19 vaccine formulations increases neutralizing antibodies, specific germinal center B cells and confers protection against SARS-CoV-2 infection.", + "rel_date": "2021-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.07.471590", + "rel_abs": "In this work we evaluated recombinant receptor binding domain (RBD) based vaccine formulation prototypes with potential for further clinical development. We assessed different formulations containing RBD plus Alum, AddaS03, AddaVax or the combination of Alum and U-Omp19: a novel Brucella spp. protease inhibitor vaccine adjuvant. Results show that the vaccine formulation composed of U-Omp19 and Alum as adjuvants have a better performance: it significantly increased mucosal and systemic neutralizing antibodies in comparison to antigen plus Alum, AddaVax or AddaS03. Antibodies induced with the formulation containing U-Omp19 not only increased their neutralization capacity against the wild-type virus but also cross neutralized alpha, lambda and gamma variants with similar potency. Also, addition of U-Omp19 to vaccine formulation increased the frequency of RBD-specific geminal center B cells and plasmablasts. Additionally, U-Omp19+Alum formulation induced RBD-specific Th1 and CD8+ T cell responses in spleens and lungs. Finally, this vaccine formulation conferred protection against an intranasal SARS-CoV-2 challenge of K18-hACE2 mice.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Lorena M Coria", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Lucas M Saposnik", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Celeste Pueblas Castro", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Eliana F Castro", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Laura A Bruno", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "William B Stone", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Paula S Perez", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS, Universidad de Buenos Aires - CONICET)" + }, + { + "author_name": "M. Laura Darriba", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Lucia B Chemes", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Julieta Alcain", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Ignacio Mazzitelli", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS, Universidad de Buenos Aires - CONICET)" + }, + { + "author_name": "Augusto Varese", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS, Universidad de Buenos Aires - CONICET)" + }, + { + "author_name": "Melisa Salvatori", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS, Universidad de Buenos Aires - CONICET)" + }, + { + "author_name": "Albert J Auguste", + "author_inst": "Virginia Polytechnic Institute and State University" + }, + { + "author_name": "Diego E Alvarez", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Karina A Pasquevich", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + }, + { + "author_name": "Juliana Cassataro", + "author_inst": "Instituto de Investigaciones Biotecnologicas Dr. Rodolfo A. Ugalde, Universidad Nacional de San Martin, Consejo Nacional de Investigaciones Cientificas y Tecnic" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.08.471814", "rel_title": "Nanotrap Particles Improve Nanopore Sequencing of SARS-CoV-2 and Other Respiratory Viruses", @@ -490948,33 +492067,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.12.06.471525", - "rel_title": "A proteomic perspective and involvement of cytokines in SARS-CoV-2 infection", - "rel_date": "2021-12-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.06.471525", - "rel_abs": "Infection with the SARS-CoV-2 virus results in manifestation of several clinical observations from asymptomatic to multi-organ failure. Biochemically, the serious effects are due to what is described as cytokine storm. The initial infection region for COVID-19 is the nasopharyngeal/oropharyngeal region which is the site where samples are taken to examine the presence of virus. We have earlier shown that several defensin genes are down regulated in cells from this region in patients who tested positive in the RTPCR test. We have now carried out detailed proteomic analysis of the nasopharyngeal/oropharyngeal swab samples collected from normal individuals and those tested positive for SARS-CoV-2 by RTPCR, involving high throughput quantitative proteomics analysis. Several proteins like annexins, cytokines and histones were found differentially regulated in the host human cells following SARS-CoV-2 infection. Genes for these proteins were also observed to be differentially regulated when their expression was analyzed. Majority of the cytokine proteins were found to be up regulated in the infected individuals. Cell to Cell signaling interaction, Immune cell trafficking and inflammatory response pathways were found associated with the differentially regulated proteins based on network pathway analysis.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sarena Banu", - "author_inst": "CSIR-Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Mohammed M Idris", - "author_inst": "CSIR-Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Ramakrishnan Nagaraj", - "author_inst": "CSIR-Centre for Cellular and Molecular Biology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.12.06.471489", "rel_title": "Production of novel Spike truncations in Chinese hamster ovary cells", @@ -491199,6 +492291,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.06.471215", + "rel_title": "The influence of new SARS-CoV-2 variant Omicron (B.1.1.529) on vaccine efficacy, its correlation to Delta Variants: a computational approach", + "rel_date": "2021-12-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.06.471215", + "rel_abs": "The newly discovered COVID variant B.1.1.529 in Botswana has more than 30 mutations in spike and many other in non-spike proteins, far more than any other SARS-CoV-2 variant accepted as a variant of concern by the WHO and officially named Omicron, and has sparked concern among scientists and the general public. Our findings provide insights into structural modification caused by the mutations in the Omicrons receptor-binding domain and look into the effects on interaction with the hosts neutralising antibodies CR3022, B38, CB6, P2B-2F6, and REGN, as well as ACE2R using an in silico approach. We have employed secondary structure prediction, structural superimposition, protein disorderness, molecular docking, and MD simulation to investigate host-pathogen interactions, immune evasion, and transmissibility caused by mutations in the RBD region of the spike protein of the Omicron variant and compared it to the Delta variants (AY.1, AY.2, & AY.3) and wild type. Computational analysis revealed that the Omicron variant has a higher binding affinity for the human ACE2 receptor than the wild and Delta (AY.1 and AY.2 strains), but lower than the Delta AY.3 strain. MD simulation and docking analysis suggest that the omicron and Delta AY.3 were found to have relatively unstable and compact RBD structures and hampered interactions with antibodies more than wild and Delta (AY.1 and AY.2), which may lead to relatively more pathogenicity and antibody escape. In addition, we observed lower binding affinity of Omicron for human monoclonal antibodies (CR3022, B38, CB6, and P2B2F6) when compared to wild and Delta (AY.1 & AY.2). However, the binding affinity of Omicron RBD variants for CR3022, B38, and P2B2F6 antibodies is lower as compared to Delta AY.3, which might promote immune evasion and reinfection and needs further experimental investigation.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Prashant Ranjan", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Neha", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Chandra Devi", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Kaviyapriya Arulmozhi Devar", + "author_inst": "Banaras Hindu University" + }, + { + "author_name": "Parimal Das", + "author_inst": "Banaras Hindu University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.07.21267442", "rel_title": "Dynamic analysis and evaluation of asymptomatic infection in the spread of COVID-19", @@ -492766,213 +493893,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.05.21267318", - "rel_title": "A nonrandomized phase 2 trial of oral thymic peptides in hospitalized patients with Covid-19", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.05.21267318", - "rel_abs": "BackgroundCoronavirus disease 2019 (Covid-19) active cases continue to demand the development of safe and effective treatments. This is the first clinical trial to evaluate the safety and efficacy of oral thymic peptides.\n\nMethodsWe conducted a nonrandomized phase 2 trial with a historic control group to evaluate the safety and efficacy of a daily 250-mg oral dose of thymic peptides in the treatment of hospitalized Covid-19 patients. Comparison based on standard care from registry data was performed after propensity score matching. The primary outcomes were survival, time to recovery and the number of participants with treatment-related adverse events or side effects by day 20.\n\nResultsA total of 44 patients were analyzed in this study, 22 in the thymic peptides group and 22 in the standard care group. There were no deaths in the intervention group, compared to 24% mortality in standard care by day 20 (log-rank P=0.02). The Kaplan-Meier analysis showed a significantly shorter time to recovery by day 20 in the thymic peptides group as compared with standard care (median, 6 days vs. 12 days; hazard ratio for recovery, 2.75 [95% confidence interval, 1.34 to 5.62]; log-rank P=0.002). No side effects or adverse events were reported.\n\nConclusionIn patients hospitalized with Covid-19, the use of thymic peptides reported no side effects, adverse events, or deaths by day 20. When compared with registry data, a significantly shorter time to recovery and mortality reduction was measured. The Catholic University of Honduras Medical Research Group (GIMUNICAH) is working on a more extensive phase 3 trial.\n\nTrial registrationClinicalTrials.gov NCT04771013. February 25, 2021.", - "rel_num_authors": 48, - "rel_authors": [ - { - "author_name": "H\u00e9ctor M. Ramos-Zald\u00edvar", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)/ Pontificia Universidad Cat\u00f3lica de Chile" - }, - { - "author_name": "Karla G. Reyes-Perdomo", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)/ Universidad Mayor, Chile." - }, - { - "author_name": "Nelson A. Espinoza-Moreno", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Ernesto Tom\u00e1s Dox-Cruz", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Thania Camila Aguirre Urbina", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Astrid Yohaly Rivera Caballero", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Eduardo Smelin Perdomo Dominguez", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Sof\u00eda Guadalupe Pe\u00f1a Calix", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Joselin Michelle Monterroso-Reyes", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Erick Fernando Caballero V\u00e1squez", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Tarek Sai Zelaya Ortiz", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Hilbron Eduardo Rodr\u00edguez-Machado", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Marcelo Andres Forgas Solis", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Iveth Sebilla Silva", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Mauricio Edgardo Zavala Galeano", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Alejandro Antonio Morga Alvarado", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Angie Mar\u00eda Nicolle Sol\u00eds Medina", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Leticia M. Guerrero-D\u00edaz", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Julia E. Jim\u00e9nez-Faraj", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Caroll Alejandra Perell\u00f3 Santos", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)/Hospital del Valle" - }, - { - "author_name": "Wilberg A. Moncada Arita", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Darwing Fabricio Valdiviezo Montufar", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Josu\u00e9 David Hern\u00e1ndez Sabill\u00f3n", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "M\u00f3nica L. Sorto G.", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Xochilt Xiomara Padilla Navarro", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Victoria A. Palomo-Berm\u00fadez", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)/Hospital del Valle" - }, - { - "author_name": "H\u00e9ctor Armando Alvarenga Andino", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Sandra Patricia Reyes Guzman", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Mar\u00eda Haydee Rivera Reyes", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Esdras Said Medina Paz", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Joselyn Rosario Alvarado Enamorado", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Yenny Mariel Sabill\u00f3n Sagastume", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Ariadna Stephanny Mejia Rivera", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Claudia Michelle Posas Sarmiento", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Xenia Vanessa Jim\u00e9nez Pineda", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Ver\u00f3nica Alejandra Hern\u00e1ndez Puerto", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Josu\u00e9 David Portillo Landaverde", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Sergio Reyes S.", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Ivin Perdomo R.", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Josu\u00e9 J. Rivera", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Wendy Cecilia Mendoza Gir\u00f3n", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Karla Melissa Tr\u00f3chez Sabill\u00f3n", - "author_inst": "Hospital Santa B\u00e1rbara Integrado" - }, - { - "author_name": "Paola Nohemy Katsumata Leiva", - "author_inst": "Triaje de Santa B\u00e1rbara" - }, - { - "author_name": "Karla Elizabeth Pineda Toro", - "author_inst": "Triaje de Santa B\u00e1rbara" - }, - { - "author_name": "Jimena A. Montes-Gambarelli", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Cristhiam Flores", - "author_inst": "Grupo de Investigaci\u00f3n M\u00e9dica de la Universidad Cat\u00f3lica de Honduras (GIMUNICAH)" - }, - { - "author_name": "Edison Salas-Huenuleo", - "author_inst": "Advanced Integrated Technologies (AINTECH), Santiago, Chile" - }, - { - "author_name": "Marcelo E. Andia", - "author_inst": "Pontificia Universidad Cat\u00f3lica de Chile" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.04.471245", "rel_title": "SARS-CoV-2 infection of olfactory epithelial cells and neurons drives acute lung injury and lethal COVID-19 in mice", @@ -493241,6 +494161,33 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.12.05.471290", + "rel_title": "Constructing a multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and co-infecting microbes", + "rel_date": "2021-12-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.05.471290", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused millions of deaths worldwide. Many efforts have focused on unraveling the mechanism of the viral infection to develop effective strategies for treatment and prevention. Previous studies have provided some clarity on the protein-protein interaction linkages occurring during the life cycle of viral infection; however, we lack a complete understanding of the full interactome, comprising human miRNAs and protein-coding genes and co-infecting microbes. To comprehensively determine this, we developed a statistical modeling method using latent Dirichlet allocation (called MLCrosstalk, for multiple-layer crosstalk) to fuse many types of data to construct the full interactome of SARS-CoV-2. Specifically, MLCrosstalk is able to integrate samples with multiple layers of information (e.g., miRNA and microbes), enforce a consistent topic distribution on all data types, and infer individual-level linkages (i.e., differing between patients). We also implement a secondary refinement with network propagation to allow our microbe-gene linkages to address larger network structures (e.g., pathways). Using MLCrosstalk, we generated a list of genes and microbes linked to SARS-CoV-2. Interestingly, we found that two of the identified microbes, Rothia mucilaginosa and Prevotella melaninogenica, show distinct patterns representing synergistic and antagonistic relationships with the virus, respectively. We also identified several SARS-COV-2-associated pathways, including the VEGFA-VEGFR2 and immune response pathways, which may provide potential targets for drug design.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Shaoke Lou", + "author_inst": "Yale University" + }, + { + "author_name": "Tianxiao Li", + "author_inst": "Yale University" + }, + { + "author_name": "Mark Gerstein", + "author_inst": "Yale university" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.05.471277", "rel_title": "A zebrafish model of COVID-19-associated cytokine storm syndrome reveals differential proinflammatory activities of Spike proteins of SARS-CoV-2 variants of concern.", @@ -494724,33 +495671,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.06.21267360", - "rel_title": "Likely community transmission of COVID-19 infections between neighboring, persistent hotspots in Ontario, Canada", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21267360", - "rel_abs": "IntroductionThis study aimed to produce community-level geo-spatial mapping of confirmed COVID-19 cases in Ontario, Canada in near real-time to support decision-making. This was accomplished by area-to-area geostatistical analysis, space-time integration, and spatial interpolation of COVID-19 positive individuals.\n\nMethodsCOVID-19 cases and locations were curated for geostatistical analyses from March 2020 through June 2021, corresponding to the first, second, and third waves of infections. Daily cases were aggregated according to designated forward sortation area [FSA], and postal codes [PC] in municipal regions covering Hamilton, Kitchener/Waterloo, London, Ottawa, Toronto, and Windsor/Essex county. Hotspots were identified with area-to-area tests including Getis-Ord Gi*, Global Morans I spatial autocorrelation, and Local Morans I asymmetric clustering and outlier analyses. Case counts were also interpolated across geographic regions by Empirical Bayesian Kriging, which localizes high concentrations of COVID-19 positive tests, independent of FSA or PC boundaries. The Geostatistical Disease Epidemiology Toolbox, which is freely-available software, automates the identification of these regions and produces digital maps for public health professionals to assist in pandemic management of contact tracing and distribution of other resources.\n\nResults/DiscussionThis study provided indicators in real-time of likely, community-level disease transmission through innovative geospatial analyses of COVID-19 incidence data. Municipal and provincial results were validated by comparisons with known outbreaks at long-term care and other high density residences and on farms. PC-level analyses revealed hotspots at higher geospatial resolution than public reports of FSAs, and often sooner. Results of different tests and kriging were compared to determine consistency among hotspot assignments. Concurrent or consecutive hotspots in close proximity suggested potential community transmission of COVID-19 from cluster and outlier analysis of neighboring PCs and by kriging. Results were also stratified by population based-categories (sex, age, and presence/absence of comorbidities). Earlier recognition of hotspots could reduce public health burdens of COVID-19 and expedite contact tracing.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Eliseos J. Mucaki", - "author_inst": "CytoGnomix" - }, - { - "author_name": "Ben C. Shirley", - "author_inst": "CytoGnomix" - }, - { - "author_name": "Peter K Rogan", - "author_inst": "University of Western Ontario/CytoGnomix" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.05.21267315", "rel_title": "Might first-hand experience of ill-health and economic hardship during the COVID-19 pandemic strengthen public support for vaccination and the reallocation of health sector funding towards health emergency preparedness in South Africa?", @@ -494939,6 +495859,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.06.21267289", + "rel_title": "Testing the Validity of the Modified Vaccine Attitude Question Battery across 22 Languages with a Large-scale International Survey Dataset", + "rel_date": "2021-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21267289", + "rel_abs": "In this study, we tested the validity of the modified version of the Vaccine Attitude Question Battery (VAQB) across 22 different languages. Validity test was conducted with a large-scale international survey dataset, COVIDiSTRESSII Global Survey, collected from 20,601 participants from 62 countries. We employed exploratory and confirmatory factor analysis, measurement invariance test, and measurement alignment for internal validity test. Moreover, we examined correlation between the VAQB score, vaccination intent, compliance with preventive measures, and trust in public health-related agents. The results reported that the modified VAQB, which included five items, showed good validity across 22 languages with measurement alignment. Furthermore, the VAQB score showed negative association with vaccination intent, compliance, and trust as expected. The findings from this study provide additional evidence supporting the validity of the modified VAQB in 22 languages for future large-scale international research on COVID-19 and vaccination.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hyemin Han", + "author_inst": "University of Alabama" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.06.21267101", "rel_title": "SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia", @@ -496618,69 +497557,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.12.01.21266670", - "rel_title": "Longitudinal study of DNA methylation and epigenetic clocks prior to and following test-confirmed COVID-19 and mRNA vaccination", - "rel_date": "2021-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.01.21266670", - "rel_abs": "The host epigenetic landscape is rapidly changed during SARS-CoV-2 infection and evidence suggests that severe COVID-19 is associated with durable scars to the epigenome. Specifically, aberrant DNA methylation changes in immune cells and alterations to epigenetic clocks in blood relate to severe COVID-19. However, a longitudinal assessment of DNA methylation states and epigenetic clocks in blood from healthy individuals prior to and following test-confirmed non-hospitalized COVID-19 has not been performed. Moreover, the impact of mRNA COVID-19 vaccines upon the host epigenome remains understudied. Here, we first examined DNA methylation states in blood of 21 participants prior to and following test confirmed COVID-19 diagnosis at a median timeframe of 8.35 weeks. 261 CpGs were identified as differentially methylated following COVID-19 diagnosis in blood at an FDR adjusted P value <0.05. These CpGs were enriched in gene body and northern and southern shelf regions of genes involved in metabolic pathways. Integrative analysis revealed overlap among genes identified in transcriptional SARS-CoV-2 infection datasets. Principal component-based epigenetic clock estimates of PhenoAge and GrimAge significantly increased in people over 50 following infection by an average of 2.1 and 0.84 years. In contrast, PCPhenoAge significantly decreased in people under 50 following infection by an average of 2.06 years. This observed divergence in epigenetic clocks following COVID-19 was related to age and immune cell-type compositional changes in CD4+ T cells, B cells, granulocytes, plasmablasts, exhausted T cells, and naive T cells. Complementary longitudinal epigenetic clock analyses of 36 participants prior to and following Pfizer and Moderna mRNA-based COVID-19 vaccination revealed vaccination significantly reduced principal component-based Horvath epigenetic clock estimates in people over 50 by an average of 3.91 years for those that received Moderna. This reduction in epigenetic clock estimates was significantly related to chronological age and immune cell-type compositional changes in B cells and plasmablasts pre- and post-vaccination. These findings suggest the potential utility of epigenetic clocks as a biomarker of COVID-19 vaccine responses. Future research will need to unravel the significance and durability of short-term changes in epigenetic age related to COVID-19 exposure and mRNA vaccination.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Alina PS Pang", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Albert T Higgins-Chen", - "author_inst": "Yale University School of Medicine, VA Connecticut Healthcare System" - }, - { - "author_name": "Florence Comite", - "author_inst": "Comite Center for Precision Medicine & Health, Lenox Hill Hospital/Northwell" - }, - { - "author_name": "Ioana Raica", - "author_inst": "Comite Center for Precision Medicine & Health" - }, - { - "author_name": "Christopher Arboleda", - "author_inst": "Comite Center for Precision Medicine & Health" - }, - { - "author_name": "Tavis Mendez", - "author_inst": "TruDiagnostic" - }, - { - "author_name": "Michael Schotsaert", - "author_inst": "Icahn School of Medicine at Mount Sinai, Global Health and Emerging Pathogens Institute" - }, - { - "author_name": "Varun Dwaraka", - "author_inst": "TruDiagnostic" - }, - { - "author_name": "Ryan Smith", - "author_inst": "TruDiagnostic" - }, - { - "author_name": "Morgan E Levine", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Lishomwa C Ndhlovu", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Michael J Corley", - "author_inst": "Weill Cornell Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.04.21267284", "rel_title": "S glycoprotein diversity of the Omicron Variant", @@ -497041,6 +497917,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.12.03.21267281", + "rel_title": "Safety and immunogenicity of the third booster dose with inactivated, viral vector, and mRNA COVID-19 vaccines in fully immunized healthy adults with inactivated vaccine", + "rel_date": "2021-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.03.21267281", + "rel_abs": "The coronavirus disease-2019 (COVID-19) pandemic has become a severe healthcare problem worldwide since the first outbreak in late December 2019. Currently, the COVID-19 vaccine has been used in many countries, but it is still unable to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection despite patients receiving full vaccination doses. Therefore, we aimed to appraise the booster effect of the different platforms of vaccines, including inactivated vaccine (BBIBP), viral vector vaccine (AZD122), and mRNA vaccine (BNT162b2) in healthy adults who received the full dose of inactivated vaccine (CoronaVac). The booster dose was safe with no serious adverse events. Moreover, the immunogenicity indicated that the booster dose with viral vector and mRNA vaccine achieved a significant proportion of Ig anti-receptor binding domain (RBD), IgG anti-RBD, and IgA anti-S1 booster response. In contrast, inactivated vaccine achieved a lower booster response than others. Consequently, the neutralization activity of vaccinated serum had a high inhibition of over 90% against SARS-CoV-2 wild-type and their variants (B.1.1.7-alpha, B.1.351-beta, and B.1.617.2-delta). In addition, IgG anti-nucleocapsid was observed only among the group that received the BBIBP booster. Our study found a significant increase in levels of interferon gamma-secreting T-cell response after the additional viral vector or mRNA booster vaccination. This study showed that administration with either viral vector (AZD1222) or mRNA (BNT162b2) boosters in individuals with a history of two doses of inactivated vaccine (CoronaVac) obtained great immunogenicity with acceptable adverse events.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Sitthichai Kanokudom", + "author_inst": "Center of Excellence in Clinical Virology, Department of Biochemistry, Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn Univ" + }, + { + "author_name": "Suvichada Assawakosri", + "author_inst": "Center of Excellence in Clinical Virology, Department of Biochemistry, Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn Univ" + }, + { + "author_name": "Nungruthai Suntronwong", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Chompoonut Auphimai", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Pornjarim Nilyanimit", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Preeyaporn Vichaiwattana", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Thanunrat Thongmee", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Ritthideach Yorsaeng", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Donchida Srimuan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Thaksaporn Thatsanatorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Sirapa Klinfueng", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Natthinee Sudhinaraset", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Nasamon Wanlapakorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Sittisak Honsawek", + "author_inst": "Department of Biochemistry, Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospita" + }, + { + "author_name": "Yong Poovorawan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Thailand and FRS(T), the Royal Society of Thailand" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.12.04.21267294", "rel_title": "Characteristics of Patients Referred to a Cardiovascular Disease Clinic for Post-Acute Sequelae of SARS-CoV-2 Infection", @@ -498440,61 +499391,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.01.21266598", - "rel_title": "Comparing human and model-based forecasts of COVID-19 in Germany and Poland", - "rel_date": "2021-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.01.21266598", - "rel_abs": "1Forecasts based on epidemiological modelling have played an important role in shaping public policy throughout the COVID-19 pandemic. This modelling combines knowledge about infectious disease dynamics with the subjective opinion of the researcher who develops and refines the model and often also adjusts model outputs. Developing a forecast model is difficult, resource- and time-consuming. It is therefore worth asking what modelling is able to add beyond the subjective opinion of the researcher alone. To investigate this, we analysed different real-time forecasts of cases of and deaths from COVID-19 in Germany and Poland over a 1-4 week horizon submitted to the German and Polish Forecast Hub. We compared crowd forecasts elicited from researchers and volunteers, against a) forecasts from two semi-mechanistic models based on common epidemiological assumptions and b) the ensemble of all other models submitted to the Forecast Hub. We found crowd forecasts, despite being overconfident, to outperform all other methods across all forecast horizons when forecasting cases (weighted interval score relative to the Hub ensemble 2 weeks ahead: 0.89). Forecasts based on computational models performed comparably better when predicting deaths (rel. WIS 1.26), suggesting that epidemiological modelling and human judgement can complement each other in important ways.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Nikos I. Bosse", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Sam Abbott", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Johannes Bracher", - "author_inst": "Chair of Statistics and Econometrics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany; Computational Statistics Group, Heidelberg Institute for Theo" - }, - { - "author_name": "Habakuk Hain", - "author_inst": "Max Planck Institute for Biophysical Chemistry" - }, - { - "author_name": "Billy J Quilty", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Mark Jit", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "- Centre for the Mathematical Modelling of Infectious Diseases COVID-19 Working Group", - "author_inst": "" - }, - { - "author_name": "Edwin van Leeuwen", - "author_inst": "Public Health England" - }, - { - "author_name": "Anne Cori", - "author_inst": "Imperial College London" - }, - { - "author_name": "Sebastian Funk", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.03.21266419", "rel_title": "Guillain-Barre Syndrome after COVID-19 Vaccination in the Vaccine Safety Datalink", @@ -498763,6 +499659,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.12.03.21266538", + "rel_title": "Introduction and community transmission of SARS-CoV-2 lineage A.2.5 in Florida with novel spike INDELS", + "rel_date": "2021-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.03.21266538", + "rel_abs": "SARS-CoV-2 (SC2) variants of concern (VOC) continue to emerge and spread globally, threatening the use of monoclonal antibody therapies and vaccine effectiveness. Several mutations in the SC2 spike glycoprotein have been associated with reduction in antibody neutralization. Genomic surveillance of SC2 variants has been imperative to inform the public health response regarding the use of clinical therapies in specific jurisdictions based on the proportion of particular variants (e.g., Gamma (P.1)) in a region. Florida Department of Health Bureau of Public Health Laboratories (BPHL) performs tiled-amplicon whole genome sequencing for baseline and targeted surveillance of SC2 isolates in Florida from clinical specimens collected from county health departments and hospitals throughout the state. Here, we describe the introduction of SC2 lineage A.2.5 in Florida, which contains S:L452R (a substitution of therapeutic concern) and two novel Spike INDELS, the deletion of 141-143 and ins215AGY, with unknown implications on immune response. The A.2.5 lineage was first detected in Florida among an outbreak at a healthcare facility in January 2021, and subsequent A.2.5 isolates were detected across all geographical regions throughout the state. A time-scaled maximum clade credibility phylogeny determined there were at least eight separate introductions of A.2.5 in the state. The time of introduction of a monophyletic Florida clade was established to be December 2020. The Spike INDELS were determined to reside in the N-terminal domain, a region associated with antibody neutralization. As community transmission of SARS-CoV-2 in Florida continues, genomic surveillance of circulating variants in Florida and the detection of emerging variants are critical for informing public health response to COVID-19.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sarah E Schmedes", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + }, + { + "author_name": "Taj Azarian", + "author_inst": "Burnett School of Biomedical Sciences, University of Central Florida" + }, + { + "author_name": "Eleonora Cella", + "author_inst": "Burnett School of Biomedical Sciences, University of Central Florida" + }, + { + "author_name": "Jessy Motes", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + }, + { + "author_name": "Omer Tekin", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + }, + { + "author_name": "James Weiss", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + }, + { + "author_name": "Nancimae Miller", + "author_inst": "Pathology Consultants of South Broward, Memorial Healthcare System" + }, + { + "author_name": "Jason Blanton", + "author_inst": "Bureau of Public Health Laboratories, Florida Department of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.03.21267155", "rel_title": "High viral loads: what drives fatal cases of COVID-19 in vaccinees? an autopsy study", @@ -500246,117 +501189,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.30.21266952", - "rel_title": "COVID-19 infection dynamics revealed by SARS-CoV-2 wastewater sequencing analysis and deconvolution", - "rel_date": "2021-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.30.21266952", - "rel_abs": "The use of RNA sequencing from wastewater samples is a valuable way for estimating infection dynamics and circulating lineages of SARS-CoV-2. This approach is independent from testing individuals and can therefore become the key tool to monitor this and potentially other viruses. However, it is equally important to develop easily accessible and scalable tools which can highlight critical changes in infection rates and dynamics over time across different locations given sequencing data from wastewater. Here, we provide an analysis of lineage dynamics in Berlin and New York City using wastewater sequencing and present PiGx SARS-CoV-2, a highly reproducible computational analysis pipeline with comprehensive reports. This end-to-end pipeline includes all steps from raw data to shareable reports, additional taxonomic analysis, deconvolution and geospatial time series analyses. Using simulated datasets (in silico generated and spiked-in samples) we could demonstrate the accuracy of our pipeline calculating proportions of Variants of Concern (VOC) from environmental as well as pre-mixed samples (spiked-in). By applying our pipeline on a dataset of wastewater samples from Berlin between February 2021 and January 2022, we could reconstruct the emergence of B.1.1.7(alpha) in February/March 2021 and the replacement dynamics from B.1.617.2 (delta) to BA.1 and BA.2 (omicron) during the winter of 2021/2022. Using data from very-short-reads generated in an industrial scale setting, we could see even higher accuracy in our deconvolution. Lastly, using a targeted sequencing dataset from New York City (receptor-binding-domain (RBD) only), we could reproduce the results recovering the proportions of the so-called cryptic lineages shown in the original study. Overall our study provides an in-depth analysis reconstructing virus lineage dynamics from wastewater, and that our tool can be used to identify new mutations and to detect any emerging new lineages with different amplification and sequencing methods. Our approach can support efforts to establish continuous monitoring and early-warning projects for detecting SARS-CoV-2 or any other pathogen.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Vic-Fabienne Schumann", - "author_inst": "Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Rafael Cuadrat", - "author_inst": "Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Emanuel Wyler", - "author_inst": "RNA Biology and Posttranscriptional Regulation, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, German" - }, - { - "author_name": "Ricardo Wurmus", - "author_inst": "Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Aylina Deter", - "author_inst": "Genomics Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Claudia Quedenau", - "author_inst": "Genomics Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Jan Dohmen", - "author_inst": "Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Miriam Faxel", - "author_inst": "Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Tatiana Borodina", - "author_inst": "Genomics Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Niclas Barke", - "author_inst": "RNA Biology and Posttranscriptional Regulation, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, German" - }, - { - "author_name": "Janine Altmueller", - "author_inst": "Genomics Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Regina Gnirss", - "author_inst": "Berliner Wasserbetriebe, Berlin, Germany" - }, - { - "author_name": "Uta Boeckelmann", - "author_inst": "Berliner Wasserbetriebe, Berlin, Germany" - }, - { - "author_name": "Frederik Zietzschmann", - "author_inst": "Berliner Wasserbetriebe, Berlin, Germany" - }, - { - "author_name": "Bora Uyar", - "author_inst": "Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Alexander Blume", - "author_inst": "Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Martin Meixner", - "author_inst": "amedes Medizinische Dienstleistungen GmbH" - }, - { - "author_name": "Jos\u00e9 Horacio Grau", - "author_inst": "amedes Medizinische Dienstleistungen GmbH" - }, - { - "author_name": "Karsten Liere", - "author_inst": "amedes Medizinische Dienstleistungen GmbH" - }, - { - "author_name": "Thomas Hackenbeck", - "author_inst": "amedes Medizinische Dienstleistungen GmbH" - }, - { - "author_name": "Vedran Franke", - "author_inst": "Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Nikolaus Rajewsky", - "author_inst": "Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - }, - { - "author_name": "Markus Landthaler", - "author_inst": "RNA Biology and Posttranscriptional Regulation, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, German" - }, - { - "author_name": "Altuna Akalin", - "author_inst": "Bioinformatics & Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max-Delbrueck-Center for Molecular Medicine Berlin, Berlin, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.30.21265428", "rel_title": "Racial and ethnic disparities in maternal mental health during COVID-19", @@ -500561,6 +501393,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.02.21267185", + "rel_title": "Tajima D test accurately forecasts Omicron / COVID-19 outbreak", + "rel_date": "2021-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21267185", + "rel_abs": "On 26 November 2021, the World Health Organization designated the SARS-CoV-2 variant B.1.1.529, Omicron, a variant of concern. However, the phylogenetic and evolutionary dynamics of this variant remain unclear. An analysis of the 131 Omicron variant sequences from November 9 to November 28, 2021 reveals that variants have diverged into at least 6 major subgroups. 86.3% of the cases have an insertion at amino acid 214 (INS214EPE) of the spike protein. Neutrality analysis of DH (-2.814, p<0.001) and Zengs E (0.0583, p=1.0) tests suggested that directional selection was the major driving force of Omicron variant evolution. The synonymous (Dsyn) and nonsynonymous (Dnonsyn) polymorphisms of the Omicron variant spike gene were estimated with Tajimas D statistic to eliminate homogenous effects. Both D ratio (Dnonsyn/Dsyn, 1.57) and {Delta}D (Dsyn-Dnonsyn, 0.63) indicate that purifying selection operates at present. The low nucleotide diversity (0.00008) and Tajima D value (-2.709, p<0.001) also confirms that Omicron variants had already spread in human population for more than the 6 weeks than has been reported. These results, along with our previous analysis of Delta and Lambda variants, also supports the validity of the Tajimas D test score, with a threshold value as -2.50, as an accurate predictor of new COVID-19 outbreaks.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ting-Yu Yeh", + "author_inst": "Institute of Marine and Environmental Technology" + }, + { + "author_name": "Gregory P. Contreras", + "author_inst": "Auxergen Inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.30.21267071", "rel_title": "Increased risk of psychiatric sequelae of COVID-19 is highest early in the clinical course", @@ -501816,173 +502671,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.11.29.21266819", - "rel_title": "SARS-CoV-2 genomic monitoring in the Sao Paulo State unveils new sublineages of the AY.43 strain", - "rel_date": "2021-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21266819", - "rel_abs": "Delta VOC is highly diverse and more than 120 sublineages have been identified in Pango lineages with the continuous description of emerging ones. Brazil is now one of the most vaccinated countries against SARS-CoV-2 in the world which can enhance the emergence of viral mutations related to improved viral fitness. In this study, we identified two novel sublineages of the AY.43 lineage which were classified as AY.43.1 and AY.43.2 as observed on the specific clustering on the obtained phylogenetic tree. The novel sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for AY.43.1 and ORF1ab:G1155C for AY.43.2. The majority of the analyzed sequences of both lineages were Brazilian, which shows that probably these two emerging sublineages have Brazilian origin. It is still unknown how these two sublineages are disseminated in Sao Paulo State and Brazil and their potential impact on the ongoing vaccination process. However, the performed study reinforces the importance of the SARS-CoV-2 genome monitoring for timely identification of emerging SARS-CoV-2 variants which can impact the ongoing SARS-CoV-2 vaccination and public health policies.", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "Alex Ranieri J. Lima", - "author_inst": "Butantan Institute" - }, - { - "author_name": "Gabriela Ribeiro", - "author_inst": "Butantan Institute" - }, - { - "author_name": "Vincent Louis Viala", - "author_inst": "Butantan Institute" - }, - { - "author_name": "Loyze Paola Oliveira Lima", - "author_inst": "Butantan Institute" - }, - { - "author_name": "Antonio Jorge Martins", - "author_inst": "Butantan Institute" - }, - { - "author_name": "Claudia Barros", - "author_inst": "Butantan Institute" - }, - { - "author_name": "Elaine Marqueze", - "author_inst": "Butantan Institute" - }, - { - "author_name": "Jardelina Bernardino", - "author_inst": "Butantan Institute" - }, - { - "author_name": "Debora Moretti", - "author_inst": "Butantan Institute" - }, - { - "author_name": "Evandra Strazza Rodrigues", - "author_inst": "University of Sao Paulo, Ribeirao Preto Medical School, Blood Center of Ribeirao Preto" - }, - { - "author_name": "Elaine Vieira Santos", - "author_inst": "University of Sao Paulo, Ribeirao Preto Medical School, Blood Center of Ribeirao Preto, Ribeirao Preto" - }, - { - "author_name": "Ricardo Augusto Brassaloti", - "author_inst": "University of Sao Paulo, Ribeirao Preto Medical School, Blood Center of Ribeirao Preto, Ribeirao Preto" - }, - { - "author_name": "Raquel Cassano", - "author_inst": "University of Sao Paulo, Ribeirao Preto Medical School, Blood Center of Ribeirao Preto, Ribeirao Preto" - }, - { - "author_name": "Pilar Mariani", - "author_inst": "NGS Solucoes Genomicas" - }, - { - "author_name": "Luan Gaspar Clemente", - "author_inst": "University of Sao Paulo, Centro de Genomica Funcional da ESALQ, Piracicaba, SP, Brazil" - }, - { - "author_name": "Patricia Akemi Assato", - "author_inst": "Sao Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil;" - }, - { - "author_name": "Felipe Allan Costa", - "author_inst": "Sao Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil;" - }, - { - "author_name": "Mirele Daiana Poleti", - "author_inst": "Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil;" - }, - { - "author_name": "Jessika Cristina Chagas Lesbon", - "author_inst": "Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil;" - }, - { - "author_name": "Elisangela Chicaroni Mattos", - "author_inst": "Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil;" - }, - { - "author_name": "Cecilia Artico Banho", - "author_inst": "Medicine School of Sao Jose do Rio Preto (FAMERP), Sao Jose do Rio Preto, Sao Paulo, Brazil;" - }, - { - "author_name": "Livia S Sacchetto", - "author_inst": "Faculdade de Medicina de Sao Jose do Rio Preto" - }, - { - "author_name": "Marilia Mazzi Moraes", - "author_inst": "Medicine School of Sao Jose do Rio Preto (FAMERP), Sao Jose do Rio Preto, Sao Paulo, Brazil;" - }, - { - "author_name": "Melissa Palmieri", - "author_inst": "Coordenacao de Vigilancia em Saude - Secretaria Municipal da Saude, Sao Paulo" - }, - { - "author_name": "Fabiana Erica Silva", - "author_inst": "Assistencia Laboratorial/ Coordenacao de Atencao Basica - Secretaria Municipal da Saude, Sao Paulo" - }, - { - "author_name": "Rejane Tommasini Grotto", - "author_inst": "Sao Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil; Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical " - }, - { - "author_name": "Jayme A. Souza-Neto", - "author_inst": "Sao Paulo State University (UNESP)" - }, - { - "author_name": "Marta Giovanetti", - "author_inst": "Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, B" - }, - { - "author_name": "Luiz Alcantara", - "author_inst": "Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, B" - }, - { - "author_name": "Mauricio L Nogueira", - "author_inst": "Faculdade de Medicina de Sao Jose do Rio Preto" - }, - { - "author_name": "Heidge Fukumasu", - "author_inst": "Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil;" - }, - { - "author_name": "Luiz Lehmann Coutinho", - "author_inst": "University of Sao Paulo, Centro de Genomica Funcional da ESALQ, Piracicaba, SP, Brazil" - }, - { - "author_name": "Simone Kashima", - "author_inst": "Hemocentro de Ribeirao Preto" - }, - { - "author_name": "Raul Machado Neto", - "author_inst": "Butantan Institute" - }, - { - "author_name": "Dimas Tadeu Covas", - "author_inst": "University of Sao Paulo, Ribeirao Preto Medical School, Blood Center of Ribeirao Preto, Ribeirao Preto, SP, Brazil; Butantan Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Svetoslav Nanev Slavov", - "author_inst": "University of Sao Paulo, Ribeirao Preto Medical School, Blood Center of Ribeirao Preto, Ribeirao Preto, SP, Brazil;" - }, - { - "author_name": "Maria Carolina Elias", - "author_inst": "Butantan Institute" - }, - { - "author_name": "Sandra Coccuzzo Sampaio", - "author_inst": "Instituto Butantan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.30.21267047", "rel_title": "Safety, tolerability, and immunogenicity of a SARS-CoV-2 recombinant spike protein vaccine: a randomised, double-blind, placebo-controlled, phase 1-2 clinical trial (ABDALA Study).", @@ -502279,6 +502967,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.11.29.21267041", + "rel_title": "COVID-19 Variant Detection with a High-Fidelity CRISPR-Cas12 Enzyme", + "rel_date": "2021-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21267041", + "rel_abs": "Laboratory tests for the accurate and rapid identification of SARS-CoV-2 variants can potentially guide the treatment of COVID-19 patients and inform infection control and public health surveillance efforts. Here we present the development and validation of a rapid COVID-19 variant DETECTR(R) assay incorporating loop-mediated isothermal amplification (LAMP) followed by CRISPR-Cas12 based identification of single nucleotide polymorphism (SNP) mutations in the SARS-CoV-2 spike (S) gene. This assay targets the L452R, E484K/Q/A, and N501Y mutations that are associated with nearly all circulating viral lineages and identifies the two circulating variants of concern, Delta and Omicron. In a comparison of three different Cas12 enzymes, only the newly identified enzyme CasDx1 was able to accurately identify all targeted SNP mutations. An analysis pipeline for CRISPR-based SNP identification from 139 clinical samples yielded an overall SNP concordance of 98% and agreement with SARS-CoV-2 lineage classification of 138/139 compared to viral whole-genome sequencing. We also showed that detection of the single E484A mutation was necessary and sufficient to accurately identify Omicron from other major circulating variants in patient samples. These findings demonstrate the utility of CRISPR-based DETECTR(R) as a faster and simpler diagnostic than sequencing for SARS-CoV-2 variant identification in clinical and public health laboratories.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Clare L Fasching", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Venice Servellita", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Bridget McKay", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Vaishnavi Nagesh", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "James P Broughton", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Noah Brazer", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Baolin Wang", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Alicia Sotomayor-Gonzalez", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Kevin Reyes", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Jessica Streithorst", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Rachel N Deraney", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Emma Stanfield", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Carley G Hendriks", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Steve Miller", + "author_inst": "University of California San Francisco" + }, + { + "author_name": "Jesus Ching", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Janice S Chen", + "author_inst": "Mammoth Biosciences" + }, + { + "author_name": "Charles Y Chiu", + "author_inst": "University of California San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.29.21267042", "rel_title": "Favipiravir for the Treatment of Coronavirus Disease 2019; a propensity score-matched cohort study", @@ -503986,25 +504757,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.28.21266967", - "rel_title": "Likelihood of infecting or getting infected with COVID-19 as a function of vaccination status, as investigated with a stochastic model for New Zealand (Aotearoa)", - "rel_date": "2021-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.28.21266967", - "rel_abs": "AimThe New Zealand government has transitioned from the Alert Level framework, which relied on government action and population level controls, to the COVID-19 Protection Framework, which relies on vaccination rates and allows for greater freedoms (for the vaccinated). Under the COVID-19 Protection Framework and current widespread community transmission of Omicron, there is significant interest in understanding the relative risk of spreading COVID-19 posed by unvaccinated, vaccinated, and boosted individuals.\n\nMethodsA stochastic branching process model is used to simulate the spread of COVID-19 for outbreaks seeded by unvaccinated, vaccinated, or boosted individuals. The likelihood of infecting or getting infected with COVID-19 is calculated based on vaccination status. The model is applied to both the Delta and Omicron variants.\n\nResultsFor the Delta variant a vaccinated traveler infected with COVID-19 is 9x less likely to seed an outbreak than an unvaccinated traveler infected with COVID-19, however, for the Omicron variant there is little difference between outbreaks seeded by unvaccinated and vaccinated individuals (boosted individuals are slightly less likely to seed large outbreaks). For the Delta variant unvaccinated individuals are responsible for 87% of all infections whereas only 3% of infections are from vaccinated to vaccinated when normalized by population. Therefore, a vaccinated individual is 6.8x more likely to be infected by an unvaccinated individual than by a vaccinated individual. For the Omicron variant unvaccinated individuals are responsible for 45% of all infections compared to 39% for vaccinated (two-doses) and 15% for boosted (three-doses) individuals when normalized by population. Despite the vaccine being less effective at preventing breakthrough transmission for Omicron, only 3% of all infections are from boosted to boosted individuals when normalized by population indicating that three doses of the vaccine provide good protection from infection and breakthrough transmission.\n\nConclusionsThis work demonstrates that most new infections are caused by unvaccinated individuals, especially for the Delta variant. These simulations illustrate the importance of vaccination in stopping individuals from becoming infected with COVID-19 and in preventing onward transmission. For Omicron, individuals vaccinated with two doses are only slightly less likely to spread COVID-19 than those who are unvaccinated. This work suggests that for the current Omicron outbreak the COVID-19 Protection Framework should potentially be updated to distinguish between those who have received two primary doses of the Pfizer-BioNTech vaccine (vaccinated individuals) and those who have received three doses (boosted individuals).", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Leighton M Watson", - "author_inst": "University of Oregon" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.28.21266969", "rel_title": "Prioritizing interventions for preventing COVID-19 outbreaks in military basic training", @@ -504157,6 +504909,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.25.21266875", + "rel_title": "COVID-19 trends and severity among symptomatic children aged 0 to 17 years in ten EU countries, 3 August 2020 to 3 October 2021", + "rel_date": "2021-11-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.25.21266875", + "rel_abs": "To guide evidence-based prevention of COVID-19 in children, we estimated risks of severe outcomes in 820,404 symptomatic paediatric cases reported by 10 EU Member States between August 2020 and October 2021. Case and hospitalisation rates rose as overall transmission increased but severe outcomes were rare: 9,611 (1.2%) were hospitalised, 640 (0.08%) required intensive care and 84 (0.01%) died. Despite increased individual risk (aOR; 95% CI for hospitalisation: 7.3; 3.3 - 16.2, ICU: 8.7; 6.2 - 12.3) in cases with comorbidities such as cancer, diabetes, cardiac or lung disease, most (83.7%) hospitalised children had no reported comorbidity.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nick Bundle", + "author_inst": "European Centre for Disease Prevention and Control (ECDC)" + }, + { + "author_name": "Nishi Dave", + "author_inst": "European Centre for Disease Prevention and Control (ECDC)" + }, + { + "author_name": "Anastasia Pharris", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "Gianfranco Spiteri", + "author_inst": "European Centre for Disease Prevention and Control (ECDC)" + }, + { + "author_name": "Charlotte Deogan", + "author_inst": "European Centre for Disease Prevention and Control (ECDC)" + }, + { + "author_name": "Jonathan E. Suk", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "- Study group members", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.29.21266976", "rel_title": "Impact of the COVID-19 pandemic on the malaria burden in northern Ghana: Analysis of routine surveillance data", @@ -505700,53 +506495,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.27.21266942", - "rel_title": "Outcomes of Anti-Spike Monoclonal Antibody Therapy in Pregnant Women with Mild to Moderate COVID-19", - "rel_date": "2021-11-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.27.21266942", - "rel_abs": "ObjectiveTo evaluate the efficacy and safety of anti-spike monoclonal antibodies (MAb) in the treatment of mild to moderate COVID-19 in high-risk patients who are pregnant.\n\nMethodsThe database of patients treated with monoclonal antibodies in the Mayo Clinic Midwest region was reviewed for patients who were pregnant at the time of infusion. Manual chart review was performed to collect demographic details as well as COVID course for both the mother and the infant if delivered. The data are presented using descriptive methods.\n\nResultsWe identified fifty-one pregnant patients with mild to moderate COVID-19 who were treated with MAb (4 with bamlanivimab monotherapy, 3 with bamlanivimab-etesevimab combination, and 44 with the casirivimab-imdevimab combination). No adverse effects were reported, and no patient required COVID-19 related hospitalization. Twenty-nine patients delivered healthy babies, there was one case of intrauterine fetal demise secondary to a congenital Ebstein anomaly (not related to MAb treatment), and twenty-one were uncomplicated pregnancies.\n\nConclusionMAb infusions were well tolerated in pregnant patients considered at high risk for COVID-19 complications, with no observed adverse effects to mother or fetus. Although preliminary data suggest MAb therapy in pregnancy is safe, further research is recommended to fully assess safety and efficacy in pregnancy.\n\nTEACHING POINTSO_LIAnti-spike monoclonal antibody therapy is well tolerated in high-risk pregnant patients with mild to moderate COVID-19\nC_LIO_LINo adverse effects of anti-spike monoclonal antibody administration were observed in either the mother or fetus.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Bright P Thilagar", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Aditya K Ghosh", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Jerome Nguyen", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Regan N Theiler", - "author_inst": "Mayo clinic" - }, - { - "author_name": "Myra J Wick", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Ryan T Hurt", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Raymund R Razonable", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Ravindra Ganesh", - "author_inst": "Mayo Clinic" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.11.28.21266956", "rel_title": "A systematic scoping review on the impact of the COVID-19 quarantine on the psychological wellbeing of medical students.", @@ -505979,6 +506727,125 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.11.24.21266812", + "rel_title": "SARS-CoV-2 Convalescent Sera Binding and Neutralizing Antibody Concentrations Compared with COVID-19 Vaccine Efficacy Estimates Against Symptomatic Infection", + "rel_date": "2021-11-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266812", + "rel_abs": "Previous vaccine efficacy (VE) studies have estimated neutralizing and binding antibody concentrations that correlate with protection from symptomatic infection; how these estimates compare to those generated in response to SARS-CoV-2 infection is unclear. Here, we assessed quantitative neutralizing and binding antibody concentrations using standardized SARS-CoV-2 assays on 3,067 serum specimens collected during July 27, 2020-August 27, 2020 from COVID-19 unvaccinated persons with detectable anti-SARS-CoV-2 antibodies using qualitative antibody assays. Quantitative neutralizing and binding antibody concentrations were strongly positively correlated (r=0.76, p<0.0001) and were noted to be several fold lower in the unvaccinated study population as compared to published data on concentrations noted 28 days post-vaccination. In this convenience sample, [~]88% of neutralizing and [~]63-86% of binding antibody concentrations met or exceeded concentrations associated with 70% COVID-19 VE against symptomatic infection from published VE studies; [~]30% of neutralizing and 1-14% of binding antibody concentrations met or exceeded concentrations associated with 90% COVID-19 VE. These data support observations of infection-induced immunity and current recommendations for vaccination post infection to maximize protection against symptomatic COVID-19.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Amy J. Schuh", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Panayampalli S. Satheshkumar", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Stephanie Dietz", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Lara Bull-Otterson", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Myrna Charles", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Chris Edens", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Jefferson M. Jones", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Kristina L. Bajema", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Kristie E.N. Clarke", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "L. Clifford McDonald", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Sadhna Patel", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Kendra Cuffe", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Natalie J. Thornburg", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Jarad Schiffer", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Kelly Chun", + "author_inst": "Labcorp" + }, + { + "author_name": "Monique Bastidas", + "author_inst": "Labcorp" + }, + { + "author_name": "Manory Fernando", + "author_inst": "Labcorp" + }, + { + "author_name": "Christos J. Petropoulos", + "author_inst": "Labcorp" + }, + { + "author_name": "Terri Wrin", + "author_inst": "Labcorp" + }, + { + "author_name": "Suqin Cai", + "author_inst": "Labcorp" + }, + { + "author_name": "Dot Adcock", + "author_inst": "Labcorp" + }, + { + "author_name": "Deborah Sesok-Pizzini", + "author_inst": "Labcorp" + }, + { + "author_name": "Stanley Letovsky", + "author_inst": "Labcorp" + }, + { + "author_name": "Alicia M. Fry", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Aron J. Hall", + "author_inst": "United States Centers for Disease Control and Prevention" + }, + { + "author_name": "Adi V. Gundlapalli", + "author_inst": "United States Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.21.21266633", "rel_title": "SARS-CoV-2 vaccination predicts COVID-19 progression and outcomes in hospitalized patients", @@ -507458,69 +508325,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.11.21.21264927", - "rel_title": "Development and Evaluation of AccuPower(R) COVID-19 Multiplex Real-Time RT-PCR Kit and AccuPower(R) SARS-CoV-2 Multiplex Real-Time RT-PCR Kit for SARS-CoV-2 Detection in Sputum, NPS/OPS, Saliva and Pooled Samples", - "rel_date": "2021-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.21.21264927", - "rel_abs": "Rapid and accurate detection of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the successful control of the current global COVID-19 pandemic. The real-time reverse transcription polymerase chain reaction (Real-time RT-PCR) is the most widely used detection technique. This research describes the development of two novel multiplex real-time RT-PCR kits, AccuPower(R) COVID-19 Multiplex Real-Time RT-PCR Kit (NCVM) specifically designed for use with the ExiStation48 system (comprised of ExiPrep48 Dx and Exicycler96 by BIONEER, Korea) for sample RNA extraction and PCR detection, and AccuPower(R) SARS-CoV-2 Multiplex Real-Time RT-PCR Kit (SCVM) designed to be compatible with manufacturers on-market PCR instruments. The limit of detection (LoD) of NCVM was 120 copies/L and the LoD of the SCVM was 2 copies/mL for both the gene and the SARS-CoV-2 gene (N gene and RdRp gene). The AccuPower(R) kits demonstrated high precision with no cross reactivity to other respiratory-related microorganisms. The clinical performance of AccuPower(R) kits was evaluated using the following clinical samples: sputum and nasopharyngeal/oropharyngeal swab (NPS/OPS) samples. Overall agreement of the AccuPower(R) kits with a Food and Drug Administration (FDA) approved emergency use authorized commercial kit (STANDARD M nCoV Real-Time Detection kit, SD BIOSENSOR, Korea) was above 95% (Cohens kappa coefficient [≥] 0.95), with a sensitivity of over 95%. The NPS/OPS specimen pooling experiment was conducted to verify the usability of AccuPower(R) kits on pooled samples and the results showed greater than 90% agreement with individual NPS/OPS samples. The clinical performance of AccuPower(R) kits with saliva samples was also compared with NPS/OPS samples and demonstrated over 95% agreement (Cohens kappa coefficient > 0.95). This study shows the BIONEER NCVM and SCVM assays are comparable with the current standard confirmation assay and are suitable for effective clinical management and control of SARS-CoV-2.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "In Bum Suh", - "author_inst": "Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea" - }, - { - "author_name": "Jaegyun Lim", - "author_inst": "Department of Laboratory Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang, Korea" - }, - { - "author_name": "Hyo Seon Kim", - "author_inst": "Research Administration Team, Institute of Clinical Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang, Korea" - }, - { - "author_name": "Guil Rhim", - "author_inst": "Department of General Affairs, Korean Association of Otorhinolaryngologists, Seoul, Korea" - }, - { - "author_name": "Heebum Kim", - "author_inst": "Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea" - }, - { - "author_name": "Hana Kim", - "author_inst": "Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea" - }, - { - "author_name": "Sae-Mi Lee", - "author_inst": "Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea" - }, - { - "author_name": "Hyun-sang Park", - "author_inst": "Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea" - }, - { - "author_name": "Hyun Ju Song", - "author_inst": "Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea" - }, - { - "author_name": "MyungKook Hong", - "author_inst": "Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea" - }, - { - "author_name": "Gyung Sook Shin", - "author_inst": "Department of Laboratory Medicine, College of Medicine, Kangwon National University, Chuncheon, Korea" - }, - { - "author_name": "Moon Jung Kim", - "author_inst": "Department of Laboratory Medicine, Myongji Hospital, Hanyang University College of Medicine, Goyang, Korea" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.22.21266690", "rel_title": "Favipiravir for treatment of outpatients with asymptomatic or uncomplicated COVID-19: a double-blind randomized, placebo-controlled, phase 2 trial", @@ -507893,6 +508697,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.22.21266692", + "rel_title": "Serological responses to COVID-19 booster vaccine in England", + "rel_date": "2021-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266692", + "rel_abs": "IntroductionThere are limited data on immune responses after COVID-19 vaccine boosters in individuals receiving primary immunisation with BNT162b2 (Pfizer-BioNTech) or AZD1222 (AstraZeneca).\n\nMethodsA prospective, cohort study to assess SARS-CoV-2 antibody responses before and after booster vaccination with BNT162b2 in adults receiving either (i) two BNT162b2 doses <30 days apart (BNT162b2-control), (ii) two BNT162b2 doses [≥]30 days apart (BNT162b2-extended) or (iii) two AZD1222 doses [≥]30 days apart (AZD1222-extended) in London, England. SARS-CoV-2 spike protein antibody geometric mean titres (GMTs) before and 2-4 weeks after booster were compared.\n\nResultsOf 750 participants, 626 provided serum samples for up to 38 weeks after their second vaccine dose. Antibody GMTs peaked at 2-4 weeks after the second dose, before declining by 68% at 36-38 weeks after dose 2 for BNT162b2-control participants, 85% at 24-29 weeks for BNT162b2-extended participants and 78% at 24-29 weeks for AZD1222-extended participants. Antibody GMTs was highest in BNT162b2-extended participants (942 [95%CI, 797-1113]) than AZD1222-extended (183 [124-268]) participants at 24-29 weeks or BNT162b2-control participants at 36-38 weeks (208; 95%CI, 150-289). At 2-4 weeks after booster, GMTs were significantly higher than after primary vaccination in all three groups: 18,104 (95%CI, 13,911-23,560; n=47) in BNT162b2-control (76.3-fold), 13,980 (11,902-16,421; n=118) in BNT162b2-extended (15.9-fold) and 10,799 (8,510-13,704; n=43) in AZD1222-extended (57.2-fold) participants. BNT162b2-control participants (median:262 days) had a longer interval between primary and booster doses than BNT162b2-extended or AZD1222-extended (both median:186 days) participants.\n\nConclusionsWe observed rapid serological responses to boosting with BNT162b2, irrespective of vaccine type or schedule used for primary immunisation, with higher post-booster responses with longer interval between primary immunisation and boosting. Boosters will not only provide additional protection for those at highest risk of severe COVID-19 but also prevent infection and, therefore, interrupt transmission, thereby reducing infections rates in the population. Ongoing surveillance will be important for monitoring the duration of protection after the booster.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Georgina Ireland", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Heather Whitaker", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Shamez N Ladhani", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Frances Baawuah", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Vani Subbarao", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Ezra Linley", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Lenesha Warrener", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Michelle O'Brien", + "author_inst": "Brondesbury Medical Centre, Kilburn, London, United Kingdom" + }, + { + "author_name": "Corrine Whillock", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Paul Moss", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Mary E Ramsay", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Gayatri Amirthalingam", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Kevin E Brown", + "author_inst": "UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.22.21266713", "rel_title": "In Vitro Nasal Tissue Model for the Validation of Nasopharyngeal and Mid-turbinate Swabs for SARS-CoV-2 Testing", @@ -509296,137 +510167,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.22.21266512", - "rel_title": "Association of COVID-19 with arterial and venous vascular diseases: a population-wide cohort study of 48 million adults in England and Wales", - "rel_date": "2021-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266512", - "rel_abs": "ImportanceThe long-term effects of COVID-19 on the incidence of vascular diseases are unclear.\n\nObjectiveTo quantify the association between time since diagnosis of COVID-19 and vascular disease, overall and by age, sex, ethnicity, and pre-existing disease.\n\nDesignCohort study based on population-wide linked electronic health records, with follow up from January 1st to December 7th 2020.\n\nSetting and participantsAdults registered with an NHS general practice in England or Wales and alive on January 1st 2020.\n\nExposuresTime since diagnosis of COVID-19 (categorised as 0-6 days, 1-2 weeks, 3-4, 5-8, 9-12, 13-26 and 27-49 weeks since diagnosis), with and without hospitalisation within 28 days of diagnosis.\n\nMain outcomes and measuresPrimary outcomes were arterial thromboses (mainly acute myocardial infarction and ischaemic stroke) and venous thromboembolic events (VTE, mainly pulmonary embolism and lower limb deep vein thrombosis). We also studied other vascular events (transient ischaemic attack, haemorrhagic stroke, heart failure and angina). Hazard ratios were adjusted for demographic characteristics, previous disease diagnoses, comorbidities and medications.\n\nResultsAmong 48 million adults, 130,930 were and 1,315,471 were not hospitalised within 28 days of COVID-19. In England, there were 259,742 first arterial thromboses and 60,066 first VTE during 41.6 million person-years follow-up. Adjusted hazard ratios (aHRs) for first arterial thrombosis compared with no COVID-19 declined rapidly from 21.7 (95% CI 21.0-22.4) to 3.87 (3.58-4.19) in weeks 1 and 2 after COVID-19, 2.80 (2.61-3.01) during weeks 3-4 then to 1.34 (1.21-1.48) during weeks 27-49. aHRs for first VTE declined from 33.2 (31.3-35.2) and 8.52 (7.59-9.58) in weeks 1 and 2 to 7.95 (7.28-8.68) and 4.26 (3.86-4.69) during weeks 3-4 and 5-8, then 2.20 (1.99-2.44) and 1.80 (1.50-2.17) during weeks 13-26 and 27-49 respectively. aHRs were higher, for longer after diagnosis, after hospitalised than non-hospitalised COVID-19. aHRs were also higher among people of Black and Asian than White ethnicity and among people without than with a previous event. Across the whole population estimated increases in risk of arterial thromboses and VTEs were 2.5% and 0.6% respectively 49 weeks after COVID-19, corresponding to 7,197 and 3,517 additional events respectively after 1.4 million COVID-19 diagnoses.\n\nConclusions and RelevanceHigh rates of vascular disease early after COVID-19 diagnosis decline more rapidly for arterial thromboses than VTEs but rates remain elevated up to 49 weeks after COVID_19. These results support continued policies to avoid COVID-19 infection with effective COVID-19 vaccines and use of secondary preventive agents in high-risk patients.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSIs COVID-19 associated with higher long-term incidence of vascular diseases?\n\nFindingsIn this cohort study of 48 million adults in England and Wales, COVID-19 was associated with higher incidence, that declined with time since diagnosis, of both arterial thromboses [week 1: adjusted HR [aHR] 21.7 (95% CI 21.0-22.4) weeks 27-49: aHR 1.34 (1.21-1.48)] and venous thromboembolism [week 1: aHR 33.2 (31.3-35.2), weeks 27-49 1.80 (1.50-2.17)]. aHRs were higher, for longer, after hospitalised than non-hospitalised COVID-19. The estimated excess number of arterial thromboses and venous thromboembolisms was 10,500.\n\nMeaningAvoidance of COVID-19 infection through vaccination, and use of secondary preventive agents after infection in high-risk patients, may reduce post-COVID-19 acute vascular diseases.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Rochelle Knight", - "author_inst": "University of Bristol" - }, - { - "author_name": "Venexia Walker", - "author_inst": "University of Bristol" - }, - { - "author_name": "Samantha Ip", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Jennifer A Cooper", - "author_inst": "University of Bristol" - }, - { - "author_name": "Thomas Bolton", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Spencer Keene", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Rachel Denholm", - "author_inst": "University of Bristol" - }, - { - "author_name": "Ashley Akbari", - "author_inst": "Swansea University" - }, - { - "author_name": "Hoda Abbasizanjani", - "author_inst": "Swansea University" - }, - { - "author_name": "Fatemeh Torabi", - "author_inst": "Swansea University" - }, - { - "author_name": "Efosa Omigie", - "author_inst": "NHS Digital" - }, - { - "author_name": "Sam Hollings", - "author_inst": "NHS Digital" - }, - { - "author_name": "Teri-Louise North", - "author_inst": "University of Bristol" - }, - { - "author_name": "Renin Toms", - "author_inst": "University of Bristol" - }, - { - "author_name": "Emanuele Di Angelantonio", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Spiros Denaxas", - "author_inst": "University College London" - }, - { - "author_name": "Johan H Thygesen", - "author_inst": "University College London" - }, - { - "author_name": "Christopher Tomlinson", - "author_inst": "University College London" - }, - { - "author_name": "Ben Bray", - "author_inst": "Kings College London" - }, - { - "author_name": "Craig J Smith", - "author_inst": "University of Manchester" - }, - { - "author_name": "Mark Barber", - "author_inst": "Glasgow Caledonian University" - }, - { - "author_name": "George Davey Smith", - "author_inst": "University of Bristol" - }, - { - "author_name": "Nishi Chaturvedi", - "author_inst": "University College London" - }, - { - "author_name": "Cathie Sudlow", - "author_inst": "Health Data Research UK" - }, - { - "author_name": "William N Whiteley", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Angela Wood", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Jonathan A C Sterne", - "author_inst": "University of Bristol" - }, - { - "author_name": "- CVD-COVID-UK/COVID-IMPACT consortium", - "author_inst": "" - }, - { - "author_name": "- Longitudinal Health and Wellbeing COVID-19 National Core Study", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.23.21266789", "rel_title": "SARS-CoV-2 within-host and in-vitro genomic variability and sub-genomic RNA levels indicate differences in viral expression between clinical and in-vitro cohorts.", @@ -509607,6 +510347,69 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.11.24.21266401", + "rel_title": "Effectiveness of BNT162b2 and ChAdOx1 against SARS-CoV-2 household transmission - a prospective cohort study in England", + "rel_date": "2021-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266401", + "rel_abs": "BackgroundThe ability of SARS-CoV-2 vaccines to protect against infection and onward transmission determines whether immunisation can control global circulation. We estimated effectiveness of BNT162b2 and ChAdOx1 vaccines against acquisition and transmission of the Alpha and Delta variants in a prospective household study in England.\n\nMethodsAdult index cases in the community and their household contacts took oral-nasal swabs on days 1, 3 and 7 after enrolment. Swabs were tested by RT-qPCR with genomic sequencing conducted on a subset. We used Bayesian logistic regression to infer vaccine effectiveness against acquisition and transmission, adjusted for age, vaccination history and variant.\n\nFindingsBetween 2 February 2021 and 10 September 2021 213 index cases and 312 contacts were followed up. After excluding households lacking genomic proximity (N=2) or with unlikely serial intervals (N=16), 195 households with 278 contacts remained of whom 113 (41%) became PCR positive. Delta lineages had 1.64 times the risk (95% Credible Interval: 1.15 - 2.44) of transmission than Alpha; contacts older than 18 years were 1.19 times (1.04 - 1.52) more likely to acquire infection than children. Effectiveness of two doses of BNT162b2 against transmission of Delta was 31% (-3%, 61%) and 42% (14%, 69%) for ChAdOx1, similar to their effectiveness for Alpha. Protection against infection with Alpha was higher than for Delta, 71% (12%,95%) vs 24% (-2%, 64%) respectively for BNT162b2 and 26% (-39%, 73%) vs 14% (-5%, 46%) respectively for ChAdOx1.\n\nInterpretationBNT162b2 and ChAdOx1 reduce transmission of the Delta variant from breakthrough infections in the household setting though their protection against infection is low.\n\nFundingThis study was funded by the UK Health Security Agency (formerly Public Health England) as part of the COVID-19 response.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Samuel Clifford", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Pauline Waight", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Jada Hackman", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Stephane Hue", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Charlotte M Gower", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Freja CM Kirsebom", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Catriona Skarnes", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Louise Letley", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Jamie Lopez Bernal", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Nick Andrews", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Stefan Flasche", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Elizabeth Miller", + "author_inst": "London School of Hygiene and Tropical Medicine, UK Health Security Agency" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.22.21266599", "rel_title": "Modeling on Wastewater Treatment Process in Saudi Arabia: a perspective of Covid-19", @@ -511190,41 +511993,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2021.11.20.469369", - "rel_title": "Decidual immune response following COVID-19 during pregnancy varies by timing of maternal SARS-CoV-2 infection", - "rel_date": "2021-11-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.20.469369", - "rel_abs": "While COVID-19 infection during pregnancy is common, fetal transmission is rare, suggesting that intrauterine mechanisms form an effective blockade against SARS-CoV-2. Key among these is the decidual immune environment of the placenta. We hypothesized that decidual leukocytes are altered by maternal SARS-CoV-2 infection in pregnancy and that this decidual immune resonse is shaped by the timing of infection during gestation. To address this hypothesis, we collected decidua basalis tissues at delivery from women with symptomatic COVID-19 during second (2nd Tri COVID, n=8) or third trimester (3rd Tri COVID, n=8) and SARS-CoV-2-negative controls (Control, n=8). Decidual natural killer (NK) cells, macrophages and T cells were evaluated using quantitative microscopy, and pro- and anti-inflammatory cytokine mRNA expression was evaluated using quantitative reverse transcriptase PCR (qRT-PCR). When compared with the Control group, decidual tissues from 3rd Tri COVID exhibited significantly increased macrophages, NK cells and T cells, whereas 2nd Tri COVID only had significantly increased T cells. In evaluating decidual cytokine expression, we noted that IL-6, IL-8, IL-10 and TNF- were significantly correlated with macrophage cell abundance. However, in 2nd Tri COVID tissues, there was significant downregulation of IL-6, IL-8, IL-10, and TNF-. Taken together, these results suggest innate and adaptive immune responses are present at the maternal-fetal interface in maternal SARS-CoV-2 infections late in pregnancy, and that infections earlier in pregnancy show evidence of a resolving immune response. Further studies are warranted to characterize the full scope of intrauterine immune responses in pregnancies affected by maternal COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Elisha M Wachman", - "author_inst": "Department of Pediatrics Boston Medical Center" - }, - { - "author_name": "Jeffery Boateng", - "author_inst": "Department of Pediatrics Boston Medical Center" - }, - { - "author_name": "Mayuri Jain", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Yoel Benarroch", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Elizabeth S Taglauer", - "author_inst": "Department of Pediatrics Boston Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.11.17.21266464", "rel_title": "Krebs von den Lungen 6 levels in COVID-19 ICU Patients are Associated with Mortality", @@ -511421,6 +512189,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.19.21266580", + "rel_title": "COVID-19 cases and hospitalizations averted by case investigation and contact tracing in the United States", + "rel_date": "2021-11-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.19.21266580", + "rel_abs": "ImportanceEvidence of the impact of COVID-19 Case Investigation and Contact Tracing (CICT) programs is lacking. Policymakers need this evidence to assess its value.\n\nObjectiveEstimate COVID-19 cases and hospitalizations averted nationwide by US states CICT programs.\n\nDesignWe combined data from US CICT programs (e.g., proportion of cases interviewed, contacts notified or monitored, and days to case and contact notification) with incidence data to model CICT impacts over 60 days period (November 25, 2020 to January 23, 2021) during the height of the pandemic. We estimated a range of impacts by varying assumed compliance with isolation and quarantine recommendations.\n\nSettingUS States and Territories\n\nParticipantsFifty-nine state and territorial health departments that received federal funding supporting COVID-19 pandemic response activities were eligible for inclusion. Of these, 22 states and 1 territory reported all measures necessary for the analysis. These 23 jurisdictions covered 42.5% of the US population (140 million persons), spanned all 4 census regions, and reported data that reflected all 59 federally funded CICT programs.\n\nInterventionPublic health case investigation and contact tracing\n\nMain Outcomes and MeasuresCases and hospitalizations averted; percent of cases averted among cases not prevented by vaccination and other non-pharmaceutical interventions (other NPIs).\n\nResultsWe estimated 1.11 million cases and 27,231 hospitalizations were averted by CICT programs under a scenario where 80% of interviewed cases and monitored contacts, and 30% of notified contacts fully complied with isolation and quarantine guidance, eliminating their contributions to future transmission. As many as 1.36 million cases and 33,527 hospitalizations could have been prevented if all interviewed cases and monitored contacts had entered into and fully complied with isolation and quarantine guidelines upon being interviewed or notified. Across all scenarios and jurisdictions, CICT averted a median of 21.2% (range: 1.3% - 65.8%) of the cases not prevented by vaccination and other NPIs.\n\nConclusions and RelevanceCICT programs likely had a substantial role in curtailing the pandemic in most jurisdictions during the winter 2020-2021 peak. Differences in impact across jurisdictions indicate an opportunity to further improve CICT effectiveness. These estimates demonstrate the potential benefits from sustaining and improving these programs.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSWhat were the health impacts of COVID-19 case investigation and contact tracing programs (CICT) in the US?\n\nFindingsBy combining CICT program data from 22 states and 1 territory with mathematical modeling, we estimate CICT averted between 1.11 to 1.36 million cases and 27,231 to 33,527 hospitalizations over 60 days during the height of the pandemic (winter 2020-21). The upper estimate assumes all interviewed cases and monitored contacts complied with isolation and quarantine guidelines, while the lower estimate assumes fractions of interviewed cases and monitored or notified contacts did so.\n\nMeaningCICT programs likely played a critical role in curtailing the pandemic.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Gabriel Rainisch", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Seonghye Jeon", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Danielle Pappas", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Kimberly Spencer", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Leah S Fischer", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Bishwa Adhikari", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Melanie Taylor", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Bradford Greening Jr.", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Patrick Moonan", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "John Oeltmann", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Emily B Kahn", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Michael Washington", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Martin I Meltzer", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.19.21266581", "rel_title": "Baseline hypocapnia is associated with intubation in COVID-19 diagnosed patients", @@ -512768,77 +513603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2021.11.17.21266451", - "rel_title": "COVID-19 Health Care Behaviour in The Gambia: a cross-sectional survey of 205 adults who went through mandatory institutional quarantine", - "rel_date": "2021-11-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266451", - "rel_abs": "BackgroundTo control the spread of the novel Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome novel Coronavirus-2 (SARS-CoV-2), countries around the world subsequently implemented several public health measures, including the adoption of mandatory institutional quarantine for close contacts. This study explored the experiences of individuals who underwent institutional quarantine in The Gambia to inform government measures to increase its effectiveness and reduce its associated negative impacts.\n\nMethodsQuestionnaires were administered via mobile phone call with data collectors calling and directly recording participant responses on a tablet in an electronic online form developed in REDCap (Research Electronic Data Capture). The questionnaire contained questions on COVID-19 related knowledge, health care behaviour, attitudes, perceptions and stigma. Data were analysed using STATA v.13 (Stata Corp, College Station, TX, USA).\n\nResultsIn total, 205 adults who observed the mandatory institutional quarantine were interviewed. There was varied knowledge of COVID-19 causes, spread, symptoms, diagnosis, treatment, and severity. Participants believed the purpose of quarantine was monitoring for signs and symptoms of coronavirus disease, testing for SARS-CoV-2, separation from the community, and protection from coronavirus disease. While a majority reported positive experiences while in quarantine, some expressed prominent dissatisfaction related to the essential services and quality of care provided. Different forms of stigma were also experienced before, during and after the quarantine experience.\n\nConclusionThis study provides important information on quarantine experiences in The Gambia during the global COVID-19 pandemic. The Ministry of Health in The Gambia and other countries could improve the experience of quarantined individuals by consistently providing psychosocial support, compensation for loss of earnings, and timely provision of SARS-CoV-2 test results. Furthermore, stigma experiences and practices should be addressed during and after individuals stay in quarantine via the provision of psychosocial support.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Penda Johm", - "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Oluwatosin Oizamsi Nkereuwem", - "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Aji Matty Manjang", - "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Omar Ceesay", - "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Lamin Leigh", - "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Amie Ceesay", - "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Mustapha Bittaye", - "author_inst": "Ministry of Health, The Gambia" - }, - { - "author_name": "Adeyemi Roberts", - "author_inst": "Ministry of Health, The Gambia" - }, - { - "author_name": "Buba Manjang", - "author_inst": "Ministry of Health, The Gambia" - }, - { - "author_name": "Sana Sambou", - "author_inst": "Ministry of Health, The Gambia" - }, - { - "author_name": "Sainey Sanneh", - "author_inst": "Ministry of Health, The Gambia" - }, - { - "author_name": "Lamin Saidy", - "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Binta Saidy", - "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Beate Kampmann", - "author_inst": "Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.19.21266615", "rel_title": "SARS-CoV2 serology assays: utility and limits of different antigen based tests through the evaluation and the comparison of four commercial tests", @@ -513127,6 +513891,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.17.21266488", + "rel_title": "Enoxaparin for thromboprophylaxis in hospitalized COVID-19 patients: comparison of 40 mg o.d. vs 40 mg b.i.d. The X-COVID19 Randomized Clinical Trial", + "rel_date": "2021-11-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266488", + "rel_abs": "It is uncertain whether higher doses of anticoagulants than recommended for thromboprophylaxis are necessary in COVID-19 patients hospitalized in general wards. This is a multicentre, open-label, randomized trial performed in 9 Italian centres, comparing 40 mg b.i.d. vs 40 mg o.d. enoxaparin in COVID-19 patients, between April 30, 2020 and April 25, 2021. Primary efficacy outcome was in-hospital incidence of venous thromboembolism (VTE): asymptomatic or symptomatic proximal deep vein thrombosis (DVT) diagnosed by serial compression ultrasonography (CUS), and/or symptomatic pulmonary embolism (PE) diagnosed by computed tomography angiography (CTA). Secondary endpoints included each individual component of the primary efficacy outcome and a composite of death, VTE, mechanical ventilation, stroke, myocardial infarction, admission to ICU. Safety outcomes included major bleeding. The study was interrupted prematurely due to slow recruitment. We included 183 (96%) of the 189 enrolled patients in the primary analysis (91 in b.i.d., 92 in o.d.). Primary efficacy outcome occurred in 6 patients (6{middle dot}5%, 0 DVT, 6 PE) in the o.d. group and 0 in the b.id. group (ARR 6{middle dot}5, 95% CI, 1{middle dot}5-11{middle dot}6). Absence of concomitant DVT and imaging characteristics suggest that most pulmonary artery occlusions were actually caused by local thrombi rather than PE. Statistically non-significant differences in secondary and safety endpoints were observed, with two major bleeding events in each arm. In conclusion, no DVT developed in COVID-19 patients hospitalized in general wards, independently of enoxaparin dosing used for thromboprophylaxis. Pulmonary artery occlusions developed only in the o.d. group. Our trial is underpowered and with few events.\n\nREGISTRATIONClinicalTrials.gov Identifier: NCT04366960\n\nEthics Commettee approvation number75/2020", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Nuccia Morici", + "author_inst": "ASST GRANDE OSPEDALE METROPOLITANO NIGUARDA" + }, + { + "author_name": "Gian Marco Podda", + "author_inst": "University of Milan; Medicina 2, ASST Santi Paolo e Carlo, Milan, Italy" + }, + { + "author_name": "Simone Birocchi", + "author_inst": "Medicina 2, ASST Santi Paolo e Carlo, Milan, Italy" + }, + { + "author_name": "Luca Bonacchini", + "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" + }, + { + "author_name": "Marco Merli", + "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" + }, + { + "author_name": "Michele Trezzi", + "author_inst": "Struttura Operativa Complessa (SOC) Malattie Infettive II, AUSL Toscana Centro, Ospedale San Jacopo, Pistoia, Italy" + }, + { + "author_name": "Gianluca Massaini", + "author_inst": "Struttura Operativa Semplice (SOS) Chirurgia vascolare, AUSL Toscana Centro, Ospedale San Jacopo, Pistoia, Italy" + }, + { + "author_name": "Marco Agostinis", + "author_inst": "Emergency Department, Ospedale San Carlo Borromeo, ASST Santi Paolo e Carlo, Milano, Italy" + }, + { + "author_name": "Giulia Carioti", + "author_inst": "Emergency Department, Ospedale San Carlo Borromeo, ASST Santi Paolo e Carlo, Milano, Italy" + }, + { + "author_name": "Francesco Saverio Serino", + "author_inst": "ASL 4 Veneto, Covid Hospital, Jesolo, Italy" + }, + { + "author_name": "Gianluca Gazzaniga", + "author_inst": "Postgraduate School of Clinical Pharmacology and Toxicology, Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy" + }, + { + "author_name": "Daniela Barberis", + "author_inst": "ASST Grande Ospedale Metropolitano Niguarda" + }, + { + "author_name": "Laura Antolini", + "author_inst": "Center of Bioinformatics, Biostatistics and Bioimaging, School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy" + }, + { + "author_name": "Maria Grazia Valsecchi", + "author_inst": "Center of Bioinformatics, Biostatistics and Bioimaging, School of Medicine and Surgery, University of Milano Bicocca, Monza, Italy" + }, + { + "author_name": "Marco Cattaneo", + "author_inst": "University of Milan; Medicina 2, ASST Santi Paolo e Carlo, Milan, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.17.21266367", "rel_title": "A prospective study of asymptomatic SARS-CoV-2 infection among individuals involved in academic research under limited operations during the COVID-19 pandemic", @@ -514482,85 +515321,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.17.21266274", - "rel_title": "Anti-SARS-CoV-2 antibodies seroprevalence among patients submitted to treatment for tuberculosis in Rio de Janeiro, Brazil: a cross-sectional study.", - "rel_date": "2021-11-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266274", - "rel_abs": "Due to tuberculosis (TB) patients pulmonary damages, some authors believe that a SARS-CoV-2 coinfection may result in unfavorable outcomes. A cross-sectional anti-SARS-CoV-2 antibodies seroprevalence study was conducted at a TB treatment tertiary referral unit in Rio de Janeiro, Brazil, to estimate the proportion (in %) of TB patients exposed to the new coronavirus and their main outcomes. Of 83 patients undergoing TB treatment, 26.5% have already been infected by the new coronavirus. Most patients were asymptomatic (69%) or had mild COVID-19 cases (31%). Only one patient required hospitalization. Among the symptoms and signs presented, the most frequently reported were: fever, headache, and myalgia. People with less education and less purchasing power seemed to had been more exposed to SARS-CoV-2.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Karen Machado Gomes", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Suzanne Pereira Leite", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Maria Helena Vieira Moutinho", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Thatiana Alfena de Souza", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Rita de Cassia Batista", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Luiz Claudio Motta de Oliveira", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Paulo Redner", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Jesus Pais Ramos", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Fatima Maria Gomes da Rocha", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Gisele Pinto de Oliveira", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Antonio Teva", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Fernando do Couto Motta", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Marilda Agudo Mendonca Teixeira de Siqueira", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Rafael Silva Duarte", - "author_inst": "Universidade Federal do Rio de Janeiro" - }, - { - "author_name": "Francisco Inacio Pinkusfeld Monteiro Bastos", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Paulo Victor de Sousa Viana", - "author_inst": "Fundacao Oswaldo Cruz" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.17.21266051", "rel_title": "The unmitigated profile of COVID-19 infectiousness", @@ -514709,6 +515469,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.14.21266334", + "rel_title": "Attenuation of antibody titres during 3-6 months after the second dose of the BNT162b2 vaccine depends on sex, with age and smoking as risk factors for lower antibody titres at 6 months", + "rel_date": "2021-11-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.14.21266334", + "rel_abs": "ObjectiveWe aimed to determine antibody titres at 6 months and their rate of change during 3-6 months after the second dose of the BNT162b2 coronavirus disease 2019 (COVID-19) mRNA vaccine (Pfizer/BioNTech) and to explore clinical variables associated with titres in Japan.\n\nMethodsWe enrolled 365 healthcare workers (250 women, 115 men) whose 3-month antibody titres were analyzed in our previous study and whose blood samples were collected 183 {+/-} 15 days after the second dose. Participant characteristics collected previously were used. The relationships of these factors with antibody titres at 6 months and rates of change in antibody titres during 3-6 months were analyzed.\n\nResultsMedian age was 44 years. Median antibody titre at 6 months was 539 U/mL. Older participants had significantly lower antibody titres (20s, 752 U/mL; 60s-70s, 365 U/mL). In age-adjusted analysis, smoking was the only factor associated with lower antibody titres. Median rate of change in antibody titres during 3-6 months was -29.4%. The only factor significantly associated with the rate of change in Ab titres was not age or smoking, but sex (women, -31.6%; men, -25.1%).\n\nConclusionThe most important factors associated with lower antibody titres at 6 months were age and smoking, as at 3 months, probably reflecting their effect on peak antibody titres. However, antibody titres significantly attenuated during 3-6 months in women alone, which reduced the sex difference in antibody titres seen during the first 3 months. Antibody titres may be affected by different factors at different time points.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yushi Nomura", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Michiru Sawahata", + "author_inst": "Jichi Medical University" + }, + { + "author_name": "Yosikazu Nakamura", + "author_inst": "Jichi Medical University" + }, + { + "author_name": "Ryousuke Koike", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Otohiro Katsube", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Koichi Hagiwara", + "author_inst": "Jichi Medical University" + }, + { + "author_name": "Seiji Niho", + "author_inst": "Dokkyo Medical University" + }, + { + "author_name": "Norihiro Masuda", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Takaaki Tanaka", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + }, + { + "author_name": "Kumiya Sugiyama", + "author_inst": "National Hospital Organization Utsunomiya National Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.16.21266414", "rel_title": "Unraveling the spatiotemporal spread of COVID-19 in Brazil through spatial network connectivity", @@ -516196,49 +517011,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.15.21265753", - "rel_title": "Continued Effectiveness of COVID-19 Vaccination among Urban Healthcare Workers during Delta Variant Predominance", - "rel_date": "2021-11-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.15.21265753", - "rel_abs": "BackgroundData on COVID-19 vaccine effectiveness (VE) among healthcare workers (HCWs) during periods of delta variant predominance are limited.\n\nMethodsWe followed a population of urban Massachusetts HCWs (45% non-White) subject to epidemiologic surveillance. We accounted for covariates such as demographics and community background infection incidence, as well as information bias regarding COVID-19 diagnosis and vaccination status.\n\nResults and DiscussionDuring the study period (December 16, 2020 to September 30, 2021), 4615 HCWs contributed to a total of 1,152,486 person-days at risk (excluding 309 HCWs with prior infection) and had a COVID-19 incidence rate of 5.2/10,000 (114 infections out of 219,842 person-days) for unvaccinated person-days and 0.6/10,000 (49 infections out of 830,084 person-days) for fully vaccinated person-days, resulting in an adjusted VE of 82.3% (95% CI: 75.1-87.4%). For the secondary analysis limited to the period of delta variant predominance in Massachusetts (i.e., July 1 to September 30, 2021), we observed an adjusted VE of 76.5% (95% CI: 40.9-90.6%). Independently, we found no re-infection among those with prior COVID-19, contributing to 74,557 re-infection-free person-days, adding to the evidence base for the robustness of naturally acquired immunity.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Fan-Yun Lan", - "author_inst": "Cambridge Health Alliance, Harvard Medical School" - }, - { - "author_name": "Amalia Sidossis", - "author_inst": "Cambridge Health Alliance, Harvard Medical School" - }, - { - "author_name": "Eirini Iliaki", - "author_inst": "Cambridge Health Alliance, Harvard Medical School" - }, - { - "author_name": "Jane Buley", - "author_inst": "Cambridge Health Alliance, Harvard Medical School" - }, - { - "author_name": "Neetha Nathan", - "author_inst": "Cambridge Health Alliance, Harvard Medical School" - }, - { - "author_name": "Lou Ann Bruno-Murtha", - "author_inst": "Cambridge Health Alliance, Harvard Medical School" - }, - { - "author_name": "Stefanos N. Kales", - "author_inst": "Cambridge Health Alliance, Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.15.21266255", "rel_title": "COVID-19 vaccination, risk-compensatory behaviours, and social contacts in four countries in the UK", @@ -516419,6 +517191,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2021.11.15.21265526", + "rel_title": "COVID-19 in the Republic of Belarus: pandemic features and the interim safety and efficacy assessment of the Gam-COVID-Vac vaccine", + "rel_date": "2021-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.15.21265526", + "rel_abs": "ObjectiveTo study the COVID-19 pandemic features among the population of the Republic of Belarus from February 2020 to September 2021 and assess the safety (tolerance) and epidemiological efficacy of the Gam-COVID-Vac vaccine (Sputnik V).\n\nMaterials and methodsA retrospective analysis of COVID-19 cases in the Republic of Belarus from the beginning of registration (February 28, 2020) to September 12, 2021 was performed. To assess the COVID-19 case detection dynamics, official registration data available on the website of the Ministry of Health of the Republic of Belarus were used.\n\nVaccine safety (tolerance) and efficacy were assessed in an observational study. Safety (tolerance) was assessed by presence/absence of adverse reactions: general and local ones.\n\nThe efficacy rate (E) and the epidemiological efficacy index (K) was calculated according to the formula: E(%)=100*(b-a)/b, K=b/a.\n\nResultsOur data show that The COVID-19 pandemic in the Republic of Belarus is characterized by successive development stages: the first is the absence of COVID-19 cases in the country; the second is the registration of individual infection cases that came from abroad followed by local pathogen spread among the countrys population; the third is a local spread of COVID-19 among individuals who had contact with infected people; the fourth is the detection of cases where patients had no history of exposure to COVID-19 patients.\n\nAs of calendar week 26, 2021 Delta variant of SARS-CoV-2 has become the prevalent in the country.\n\nFollow-up results in January-August 2021 showed that the Sputnik V vaccine was well tolerated, with 80,832 adverse reactions reported (2.99% (95% CI 2.9-3.0) of the total number of vaccine doses administered). In terms of severity, adverse reactions were mild (91.4% (95% CI 91.2-91.6)) and moderate (8.6% (95% CI 8.6-8.8)). The epidemiological efficacy rate was 96.3%, the epidemiological efficacy index was 26.7. Thus, the results obtained testify to high prophylactic efficacy of the Sputnik V vaccine.\n\nConclusionsThe COVID-19 pandemic in the Republic of Belarus is characterized by successive development stages: from no cases in early 2020 to detected cases where most individuals had no history of contact with COVID-19 patients; periods of rising and falling incidence. The Sputnik V vaccine has demonstrated a high safety profile and epidemiological efficacy throughout mass vaccination in the Republic of Belarus.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ala M Dashkevich", + "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health" + }, + { + "author_name": "Veronika S Vysotskaya", + "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health" + }, + { + "author_name": "Iryna N Hlinskaya", + "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health" + }, + { + "author_name": "Anzhela L Skuranovich", + "author_inst": "Republican Centre of Hygiene, Epidemiology and Public Health" + }, + { + "author_name": "Aliaksandr A Tarasenka", + "author_inst": "Ministry of Health of the Republic of Belarus" + }, + { + "author_name": "Inna A Karaban", + "author_inst": "Ministry of Health of the Republic of Belarus" + }, + { + "author_name": "Natalia D Kolomiets", + "author_inst": "Belarusian Medical Academy of Postgraduate Education" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.16.21266391", "rel_title": "From online data collection to identification of disease mechanisms: The IL-1beta, IL-6 and TNF-alpha; cytokine triad is associated with post-acute sequelae of COVID-19 in a digital research cohort", @@ -518338,45 +519153,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.11.12.21266257", - "rel_title": "Using the Health Belief Model to design a questionnaire aimed at measuring people's perceptions regarding COVID-19 immunity certificates", - "rel_date": "2021-11-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.12.21266257", - "rel_abs": "The present short communication paper describes the methodological approach of applying the Health Belief Model to the use COVID-19 immunity certificates in the UK. We designed an online survey including an adaptation of the following Health Belief Model constructs: perceived COVID-19 susceptibility, perceived COVID-19 severity, perceived benefits of using immunity certificates, perceived barriers from using immunity certificates, perceived severity of not using immunity certificates, and perceived vaccination views. The online cross-sectional survey conducted on the 3rd of August 2021 gathered responses from 534 participants aged 18 and older, representative of the UK population in terms of gender, age, and ethnicity.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Corina Elena Niculaescu", - "author_inst": "Department of Computer Science, Brunel University London and ICMA Centre University of Reading" - }, - { - "author_name": "Isabel Karen Sassoon", - "author_inst": "Department of Computer Science, Brunel University London" - }, - { - "author_name": "Irma Cecilia Landa-Avila", - "author_inst": "School of Design and Creative Arts, Loughborough University" - }, - { - "author_name": "Ozlem Colak", - "author_inst": "School of Design and Creative Arts, Loughborough University" - }, - { - "author_name": "Gyuchan Thomas Jun", - "author_inst": "School of Design and Creative Arts, Loughborough University" - }, - { - "author_name": "Panagiotis Balatsoukas", - "author_inst": "School of Design and Creative Arts, Loughborough University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.13.21266310", "rel_title": "Implementation of Unassisted and Community-Based HIV Self-Testing (HIVST) during the COVID-19 pandemic among Men-who-have-sex-with-Men (MSM) and Transgender Women (TGW): A Demonstration Study in Metro Manila, Philippines", @@ -518621,6 +519397,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.11.12.21266292", + "rel_title": "Covid-19 Pandemic and its Effect on Residents' Mental Well-Being", + "rel_date": "2021-11-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.12.21266292", + "rel_abs": "Concerns about COVID-19s long-term consequences on the mental health of frontline health professionals are mounting as the entire world strives anew to contain it. The primary objective of this research is to describe the impact of working during the COVID-19 pandemic on junior doctors mental health and to investigate the effect of the COVID-19 pandemic on junior doctors training and professional performance. A cross-sectional online survey using the Google Forms platform was conducted from May 1st to May 30th, 2021, in 311 healthcare workers who were currently enrolled in a residency program at the Kuwait Institutional of Medical Specialization (KIMS). Socio-demographic details of each health worker were collected and the scores related to depression, anxiety, and stress were measured using the previously validated depression anxiety stress scale-21 (DASS-21). Higher stress scores were seen in those who were devoid of the option to work with COVID-19 patients (adjusted {beta} 5.1 (95%CI:1.2-9);p=0.01), who reported that working during the pandemic affected their study schedule (adjusted {beta} 4.8 (95%CI:1.6-8.1);p= 0.004), and who lost off service training time (adjusted {beta} 2.7 (95%CI:0.13-5.2); p=0.034). Further, the anxiety scores were significantly higher in females. The impact of the ongoing pandemic on residents mental health is grave, necessitating psychological treatment and support. The study discovered various factors linked to depression, anxiety, and stress. As a result, these aspects must be regarded to protect the residents mental health.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Anwar Yazdani", + "author_inst": "Anesthesia and ICU Department, AlSabah Hospital, Kuwait" + }, + { + "author_name": "Hend Esmaeili", + "author_inst": "Department of Anesthesia and Critical Care, Farwaniya Hospital, Kuwait" + }, + { + "author_name": "Abdulla K AlSaleh", + "author_inst": "Anesthesia and ICU Department, Amiri Hospital, Kuwait" + }, + { + "author_name": "Ahmed Sultan", + "author_inst": "Anesthesia and ICU Department, Amiri Hospital, Kuwait" + }, + { + "author_name": "Esam Alamad", + "author_inst": "Anesthesia and ICU Department, Al Adan Hospital, Kuwait" + }, + { + "author_name": "Ali Bandar", + "author_inst": "Department of Anesthesia and critical care, Jaber Hospital, Kuwait" + }, + { + "author_name": "Hanouf Rawdhan", + "author_inst": "Department of Anesthesia Kuwait Cancer Control Center" + }, + { + "author_name": "Mariam Ayed", + "author_inst": "Ministry of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.11.10.21266063", "rel_title": "Case Series of Thrombosis with Thrombocytopenia Syndrome following COVID-19 vaccination--United States, December 2020-August 2021", @@ -520096,33 +520919,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2021.11.11.21266209", - "rel_title": "Rapid, Reliable and Robust approach for extraction-free RT-PCR based detection of SARS-CoV-2 in clinical setting to expedite large scale screening", - "rel_date": "2021-11-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.11.21266209", - "rel_abs": "Rapid, reliable and robust method for the detection of SARS-CoV-2 is an indispensable need for diagnostics. The development of diagnostic method will aid to address further waves of the pandemic potentially with rapid surveillance of disease; and to allay the fears. To meet this challenge, we have developed a rapid RT-qPCR method for the detection of 3 target genes or confirmatory genes in less than 30 minutes. The assay showed 100% sensitivity and 100% specificity when tested on 120 samples. We compared a conventional extraction based method with extraction-free method, and then further reduced the run time of extraction free method. Additionally, we have validated our rapid RT-qPCR method for the assessment of pooled sample. We hereby propose a most reliable approach for the mass screening of samples with ease of operation at low cost. Finally we designed a single tube analysis method which provides qualitative as well as quantitative results in minimum time.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Abhilasha Dubey", - "author_inst": "Medilab diagnostic" - }, - { - "author_name": "Sanjay Upadhyay", - "author_inst": "Medilab diagnostic" - }, - { - "author_name": "Manjeet Mehta", - "author_inst": "Lifenity wellness" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.10.21266138", "rel_title": "SARS-CoV-2 RNA is enriched by orders of magnitude in solid relative to liquid wastewater at publicly owned treatment works", @@ -520495,6 +521291,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.11.21266216", + "rel_title": "Effectiveness of non-pharmaceutical measures (NPIs) on COVID-19 in Europe: A systematic literature review", + "rel_date": "2021-11-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.11.21266216", + "rel_abs": "BackgroundThe study objective was to conduct a systematic review to assess the effectiveness of non-pharmaceutical interventions (NPIs) to reduce the transmission of SARS-CoV-2 in Europe during the first wave of the pandemic.\n\nMethodsWe searched OVID Medline, EMBASE, and the Cochrane and Campbell Databases for Systematic Reviews published up to April 15th 2021. Focusing on community (meso-level) and society (macro-level) level NPIs, we included all study designs, while a geographic restriction was limited to the EU, UK and European Economic Area (EEA) countries. Using the PICO framework, two reviewers independently extracted data and assessed quality using appropriate quality appraisal tools. A qualitative synthesis was performed, with NPIs grouped initially by a) Physical Distancing measures, b) Case detection and management measures, and c) hygiene measures and subsequently by country.\n\nResultsOf 17,692 studies initially assessed, 45 met all inclusion criteria. Most studies (n=30) had a modelling study design, while 13 were observational, one quasi-experimental and one experimental. Evidence from across the European continent, presented by country, indicates that the implementations of physical distancing measures (i.e., lockdowns/quarantines), preferably earlier in the pandemic, reduce the number of cases and hospitalisation across settings and for which the timing and duration are essential parameters. Case detection and management measures were also identified as effective measures at certain levels of testing and incidence, while hygiene and safety measures complemented the implementation of physical distancing measures.\n\nConclusionsThis literature review represents a comprehensive assessment of the effectiveness of NPIs in Europe up to April 2021. Despite heterogeneity across studies, NPIs, as assessed within the context of this systematic review at the macro and meso level, are effective in reducing SARS-CoV-2 transmission rates and COVID-19 hospitalisation rates and deaths in the European Region and may be applied as response strategies to reduce the burden of COVID-19 in forthcoming waves.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Constantine Vardavas", + "author_inst": "University of Crete" + }, + { + "author_name": "Katerina Nikitara", + "author_inst": "University of Crete" + }, + { + "author_name": "Katerina Aslanoglou", + "author_inst": "University of Crete" + }, + { + "author_name": "Michele Hilton Boon", + "author_inst": "WISE Centre for Economic Justice, Glasgow Caledonian University" + }, + { + "author_name": "Revati Phalkey", + "author_inst": "Climate Change and Health Group, Public Health England, United Kingdom" + }, + { + "author_name": "Jo Leonardi-Bee", + "author_inst": "Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" + }, + { + "author_name": "Gkikas Magiorkinis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Paraskevi Katsaounou", + "author_inst": "Department of Respiratory Medicine, National and Kapodistrian University of Athens, Athens, Greece" + }, + { + "author_name": "Anastasia Pharris", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "Ettore Severi", + "author_inst": "European Centre for Disease Prevention and Control" + }, + { + "author_name": "Jonathan E. Suk", + "author_inst": "European Centre for Disease Prevention and Control" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.10.21266124", "rel_title": "Differences in COVID-19 vaccination coverage by occupation in England: a national linked data study", @@ -522150,49 +523005,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.10.21266166", - "rel_title": "Unexposed populations and potential COVID-19 burden in European countries", - "rel_date": "2021-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.10.21266166", - "rel_abs": "We estimate the potential remaining COVID-19 burden in 19 European countries by estimating the proportion of each countrys population that has acquired immunity to severe disease through infection or vaccination. Our results suggest that many European countries could still face a substantial burden of hospitalisations and deaths, particularly those with lower vaccination coverage, less historical transmission, and/or older populations. Continued non-pharmaceutical interventions and efforts to achieve high vaccination coverage are required in these countries to limit severe COVID-19 outcomes.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Lloyd A C Chapman", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Rosanna C Barnard", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Timothy W Russell", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Sam Abbott", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Kevin van Zandvoort", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Nicholas G Davies", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Adam J Kucharski", - "author_inst": "London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.09.21266110", "rel_title": "Characterization of the humoral immune response to BNT162b2 in elderly residents of long-term care facilities five to seven months after vaccination", @@ -522417,6 +523229,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.09.21266145", + "rel_title": "Viral kinetic modeling and clinical trial simulation predicts disruption of respiratory disease trials by non-pharmaceutical COVID-19 interventions", + "rel_date": "2021-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.09.21266145", + "rel_abs": "Clinical research in infectious respiratory diseases has been profoundly affected by non-pharmaceutical interventions (NPIs) against COVID-19. On top of trial delays or even discontinuation which have been observed in all disease areas, NPIs altered transmission pattern of many seasonal respiratory viruses which followed regular patterns for decades before the pandemic. Clinical trial design based on pre-pandemic historical data therefore needs to be put in question. In this article, we show how knowledge-based mathematical modeling can be used to address this issue. We set up an epidemiological model of respiratory tract infection (RTI) sensitive to a time dependent between-host transmission rate and coupled this model to a mechanistic description of viral RTI episodes in an individual patient. By reducing the transmission rate when the lockdown was introduced in the United Kingdom in March 2020, we were able to reproduce the perturbed 2020 RTI disease burden data. Using this setup, we simulated several NPIs scenarios of various strength (none, mild, medium, strong) and conducted placebo-controlled in silico clinical trials in pediatric patients with recurrent RTIs (RRTI) quantifying annual RTI rate distributions. In interventional arms, virtual patients aged 1-5 years received the bacterial lysate OM-85 (approved in several countries for the prevention of pediatric RRTIs) through a pro-type I immunomodulation mechanism of action described by a physiologically based pharmacokinetics and pharmacodynamics approach (PBPK/PD). Our predictions showed that sample size estimates based on the ratio of RTI rates (or the post-hoc power of fixed sample size trials) are not majorly impacted under NPIs which are less severe (none, mild and medium NPIs) than a strict lockdown (strong NPI). However, NPIs show a stronger impact on metrics more relevant for assessing the clinical relevance of the effect such as absolute benefit. This dichotomy shows the risk that successful trials (even with their primary endpoints being met) still get challenged in risk benefit assessment during the review of market authorization. Furthermore, we found that a mild NPI scenario already affected the time to recruit significantly when sticking to eligibility criteria complying with historical data. In summary, our model predictions can help rationalize and forecast post-COVID-19 trial feasibility. They advocate for gauging absolute and relative benefit metrics as well as clinical relevance for assessing efficacy hypotheses in trial design and they question eligibility criteria misaligned with the actual disease burden.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Simon Ars\u00e8ne", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Claire Couty", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Igor Faddeenkov", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Natacha Go", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Sol\u00e8ne Granjeon-Noriot", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Daniel \u0160m\u00edt", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Riad Kahoul", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Ben Illigens", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Jean-Pierre Boissel", + "author_inst": "Novadiscovery" + }, + { + "author_name": "Aude Chevalier", + "author_inst": "OM Pharma" + }, + { + "author_name": "Lorenz Lehr", + "author_inst": "OM Pharma" + }, + { + "author_name": "Christian Pasquali", + "author_inst": "OM Pharma" + }, + { + "author_name": "Alexander Kulesza", + "author_inst": "Novadiscovery" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.09.467827", "rel_title": "A novel histone deacetylase inhibitor-based approach to eliminate microglia and retain astrocyte properties in glial cell culture.", @@ -523827,53 +524706,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.05.21265958", - "rel_title": "Patient trajectories among hospitalised COVID-19 patients vaccinated with an mRNA vaccine in Norway: a register-based cohort study", - "rel_date": "2021-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.05.21265958", - "rel_abs": "ObjectivesWith most of the Norwegian population vaccinated against COVID-19, an increasing number and proportion of COVID-19 related hospitalisations are occurring among vaccinated patients. We estimated the length of stay (LoS) in hospital and an intensive care unit (ICU), and risk of admission to ICU and in-hospital death among COVID-19 patients [≥]18 years who had been fully vaccinated with an mRNA vaccine, compared to unvaccinated patients.\n\nMethodsUsing national registry data, we conducted a cohort study on SARS-CoV-2 positive patients hospitalised in Norway between 1 February and 30 November 2021, with COVID-19 as the main cause of hospitalisation. We ran Cox proportional hazards models to analyse differences in our outcomes. Explanatory variables included vaccination status, age, sex, county of residence, regional health authority, date of admission, country of birth, virus variant and underlying risk factors.\n\nResultsWe included 3,203 patients, of whom 716 (22%) were fully vaccinated (at least two doses or one dose and previous SARS-CoV-2 infection). Fully vaccinated patients had a shorter overall LoS in hospital (aHR for discharge: 1.61, 95%CI: 1.24-2.08), shorter LoS without ICU (aHR: 1.27, 95%CI: 1.07-1.52), and lower risk of ICU admission (aHR: 0.50, 95%CI: 0.37-0.69) compared to unvaccinated patients. We observed no difference in the LoS in ICU, nor risk of in-hospital death between fully vaccinated and unvaccinated patients.\n\nConclusionsFully vaccinated patients hospitalised with COVID-19 in Norway have a shorter LoS and lower risk of ICU admission than unvaccinated patients. These findings can support patient management and ongoing capacity planning in hospitals.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Robert Whittaker", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Anja Brathen Kristofferson", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Beatriz Valcarcel Salamanca", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Elina Seppala", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Karan Golestani", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Reidar Kvale", - "author_inst": "Haukeland University Hospital" - }, - { - "author_name": "Sara Watle", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Eirik Buanes", - "author_inst": "Haukeland University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.08.21266083", "rel_title": "Regional and temporal variations affect the accuracy of variant-specific SARS-CoV-2 PCR assays", @@ -524006,6 +524838,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.11.09.21266122", + "rel_title": "The effects of the first national lockdown in England on geographical inequalities in the evolution of COVID-19 case rates: An ecological study", + "rel_date": "2021-11-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.09.21266122", + "rel_abs": "BackgroundSocio-economic inequalities in COVID-19 case rates have been noted worldwide. Previous studieshave compared case rates over set phases. There has been no analysis of how inequalities in cases changed overtime and were shaped by national mitigation strategies (e.g. lock downs). This paper provides the first analysis of the evolution of area-level inequalities in COVID-19 cases by deprivation levels in the first wave of the pandemic (January to July 2020) in England - with a focus on the effects of the first national lockdown (March - July 2020).\n\nMethodsWeekly case rates per Middle Super Output Area (MSOA, n=4412) in England from 2020-03-15 to 2020-07-04 were obtained, and characteristics of local epidemics were calculated, e.g. the highest case rate per area. Simple linear and logistic regression analyses were employed to assess the association of these metrics with index of multiple deprivation (IMD). Local authority-level (n=309) cases were used similarly in a sensitivity analysis, as these data were available daily and extended further back in time. The impact of lockdown was assessed by comparing the cumulative case rate in the most deprived 20% of MSOAs to the least deprived 20%, for the periods before the lockdown, and by the end of lockdown.\n\nFindingsLess deprived areas began recording COVID-19 cases earlier than more deprived areas and were more likely to have peaked by March 2020. More deprived areas case rates grew faster and peaked higher than less deprived areas. During the first national lockdown in the UK, the relative excess in case rates in the most deprived areas increased to 130% of that of the least deprived ones.\n\nInterpretationThe pattern of disease spread in England confirm the hypothesis that initial cases of a novel infectious disease are likely to occur in more affluent communities, but more deprived areas will overtake them once national mitigation strategies begin, and bear the brunt of the total case load. The strict first national lockdown served to increase case rate inequalities in England.\n\nFundingThis work was supported by a grant from The Health Foundation (Ref: 2211473), who took no part in the design, analysis or writing of this study.\n\nResearch in Context\n\nEvidence before this studyThe magnitude and distribution of deprivation-related inequalities in COVID-19 cases have been reported for England and many other countries, however, none have yet investigated the initial evolution of these inequalities, nor the effects of the first national lockdown.\n\nAdded value of this studyWe leverage the benefits of two separate datasets of COVID-19 case counts to investigate the initiation and evolution in inequalities in disease burden by deprivation. We found that cases were first recorded in less deprived areas before rising faster in more deprived areas. The first national lockdown led to an increase in these geographical inequalities.\n\nImplications of all the available evidenceNational lockdowns are an important tool in the armoury of pandemic control, but their timing and duration must be carefully decided and be locally specific. Because case rate inequalities were already present before lockdown in England, movement restrictions served to further increase them.\n\nSummary Box\n\nSection 1: What is already known on this subjectGeographical inequalities in COVID-19 case rates have been noted worldwide, and in England. However, how these inequalities were affected by policy responses - such as national lockdowns - has yet to be investigated.\n\nSection 2: What this study addsWe examined geographical inequalities in COVID-19 case rates by deprivation during the first English lock down (March - July, 2020). We find that cases were first reported in the less deprived areas of England, but this pattern quickly reversed and large excesses of cases occurred in the most deprived areas during the first national lockdown. Case rates in more deprived areas also rose more sharply, peaked higher, and then dropped faster than in less deprived areas. Inequality in cumulative case rates grew over the lockdown, increasing inequalities in disease burden.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Claire E Welsh", + "author_inst": "Newcastle University" + }, + { + "author_name": "Viviana Albani", + "author_inst": "Newcastle University" + }, + { + "author_name": "Fiona E Matthews", + "author_inst": "Newcastle University" + }, + { + "author_name": "Clare Bambra", + "author_inst": "Newcastle University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.08.21266055", "rel_title": "Immunity to COVID-19 in India through vaccination and natural infection", @@ -525441,185 +526304,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.08.21265380", - "rel_title": "Describing the population experiencing COVID-19 vaccine breakthrough following second vaccination in England: A cohort study from OpenSAFELY", - "rel_date": "2021-11-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21265380", - "rel_abs": "BackgroundWhile the vaccines against COVID-19 are considered to be highly effective, COVID-19 vaccine breakthrough is likely and a small number of people will still fall ill, be hospitalised, or die from COVID-19, despite being fully vaccinated. With the continued increase in numbers of positive SARS-CoV-2 tests, describing the characters of individuals who have experienced a COVID-19 vaccine breakthrough could be hugely important in helping to determine who may be at greatest risk.\n\nMethodWith the approval of NHS England we conducted a retrospective cohort study using routine clinical data from the OpenSAFELY TPP database of fully vaccinated individuals, linked to secondary care and death registry data, and described the characteristics of those experiencing a COVID-19 vaccine breakthrough.\n\nResultsAs of 01st November 2021, a total of 15,436,455 individuals were identified as being fully vaccinated against COVID-19, with a median follow-up time of 149 days (IQR: 107-179). From within this population, a total of 577245 (<4%) individuals reported a positive SARS-CoV-2 test. For every 1000 years of patient follow-up time, the corresponding incidence rate was 98.02 (95% CI 97.9-98.15). There were 16,120 COVID-19-related hospital admissions, 1,100 COVID-19 critical care admission patients and 3,925 COVID-19-related deaths; corresponding incidence rates of 2.72 (95% C 2.7-2.74), 0.19 (95% C 0.18-0.19) and 0.66 (95% C 0.65-0.67), respectively. When broken down by the initial priority group, higher rates of hospitalisation and death were seen in those in care homes and those over 80 years of age. Comorbidities with the highest rates of breakthrough COVID-19 included chronic kidney disease, dialysis, transplant, haematological malignancy, and immunocompromised.\n\nConclusionThe majority of COVID-19 vaccine breakthrough cases in England were mild with relatively few fully vaccinated individuals being hospitalised or dying as a result. However, some concerning differences in rates of breakthrough cases were identified in several clinical and demographic groups. While it is important to note that these findings are simply descriptive and cannot be used to answer why certain groups have higher rates of COVID-19 breakthrough than others, the emergence of the Omicron variant of COVID-19 coupled with the continued increase in numbers of positive SARS-CoV-2 tests are concerning. As numbers of fully vaccinated individuals increases and follow-up time lengthens, so too will the number of COVID-19 breakthrough cases. Additional analyses, aimed at identifying individuals at higher risk, are therefore required.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "Amelia CA Green", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "University of Oxford" - }, - { - "author_name": "William J Hulme", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elizabeth J Williamson", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Helen I McDonald", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Krishnan Bhaskaran", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Christopher T Rentsch", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Anna Schultze", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "University of Oxford" - }, - { - "author_name": "Viyaasan Mahalingasivam", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Laurie Tomlinson", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Alex J Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Louis Fisher", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jon Massey", - "author_inst": "University of Oxford" - }, - { - "author_name": "Colm D Andrews", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lisa E M Hopcroft", - "author_inst": "University of Oxford" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Richard Croker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jessica Morley", - "author_inst": "University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sebastian CJ Bacon", - "author_inst": "University of Oxford" - }, - { - "author_name": "David Evans", - "author_inst": "University of Oxford" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "University of Oxford" - }, - { - "author_name": "George Hickman", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tom Ward", - "author_inst": "University of Oxford" - }, - { - "author_name": "Simon Davy", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rohini Mathur", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "John Tazare", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Kevin Wing", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Angel YS Wong", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Harriet Forbes", - "author_inst": "University of Bristol" - }, - { - "author_name": "Christopher Bates", - "author_inst": "TPP" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP" - }, - { - "author_name": "John Parry", - "author_inst": "TPP" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP" - }, - { - "author_name": "Ian J Douglas", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Stephen JW Evans", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Liam Smeeth", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.05.21265810", "rel_title": "National and subnational short-term forecasting of COVID-19 in Germany and Poland, early 2021", @@ -525908,6 +526592,101 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.11.03.21265533", + "rel_title": "Effect of the Neutralizing SARS-CoV-2 Antibody Sotrovimab in Preventing Progression of COVID-19: A Randomized Clinical Trial", + "rel_date": "2021-11-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265533", + "rel_abs": "ImportanceOlder patients and those with underlying comorbidities infected with SARS-CoV-2 may be at increased risk of hospitalization and death from COVID-19. Sotrovimab is a neutralizing antibody designed for treatment of high-risk patients to prevent COVID-19 progression.\n\nObjectiveTo evaluate the efficacy and safety of sotrovimab in preventing progression of mild to moderate COVID-19 to severe disease.\n\nDesignRandomized, double-blind, multicenter, placebo-controlled, phase 3 study.\n\nSetting57 centers in 5 countries.\n\nParticipantsNonhospitalized patients with symptomatic, mild to moderate COVID-19 and at least 1 risk factor for disease progression.\n\nInterventionPatients were randomized (1:1) to an intravenous infusion of sotrovimab 500 mg or placebo.\n\nMain Outcomes and MeasuresThe primary efficacy outcome was the proportion of patients with COVID-19 progression, defined as all-cause hospitalization longer than 24 hours for acute illness management or death through day 29. Key secondary outcomes included the proportion of patients with COVID-19 progression, defined as emergency room visit, hospitalization of any duration, or death, and proportion of patients developing severe/critical respiratory COVID-19 requiring supplemental oxygen.\n\nResultsAmong 1057 patients randomized (sotrovimab, 528; placebo, 529), all-cause hospitalization longer than 24 hours or death was significantly reduced with sotrovimab (6/528 [1%]) vs placebo (30/529 [6%]) by 79% (95% CI, 50% to 91%; P<.001). Secondary outcome results further demonstrated the effect of sotrovimab in reducing emergency room visits, hospitalization of any duration, or death, which was reduced by 66% (95% CI, 37% to 81%; P<.001), and severe/critical respiratory COVID-19, which was reduced by 74% (95% CI, 41% to 88%; P=.002). No patients receiving sotrovimab required high-flow oxygen, oxygen via nonrebreather mask, or mechanical ventilation compared with 14 patients receiving placebo. The proportion of patients reporting adverse events was similar between treatment groups; sotrovimab was well tolerated, and no safety concerns were identified.\n\nConclusions and RelevanceAmong nonhospitalized patients with mild to moderate COVID-19, a single 500-mg intravenous dose of sotrovimab prevented progression of COVID-19, with a reduction in hospitalization and need for supplemental oxygen. Sotrovimab is a well-tolerated, effective treatment option for patients at high risk for severe morbidity and mortality from COVID-19.\n\nTrial RegistrationClinicalTrials.gov Identifier: NCT04545060", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Anil Gupta", + "author_inst": "Albion Finch Medical, William Osler Health Centre" + }, + { + "author_name": "Yaneicy Gonzalez-Rojas", + "author_inst": "Optimus U, Corp." + }, + { + "author_name": "Erick Juarez", + "author_inst": "Florida International Medical Research" + }, + { + "author_name": "Manuel Crespo", + "author_inst": "Alvaro Cunqueiro Hospital, IIS Galicia Sur" + }, + { + "author_name": "Jaynier Moya", + "author_inst": "Pines Care Research Center" + }, + { + "author_name": "Diego Falci", + "author_inst": "Hospital de Clinicas de Porto Alegre" + }, + { + "author_name": "Elias Sarkis", + "author_inst": "Sarkis Clinical Trials" + }, + { + "author_name": "Joel Solis", + "author_inst": "Centex Studies" + }, + { + "author_name": "Hanzhe Zheng", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Nicola Scott", + "author_inst": "GlaxoSmithKline" + }, + { + "author_name": "Andrea L. Cathcart", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Sergio Parra", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Jennifer E. Sager", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Daren J Austin", + "author_inst": "GlaxoSmithKline" + }, + { + "author_name": "Amanda Peppercorn", + "author_inst": "GlaxoSmithKline" + }, + { + "author_name": "Elizabeth Alexander", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Wendy W. Yeh", + "author_inst": "Vir Biotechnology, Inc" + }, + { + "author_name": "Cynthia Brinson", + "author_inst": "Central Texas Clinical Research" + }, + { + "author_name": "Melissa Aldinger", + "author_inst": "Vir Biotechnology, Inc." + }, + { + "author_name": "Adrienne E Shapiro", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.05.21265763", "rel_title": "Surveillance of COVID-19 in a Vaccinated Population: A Rapid Literature Review", @@ -527427,101 +528206,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.11.04.467308", - "rel_title": "SARS-CoV-2 infection in free-ranging white-tailed deer (Odocoileus virginianus)", - "rel_date": "2021-11-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.04.467308", - "rel_abs": "Human-to-animal spillover of SARS-CoV-2 virus has occurred in a wide range of animals, but thus far, the establishment of a new natural animal reservoir has not been detected. Here, we detected SARS-CoV-2 virus using rRT-PCR in 129 out of 360 (35.8%) free-ranging white-tailed deer (Odocoileus virginianus) from northeast Ohio (USA) sampled between January-March 2021. Deer in 6 locations were infected with at least 3 lineages of SARS-CoV-2 (B.1.2, B.1.596, B.1.582). The B.1.2 viruses, dominant in Ohio at the time, spilled over multiple times into deer populations in different locations. Deer-to-deer transmission may have occurred in three locations. The establishment of a natural reservoir of SARS-CoV-2 in white-tailed deer could facilitate divergent evolutionary trajectories and future spillback to humans, further complicating long-term COVID-19 control strategies.\n\nOne-Sentence SummaryA significant proportion of SARS-CoV-2 infection in free-ranging US white-tailed deer reveals a potential new reservoir.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Vanessa L Hale", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Patricia M Dennis", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Dillon S McBride", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Jacqueline M Nolting", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Christopher Madden", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Devra Huey", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Margot Ehrlich", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Jennifer Grieser", - "author_inst": "Cleveland Metroparks" - }, - { - "author_name": "Jenessa A Winston", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Dusty Lombardi", - "author_inst": "Ohio Wildlife Center" - }, - { - "author_name": "Stormy Gibson", - "author_inst": "Ohio Wildlife Center" - }, - { - "author_name": "Linda Saif", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Mary Lea Killian", - "author_inst": "USDA APHIS" - }, - { - "author_name": "Kristina Lantz", - "author_inst": "USDA APHIS VS: USDA Veterinary Services" - }, - { - "author_name": "Rachel M Tell", - "author_inst": "USDA APHIS" - }, - { - "author_name": "Mia Kim Torchetti", - "author_inst": "USDA Animal and Plant Health Inspection Service" - }, - { - "author_name": "Suelee Robbe-Austerman", - "author_inst": "United States Department of Agriculure" - }, - { - "author_name": "Martha I Nelson", - "author_inst": "National Institute of Allergy and Infectious Diseases, National Institutes of Health" - }, - { - "author_name": "Seth A Faith", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Andrew Bowman", - "author_inst": "Ohio State University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.11.04.467344", "rel_title": "Brilacidin, a COVID-19 Drug Candidate, demonstrates broad-spectrum antiviral activity against human coronaviruses OC43, 229E and NL63 through targeting both the virus and the host cell", @@ -527726,6 +528410,33 @@ "type": "new results", "category": "synthetic biology" }, + { + "rel_doi": "10.1101/2021.11.04.21265937", + "rel_title": "Estimation of the basic reproduction number of COVID-19 from the incubation period distribution", + "rel_date": "2021-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.04.21265937", + "rel_abs": "BackgroundThe estimates of future course of spreading of the SARS-CoV-2 virus are frequently based on Markovian models in which the transitions between the compartments are exponentially distributed. Specifically, the basic reproduction number R0 is also determined from formulae where it is related to the parameters of such models. The observations show that the start of infectivity of an individual appears nearly at the same time as the onset of symptoms, while the distribution of the incubation period is not an exponential.\n\nMethodsWe propose a method for estimation of R0 for COVID-19 based on the empirical incubation period distribution and assumed very short infectivity period that lasts only few days around the onset of symptoms. It is tested on daily new cases in six major countries in Europe, in the first wave of epidemic in spring, 2020.\n\nResultsThe calculations show that even if the infectivity starts two days before the onset of symptoms and stops immediately when they appear, the value of R0 is larger than that from the classical, Markovian approach. For more realistic cases, when only individuals with mild symptoms spread the virus for few days after onset of symptoms, the respective values are even larger.\n\nConclusionsThe calculations of R0 and other characteristics of spreading of COVID-19 based on the classical, Markovian approaches should be taken very cautiously. Instead, non-Markovian models with general distribution functions of transition between compartments should be considered as more appropriate.\n\nKey messagesO_LIAlthough formulae for estimate of the basic reproduction number R0, by using general-form functions of infectivity are known since the earliest works in epidemiology, majority of studies are based on exponential distribution function.\nC_LIO_LIWe introduce a new methodology of calculating R0 with an infectivity function obtained by combining empirical incubation period distribution with infectivity window function that is localized around the onset of symptoms.\nC_LIO_LIEstimates of R0 for the first wave of COVID - 19 in the spring 2020, by the proposed methodology are larger than those from the classical SIR model.\nC_LIO_LIWhen possible, the estimates of R0 should be based on empirical distributions of the infectivity functions, while the values obtained with the conventional epidemic spreading models should be taken with caution.\nC_LI", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lasko Basnarkov", + "author_inst": "SS Cyril and Methodius University in Skopje, Macedonia" + }, + { + "author_name": "Igor Tomovski", + "author_inst": "Macedonian Academy of Sciences and Arts" + }, + { + "author_name": "Florin Avram", + "author_inst": "Universite de Pau, France" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.04.21265910", "rel_title": "SARS-CoV-2 Aerosol Transmission Indoors: A Closer Look at Viral Load, Infectivity, the Effectiveness of Preventive Measures and a Simple Approach for Practical Recommendations", @@ -529061,37 +529772,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.03.21265863", - "rel_title": "Downsizing of contact tracing during COVID-19 vaccine roll-out", - "rel_date": "2021-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265863", - "rel_abs": "Contact tracing is a key component of successful management of COVID-19. Contacts of infected individuals are asked to quarantine, which can significantly slow down (or prevent) community spread. Contact tracing is particularly effective when infections are detected quickly (e.g., through rapid testing), when contacts are traced with high probability, when the initial number of cases is low, and when social distancing and border restrictions are in place. However, the magnitude of the individual contribution of these factors in reducing epidemic spread and the impact of vaccination in determining contact tracing outputs is not fully understood. We present a delayed differential equation model to investigate how vaccine roll-out and the relaxation of social distancing requirements affect contact tracing practises. We provide an analytical criteria to determine the minimal contact tracing efficiency (defined as the the probability of identifying and quarantining contacts of symptomatic individuals) required to keep an outbreak under control, with respect to the contact rate and vaccination status of the population. Additionally, we consider how delays in outbreak detection and increased case importation rates affect the number of contacts to be traced daily. We show that in vaccinated communities a lower contact tracing efficiency is required to avoid uncontrolled epidemic spread, and delayed outbreak detection and relaxation of border restrictions do not lead to a significantly higher risk of overwhelming contact tracing. We find that investing in testing programs, rather than increasing the contact tracing capacity, has a larger impact in determining whether an outbreak will be controllable. This is because early detection activates contact tracing, which will slow, and eventually reverse exponential growth, while the contact tracing capacity is a threshold that will easily become overwhelmed if exponential growth is not curbed. Finally, we evaluate quarantine effectiveness during vaccine roll-out, by considering the proportion of people that will develop an infection while in isolation in relation to the vaccination status of the population and for different viral variants. We show that quarantine effectiveness decreases with increasing proportion of fully vaccinated individuals, and increases in the presence of more transmissible variants. These results suggest that a cost-effective approach during vaccine roll-out is to establish different quarantine rules for vaccinated and unvaccinated individuals, where rules should depend on viral trans-missibility. Altogether, our study provides quantitative information for contact tracing downsizing during vaccine roll-out, to guide COVID-19 exit strategies.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Maria M Martignoni", - "author_inst": "Memorial University of Newfoundland" - }, - { - "author_name": "Joshua Renault", - "author_inst": "Memorial University of Newfoundland" - }, - { - "author_name": "Joseph Baafi", - "author_inst": "Memorial University of Newfoundland" - }, - { - "author_name": "Amy Hurford", - "author_inst": "Memorial University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.03.21260184", "rel_title": "Whole-Blood Methylation Analysis Reveals Respiratory Environmental Functional Pathways Involved in Severity Following SARS-CoV-2 Infection", @@ -529604,6 +530284,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.02.466951", + "rel_title": "Drug targeting Nsp1-ribosomal complex shows antiviral activity against SARS-CoV-2", + "rel_date": "2021-11-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.02.466951", + "rel_abs": "The SARS-Cov-2 non-structural protein 1 (Nsp1) contains an N-terminal domain and C-terminal helices connected by a short linker region. The C-terminal helices of Nsp1 (Nsp1-C-ter) from SARS-Cov-2 bind in the mRNA entry channel of the 40S ribosomal subunit and block the entry of mRNAs thereby shutting down host protein synthesis. Nsp1 suppresses the host immune function and is vital for viral replication. Hence, Nsp1 appears to be an attractive target for therapeutics. In this study, we have in silico screened Food and Drug Administration (FDA)-approved drugs against Nsp1-C-ter and find that montelukast sodium hydrate binds to Nsp1-C-ter with a binding affinity (KD) of 10.8{+/-}0.2 M in vitro and forms a stable complex with it in simulation runs with a binding energy of -76.71{+/-}8.95 kJ/mol. The drug also rescues the inhibitory effect of Nsp1 in host protein synthesis as demonstrated by the expression of firefly luciferase reporter gene in cells. Importantly, montelukast sodium hydrate demonstrates antiviral activity against SARS-CoV-2 with reduced viral replication in HEK cells expressing ACE2 and Vero-E6 cells. We therefore propose montelukast sodium hydrate may help in combatting SARS-CoV-2 infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tanweer Hussain", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Mohammad Afsar", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Rohan Narayan", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Md Noor Akhtar", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Huma Rahil", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Sandeep Eswarappa", + "author_inst": "Indian Institute of Science Bangalore" + }, + { + "author_name": "Shashank Tripathi", + "author_inst": "Indian Institute of Science" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.11.03.21265876", "rel_title": "Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility", @@ -531759,37 +532482,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.30.21265430", - "rel_title": "Automated Interpretable Discovery of Heterogeneous Treatment Effectiveness: A Covid-19 Case Study", - "rel_date": "2021-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.30.21265430", - "rel_abs": "Testing multiple treatments for heterogeneous (varying) effectiveness with respect to many underlying risk factors requires many pairwise tests; we would like to instead automatically discover and visualize patient archetypes and predictors of treatment effectiveness using multitask machine learning. In this paper, we present a method to estimate these heterogeneous treatment effects with an interpretable hierarchical framework that uses additive models to visualize expected treatment benefits as a function of patient factors (identifying personalized treatment benefits) and concurrent treatments (identifying combinatorial treatment benefits). This method achieves state-of-the-art predictive power for Covid-19 in-hospital mortality and interpretable identification of heterogeneous treatment benefits. We first validate this method on the large public MIMIC-IV dataset of ICU patients to test recovery of heterogeneous treatment effects. Next we apply this method to a proprietary dataset of over 3000 patients hospitalized for Covid-19, and find evidence of heterogeneous treatment effectiveness predicted largely by indicators of inflammation and throm-bosis risk: patients with few indicators of thrombosis risk benefit most from treatments against inflammation, while patients with few indicators of inflammation risk benefit most from treatments against thrombosis. This approach provides an automated methodology to discover heterogeneous and individualized effectiveness of treatments.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Benjamin J Lengerich", - "author_inst": "MIT" - }, - { - "author_name": "Mark E. Nunnally", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Yin J Aphinyanaphongs", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Rich Caruana", - "author_inst": "Microsoft Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.31.21265714", "rel_title": "Azithromycin consumption during the COVID-19 pandemic in Croatia, 2020", @@ -531982,6 +532674,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.01.21265653", + "rel_title": "Modelling COVID-19 Pandemic Dynamics Using Transparent, Interpretable, Parsimonious and Simulatable (TIPS) Machine Learning Models: A Case Study from Systems Thinking and System Identification Perspectives", + "rel_date": "2021-11-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265653", + "rel_abs": "Since the outbreak of COVID-19, an astronomical number of publications on the pandemic dynamics appeared in the literature, of which many use the susceptible infected removed (SIR) and susceptible exposed infected removed (SEIR) models, or their variants, to simulate and study the spread of the coronavirus. SIR and SEIR are continuous-time models which are a class of initial value problems (IVPs) of ordinary differential equations (ODEs). Discrete-time models such as regression and machine learning have also been applied to analyze COVID-19 pandemic data (e.g. predicting infection cases), but most of these methods use simplified models involving a small number of input variables pre-selected based on a priori knowledge, or use very complicated models (e.g. deep learning), purely focusing on certain prediction purposes and paying little attention to the model interpretability. There have been relatively fewer studies focusing on the investigations of the inherent time-lagged or time-delayed relationships e.g. between the reproduction number (R number), infection cases, and deaths, analyzing the pandemic spread from a systems thinking and dynamic perspective. The present study, for the first time, proposes using systems engineering and system identification approach to build transparent, interpretable, parsimonious and simulatable (TIPS) dynamic machine learning models, establishing links between the R number, the infection cases and deaths caused by COVID-19. The TIPS models are developed based on the well-known NARMAX (Nonlinear AutoRegressive Moving Average with eXogenous inputs) model, which can help better understand the COVID-19 pandemic dynamics. A case study on the UK COVID-19 data is carried out, and new findings are detailed. The proposed method and the associated new findings are useful for better understanding the spread dynamics of the COVID-19 pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hua-Liang Wei", + "author_inst": "The University Of Sheffield" + }, + { + "author_name": "Stephen A Billings", + "author_inst": "The University of Sheffield" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.01.21265729", "rel_title": "Quantifying the effects of non-pharmaceutical and pharmaceutical interventions against COVID-19 epidemic in the Republic of Korea: Mathematical model-based approach considering age groups and the Delta variant", @@ -533393,45 +534108,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.29.21265683", - "rel_title": "Label-Free SARS-CoV-2 Detection on Flexible Substrates", - "rel_date": "2021-10-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.29.21265683", - "rel_abs": "One of the most important strategies for mitigation and managing pandemics is widespread, rapid and inexpensive testing and isolation of infected patients. In this study, we demonstrate large area, label-free, and rapid testing sensor platforms fabricated on both rigid and flexible substrates for fast and accurate detection of SARS-CoV-2. SERS enhancing metal insulator metal (MIM) nanostructures are modeled using finite element simulations and then fabricated using nanoimprint lithography (NIL) and transfer printing. The SERS signal of various viral samples, including spiked saliva, was analyzed using machine learning classifiers. We observe that our approach can obtain the test results typically within 25 minutes with a detection accuracy of at least 83% for the viral samples. We envision that this approach which features large area nanopatterning, fabrication in both rigid and flexible formats for wearables, SERS spectroscopy and machine learning can enable new types of rapid, label-free biosensors for screening pathogens and managing current and future pandemics.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Debadrita Paria", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Kam Sang Kwok", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Piyush Raj", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Peng Zheng", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "David Gracias", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Ishan Barman", - "author_inst": "Johns Hopkins University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.30.21265699", "rel_title": "Measuring College Student Attitudes Toward COVID-19 Vaccinations", @@ -533656,6 +534332,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.10.28.21265499", + "rel_title": "Time of day of vaccination affects SARS-CoV-2 antibody responses in an observational study of healthcare workers", + "rel_date": "2021-10-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265499", + "rel_abs": "The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global crisis with unprecedented challenges for public health. Vaccinations against SARS-CoV-2 have slowed the incidence of new infections and reduced disease severity. As the time-of-day of vaccination has been reported to influence host immune responses to multiple pathogens, we quantified the influence of SARS-CoV-2 vaccination time, vaccine type, age, sex, and days post-vaccination on anti-Spike antibody responses in healthcare workers. The magnitude of the anti-Spike antibody response associated with the time-of-day of vaccination, vaccine type, participant age, sex, and days post vaccination. These results may be relevant for optimizing SARS-CoV-2 vaccine efficacy.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Wei Wang", + "author_inst": "Division of Sleep and Circadian Disorders, Brigham and Womens Hospital; Division of Sleep Medicine, Harvard Medical School, US." + }, + { + "author_name": "Peter Balfe", + "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, UK" + }, + { + "author_name": "David W Eyre", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sheila F Lumley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Denise O'Donnell", + "author_inst": "Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK" + }, + { + "author_name": "Fiona Warren", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK" + }, + { + "author_name": "Derrick W Crook", + "author_inst": "NIHR Oxford Biomedical Research Centre" + }, + { + "author_name": "Katie Jeffery", + "author_inst": "Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, and\tRadcliffe Department of Medic" + }, + { + "author_name": "Philippa C Matthews", + "author_inst": "Nuffield Department of Medicine, and 4.\tDepartment of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hos" + }, + { + "author_name": "Elizabeth B Klerman", + "author_inst": "Massachusetts General Hospital/Harvard Medical School" + }, + { + "author_name": "Jane McKeating", + "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.28.21265544", "rel_title": "In vitro characterisation and clinical evaluation of the diagnostic accuracy of a new antigen test for SARS-CoV-2 detection.", @@ -535219,65 +535954,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.10.29.466408", - "rel_title": "The glycosylated extracellular domain of MUC1 protects against SARS-CoV-2 infection at the respiratory surface", - "rel_date": "2021-10-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.29.466408", - "rel_abs": "Mucins play an essential role in protecting the respiratory tract against microbial infections but can also serve as binding sites for bacterial and viral adhesins. The heavily O-glycosylated gel-forming mucins MUC5AC and MUC5B eliminate pathogens by mucociliary clearance while transmembrane mucins MUC1, MUC4, and MUC16 can restrict microbial invasion at the apical surface of the epithelium. In this study, we determined the impact of host mucins and mucin glycans on SARS-CoV-2 epithelial entry. Human lung epithelial Calu-3 cells express the SARS-CoV-2 entry receptor ACE2 and high levels of glycosylated MUC1, but not MUC4 and MUC16, on their cell surface. The O-glycan-specific mucinase StcE specifically removed the glycosylated part of the MUC1 extracellular domain while leaving the underlying SEA domain and cytoplasmic tail intact. StcE treatment of Calu-3 cells significantly enhanced infection with SARS-CoV-2 pseudovirus and authentic virus, while removal of sialic acid and fucose from the epithelial surface did not impact viral entry. Both MUC1 and MUC16 are expressed on the surface of human air-liquid interface (ALI) differentiated airway organoids and StcE treatment led to mucin removal and increased levels of SARS-CoV-2 entry and replication. On the surface of Calu-3 cells, the transmembrane mucin MUC1 and ACE2 are often co-expressed and StcE treatment results in enhanced binding of purified spike protein and SARS-CoV-2 pseudovirus. This study points at an important role for glycosylated mucin domains as components of the host defense that can restrict SARS-CoV-2 infection.\n\nAuthor summarySARS-CoV-2, the virus that has caused the devastating COVID-19 pandemic, causes a range of symptoms in infected individuals, from mild respiratory illness to acute respiratory distress syndrome. A fundamental understanding of host factors influencing viral entry is critical to elucidate SARS-CoV-2-host interactions and identify novel therapeutic targets. In this study, we investigated the role of host mucins and mucin glycans on SARS-CoV-2 entry into the airway epithelial cells. Mucins are a family of high molecular weight O-glycosylated proteins that play an essential role in protecting the respiratory tract against viral and bacterial infections. The gel-forming mucins MUC5AC and MUC5B clear pathogens by mucociliary clearance while transmembrane mucins MUC1, MUC4, and MUC16 can restrict or facilitate microbial invasion at the apical surface of the epithelium. The mucin-selective protease StcE specifically cleaves the glycosylated extracellular part of the mucins without perturbing the underlying domains. We show that removal of mucins from the surface of Calu-3 cells and primary airway epithelial cultures with StcE mucinase increases binding of the SARS-CoV-2 spike protein to the respiratory surface and greatly enhances infection. This study demonstrates the important role of glycosylated extracellular mucin domains as a host defense mechanism during SARS-CoV-2 entry. Future efforts should be focused on characterizing the role of specific soluble and transmembrane mucins during the different stages of SARS-CoV-2 infection.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Maitrayee Chatterjee", - "author_inst": "Utrecht University" - }, - { - "author_name": "Liane Z.X Huang", - "author_inst": "Utrecht University" - }, - { - "author_name": "Anna Z Mykytyn", - "author_inst": "Erasmus Medical Centre" - }, - { - "author_name": "Chunyan Wang", - "author_inst": "Utrecht University" - }, - { - "author_name": "Mart M. Lamers", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Bart Westendorp", - "author_inst": "Utrecht University" - }, - { - "author_name": "Richard W Wubbolts", - "author_inst": "Utrecht University" - }, - { - "author_name": "Jos P.M van Putten", - "author_inst": "Utrecht University" - }, - { - "author_name": "Berend Jan Bosch", - "author_inst": "Utrecht University" - }, - { - "author_name": "Bart Haagmans", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Karin Strijbis", - "author_inst": "Utrecht University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.10.26.21265146", "rel_title": "Detection of SARS-CoV-2 RNA Throughout Wastewater Treatment Plants and A Modeling Approach to Understand COVID-19 Infection Dynamics in Winnipeg, Canada", @@ -535522,6 +536198,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.27.21265574", + "rel_title": "Boosting of Cross-Reactive Antibodies to Endemic Coronaviruses by SARS-CoV-2 Infection but not Vaccination with Stabilized Spike", + "rel_date": "2021-10-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.27.21265574", + "rel_abs": "Pre-existing antibodies to endemic coronaviruses (CoV) that cross-react with SARS-CoV-2 have the potential to influence the antibody response to COVID-19 vaccination and infection for better or worse. In this observational study of mucosal and systemic humoral immunity in acutely infected, convalescent, and vaccinated subjects, we tested for cross reactivity against endemic CoV spike (S) protein at subdomain resolution. Elevated responses, particularly to the {beta}-CoV OC43, were observed in all natural infection cohorts tested and were correlated with the response to SARS-CoV-2. The kinetics of this response and isotypes involved suggest that infection boosts preexisting antibody lineages raised against prior endemic CoV exposure that cross react. While further research is needed to discern whether this recalled response is desirable or detrimental, the boosted antibodies principally targeted the better conserved S2 subdomain of the viral spike and were not associated with neutralization activity. In contrast, vaccination with a stabilized spike mRNA vaccine did not robustly boost cross-reactive antibodies, suggesting differing antigenicity and immunogenicity. In sum, this study provides evidence that antibodies targeting endemic CoV are robustly boosted in response to SARS-CoV-2 infection but not to vaccination with stabilized S, and that depending on conformation or other factors, the S2 subdomain of the spike protein triggers a rapidly recalled, IgG-dominated response that lacks neutralization activity.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=61 SRC=\"FIGDIR/small/21265574v1_figA1.gif\" ALT=\"Figure 1\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@168d38aorg.highwire.dtl.DTLVardef@1183afcorg.highwire.dtl.DTLVardef@1c88b77org.highwire.dtl.DTLVardef@13c6e0a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO Antibody responses to SARS-CoV-2 and endemic CoV spike proteins were measured in diverse cohorts. While antibodies to SARS-CoV-2 were induced across all isotypes, only IgA and IgG responses to endemic CoV were robustly boosted, and only among naturally-infected but not vaccinated individuals. These recalled, cross-reactive responses to endemic CoV primarily recognized the better conserved S2 domain and were non-neutralizing. While other antiviral activities of broadly cross-reactive S2-specifc antibodies are not known, the differing antigenicity of natural infection and vaccination with stabilized pre-fusion spike has potential implications for the breadth and level of protection afforded by each.\n\nC_FIG", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Andrew R Crowley", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Harini Natarajan", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Andrew P Hederman", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Carly A Bobak", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Joshua A Weiner", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Wendy F. Wieland-Alter", + "author_inst": "Dartmouth Hitchcock Medical Center" + }, + { + "author_name": "Jiwon Lee", + "author_inst": "Dartmouth College" + }, + { + "author_name": "Evan M Bloch", + "author_inst": "Johns Hopkins Medicine" + }, + { + "author_name": "Aaron AR Tobian", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Andrew Redd", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Joel N. Blankson", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Dana Wolf", + "author_inst": "Hadassah University Medical Center" + }, + { + "author_name": "Tessa Goetghebuer", + "author_inst": "CHU St. Pierre" + }, + { + "author_name": "Arnaud Marchant", + "author_inst": "Universite libre de Bruxelles" + }, + { + "author_name": "Ruth I Connor", + "author_inst": "Dartmouth Hitchcock Medical Center" + }, + { + "author_name": "Peter F Wright", + "author_inst": "Dartmouth Hitchcock Medical Center" + }, + { + "author_name": "Margaret E Ackerman", + "author_inst": "Dartmouth College" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.27.21265591", "rel_title": "How many lives do COVID vaccines save? Evidence from Israel.", @@ -536981,33 +537740,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.20.21265254", - "rel_title": "COVID-19 Observations from Hospitalized Ward Patients in the Northern Emirates: A Practice Only Preached.", - "rel_date": "2021-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265254", - "rel_abs": "BackgroundThe COVID-19 pandemic has established itself as the defining global health crisis of this time. The study describes the clinical profile of hospitalized, non-ICU patients with COVID-19 in the United Arab Emirates (UAE) during its second wave, through January-March 2021. It also highlights the use of antibiotic stewardship principles in patients admitted with COVID-19.\n\nMethodologyAn observational, retrospective study was conducted with 110 participants from Sheikh Khalifa General Hospital - Umm Al Quwain in the UAE. Pregnant women, patients who were admitted to/transferred to/discharged from the intensive care unit, patients who were receiving antibiotics prior to admission were excluded from the study.\n\nResultsPopulation was 58.2% male with a mean age of 51.2 ({+/-} 14.6) years; 69.1% had at least one comorbidity and 61.8% were classified as severe COVID-19 disease. Mean WBC count was 6.03 {+/-} 2.70 x 109 cells/L with a mean CRP of 83.3 {+/-} 14.6 mg/L. 4.2% of the tested (20.9%) blood cultures performed were positive. Immunomodulators (67.26%), prophylactic anticoagulants (90%), anti-viral drugs (83.61%) were primary modalities of therapy. Empiric antibiotic use was limited to 9.1% of population.\n\nConclusionOur study highlighted that the population admitted to the hospital in the second wave of the COVID-19 pandemic in the UAE were mostly male, older with higher prevalence of comorbidities. Given the limited knowledge of the new disease, we took bold but calculated clinical measures to maintain antibiotic stewardship practice and brought antibiotic prescribing to extraordinary low level not seen during the COVID-19 pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Shahab Qureshi", - "author_inst": "University of Sharjah" - }, - { - "author_name": "Drishti Dhirendra Kampani", - "author_inst": "University of Sharjah" - }, - { - "author_name": "Tara Ali Hassan Al-Qutbi", - "author_inst": "University of Sharjah" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.20.21265171", "rel_title": "Neutralizing Antibody Response to Pseudotype SARS-CoV-2 Differs between mRNA-1273 and BNT162b2 COVID-19 Vaccines and by History of SARS-CoV-2 Infection", @@ -537300,6 +538032,97 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.10.25.465714", + "rel_title": "Nanobodies recognizing conserved hidden clefts of all SARS-CoV-2 spike variants", + "rel_date": "2021-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.25.465714", + "rel_abs": "We are in the midst of the historic coronavirus infectious disease 2019 (COVID-19) pandemic caused by severe respiratory syndrome coronavirus 2 (SARS-CoV-2). Although countless efforts to control the pandemic have been attempted--most successfully, vaccination1-3--imbalances in accessibility to vaccines, medicines, and diagnostics among countries, regions, and populations have been problematic. Camelid variable regions of heavy chain-only antibodies (VHHs or nanobodies)4 have unique modalities: they are smaller, more stable, easier to customize, and, importantly, less expensive to produce than conventional antibodies5, 6. We present the sequences of nine alpaca nanobodies that detect the spike proteins of four SARS-CoV-2 variants of concern (VOCs)--namely, the alpha, beta, gamma, and delta variants. We show that they can quantify or detect spike variants via ELISA and lateral flow, kinetic, flow cytometric, microscopy, and Western blotting assays7. The panel of nanobodies broadly neutralized viral infection by pseudotyped SARS-CoV-2 VOCs. Structural analyses showed that a P86 clone targeted epitopes that were conserved yet unclassified on the receptor-binding domain (RBD) and located inside the N-terminal domain (NTD). Human antibodies have hardly accessed both regions; consequently, the clone buries hidden crevasses of SARS-CoV-2 spike proteins undetected by conventional antibodies and maintains activity against spike proteins carrying escape mutations.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Ryota Maeda", + "author_inst": "Kyoto University & COGNANO Inc." + }, + { + "author_name": "Junso Fujita", + "author_inst": "Osaka University" + }, + { + "author_name": "Yoshinobu Konishi", + "author_inst": "Kyoto University" + }, + { + "author_name": "Yasuhiro Kazuma", + "author_inst": "Kyoto University" + }, + { + "author_name": "Hiroyuki Yamazaki", + "author_inst": "COGNANO Inc." + }, + { + "author_name": "Itsuki Anzai", + "author_inst": "Osaka University" + }, + { + "author_name": "Keishi Yamaguchi", + "author_inst": "Osaka University" + }, + { + "author_name": "Kazuki Kasai", + "author_inst": "Kyoto University & COGNANO Inc." + }, + { + "author_name": "Kayoko Nagata", + "author_inst": "Kyoto University" + }, + { + "author_name": "Yutaro Yamaoka", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Kei Miyakawa", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Akihide Ryo", + "author_inst": "Yokohama City University" + }, + { + "author_name": "Kotaro Shirakawa", + "author_inst": "Kyoto University" + }, + { + "author_name": "Fumiaki Makino", + "author_inst": "Osaka University & JEOL Ltd." + }, + { + "author_name": "Yoshiharu Matsuura", + "author_inst": "Osaka University" + }, + { + "author_name": "Tsuyoshi Inoue", + "author_inst": "Osaka University" + }, + { + "author_name": "Akihiro Imura", + "author_inst": "COGNANO Inc." + }, + { + "author_name": "Keiichi Namba", + "author_inst": "Osaka University & JEOL YOKOGUSHI Research Alliance Laboratories & RIKEN Center for Biosystems Dynamics Research and SPring-8 Center" + }, + { + "author_name": "Akifumi Takaori-Kondo", + "author_inst": "Kyoto University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.10.22.21265188", "rel_title": "Response to the coronavirus disease 2019 (COVID-19) pandemic at private retail pharmacies in Kenya: a mixed methods study", @@ -538815,57 +539638,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.23.21265407", - "rel_title": "Relationship among work-treatment balance, job stress, and work engagement in Japan: A cross-sectional study", - "rel_date": "2021-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.23.21265407", - "rel_abs": "There is a drive to support workers undergoing medical treatment who wish to continue working in Japan, known as the work-treatment balance. It is hoped that this support for the work-treatment balance could boost their mental health. This study examines the relationship among the work-treatment balance, job stress, and work engagement. This study was conducted in December 2020 in Japan, with 27,036 participants. We divided the participants into three groups by the receipt state of support for the work-treatment balance: control group (no need the support), unsupported group, and supported group. The scores of the parameters of the job content questionnaire and the Utrecht Work Engagement Scale (UWES-3) were compared among groups using a multilevel regression with age-sex or multivariate-adjusted models. In the two models, the job control score of the unsupported group was significantly lower than that of the control group. The two social support scores of the supported group were significantly higher than those of the control group. The scores of the UWES-3 of the unsupported group were significantly lower than those of the control group. The support of work-treatment balance for workers could have a positive impact on their mental health.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kazunori Ikegami", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Hajime Ando", - "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health" - }, - { - "author_name": "Hisashi Eguchi", - "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Koji Mori", - "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health" - }, - { - "author_name": "Keiji Muramatsu", - "author_inst": "University of Occupational and Environmental Health" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Akira Ogami", - "author_inst": "Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.10.25.21265494", "rel_title": "Health workers Motivators to uptake of the Covid-19 vaccine at Iganga Hospital Eastern Uganda, and Mengo Hospital Kampala Uganda; A qualitative study", @@ -539226,6 +539998,189 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.10.18.21264530", + "rel_title": "Integrated Genomic Surveillance reveals extensive onward transmission of travel-imported SARS-CoV-2 infections in the community", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.18.21264530", + "rel_abs": "Integration of genomic surveillance with contact tracing provides a powerful tool for the reconstruction of person-to-person pathogen transmission chains. We report two large clusters of SARS-CoV-2 cases (\"Delta\" clade, 110 cases combined) detected in July 2021 by Integrated Genomic Surveillance in Dusseldorf. Structured interviews and deep contact tracing demonstrated an association to a single SARS-CoV-2 infected return traveller (Cluster 1) and to return travel from Catalonia and other European countries (Cluster 2), highlighting the importance of containing travel-imported SARS-CoV-2 infections.", + "rel_num_authors": 42, + "rel_authors": [ + { + "author_name": "Torsten Houwaart", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Samir Belhaj", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Emran Tawalbeh", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Dirk Nagels", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Patrick Finzer", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany; Zotz | Klimas, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Lisa Stiller", + "author_inst": "Medizinische Laboratorien D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Jacqueline Blum", + "author_inst": "Medizinische Laboratorien D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Christian Lange", + "author_inst": "Medizinische Laboratorien D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Yara Fr\u00f6hlich", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Assia Benmoumene", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Dounia Asskali", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Hussein Haidar", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Janina von Dahlen", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Carla Adelmann", + "author_inst": "Solingen Health Authority (Gesundheitsamt Solingen)" + }, + { + "author_name": "Britta Schroer", + "author_inst": "Solingen Health Authority (Gesundheitsamt Solingen)" + }, + { + "author_name": "Ute Osmers", + "author_inst": "MVZ SYNLAB Leverkusen GmbH" + }, + { + "author_name": "Christiane Grice", + "author_inst": "MVZ SYNLAB Leverkusen GmbH" + }, + { + "author_name": "Phillipp P. Kirfel", + "author_inst": "MVZ SYNLAB Leverkusen GmbH" + }, + { + "author_name": "Hassan Jomaa", + "author_inst": "MVZ SYNLAB Leverkusen GmbH" + }, + { + "author_name": "Moritz Pigulla", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Pascal Kreuzer", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Alona Tyshaieva", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Jonas Weber", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Daniel Strelow", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Jessica Nicolai", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Tobias Wienemann", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Malte Kohns Vasconcelos", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Lisanna H\u00fclse", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Katrin Hoffmann", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Nadine L\u00fcbke", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Sandra Hauka", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Marcel Andree", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Claus J\u00fcrgen Scholz", + "author_inst": "Labor Dr. Wisplinghoff, Cologne, Germany" + }, + { + "author_name": "Nathalie Jazmati", + "author_inst": "Labor Dr. Wisplinghoff, Cologne, Germany" + }, + { + "author_name": "Klaus G\u00f6bels", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Rainer Zotz", + "author_inst": "Zotz | Klimas, D\u00fcsseldorf, Germany; Labor Dr. Wisplinghoff, Cologne, Germany" + }, + { + "author_name": "Klaus Pfeffer", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "J\u00f6rg Timm", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Lutz Ehlkes", + "author_inst": "D\u00fcsseldorf Health Authority (Gesundheitsamt D\u00fcsseldorf), D\u00fcsseldorf, Germany" + }, + { + "author_name": "Andreas Walker", + "author_inst": "Institute of Virology, University Hospital D\u00fcsseldorf, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "Alexander T. Dilthey", + "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Heinrich Heine University D\u00fcsseldorf, D\u00fcsseldorf, Germany" + }, + { + "author_name": "- German COVID-19 OMICS Initiative (DeCOI)", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.24.465626", "rel_title": "SARS-CoV-2 infects human adipose tissue and elicits an inflammatory response consistent with severe COVID-19", @@ -540745,33 +541700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.23.21265403", - "rel_title": "The 1968 Influenza Pandemic and COVID-19 Outcomes", - "rel_date": "2021-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.23.21265403", - "rel_abs": "Past pandemic experience can affect health outcomes in future pandemics. This paper focuses on the last major influenza pandemic in 1968 (H3N2), which killed up to 100,000 people in the US. We find that places with high influenza mortality in 1968 experienced 1-4% lower COVID-19 death rates. Our identification strategy isolates variation in COVID-19 rates across people born before and after 1968. In places with high 1968 influenza incidence, older cohorts experience lower COVID-19 death rates relative to younger ones. The relationship holds using county and patient-level data, as well as in hospital and nursing home settings. Results do not appear to be driven by systemic or policy-related factors, instead suggesting an individual-level response to prior influenza pandemic exposure. The findings merit investigation into potential biological and immunological mechanisms that account for these differences--and their implications for future pandemic preparedness.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Charles A Taylor", - "author_inst": "Columbia University; University of California, Berkeley" - }, - { - "author_name": "Christopher Boulos", - "author_inst": "Columbia University" - }, - { - "author_name": "Matthew J Memoli", - "author_inst": "National Institute of Allergy and Infectious Diseases (NIAID)" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.23.21265086", "rel_title": "Disease waves of SARS-CoV-2 in Iran closely mirror global pandemic trends", @@ -541204,6 +542132,145 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.10.22.465476", + "rel_title": "The humanized nanobody RBD-1-2G tolerates the spike N501Y mutation to neutralize SARS-CoV-2", + "rel_date": "2021-10-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.22.465476", + "rel_abs": "Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) ex vivo model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Ying Fu", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Juliana da Fonseca Rezende e Mello", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Bryan D Fleming", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Alex Renn", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Catherine Z. Chen", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Xin Hu", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Miao Xu", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Kirill Gorshkov", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Quinlin Hanson", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Wei Zheng", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Emily M Lee", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Lalith Perera", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Robert Petrovich", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Manisha Pradhan", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Richard T Eastman", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Zina Itkin", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Thomas Stanley", + "author_inst": "National Institute of Environmental Health Services" + }, + { + "author_name": "Allen Hsu", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Venkata Dandey", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "William Gillette", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Troy Taylor", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Nitya Ramakrishnan", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Shelley Perkins", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Dominic Esposito", + "author_inst": "Frederick National Laboratory for Cancer Research" + }, + { + "author_name": "Eunkeu Oh", + "author_inst": "Naval Research Laboratory" + }, + { + "author_name": "Kimihiro Susumu", + "author_inst": "Jacobs Corporation" + }, + { + "author_name": "Mason Wolak", + "author_inst": "Naval Research Laboratory" + }, + { + "author_name": "Marc Ferrer", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Matthew D. Hall", + "author_inst": "National Center for Advancing Translational Sciences" + }, + { + "author_name": "Mario J Borgnia", + "author_inst": "National Institute of Environmental Health Sciences" + }, + { + "author_name": "Anton Simeonov", + "author_inst": "National Center for Advancing Translational Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "synthetic biology" + }, { "rel_doi": "10.1101/2021.10.23.465542", "rel_title": "Protection from SARS-CoV-2 Delta one year after mRNA-1273 vaccination in nonhuman primates is coincident with an anamnestic antibody response in the lower airway", @@ -542907,81 +543974,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.19.21264954", - "rel_title": "Public awareness and support for use of wastewater for SARS-CoV-2 monitoring: A community survey in Louisville, Kentucky", - "rel_date": "2021-10-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.19.21264954", - "rel_abs": "The majority of sewer systems in the United States and other countries, are operated by public utilities. In the absence of any regulation, public perception of monitoring wastewater for population health biomarkers is an important consideration for a public utility commission when allocating resources for this purpose. In August 2021, we conducted a survey as part of an ongoing COVID-19 community prevalence study in Louisville/Jefferson County, KY. The survey comprised of seven questions about awareness of and privacy concerns and was sent to 32,000 households randomly distributed within the county. A total of 1,220 sampled adults participated in the probability sample, and 981 were used in analysis. A total of 2,444 adults additionally responded in the convenience sample, and 1,751 were used in analysis. The samples were weighted to produce estimates representative of all adults in the county. Public awareness of tracking COVID-19 virus in the sewers was low. Opinions about how data from this activity are shared strongly supported public disclosure of monitoring results. Responses showed more support for measuring the largest areas (>30,000 to 50,000 households) typically representing population levels found in a community or regional wastewater treatment plant. Those who had a history of COVID-19 infection were more likely to support highly localized monitoring. Understanding wastewater surveillance strategies and thresholds of privacy concerns requires in-depth, comprehensive analysis of public opinion for continued success and efficacy of public health monitoring.\n\nGraphic for Table of Contents (TOC)/Abstract Art\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=44 SRC=\"FIGDIR/small/21264954v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@8774aforg.highwire.dtl.DTLVardef@fdbeaborg.highwire.dtl.DTLVardef@f0fc3forg.highwire.dtl.DTLVardef@14097dd_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Rochelle H. Holm", - "author_inst": "University of Louisville" - }, - { - "author_name": "J. Michael Brick", - "author_inst": "Westat, Inc." - }, - { - "author_name": "Alok R. Amraotkar", - "author_inst": "University of Louisville" - }, - { - "author_name": "Joy L. Hart", - "author_inst": "University of Louisville" - }, - { - "author_name": "Anish Mukherjee", - "author_inst": "University of Louisville" - }, - { - "author_name": "Jacob Zeigler", - "author_inst": "University of Louisville" - }, - { - "author_name": "Adrienne M. Bushau-Sprinkle", - "author_inst": "University of Louisville" - }, - { - "author_name": "Lauren B. Anderson", - "author_inst": "University of Louisville" - }, - { - "author_name": "Kandi L. Walker", - "author_inst": "University of Louisville" - }, - { - "author_name": "Daymond Talley", - "author_inst": "Louisville/Jefferson County Metropolitan Sewer District" - }, - { - "author_name": "Rachel Keith", - "author_inst": "University of Louisville" - }, - { - "author_name": "Shesh Rai", - "author_inst": "University of Louisville" - }, - { - "author_name": "Kenneth E. Palmer", - "author_inst": "University of Louisville" - }, - { - "author_name": "Aruni Bhatnagar", - "author_inst": "University of Louisville" - }, - { - "author_name": "Ted R Smith", - "author_inst": "University of Louisville" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.10.19.21265028", "rel_title": "Small Airway Disease as long-term Sequela of COVID-19: Use of Expiratory CT despite Improvement in Pulmonary Function test", @@ -543153,6 +544145,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.10.20.21265149", + "rel_title": "Differences in COVID-19 Risk by Race and County-Level Social Determinants of Health Among Veterans", + "rel_date": "2021-10-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265149", + "rel_abs": "COVID-19 disparities by area-level social determinants of health (SDH) may be impacting U.S. Veterans. This retrospective analysis utilized COVID-19 data from the U.S. Department of Veterans Affairs (VA)s EHR and geographically linked county-level data from 18 area-based socioeconomic measures. The risk of testing positive with Veterans county-level SDHs adjusting for demographics, comorbidities, and facility characteristics was calculated using generalized linear models. We found an exposure-response relationship whereby individual COVID-19 infection risk increased with each increasing quartile of adverse county-level SDH such as the percentage of residents in a county without a college degree, eligible for Medicaid, and living in crowded housing.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Hoda S. Abdel Magid", + "author_inst": "Stanford University; Veterans Affairs Palo Alto Healthcare System" + }, + { + "author_name": "Jacqueline M Ferguson", + "author_inst": "Stanford University; Veterans Affairs Palo Alto Healthcare System" + }, + { + "author_name": "Raymond V Cleve", + "author_inst": "Stanford University; Veterans Affairs Palo Alto Healthcare System" + }, + { + "author_name": "Amanda Purnell", + "author_inst": "Veterans Affairs Central Office" + }, + { + "author_name": "Thomas F Osborne", + "author_inst": "Stanford University; Veterans Affairs Palo Alto Healthcare System" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.21.21265133", "rel_title": "Post COVID-19 in children, adolescents, and adults: results of a matched cohort study including more than 150,000 individuals with COVID-19", @@ -544900,37 +545927,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.10.18.464828", - "rel_title": "Transcriptome data from human nasal epithelial cells infected by H3N2 influenza virus indicate early unbalanced ROS/RNA levels, temporarily increased aerobic fermentation linked to enhanced \u03b1-tubulin and rapid energy-dependent IRF9-marked immunization", - "rel_date": "2021-10-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.18.464828", - "rel_abs": "BackgroundTranscriptome studies of a selected gene set (ReprogVirus) had identified unbalanced ROS/RNS levels, which connected to increased aerobic fermentation that linked to alpha-tubulin-based cell restructuration and cell cycle control, as a major complex trait for early de novo programming (CoV-MAC-TED) upon SARS-CoV-2 infection. Recently, CoV-MAC-TED was confirmed as promising marker by using primary target human nasal epithelial cells (NECs) infected by two SARS-CoV-2 variants with different effects on disease severity. To further explore this marker/cell system as a standardized tool for identifying anti-viral targets in general, testing of further virus types is required. Results: Transcriptome level profiles of H3N2 influenza-infected NECs indicated ROS/RNS level changes and increased transcript accumulation of genes related to glycolysis, lactic fermentation and -tubulin at 8 hours post infection. These early changes linked to energy-dependent, IRF9-marked rapid immunization. However, ReprogVirus-marker genes indicated the absence of initial cell cycle progress, which contrasted our findings during infections with two SARS-CoV-2 variants, where cell cycle progress was linked to delayed IRF9 response. Our results point to the possibility of CoV-MAC-TED-assisted, rapid individual host cell response identification upon virus infections. Conclusion: The complex trait CoV-MAC-TED can identify similar and differential early responses of SARS-CoV-2 and influenza H3N2 viruses. This indicates its appropriateness to search for anti-viral targets in view of therapeutic design strategies. For standardization, human NECs can be used. This marker/cell system is promising to identify differential early cell responses upon viral infections also depending on cell origins.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jose Helio Costa", - "author_inst": "Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil" - }, - { - "author_name": "Shahid Aziz", - "author_inst": "Functional Genomics and Bioinformatics Group, Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil" - }, - { - "author_name": "Birgit Arnholdt-Schmitt", - "author_inst": "Non-Institutional Competence Focus (NICFocus) FunCROP" - }, - { - "author_name": "Carlos Noceda", - "author_inst": "Plant Molecular and Cellular Biotechnology / Industrial Biotechnology and Bioproducts. Department of Life and Agricultural Sciences. Universidad de las Fuerzas " - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.10.19.465036", "rel_title": "Discovery of Potent Triple Inhibitors of Both SARS-CoV-2 Proteases and Human Cathepsin L", @@ -545299,6 +546295,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.18.21265057", + "rel_title": "Impact of routine asymptomatic screening on COVID-19 incidence in a highly vaccinated university population", + "rel_date": "2021-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.18.21265057", + "rel_abs": "BackgroundWith the return of in-person classes, an understanding of COVID-19 transmission in vaccinated university campuses is essential. Given the context of high anticipated vaccination rates and other measures, there are outstanding questions of the potential impact of campus-based asymptomatic screening.\n\nMethodsWe estimated the expected number of cases and hospitalizations in one semester using rates derived for British Columbia (BC), Canada up to September 15th, 2021 and age-standardizing to a University population. To estimate the expected number of secondary cases averted due to routine tests of unvaccinated individuals in a BC post-secondary institution, we used a probabilistic model based on the incidence, vaccination effectiveness, vaccination coverage and R0. We examined multiple scenarios of vaccine coverage, screening frequency, and pre-vaccination R0.\n\nResultsFor one 12 week semester, the expected number of cases is 67 per 50,000 for 80% vaccination coverage and 37 per 50,000 for 95% vaccination coverage. Screening of the unvaccinated population averts an expected 6-16 cases per 50,000 at 80% decreasing to 1-2 averted cases per 50,000 at 95% vaccination coverage for weekly to daily screening. Further scenarios can be explored using a web-based application.\n\nInterpretationRoutine screening of unvaccinated individuals may be of limited benefit if vaccination coverage is 80% or greater within a university setting.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Rebeca Cardim Falcao", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Michael Otterstatter", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "May A. Ahmed", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Michelle Spencer", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Sarafa Iyaniwura", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Naveed Z. Janjua", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Geoff McKee", + "author_inst": "BC Centre for Disease Control" + }, + { + "author_name": "Michael A. Irvine", + "author_inst": "BC Centre for Disease Control" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.15.21265037", "rel_title": "Extreme COVID-19 waves reveal hyperexponential growth and finite-time singularity", @@ -546645,185 +547688,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.13.21264937", - "rel_title": "Comparative effectiveness of ChAdOx1 versus BNT162b2 COVID-19 vaccines in Health and Social Care workers in England: a cohort study using OpenSAFELY", - "rel_date": "2021-10-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264937", - "rel_abs": "ObjectivesTo compare the effectiveness of the BNT162b2 mRNA (Pfizer-BioNTech) and the ChAdOx1 (Oxford-AstraZeneca) COVID-19 vaccines against infection and COVID-19 disease in health and social care workers.\n\nDesignCohort study, emulating a comparative effectiveness trial.\n\nSettingLinked primary care, hospital, and COVID-19 surveillance records available within the OpenSAFELY-TPP research platform.\n\nParticipants317,341 health and social care workers vaccinated between 4 January and 28 February 2021, registered with a GP practice using the TPP SystmOne clinical information system in England, and not clinically extremely vulnerable.\n\nInterventionsVaccination with either BNT162b2 or ChAdOx1 administered as part of the national COVID-19 vaccine roll-out.\n\nMain outcome measuresRecorded SARS-CoV-2 positive test, or COVID-19 related Accident and Emergency attendance or hospital admission occurring within 20 weeks of vaccination.\n\nResultsThe cumulative incidence of each outcome was similar for both vaccines during the first 20 weeks post-vaccination. The cumulative incidence of recorded SARS-CoV-2 infection 6 weeks after vaccination with BNT162b2 was 19.2 per 1000 people (95%CI 18.6 to 19.7) and with ChAdOx1 was 18.9 (95%CI 17.6 to 20.3), representing a difference of -0.24 per 1000 people (95%CI -1.71 to 1.22). The difference in the cumulative incidence per 1000 people of COVID-19 accident and emergency attendance at 6 weeks was 0.01 per 1000 people (95%CI -0.27 to 0.28). For COVID-19 hospital admission, this difference was 0.03 per 1000 people (95%CI -0.22 to 0.27).\n\nConclusionsIn this cohort of healthcare workers where we would not anticipate vaccine type to be related to health status, we found no substantial differences in the incidence of SARS-CoV-2 infection or COVID-19 disease up to 20 weeks after vaccination. Incidence dropped sharply after 3-4 weeks and there were very few COVID-19 hospital attendance and admission events after this period. This is in line with expected onset of vaccine-induced immunity, and suggests strong protection against COVID-19 disease for both vaccines.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "William J Hulme", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Elizabeth J Williamson", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Amelia CA Green", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Krishnan Bhaskaran", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Helen I McDonald", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Christopher T Rentsch", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Anna Schultze", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "John Tazare", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Alex J Walker", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Laurie Tomlinson", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Tom M Palmer", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK" - }, - { - "author_name": "Elsie Horne", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Louis Fisher", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Sebastian CJ Bacon", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "David Evans", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "George Hickman", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Simon Davy", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Tom Ward", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Richard Croker", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Angel YS Wong", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Rohini Mathur", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Kevin Wing", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Harriet Forbes", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Daniel J Grint", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Ian J Douglas", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Stephen JW Evans", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Liam Smeeth", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Christopher Bates", - "author_inst": "TPP, Horsforth, Leeds, UK" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP, Horsforth, Leeds, UK" - }, - { - "author_name": "John Parry", - "author_inst": "TPP, Horsforth, Leeds, UK" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP, Horsforth, Leeds, UK" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP, Horsforth, Leeds, UK" - }, - { - "author_name": "Jonathan AC Sterne", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Bristol, Biomedical Research Centre, Bristol, UK" - }, - { - "author_name": "Miguel A Hernan", - "author_inst": "CAUSALab, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Departments of Epidemiology and Biostatistics, Harvard T.H. Chan School of Public Health, " - }, - { - "author_name": "Ben Goldacre", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.13.21264916", "rel_title": "Combination therapy of infliximab and thiopurines, but not monotherapy with infliximab or vedolizumab, is associated with attenuated IgA and neutralisation responses to SARS-CoV-2 in inflammatory bowel disease.", @@ -547104,6 +547968,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.13.21264919", + "rel_title": "Agile design and development of a high throughput cobas(R) SARS-CoV-2 RT-PCR diagnostic test", + "rel_date": "2021-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264919", + "rel_abs": "Diagnostic testing is essential for management of the COVID-19 pandemic. An agile assay design methodology, optimized for the cobas(R) 6800/8800 system, was used to develop a dual-target, qualitative SARS-CoV-2 RT-PCR test using commercially available reagents and existing sample processing and thermocycling profiles. The limit of detection was 0.004 to 0.007 TCID50/mL for USA-WA1/2020. Assay sensitivity was confirmed for SARS-CoV-2 variants Alpha, Beta, Gamma, Delta and Kappa. The coefficients of variation of the cycle threshold number (Ct) were between 1.1 and 2.2%. There was no difference in Ct using nasopharyngeal compared to oropharyngeal swabs in universal transport medium (UTM). A small increase in Ct was observed with specimens collected in cobas(R) PCR medium compared to UTM. In silico analysis indicated that the dual-target test is capable of detecting all >1,800,000 SARS-CoV-2 sequences in the GISAID database. Our agile assay design approach facilitated rapid development and deployment of this SARS-CoV-2 RT-PCR test.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Chitra Manohar", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Jingtao Sun", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Peter Schlag", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Chris Santini", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Marcel Fontecha", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Pirmin Lotscher", + "author_inst": "Roche Diagnostics International AG, Rotkreuz, Switzerland" + }, + { + "author_name": "Carolin Bier", + "author_inst": "Roche Diagnostics International AG, Rotkreuz, Switzerland" + }, + { + "author_name": "Kristina Goepfert", + "author_inst": "Roche Diagnostics International AG, Rotkreuz, Switzerland" + }, + { + "author_name": "Dana Duncan", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Gene Spier", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Daniel Jarem", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + }, + { + "author_name": "Dmitriy Kosarikov", + "author_inst": "Roche Molecular Systems, Inc., Pleasanton, United States" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.14.21265010", "rel_title": "How frequent are acute reactions to COVID-19 vaccination and who is at risk?", @@ -548359,53 +549286,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.16.21265097", - "rel_title": "Public Perception of COVID-19 Vaccines on Twitter in the United States", - "rel_date": "2021-10-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.16.21265097", - "rel_abs": "BackgroundCOVID-19 vaccines play a vital role in combating the COVID-19 pandemic. Social media provides a rich data source to study public perception of COVID-19 vaccines.\n\nObjectiveIn this study, we aimed to examine public perception and discussion of COVID-19 vaccines on Twitter in the US, as well as geographic and demographic characteristics of Twitter users who discussed about COVID-19 vaccines.\n\nMethodsThrough Twitter streaming Application Programming Interface (API), COVID-19-related tweets were collected from March 5th, 2020 to January 25th, 2021 using relevant keywords (such as \"corona\", \"covid19\", and \"covid\"). Based on geolocation information provided in tweets and vaccine-related keywords (such as \"vaccine\" and \"vaccination\"), we identified COVID-19 vaccine-related tweets from the US. Topic modeling and sentiment analysis were performed to examine public perception and discussion of COVID-19 vaccines. Demographic inference using computer vision algorithm (DeepFace) was performed to infer the demographic characteristics (age, gender and race/ethnicity) of Twitter users who tweeted about COVID-19 vaccines.\n\nResultsOur longitudinal analysis showed that the discussion of COVID-19 vaccines on Twitter in the US reached a peak at the end of 2020. Average sentiment score for COVID-19 vaccine-related tweets remained relatively stable during our study period except for two big peaks, the positive peak corresponds to the optimism about the development of COVID-19 vaccines and the negative peak corresponds to worrying about the availability of COVID-19 vaccines. COVID-19 vaccine-related tweets from east coast states showed relatively high sentiment score. Twitter users from east, west and southern states of the US, as well as male users and users in age group 30-49 years, were more likely to discuss about COVID-19 vaccines on Twitter.\n\nConclusionsPublic discussion and perception of COVID-19 vaccines on Twitter were influenced by the vaccine development and the pandemic, which varied depending on the geographics and demographics of Twitter users.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Zidian Xie", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Xueting Wang", - "author_inst": "University of Rochester" - }, - { - "author_name": "Yan Jiang", - "author_inst": "University of Rochester" - }, - { - "author_name": "Yuhan Chen", - "author_inst": "University of Rochester" - }, - { - "author_name": "Shengyuan Huang", - "author_inst": "University of Rochester" - }, - { - "author_name": "Haoxuan Ma", - "author_inst": "University of Rochester" - }, - { - "author_name": "Ajay Anand", - "author_inst": "University of Rochester" - }, - { - "author_name": "Dongmei Li", - "author_inst": "University of Rochester Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.17.21265114", "rel_title": "Self-reported safety of the BBIBP-CorV (Sinopharm) COVID-19 vaccine among Iranian people with multiple sclerosis", @@ -548674,6 +549554,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.17.21265101", + "rel_title": "Time-varying effectiveness of the mRNA-1273, BNT162b2 and Ad26.COV2.S vaccines against SARS-CoV-2 infections and COVID-19 hospitalizations and deaths: an analysis based on observational data from Puerto Rico", + "rel_date": "2021-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.17.21265101", + "rel_abs": "BackgroundAs of October 1, 2021 2,217,547 individuals were fully vaccinated against COVID-19 in Puerto Rico. Since the vaccination process commenced on December 15, 2020 111,052 laboratory-confirmed SARS-CoV-2 infections have been reported. These data permitted us to quantify the benefits of the immunization campaign and to compare effectiveness of the mRNA-1273 (Moderna), BNT162b2 (Pfizer), and Ad26.COV2.S (J&J) vaccines.\n\nMethodsDepartment of Health databases holding vaccination status, SARS-CoV-2 test results, and COVID-19 hospitalizations and deaths were integrated. We fit a statistical model that adjusted for time-varying incidence rates and age to estimate vaccine effectiveness and hospitalization and death relative risks. Code and data are provided here: https://github.com/rafalab/vax-eff-pr.\n\nResultsAt the peak of their protection, mRNA-1273, BNT162b2, and Ad26.COV2.S had an effectiveness of 90% (88%-91%), 87% (85%-89%), and 58% (51%-65%), respectively. After four months, effectiveness waned to about 70%, 60%, and 30%. We found no evidence that effectiveness was different after the Delta variant became dominant. For those infected, the vaccines provided further protection against hospitalization and deaths across all age groups. All vaccines had a lower effectiveness for those over 85 years, with a larger decrease for the Ad26.COV2.S vaccine. Overall, thousands of hospitalizations and deaths were avoided thanks to the vaccines.\n\nConclusionsThe mRNA-1273 and BNT162b2 vaccines were highly effective across all age groups. They were still effective after four months although the protection waned. The Ad26.COV2.S vaccine was effective but to a lesser degree, especially for older age groups.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Monica M. Robles-Fontan", + "author_inst": "Departamento de Salud de Puerto Rico" + }, + { + "author_name": "Elvis G. Nieves", + "author_inst": "Departamento de Salud de Puerto Rico" + }, + { + "author_name": "Iris Cardona-Gerena", + "author_inst": "Departamento de Salud de Puerto Rico" + }, + { + "author_name": "Rafael A Irizarry", + "author_inst": "Dana-Farber Cancer Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.18.21265046", "rel_title": "Comparative assessment of methods for short-term forecasts of COVID-19 admissions in England at the local level", @@ -550084,433 +550995,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.10.07.21264644", - "rel_title": "Genomic epidemiology reveals how restriction measures shaped the SARS-CoV-2 epidemic in Brazil", - "rel_date": "2021-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.07.21264644", - "rel_abs": "Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.", - "rel_num_authors": 103, - "rel_authors": [ - { - "author_name": "Marta Giovanetti", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Svetoslav Nanev Slavov", - "author_inst": "University of SAo Paulo, RibeirAo Preto Medical School, Blood Center of Ribeirao Preto, Ribeirao Preto, SP, Brazil; Butantan Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Vagner Fonseca", - "author_inst": "Laboratorio de Genetica Celular e Molecular, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Eduan Wilkinson", - "author_inst": "KwaZulu, Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu,Natal, Durban, Sou" - }, - { - "author_name": "Houriiyah Tegally", - "author_inst": "KwaZulu, Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu,Natal, Durban, Sou" - }, - { - "author_name": "Jose Patane", - "author_inst": "Instituto Butantan" - }, - { - "author_name": "Vincent Louis Viala", - "author_inst": "Butantan Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Emmanuel James San", - "author_inst": "KwaZulu, Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu,Natal, Durban, Sou" - }, - { - "author_name": "Evandra Strazza Rodrigues", - "author_inst": "University of Sao Paulo, Ribeirao Preto Medical School, Blood Center of Ribeirao Preto, Ribeirao Preto, SP, Brazil" - }, - { - "author_name": "Elaine Vieira Santos", - "author_inst": "University of Sao Paulo, Ribeirao Preto Medical School, Blood Center of Ribeirao Preto, Ribeirao Preto, SP, Brazil" - }, - { - "author_name": "Flavia Aburjaile", - "author_inst": "Laboratorio de Genetica Celular e Molecular, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Joilson Xavier", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Minas Gerais, Fundacao Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Hegger Fritsch", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Minas Gerais, Fundacao Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Talita Emile Ribeiro Adelino", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Minas Gerais, Fundacao Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Felicidade Pereira", - "author_inst": "Laboratorio Central de Saude Publica da Bahia, LACEN BA, Salvador, Bahia, Brazil" - }, - { - "author_name": "Arabela Leal", - "author_inst": "Laboratorio Central de Saude Publica da Bahia, LACEN BA, Salvador, Bahia, Brazil" - }, - { - "author_name": "Felipe Campos de Melo Iani", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Minas Gerais, Fundacao Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Glauco de Carvalho Pereira", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Minas Gerais, Fundacao Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Cynthia Vazquez", - "author_inst": "Laboratorio Central de Salud Publica, Asuncion, Paraguay" - }, - { - "author_name": "Gladys Mercedes Estigarribia Sanabria", - "author_inst": "Universidad Nacional del Caaguazu, Instituto Regional de Investigacion en Salud Laboratorio de Biologia Molecular, Hospital Regional de Coronel Oviedo, Minister" - }, - { - "author_name": "Elaine Cristina de Oliveira", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Mato Grosso, Cuiaba, Brazil" - }, - { - "author_name": "Luiz Demarchi", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil" - }, - { - "author_name": "Julio Croda", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Rafael Dos Santos Bezerra Sr.", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Loyze Paola Oliveira de Lima", - "author_inst": "Butantan Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Antonio Jorge Martins", - "author_inst": "Butantan Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Claudia Renata dos Santos Barros", - "author_inst": "Butantan Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Elaine Cristina Marqueze", - "author_inst": "Butantan Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Jardelina de Souza Todao Bernardino", - "author_inst": "Butantan Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Debora Botequio Moretti", - "author_inst": "Butantan Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Ricardo Augusto Brassaloti", - "author_inst": "University of Sao Paulo, Centro de Genomica Funcional da ESALQ, Piracicaba, SP, Brazil" - }, - { - "author_name": "Raquel de Lello Rocha Campos Cassano", - "author_inst": "University of Sao Paulo, Centro de Genomica Funcional da ESALQ, Piracicaba, SP, Brazil" - }, - { - "author_name": "Pilar Drummond Sampaio Correa Mariani", - "author_inst": "NGS Solucoes Genomicas, Piracicaba, SP, Brazil" - }, - { - "author_name": "Joao Paulo Kitajima", - "author_inst": "Mendelics Analise Genomica" - }, - { - "author_name": "Bibiana Santos", - "author_inst": "Mendelics Analise Genomica" - }, - { - "author_name": "Rodrigo Proto Siqueira", - "author_inst": "Instituto de Biologia Molecular, Laboratorio Antonello, Rio Grande do Sul, Brazil" - }, - { - "author_name": "Vlademir Vicente Cantarelli", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre (UFCSPA), Universidade Feevale, Grupo Exame Laboratorios, Rio Grande do Sul, Brazil" - }, - { - "author_name": "Stephane Tosta", - "author_inst": "Laboratorio Central de Saude Publica da Bahia, LACEN BA, Salvador, Bahia, Brazil" - }, - { - "author_name": "Vanessa Brandao Nardy", - "author_inst": "Laboratorio Central de Saude Publica da Bahia LACEN BA, Salvador, Bahia, Brazil" - }, - { - "author_name": "Luciana Reboredo de Oliveira da Silva", - "author_inst": "Laboratorio Central de Saude Publica da Bahia LACEN BA, Salvador, Bahia, Brazil" - }, - { - "author_name": "Marcela Kelly Astete Gomez", - "author_inst": "Laboratorio Central de Saude Publica da Bahia LACEN BA, Salvador, Bahia, Brazil" - }, - { - "author_name": "Jaqueline Gomes Lima", - "author_inst": "Laboratorio Central de Saude Publica da Bahia LACEN BA, Salvador, Bahia, Brazil" - }, - { - "author_name": "Adriana Aparecida Ribeiro", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Minas Gerais, Fundacao Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Natalia Rocha Guimaraes", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Minas Gerais, Fundacao Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Luiz Takao Watanabe", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Mato Grosso, Cuiaba, Brazil" - }, - { - "author_name": "Luana Barbosa Da Silva", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Mato Grosso, Cuiaba, Brazil" - }, - { - "author_name": "Raquel da Silva Ferreira", - "author_inst": "Laboratorio Central de Saude Publica do Estado de Mato Grosso, Cuiaba, Brazil" - }, - { - "author_name": "Mara Patricia F. da Penha", - "author_inst": "Vigilancia em Saude, do Estado de Mato Grosso, Cuiaba, Brazil" - }, - { - "author_name": "Maria Jose Ortega", - "author_inst": "Laboratorio Central de Salud Publica de Paraguay" - }, - { - "author_name": "Andrea Gomez de la Fuente", - "author_inst": "Laboratorio Central de Salud Publica de Paraguay" - }, - { - "author_name": "Shirley Villalba", - "author_inst": "Laboratorio Central de Salud Publica de Paraguay" - }, - { - "author_name": "Juan Torales", - "author_inst": "Laboratorio Central de Salud Publica de Paraguay" - }, - { - "author_name": "Maria Liz Gamarra", - "author_inst": "Laboratorio Central de Salud Publica de Paraguay" - }, - { - "author_name": "Carolina Aquino", - "author_inst": "Laboratorio Central de Salud Publica de Paraguay" - }, - { - "author_name": "Gloria Patricia Martinez Figueredo", - "author_inst": "Universidad Nacional del Caaguazu, Instituto Regional de Investigacion en Salud Laboratorio de Biologia Molecular, Hospital Regional de Coronel Oviedo, Minister" - }, - { - "author_name": "Wellington Santos Fava", - "author_inst": "Universidade Federal do Mato Grosso do Sul" - }, - { - "author_name": "Ana Rita C. Motta Castro", - "author_inst": "Universidade Federal do Mato Grosso do Sul" - }, - { - "author_name": "James Venturini", - "author_inst": "Universidade Federal do Mato Grosso do Sul" - }, - { - "author_name": "Sandra Maria do Vale Leone de Oliveira", - "author_inst": "Universidade Federal do Mato Grosso do Sul" - }, - { - "author_name": "Crhistinne Cavalheiro Maymone Goncalves", - "author_inst": "Secretaria de Saude do Estado do Mato Grosso do Sul" - }, - { - "author_name": "Maria do Carmo Debur Rossa", - "author_inst": "Laboratorio Central do Estado do Parana (Lacen PR)" - }, - { - "author_name": "Guilherme Nardi Becker", - "author_inst": "Laboratorio Central do Estado do Parana (Lacen PR)" - }, - { - "author_name": "Mayra Marinho Presibella", - "author_inst": "Laboratorio Central do Estado do Parana (Lacen PR)" - }, - { - "author_name": "Nelson Quallio Marques", - "author_inst": "Laboratorio Central do Estado do Parana (Lacen PR)" - }, - { - "author_name": "Irina Nastassja Riediger", - "author_inst": "Laboratorio Central do Estado do Parana (Lacen PR)" - }, - { - "author_name": "Sonia Raboni", - "author_inst": "Hospital de Clinicas da Universidade Federal do Parana, Curitiba, PR" - }, - { - "author_name": "Gabriela Mattoso", - "author_inst": "Laboratorio de Virologia Molecular Instituto Carlos Chagas Fiocruz PR, Curitiba, PR" - }, - { - "author_name": "Allan D. Cataneo", - "author_inst": "Laboratorio de Virologia Molecular Instituto Carlos Chagas Fiocruz PR, Curitiba, PR" - }, - { - "author_name": "Camila Zanluca", - "author_inst": "Laboratorio de Virologia Molecular Instituto Carlos Chagas Fiocruz PR, Curitiba, PR" - }, - { - "author_name": "Claudia N Duarte dos Santos", - "author_inst": "Laboratorio de Virologia Molecular Instituto Carlos Chagas Fiocruz PR, Curitiba, PR" - }, - { - "author_name": "Patricia Akemi Assato", - "author_inst": "Sao Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil" - }, - { - "author_name": "Felipe Allan da Silva da Costa", - "author_inst": "Sao Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil" - }, - { - "author_name": "Mirele Daiana Poleti", - "author_inst": "Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil" - }, - { - "author_name": "Jessika Cristina Chagas Lesbon", - "author_inst": "Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil" - }, - { - "author_name": "Elisangela Chicaroni Mattos", - "author_inst": "Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil" - }, - { - "author_name": "Cecilia Artico Banho", - "author_inst": "Medicine School of Sao Jose do Rio Preto (FAMERP), Sao Jose do Rio Preto, Sao Paulo, Brazil" - }, - { - "author_name": "Livia S Sacchetto", - "author_inst": "Faculdade de Medicina de Sao Jose do Rio Preto" - }, - { - "author_name": "Marilia Mazzi Moraes", - "author_inst": "Medicine School of Sao Jose do Rio Preto (FAMERP), Sao Jose do Rio Preto, Sao Paulo, Brazil" - }, - { - "author_name": "Rejane Maria Tommasini Grotto", - "author_inst": "Sao Paulo State University (UNESP), School of Agricultural Sciences, Botucatu, Brazil; Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical " - }, - { - "author_name": "Jayme A. Souza-Neto", - "author_inst": "Sao Paulo State University (UNESP)" - }, - { - "author_name": "Mauricio L Nogueira", - "author_inst": "Faculdade de Medicina de Sao Jose do Rio Preto" - }, - { - "author_name": "Heidge Fukumasu", - "author_inst": "Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, Brazil" - }, - { - "author_name": "Luiz Lehmann Coutinho", - "author_inst": "University of Sao Paulo, Centro de Genomica Funcional da ESALQ, Piracicaba, SP, Brazil" - }, - { - "author_name": "Rodrigo Tocantins Calado", - "author_inst": "University of Sao Paulo, Ribeirao Preto Medical School, Blood Center of Ribeirao Preto, Ribeirao Preto, SP, Brazil" - }, - { - "author_name": "Raul Machado Neto", - "author_inst": "Butantan Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Ana Maria Bispo de Filippis", - "author_inst": "Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil" - }, - { - "author_name": "Rivaldo Venancio da Cunha", - "author_inst": "Fundacao Oswaldo Cruz, Bio Manguinhos, Rio de Janeiro, Rio de Janeiro, Brazil" - }, - { - "author_name": "Carla Freitas", - "author_inst": "Ministerio da Saude Brazil" - }, - { - "author_name": "Cassio Roberto Leonel Peterka", - "author_inst": "Ministerio da Saude Brazil" - }, - { - "author_name": "Cassia de Fatima Rangel Fernandes", - "author_inst": "Ministerio da Saude Brazil" - }, - { - "author_name": "Wildo Navegantes", - "author_inst": "OPAS" - }, - { - "author_name": "Rodrigo Fabiano do Carmo Said", - "author_inst": "OPAS" - }, - { - "author_name": "Maria Almiron", - "author_inst": "OPAS" - }, - { - "author_name": "Carlos F Campelo de A e Melo", - "author_inst": "OPAS" - }, - { - "author_name": "Jose Lourenco", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "University of KwaZulu-Natal" - }, - { - "author_name": "Edward C Holmes", - "author_inst": "University of Sydney" - }, - { - "author_name": "Ricardo Haddad", - "author_inst": "Butantan Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Sandra Coccuzzo Sampaio", - "author_inst": "Instituto Butantan" - }, - { - "author_name": "Maria Carolina Elias", - "author_inst": "Butantan Institute, Sao Paulo, Brazil" - }, - { - "author_name": "Simone Kashima", - "author_inst": "Hemocentro de Ribeirao Preto" - }, - { - "author_name": "Luiz Carlos Junior Alcantara", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Dimas Tadeu Covas", - "author_inst": "University of Sao Paulo, Ribeirao Preto Medical School, Blood Center of Ribeirao Preto, Ribeirao Preto, SP, Brazil; Butantan Institute, Sao Paulo, Brazil" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.10.11.21264724", "rel_title": "Transmission of SARS-CoV-2 associated with cruise ship travel: protocol for a systematic review (Version 1)", @@ -550695,6 +551179,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.10.11.21264709", + "rel_title": "Quantitative chest CT combined with plasma cytokines predict outcomes in COVID-19 patients", + "rel_date": "2021-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.11.21264709", + "rel_abs": "Despite extraordinary international efforts to dampen the spread and understand the mechanisms behind SARS-CoV-2 infections, accessible predictive biomarkers directly applicable in the clinic are yet to be discovered. Recent studies have revealed that diverse types of assays bear limited predictive power for COVID-19 outcomes. Here, we harness the predictive power of chest CT in combination with plasma cytokines using a machine learning approach for predicting death during hospitalization and maximum severity degree in COVID-19 patients. Patients (n=152) from the Mount Sinai Health System in New York with plasma cytokine assessment and a chest CT within 5 days from admission were included. Demographics, clinical, and laboratory variables, including plasma cytokines (IL-6, IL-8, and TNF-) were collected from the electronic medical record. We found that chest CT combined with plasma cytokines were good predictors of death (AUC 0.78) and maximum severity (AUC 0.82), whereas CT quantitative was better at predicting severity (AUC 0.81 vs 0.70) while cytokine measurements better predicted death (AUC 0.70 vs 0.66). Finally, we provide a simple scoring system using plasma IL-6, IL-8, TNF-, GGO to aerated lung ratio and age as novel metrics that may be used to monitor patients upon hospitalization and help physicians make critical decisions and considerations for patients at high risk of death for COVID-19.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Guillermo Carbonell", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Diane Marie Del Valle", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Edgar E Gonzalez-Kozlova", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Brett Marinelli", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Emma Klein", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Maria El Homsi", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Daniel Stocker", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Michael Chung", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adam Bernheim", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Nicole Simons", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jiani Xiang", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sharon Nirenberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Patricia Kovatch", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sara Lewis", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Miriam Merad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sacha Gnjatic", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Bachir Taouli", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2021.10.12.21264890", "rel_title": "Breastfeeding infants receive neutralizing antibodies and cytokines from mothers immunized with a COVID-19 mRNA vaccine", @@ -552266,41 +552833,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.13.464299", - "rel_title": "Variable inhibition of unwinding rates of DNA catalyzed by the SARS-Cov-2 (COV19) helicase nsp13 by structurally distinct single DNA lesions.", - "rel_date": "2021-10-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.13.464299", - "rel_abs": "The SARS 2 (Covid 19) helicase nsp13 plays a critically important role in the replication of the Corona virus by unwinding double-stranded RNA (and DNA) with a 5{longrightarrow}3 strand polarity. Here we explored the impact of single, structurally defined covalent DNA lesions on the helicase activity of nsp13 in aqueous solutions, The objectives were to derive mechanistic insights into the relationships between the structures of DNA lesions, the DNA distortions that they engender, and the inhibition of helicase activity. The lesions included two bulky stereoisomeric N2-guanine adducts derived from the reactions of benzo[a]pyrene diol epoxide with DNA. The trans-adduct assumes a minor groove conformation, while the cis-product adopts a base-displaced intercalated conformation. The non-bulky DNA lesions included the intra-strand cross-linked thymine dimers, the cis-syn-cyclobutane pyrimidine dimer, and the pyrimidine (6-4) pyrimidone photoproduct. All four lesions strongly inhibit the helicase activity of nsp13, The UV photolesions feature a 2 - 5-fold smaller inhibition of the nsp13 unwinding activity than the bulky DNA adducts, and the kinetics of these two pairs of DNA lesions are also different. The connections between the structural features of these four DNA lesions and their impact on nsp13 unwinding efficiencies are discussed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ana H. Sales", - "author_inst": "New York University" - }, - { - "author_name": "Sam Ciervo", - "author_inst": "New Yok University" - }, - { - "author_name": "Tania Lupoli", - "author_inst": "New York University" - }, - { - "author_name": "Vladimir Shafirovich", - "author_inst": "New York University" - }, - { - "author_name": "Nicholas E Geacintov", - "author_inst": "New York University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.10.14.21264999", "rel_title": "Social and mental health risks faced by undocumented migrants during the COVID-19 pandemic: Evidence from three surveys in France", @@ -552517,6 +553049,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.10.13.21264975", + "rel_title": "Disparities in SARS-CoV-2 exposure: evidence from a citywide seroprevalence study in Holyoke, Massachusetts, USA", + "rel_date": "2021-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264975", + "rel_abs": "BackgroundSeroprevalence studies are important tools to estimate the prevalence of prior or recent SARS-CoV-2 infections, identifying hotspots and high-risk groups and informing public health responses to the COVID-19 pandemic. We conducted a city-level seroprevalence study in Holyoke, Massachusetts, USA to estimate the seroprevalence of SARS-CoV-2 antibodies and risk factors for seropositivity.\n\nMethodsWe invited inhabitants of 2,000 randomly sampled addresses between November 5 and December 31, 2020. Participants completed questionnaires measuring sociodemographic and health characteristics, and COVID-19 exposure history, and provided dried blood spots for measurement of SARS-CoV-2 IgG and IgM antibodies. We calculate total and subgroup seroprevalence estimates based on presence of IgG antibodies using a Bayesian procedure that incorporates uncertainty in antibody test sensitivity and specificity. We account for clustering by household and weighting based on demographic characteristics to ensure estimates represented the citys population.\n\nFindingsWe enrolled 280 households including 472 individuals. 328 underwent antibody testing. The citywide seroprevalence estimate of SARS-CoV-2 IgG was 13.1% (95%CI 6.9-22.3) compared to 9.8% based on publicly reported case counts. Seroprevalence was 16.1% (95%CI 6.2-31.8) among individuals identifying as Hispanic compared to 9.4% (95%CI 4.6-16.4) among those identifying as non-Hispanic white. Seroprevalence was higher among Spanish speaking households (21.9%; 95% CI 8.3-43.9) compared to English speaking households (10.2%; 95% CI 5.2-18.0) and among individuals living in high vulnerability areas (14.4%; 95% CI 7.1-25.5) compared to low vulnerability areas (8.2%; 95% CI 3.1-16.9).\n\nInterpretationThe measured SARS-CoV-2 seroprevalence of IgG antibodies in Holyoke was only 13.1% during the second surge of SARS-CoV-2 in this region, far from accepted thresholds for \"herd immunity.\" Already vulnerable communities were at highest risk of prior infection. Implementation of local serosurveys in tandem with proactive public health interventions that address disparities in SARS-CoV-2 exposure are crucial to ensure at-risk communities have appropriate educational materials and access to vaccines, testing, and timely treatment.\n\nFundingThe Sullivan Family Foundation, Harvard Data Science Institute Bias2 program, the US Centers for Disease Control and Prevention.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Wilfredo Rafael Matias", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Division of Infectious Diseases, Brigham and Womens Hospital, Boston, MA; Center fo" + }, + { + "author_name": "Isabel R Fulcher", + "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA; Harvard Data Science Initiative, Cambridge, MA" + }, + { + "author_name": "Sara M Sauer", + "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Cody P Nolan", + "author_inst": "Department of Medicine, Brigham and Womens Hospital, Boston, MA" + }, + { + "author_name": "Yodeline Guillaume", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Jack Zhu", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Francisco J Molano", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Elizabeth Uceta", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Shannon Collins", + "author_inst": "Center for Global Health, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Damien M Slater", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Vanessa M Sanchez", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Serina Moheed", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA" + }, + { + "author_name": "Jason B Harris", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Richelle C Charles", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Department of Medicine, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Ryan M Paxton", + "author_inst": "Holyoke Board of Health, Holyoke, MA" + }, + { + "author_name": "Sean F Gonsalves", + "author_inst": "Holyoke Board of Health, Holyoke, MA" + }, + { + "author_name": "Molly F Franke", + "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Louise C Ivers", + "author_inst": "Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA; Center for Global Health, Massachusetts General Hospital, Boston, MA; Department of" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.13.21264901", "rel_title": "Soluble angiotensin-converting enzyme 2 as a prognostic biomarker for disease progression in patients infected with SARS-CoV-2", @@ -554112,45 +554731,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.10.11.21264863", - "rel_title": "Characterizing menstrual bleeding changes occurring after SARS-CoV-2 vaccination", - "rel_date": "2021-10-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.11.21264863", - "rel_abs": "Early in 2021, many people began sharing that they experienced unexpected menstrual bleeding after SARS-CoV-2 inoculation. We investigated this emerging phenomenon of changed menstrual bleeding patterns among a convenience sample of currently and formerly menstruating people using a web-based survey. In this sample, 42% of people with regular menstrual cycles bled more heavily than usual while 44% reported no change after being vaccinated. Among respondents who typically do not menstruate, 71% of people on long-acting reversible contraceptives, 39% of people on gender-affirming hormones, and 66% of post-menopausal people reported breakthrough bleeding. We found increased/breakthrough bleeding was significantly associated with age, systemic vaccine side effects (fever, fatigue), history of pregnancy or birth, and ethnicity. Generally, changes to menstrual bleeding are not uncommon nor dangerous, yet attention to these experiences is necessary to build trust in medicine.\n\nTeaserIncreased bleeding can occur post SARS-CoV-2 vaccines; this study investigates patterns in who experiences these changes.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Katharine MN Lee", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Eleanor J Junkins", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Chongliang Luo", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Urooba A Fatima", - "author_inst": "University of Illinois Urbana-Champaign" - }, - { - "author_name": "Maria L Cox", - "author_inst": "University of Illinois Urbana-Champaign" - }, - { - "author_name": "Kathryn BH Clancy", - "author_inst": "University of Illinois Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.10.11.463689", "rel_title": "Mutating novel interaction sites in NRP1 reduces SARS-CoV-2 spike protein internalization", @@ -554299,6 +554879,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.10.09.21264794", + "rel_title": "Covid-19 Epidemic Prediction in France: the Multimodal Case.", + "rel_date": "2021-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.09.21264794", + "rel_abs": "In two previous papers we have proposed models to estimate the Covid-19 epidemic when the number of daily positive cases has a bell shaped form that we call a mode. We have observed that each Covid variant produces this type of epidemic shape at a different moment, resulting in a multimodal epidemic shape. We will show in this document that each mode can still be estimated with models described in the two previous papers provides we replace the cumulated number of positive cases y by the cumulated number of positive cases reduced by a parameter P to be estimated. Therefore denoting z the logarithm of y -P, z follows approximately the differential equation [z] = b -azr where a, b, r have also to be estimated from the observed data. We will show the obtained predictions on the four French modes April, November 2020, May and September 2021. The comparison between the prediction obtained before the containment decisions made by the French government and the observed data afterwards suggests the inefficiency of the epidemic lockdowns.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jean-Pierre Quadrat", + "author_inst": "Retired from INRIA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.11.463917", "rel_title": "Secondary structure of subgenomic RNA M of SARS-CoV-2", @@ -555793,165 +556392,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.06.21264584", - "rel_title": "SARS-CoV-2 DNA Vaccine INO-4800 Induces Durable Immune Responses Capable of Being Boosted in a Phase 1 Open-Label Trial", - "rel_date": "2021-10-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.06.21264584", - "rel_abs": "BackgroundAdditional SARS-CoV-2 vaccines that are safe and effective as primary vaccines and boosters remain urgently needed to combat the COVID-19 pandemic. We describe the safety and durability of the immune responses following two primary doses and a homologous booster dose of an investigational DNA vaccine (INO-4800) targeting the full-length spike antigen.\n\nMethodsThree dosage strengths of INO-4800 (0.5 mg, 1.0 mg, and 2.0 mg) were evaluated in 120 age-stratified healthy adults. Intradermal injection of INO-4800 followed by electroporation at 0 and 4 weeks preceded an optional booster 6-10.5 months after the second dose.\n\nResultsINO-4800 appeared well tolerated, with no treatment-related serious adverse events. Most adverse events were mild and did not increase in frequency with age and subsequent dosing. A durable antibody response was observed 6 months following the second dose; a homologous booster dose significantly increased immune responses. Cytokine producing T cells and activated CD8+ T cells with lytic potential were significantly increased in the 2.0 mg dose group.\n\nConclusionINO-4800 was well tolerated in a 2-dose primary series and as a homologous booster in all adults, including the elderly. These results support further development of INO-4800 for use as a primary vaccine and as a booster.\n\nTrial Registration: ClinicalTrials.gov NCT04336410\n\nSummaryTwo-milligram dose of INO-4800, a DNA-based vaccine encoding the SARS-CoV-2 spike protein, appears safe and well-tolerated and elicits humoral and cell-mediated immunity persisting to 6 months after a second dose. A third dose 6-10.5 months later significantly boosts immune responses.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Kimberly A Kraynyak", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Elliott Blackwood", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Joseph Agnes", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Pablo Tebas", - "author_inst": "Hospital of the University of Pennsylvania" - }, - { - "author_name": "Mary Giffear", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Dinah Amante", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Emma L Reuschel", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Mansi Purwar", - "author_inst": "Vaccine and Immunotherapy Center, Wistar Institute" - }, - { - "author_name": "Aaron Christensen-Quick", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Neiman Liu", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Viviane Andrade", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Malissa Diehl", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Snehal Wani", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Martyna Lupicka", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Albert Sylvester", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Matthew P Morrow", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Patrick Pezzoli", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Trevor McMullan", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Abhijeet J Kulkarni", - "author_inst": "Vaccine and Immunotherapy Center, Wistar Institute" - }, - { - "author_name": "Faraz I Zaidi", - "author_inst": "Vaccine and Immunotherapy Center, Wistar Institute" - }, - { - "author_name": "Drew Frase", - "author_inst": "Vaccine and Immunotherapy Center, Wistar Institute" - }, - { - "author_name": "Kevin Liaw", - "author_inst": "Vaccine and Immunotherapy Center, Wistar Institute" - }, - { - "author_name": "Trevor R.F. Smith", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Stephanie J Ramos", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "John Ervin", - "author_inst": "Alliance for Multispecialty Research" - }, - { - "author_name": "Mark Adams", - "author_inst": "Alliance for Multispecialty Research" - }, - { - "author_name": "Jessica Lee", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Michael Dallas", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Ami Shah Brown", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Jacqueline E Shea", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "J Joseph Kim", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "David B Weiner", - "author_inst": "Vaccine and Immunotherapy Center, Wistar Institute" - }, - { - "author_name": "Kate E Broderick", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Laurent M Humeau", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Jean D Boyer", - "author_inst": "Inovio Pharmaceuticals" - }, - { - "author_name": "Mammen P Mammen Jr.", - "author_inst": "Inovio Pharmaceuticals" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.05.21264567", "rel_title": "Efficacy and Safety of NVX-CoV2373 in Adults in the United States and Mexico", @@ -556228,6 +556668,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.07.21264419", + "rel_title": "Higher education responses to COVID-19 in the United States: Evidence for the impacts of university policy", + "rel_date": "2021-10-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.07.21264419", + "rel_abs": "With a dataset of testing and case counts from over 1,400 institutions of higher education (IHEs) in the United States, we analyze the number of infections and deaths from SARS-CoV-2 in the counties surrounding these IHEs during the Fall 2020 semester (August to December, 2020). We used a matching procedure designed to create groups of counties that are aligned along age, race, income, population, and urban/rural categories--socio-demographic variables that have been shown to be correlated with COVID-19 outcomes. We find that counties with IHEs that remained primarily online experienced fewer cases and deaths during the Fall 2020 semester; whereas before and after the semester, these two groups had almost identical COVID-19 incidence. Additionally, we see fewer deaths in counties with IHEs that reported conducting any on-campus testing compared to those that reported none. We complement the statistical analysis with a case study of IHEs in Massachusetts--a rich data state in our dataset--which further highlights the importance of IHE-affiliated testing for the broader community. The results in this work suggest that campus testing can itself be thought of as a mitigation policy and that allocating additional resources to IHEs to support efforts to regularly test students and staff would be beneficial to mitigating the spread of COVID-19 in the general population.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Brennan Klein", + "author_inst": "Northeastern University Network Science Institute" + }, + { + "author_name": "Nicholas Generous", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Northeastern University" + }, + { + "author_name": "Zarana Bhadricha", + "author_inst": "Northeastern University" + }, + { + "author_name": "Rishab Gunashekar", + "author_inst": "Northeastern University" + }, + { + "author_name": "Preeti Kori", + "author_inst": "Northeastern University" + }, + { + "author_name": "Bodian Li", + "author_inst": "Northeastern University" + }, + { + "author_name": "Stefan McCabe", + "author_inst": "Northeastern University" + }, + { + "author_name": "Jon Green", + "author_inst": "Northeastern University" + }, + { + "author_name": "David Lazer", + "author_inst": "Northeastern University" + }, + { + "author_name": "Christopher R. Marsicano", + "author_inst": "Davidson College" + }, + { + "author_name": "Samuel V. Scarpino", + "author_inst": "The Rockefeller Foundation Pandemic Prevention Institute" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Northeastern University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.08.21264749", "rel_title": "Longitudinal changes in home confinement and mental health implications: A 17-month follow-up study in England during the COVID-19 pandemic", @@ -557647,61 +558154,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.05.21264550", - "rel_title": "Comparison of antibody immune responses between BNT162b2 and mRNA-1273 SARS-CoV-2 vaccines in naive and previously infected individuals", - "rel_date": "2021-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.05.21264550", - "rel_abs": "Two mRNA vaccines, Pfizer-BNT162b2 and Moderna-mRNA-1273, were granted the US Food and Drug Administration Emergency Use Authorization for preventing COVID-19. However, little is known about the difference in antibody responses induced by the two mRNA vaccines in naive and individuals with a previous history of infections (PI group). Therefore, we investigated the levels of anti-S-RBD total antibodies (IgM, IgA, and IgG), anti-S-RBD IgG, and anti-S-RBD IgA in these two groups 1-13 (median=6) weeks following administration of two doses of mRNA-1273 or BNT162b2 vaccines. Results showed that in naive-vaccinated group, the mRNA-1327 vaccine induces significantly higher levels of S-RBD total antibodies (3.5-fold; p<0.001), S-RBD IgG (2-fold-p<0.01), and S-IgA (2.1-fold, p<0.001) than the BNT162b2 vaccine. In the PI-vaccinated group, both vaccines produce significantly higher S-RBD total antibodies level than those of the naive-vaccinated group. The PI group produced a higher level of S-RBD IgG than the naive-BNT162b2 (p=0.05) but not more than the naive-mRNA-1273 (p=0.9) group. Interestingly, the PI-vaccinated group produced a comparable level of IgA ratio to the naive-mRNA-1273 group but significantly higher than the naive-BNT162b2 group (1.6-fold, p<0.001). Our results showed that the mRNA-1327 vaccine is more immunogenic and induces a greater antibody response than the BNT162b2 vaccine.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Duaa Al-Sadeq", - "author_inst": "Qatar University" - }, - { - "author_name": "Farah Shurrab", - "author_inst": "Qatar University" - }, - { - "author_name": "Ahmed Ismail", - "author_inst": "Ministry of Public Health" - }, - { - "author_name": "Fathima Humaira Amanullah", - "author_inst": "Qatar University" - }, - { - "author_name": "Swapna Thomas", - "author_inst": "Qatar University" - }, - { - "author_name": "Nader Aldewik", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Hadi M. Yassine", - "author_inst": "Qatar University" - }, - { - "author_name": "Hanan Abdul Rahim", - "author_inst": "Qatar University" - }, - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Gheyath Nasrallah", - "author_inst": "Qatar University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.05.21264545", "rel_title": "Serum but not mucosal antibody responses are predicted by pre-existing SARS-CoV-2 spike cross-reactive CD4+ T cells following BNT162b2 vaccination in the elderly", @@ -558134,6 +558586,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.04.21264540", + "rel_title": "Detailed reconstruction of the Iranian COVID-19 epidemic reveals high attack rates of SARS-CoV-2 in several provinces", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.04.21264540", + "rel_abs": "Detailed reconstruction of the SARS-CoV-2 transmission dynamics and assessment of its burden in several parts of the world has still remained largely unknown due to the scarcity of epidemiological analyses and limited testing capacities of different countries to identify cases and deaths attributable to COVID-19 [1-4]. Understanding the true burden of the Iranian COVID-19 epidemic is subject to similar challenges with limited clinical and epidemiological studies at the subnational level [5-9]. To address this, we develop a new quantitative framework that enables us to fully reconstruct the transmission dynamics across the country and assess the level of under-reporting in infections and deaths using province-level, age-stratified all-cause mortality data. We show that excess mortality aligns with seroprevalence estimates in each province and subsequently estimate that as of 2021-10-22, only 48% (95% confidence interval: 43-55%) of COVID-19 deaths in Iran have been reported. We find that in the most affected provinces such as East Azerbaijan, Qazvin, and Qom approximately 0.4% of the population have died of COVID-19 so far. We also find significant heterogeneity in the estimated attack rates across the country with 11 provinces reaching close to or higher than 100% attack rates. Despite a relatively young age structure in Iran, our analysis reveals that the infection fatality rate in most provinces is comparable to high-income countries with a larger percentage of older adults, suggesting that limited access to medical services, coupled with undercounting of COVID-19-related deaths, can have a significant impact on accurate estimation of COVID-19 fatalities. Our estimation of high attack rates in provinces with largely unmitigated epidemics whereby, on average, between 10% to 25% individuals have been infected with COVID-19 at least twice over the course of 20 months also suggests that, despite several waves of infection, herd immunity through natural infection has not been achieved in the population.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mahan Ghafari", + "author_inst": "University of Oxford" + }, + { + "author_name": "Oliver J Watson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ariel Karlinsky", + "author_inst": "Hebrew University of Jerusalem" + }, + { + "author_name": "Luca Ferretti", + "author_inst": "Nuffield Department of Medicine" + }, + { + "author_name": "Aris Katzourakis", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.06.21264645", "rel_title": "A joint hierarchical model for the number of cases and deaths due to COVID-19 across the boroughs of Montreal", @@ -560025,69 +560512,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.10.03.21264451", - "rel_title": "Safety and Immunogenicity of CoronaVac and ChAdOx1 Against the SARS-CoV-2 Circulating Variants of Concern (Alpha, Delta, Beta) in Thai Healthcare Workers", - "rel_date": "2021-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.03.21264451", - "rel_abs": "ImportanceInactivated vaccine (CoronaVac) and chimpanzee adenovirus-vector vaccine (ChAdOx1) have been more available in resource-limited settings. However, the data comparing between these two vaccines in the same setting are limited.\n\nObjectivesTo determine adverse events (AEs) and immunogenicity of CoronaVac and ChAdOx1 in health care workers (HCWs).\n\nDesignThis prospective study was conducted from February to July 2021.\n\nSettingA single center, university-based tertiary care center in Bangkok.\n\nParticipantsHealthy HCWs.\n\nExposureTwo doses of CoronaVac (4 weeks apart) or ChAdOx1 (8 weeks apart) intramuscularly.\n\nMain Outcomes and MeasuresSelf-reported AEs were collected for 7 days following each vaccination using electronic diary. The immunogenicity was determined by the level of IgG antibodies against receptor binding domain (RBD) of the SARS-CoV-2 spike protein (S1 subunit). The 50% plaque reduction neutralization tests against original Wuhan strain and circulating VOCs were performed in subset of samples at 2 weeks after the second dose.\n\nResultsOf the 360 HCWs, 180 received each vaccine. The median (interquartile range: IQR) age was 35 (29-44) years old and 84.2% were female. Participants who received ChAdOx1 reported higher frequency of AEs than those received CoronaVac after both the first dose (84.4% vs. 66.1%, P < 0.001) and second dose (75.6% vs. 60.6%, P = 0.002), with more AEs in those younger than 30 years of age for both vaccines. The seroconversion rate was 75.6% and 100% following the first dose of CoronaVac and ChAdOx1, respectively. All participants seroconverted at 2 weeks after the second dose. The anti-SARS-CoV-2 RBD IgG levels induced by CoronaVac was lower than ChAdOX1 with geometric means of 164.4 and 278.5 BAU/mL, respectively (P = 0.0066). Both vaccines induced similar levels of neutralizing antibodies against the Wuhan strain, geometric mean titer (GMT) of 337.4 vs 331.2; however, CoronaVac induced significantly lower GMT against Alpha (23.1 vs. 92.5), Delta (21.2 vs. 69.7), and Beta (10.2 vs. 43.6) variants, respectively.\n\nConclusions and RelevanceCoronaVac induces lower measurable antibodies but with lower frequency of AEs than ChAdOx1. The low neutralizing antibodies against the circulating VOCs induced by CoronaVac supports the need for earlier boosting to prevent breakthrough infections.\n\nTrial RegistrationTCTR20210720002 https://www.thaiclinicaltrials.org/\n\nQuestionWhat is the difference between CoronaVac and ChAdOx1 vaccines on safety and immunogenicity against the circulating variants of concern (VOCs) in the same setting?\n\nFindingsThis prospective study in 360 healthy health care workers reported higher frequency of adverse events following ChAdOx1 than CoronaVac particularly in those younger than 30 years old. The ChAdOx1 induced 3.3-4.3 times higher neutralising antibodies against VOCs than CoronaVac.\n\nMeaningThe 2-dose CoronaVac vaccination induced significantly lower level of neutralizing antibody against the circulating VOCs. An earlier booster may be needed to prevent breakthrough infection.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Nasikarn Angkasekwinai", - "author_inst": "Siriraj Hospital" - }, - { - "author_name": "Jaturong Sewatanon", - "author_inst": "Siriraj Hospital" - }, - { - "author_name": "Suvimol Niyomnaitham", - "author_inst": "Siriraj Hospital" - }, - { - "author_name": "Supaporn Phumiamorn", - "author_inst": "Department of Medical Sciences, Ministry of Public Health" - }, - { - "author_name": "Kasama Sukapirom", - "author_inst": "Siriraj Hospital" - }, - { - "author_name": "Sompong Sapsutthipas", - "author_inst": "Department of Medical Sciences, Ministry of Public Health" - }, - { - "author_name": "Rujipas Sirijatuphat", - "author_inst": "Siriraj Hospital" - }, - { - "author_name": "Orasri Wittawatmongkol", - "author_inst": "Siriraj Hospital" - }, - { - "author_name": "Sansnee Senawong", - "author_inst": "Siriraj Hospital" - }, - { - "author_name": "Surakameth Mahasirimongkol", - "author_inst": "Department of Medical Sciences, Ministry of Public Health" - }, - { - "author_name": "Sakalin Trisiriwanich", - "author_inst": "Department of Medical Sciences, Ministry of Public Health" - }, - { - "author_name": "Kulkanya Chokephaibulkit", - "author_inst": "Siriraj Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.04.21263131", "rel_title": "Sero Prevalence of COVID-19 in Palestine in 2020", @@ -560292,6 +560716,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.10.05.21264548", + "rel_title": "Feasibility and acceptability of daily testing at school as an alternative to self-isolation following close contact with a confirmed case of COVID-19: A qualitative analysis", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.05.21264548", + "rel_abs": "BackgroundDaily testing using a rapid Lateral Flow Device (LFD) has been suggested as an alternative to self-isolation. A randomised trial comparing daily contact testing (DCT) in schools with self-isolation found that SARS-CoV-2 transmission within school was comparable and low in both groups. However, if this approach is to be adopted widely, it is critical that we understand the perspective of those who will be delivering and receiving DCT. The aim of this qualitative process study embedded in the randomised controlled trial (RCT) was to improve understanding of a range of behavioural factors that could influence implementation.\n\nMethodsInterviews were conducted with 63 participants, including staff, students, and parents of students who had been identified as being in close contact with someone with COVID-19. The topic guide explored perceptions of daily testing, understanding of positive and negative test results, and adherence to guidance. Data were analysed using an inductive thematic approach.\n\nResultsResults were organised under three main headings: (1) factors influencing daily testing (2) interpretation of test results (3) behaviour during testing period. Participants recognized that daily testing may allow students to remain in school, which was viewed as necessary for both education and social needs. Whilst some felt safer as a result of daily testing, others raised concerns about safety. Participants did not always understand how to interpret and respond to test results, and although participants reported high levels of adherence to the guidance, improved communications were desired.\n\nConclusionDaily testing may be a feasible and acceptable alternative to self-isolation among close contacts of people who test positive. However, improved communications are needed to ensure that all students and parents have a good understanding of the rationale for testing, what test results mean, how test results should be acted on, and how likely students are to test positive following close contact. Support is needed for students and parents of students who have to self-isolate and for those who have concerns about the safety of daily testing.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sarah Denford", + "author_inst": "University of Bristol" + }, + { + "author_name": "Lauren Towler", + "author_inst": "University of Southampton" + }, + { + "author_name": "Behiye Ali", + "author_inst": "University of Bristol" + }, + { + "author_name": "Georgia Treneman-Evans", + "author_inst": "University of Bristol" + }, + { + "author_name": "Rachael Bloomer", + "author_inst": "University of Bristol" + }, + { + "author_name": "Tim E Peto", + "author_inst": "oxford university" + }, + { + "author_name": "Bernadette C Young", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lucy Yardley", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.05.463205", "rel_title": "SARS-CoV-2 causes human BBB injury and neuroinflammation indirectly in a linked organ chip platform", @@ -562399,65 +562870,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.10.04.21264483", - "rel_title": "Fourteen-days Evolution of COVID-19 Symptoms During the Third Wave in Non-vaccinated Subjects and Effects of Hesperidin Therapy: A randomized, double-blinded, placebo-controlled study.", - "rel_date": "2021-10-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.04.21264483", - "rel_abs": "COVID-19 symptoms can cause substantial disability, yet no therapy can currently reduce their frequency or duration. We conducted a double-blind placebo-controlled trial of hesperidin 1000 mg once-daily for 14 days in 216 symptomatic non-vaccinated COVID-19 subjects. Thirteen symptoms were recorded after 3, 7, 10 and 14 days. The primary endpoint was the proportion of subjects with any of four cardinal (group A) symptoms: fever, cough, shortness of breath or anosmia. At baseline, symptoms in decreasing frequency were: cough (53.2%), weakness (44.9%), headache (42.6%), pain (35.2%), sore throat (28.7%), runny nose (26.9%), chills (22.7%), shortness of breath (22.2%), anosmia (18.5%), fever (16.2%), diarrhea (6.9%), nausea/vomiting (6.5%) and irritability/confusion (3.2%). Group A symptoms in the placebo vs hesperidin group was 88.8% vs 88.5% (day 1) and reduced to 58.5 vs 49.4 % at day 14 (OR 0.69, 95% CI 0.38-1.27, p = 0.23). At day 14, 15 subjects in the placebo group and 28 in the hesperidin group failed to report their symptoms. In an attrition bias analysis imputing \"no symptoms\" to missing values, the hesperidin group shows reduction of 14.5 % of group A symptoms from 50.9% to 36.4% (OR: 0.55, 0.32-0.96, p = 0.03). Anosmia, the most frequent persisting symptom (29.3%), was lowered by 7.3% at 25.3 % in the hesperidin group vs 32.6% in the placebo group (p = 0.29). Mean number of symptoms in placebo and hesperidin was 5.10 {+/-} 2.26 vs 5.48 {+/-} 2.35 (day 1) and 1.40 {+/-} 1.65 vs 1.38 {+/-} 1.76 (day 14) (p = 0.92). In conclusion, most non-vaccinated COVID-19 infected subjects remain symptomatic after 14 days with anosmia being the most frequently persisting symptom. Hesperidin 1g daily may help reduce group A symptoms. Earlier treatment of longer duration and/or higher dosage should be tested.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Jocelyn Dupuis", - "author_inst": "Montreal Heart Institute" - }, - { - "author_name": "Pierre Laurin", - "author_inst": "Ingenew Pharma Inc." - }, - { - "author_name": "Jean-Claude Tardif", - "author_inst": "Montreal Heart Institute" - }, - { - "author_name": "Leslie Hausermann", - "author_inst": "Montreal Heart Institute" - }, - { - "author_name": "Camille Rosa", - "author_inst": "Montreal Health Innovations Coordinating Center" - }, - { - "author_name": "Marie-Claude Guertin", - "author_inst": "Montreal Health Innovations Coordinating Center" - }, - { - "author_name": "Karen Thibaudeau", - "author_inst": "Ingenew Pharma Inc." - }, - { - "author_name": "Lyne Gagnon", - "author_inst": "Ingenew Pharma Inc." - }, - { - "author_name": "Frank Cesari", - "author_inst": "Ingenew Pharma Inc." - }, - { - "author_name": "Martin Robitaille", - "author_inst": "Ingenew Pharma Inc." - }, - { - "author_name": "John E Moran", - "author_inst": "Ingenew Pharma Inc." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.04.21264522", "rel_title": "A randomized, double-blind phase I clinical trial of two recombinant dimeric RBD COVID-19 vaccine candidates: safety, reactogenicity and immunogenicity", @@ -562690,6 +563102,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.10.02.21264210", + "rel_title": "SARS-CoV-2 multi-variant graphene biosensor based on engineered dimeric ACE2 receptor", + "rel_date": "2021-10-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.02.21264210", + "rel_abs": "Fast, reliable and point-of-care systems to detect the SARS-CoV-2 infection are crucial to contain viral spreading and to adopt timely clinical treatments. Many of the rapid detection tests currently in use are based on antibodies that bind viral proteins1. However, newly appearing virus variants accumulate mutations in their RNA sequence and produce proteins, such as Spike, that may show reduced binding affinity to these diagnostic antibodies, resulting in less reliable tests and in the need for continuous update of the sensing systems2. Here we propose a graphene field-effect transistor (gFET) biosensor which exploits the key interaction between the Spike protein and the human ACE2 receptor. This interaction is one of the determinants of host infections and indeed recently evolved Spike variants were shown to increase affinity for ACE2 receptor3. Through extensive computational analyses we show that a chimeric ACE2-Fc construct mimics the ACE2 dimer, normally present on host cells membranes, better than its soluble truncated form. We demonstrate that ACE2-Fc functionalized gFET is effective for in vitro detection of Spike and outperforms the same chip functionalized with either a diagnostic antibody or the soluble ACE2. Our sensor is implemented in a portable, wireless, point-of-care device and successfully detected both alpha and gamma virus variants in patients clinical samples. As incomplete immunization, due to vaccine roll-out, may offer new selective grounds for antibody-escaping virus variants4, our biosensor opens to a class of highly sensitive, rapid and variant-robust SARS-CoV-2 detection systems.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Mattia D'Agostino", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Eleonora Pavoni", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Alice Romagnoli", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy. New York-Marche Structural Biology Ce" + }, + { + "author_name": "Chiara Ardiccioni", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy. New York-Marche Structural Biology Ce" + }, + { + "author_name": "Stefano Motta", + "author_inst": "Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy." + }, + { + "author_name": "Paolo Crippa", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Giorgio Biagetti", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Valentina Notarstefano", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Simone Barocci", + "author_inst": "Department of Clinical Pathology, ASUR Marche AV1, Urbino, PU, Italy." + }, + { + "author_name": "Brianna K Costabile", + "author_inst": "Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA." + }, + { + "author_name": "Gabriele Colasurdo", + "author_inst": "OMME GEARS, Falconara M.am, Zona Ind. CIAF, 60015, Ancona, Italy." + }, + { + "author_name": "Sara Caucci", + "author_inst": "Virology Unit, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Torrette, 60126 Ancona, Italy." + }, + { + "author_name": "Davide Mencarelli", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Claudio Turchetti", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Marco Farina", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Luca Pierantoni", + "author_inst": "Department of Information Engineering, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Anna La Teana", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy. New York-Marche Structural Biology Ce" + }, + { + "author_name": "Richard Al Hadi", + "author_inst": "Alcatera Inc, Los Angeles, CA 90024, USA." + }, + { + "author_name": "Mauro Chinappi", + "author_inst": "Department of Industrial Engineering, University of Rome Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy." + }, + { + "author_name": "Emiliano Trucchi", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy." + }, + { + "author_name": "Filippo Mancia", + "author_inst": "Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA." + }, + { + "author_name": "Blasco Morozzo della Rocca", + "author_inst": "Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica 1, 00133 Rome, Italy." + }, + { + "author_name": "Ilda D'Annessa", + "author_inst": "Institute of Chemical Science and Technologies, SCITEC-CNR, Via Mario Bianco 9, 20131, Milan, Italy." + }, + { + "author_name": "Daniele Di Marino", + "author_inst": "Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy. New York-Marche Structural Biology Ce" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.01.452232", "rel_title": "Characterization and Structural Prediction of ORF10, ORF7b, ORF7a, ORF6, Membrane Glycoprotein, and Envelope Protein in SARS-CoV-2 Bangladeshi Variant through Bioinformatics Approach", @@ -563965,85 +564488,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.01.21264400", - "rel_title": "Recombinant adjuvanted zoster vaccine and reduced risk of COVID-19 diagnosis and hospitalization in older adults", - "rel_date": "2021-10-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21264400", - "rel_abs": "BackgroundVaccines may elicit long-term boosting of innate immune responses that can help protect against COVID-19. We evaluated the association between recombinant adjuvanted zoster vaccine (RZV) and COVID-19 outcomes at Kaiser Permanente Southern California.\n\nMethodsIn a cohort design, adults aged [≥]50 years who received [≥]1 RZV dose prior to 3/1/2020 were matched 1:2 to unvaccinated individuals and followed until 12/31/2020. Adjusted hazard ratios (aHR) and 95% confidence intervals (CIs) for COVID-19 outcomes were estimated using Cox proportional hazards regression. In a test-negative design, cases had a positive SARS-CoV-2 test and controls had only negative tests, from 3/1/2020-12/31/2020. Adjusted odds ratios (aOR) and 95% CIs for prior receipt of RZV were estimated using logistic regression.\n\nResultsIn the cohort design, 149,244 RZV recipients were matched to 298,488 unvaccinated individuals. The aHRs (95% CI) for COVID-19 diagnosis and hospitalization were 0.84 (0.81-0.87) and 0.68 (0.64-0.74), respectively. In the test-negative design, 8.4% of 75,726 test-positive cases and 13.1% of 340,898 test-negative controls had received [≥]1 RZV dose. The aOR (95% CI) was 0.84 (0.81-0.86).\n\nConclusionRZV vaccination was associated with a 16% lower risk of COVID-19 diagnosis and 32% lower risk of hospitalization, suggesting RZV elicits heterologous protection, possibly through trained immunity.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Katia J Bruxvoort", - "author_inst": "Department of Research & Evaluation, Kaiser Permanente Southern California, 100 S Los Robles, Pasadena, CA 91101, USA" - }, - { - "author_name": "Bradley Ackerson", - "author_inst": "Department of Research & Evaluation, Kaiser Permanente Southern California, 100 S Los Robles, Pasadena, CA 91101, USA" - }, - { - "author_name": "Lina S Sy", - "author_inst": "Department of Research & Evaluation, Kaiser Permanente Southern California, 100 S Los Robles, Pasadena, CA 91101, USA" - }, - { - "author_name": "Amit Bhavsar", - "author_inst": "GSK, 20 Avenue Fleming, 1300 Wavre, Belgium" - }, - { - "author_name": "Hung Fu Tseng", - "author_inst": "Department of Research & Evaluation, Kaiser Permanente Southern California, 100 S Los Robles, Pasadena, CA 91101, USA" - }, - { - "author_name": "Ana Florea", - "author_inst": "Department of Research & Evaluation, Kaiser Permanente Southern California, 100 S Los Robles, Pasadena, CA 91101, USA" - }, - { - "author_name": "Yi Luo", - "author_inst": "Department of Research & Evaluation, Kaiser Permanente Southern California, 100 S Los Robles, Pasadena, CA 91101, USA" - }, - { - "author_name": "Yun Tian", - "author_inst": "Department of Research & Evaluation, Kaiser Permanente Southern California, 100 S Los Robles, Pasadena, CA 91101, USA" - }, - { - "author_name": "Zendi Solano", - "author_inst": "Department of Research & Evaluation, Kaiser Permanente Southern California, 100 S Los Robles, Pasadena, CA 91101, USA" - }, - { - "author_name": "Robyn Widenmaier", - "author_inst": "GSK, 14200 Shady Grove Road, Rockville, MD 20850, USA" - }, - { - "author_name": "Meng Shi", - "author_inst": "GSK, 14200 Shady Grove Road, Rockville, MD 20850, USA" - }, - { - "author_name": "Robbert Van Der Most", - "author_inst": "GSK, 89 Rue de l Institut, 1330 Rixensart, Belgium" - }, - { - "author_name": "Johannes Eberhard Schmidt", - "author_inst": "GSK, 1 Via Fiorentina, 53100 Siena, Italy" - }, - { - "author_name": "Jasur Danier", - "author_inst": "GSK, 14200 Shady Grove Road, Rockville, MD 20850, USA" - }, - { - "author_name": "Thomas Breuer", - "author_inst": "GSK, 20 Avenue Fleming, 1300 Wavre, Belgium" - }, - { - "author_name": "Lei Qian", - "author_inst": "Department of Research & Evaluation, Kaiser Permanente Southern California, 100 S Los Robles, Pasadena, CA 91101, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.01.21264411", "rel_title": "Forgoing healthcare during the COVID-19 pandemic in Geneva, Switzerland - a cross-sectional population-based study", @@ -564276,6 +564720,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.10.01.21264412", + "rel_title": "Initial SARS-CoV-2 viral load is associated with disease severity: a retrospective cohort study", + "rel_date": "2021-10-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21264412", + "rel_abs": "BackgroundWe aimed to assess the association between initial SARS-CoV-2 viral load and the subsequent hospital and intensive care unit (ICU) admission and overall survival.\n\nMethodsAll persons with a positive SARS-CoV-2 RT-PCR result from a combined nasopharyngeal (NP) and oropharyngeal (OP) swab (first samples from unique persons only) that was collected between March 17, 2020, and March 31, 2021, in Public Health testing facilities in the region Kennemerland, province of North Holland, the Netherlands were included. Data on hospital (and ICU) admission were collected from the two large teaching hospitals in the region Kennemerland.\n\nResultsIn total, 20,207 SARS-CoV-2 positive persons were included in this study, of whom 310 (1.5%) were hospitalized in a regional hospital within 30 days of their positive SARS-CoV-2 RT-PCR test. When persons were categorized in three SARS-CoV-2 viral load groups, the high viral load group (Cp < 25) was associated with an increased risk of hospitalization as compared to the low viral load group (Cp > 30) (ORadjusted [95%CI]: 1.57 [1.11-2.26], p-value=0.012), adjusted for age and sex. The same association was seen for ICU admission (ORadjusted [95%CI]: 7.06 [2.15-43.57], p-value=0.007). For a subset of 243 of the 310 hospitalized patients, the association of initial SARS-CoV-2 Cp-value with in-hospital mortality was analyzed. The initial SARS-CoV-2 Cp-value of the 17 patients who deceased in the hospital was significantly lower (indicating a higher viral load) compared to the 226 survivors: median Cp-value [IQR]: 22.7 [3.4] vs. 25.0 [5.2], OR[95%CI]: 0.81 [0.68-0.94], p-value = 0.010.\n\nConclusionsOur data show that higher initial SARS-CoV-2 viral load is associated with an increased risk of hospital admission, ICU admission, and in-hospital mortality. We believe that our findings emphasize the added value of reporting SARS-CoV-2 viral load based on Cp-values to identify persons who are at the highest risk of adverse outcomes such as hospital or ICU admission and who therefore may benefit from more intensive monitoring.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Dennis Souverein", + "author_inst": "Regional Public Health Laboratory Kennemerland" + }, + { + "author_name": "Karlijn van Stralen", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Steven van Lelyveld", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Claudia van Gemeren", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Milly Haverkort", + "author_inst": "Public Health Service Kennemerland" + }, + { + "author_name": "Dominic Snijders", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Robin Soetekouw", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Erik Kapteijns", + "author_inst": "Rode Kruis Ziekenhuis" + }, + { + "author_name": "Evelien de Jong", + "author_inst": "Rode Kruis Ziekenhuis" + }, + { + "author_name": "Gonneke Hermanides", + "author_inst": "Rode Kruis Ziekenhuis" + }, + { + "author_name": "Sem Aronson", + "author_inst": "Spaarne Gasthuis" + }, + { + "author_name": "Alex Wagemakers", + "author_inst": "Regional Public Health Laboratory Kennemerland" + }, + { + "author_name": "Sjoerd Euser", + "author_inst": "Regional Public Health Laboratory Kennemerland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.01.21264428", "rel_title": "Risk factors for infection, predictors of severe disease and antibody response to COVID-19 in patients with rheumatic diseases in Portugal - a multicentre, nationwide study", @@ -565699,61 +566210,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.30.21264181", - "rel_title": "Equivalence of saliva RT-qPCR testing to nasal-throat/nasopharyngeal swab testing in the general practitioner's setting to detect SARS-CoV-2", - "rel_date": "2021-10-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.30.21264181", - "rel_abs": "Study designSaliva has been proposed as valid alternative for nasopharyngeal swab for RT-qPCR detection of SARS-CoV-2. The sensitivity is generally equivalent, and it comes with much less discomfort for the patient. While there is an overall good performance in the literature for adults, there is much less information on the use of saliva in children or in the general practitioners setting.\n\nMethodsWe tested a novel commercially available saliva collection kit with a virus inactivating and RNA stabilizing buffer (InActiv Blue(R)) in matched saliva and swab samples from 245 individuals, including 216 children, collected by general practitioners.\n\nResultsBlind RT-qPCR testing of the saliva samples confirmed all 23 positives identified by swab testing (100% concordance), irrespective of age, presence of symptoms, or high-risk status. One childs saliva sample was found low positive while negative on the nasopharyngeal swab, resulting in an overall relative sensitivity of RT-qPCR saliva testing of 104.3%.\n\nConclusionSaliva collected in InActiv Blue(R) can be a valid alternative for SARS-CoV-2 RT-qPCR testing in the general practitioners setting, including children.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ilse Jonckheere", - "author_inst": "InActiv Blue" - }, - { - "author_name": "Liesbeth Faes", - "author_inst": "InActiv Blue" - }, - { - "author_name": "Yarah Overmeire", - "author_inst": "Labo Nuytinck" - }, - { - "author_name": "An De Vleeschauwer", - "author_inst": "Labo Nuytinck" - }, - { - "author_name": "Laura Vanden Daele", - "author_inst": "Labo Nuytinck" - }, - { - "author_name": "Nathalie Van Bruaene", - "author_inst": "Labo Nuytinck" - }, - { - "author_name": "Ilse Vandecandelaere", - "author_inst": "Medisch Labo Bruyland" - }, - { - "author_name": "Britt Merlaen", - "author_inst": "Biogazelle" - }, - { - "author_name": "Joannes van Cann", - "author_inst": "Biogazelle" - }, - { - "author_name": "Jo Vandesompele", - "author_inst": "Ghent University, InActiv Blue, Biogazelle" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.30.21264335", "rel_title": "Humoral and cellular immune responses upon SARS-CoV-2 vaccines in patients with anti-CD20 therapies: A systematic review and meta-analysis of 1342 patients", @@ -565998,6 +566454,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.10.01.21264382", + "rel_title": "COVID-19 Pandemic Response in a Migrant Farmworker Community: Excess Mortality, Testing Access and Contact Tracing in Immokalee, Florida", + "rel_date": "2021-10-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21264382", + "rel_abs": "IntroductionWe aim to estimate the impact of COVID-19 in Immokalee, FL and assess community experiences with workplace conditions, access to testing, sources of information, and contact tracing to inform and strengthen local public health sector efforts in reaching and providing high-quality care to the community.\n\nMethodsWe conducted a descriptive analysis of data on COVID-19 deaths for Collier County from May-August 2020. We surveyed a cross-sectional, randomized representative sample of 318 adults living in Immokalee from March-November 2020 to assess socio-demographics, sources of information, ability to follow guidelines, and experiences with local programs. Results were compared across language groups.\n\nResultsAverage excess mortality in Collier County was 108%. The majority surveyed in Immokalee had socio-demographic factors associated with higher COVID risk. Non-English speakers had higher workplace risk due to less ability to work from home. Haitian Creole speakers were less likely to be tested, though all participants were willing to get symptomatic testing and quarantine. Those participants who tested positive or had COVID-19 exposures had low engagement with the contact tracing program, and Spanish-speakers reported lower quality of contact tracing than English speakers.\n\nConclusionsThe community of Immokalee, FL is a vulnerable population that suffered disproportionate deaths from COVID-19. This study reveals language inequities in COVID testing and contact tracing should be targeted in future pandemic response in Immokalee and other migrant farmworker communities.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Neha Limaye", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Brennan Ninesling", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Frantzso Marcelin", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Cody Nolan", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Walter Sobba", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Matthew Hing", + "author_inst": "David Geffen School of Medicine at UCLA" + }, + { + "author_name": "Emily Ptaszek", + "author_inst": "Healthcare Network of Southwest Florida" + }, + { + "author_name": "Fernet Leandre", + "author_inst": "Partners in Health" + }, + { + "author_name": "Daniel Palazuelos", + "author_inst": "Brigham and Women's Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.01.462460", "rel_title": "ZBP1 induces inflammatory signaling via RIPK3 and promotes SARS-CoV-2-induced cytokine expression", @@ -568005,49 +568512,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.27.21264202", - "rel_title": "The effects of communicating uncertainty around statistics on public trust: an international study", - "rel_date": "2021-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264202", - "rel_abs": "A growing body of research indicates that transparent communication of statistical uncertainty around facts and figures does not undermine credibility. However, the extent to which these findings apply in the context of the COVID-19 pandemic--rife with uncertainties--is unclear. In a large international survey experiment, (Study 1; N = 10,519) we report that communicating uncertainty around COVID-19 statistics in the form of a numeric range (vs. no uncertainty) may lead to slightly lower trust in the number presented but has no impact on trust in the source of the information. We also report the minimal impact of numeric uncertainty on trust is consistent across estimates of current or future COVID-19 statistics (Study 2) and figures relating to environmental or economic research, rather than the pandemic (Study 3). Conversely, we find imprecise statements about the mere existence of uncertainty without quantification can undermine both trust in the numbers and their source - though effects vary across countries and contexts. Communicators can be transparent about statistical uncertainty without concerns about undermining perceptions of their trustworthiness, but ideally should aim to use numerical ranges rather than verbal statements.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "John R Kerr", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Anne Marthe van der Bles", - "author_inst": "University of Groningen" - }, - { - "author_name": "Claudia Schneider", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Sarah Dryhurst", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Vivien Chopurian", - "author_inst": "Humboldt-Universitat zu Berlin" - }, - { - "author_name": "Alexandra LJ Freeman", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Sander van der Linden", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.27.21264191", "rel_title": "Monoclonal antibodies against SARS-CoV-2: potential game-changer still underused", @@ -568260,6 +568724,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.27.21264174", + "rel_title": "Counter-intuitive COVID-19 Trajectories - Explanations, Early Warning Indicator and Mitigation Strategies", + "rel_date": "2021-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264174", + "rel_abs": "The COVID-19 trajectories worldwide have shown several surprising features which are outside the purview of classical epidemiological models. These include (a) almost constant and low daily case rates over extended periods of time, (b) sudden waves emerging from the above solution despite no or minimal change in the level of non-pharmaceutical interventions (NPI), and (c) reduction or flattening of case counts even after relaxation of NPI. To explain these phenomena, we add contact tracing to our recently developed cluster seeding and transmission (CST) model, which is predicated on heterogeneous rather than homogeneous mixing of people in society. With this addition, we find no fewer than four effects which make prediction of epidemic trajectories uncertain. These are (a) cryptogenic instability, where a small increase in population-averaged contact rate causes a large increase in cases, (b) critical mass effect, where a wave can manifest after weeks of quiescence with no change in parameter values, (c) knife-edge effect, where a small change in parameter across a critical value can cause a huge change in the response of the system, and (d) hysteresis effect, where the timing and not just the strength of a particular NPI determines the subsequent evolution of the epidemic. Despite these effects however, it is a robust conclusion that a good contact tracing program can effectively substitute for much more invasive measures. We further find that the contact tracing capacity ratio - a metric of the stress to which the tracers are subject - can act as a reliable early warning indicator of an imminent epidemic wave. Extensive simulations demonstrate that whenever there is a drop in capacity ratio during a period of low daily infections, there is a very high probability of the case counts rising significantly in the immediate future.\n\nAuthor summaryClose to two years into the pandemic, the trajectories of COVID-19 in different places and at different times have shown wild variations and confounded modeling and forecasting efforts. Our new mathematical model can help to explain these variations. Some solutions of our model are non-standard but realistic. For example, we find an epidemic curve where daily cases remain on a plateau for a long time before suddenly exploding into a wave, despite interventions remaining constant throughout. We also find solutions showing that a specific intervention, for example capacity reduction at public gatherings, is very effective if implemented early on in a wave but useless if implemented a little later. Our proposed early warning indicator can be a game-changer for epidemic forecasting and model-based intervention strategies. Current forecasting algorithms have the weakest performance at the inflection points where there is an abrupt change in trend in the daily infection rates. The early warning indicator can give us advance notice of an approaching inflection point, and enable the authorities to take preventive measures before a wave actually arrives. Our results indicate that close communication between contact tracing personnel and public health authorities can achieve synergistic mitigation of the pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "B Shayak", + "author_inst": "Cornell University" + }, + { + "author_name": "Mohit Manoj Sharma", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.29.21264261", "rel_title": "World Science against COVID-19: Gender and Geographical Distribution of Research.", @@ -570103,57 +570590,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.09.29.462373", - "rel_title": "SARS-CoV-2 variants of concern infect the respiratory tract and induce inflammatory response in wild-type laboratory mice", - "rel_date": "2021-09-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.29.462373", - "rel_abs": "The emergence of new severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern poses a major threat to the public health due to possible enhanced virulence, transmissibility and immune escape. These variants may also adapt to new hosts in part through mutations in the spike protein. In this study, we evaluated the infectivity and pathogenicity of SARS-CoV-2 variants of concern in wild-type C57BL/6 mice. Six-week-old mice were inoculated intranasally with a representative virus from the original B.1 lineage or emerging B.1.1.7 and B.1.351 lineages. We also infected a group of mice with a mouse-adapted SARS-CoV-2 (MA10). Viral load and mRNA levels of multiple cytokines and chemokines were analyzed in the lung tissues on day 3 after infection. Our data show that unlike the B.1 virus, the B.1.1.7 and B.1.351 viruses are capable of infecting C57BL/6 mice and replicating at high concentrations in the lungs. The B.1.351 virus replicated to higher titers in the lungs compared to the B.1.1.7 and MA10 viruses. The levels of cytokines (IL-6, TNF-, IL-1{beta}) and chemokine (CCL2) were upregulated in response to the B.1.1.7 and B.1.351 infection in the lungs. Overall, these data indicate a greater potential for infectivity and adaptation to new hosts by emerging SARS-CoV-2 variants.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Shannon Stone", - "author_inst": "Georgia State University" - }, - { - "author_name": "Hussin A. Rothan", - "author_inst": "Georgia State University" - }, - { - "author_name": "Janhavi P Natekar", - "author_inst": "Georgia State University" - }, - { - "author_name": "Pratima Kumari", - "author_inst": "Georgia State University" - }, - { - "author_name": "Shaligram Sharma", - "author_inst": "Georgia State University" - }, - { - "author_name": "Heather Pathak", - "author_inst": "Georgia State University" - }, - { - "author_name": "Komal Arora", - "author_inst": "Georgia State University" - }, - { - "author_name": "Tabassum T Aurani", - "author_inst": "Georgia State University" - }, - { - "author_name": "Mukesh Kumar", - "author_inst": "Georgia State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.09.29.462406", "rel_title": "Full genome Nobecovirus sequences from Malagasy fruit bats define a unique evolutionary history for this coronavirus clade", @@ -570402,6 +570838,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.09.27.21264044", + "rel_title": "Sub-Saharan African Countries' COVID-19 Research: An analysis of the External and Internal Contributions, Collaboration Patterns and Funding Sources", + "rel_date": "2021-09-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264044", + "rel_abs": "This study aims at providing some evidence-based insight into Sub-Saharan Africas first eighteen months of COVID-19 research by evaluating its research contributions, patterns of collaboration, and funding sources. Eighteen months (2020 January 1-2021 June 30) COVID-19 publication data of 46 Sub-Saharan African countries was collected from Scopus for analysis. Country of affiliation of the authors and funding agencies data was analyzed to understand country contributions, collaboration pattern and funding sources. USA (23.08%) and the UK (19.63%), the top two external contributors, collaborated with Sub-Saharan African countries about three times more than other countries. Collaborative papers between Sub-Saharan African countries - without contributions from outside the region-made up less than five percent of the sample, whereas over 50% of the papers were written in collaboration with researchers from outside the region. Organizations that are in USA and the UK funded 45% of all the COVID-19 research from Sub-Saharan Africa. 53.44% of all the funding from Sub-Saharan African countries came from South African organizations. This study provides evidence that pan-African COVID-19 research collaboration is low, perhaps due to poor funding and lack of institutional support within Sub-Saharan Africa. This mirrors the collaborative features of science in Sub-Saharan Africa before the COVID-19 pandemic. The high volume of international collaboration during the pandemic is a good development. There is also a strong need to forge more robust pan-African research collaboration networks, through funding from Africas national and regional government organizations, with the specific objective of meeting local COVID-19 and other healthcare needs.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Toluwase Victor Asubiaro", + "author_inst": "University of Western Ontario" + }, + { + "author_name": "Hafsah Shaik", + "author_inst": "Independent Researcher" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.27.21264130", "rel_title": "Effectiveness of the mRNA BNT162b2 vaccine against SARS-CoV-2 severe infections in the Israeli over 60 population: a temporal analysis done by using the national surveillance data.", @@ -571653,117 +572112,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.25.21264117", - "rel_title": "Lasting changes to circulating leukocytes in people with mild SARS-CoV-2 infections", - "rel_date": "2021-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.25.21264117", - "rel_abs": "Survivors of severe SARS-CoV-2 infections frequently suffer from a range of post-infection sequelae. Whether survivors of mild or asymptomatic infections can expect any long-term health consequences is not yet known. Herein we investigated lasting changes to soluble inflammatory factors and cellular immune phenotype and function in individuals who had recovered from mild SARS-CoV-2 infections (n=22) compared to those that had recovered from other mild respiratory infections (n=11). Individuals who had mild SARS-CoV-2 infections had elevated levels of C-reactive protein 1-3 months after symptom onset, and changes in phenotype and function of circulating T cells that were not apparent in individuals 6-9 months post-symptom onset. Markers of monocyte activation and expression of adherence and chemokine receptors indicative of altered migratory capacity were also higher at 1-3 months post-infection in individuals who had mild SARS-CoV-2, but these were no longer elevated by 6-9 months post-infection. Perhaps most surprisingly, polyclonal activation of T cells was higher in individuals who had recently experienced a mild SARS-CoV-2 infection compared to individuals with other recent respiratory infections. These data are indicative of prolonged immune activation and systemic inflammation that persists for up to three months after mild or asymptomatic SARS-CoV-2 infections.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Allison E Kennedy", - "author_inst": "McMaster University" - }, - { - "author_name": "Laura Cook", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Jessica A Breznik", - "author_inst": "McMaster University" - }, - { - "author_name": "Braeden Cowbrough", - "author_inst": "McMaster University" - }, - { - "author_name": "Jessica G Wallace", - "author_inst": "McMaster University" - }, - { - "author_name": "Angela Huynh", - "author_inst": "McMaster University" - }, - { - "author_name": "James W Smith", - "author_inst": "McMaster University" - }, - { - "author_name": "Kiho Son", - "author_inst": "McMaster University" - }, - { - "author_name": "Hannah Stacey", - "author_inst": "McMaster University" - }, - { - "author_name": "Jann Ang", - "author_inst": "McMaster University" - }, - { - "author_name": "Allison McGeer", - "author_inst": "Sinai Health" - }, - { - "author_name": "Brenda L Coleman", - "author_inst": "Sinai Health" - }, - { - "author_name": "Maggie Larche", - "author_inst": "McMaster University" - }, - { - "author_name": "Mark Larche", - "author_inst": "McMaster University" - }, - { - "author_name": "Nathan Hambly", - "author_inst": "McMaster University" - }, - { - "author_name": "Parameswaran Nair", - "author_inst": "McMaster University" - }, - { - "author_name": "Kjetil Ask", - "author_inst": "McMaster University" - }, - { - "author_name": "Matthew S Miller", - "author_inst": "McMaster University" - }, - { - "author_name": "Jonathan Bramson", - "author_inst": "McMaster University" - }, - { - "author_name": "Megan K Levings", - "author_inst": "University of British Colombia" - }, - { - "author_name": "Ishac Nazy", - "author_inst": "McMaster University" - }, - { - "author_name": "Sarah Svenningsen", - "author_inst": "McMaster University" - }, - { - "author_name": "Manali Mukherjee", - "author_inst": "McMaster University" - }, - { - "author_name": "Dawn ME Bowdish", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.25.21263542", "rel_title": "COVID-19 attack ratio among children critically depends on the time to removal and activity levels", @@ -571952,6 +572300,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.25.21264082", + "rel_title": "Contact surveys reveal heterogeneities in age-group contributions to SARS-CoV-2 dynamics in the United States", + "rel_date": "2021-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.25.21264082", + "rel_abs": "SARS-CoV-2 is spread primarily through person-to-person contacts. Quantifying population contact rates is important for understanding the impact of physical distancing policies and for modeling COVID-19, but contact patterns have changed substantially over time due to shifting policies and behaviors. There are surprisingly few empirical estimates of age-structured contact rates in the United States both before and throughout the COVID-19 pandemic that capture these changes. Here, we use data from six waves of the Berkeley Interpersonal Contact Survey (BICS), which collected detailed contact data between March 22, 2020 and February 15, 2021 across six metropolitan designated market areas (DMA) in the United States. Contact rates were low across all six DMAs at the start of the pandemic. We find steady increases in the mean and median number of contacts across these localities over time, as well as a greater proportion of respondents reporting a high number of contacts. We also find that young adults between ages 18 and 34 reported more contacts on average compared to other age groups. The 65 and older age group consistently reported low levels of contact throughout the study period. To understand the impact of these changing contact patterns, we simulate COVID-19 dynamics in each DMA using an age-structured mechanistic model. We compare results from models that use BICS contact rate estimates versus commonly used alternative contact rate sources. We find that simulations parameterized with BICS estimates give insight into time-varying changes in relative incidence by age group that are not captured in the absence of these frequently updated estimates. We also find that simulation results based on BICS estimates closely match observed data on the age distribution of cases, and changes in these distributions over time. Together these findings highlight the role of different age groups in driving and sustaining SARS-CoV-2 transmission in the U.S. We also show the utility of repeated contact surveys in revealing heterogeneities in the epidemiology of COVID-19 across localities in the United States.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Taylor Chin", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Dennis M. Feehan", + "author_inst": "UC Berkeley" + }, + { + "author_name": "Caroline O. Buckee", + "author_inst": "Harvard School of Public Health" + }, + { + "author_name": "Ayesha S. Mahmud", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.26.21264145", "rel_title": "Racial and ethnic inequalities in COVID-19 mortality within carceral settings: An analysis of Texas prisons and jails", @@ -573815,97 +574194,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.21.21263713", - "rel_title": "Prevalence of SARS-CoV-2 infection among people experiencing homelessness in Toronto during the first wave of the COVID-19 pandemic", - "rel_date": "2021-09-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.21.21263713", - "rel_abs": "BackgroundPeople experiencing homelessness are at increased risk of SARS-CoV-2 infection. This study reports the point prevalence of SARS-CoV-2 infection during testing conducted at sites serving people experiencing homelessness in Toronto during the first wave of the COVID-19 pandemic. We also explored the association between site characteristics and prevalence rates.\n\nMethodsThe study included individuals who were staying at shelters, encampments, COVID-19 physical distancing sites, and drop-in and respite sites and completed outreach-based testing for SARS-CoV-2 during the period April 17 to July 31, 2020. We examined test positivity rates over time and compared them to rates in the general population of Toronto. Negative binomial regression was used to examine the relationship between each shelter-level characteristic and SARS-CoV-2 positivity rates. We also compared the rates across 3 time periods (T1: April 17-April 25; T2: April 26-May 23; T3: May 24-June 25).\n\nResultsThe overall prevalence of SARS-CoV-2 infection was 8.5% (394/4657). Site-specific rates showed great heterogeneity with infection rates ranging from 0% to 70.6%. Compared to T1, positivity rates were 0.21 times lower (95% CI: 0.06, 0.75) during T2 and 0.14 times lower (95% CI: 0.043, 0.44) during T3. Most cases were detected during outbreak testing (384/394 [97.5%]) rather than active case finding.\n\nInterpretationDuring the first wave of the pandemic, rates of SARS-CoV-2 infection at sites for people experiencing homelessness in Toronto varied significantly over time. The observation of lower rates at certain sites may be attributable to overall time trends, expansion of outreach-based testing to include sites without known outbreaks and/or individual site characteristics.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Linh Luong", - "author_inst": "Unity Health Toronto" - }, - { - "author_name": "Michaela Beder", - "author_inst": "University of Toronto" - }, - { - "author_name": "Rosane Nisenbaum", - "author_inst": "Unity Health Toronto" - }, - { - "author_name": "Aaron Orkin", - "author_inst": "University of Toronto" - }, - { - "author_name": "Jonathan Wong", - "author_inst": "Inner City Health Associates" - }, - { - "author_name": "Cynthia Damba", - "author_inst": "Ontario Health Toronto" - }, - { - "author_name": "Ryan Emond", - "author_inst": "Ontario Health Toronto" - }, - { - "author_name": "Suvendrini Lena", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Vanessa Wright", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Mona Loutfy", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Cindy Bruce-Barrett", - "author_inst": "The Hospital for Sick Children" - }, - { - "author_name": "Wilfred Cheung", - "author_inst": "Ontario Health Toronto" - }, - { - "author_name": "Yick Kan Cheung", - "author_inst": "Ontario Health Toronto" - }, - { - "author_name": "Victoria Williams", - "author_inst": "Ontario Health Toronto" - }, - { - "author_name": "Miriam Vanmeurs", - "author_inst": "Ontario Health Toronto" - }, - { - "author_name": "Andrew Boozary", - "author_inst": "University Health Network" - }, - { - "author_name": "Harvey Manning", - "author_inst": "Anishnawbe Health Toronto" - }, - { - "author_name": "Joe Hester", - "author_inst": "Anishnawbe Health Toronto" - }, - { - "author_name": "Stephen W. Hwang", - "author_inst": "Unity Health Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.22.21263900", "rel_title": "Prevalence and risk factors for in-school transmission of SARS-CoV-2 in Massachusetts K-12 public schools, 2020-2021", @@ -574086,6 +574374,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.23.21264014", + "rel_title": "Neutralizing efficacy of vaccines against the SARS-CoV-2 Mu variant", + "rel_date": "2021-09-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.23.21264014", + "rel_abs": "The rise of mutant strains of SARS-CoV-2 poses an additional problem to the existing pandemic of COVID-19. There are rising concerns about the Mu variant which can escape humoral immunity acquired from infections from previous strains or vaccines. We examined the neutralizing efficacy of the BNT162b2 mRNA vaccine against the Mu variant and report that the vaccine has 76% neutralizing effectiveness against the Mu compared to 96% with the original strain. We also show that Mu, similar to the Delta variant, causes cell-to-cell fusion which can be an additional factor for the variant to escape vaccine-mediated humoral immunity. Despite the rise in vaccine escape strains, the vaccine still possesses adequate ability to neutralize majority of the mutants.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kei Miyakawa", + "author_inst": "Yokohama City University School of Medicine" + }, + { + "author_name": "Sundararaj Stanleyraj Jeremiah", + "author_inst": "Yokohama City University School of Medicine" + }, + { + "author_name": "Hideaki Kato", + "author_inst": "Yokohama City University Hospital" + }, + { + "author_name": "Akihide Ryo", + "author_inst": "Yokohama City University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.21.21263902", "rel_title": "Quantification and prognostic significance of interferon-\u03b3 secreting SARS-CoV-2 responsive T cells in hospitalised patients with acute COVID-19", @@ -575577,53 +575896,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.23.21262329", - "rel_title": "A multiplex serological assay for the characterization of IgG immune response to SARS-CoV-2", - "rel_date": "2021-09-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.23.21262329", - "rel_abs": "BackgroundIn the fight against SARS-COV-2, the development of serological assays based on different antigenic domains represent a versatile tool to get a comprehensive picture of the immune response or differentiate infection from vaccination beyond simple diagnosis.\n\nObjectivesHere we use a combination of the Nucleoprotein (NP), the Spike 1 (S1) and Spike 2 (S2) subunits, and the receptor binding domain (RBD) and N-terminal domain (NTD) of the Spike antigens from the Syrius-CoViDiag(R) multiplex IgG assay, to follow the immune response to SARS-CoV-2 infection over a long time period and depending on disease severity.\n\nResultsUsing a panel of 209 sera collected from 61 patients up to eight months after infection, we observed that most patients develop an immune response against multiple viral epitope, but anti-S2 antibodies seemed to last longer. For all the tested IgGs, we have found higher titers for hospitalized patients than for non-hospitalized ones. Moreover the combination of the five different IgG titers increased the correlation to the neutralizing antibody titers than if considered individually.\n\nConclusionMultiplex immunoassays have the potential to improve diagnostic performances, especially for ancient infection or mild form of the disease presenting weaker antibody titers. Also the combined detection of anti-NP and anti-Spike-derived domains can be useful to differentiate vaccination from viral infection and accurately assess the antibody potential to neutralize the virus.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Etienne Brochot", - "author_inst": "University of Picardie" - }, - { - "author_name": "Vianney Souplet", - "author_inst": "Innobiochips" - }, - { - "author_name": "Pauline Follet", - "author_inst": "Innobiochips" - }, - { - "author_name": "Pauline Ponthieu", - "author_inst": "Innobiochips" - }, - { - "author_name": "Christophe Olivier", - "author_inst": "Innobiochips" - }, - { - "author_name": "Gael Even", - "author_inst": "GD Biotech" - }, - { - "author_name": "Christophe Audebert", - "author_inst": "GD Biotech" - }, - { - "author_name": "Remi Malbec", - "author_inst": "GD Biotech" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.23.21260526", "rel_title": "Validation of the Panbio COVID-19 Antigen Rapid Test (Abbott) to screen for SARS-CoV-2 infection in Sint Maarten: a diagnostic accuracy study", @@ -575804,6 +576076,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.09.23.461605", + "rel_title": "Apixaban, an orally available anticoagulant, inhibits SARS-CoV-2 replication by targeting its major protease in a non-competitive way", + "rel_date": "2021-09-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.23.461605", + "rel_abs": "Anticoagulants are associated with clinical benefit against the 2019 coronavirus disease (COVID-19), preventing COVID-19 associated coagulopathy. Blood coagulation factor Xa (FXa) and SARS-CoV-2 major protease (Mpro) share over 80% homology at the three-dimensional protein level. Thus, it is worth interrogating whether there is crosstalk between inhibitors and substrates between these enzymes. Here, we found that the clinically-approved FXa inhibitor apixaban targets SARS-CoV-2 Mpro with a 21-fold higher potency than boceprevir (GC376). Apixaban displayed a non-competitive mechanism of inhibition towards Mpro, since it targets the enzyme/substrate complex and the allosteric site onto the viral protease. Enzymatic assays were further validated in infected Calu-3 cells, which reveal that apixaban decreases the production of infectious viral particles in a dose-dependent manner, with an inhibitory potency in the micromolar range. Our results are in line with the proposed early use of anticoagulants, including FXa inhibitors, to improve clinical outcome of COVID-19 patients. In this context, apixaban may display a dual mechanism of action by targeting FXa to prevent coagulopathy and, at some level, SARS-CoV-2 Mpro.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Otavio Augusto Chaves", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Carolina Q. Sacramento", + "author_inst": "FIOCRUZ" + }, + { + "author_name": "Natalia Fintelman-Rodrigues", + "author_inst": "FIOCRUZ" + }, + { + "author_name": "Jairo Ramos Temerozo", + "author_inst": "Oswaldo Cruz Institute" + }, + { + "author_name": "Filipe Pereira-Dutra", + "author_inst": "Oswaldo Cruz Foundation" + }, + { + "author_name": "Daniella M. Mizurini", + "author_inst": "UFRJ" + }, + { + "author_name": "Robson Q. Monteiro", + "author_inst": "UFRJ" + }, + { + "author_name": "Leonardo Vazquez", + "author_inst": "Fiocruz" + }, + { + "author_name": "Patricia T. Bozza", + "author_inst": "Lab Imunofarmacologia, Instituto Oswaldo Cruz, FIOCRUZ" + }, + { + "author_name": "Hugo Caire Castro-Faria-Neto", + "author_inst": "Fiocruz" + }, + { + "author_name": "Thiago Moreno L. Souza", + "author_inst": "Oswaldo Cruz Foundation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.09.23.21262822", "rel_title": "Plasma S-Adenosylmethionine is Associated with Lung Injury in COVID-19", @@ -577251,41 +577582,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.22.21263515", - "rel_title": "The impact of heating, ventilation and air conditioning (HVAC) design features on the transmission of viruses, including SARS-CoV-2: an overview of reviews", - "rel_date": "2021-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.22.21263515", - "rel_abs": "BackgroundThe 2019 novel coronavirus or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak was declared a pandemic by the World Health Organization (WHO) in March 2020. Almost two years later (early-February 2022), the WHO reported over 383 million cases of the disease caused by the virus with over 5.6 million deaths worldwide. Debate regarding routes of transmission was substantial early in the pandemic; however, airborne transmission emerged as an important consideration. Infectious airborne agents can spread within the built environment through heating, ventilation, and air conditioning (HVAC) systems. Multiple features of HVAC systems can influence transmission (e.g., ventilation, filtration, ultraviolet radiation, humidity). Understanding how HVAC features influence airborne transmission is critical to mitigate the spread of infectious agents.\n\nObjectiveGiven airborne transmission of SARS-CoV-2, an overview of reviews was conducted to understand what is already known from the scientific literature about how virus transmission may be affected by HVAC design features in the built environment.\n\nMethodsOvid MEDLINE and Compendex were searched from inception to January 2021. Two reviewers independently screened titles and abstracts and full text of potentially relevant reviews, using a priori inclusion criteria. Inclusion criteria were systematic reviews examining effects of HVAC design features on virus transmission. Two reviewers independently assessed methodological quality using AMSTAR2.\n\nResultsSearching identified 361 citations, 45 were potentially relevant, and 7 were included. Reviews were published between 2007 and 2021, and included 47 virus studies. Two earlier reviews (2007, 2016) of 21 studies found sufficient evidence that mechanical ventilation (airflow patterns, ventilation rates) plays a role in airborne transmission; however, both found insufficient evidence to quantify minimum mechanical ventilation requirements. One review (2017) of 9 studies examining humidity and indoor air quality found that influenza virus survival was lowest between 40% and 80% relative humidity; authors noted that ventilation rates were a confounding variable. Two reviews (2021) examined mitigation strategies for coronavirus transmission, finding that transmission decreased with increasing temperature and relative humidity. One review (2020) identified 14 studies examining coronavirus transmission in air conditioning systems, finding HVAC systems played a role in virus spread during previous coronavirus outbreaks. One review (2020) examined virus transmission interventions on public ground transportation, finding ventilation and filtration to be effective.\n\nConclusionsSeven reviews synthesizing 47 studies demonstrate a role for HVAC in mitigating airborne virus transmission. Ventilation, humidity, temperature, and filtration can play a role in viability and transmission of viruses, including coronaviruses. Recommendations for minimum standards were not possible due to few studies investigating a given HVAC parameter. This overview examining HVAC design features and their effects on airborne transmission of viruses serves as a starting point for future systematic reviews and identifying priorities for primary research.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Gail M. Thornton", - "author_inst": "University of Alberta" - }, - { - "author_name": "Emily Kroeker", - "author_inst": "University of Alberta" - }, - { - "author_name": "Brian A. Fleck", - "author_inst": "University of Alberta" - }, - { - "author_name": "Lexuan Zhong", - "author_inst": "University of Alberta" - }, - { - "author_name": "Lisa Hartling", - "author_inst": "University of Alberta" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.22.21263956", "rel_title": "An artificial intelligence system for predicting mortality in COVID-19 patients using chest X-rays: a retrospective study", @@ -577514,6 +577810,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.09.18.21263773", + "rel_title": "COVID-19 Acceleration and Vaccine Status in France - August 2021", + "rel_date": "2021-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.18.21263773", + "rel_abs": "ObjectivesThis note provides an assessment of COVID-19 acceleration among groups with different vaccine status in France.\n\nMethodsWe assess viral acceleration using a novel indicator introduced in Baunez et al. (2021). The acceleration index relates the percentage change of tests that have been performed on a given day to the percentage change in the associated positive cases that same day. We compare viral acceleration among vaccinated and unvaccinated individuals in France over the period May 31st - August 29, 2021.\n\nResultsOnce the state of the epidemic within each groups is accounted for, it turns out that viral acceleration has since mid-July converged to similar levels among vaccinated and unvaccinated individuals in France, even though viral speed is larger for the latter group compared to the former.\n\nConclusionOur results call for an increasing testing effort for both vaccinated and unvaccinated individuals, in view of the fact that viral circulation is currently accelerating at similar levels for both groups in France.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Christelle Baunez", + "author_inst": "Institut Neurosciences Timone" + }, + { + "author_name": "Mickael Degoulet", + "author_inst": "Institut Neurosciences Timone" + }, + { + "author_name": "Stephane Luchini", + "author_inst": "Aix-Marseille School of Economics" + }, + { + "author_name": "Patrick Pintus", + "author_inst": "Aix-Marseille University and CNRS" + }, + { + "author_name": "Miriam Teschl", + "author_inst": "Aix-Marseille School of Economics" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.09.19.21262487", "rel_title": "Genomic analysis of SARS-CoV-2 breakthrough infections from Varanasi, India", @@ -579225,41 +579556,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.15.21263647", - "rel_title": "Modeling the systemic risks of COVID-19 on the wildland firefighting workforce", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.15.21263647", - "rel_abs": "Wildfire management in the US relies on a complex nationwide network of shared resources that are allocated based on regional need. While this network bolsters firefighting capacity, it may also provide pathways for COVID-19 transmission between fire sites. We develop an agent-based model of COVID-19 built on historical wildland fire assignments using detailed dispatch data from 2016-2018, which form a network of firefighters dispersed spatially and temporally across the US. We use this model to simulate SARS-CoV-2 transmission under several intervention scenarios including vaccination and social distancing. We find vaccination and social distancing are effective at reducing transmission at fire incidents. Under a scenario assuming High Compliance with recommended mitigations (including vaccination), infection rates, number of outbreaks, and worker days missed are effectively negligible. Under a contrasting Low Compliance scenario, it is possible for cascading outbreaks to emerge leading to relatively high numbers of worker days missed. The current set of interventions in place successfully mitigate the risk of cascading infections between fires, and off-assignment infection may be the dominant infection concern in the 2021 season. COVID-19 control measures in place in wildfire management are highly beneficial at decreasing both the health and resource impacts of the ongoing pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Erin J Belval", - "author_inst": "United States Forest Service" - }, - { - "author_name": "Jude Bayham", - "author_inst": "Colorado State University" - }, - { - "author_name": "Matthew P Thompson", - "author_inst": "United States Forest Service" - }, - { - "author_name": "Jacob Dilliott", - "author_inst": "Colorado State University" - }, - { - "author_name": "Andrea G Buchwald", - "author_inst": "University of Maryland School of Medicine" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.21.21263891", "rel_title": "Did the COVID-19 pandemic result in more family physicians stopping practice? Results from Ontario, Canada", @@ -579480,6 +579776,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.09.16.21263576", + "rel_title": "Impact of prior SARS-CoV-2 infection on post-vaccination SARS-CoV-2 spike IgG antibodies in a longitudinal cohort of healthcare workers", + "rel_date": "2021-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.16.21263576", + "rel_abs": "Waning serum antibodies against SARS-CoV-2 have sparked discussions about long-term immunity and need for vaccine boosters. We examined SARS-CoV-2 spike IgG antibodies in a longitudinal cohort, comparing antibody decay in individuals who received an mRNA SARS-CoV-2 vaccine, with and without prior SARS-CoV-2 infection. We completed a longitudinal cohort of healthcare workers (HWs) between June 2020 and September 2021. HWs were included if they had a serum sample collected after SARS-CoV-2 infection and/or a serum sample collected [≥] 14 days after second dose of an mRNA SARS-CoV-2 vaccine. Linear regression models adjusting for vaccine type, age, and sex were used to compare post-vaccination antibody levels between 1) HWs with and without prior SARS-CoV-2 infection and 2) HWs with prior SARS-CoV-2 infection [≤] 90 days and > 90 days prior to first vaccine. Serum was collected from 98 HWs after SARS-CoV-2 infection and before vaccine, and 1960 HWs [≥] 14 days following second vaccine dose. Serum spike antibody levels were higher after vaccination than after natural infection. Compared to SARS-CoV-2 naive individuals, those with prior infection maintained higher post-vaccination mean spike IgG values at 1, 3, and 6 months, after adjusting for age, sex, and vaccine type. Individuals with PCR-confirmed infection > 90 days before vaccination had higher post-vaccination antibody levels than individuals infected [≤] 90 days before vaccination. Individuals with three exposures to spike protein maintain the highest antibody levels particularly when first and second exposures were greater than 90 days apart. A booster dose provides a third exposure and may similarly induce a more durable antibody response.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Diana Zhong", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Shaoming Xiao", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Amanda K Debes", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Emily R Egbert", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Patrizio Caturegli", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Elizabeth Colantuoni", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Aaron M Milstone", + "author_inst": "Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.20.21263875", "rel_title": "Comparative single-dose mRNA and ChAdOx1 vaccine effectiveness against SARS-CoV-2, including early variants of concern: a test-negative design, British Columbia, Canada", @@ -580760,37 +581099,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.17.21263721", - "rel_title": "Influence of Built Environment on Bike Sharing Usage under COVID-19", - "rel_date": "2021-09-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.17.21263721", - "rel_abs": "Bike sharing, as an important component of urban public transportation, has played a more important role during the COVID-19 pandemic because users could ride bikes in open space and avoid the risk of infection. Leveraging the trip data of the Divvy bike sharing system in Chicago, this study sets to explore the change of ridership that COVID-19 has brought and the built environment factors that influence the spatial variation of ridership under the pandemic. Results show that the ridership declines by xx% in total. To account for the spatially heterogeneous relationship between the built environment and the ridership, the geographically weighted regression (GWR) model and the semi-parametric GWR (S-GWR) model are constructed. By comparing the model results, we find that the S-GWR model outperforms the GWR and the multiple linear regression model. The results of the S-GWR model indicates that education employment density, distance to subway, COVID-19 cases and ridership before COVID-19 are global variables. The ridership between residential density, office employment density and the ridership vary across space. The results of this study could provide useful reference to transportation planners and bike sharing operators to determine the high bike sharing demand area under the pandemic and to make adjustment on the locations and capacity of the stations and the rebalancing schemes accordingly.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Hongtai Yang", - "author_inst": "Southwest Jiaotong University" - }, - { - "author_name": "Zishuo Guo", - "author_inst": "Southwest Jiaotong University" - }, - { - "author_name": "Jinghai Huo", - "author_inst": "Southwest Jiaotong University" - }, - { - "author_name": "Linchuan Yang", - "author_inst": "Southwest Jiaotong University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.16.21263575", "rel_title": "SARS-CoV-2 wastewater surveillance in Germany: long-term PCR monitoring, suitability of primer/probe combinations and biomarker stability", @@ -580943,6 +581251,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.17.21263723", + "rel_title": "Optimized Post-Vaccination Strategies and Preventative Measures for SARS-CoV-2", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.17.21263723", + "rel_abs": "IntroductionSince March of 2020, over 210 million SARS-CoV-2 cases have been reported and roughly five billion doses of a SARS-CoV-2 vaccine have been delivered. The rise of the more infectious delta variant has recently indicated the value of reinstating previously relaxed non-pharmacological and test-driven preventative measures. These efforts have been met with resistance, due, in part, to a lack of site-specific quantitative evidence which can justify their value. As vaccination rates continue to increase, a gap in knowledge exists regarding appropriate thresholds for escalation and de-escalation of COVID-19 preventative measures.\n\nMethodsWe conducted a series of simulation experiments, trialing the spread of SARS-CoV-2 virus in a hypothesized working environment that is subject to COVID-19 infections from the surrounding community. We established cohorts of individuals who would, in simulation, work together for a set period of time. With these cohorts, we tested the rates of workplace and community acquired infections based on applied isolation strategies, community infection rates (CIR), scales of testing, non-pharmaceutical interventions, variant predominances and testing strategies, vaccination coverages, and vaccination efficacies of the members included. Permuting through each combination of these variables, we estimated expected case counts for 33,462 unique workplace scenarios.\n\nResultsWhen the CIR is 5 new confirmed cases per 100,000 or fewer, and at 50% of the workforce is vaccinated with a 95% efficacious vaccine, then testing daily with an antigen-based or PCR based test in only unvaccinated workers will result in less than one infection through 4,800 person weeks. When the community infection rate per 100,000 persons is less than or equal to 60, and the vaccination coverage of the workforce is 100% with 95% vaccine efficacy then no masking or routine testing + isolation strategies are needed to prevent workplace acquired infections regardless of variant predominance. Identifying and isolating workers with antigen-based SARS-CoV-2 testing methods results in the same or fewer workplace acquired infections than testing with polymerase chain reaction (PCR) methods.\n\nConclusionsSpecific scenarios exist in which preventative measures taken to prevent SARS-CoV-2 spread, including masking, and testing plus isolation strategies can safely be relaxed. Further, efficacious testing with quarantine strategies exist for implementation in only unvaccinated cohorts in a workplace. Due to shorter turnaround time, antigen-based testing with lower sensitivity is more effective than PCR testing with higher sensitivities in comparable testing strategies. The general reference interactive heatmap we provide can be used for site specific, immediate, parameter-based case count predictions to inform appropriate institutional policy making.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Rowland W Pettit", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Bo Peng", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Patrick Yu", + "author_inst": "Corporate Medical Advisors, Houston, Texas, USA" + }, + { + "author_name": "Peter Matos", + "author_inst": "Corporate Medical Advisors, Houston, Texas, USA" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "Laboratory Medicine, University of Washington" + }, + { + "author_name": "Julie McCashin", + "author_inst": "International S.O.S., Houston, TX" + }, + { + "author_name": "Christopher Ian Amos", + "author_inst": "Baylor College of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.09.16.21263714", "rel_title": "The Relationship of Vaccine Uptake and COVID-19 Infections among Nursing Home Staff and Residents in Missouri", @@ -582182,125 +582533,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.16.21263686", - "rel_title": "Germinal center responses to SARS-CoV-2 mRNA vaccines in healthy and immunocompromised individuals", - "rel_date": "2021-09-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.16.21263686", - "rel_abs": "Vaccine-mediated immunity often relies on the generation of protective antibodies and memory B cells, which commonly stem from germinal center (GC) reactions. An in-depth comparison of the GC responses elicited by SARS-CoV-2 mRNA vaccines in healthy and immunocompromised individuals has not yet been performed due to the challenge of directly probing human lymph nodes. In this study, through a fine-needle-aspiration-based approach, we profiled the immune responses to SARS-CoV-2 mRNA vaccines in lymph nodes of healthy individuals and kidney transplant (KTX) recipients. We found that, unlike healthy subjects, KTX recipients presented deeply blunted SARS-CoV-2-specific GC B cell responses coupled with severely hindered T follicular helper cells, SARS-CoV-2 receptor-binding-domain-specific memory B cells and neutralizing antibodies. KTX recipients also displayed reduced SARS-CoV-2-specific CD4 and CD8 T cell frequencies. Broadly, these data indicate impaired GC-derived immunity in immunocompromised individuals, and suggest a GC-origin for certain humoral and memory B cell responses following mRNA vaccination.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Katlyn Lederer", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Kalpana Parvathaneni", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Mark M Painter", - "author_inst": "Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Emily Bettini", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Divyansh Agarwal", - "author_inst": "Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA" - }, - { - "author_name": "Kendall A Lundgreen", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Madison Weirick", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Rishi R Goel", - "author_inst": "Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Xiaoming Xu", - "author_inst": "Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Elizabeth M Drapeau", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Sigrid Gouma", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Allison R Greenplate", - "author_inst": "Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Carole Le Coz", - "author_inst": "Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Neil Romberg", - "author_inst": "Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Lisa Jones", - "author_inst": "Department of Radiology, Division of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Mark Rosen", - "author_inst": "Department of Radiology, Division of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Behdad Besharatian", - "author_inst": "Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Mary Kaminiski", - "author_inst": "Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA" - }, - { - "author_name": "Scott E Hensley", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Paul Bates", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "E John Wherry", - "author_inst": "Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Ali Naji", - "author_inst": "Department of Surgery, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Vijay Bhoj", - "author_inst": "Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Michela Locci", - "author_inst": "Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.09.14.21263596", "rel_title": "Distributed Counterfactual Modeling Approach for Investigating Hospital-Associated Racial Disparities in COVID-19 Mortality", @@ -582553,6 +582785,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.14.21262977", + "rel_title": "Spatiotemporal analyses illuminate the competitive advantage of a SARS-CoV-2 variant of concern over a variant of interest", + "rel_date": "2021-09-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21262977", + "rel_abs": "The emergence of novel SARS-CoV-2 variants in late 2020 and early 2021 raised alarm worldwide and prompted reassessment of the management, surveillance, and projected future of COVID-19. Mutations that confer competitive advantages by increasing transmissibility or immune evasion have been associated with the localized dominance of single variants. Thus, elucidating the evolutionary and epidemiological dynamics among novel variants is essential for understanding the trajectory of the COVID-19 pandemic. Here we show the interplay between B.1.1.7 (Alpha) and B.1.526 (Iota) in New York (NY) from December 2020 to April 2021 through phylogeographic analyses, space-time scan statistics, and cartographic visualization. Our results indicate that B.1.526 likely evolved in the Bronx in late 2020, providing opportunity for an initial foothold in the heavily interconnected New York City (NYC) region, as evidenced by numerous exportations to surrounding locations. In contrast, B.1.1.7 became dominant in regions of upstate NY where B.1.526 had limited presence, suggesting that B.1.1.7 was able to spread more efficiently in the absence of B.1.526. Clusters discovered from the spatial-time scan analysis supported the role of competition between B.1.526 and B.1.1.7 in NYC in March 2021 and the outsized presence of B.1.1.7 in upstate NY in April 2021. Although B.1.526 likely delayed the rise of B.1.1.7 in NYC, B.1.1.7 became the dominant variant in the Metro region by the end of the study period. These results reveal the advantages endemicity may grant to a variant (founder effect), despite the higher fitness of an introduced lineage. Our research highlights the dynamics of inter-variant competition at a time when B.1.617.2 (Delta) is overtaking B.1.1.7 as the dominant lineage worldwide. We believe our combined spatiotemporal methodologies can disentangle the complexities of shifting SARS-CoV-2 variant landscapes at a time when the evolution of variants with additional fitness advantages is impending.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Alexis Russell", + "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Collin O'Connor", + "author_inst": "Division of Epidemiology, New York State Department of Health" + }, + { + "author_name": "Erica Lasek-Nesselquist", + "author_inst": "Bioinformatics Core, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Jonathan Plitnick", + "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "John P Kelly", + "author_inst": "Applied Genomic Technology Core, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Daryl M Lamson", + "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Kirsten St George", + "author_inst": "Laboratory of Viral Diseases, Wadsworth Center, New York State Department of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.14.21263153", "rel_title": "Evolution of COVID-19 mortality over time: results from the Swiss hospital surveillance system (CH-SUR)", @@ -584640,77 +584915,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.13.21263535", - "rel_title": "Seroresponse to SARS-CoV-2 vaccines among maintenance dialysis patients over six months", - "rel_date": "2021-09-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263535", - "rel_abs": "Background and ObjectivesWhile most maintenance dialysis patients exhibit initial seroresponse to vaccination, concerns remain regarding the durability of this antibody response. This study evaluated immunity over time.\n\nDesign, setting, participants, and measurementsThis retrospective cohort study included maintenance dialysis patients from a midsize national dialysis provider who received a complete SARS-CoV-2 vaccine series and had at least one antibody titer checked after full vaccination. Immunoglobulin G spike antibodies (SAb-IgG) titers were assessed monthly with routine labs beginning after full vaccination and followed over time; the semiquantitative SAb-IgG titer reported a range between 0 and [≥] 20 U/L. Descriptive analyses compared trends over time by prior history of COVID-19 and type of vaccine received. Time-to-event analyses were conducted for the outcome of loss of seroresponse (SAb-IgG < 1 U/L or development of COVID-19). Cox proportional hazards regression was used to adjust for additional clinical characteristics of interest.\n\nResultsAmong 1898 maintenance dialysis patients, 1567 (84%) had no prior history of COVID-19. Patients without a history of COVID-19 had declining titers over time. Among 441 BNT162b2/Pfizer recipients, median [IQR] SAb-IgG titer declined from 20 [5.99-20] U/L in month 1 to 1.30 [0.15-3.59] U/L by month 6. Among 779 mRNA-1273/Moderna recipients, median [IQR] SAb-IgG titer declined from 20 [20-20] in month 1 to 6.20 [1.74-20] by month 6. The 347 Ad26.COV2.S/Janssen recipients had a lower titer response than mRNA vaccine recipients over all time periods. In time-to-event analyses, Ad26.COV2.S/Janssen and mRNA-1273/Moderna recipients had the shortest and longest time to loss of seroresponse, respectively. The maximum titer reached in the first two months after full vaccination was predictive of the durability of the SAb-IgG seroresponse; patients with SAb-IgG titer 1-19.99 U/L were more likely to have loss of seroresponse compared to patients with SAb-IgG titer [≥] 20 U/L (HR 23.9 [95% CI: 16.1-35.5]).\n\nConclusionsVaccine-induced seroresponse wanes over time among maintenance dialysis patients across vaccine types. Early titers after full vaccination predict the durability of seroresponse.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Caroline M Hsu", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Daniel E Weiner", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Harold J Manley", - "author_inst": "Dialysis Clinic Inc." - }, - { - "author_name": "Gideon N Aweh", - "author_inst": "Dialysis Clinic Inc." - }, - { - "author_name": "Vladimir Ladik", - "author_inst": "Dialysis Clinic Inc." - }, - { - "author_name": "Jill Frament", - "author_inst": "Dialysis Clinic Inc." - }, - { - "author_name": "Dana Miskulin", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Christos Agyropoulos", - "author_inst": "University of New Mexico" - }, - { - "author_name": "Kenneth Abreo", - "author_inst": "Louisiana State University Health Sciences Center, Shreveport" - }, - { - "author_name": "Andrew Chin", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Reginald Gladish", - "author_inst": "Nephrology of North Alabama" - }, - { - "author_name": "Loay Salman", - "author_inst": "Albany Medical College" - }, - { - "author_name": "Doug Johnson", - "author_inst": "Dialysis Clinic Inc." - }, - { - "author_name": "Eduardo K Lacson", - "author_inst": "Dialysis Clinic Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.09.14.21263505", "rel_title": "Women's views and experiences of accessing vaccination in pregnancy during the COVID-19 pandemic: A multi-methods study in the United Kingdom", @@ -584955,6 +585159,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.09.13.21263487", + "rel_title": "SARS-CoV-2 anti-spike IgG antibody responses after second dose of ChAdOx1 or BNT162b2 in the UK general population", + "rel_date": "2021-09-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21263487", + "rel_abs": "We investigated anti-spike IgG antibody responses and correlates of protection following second doses of ChAdOx1 or BNT162b2 SARS-CoV-2 vaccines in the UK general population. In 222,493 individuals, we found significant boosting of anti-spike IgG by second doses of both vaccines in all ages and using different dosing intervals, including the 3-week interval for BNT162b2. After second vaccination, BNT162b2 generated higher peak levels than ChAdOX1. Older individuals and males had lower peak levels with BNT162b2 but not ChAdOx1, while declines were similar across ages and sexes with ChAdOX1 or BNT162b2. Prior infection significantly increased antibody peak level and half-life with both vaccines. Anti-spike IgG levels were associated with protection from infection after vaccination and, to an even greater degree, after prior infection. At least 67% protection against infection was estimated to last for 2-3 months after two ChAdOx1 doses and 5-8 months after two BNT162b2 doses in those without prior infection, and 1-2 years for those unvaccinated after natural infection. A third booster dose may be needed, prioritised to ChAdOx1 recipients and those more clinically vulnerable.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Jia Wei", + "author_inst": "University of Oxford" + }, + { + "author_name": "Koen B. Pouwels", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nicole Stoesser", + "author_inst": "University of Oxford" + }, + { + "author_name": "Philippa C. Matthews", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ian Diamond", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ruth Studley", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Emma Rourke", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Duncan Cook", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "John I Bell", + "author_inst": "University of Oxford" + }, + { + "author_name": "John N Newton", + "author_inst": "Public Health England" + }, + { + "author_name": "Jeremy Farrar", + "author_inst": "Wellcome Trust" + }, + { + "author_name": "Alison Howarth", + "author_inst": "University of Oxford" + }, + { + "author_name": "Brian D. Marsden", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sarah Hoosdally", + "author_inst": "University of Oxford" + }, + { + "author_name": "E Yvonne Jones", + "author_inst": "University of Oxford" + }, + { + "author_name": "David I Stuart", + "author_inst": "University of Oxford" + }, + { + "author_name": "Derrick W. Crook", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tim E.A. Peto", + "author_inst": "University of Oxford" + }, + { + "author_name": "A.Sarah Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "David W. Eyre", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.09.21263348", "rel_title": "Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multi-target approach", @@ -586686,61 +586985,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, - { - "rel_doi": "10.1101/2021.09.07.21261607", - "rel_title": "High viral SARS-CoV-2 load in placenta of patients with hypertensive disorders after COVID-19 during pregnancy", - "rel_date": "2021-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21261607", - "rel_abs": "IntroductionStudies described an increased frequency of hypertensive disorders of pregnancy after a COVID-19 episode. There is limited evidence about SARS-CoV-2 viral load in placenta. This study aimed to investigate the relationship between SARS-CoV-2 viral load in placenta and clinical development of HDP after COVID-19 throughout different periods of gestation.\n\nMethodsThis was a case-control study in women with and without gestational hypertensive disorders (HDP) after SARS-CoV-2 infection diagnosed by RT-PCR during pregnancy. Patients were matched by gestational age at the moment of COVID-19 diagnosis. We performed an analysis of SARS-CoV-2 RNA levels in placenta.\n\nResultsA total of 28 women were enrolled. Sixteen patients were diagnosed with COVID-19 during the third trimester and the remaining twelve patients in the others trimesters. Ten placentas (35.7%) were positive for SARS-CoV-2, nine of them (90%) belonged to the HDP group versus one (10%) in control group (p=0.009). Those cases with the highest loads of viral RNA developed severe-preeclampsia.\n\nConclusionThe presence of SARS-CoV-2 was more frequent in placentas of patients with HDP after COVID-19. There seems to be a relationship between high viral load in the placenta and the development of hypertensive disorders. We found SARS-CoV-2 viral load in placenta after birth in mothers infected at the first half of pregnancy, but with negative nasopharyngeal RT-PCR at delivery. Our data suggest that SARS-CoV-2 infection during pregnancy could trigger gestational hypertensive disorders through placenta-related mechanisms.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "MARTA FABRE", - "author_inst": "Instituto de Investigacion Sanitario de Aragon (IIS Aragon)" - }, - { - "author_name": "PILAR CALVO", - "author_inst": "Instituto de Investigacion Sanitario de Aragon (IIS Aragon)" - }, - { - "author_name": "SARA RUIZ-MARTINEZ", - "author_inst": "Instituto de Investigacion Sanitario de Aragon (IIS Aragon)" - }, - { - "author_name": "MARIA PERAN", - "author_inst": "Instituto de Investigacion Sanitario de Aragon (IIS Aragon)" - }, - { - "author_name": "DANIEL OROS", - "author_inst": "Instituto de Investigacion Sanitario de Aragon (IIS Aragon)" - }, - { - "author_name": "ANA MEDEL", - "author_inst": "Instituto Aragones de Ciencias de la Salud (IACS)" - }, - { - "author_name": "MARK STRUNK", - "author_inst": "Instituto Aragones de Ciencias de la Salud (IACS)" - }, - { - "author_name": "RAFAEL BENITO", - "author_inst": "Hospital Clinico Universitario Lozano Blesa" - }, - { - "author_name": "JON SCHOORLEMMER", - "author_inst": "Instituto Aragones de Ciencias de la Salud (IACS)" - }, - { - "author_name": "CRISTINA PAULES", - "author_inst": "Instituto de Investigacion Sanitario de Aragon (IIS Aragon)," - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.09.10.21263383", "rel_title": "Social-economic drivers overwhelm climate in underlying the COVID-19 early growth rate", @@ -586997,6 +587241,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.10.21263072", + "rel_title": "VALIDATION OF A SALIVA-BASED TEST FOR THE MOLECULAR DIAGNOSIS OF SARS-CoV-2 INFECTION", + "rel_date": "2021-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.10.21263072", + "rel_abs": "BackgroundSince the beginning of the pandemic, clinicians and researchers have been searching for alternative tests to improve screening and diagnosis of SARS-CoV-2 infection (Y. Yang et al., medRxiv 2020; W. Wang et al., 2020.3786; A Senok et al., Infect Drug Resist 2020). Currently, the gold standard for virus identification is the nasopharyngeal (NP) swab (N. Sethuraman et al., JAMA 2020; A.J. Jamal et al Clinical Infect Disease 2021). Saliva samples, however, offer clear practical and logistical advantages (K.K.W To et al, Clinical Microb and Infect; A.L. Wylle et al. N Engl J Med 2020; N. Matic et al, Eur J Clin 2021) but due to lack of collection, transport, and storage solutions, high-throughput saliva-based laboratory tests are difficult to scale up as a screening or diagnostic tool (D. Esser et al., Biomark Insights 2008; E. Kaufman et al., Crit Rev Oral Biol Med2002). With this study, we aimed to validate an intra-laboratory molecular detection method for SARS-CoV-2 on saliva samples collected in a new storage saline solution, comparing the results to NP swabs to determine the difference in sensitivity between the two tests.\n\nMethodsIn this study, 156 patients (cases) and 1005 asymptomatic subjects (controls) were enrolled and tested simultaneously for the detection of the SARS-CoV-2 viral genome by RT-PCR on both NP swab and saliva samples. Saliva samples were collected in a preservative and inhibiting saline solution (Biofarma Srl). Internal method validation was performed to standardize the entire workflow for saliva samples.\n\nResultsThe identification of SARS-CoV-2 conducted on saliva samples showed a clinical sensitivity of 95.1% and specificity of 97.8% compared to NP swabs. The positive predictive value (PPV) was 81% while the negative predictive value (NPV) was 99.5%. Test concordance was 97.6% (Cohens Kappa=0.86; 95% CI 0.81-0.91). The LoD of the test was 5 viral copies for both samples.\n\nConclusionsRT-PCR assays conducted on a stored saliva sample achieved similar performance to those on NP swabs and this may provide a very effective tool for population screening and diagnosis. Collection of saliva in a stabilizing solution makes the test more convenient and widely available; furthermore, the denaturing properties of the solution reduce the infective risks belonging to sample manipulation.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Michela Bulfoni", + "author_inst": "Department of Medicine, University of Udine, Udine, Italy; Institute of Pathology, ASU FC, Udine, Italy" + }, + { + "author_name": "Emanuela Sozio", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Barbara Marcon", + "author_inst": "Department of Laboratory Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Maria De Martino", + "author_inst": "Department of Medicine, University of Udine, Udine, Italy" + }, + { + "author_name": "Daniela Cesselli", + "author_inst": "Department of Medicine, University of Udine, Udine, Italy; Institute of Pathology, ASU FC, Udine, Italy" + }, + { + "author_name": "Chiara De Carlo", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Romina Martinella", + "author_inst": "Department of Laboratory Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Angelica Migotti", + "author_inst": "Department of Laboratory Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Eleonora Vania", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Agnese Zanus-Fortes", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Jessica De Piero", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy" + }, + { + "author_name": "Emanuele Nencioni", + "author_inst": "Biofarma Srl" + }, + { + "author_name": "Carlo Tascini", + "author_inst": "Infectious Disease Unit, Department of Medicine, ASU FC, Udine, Italy; Department of Medicine, University of Udine, Udine, Italy" + }, + { + "author_name": "Miriam Isola", + "author_inst": "Department of Medicine, University of Udine, Udine, Italy" + }, + { + "author_name": "Francesco Curcio", + "author_inst": "Department of Laboratory Medicine, ASU FC, Udine, Italy; Department of Medicine, University of Udine, Udine, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.14.460356", "rel_title": "Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display", @@ -588412,49 +588731,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.09.15.460454", - "rel_title": "Intronization enhances expression of S-protein and other transgenes challenged by cryptic splicing", - "rel_date": "2021-09-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.15.460454", - "rel_abs": "The natural habitat of SARS-CoV-2 is the cytoplasm of a mammalian cell where it replicates its genome and expresses its proteins. While SARS-CoV-2 genes and hence its codons are presumably well optimized for mammalian protein translation, they have not been sequence optimized for nuclear expression. The cDNA of the Spike protein harbors over a hundred predicted splice sites and produces mostly aberrant mRNA transcripts when expressed in the nucleus. While different codon optimization strategies increase the proportion of full-length mRNA, they do not directly address the underlying splicing issue with commonly detected cryptic splicing events hindering the full expression potential. Similar splicing characteristics were also observed in other transgenes. By inserting multiple short introns throughout different transgenes, significant improvement in expression was achieved, including >7-fold increase for Spike transgene. Provision of a more natural genomic landscape offers a novel way to achieve multi-fold improvement in transgene expression.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "K\u00e4rt Tomberg", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Liliana Antunes", - "author_inst": "University of Cambridge" - }, - { - "author_name": "YangYang Pan", - "author_inst": "University of Cambridge, Shanxi Agricultural University" - }, - { - "author_name": "Jacob Hepkema", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Dimitrios A Garyfallos", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Ahmed Mahfouz", - "author_inst": "Leiden University Medical Center, Delft University of Technology" - }, - { - "author_name": "Allan Bradley", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2021.09.14.460408", "rel_title": "Synthetic lethality-based prediction of anti-SARS-CoV-2 targets", @@ -588711,6 +588987,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.07.21262725", + "rel_title": "SARS-COV2 mutant-specific T cells and neutralizing antibodies after vaccination and up to 1 year after infection", + "rel_date": "2021-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21262725", + "rel_abs": "ObjectiveWe investigated blood samples from fully SARS-CoV2-vaccinated subjects and from previously positive tested patients up to one year after infection with SARS-CoV2, and compared short- and long-term T cell and antibody responses, with a special focus on the recently emerged delta variant (B.1.617.2).\n\nMethods and ResultsIn 23 vaccinated subjects, we documented high anti-SARS-CoV2 spike protein receptor binding domain (RBD) antibody titers. Average virus neutralization by antibodies, assessed as inhibition of ACE2 binding to RBD, was 2.2-fold reduced for delta mutant vs. wild type (wt) RBD. The mean specific antibody titers were lower one year after natural infection than after vaccination; ACE2 binding to delta mutant vs. wt RBD was 1.65-fold reduced. In an additional group, omicron RBD binding was reduced compared to delta.\n\nSpecific CD4+ T cell responses were measured after stimulation with peptides pools from wt, alpha, beta, gamma, or delta variant SARS-CoV2 spike proteins by flow cytometric intracellular cytokine staining. There was no significant difference in cytokine production of IFN-{gamma}, TNF-, or IL-2 between vaccinated subjects. T cell responses to wt or mutant SARS-CoV2 spike were significantly weaker after natural occurring infections compared to those in vaccinated individuals.\n\nConclusionAntibody neutralisation of the delta mutant was reduced compared to wt, as assessed in a novel inhibition assay with a finger prick blood drop. Strong CD4 T cell responses were present against wt and mutant SARS-CoV2 variants, including the delta (B.1.617.2) strain, in fully vaccinated individuals, whereas they were partly weaker 1 year after natural infection. Hence, immune responses after vaccination are stronger compared to those after naturally occurring infection, pointing out the need of the vaccine to overcome the pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jennifer R Richardson", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Ralph Goetz", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Vanessa Mayr", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Martin J Lohse", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Hans-Peter Holthoff", + "author_inst": "ISAR Bioscience" + }, + { + "author_name": "Martin Ungerer", + "author_inst": "ISAR Bioscience" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.09.10.21262710", "rel_title": "Antibody responses to BNT162b2 mRNA vaccine: infection-naive individuals with abdominal obesity warrant attention", @@ -590614,49 +590929,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.09.08.21263311", - "rel_title": "Determinants of hospital outcomes for COVID-19 infections in a large Pennsylvania Health System", - "rel_date": "2021-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.08.21263311", - "rel_abs": "There is growing evidence that racial and ethnic minorities bear a disproportionate burden from COVID-19. Temporal changes in the pandemic epidemiology and diversity in the clinical course require careful study to identify determinants of poor outcomes.\n\nWe analyzed 6255 individuals admitted with PCR-confirmed COVID-19 to one of 5 hospitals in the University of Pennsylvania Health System between March 2020 and March 2021, using electronic health records to assess risk factors and outcomes through 8 weeks post-admission. Discharge, readmission and mortality outcomes were analyzed in a multi-state model with multivariable Cox models for each transition.\n\nMortality varied markedly over time, with cumulative incidence (95% CI) 30 days post-admission of 19.1% (16.9, 21.3) in March-April 2020, 5.7% (4.2, 7.5) in July-October 2020 and 10.5% (9.1,12.0) in January-March 2021; 26% of deaths occurred after discharge. Average age (SD) at admission varied from 62.7 (17.6) to 54.8 (19.9) to 60.5 (18.1); mechanical ventilation use declined from 21.3% to 9-11%.\n\nCompared to Caucasian, Black race was associated with more severe disease at admission, higher rates of co-morbidities and low-income resident zip code. Between-race risk differences in mortality risk diminished in multivariable models; while admitting hospital, increasing age, admission early in the pandemic, and severe disease and low blood pressure at admission were associated with increased mortality hazard. Hispanic ethnicity was associated with fewer baseline co-morbidities and lower mortality hazard (0.57, 95% CI: 0.37, .087).\n\nMulti-state modeling allows for a unified framework to analyze multiple outcomes throughout the disease course. Morbidity and mortality for hospitalized COVID-19 patients varied over time but post-discharge mortality remained non-trivial. Black race was associated with more risk factors for morbidity and with treatment at hospitals with lower mortality. Multivariable models suggest there are not between-race differences in outcomes. Future work is needed to better understand the identified between-hospital differences in mortality.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Pamela A Shaw", - "author_inst": "Kaiser Permanente Washington Health Research Institute" - }, - { - "author_name": "Jasper B Yang", - "author_inst": "Kaiser Permanente Washington Health Research Institute" - }, - { - "author_name": "Danielle L Mowery", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Emily R. Schriver", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Kevin B Mahoney", - "author_inst": "University of Pennsylvania Health System" - }, - { - "author_name": "Katharine J Bar", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - }, - { - "author_name": "Susan S Ellenberg", - "author_inst": "University of Pennsylvania Perelman School of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.09.21263266", "rel_title": "Molecular point-of-care testing for SARS-CoV-2 using the ID NOW(TM) System in Emergency Department: Prospective Evaluation and Implementation in the Care Process", @@ -590893,6 +591165,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.13.460111", + "rel_title": "Therapeutic efficacy of an oral nucleoside analog of remdesivir against SARS-CoV-2 pathogenesis in mice.", + "rel_date": "2021-09-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.13.460111", + "rel_abs": "The COVID-19 pandemic remains uncontrolled despite the rapid rollout of safe and effective SARS-CoV-2 vaccines, underscoring the need to develop highly effective antivirals. In the setting of waning immunity from infection and vaccination, breakthrough infections are becoming increasingly common and treatment options remain limited. Additionally, the emergence of SARS-CoV-2 variants of concern with their potential to escape therapeutic monoclonal antibodies emphasizes the need to develop second-generation oral antivirals targeting highly conserved viral proteins that can be rapidly deployed to outpatients. Here, we demonstrate the in vitro antiviral activity and in vivo therapeutic efficacy of GS-621763, an orally bioavailable prodrug of GS-441524, the parental nucleoside of remdesivir, which targets the highly conserved RNA-dependent RNA polymerase. GS-621763 exhibited significant antiviral activity in lung cell lines and two different human primary lung cell culture systems. The dose-proportional pharmacokinetic profile observed after oral administration of GS-621763 translated to dose-dependent antiviral activity in mice infected with SARS-CoV-2. Therapeutic GS-621763 significantly reduced viral load, lung pathology, and improved pulmonary function in COVID-19 mouse model. A direct comparison of GS-621763 with molnupiravir, an oral nucleoside analog antiviral currently in human clinical trial, proved both drugs to be similarly efficacious. These data demonstrate that therapy with oral prodrugs of remdesivir can significantly improve outcomes in SARS-CoV-2 infected mice. Thus, GS-621763 supports the exploration of GS-441524 oral prodrugs for the treatment of COVID-19 in humans.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Alexandra Schafer", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "David R Martinez", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "John J Won", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Fernanado R Moreira", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Ariane J Brown", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Kendra L Gully", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Rao Kalla", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Kwon Chun", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Venice Du Pont", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Darius Babusis", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Jennifer Tang", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Eisuke Murakami", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Raju Subramanian", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Kimberly T Barrett", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Blake J. Bleier", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Roy Bannister", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Joy Y. Feng", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "John P. Bilello", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Tomas Cihlar", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Richard L. Mackman", + "author_inst": "Gilead Sciences, Inc" + }, + { + "author_name": "Stephanie A. Montgomery", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Timothy P. Sheahan", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.09.13.460130", "rel_title": "Elucidation of the interactions between SARS-CoV-2 Spike protein and wild and mutant types of IFITM proteins by in silico methods", @@ -592276,49 +592655,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.08.21263268", - "rel_title": "Combined Impact of Prior SARS-CoV-2 Infection and Vaccination on Antibody Presence", - "rel_date": "2021-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.08.21263268", - "rel_abs": "As COVID-19 continues to spread rapidly and vaccine uptake stagnates, questions remain about the amount of SARS-CoV-2 antibodies present in the population induced by either SARS-CoV-2 infection, by a COVID-19 vaccine, or both.\n\nThe TEXAS Coronavirus Antibody REsponse Survey (CARES) is a statewide seroprevalence program which utilizes the Roche S-test to detect antibodies to the SARS-CoV-2 spike protein and the Roche N-test to detect antibodies to the SARS-CoV-2 nucleocapsid protein, to monitor the combined impact of prior infection and the COVID-19 vaccine. The current sample size having both S- and N-test data and reported vaccination status is 8,846.\n\nParticipants with prior infection (i.e. N+) and with either partial or full vaccination have the highest proportion of those showing the maximum value of the S-test (80.95% and 83.07%, respectively). Using a permutation test, there is no statistically significant difference between the median S-test value for those that have had prior infection and are partially vaccinated versus those that have had prior infection and are fully vaccinated. These groups both show significantly higher median amount compared to the other three groups: N+/not vaccinated, N-/partially vaccinated, and N-/fully vaccinated (all p-values < 0.0001).\n\nUnvaccinated individuals with prior infection have one of the lowest median S-test values. For participants with previous SARS-CoV-2 infection and a COVID-19 vaccine, the median S-test value is high and is not statistically different between those who are partially vaccinated and those who are fully vaccinated.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Eric Boerwinkle", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "Jennifer A Shuford", - "author_inst": "Texas Department of State Health Services, Austin, TX USA" - }, - { - "author_name": "Michael D Swartz", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "David L Lakey", - "author_inst": "The University of Texas System, Austin, TX, USA" - }, - { - "author_name": "Kimberly A Aguillard", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "Stephen J Pont", - "author_inst": "Texas Department of State Health Services, Austin, TX USA" - }, - { - "author_name": "Melissa A Valerio-Shewmaker", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Brownsville, Brownsville, TX, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.08.21263283", "rel_title": "Nationwide trends in COVID-19 cases and SARS-CoV-2 wastewater concentrations in the United States", @@ -592499,6 +592835,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.09.11.459891", + "rel_title": "Phylogenetic evidence for asparagine to aspartic acid protein editing of N-glycosylated SARS-CoV-2 viral proteins by NGLY1 deglycosylation/deamidation suggests an unusual vaccination strategy", + "rel_date": "2021-09-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.11.459891", + "rel_abs": "Many viral proteins, including multiple SARS-CoV-2 proteins, are secreted via the endoplasmic reticulum, and viral particles are assembled and exported in ER-associated replication compartments. Viral coat proteins such as the SARS-CoV-2 Spike protein are N-glycosylated at NxS/T sites as they enter the ER. N-glycosylated sites in many eukaryotic proteins are deglycosylated by the NGLY1/PNG-1 deglycosylation enzyme which also deamidates the N-glycosylated asparagine to aspartic acid, thus editing the target protein sequence. Proteomic analysis of mammalian cell lines has revealed deamidation of many host N-glycosylated asparagines to aspartic acid by NGLY1/PNG-1 on peptides that are presented by mammalian HLA for immune surveillance. The key client protein for NGLY1/PNG-1 deglycosylation and N to D protein editing was revealed by genetic analysis of C. elegans proteasome regulation to be the intact endoplasmic reticulum-transiting SKN-1A transcription factor. Strikingly, an analysis of cancer cell genetic dependencies for growth revealed that the mammalian orthologue of SKN-1A, NRF1 (also called NFE2L1) is required by a highly correlated set of cell lines as NGLY1/PNG-1, supporting that NGLY1/PNG-1 and NRF1 act in the same pathway. NGLY1/PNG-1 edits N-glycosylated asparagines on the intact SKN-1 protein as it is retrieved by ERAD from the ER to in turn activate the transcription of target proteasomal genes. The normal requirement for NGLY1/PNG-1 editing of SKN-1A can be bypassed by a genomic substituion of N to D in four NxS/T N-glycosylation motifs of SKN-1A. Thus NGLY1/PNG-1-mediated N to D protein editing is more than a degradation step for the key client protein for proteasomal homeostasis in C. elegans or tumor growth in particular mammalian cell lines, SKN-1A/NRF1. In addition, such N to D substitutions in NxS/T N-glycosylation motifs occur in evolution: N to D substitutions are observed in phylogenetic comparisons of SKN-1A between nematode species that diverged hundreds of millions of years ago or of the vertebrate NRF1 between disparate vertebrates. Genomic N to D mutations bypass the many steps in N-glycosylation in the ER and deglycosylation-based editing of N to D, perhaps based on differences in the competency of divergent species for various N-glycosylation or deglycosylation steps.\n\nWe surveyed the N-glycosylation sites in coronavirus proteins for such phylogenetic evidence for N to D protein editing in viral life cycles, and found evidence for preferential N to D residue substitutions in NxS/T N-glycosylation sites in comparisons of the genome sequences of hundreds of coronaviruses. This suggests that viruses use NGLY1/PNG-1 in some hosts, for example humans, to edit particular N-glycosylated residues to aspartic acid, but that in other hosts, often in bats, an N to D substitution mutation in the virus genome is selected. Single nucleotide mutations in Asp or Asn codons can produce viruses with N to D or D to N substitutions that might be selected in different animal hosts from the population of viral variants produced in any previous host. NGLY1/PNG-1 has been implicated in viral immunity in mammalian cell culture, favoring this hypothesis.\n\nBecause of the phylogenetic evidence that the NGLY1/PNG-1 editing of protein sequences has functional importance for SKN-1A/NRF1 and viruses, and because most immunization protocols do not address the probable editing and functional importance of N-glycosylated aspargines to aspartic acid in normal viral infections, we suggest that immunization with viral proteins engineered to substitute D at genomically encoded NxS/T sites of N-glycosylated viral proteins that show a high frequency of N to D substitution in viral phylogeny may enhance immunological response to peptide antigens. Such genomically-edited peptides would not require ER-localization for N-glycosylation or other cell compartment localization for NGLY1/PNG-1 N to D protein editing. In addition, such N to D edited protein vaccines could be produced in bacteria since N-glycosylation and deglycosylation which do not occur in bacteria would no longer be required to immunize with a D-substituted peptide. Bacterially-expressed vaccines would be much lower cost and with fewer failure modes than attenuated viral vaccines or recombinant animal viruses produced in chicken eggs, mammalian tissue culture cells, or delivered by mRNA vectors to the patient directly. Because N to D edited peptides are clearly produced by NGLY1/PNG-1, and may be and presented by mammalian HLA, such peptides may more robustly activate T-cell killing or B-cell maturation to mediate more robust viral immunity.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gary Ruvkun", + "author_inst": "Massachusetts General Hospital and Harvard Medical School" + }, + { + "author_name": "Ruslan Sadreyev", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Fei Ji", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2021.09.06.21263168", "rel_title": "Coronavirus disease (COVID-19) associated Mucormycosis: An Anaesthesiologist's Perspective", @@ -594178,65 +594541,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.03.21262885", - "rel_title": "Seroprevalence of anti-SARS-CoV-2 IgG and IgA antibodies before the launch of COVID-19 vaccination in Kazakhstan.", - "rel_date": "2021-09-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21262885", - "rel_abs": "BackgroundCOVID-19 exposure in Central Asia appears underestimated and SARS-CoV-2 seroprevalence data are urgently needed to inform ongoing vaccination efforts and other strategies to mitigate the regional pandemic. Here, we assessed the prevalence of anti-SARS-CoV-2 antibody-mediated immunity in a heterogeneous cohort of public university employees in Karaganda, Kazakhstan.\n\nMethodsAsymptomatic subjects (n=100) were recruited prior to their first COVID-19 vaccination. Questionnaires were administered to capture a range of demographic and clinical characteristics. Nasopharyngeal swabs were collected for SARS-CoV-2 RT-qPCR testing. Serological assays were performed to detect spike (S)-reactive IgG and IgA and to assess virus neutralization. Pre-pandemic samples were used to validate the assay positivity thresholds.\n\nResultsAnti-S IgG and IgA seropositivity rates among SARS-CoV-2 PCR-negative participants (n=100) were 42% (95% CI [32.2-52.3]) and 59% (95% CI [48.8-69.0]), respectively, and 64% (95% CI [53.4-73.1]) of the cohort tested positive for at least one of the antibodies. Anti-S IgG titres correlated with virus neutralization activity, detectable in 49% of the tested subset with prior COVID-19 history. Serologically confirmed history of COVID-19 was associated with Kazakh ethnicity and self-reported history of respiratory illness since March 2020.\n\nConclusionsSARS-CoV-2 exposure in this cohort is [~]15-fold higher compared to the reported all-time national and regional COVID-19 prevalence. Continuous serological surveillance is critical for understanding the COVID-19 transmission dynamics and should be nationally implemented to better inform the public health response in Central Asia.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Irina Kadyrova", - "author_inst": "Karaganda Medical University, Karaganda, Kazakhstan" - }, - { - "author_name": "Sergey Yegorov", - "author_inst": "McMaster University, Hamilton, ON, Canada." - }, - { - "author_name": "Baurzhan Negmetzhanov", - "author_inst": "Nazarbayev University, Nur-Sultan, Republic of Kazakhstan" - }, - { - "author_name": "Yevgeniya Kolesnikova", - "author_inst": "Karaganda Medical University, Karaganda, Kazakhstan" - }, - { - "author_name": "Svetlana Kolesnichenko", - "author_inst": "Karaganda Medical University, Karaganda, Kazakhstan" - }, - { - "author_name": "Ilya Korshukov", - "author_inst": "Karaganda Medical University, Karaganda, Kazakhstan" - }, - { - "author_name": "Dmitriy Vazenmiller", - "author_inst": "Karaganda Medical University, Karaganda, Kazakhstan" - }, - { - "author_name": "Anar Turmukhambetova", - "author_inst": "Karaganda Medical University, Karaganda, Kazakhstan" - }, - { - "author_name": "Matthew S. Miller", - "author_inst": "McMaster University, Hamilton, ON, Canada." - }, - { - "author_name": "Gonzalo Hortelano", - "author_inst": "Nazarbayev University, Nur-Sultan, Republic of Kazakhstan." - }, - { - "author_name": "Dmitriy Babenko", - "author_inst": "Karaganda Medical University, Karaganda, Kazakhstan" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.03.21263028", "rel_title": "Induction of trained immunity by influenza vaccination - impact on COVID-19", @@ -594557,6 +594861,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.02.21263033", + "rel_title": "Epidemic Models for COVID-19 during the First Wave from February to May 2020: a Methodological Review", + "rel_date": "2021-09-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.02.21263033", + "rel_abs": "We review epidemiological models for the propagation of the COVID-19 pandemic during the early months of the outbreak: from February to May 2020. The aim is to propose a methodological review that highlights the following characteristics: (i) the epidemic propagation models, (ii) the modeling of intervention strategies, (iii) the models and estimation procedures of the epidemic parameters and (iv) the characteristics of the data used. We finally selected 80 articles from open access databases based on criteria such as the theoretical background, the reproducibility, the incorporation of interventions strategies, etc. It mainly resulted to phenomenological, compartmental and individual-level models. A digital companion including an online sheet, a Kibana interface and a markdown document is proposed. Finally, this work provides an opportunity to witness how the scientific community reacted to this unique situation.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Marie Garin", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli, F-91190 Gif-sur-Yvette, France" + }, + { + "author_name": "Myrto Limnios", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli, F-91190 Gif-sur-Yvette, France" + }, + { + "author_name": "Alice Nicolai", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Ioannis Bargiotas", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Olivier Boulant", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Stephen E. Chick", + "author_inst": "INSEAD, Boulevard de Constance, 77300 Fontainebleau, France" + }, + { + "author_name": "Amir Dib", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Theodoros Evgeniou", + "author_inst": "INSEAD, Boulevard de Constance, 77300 Fontainebleau, France" + }, + { + "author_name": "Mathilde Fekom", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Argyris Kalogeratos", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Christophe Labourdette", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + }, + { + "author_name": "Anton Ovchinnikov", + "author_inst": "INSEAD, Boulevard de Constance, 77300 Fontainebleau, France and Smith School of Business, Queen's University, Kingston, ON, K7L3N6, Canada" + }, + { + "author_name": "Rapha\u00ebl Porcher", + "author_inst": "Universit\u00e9 de Paris CRESS, INSERM, INRA, 75004 Paris, France" + }, + { + "author_name": "Camille Pouchol", + "author_inst": "MAP5 Laboratory, FP2M, CNRS FR 2036, Universit\u00e9 de Paris, 75006 Paris, France" + }, + { + "author_name": "Nicolas Vayatis", + "author_inst": "Universit\u00e9 Paris-Saclay, ENS Paris-Saclay, CNRS, Centre Borelli" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.09.21263328", "rel_title": "COVID-19 Vaccine Concerns about Safety, Effectiveness and Policies in the United States, Canada, Sweden, and Italy among Unvaccinated Individuals", @@ -596344,113 +596723,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.09.08.459430", - "rel_title": "Age-related differences in immune dynamics during SARS-CoV-2 infection in rhesus macaques", - "rel_date": "2021-09-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.08.459430", - "rel_abs": "Advanced age is a key predictor of severe COVID-19. To gain insight into this relationship, particularly with respect to immune responses, we utilized the rhesus macaque model of SARS-CoV-2 infection. Two cohorts of eight older (16-23 years) and eight younger (3-5 years) rhesus macaques were inoculated with SARS-CoV-2. Animals were evaluated using viral RNA quantification, clinical observations, thoracic radiographs, single-cell transcriptomics, multiparameter flow cytometry, multiplex immunohistochemistry, cytokine detection, and lipidomics analysis at pre-defined timepoints in various tissues. Differences in clinical signs, pulmonary infiltrates, and virus replication dynamics were limited between age cohorts. Transcriptional signatures of inflammation-associated genes in cells isolated from bronchoalveolar lavage fluid at 3 dpi revealed efficient mounting of innate immune defenses in both younger and older animals. These findings suggested that age did not substantially skew major facets of acute disease in this model. However, age-specific divergence of immune responses emerged during the post-acute phase of infection (7-21 dpi). Older animals exhibited sustained local inflammatory innate responses while local effector T-cell responses were induced earlier in the younger animals. Circulating lipid mediator and cytokine levels highlighted increased repair-associated signals in the younger animals, in contrast to persistent pro-inflammatory responses in the older animals. In summary, despite similar disease outcomes, multi-omics profiling in SARS-CoV-2-infected rhesus macaques suggests that age may delay or impair the induction of anti-viral cellular immune responses and delay efficient return to immune homeostasis following acute infection.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Emily Speranza", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Jyothi N. Purushotham", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Julia Rebecca Port", - "author_inst": "NIAID Rocky Mountain Laboratories" - }, - { - "author_name": "Benjamin Schwarz", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Meaghan Flagg", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Brandi N. Williamson", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Friederike Feldmann", - "author_inst": "NIAID/NIH" - }, - { - "author_name": "Manmeet Singh", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Lizzette Perez-Perez", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Gail L. Sturdevant", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Lydia M. Roberts", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Aaron Carmody", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Jonathan E. Schulz", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Neeltje van Doremalen", - "author_inst": "NIH" - }, - { - "author_name": "Atsushi Okumura", - "author_inst": "NIAID/NIH" - }, - { - "author_name": "Jamie Lovaglio", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Patrick Hanley", - "author_inst": "National Institute of Allergy and Infectious Diseases" - }, - { - "author_name": "Carl Shaia", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Ron Germain", - "author_inst": "-" - }, - { - "author_name": "Sonja Best", - "author_inst": "NIAID/NIH" - }, - { - "author_name": "Vincent Munster", - "author_inst": "NIAID" - }, - { - "author_name": "Catharine Bosio", - "author_inst": "Rocky Mountain Laboratories" - }, - { - "author_name": "Emmie de Wit", - "author_inst": "NIAID, NIH" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.08.30.21262866", "rel_title": "SARS-CoV-2 mRNA Vaccination-Associated Myocarditis in Children Ages 12-17: A Stratified National Database Analysis", @@ -596667,6 +596939,137 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.09.08.459480", + "rel_title": "Targeted isolation of panels of diverse human broadly neutralizing antibodies against SARS-like viruses", + "rel_date": "2021-09-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.08.459480", + "rel_abs": "The emergence of current SARS-CoV-2 variants of concern (VOCs) and potential future spillovers of SARS-like coronaviruses into humans pose a major threat to human health and the global economy 1-7. Development of broadly effective coronavirus vaccines that can mitigate these threats is needed 8, 9. Notably, several recent studies have revealed that vaccination of recovered COVID-19 donors results in enhanced nAb responses compared to SARS-CoV-2 infection or vaccination alone 10-13. Here, we utilized a targeted donor selection strategy to isolate a large panel of broadly neutralizing antibodies (bnAbs) to sarbecoviruses from two such donors. Many of the bnAbs are remarkably effective in neutralization against sarbecoviruses that use ACE2 for viral entry and a substantial fraction also show notable binding to non-ACE2-using sarbecoviruses. The bnAbs are equally effective against most SARS-CoV-2 VOCs and many neutralize the Omicron variant. Neutralization breadth is achieved by bnAb binding to epitopes on a relatively conserved face of the receptor binding domain (RBD) as opposed to strain-specific nAbs to the receptor binding site that are commonly elicited in SARS-CoV-2 infection and vaccination 14-18. Consistent with targeting of conserved sites, select RBD bnAbs exhibited in vivo protective efficacy against diverse SARS-like coronaviruses in a prophylaxis challenge model. The generation of a large panel of potent bnAbs provides new opportunities and choices for next-generation antibody prophylactic and therapeutic applications and, importantly, provides a molecular basis for effective design of pan-sarbecovirus vaccines.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Wan-ting He", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Rami Musharrafieh", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Ge Song", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Katharina Dueker", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Longping V. Tse", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "David R. Martinez", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Alexandra Schafer", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Sean Callaghan", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Peter Yong", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Nathan Beutler", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Jonathan L. Torres", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Reid M. Volk", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Panpan Zhou", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Meng Yuan", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Hejun Liu", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Fabio Anzanello", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Tazio Capozzola", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Mara Parren", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Elijah Garcia", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Stephen A. Rawlings", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." + }, + { + "author_name": "Davey M. Smith", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." + }, + { + "author_name": "Ian A. Wilson", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Yana Safonova", + "author_inst": "Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA" + }, + { + "author_name": "Andrew B. Ward", + "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Thomas Rogers", + "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Lisa E. Gralinski", + "author_inst": "Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA." + }, + { + "author_name": "Dennis R. Burton", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + }, + { + "author_name": "Raiees Andrabi", + "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.09.08.459260", "rel_title": "Artemisia annua hot-water extracts show potent activity in vitro against Covid-19 variants including delta", @@ -598162,49 +598565,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.09.07.459123", - "rel_title": "Entrectinib - a SARS-CoV-2 inhibitor in Human Lung Tissue (HLT) cells", - "rel_date": "2021-09-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.07.459123", - "rel_abs": "Since the start of the COVID-19 outbreak, pharmaceutical companies and research groups have focused on the development of vaccines and antiviral drugs against SARS-CoV-2. Here, we apply a drug repurposing strategy to identify potential drug candidates that are able to block the entrance of the virus into human cells. By combining virtual screening with in vitro pseudovirus assays and antiviral assays in Human Lung Tissue (HLT) cells, we identify entrectinib as a promising antiviral drug. We found that part of the antiviral action of entrectinib is mediated by a non-specific mechanism, likely occurring at the viral membrane level. Such a profile could provide entrectinib with protection against the development of drug resistance by emerging SARS-CoV-2 variants.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alejandro Peralta-Garcia", - "author_inst": "Pompeu Fabra University & IMIM" - }, - { - "author_name": "Mariona Torrens-Fontanals", - "author_inst": "Pompeu Fabra University & IMIM" - }, - { - "author_name": "Tomasz Maciej Stepniewski", - "author_inst": "Pompeu Fabra University & IMIM; InterAx Biotech AG" - }, - { - "author_name": "Vikram Ayinampudi", - "author_inst": "InterAx Biotech AG" - }, - { - "author_name": "Maria Waldhoer", - "author_inst": "InterAx Biotech AG" - }, - { - "author_name": "Mirjam Zimmermann", - "author_inst": "InterAx Biotech AG" - }, - { - "author_name": "Jana Selent", - "author_inst": "Pompeu Fabra University & IMIM" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.09.01.21262791", "rel_title": "Descriptive epidemiology of COVID-19 deaths during the first wave of pandemic in India - a single center experience", @@ -598357,6 +598717,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.03.21257002", + "rel_title": "Long COVID: Assessment of Neuropsychiatric Symptoms in Children and Adolescents - A Clinical Data Analysis", + "rel_date": "2021-09-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21257002", + "rel_abs": "COVID-19 infections in adults often result in medical, neuropsychiatric, and unspecific symptoms, called Long COVID, and the premorbid functional status cannot be achieved. Regarding the course in children and adolescents, however, reliable data are not yet available.\n\nObjective380 children and adolescents/young adults aged between 6 and 21 years, being treated for various psychiatric diseases in an outpatient clinical service, were examined for COVID-19 infections and Long COVID symptoms following a structured protocol.\n\nResultsThree patients had COVID-19; one patient had symptoms of Long COVID in his medical history, but they could not be objectivized in an in-depth neuropsychiatric and neuropsychological assessment.\n\nConclusionsLong COVID seems to occur rarely in children and adolescents. Objectivizing the symptoms is a difficult task that requires various diagnostic considerations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jan Froelich", + "author_inst": "Central Institute of Mental Health Department of Child and Adolescent Psychiatry, University of Heidelberg - Faculty of Medicine Mannheim" + }, + { + "author_name": "Tobias Banaschewski", + "author_inst": "Central Institute of Mental Health Department of Child and Adolescent Psychiatry, University of Heidelberg - Faculty of Medicine Mannheim" + }, + { + "author_name": "Annabelle Ulmer", + "author_inst": "Practice for Child and Adolescent Psychiatry and Psychotherapy Dr. Dr. Jan Froelich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.09.02.21263038", "rel_title": "COVID-19 Vaccine Efficacy in a Diverse Urban Healthcare Worker Population", @@ -599596,49 +599983,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.31.21262919", - "rel_title": "Expected Rates of Select Adverse Events following Immunization for COVID-19 Vaccine Safety Monitoring", - "rel_date": "2021-09-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.31.21262919", - "rel_abs": "BackgroundKnowledge of expected rates of potential adverse events of special interest (AESI) that may occur coincidentally following COVID-19 vaccination is essential for vaccine safety surveillance and assessment. We calculated the expected rates of 21 potential AESI following COVID-19 vaccination among vaccinated persons within 1 day, 7 days, and 42 days of vaccination.\n\nMethodsWe used meta-analytic methods to estimate background rates of 21 medical conditions considered potential AESI and calculated expected rates of each potential AESI within 1 day, 7 days, and 42 days of vaccination.\n\nResultsBackground rates of three commonly monitored AESI, Guillain-Barre syndrome (GBS), myopericarditis, and all-cause deaths were 2.0 GBS cases/100,000 person-years, 1.3 myopericarditis cases/100,000 person-years, and 863.8 all-cause deaths/100,000 person-years, respectively. Based on these background rates, if 10,000,000 persons are vaccinated, we would expect 0.5, 3.7, and 22.5 GBS cases; 0.3, 2.4, and 14.3 myopericarditis cases; and 236.5, 1655.5, and 9932.8 all-cause deaths to occur in coincident temporal association (i.e., as a result of background incidence) within 1 day, 7 days, and 42 days of vaccination, respectively.\n\nConclusionKnowledge of expected rates of potential AESI can help contextualize adverse health events associated temporally with immunization, aid in safety signal detection, guide COVID-19 vaccine public health communication, and inform benefit-risk assessments of COVID-19 vaccines.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Winston E. Abara", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Julianne Gee", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Yi Mu", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Mark J Delorey", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Tun Ye", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "David K Shay", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Tom Shimabukuro", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.02.21263017", "rel_title": "Monitoring populations at increased risk for SARS-CoV-2 infection in the community", @@ -599875,6 +600219,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.09.03.458854", + "rel_title": "The genetics of eating behaviors: research in the age of COVID-19", + "rel_date": "2021-09-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.03.458854", + "rel_abs": "How much pleasure we take in eating is more than just how much we enjoy the taste of food. Food involvement - the amount of time we spend on food beyond the immediate act of eating and tasting - is key to the human food experience. We took a biological approach to test whether food-related behaviors, together capturing food involvement, have genetic components and are partly due to inherited variation. We collected data via an internet survey from a genetically informative sample of 419 adult twins (114 monozygotic twin pairs, 31 dizygotic twin pairs, and 129 singletons). Because we conducted this research during the pandemic, we also ascertained how many participants had experienced COVID-19-associated loss of taste and smell. Since these respondents had previously participated in research in person, we measured their level of engagement to evaluate the quality of their online responses. Additive genetics explained 16-44% of the variation in some measures of food involvement, most prominently various aspects of cooking, suggesting some features of the human food experience may be inborn. Other features reflected shared (early) environment, captured by respondents twin status. About 6% of participants had a history of COVID-19 infection, many with transitory taste and smell loss, but all but one had recovered before the survey. Overall, these results suggest that people may have inborn as well as learned variations in their involvement with food. We also learned to adapt to research during a pandemic by considering COVID-19 status and measuring engagement in online studies of human eating behavior.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Mackenzie E. Hannum", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Cailu Lin", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Katherine A Bell", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Aurora K Toskala", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Riley R Koch", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Tharaka Galaniha", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Alissa Nolden", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Danielle R. Reed", + "author_inst": "Monell Chemical Senses Center" + }, + { + "author_name": "Paule Valery Joseph", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2021.08.27.21262422", "rel_title": "Characteristics associated with COVID-19 vaccine uptake among adults in England (08 December to 17 May 2021)", @@ -601422,61 +601817,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.31.21262625", - "rel_title": "High-Throughput Adaptable SARS-CoV-2 Screening for Rapid Identification of Dominant and Emerging Regional Variants", - "rel_date": "2021-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.31.21262625", - "rel_abs": "ObjectivesEmerging SARS-CoV-2 variant strains can be associated with increased transmissibility, more severe disease, and reduced effectiveness of treatments. To improve the availability of regional variant surveillance, we describe a variant genotyping system that is rapid, accurate, adaptable, and able to detect new low-level variants built with existing hospital infrastructure.\n\nMethodsWe use a tiered high-throughput SARS-CoV-2 screening program to characterizes variants in a supra-regional health system over 76 days. Combining targeted qPCR and selective sequencing, we screen positive SARS-CoV-2 samples from all hospitals within our health care system for genotyping dominant and emerging variants.\n\nResultsThe median turnaround for genotyping was two days using the high-throughput qPCR-based screen, allowing us to rapidly characterize the emerging Delta variant. In our population, the Delta variant is associated with a lower CT value, lower age at infection, and increased vaccine breakthrough cases. Detection of low-level and potentially emerging variants highlights the utility of a tiered approach.\n\nConclusionsThese findings underscore the need for fast, low-cost, high-throughput monitoring of regional viral sequences as the pandemic unfolds and the emergence of SARS-CoV-2 variants increases. Combing qPCR-based screening with selective sequencing allows for rapid genotyping of variants and dynamic system improvement.\n\nKey messagesO_LIA tiered approach that uses qPCR-based screening to identify dominant variants and sequencing for unique variants maximizes throughput, turnaround time, and information gleaned from each sample.\nC_LIO_LIIn our population, the Delta variant became dominant in less than a month and is associated with lower CT, lower age at infection, and increased breakthrough cases.\nC_LIO_LIWe identified low-level variants, including the variant of interest B.1.621 and a Delta variant with an E484K mutation in our population using existing hospital infrastructure.\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Zita Hubler", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Xiao Song", - "author_inst": "University Hospitals Cleveland Medical Center" - }, - { - "author_name": "Cameron Norris", - "author_inst": "University Hospitals Cleveland Medical Center" - }, - { - "author_name": "Mehul Jani", - "author_inst": "University Hospitals Cleveland Medical Center" - }, - { - "author_name": "David Alouani", - "author_inst": "University Hospitals Cleveland Medical Center" - }, - { - "author_name": "Maureen Atchley", - "author_inst": "University Hospitals Cleveland Medical Center" - }, - { - "author_name": "Lisa M Stempak", - "author_inst": "University Hospitals Cleveland Medical Center" - }, - { - "author_name": "Sree S Cherian", - "author_inst": "University Hospitals Cleveland Medical Center" - }, - { - "author_name": "Christine L Schmotzer", - "author_inst": "University Hospitals Cleveland Medical Center" - }, - { - "author_name": "Navid Sadri", - "author_inst": "University Hospitals Cleveland Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.08.30.21262819", "rel_title": "Predicting transitions between longitudinal classes of posttraumatic stress disorder, adjustment disorder, and well-being during the COVID-19 pandemic: Protocol of a latent transition model in a general Dutch sample", @@ -601869,6 +602209,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.30.21262341", + "rel_title": "Modelling the potential role of super spreaders on COVID-19 transmission dynamics", + "rel_date": "2021-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.30.21262341", + "rel_abs": "Superspreading phenomenon has been observed in many infectious diseases and contributes significantly to public health burden in many countries. Superspreading events have recently been reported in the transmission of the COVID-19 pandemic. The present study uses a set of nine ordinary differential equations to investigate the impact of superspreading on COVID-19 dynamics. The model developed in this study addresses the heterogeineity in infectiousness by taking into account two forms of transmission rate functions for superspreaders based on clinical (infectivity level) and social or environmental (contact level). The basic reproduction number has been derived and the contribution of each infectious compartment towards the generation of new COVID-19 cases is ascertained. Data fitting was performed and parameter values were estimated within plausible ranges. Numerical simulations performed suggest that control measures that decrease the effective contact radius and increase the transmission rate exponent will be greatly beneficial in the control of COVID-19 in the presence of superspreading phenomena.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Josiah Mushanyu", + "author_inst": "University of zimbabwe" + }, + { + "author_name": "Williams Chukwu", + "author_inst": "University of Johannesburg" + }, + { + "author_name": "Farai Nyabadza", + "author_inst": "University of Johannesburg" + }, + { + "author_name": "Gift Muchatibaya", + "author_inst": "university of Zimbabwe" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.01.458644", "rel_title": "Co-expression analysis to identify key modules and hub genes associated with COVID19 in Platelets", @@ -603536,41 +603907,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.08.30.458244", - "rel_title": "(Machine) Learning the mutation signatures of SARS-CoV-2: a primer for predictive prognosis", - "rel_date": "2021-08-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.30.458244", - "rel_abs": "MotivationContinuous emergence of new variants through appearance, accumulation and disappearance of mutations in viruses is a hallmark of many viral diseases. SARS-CoV-2 and its variants have particularly exerted tremendous pressure on global healthcare system owing to their life threatening and debilitating implications. The sheer plurality of the variants and huge scale of genome sequence data available for Covid19 have added to the challenges of traceability of mutations of concern. The latter however provides an opportunity to utilize SARS-CoV-2 genomes and the mutations therein as big data records to comprehensively classify the variants through the (machine) learning of mutation patterns. The unprecedented sequencing effort and tracing of disease outcomes provide an excellent ground for identifying important mutations by developing machine learnt models or severity classifiers using mutation profile of SARS-CoV-2. This is expected to provide a significant impetus to the efforts towards not only identifying the mutations of concern but also exploring the potential of mutation driven predictive prognosis of SARS-CoV-2.\n\nResultsWe describe how a graduated approach of building various severity specific machine learning classifiers, using only the mutation corpus of SARS-CoV-2 genomes, can potentially lead to the identification of important mutations and guide potential prognosis of infection. We demonstrate the applicability of model derived important mutations and use of Shapley values in order to identify the significant mutations of concern as well as for developing sparse models of outcome classification. A total of 77,284 outcome traced SARS-CoV-2 genomes were employed in this study which represented a total corpus of 30346 unique nucleotide mutations and 18647 amino acid mutations. Machine learning models pertaining to graduated classifiers of target outcomes namely Asymptomatic, Mild, Symptomatic/Moderate, Severe and Fatal were built considering the TRIPOD guidelines for predictive prognosis. Shapley values for model linked important mutations were employed to select significant mutations leading to identification of less than 20 outcome driving mutations from each classifier. We additionally describe the significance of adopting a temporal modeling approach to benchmark the predictive prognosis linked with continuously evolving pathogens. A chronologically distinct sampling is important in evaluating the performance of models trained on past data in accurately classifying prognosis linked with genomes of future (observed with new mutations). We conclude that while machine learning approach can play a vital role in identifying relevant mutations, caution should be exercised in using the mutation signatures for predictive prognosis in cases where new mutations have accumulated along with the previously observed mutations of concern.\n\nContactsharmila.mande@tcs.com\n\nSupplementary informationSupplementary data are enclosed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sunil Nagpal", - "author_inst": "TCS Research, Tata Consultancy Services Ltd & CSIR IGIB, Delhi India" - }, - { - "author_name": "Nishal Kumar Pinna", - "author_inst": "TCS Research, Tata Consultancy Services Ltd" - }, - { - "author_name": "Divyanshu Srivastava", - "author_inst": "TCS Research, Tata Consultancy Services Ltd" - }, - { - "author_name": "Rohan Singh", - "author_inst": "TCS Research, Tata Consultancy Services Ltd" - }, - { - "author_name": "Sharmila S Mande", - "author_inst": "TCS Research, Tata Consultancy Services Ltd" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.08.30.458099", "rel_title": "Strikingly different roles of SARS-CoV-2 fusion peptides uncovered by neutron scattering", @@ -603835,6 +604171,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.24.21262245", + "rel_title": "Symptomatology associated with the diffusion of the SARS-CoV-2 Lambda variant in Peru: An infodemiologic analysis", + "rel_date": "2021-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.24.21262245", + "rel_abs": "The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) Lambda variant rapidly diffused across Peru following its identification in December 2020, and had now spread worldwide. In this study, we investigated infodemiologic trends in symptomatology associated with the Coronavirus Disease 2019 (COVID-19) following the spread of SARS-CoV-2 Lambda variant in Peru, enabling infodemiologic surveillance of SARS-CoV-2 in regions with high circulation of this new variant. Weekly Google Trends scores were obtained for key symptom keywords between March 1st, 2020 and July 4th, 2021, whilst case count data were obtained from Peruvian Ministry of Health. Multiple time series linear regression was used to assess trends in each score series, using the week of December 27th as cutoff for emergence of the Lambda variant. The significance of such trends was tested for each time period, before and after the cutoff date. A total 2,075,484 confirmed SARS-CoV-2 infections in Peru in relation to Google Trends data were analyzed. After Lambda variant emergence, searches for \"diarrhea\" demonstrated a change from a negative to positive correlation with weekly case counts and anticipated dynamic changes in case counts by 1-5 weeks. Searches for \"shortness of breath\" and \"headache\" remained consistently positively correlated to weekly case counts before and after Lambda emergence. No changes in searches for other common cold symptoms were observed, while no specific trends were observed for \"taste loss\" or \"smell loss\". Diarrhea, headache, and shortness of breath appear to be the most important symptoms for infodemiologic tracking the current outbreak in Peru and other regions with high circulation of SARS-CoV-2 Lambda variant.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Brandon Michael Henry", + "author_inst": "Clinical Laboratory, Division of Nephrology and Hypertension, Cincinnati Children Hospital Medical Center, Cincinnati, OH, USA" + }, + { + "author_name": "Maria Helena Santos de Oliveira", + "author_inst": "Department of Biostatistics, State University of Maringa, Maringa, Brazil" + }, + { + "author_name": "Thais Barbosa de Oliveira", + "author_inst": "Department of Biostatistics, State University of Maringa, Maringa, Brazil" + }, + { + "author_name": "Kin Israel Notarte", + "author_inst": "Faculty of Medicine and Surgery, University of Santo Tomas, Manila 1008, Philippines" + }, + { + "author_name": "Giuseppe Lippi", + "author_inst": "Section of Clinical Biochemistry, Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.23.21262413", "rel_title": "Towards the global equilibrium of COVID-19: statistical analysis of country-level data", @@ -605586,153 +605957,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.08.22.21262168", - "rel_title": "Intramuscular SARS-CoV-2 vaccines elicit varying degrees of plasma and salivary antibody responses as compared to natural infection", - "rel_date": "2021-08-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.22.21262168", - "rel_abs": "Vaccination induced antibody and T-cell immune responses are important for systemic protection from COVID-19. Because SARS-CoV-2 infects and is transmitted by oral-pharyngeal mucosa, we wished to test mucosal antibodies elicited by natural infection or intramuscular vaccine injection. In a non-randomized observational study, we measured antibodies against the SARS-CoV-2 RBD in plasma and saliva from convalescent or vaccinated individuals and tested their neutralizing potential using a replication competent rVSV-eGFP-SARS-CoV-2. We found IgG and IgA anti-RBD antibodies as well as neutralizing activity in convalescent plasma and saliva. Two doses of mRNA vaccination (BNT162b2 or mRNA-1273) induced high levels of IgG anti-RBD in saliva, a subset of whom also had IgA, and significant neutralizing activity. We detected anti-RBD IgG and IgA with significant neutralizing potential in the plasma of single dose Ad26.COV2.S vaccinated individuals, and we detected slight amounts of anti-RBD antibodies in matched saliva. The role of salivary antibodies in protection against SARS-CoV-2 infection is unknown and merits further investigation. This study was not designed to, nor did it study the full kinetics of the antibody response or protection from infection, nor did it address variants of SARS-CoV-2.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "George Ronald Nahass", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Rachel E Salomon-Shulman", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Grace Blacker", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Kazim Haider", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Rich Brotherton", - "author_inst": "Clinical and Translational Research Unit (CTRU), Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Kristine Teague", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Ying Ying Yiu", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Rachel E. Brewer", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Sarah Danielle Galloway", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Paige Hansen", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA; Department of" - }, - { - "author_name": "Gabriel Marquez-Arreguin", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine" - }, - { - "author_name": "Salma Sheikh-Mohamed", - "author_inst": "Department of Immunology, University of Toronto, Toronto, Canada" - }, - { - "author_name": "Gary Y.C. Chao", - "author_inst": "Department of Immunology, University of Toronto, Toronto, Canada" - }, - { - "author_name": "Baweleta Isho", - "author_inst": "Department of Immunology, University of Toronto, Toronto, Canada" - }, - { - "author_name": "Evan Do", - "author_inst": "Sean N. Parker Center for Allergy and Asthma Research, Stanford University School Medicine, Stanford, CA, USA" - }, - { - "author_name": "Iris Chang", - "author_inst": "Sean N. Parker Center for Allergy and Asthma Research, Stanford University School Medicine, Stanford, CA, USA" - }, - { - "author_name": "Theo Snow", - "author_inst": "Sean N. Parker Center for Allergy and Asthma Research, Stanford University School Medicine, Stanford, CA, USA" - }, - { - "author_name": "Alexandra S. Lee", - "author_inst": "Sean N. Parker Center for Allergy and Asthma Research, Stanford University School Medicine, Stanford, CA, USA" - }, - { - "author_name": "- STANFORD COVID-19 BIOBANK", - "author_inst": "Stanford COVID-19 Biobank, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Monali Manohar", - "author_inst": "Sean N. Parker Center for Allergy and Asthma Research, Stanford University School Medicine, Stanford, CA, USA" - }, - { - "author_name": "Samuel Yang", - "author_inst": "Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Andra L. Blomkalns", - "author_inst": "Department of Emergency Medicine, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Angela J. Rogers", - "author_inst": "Department of Medicine, Stanford University School of Medicine, Stanford, CA USA" - }, - { - "author_name": "Allison McGeer", - "author_inst": "Lunenfeld-Tanenbaum Research Institute and Mount Sinai Hospital, Toronto, Canada Department of Immunology, University of Toronto, Toronto, Canada" - }, - { - "author_name": "Anne-Claude Gingras", - "author_inst": "Lunenfeld-Tanenbaum Research Institute and Mount Sinai Hospital, Toronto, Canada Department of Immunology, University of Toronto, Toronto, Canada; Department of" - }, - { - "author_name": "Sharon Straus", - "author_inst": "Li Ka Shing Knowledge Institute of St. Michael?s Hospital, Unity Health Toronto, Canada" - }, - { - "author_name": "Phillip Grant", - "author_inst": "Department of Medicine, Stanford University School of Medicine, Stanford, CA USA" - }, - { - "author_name": "Kari C. Nadeau", - "author_inst": "Sean N. Parker Center for Allergy and Asthma Research, Stanford University School Medicine, Stanford, CA, USA" - }, - { - "author_name": "Catherine A. Blish", - "author_inst": "Department of Medicine, Stanford University School of Medicine, Stanford, CA USA" - }, - { - "author_name": "Jennifer L. Gommerman", - "author_inst": "Department of Immunology, University of Toronto, Toronto, Canada" - }, - { - "author_name": "Erin C. Sanders", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA; Department of" - }, - { - "author_name": "Irving L. Weissman", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Michal Caspi Tal", - "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine and the Ludwig Cancer Center, Stanford University School of Medicine, Stanford, CA, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.08.27.21262629", "rel_title": "Can tracking mobility be used as a public health tool against COVID-19 following the expiration of stay-at-home mandates?", @@ -605985,6 +606209,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.08.20.21261687", + "rel_title": "Randomized trials on non-pharmaceutical interventions for COVID-19 as of August 2021: a meta-epidemiological analysis", + "rel_date": "2021-08-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.20.21261687", + "rel_abs": "BackgroundNumerous non-pharmaceutical interventions (NPIs) were taken worldwide to contain the spread of the COVID-19 pandemic. We aimed at providing an overview of randomized trials assessing NPIs to prevent COVID-19.\n\nMethodsWe included all randomized trials assessing NPIs to prevent COVID-19 in any country and setting registered in ClinicalTrials.gov and the World Health Organization International Clinical Trials Registry Platform using the COVID-evidence platform (until 17 August 2021). We searched for corresponding publications in MEDLINE/PubMed, Google Scholar, the Living Overview of Evidence platform (L-OVE), and the Cochrane COVID-19 registry as well as for results posted in registries.\n\nResultsWe identified 41 randomized trials. Of them, 11 were completed (26.8%) including 7 with published results. The 41 trials planned to recruit a median of 1,700 participants (IQR, 588 to 9,500, range 30 to 35,256,399) with a median planned duration of 8 months (IQR, 3 to 14, range 1 to 24). Most came from the United States (n=11, 26.8%). The trials mostly assessed protective equipment (n=11, 26.8%), COVID-19-related information and education programs (n=9, 22.0%), access to mass events under specific safety measures (n=5, 12.2%), testing and screening strategies (n=5, 12.2%), and hygiene management (n=5, 12.2%).\n\nConclusionsWorldwide, 41 randomized trials assessing NPIs have been initiated with published results available to inform policy decisions for only 7 of them. A long-term research agenda including behavioral, environmental, social, and systems level interventions is urgently needed to guide policies and practices in the current and future public health emergencies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Julian Hirt", + "author_inst": "Department of Clinical Research, University Hospital Basel, University of Basel" + }, + { + "author_name": "Perrine Janiaud", + "author_inst": "Department of Clinical Research, University Hospital Basel, University of Basel" + }, + { + "author_name": "Lars G. Hemkens", + "author_inst": "Department of Clinical Research, University Hospital Basel, University of Basel" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.29.458083", "rel_title": "Allosteric regulation of 3CL protease of SARS-CoV-2 and SARS-CoV observed in the crystal structure ensemble", @@ -607336,69 +607587,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.25.21262583", - "rel_title": "Clinical Evaluation of the Novel Rapid Nucleic Acid Amplification Point-of-Care Test (Smart Gene SARS-CoV-2) in the analysis of Nasopharyngeal and Anterior Nasal samples.", - "rel_date": "2021-08-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.25.21262583", - "rel_abs": "IntroductionSmart Gene is a point-of-care (POC)-type automated molecular testing platform that can be performed with 1 minute of hands-on-time. Smart Gene SARS-CoV-2 is a newly developed Smart Gene molecular assay for the detection of SARS-CoV-2. The analytical and clinical performance of Smart Gene SARS-CoV-2 has not been evaluated.\n\nMethodsNasopharyngeal and anterior nasal samples were prospectively collected from subjects referred to the local PCR center from March 25 to July 5, 2021. Two swabs were simultaneously obtained for the Smart Gene SARS-CoV-2 assay and the reference real-time RT-PCR assay, and the results of Smart Gene SARS-CoV-2 were compared to the reference real-time RT-PCR assay.\n\nResultsAmong a total of 1150 samples, 68 of 791 nasopharyngeal samples and 51 of 359 anterior nasal samples were positive for SARS-CoV-2 in the reference real-time RT-PCR assay. In the testing of nasopharyngeal samples, Smart Gene SARS-CoV-2 showed the total, positive and negative concordance of 99.2% (95% confidence interval [CI]: 98.4-99.7%), 94.1% (95% CI: 85.6-98.4%) and 99.7% (95% CI: 99.0-100%), respectively. For anterior nasal samples, Smart Gene SARS-CoV-2 showed the total, positive and negative concordance of 98.9% (95% CI: 97.2-99.7%), 98.0% (95% CI: 89.6-100%) and 99.0% (95% CI: 97.2-99.8%), respectively. In total, 5 samples were positive in the reference real-time RT-PCR and negative in Smart Gene SARS-CoV-2, whereas 5 samples were negative in the reference real-time RT-PCR and positive in Smart Gene SARS-CoV-2.\n\nConclusionSmart Gene SARS-CoV-2 showed sufficient analytical performance for the detection of SARS-CoV-2 in nasopharyngeal and anterior nasal samples.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Yoshihiko Kiyasu", - "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital" - }, - { - "author_name": "Masato Owaku", - "author_inst": "Mizuho Medy Co., Ltd." - }, - { - "author_name": "Yusaku Akashi", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Tsukuba Medical Center Hospital" - }, - { - "author_name": "Yuto Takeuchi", - "author_inst": "Department of Infectious Diseases, University of Tsukuba Hospital" - }, - { - "author_name": "Kenji Narahara", - "author_inst": "Mizuho Medy Co., Ltd." - }, - { - "author_name": "Sunao Mori", - "author_inst": "Mizuho Medy Co., Ltd." - }, - { - "author_name": "Takashi Nagano", - "author_inst": "Mizuho Medy Co., Ltd." - }, - { - "author_name": "Shigeyuki Notake", - "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital" - }, - { - "author_name": "Atsuo Ueda", - "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital" - }, - { - "author_name": "Koji Nakamura", - "author_inst": "Department of Clinical Laboratory, Tsukuba Medical Center Hospital" - }, - { - "author_name": "Hiroichi Ishikawa", - "author_inst": "Department of Respiratory Medicine, Tsukuba Medical Center Hospital" - }, - { - "author_name": "Hiromichi Suzuki", - "author_inst": "Department of Infectious Diseases, Faculty of Medicine, University of Tsukuba" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.27.457964", "rel_title": "Structural dynamics of SARS-CoV-2 nucleocapsid protein induced by RNA binding", @@ -607691,6 +607879,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.08.25.21262636", + "rel_title": "Impact of Covid-19 Pandemic on Racial/Ethnic Differences in Mortality by Cause of Death", + "rel_date": "2021-08-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.25.21262636", + "rel_abs": "ObjectivesTo quantify changes in all-cause and cause-specific mortality by race and ethnicity between 2019 and 2020.\n\nMethodsUsing 2019 and 2020 provisional death counts from the National Center for Health Statistics and population estimates from the US Census Bureau, we estimate age-standardized death rates by race/ethnicity and attribute changes in mortality to various causes of death. We also examine how patterns of change across racial/ethnic groups vary by age and sex.\n\nResultsCovid-19 death rates in 2020 were highest in the Hispanic community whereas Black individuals had the largest increase in all-cause mortality between 2019 and 2020. Increases in mortality from heart disease, diabetes, and external causes of death accounted for the adverse trend in all-cause mortality within the Black population. Percentage increases in all-cause mortality were similar for men and women and for ages 25-64 and 65+ for Black and White populations, but increases were greatest for working-aged men among the Hispanic population.\n\nConclusionsExamining increases in non-Covid-19 causes of death is essential for fully capturing both the direct and indirect impact of the Covid-19 pandemic on racial/ethnic mortality disparities.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anneliese N. Luck", + "author_inst": "Department of Sociology and Population Studies Center, University of Pennsylvania, Philadelphia, PA, USA" + }, + { + "author_name": "Samuel H. Preston", + "author_inst": "Department of Sociology and Population Studies Center, University of Pennsylvania, Philadelphia, PA, USA" + }, + { + "author_name": "Irma T. Elo", + "author_inst": "Department of Sociology and Population Studies Center, University of Pennsylvania, Philadelphia, PA, USA" + }, + { + "author_name": "Andrew C. Stokes", + "author_inst": "Department of Global Health, Boston University School of Public Health, Boston, MA, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.25.21262614", "rel_title": "Democratic governance and excess mortality during the COVID-19 pandemic", @@ -609558,53 +609777,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.08.26.457874", - "rel_title": "From Alpha to Zeta: Identifying variants and subtypes of SARS-CoV-2 via clustering", - "rel_date": "2021-08-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.26.457874", - "rel_abs": "The availability of millions of SARS-CoV-2 sequences in public databases such as GISAID and EMBL-EBI (UK) allows a detailed study of the evolution, genomic diversity and dynamics of a virus like never before. Here we identify novel variants and sub-types of SARS-CoV-2 by clustering sequences in adapting methods originally designed for haplotyping intra-host viral populations. We asses our results using clustering entropy -- the first time it has been used in this context.\n\nOur clustering approach reaches lower entropies compared to other methods, and we are able to boost this even further through gap filling and Monte Carlo based entropy minimization. Moreover, our method clearly identifies the well-known Alpha variant in the UK and GISAID datasets, but is also able to detect the much less represented (< 1% of the sequences) Beta (South Africa), Epsilon (California), Gamma and Zeta (Brazil) variants in the GISAID dataset. Finally, we show that each variant identified has high selective fitness, based on the growth rate of its cluster over time. This demonstrates that our clustering approach is a viable alternative for detecting even rare subtypes in very large datasets.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Andrew Melnyk", - "author_inst": "Georgia State University" - }, - { - "author_name": "Fatemeh Mohebbi", - "author_inst": "Georgia State University" - }, - { - "author_name": "Sergey Knyazev", - "author_inst": "Georgia State University" - }, - { - "author_name": "Bikram Sahoo", - "author_inst": "Georgia State University" - }, - { - "author_name": "Roya Hosseini", - "author_inst": "Georgia State University" - }, - { - "author_name": "Pavel Skums", - "author_inst": "Georgia State University" - }, - { - "author_name": "Alexandr Zelikovskiy", - "author_inst": "Georgia State University" - }, - { - "author_name": "Murray D Patterson", - "author_inst": "Georgia State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.08.26.457884", "rel_title": "A vimentin-targeting oral compound with host-directed antiviral and anti-inflammatory actions addresses multiple features of COVID-19 and related diseases", @@ -609933,6 +610105,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.23.21262477", + "rel_title": "Low risk of SARS-CoV-2 transmission via fomite, even in cold-chain", + "rel_date": "2021-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262477", + "rel_abs": "BackgroundCountries continue to debate the need for decontamination of cold-chain food packaging to reduce possible SARS-CoV-2 fomite transmission among workers. While laboratory-based studies demonstrate persistence of SARS-CoV-2 on surfaces, the likelihood of fomite-mediated transmission under real-life conditions is uncertain.\n\nMethodsUsing a quantitative risk assessment model, we simulated in a frozen food packaging facility 1) SARS-CoV-2 fomite-mediated infection risks following worker exposure to contaminated plastic packaging; and 2) reductions in these risks attributed to masking, handwashing, and vaccination.\n\nFindingsIn a representative facility with no specific interventions, SARS-CoV-2 infection risk to a susceptible worker from contact with contaminated packaging was 2{middle dot}8 x 10-3 per 1h-period (95%CI: 6{middle dot}9 x 10-6, 2{middle dot}4 x 10-2). Implementation of standard infection control measures, handwashing and masks (9{middle dot}4 x 10-6 risk per 1h-period, 95%CI: 2{middle dot}3 x 10-8, 8{middle dot}1 x 10-5), substantially reduced risk (99{middle dot}7%). Vaccination of the susceptible worker (two doses Pfizer/Moderna, vaccine effectiveness: 86-99%) combined with handwashing and masking reduced risk to less than 1{middle dot}0 x 10-6. Simulating increased infectiousness/transmissibility of new variants (2-, 10-fold viral shedding) among a fully vaccinated workforce, handwashing and masks continued to mitigate risk (2{middle dot}0 x 10-6 -1{middle dot}1 x 10-5 risk per 1h-period). Decontamination of packaging in addition to these interventions reduced infection risks to below the 1{middle dot}0 x 10-6 risk threshold.\n\nInterpretationFomite-mediated SARS-CoV-2 infection risks were very low under cold-chain conditions. Handwashing and masking provide significant protection to workers, especially when paired with vaccination.\n\nFundingU.S. Department of Agriculture", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Julia S. Sobolik", + "author_inst": "Emory University" + }, + { + "author_name": "Elizabeth T. Sajewski", + "author_inst": "Emory University" + }, + { + "author_name": "Lee-Ann Jaykus", + "author_inst": "North Carolina State University" + }, + { + "author_name": "D. Kane Cooper", + "author_inst": "Emory University" + }, + { + "author_name": "Ben A. Lopman", + "author_inst": "Emory University" + }, + { + "author_name": "Alicia NM. Kraay", + "author_inst": "Emory University" + }, + { + "author_name": "P. Barry Ryan", + "author_inst": "Emory University" + }, + { + "author_name": "Jodie L. Guest", + "author_inst": "Emory University" + }, + { + "author_name": "Amy Webb-Girard", + "author_inst": "Emory University" + }, + { + "author_name": "Juan S. Leon", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.23.21262499", "rel_title": "Comparative analyses of all FDA EUA-approved rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation", @@ -611588,33 +611815,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.22.21262447", - "rel_title": "A Lagrangian Approach Towards Quantitative Analysis Of Flow-mediated Infection Transmission In Indoor Spaces With Application To SARS-COV-2", - "rel_date": "2021-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.22.21262447", - "rel_abs": "The ongoing SARS-CoV-2 (Covid-19) pandemic has ushered an unforeseen level of global health and economic burden. As a respiratory infection, Covid-19 is known to have a dominant airborne transmission modality, wherein fluid flow plays a central role. Quantification of complex non-intuitive dynamics and transport of pathogen laden respiratory particles in indoor flows has been of specific interest. Here we present a Lagrangian computational approach towards quantification of human-to-human exposure quantifiers, and identification of pathways by which flow organizes transmission. We develop a Lagrangian viral exposure index in a parametric form, accounting for key parameters such as building and layout, ventilation, occupancy, biological variables. We also employ a Lagrangian computation of the Finite Time Lyapunov Exponent field to identify hidden patterns of transport. A systematic parametric study comprising a set of 120 simulations, yielding a total of 1,320 different exposure index computations are presented. Results from these simulations enable: (a) understanding the otherwise hidden ways in which air flow organizes the long-range transport of such particles; and (b) translating the micro-particle transport data into a quantifier for understanding infection exposure risks.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Joseph Wilson", - "author_inst": "University of Colorado Boulder" - }, - { - "author_name": "Shelly L Miller", - "author_inst": "University of Colorado Boulder" - }, - { - "author_name": "Debanjan Mukherjee", - "author_inst": "University of Colorado Boulder" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.22.21262186", "rel_title": "Temporal Increase in Neutralization Potency of SARS-CoV-2 Antibodies and Reduced Viral Variant Escape after Sputnik V Vaccination", @@ -612023,6 +612223,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.19.21262139", + "rel_title": "Predominance of antibody-resistant SARS-CoV-2 variants in vaccine breakthrough cases from the San Francisco Bay Area, California", + "rel_date": "2021-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.19.21262139", + "rel_abs": "Associations between vaccine breakthrough cases and infection by SARS coronavirus 2 (SARS-CoV-2) variants have remained largely unexplored. Here we analyzed SARS-CoV-2 whole-genome sequences and viral loads from 1,373 persons with COVID-19 from the San Francisco Bay Area from February 1 to June 30, 2021, of which 125 (9.1%) were vaccine breakthrough infections. Fully vaccinated were more likely than unvaccinated persons to be infected by variants carrying mutations associated with decreased antibody neutralization (L452R, L452Q, E484K, and/or F490S) (78% versus 48%, p = 1.96e-08), but not by those associated with increased infectivity only (N501Y) (85% versus 77%, p = 0.092). Differences in viral loads were non-significant between unvaccinated and fully vaccinated persons overall (p = 0.99) and according to lineage (p = 0.09 - 0.78). Viral loads were significantly higher in symptomatic as compared to asymptomatic vaccine breakthrough cases (p < 0.0001), and symptomatic vaccine breakthrough infections had similar viral loads to unvaccinated infections (p = 0.64). In 5 cases with available longitudinal samples for serologic analyses, vaccine breakthrough infections were found to be associated with low or undetectable neutralizing antibody levels attributable to immunocompromised state or infection by an antibody-resistant lineage. Taken together, our results suggest that vaccine breakthrough infecions are overrepresnted by circulating antibody-resistant SARS-CoV-2 variants, and that symptomatic breakthrough infections may potentially transmit COVID-19 as efficiently as unvaccinated infections, regardless of the infecting lineage.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Venice Servellita", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alicia Sotomayor-Gonzalez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Amelia Gliwa", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Erika Torres", + "author_inst": "Color Genomics" + }, + { + "author_name": "Noah Brazer", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alicia Zhou", + "author_inst": "Color Genomics" + }, + { + "author_name": "Katherine Hernandez", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Madeline Sankaran", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Baolin Wang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Daniel Wong", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Candace Wang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Yueyuan Zhang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kevin Reyes", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Dustin Glasner", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Wayne Deng", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jessica Streithorst", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Steve Miller", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Edwin Frias", + "author_inst": "Abbott Laboratories" + }, + { + "author_name": "John Hackett", + "author_inst": "Abbott Laboratories" + }, + { + "author_name": "Susan Philip", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Scott Topper", + "author_inst": "Color Genomics" + }, + { + "author_name": "Darpun Sachdev", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Charles Y Chiu", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.24.21262415", "rel_title": "Comparing SARS-CoV-2 natural immunity to vaccine-induced immunity: reinfections versus breakthrough infections", @@ -613589,41 +613896,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.23.21262114", - "rel_title": "Child Mortality in England During the First Year of the COVID-19 Pandemic", - "rel_date": "2021-08-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262114", - "rel_abs": "OBJECTIVESThe aim of this analysis was to quantify the relative risk of childhood deaths across the whole of England during the first year of the COVID pandemic, compared to a similar period of 2019.\n\nDESIGNThis work is based on data collected by the National Child Mortality Database (NCMD) which collates data on all children who die in England. The number of deaths, and their characteristics, from 1st April 2020 until 31st of March 2021 (2020-21), were compared to those from the same period of 2019-20. Relative risk and excess mortality were derived for deaths in 2020-21 vs 2019-20.\n\nSETTINGAll deaths reported to NCMD in England of children under 18 years of age, between April 2019 and March 2021.\n\nPARTICIPANTS6490 deaths of children, under the age of 18 years, reported to the NCMD over the study period.\n\nRESULTSChildren who died between April 2020 and March 2021 had similar demographics to those who died in 2019-20. Overall, there were 356 (198 to 514) fewer deaths in 2020-21 than in 2019-20 (RR 0.90 (0.85-0.94), p<0.001). Repeating the analysis by category of death, suggested that deaths from infection (RR 0.49 (0.38-0.64)) and from other underlying medical conditions (RR 0.75 (0.68-0.82)) were lower in 2020-21 than 2019-20, and weak evidence (p=0.074) that this was also true of deaths from substance abuse.\n\nCONCLUSIONSChildhood mortality in England during the first year of the SARS-CoV-2 pandemic was the lowest on record, with over 300 fewer deaths than the preceding 12 months. The greatest reduction was seen in children less than 10 years old. It is important that we learn from this effect, that potentially offers alternative ways to improve the outcome for the most vulnerable children in our society.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "David E Odd", - "author_inst": "Cardiff University" - }, - { - "author_name": "Sylvia Stoianova", - "author_inst": "Unversity of Bristol" - }, - { - "author_name": "Tom Williams", - "author_inst": "Unversity of Bristol" - }, - { - "author_name": "Peter Fleming", - "author_inst": "University of Bristol" - }, - { - "author_name": "Karen Luyt", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.08.17.21261993", "rel_title": "Segregation of children into small groups for in-person learning during the COVID-19 pandemic", @@ -613776,6 +614048,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.16.21262150", + "rel_title": "The IHME vs Me: Modeling USA CoVID-19 Spread, Early Data to the Fifth Wave", + "rel_date": "2021-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.16.21262150", + "rel_abs": "Epidemiologists have never had such high-quality real-time pandemic data. Modeling CoVID-19 pandemic data became a predictive tool in-stead of an afterwards analysis. How early CoVID-19 model predictions impacted US Government policies and practices is first reviewed here as an important part of the pandemic history. It spurred independent modeling efforts, such as this, to help develop a better understanding of CoVID-19 spread, and to provide a substitute for the IHME (Institute for Health Metrics & Evaluation, U. Washington) 4-month predictions for the expected pandemic evolution, which they had to revise every couple of weeks. Our alternative model, which was developed over the course of several earlier medrxiv.org preprints, is shown here to provide a good description for the entire USA CoVID-19 pandemic to date, covering: (1) the original CoVID-19 wave [3/21/20-6/07/20], (2) the Summer 2020 Resurgence [6/07/20-9/25/20], (3) the large Winter 2020 Resurgence [9/25/20-3/19/21], (4) a small Spring 2021 \"Fourth Wave\", [3/19/21-6/07/21], and (5) the present-day Summer 2021 \"Fifth Wave\" [6/07/21-present], which the USA is now in the midst of. Our analysis of the initial \"Fifth Wave\" data shows that this wave presently has the capacity to infect virtually all susceptible non-vaccinated persons who practice NO Mask-Wearing and minimal Social Distancing.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Genghmun Eng", + "author_inst": "Retired Scientist" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.18.21262061", "rel_title": "Closed Doors: Predictors of Stress, Anxiety, Depression, and PTSD During the Onset of COVID-19 Pandemic in Brazil", @@ -615391,53 +615682,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.08.23.457314", - "rel_title": "Switching of OAS1 splicing isoforms mitigates SARS-CoV-2 infection", - "rel_date": "2021-08-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.23.457314", - "rel_abs": "BackgroundThe rapidly accumulating disease susceptibility information collected from coronavirus disease (COVID-19) patient genomes must be urgently utilized to develop therapeutic interventions for SARS-CoV-2 infection. Chromosome 12q24.13, which encodes the 2-5-oligoadenylate synthetase (OAS) family of proteins that sense viral genomic RNAs and trigger an antiviral response, is identified as one of the genomic regions that contains SNPs associated with COVID-19 severity. A high-risk SNP identified at the splice acceptor site of OAS1 exon 6 is known to change the proportions of the various splicing isoforms and the activity of the enzyme.\n\nMethodsWe employed in-silico motif search and RNA pull-down assay to define a factor responsible for the OAS1 splicing. Next, we rationally selected a candidate for slicing modulator to modulate this splicing.\n\nResultsWe found that inhibition of CDC-like kinase with a small chemical compound induces switching of OAS1 splice isoforms in human lung cells. In this condition, increased resistance to SARS-CoV-2 infection, enhanced RNA degradation, and transcriptional activation of interferon {beta}1, were also observed.\n\nConclusionsThe results indicate the possibility of using chemical splicing modifiers aided by genome-based precision medicine to boost the innate immune response against SARS-CoV-2 infection.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Kei Iida", - "author_inst": "Kyoto University" - }, - { - "author_name": "Masahiko Ajiro", - "author_inst": "Kyoto University" - }, - { - "author_name": "Yukiko Muramoto", - "author_inst": "Kyoto University" - }, - { - "author_name": "Toru Takenaga", - "author_inst": "Kyoto University" - }, - { - "author_name": "Masatsugu Denawa", - "author_inst": "Kyoto University" - }, - { - "author_name": "Ryo Kurosawa", - "author_inst": "Kyoto University" - }, - { - "author_name": "Takeshi Noda", - "author_inst": "Kyoto University" - }, - { - "author_name": "Masatoshi Hagiwara", - "author_inst": "Kyoto University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.08.19.21262323", "rel_title": "EFFECT OF EARLY TREATMENT WITH FLUVOXAMINE ON RISK OF EMERGENCY CARE AND HOSPITALIZATION AMONG PATIENTS WITH COVID-19: THE TOGETHER RANDOMIZED PLATFORM CLINICAL TRIAL", @@ -615858,6 +616102,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.08.23.457408", + "rel_title": "Deep immune profiling of the maternal-fetal interface with mild SARS-CoV-2 infection", + "rel_date": "2021-08-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.23.457408", + "rel_abs": "Pregnant women are an at-risk group for severe COVID-19, though the majority experience mild/asymptomatic disease. Although severe COVID-19 has been shown to be associated with immune activation at the maternal-fetal interface even in the absence of active viral replication, the immune response to asymptomatic/mild COVID-19 remains unknown. Here, we assessed immunological adaptations in both blood and term decidua from 9 SARS-exposed pregnant women with asymptomatic/mild disease and 15 pregnant SARS-naive women. In addition to selective loss of tissue-resident decidual macrophages, we report attenuation of antigen presentation and type I IFN signaling but upregulation of inflammatory cytokines and chemokines in blood monocyte derived decidual macrophages. On the other hand, infection was associated with remodeling of the T cell compartment with increased frequencies of activated CD69+ tissue-resident T cells and decreased abundance of Tregs. Interestingly, frequencies of cytotoxic CD4 and CD8 T cells increased only in the blood, while CD8 effector memory T cells were expanded in the decidua. In contrast to decidual macrophages, signatures of type I IFN signaling were increased in decidual T cells. Finally, T cell receptor diversity was significantly reduced with infection in both compartments, albeit to a much greater extent in the blood. The resulting aberrant immune activation in the placenta, even with asymptomatic disease may alter the exquisitely sensitive developing fetal immune system, leading to long-term adverse outcomes for offspring.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Suhas Sureshchandra", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Michael Z. Zulu", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Brianna Doratt", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Allen Jankeel", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Delia Tifrea", + "author_inst": "University of California,Irvine" + }, + { + "author_name": "Robert A Edwards", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Monica Rincon", + "author_inst": "Oregon Health and Sciences University" + }, + { + "author_name": "Nicole E. Marshall", + "author_inst": "Oregon Health and Science University" + }, + { + "author_name": "Ilhem Messaoudi", + "author_inst": "University of California Irvine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.08.23.457328", "rel_title": "Presence and Stability of SARS-CoV-2 on Environmental Currency and Money Cards", @@ -617357,65 +617652,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.19.21262303", - "rel_title": "Using routine emergency department data for syndromic surveillance of acute respiratory illness before and during the COVID-19 pandemic in Germany, week 10-2017 and 10-2021", - "rel_date": "2021-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.19.21262303", - "rel_abs": "BackgroundThe Coronavirus disease 2019 (COVID-19) pandemic expanded the need for timely information on acute respiratory illness on the population level.\n\nAimWe explored the potential of routine emergency department data for syndromic surveillance of acute respiratory illness in Germany.\n\nMethodsWe included routine attendance data from emergency departments who continuously transferred data between week 10-2017 and 10-2021, with ICD-10 codes available for >75% of the attendances. Case definitions for acute respiratory illness (ARI), severe ARI (SARI), influenza-like illness (ILI), respiratory syncytial virus disease (RSV) and COVID-19 were based on a combination of ICD-10 codes, and/or chief complaints, sometimes combined with information on hospitalisation and age.\n\nResultsWe included 1,372,958 attendances from eight emergency departments. The number of attendances dropped in March 2020, increased during summer, and declined again during the resurge of COVID-19 cases in autumn and winter of 2020/2021. A pattern of seasonality of acute respiratory infections could be observed. By using different case definitions (i.e. for ARI, SARI, ILI, RSV) both the annual influenza seasons in the years 2017-2020 and the dynamics of the COVID-19 pandemic in 2020-2021 were apparent. The absence of the 2020/2021 flu season was visible, parallel to the resurge of COVID-19 cases. The percentage SARI among ARI cases peaked in April-May 2020 (17%) and November 2020-January 2021 (14%).\n\nConclusionSyndromic surveillance using routine emergency department data has the potential to monitor the trends, timing, duration, magnitude and severity of illness caused by respiratory viruses, including both influenza and SARS-CoV-2.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "T Sonia Boender", - "author_inst": "Robert Koch Institute, Berlin, Germany" - }, - { - "author_name": "Wei Cai", - "author_inst": "Robert Koch Institute, Berlin, Germany" - }, - { - "author_name": "Madlen Schranz", - "author_inst": "Robert Koch Institute; Charite Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt Universitaet zu Berlin, Institute of Publ" - }, - { - "author_name": "Theresa Kocher", - "author_inst": "Robert Koch Institute, Berlin, Germany" - }, - { - "author_name": "Birte Wagner", - "author_inst": "Robert Koch Institute, Berlin, Germany" - }, - { - "author_name": "Alexander Ullrich", - "author_inst": "Robert Koch Institute, Berlin, Germany" - }, - { - "author_name": "Silke Buda", - "author_inst": "Robert Koch Institute, Berlin, Germany" - }, - { - "author_name": "Rebecca Zoellner", - "author_inst": "Health Protection Authority, Frankfurt am Main, Germany" - }, - { - "author_name": "Felix Greiner", - "author_inst": "Department of Trauma Surgery, Otto von Guericke University Magdeburg; AKTIN Emergency Department Data Registry; Institute for Occupational and Maritime Medicine" - }, - { - "author_name": "Michaela Diercke", - "author_inst": "Robert Koch Institute, Berlin, Germany" - }, - { - "author_name": "Linus Grabenhenrich", - "author_inst": "Robert Koch Institute, Berlin, Germany" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.20.21262364", "rel_title": "Effect of familiarity with COVID-19 infection--history of infection or close contact--on outing behaviors when a state of emergency is declared", @@ -617640,6 +617876,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.14.21262042", + "rel_title": "Longitudinal monitoring of SARS-CoV-2-specific immune responses", + "rel_date": "2021-08-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.14.21262042", + "rel_abs": "The Lower Austrian Wachau region was an early COVID-19 hotspot of infection. As previously reported, in June 2020, after the first peak of infections, we determined that 8.5% and 9.0% of the participants in Wei{beta}enkirchen and surrounding communities in the Wachau region were positive for SARS-CoV-2-specific immunoglobulin G (IgG) and immunoglobulin A (IgA) antibodies, respectively. Here, we present novel data obtained eight months later (February 2021) from Wei{beta}enkirchen, after the second peak of infection, with 25.0% (138/552) and 23.6% (130/552) of participants that are positive for IgG and IgA, respectively. In participants with previous IgG/IgA positivity (June 2020), we observed a 24% reduction in IgG levels, whereas the IgA levels remained stable in February 2021. This subgroup was further analyzed for SARS-CoV-2-induced T cell activities. Although 76% (34/45) and 76% (34/45) of IgG positive and IgA positive participants, respectively, showed specific T cell activities, those were not significantly correlated with the levels of IgG or IgA. Thus, the analyses of antibodies cannot surrogate the measurement of T cell activities. For a comprehensive view on SARS-CoV-2-triggered immune responses, the measurement of different classes of antibodies should be complemented with the determination of T cell activities.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Heike Rebholz", + "author_inst": "Danube Private University" + }, + { + "author_name": "Ralf J. Braun", + "author_inst": "Danube Private University" + }, + { + "author_name": "Titas Saha", + "author_inst": "Danube Private University" + }, + { + "author_name": "Oliver Harzer", + "author_inst": "Danube Private University" + }, + { + "author_name": "Miriam Schneider", + "author_inst": "Danube Private University" + }, + { + "author_name": "Dennis Ladage", + "author_inst": "Danube Private University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.15.21262087", "rel_title": "The impact of ongoing COVID-19 lockdown on family finances and mental health", @@ -619127,33 +619402,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.13.21261983", - "rel_title": "Estimating data-driven COVID-19 mitigation strategies for safe university reopening", - "rel_date": "2021-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.13.21261983", - "rel_abs": "After one pandemic year of remote or hybrid instructional modes, universities in the United States are now planning for an in-person fall semester in 2021. However, it is uncertain what the vaccination rate will look like after students, faculty, and staff return to campus. To help inform university-reopening policies, we collected survey data on social contact patterns and developed an agent-based model to simulate the spread of COVID-19 in university settings. In this paper, we aim to identify the immunity threshold that, if exceeded, would lead to a relatively safe on-campus experience for the university population. With relaxed non-pharmaceutical interventions, we estimated that immunity in at least 60% of the university population is needed for safe university reopening. Still, attention needs to be paid to extreme events that could lead to huge infection size spikes. At an immune level of 60%, continuing non-pharmaceutical interventions, such as wearing masks, could lead to an 89% reduction in the maximum cumulative infection, which reflects the possible non-negligible infection size from extreme events.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Qihui Yang", - "author_inst": "Kansas State University" - }, - { - "author_name": "Don M. Gruenbacher", - "author_inst": "Kansas State University" - }, - { - "author_name": "Caterina M. Scoglio", - "author_inst": "Kansas State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.13.21261151", "rel_title": "A systematic review of the impact of the Alpha and Gamma variants of concern on hospitalization and symptomatic rate of SARS-CoV-2", @@ -619498,6 +619746,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.13.21262039", + "rel_title": "A sensitive and rapid wastewater test for SARS-COV-2 and its use for the early detection of a cluster of cases in a remote community", + "rel_date": "2021-08-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.13.21262039", + "rel_abs": "Throughout the COVID-19 pandemic, wastewater surveillance has been used to monitor trends in SARS-CoV-2 prevalence in the community. A major challenge in establishing wastewater surveillance programs, especially in remote areas, is the need for a well-equipped laboratory for sample analysis. Currently, no options exist for rapid, sensitive, mobile, and easy-to-use wastewater tests for SARS-CoV-2. The performance of the GeneXpert System, which offers cartridge-based, rapid molecular clinical testing for SARS-CoV-2 in a portable platform, was evaluated using wastewater as the input. The GeneXpert demonstrated a SARS-CoV-2 limit of detection in wastewater below 32 copies/mL with a sample processing time of less than an hour. Using wastewater samples collected from multiple sites across Canada during February and March 2021, a high overall agreement (97.8%) was observed between the GeneXpert assay and laboratory-developed tests regarding the presence or absence of SARS-CoV-2. Additionally, with the use of centrifugal filters the detection threshold of the GeneXpert system was improved to <10 copies/mL in wastewater. Finally, to support on-site wastewater surveillance, GeneXpert testing was implemented in Yellowknife, a remote community in Northern Canada where its use successfully alerted public health authorities to undetected transmission of COVID-19. The identification of SARS-CoV-2 in wastewater triggered clinical testing of recent travelers and identification of new COVID-19 cases/clusters. Taken together, these results suggest the GeneXpert is a viable option for surveillance of SARS-CoV-2 in wastewater in locations that do not have access to established testing laboratories.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jade Daigle", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Kathleen Racher", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Justin Hazenberg", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Allan Yeoman", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Heather Hannah", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Diep Duong", + "author_inst": "Government of the Northwest Territories" + }, + { + "author_name": "Umar Mohammed", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Dave Spreitzer", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Branden S. J. Gregorchuk", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Breanne M. Head", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Adrienne F. A. Meyers", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Paul A. Sandstrom", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Anil Nichani", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "James I. Brooks", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Michael R. Mulvey", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Chand S. Mangat", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Michael G. Becker", + "author_inst": "Public Health Agency of Canada" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.14.21261996", "rel_title": "Association between interruption to medical care and sickness presenteeism during the COVID-19 pandemic: a cross-sectional study in Japan", @@ -620877,33 +621208,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.08.16.21262116", - "rel_title": "To share or not to share - What the general public thinks about global COVID-19 vaccine distribution", - "rel_date": "2021-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.16.21262116", - "rel_abs": "BackgroundDespite ongoing calls for more equity in the global distribution of COVID-19 vaccines, there remains a great disparity between high- and low- or middle-income countries. Based on the principles of distributive justice, we assessed the public opinion on this issue in the United States and Germany as examples for high-income countries with a high potential for redistribution.\n\nMethodsWe conducted representative surveys among the adult population in the United States (N=1,000) and Germany (N=1,003) in June 2021 using two instances of an analytic hierarchy process (AHP) to elicit how the public weighs different principles and criteria according to which the vaccines should be allocated as well as discrete choice experiments to split a limited supply of vaccine doses between a hypothetical high-income and low-income country.\n\nFindingsIn the first AHP, respondents in the United States and Germany gave weight to \"medical urgency\" by 37{middle dot}4% (37{middle dot}2-37{middle dot}5) and 49{middle dot}4% (49{middle dot}2-49{middle dot}5), \"equal access for all\" 32{middle dot}7% (32{middle dot}6-32{middle dot}8) and 25{middle dot}4% (25{middle dot}2-25{middle dot}5), \"production contribution\" 13{middle dot}7% (13{middle dot}6-13{middle dot}8) and 13{middle dot}3% (13{middle dot}2-13{middle dot}4), and \"free market rules\" 16{middle dot}3% (16{middle dot}2-16{middle dot}4) and 12{middle dot}0% (11{middle dot}9-12{middle dot}1), respectively. In the discrete choice experiment responds in the United States split available vaccine doses such that the low-income country on average received 53{middle dot}9 percent (95% CI: 52{middle dot}6-55{middle dot}1). For Germany this number was 57{middle dot}5 percent (95% CI: 56{middle dot}3-58{middle dot}7). The low-income country had three times as many inhabitants as the high-income country. When facing the dilemma where a vulnerable family member was waiting for a vaccine as opposed to when there was no clear self-interest, 20{middle dot}7% (18{middle dot}2-23{middle dot}3) of respondents in the United States and 18{middle dot}2% (15{middle dot}8-20{middle dot}6) in Germany reduced the amount they allocated to the low-income country\n\nInterpretationsThe public in the United States and Germany favours utilitarian and egalitarian distribution principles of vaccines for COVID-19 over the currently prevailing libertarian or meritocratic principles. This implies that political approaches and decision favouring higher levels of redistribution would be supported by the public opinion in these two countries.\n\nFundingGerman Research Foundation DFG RTG 1723.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Matthias Klumpp", - "author_inst": "Georg-August-University of Goettingen" - }, - { - "author_name": "Ida G. Monfared", - "author_inst": "Georg-August-University of Goettingen" - }, - { - "author_name": "Sebastian Vollmer", - "author_inst": "Georg-August-University of Goettingen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.08.18.456880", "rel_title": "Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-care Platform", @@ -621072,6 +621376,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.10.21261836", + "rel_title": "Efficacy and Safety of Ayurveda Intervention AYUSH 64 as add-on therapy for patients with COVID 19 infections: An open labelled, Parallel Group, Randomized controlled clinical trial", + "rel_date": "2021-08-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.10.21261836", + "rel_abs": "The authors have withdrawn this manuscript because they found a serious issue in data-analysis which leads to wrong interpretation of the results. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Pankaj Bhardwaj", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Pawan Kumar Godatwar", + "author_inst": "National Institute of Ayurveda, Jaipur, Rajasthan" + }, + { + "author_name": "Jaykaran Charan", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Sanjeev Sharma", + "author_inst": "National Institute of Ayurveda, Jaipur, Rajasthan" + }, + { + "author_name": "Shazia Shafi", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Nishant Chauhan", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Pratibha Vyas", + "author_inst": "NIIR NCD Jodhpur" + }, + { + "author_name": "Naveen Dutt", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Naresh Midha", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Ramniwas Jalandra", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Meenakshi Sharma", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Vijaya Lakshmi Nag", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + }, + { + "author_name": "Suman Sharma", + "author_inst": "National Institute of Ayurveda, Jaipur, Rajasthan" + }, + { + "author_name": "Sarvesh Kumar Singh", + "author_inst": "National Institute of Ayurveda Jaipur" + }, + { + "author_name": "Praveen Sharma", + "author_inst": "All India Institute of Medical Sciences Jodhpur" + }, + { + "author_name": "Sanjeev Misra", + "author_inst": "All India Institute of Medical Sciences, Jodhpur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.15.21262000", "rel_title": "Seasonal betacoronavirus antibodies expansion post BNT161b2 vaccination associates with reduced SARS-CoV-2 VoCs neutralization", @@ -622583,25 +622966,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2021.08.11.21261903", - "rel_title": "The fomite contribution to the transmission of COVID-19 in the UK: an evolutionary population estimate", - "rel_date": "2021-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261903", - "rel_abs": "A SEIR model with an added fomite term is used to constrain the contribution of fomites to the spread of COVID-19 under the Spring 2020 lockdown in the UK. Assuming uniform priors on the reproduction number in lockdown and the fomite transmission rate, an upper limit is found on the fomite transmission rate of less than 1 contaminated object in 7 per day per infectious person (95% CL). Basing the prior on the reproduction rate during lockdown instead on the CoMix study results for the reduction in social contacts under lockdown, and assuming the reproduction number scales with the number of social contacts, provides a much more restrictive upper limit on the transmission rate by contaminated objects of fewer than 1 in 30 per day per infectious person (95% CL). Applied to postal deliveries and groceries, the upper limit on the fomite transmission rate corresponds to a probability below 1 in 70 (95% CL) that a contaminated object transmits the infection. Fewer than about half (95% CL) of the total number of deaths during the lockdown are found to arise from fomites, and most likely fewer than a quarter. These findings apply only to fomites with a transmission rate that is unaffected by a lockdown.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Avery Meiksin", - "author_inst": "University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.11.21261950", "rel_title": "Emergence of SARS-CoV-2 variant B.1.575.2 containing the E484K mutation in the spike protein in Pamplona (Spain) May-June 2021", @@ -622818,6 +623182,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.08.11.21261946", + "rel_title": "A Novel Convolutional Neural Network for COVID-19 detection and classification using Chest X-Ray images", + "rel_date": "2021-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261946", + "rel_abs": "The early and rapid diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), the main cause of fatal pandemic coronavirus disease 2019 (COVID-19), with the analysis of patients chest X-ray (CXR) images has life-saving importance for both patients and medical professionals. In this research a very simple novel and robust deep-learning convolutional neural network (CNN) model with less number of trainable-parameters is proposed to assist the radiologists and physicians in the early detection of COVID-19 patients. It also helps to classify patients into COVID-19, pneumonia and normal on the bases of analysis of augmented X-ray images. This augmented dataset contains 4803 COVID-19 from 686 publicly available chest X-ray images along with 5000 normal and 5000 pneumonia samples. These images are divided into 80% training and 20 % validation. The proposed CNN model is trained on training dataset and then tested on validation dataset. This model has a promising performance with a mean accuracy of 92.29%, precision of 99.96%, Specificity of 99.85% along with Sensitivity value of 85.92%. The result can further be improved if more data of expert radiologist is publically available.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Muhammad Talha Nafees", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Irshad ullah", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Muhammad Rizwan", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Maaz ullah", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Muhammad Irfanullah Khan", + "author_inst": "University of Engineering and Technology Peshawar" + }, + { + "author_name": "Muhammad Farhan", + "author_inst": "University of Engineering and Technology Peshawar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2021.08.11.21261793", "rel_title": "Development and use analysis of 'gestioemocional.cat', a web app for promoting emotional self-care and access to professional mental health resources during the covid-19 pandemic", @@ -624461,37 +624864,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.13.21262002", - "rel_title": "How did people cope during the COVID-19 pandemic? A Structural Topic Modelling Analysis of Free-Text Data from 11,000 UK Adults", - "rel_date": "2021-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.13.21262002", - "rel_abs": "BackgroundThe COVID-19 pandemic has had substantial impacts on lives across the globe. Job losses have been widespread, and individuals have experienced significant restrictions on their usual activities, including extended isolation from family and friends. While studies suggest population mental health worsened from before the pandemic, not all individuals appear to have experienced poorer mental health. This raises the question of how people managed to cope during the pandemic.\n\nMethodsTo understand the coping strategies individuals employed during the COVID-19 pandemic, we used structural topic modelling, a text mining technique, to extract themes from free-text data on coping from over 11,000 UK adults, collected between 14 October and 26 November 2020.\n\nResultsWe identified 16 topics. The most discussed coping strategy was thinking positively and involved themes of gratefulness and positivity. Other strategies included engaging in activities and hobbies (such as doing DIY, exercising, walking and spending time in nature), keeping routines, and focusing on one day at a time. Some participants reported more avoidant coping strategies, such as drinking alcohol and binge eating. Coping strategies varied by respondent characteristics including age, personality traits and sociodemographic characteristics and some coping strategies, such as engaging in creative activities, were associated with more positive lockdown experiences.\n\nConclusionA variety of coping strategies were employed by individuals during the COVID-19 pandemic. The coping strategy an individual adopted was related to their overall lockdown experiences. This may be useful for helping individuals prepare for future lockdowns or other events resulting in self-isolation.\n\nCorrectionDue to an error in the analytical syntax, in an earlier version of this manuscript (posted August 13, 2021), topic labels in Figure 2 were mixed up. This - and the resulting discussion - have now been corrected.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC=\"FIGDIR/small/21262002v2_fig2.gif\" ALT=\"Figure 2\">\nView larger version (52K):\norg.highwire.dtl.DTLVardef@62f742org.highwire.dtl.DTLVardef@15748b9org.highwire.dtl.DTLVardef@1678a2borg.highwire.dtl.DTLVardef@a04c58_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 2:C_FLOATNO Association between document topic proportion and participants age (+ 95% confidence intervals). Derived from OLS regression models including adjustment for gender, ethnicity, age, education level, living arrangement, psychiatric diagnosis, long-term physical health conditions, self-isolation status, Big-5 personality traits and keyworker status.\n\nC_FIG", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Liam Wright", - "author_inst": "University College London" - }, - { - "author_name": "Meg E Fluharty", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Steptoe", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.11.21261760", "rel_title": "THE EFFECT OF BARICITANIB USAGE ON THE CLINICAL AND BIOCHEMICAL PROFILES OF COVID-19 PATIENTS- A RETROSPECTIVE OBSERVATIONAL STUDY", @@ -624712,6 +625084,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.12.456168", + "rel_title": "SARS-CoV-2 spike opening dynamics and energetics reveal the individual roles of glycans and their collective impact", + "rel_date": "2021-08-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.12.456168", + "rel_abs": "The trimeric spike (S) glycoprotein, which protrudes from the SARS-CoV-2 viral envelope, binds to human ACE2, initiated by at least one protomers receptor binding domain (RBD) switching from a \"down\" (closed) to an \"up\" (open) state. Here, we used large-scale molecular dynamics simulations and two-dimensional replica exchange umbrella sampling calculations with more than a thousand windows and an aggregate total of 160 {micro}s of simulation to investigate this transition with and without glycans. We find that the glycosylated spike has a higher barrier to opening and also energetically favors the down state over the up state. Analysis of the S-protein opening pathway reveals that glycans at N165 and N122 interfere with hydrogen bonds between the RBD and the N-terminal domain in the up state, while glycans at N165 and N343 can stabilize both the down and up states. Finally we estimate how epitope exposure for several known antibodies changes along the opening path. We find that the BD-368-2 antibodys epitope is continuously exposed, explaining its high efficacy.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yui Tik Pang", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Atanu Acharya", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Diane Lynch", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Anna Pavlova", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "James Gumbart", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.08.13.456066", "rel_title": "SARS-CoV-2 Neutralization in Commercial Lots of Plasma-derived Immunoglobulin", @@ -626711,37 +627118,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.10.21261846", - "rel_title": "Impact of the COVID-19 Pandemic on Early Child Cognitive Development: Initial Findings in a Longitudinal Observational Study of Child Health", - "rel_date": "2021-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.10.21261846", - "rel_abs": "ObjectiveTo characterize cognitive function in young children under 3 years of age over the past decade, and test whether children exhibit different cognitive development profiles through the COVID-19 pandemic.\n\nStudy DesignNeurocognitive data (Mullen Scales of Early Learning, MSEL) were drawn from 700 healthy and neurotypically developing children between 2011 to 2021 without reported positive tests or clinical diagnosis of SARS-CoV-2 infection. We compared MSEL composite measures (general cognition, verbal, and non-verbal development) to test if those measured during 2020 and 2021 differed significantly from historical 2011-2019 values. We also compared MSEL values in a sub-cohort comprising infants 0-16 months of age born during the pandemic vs. infants born prior. In all analyses, we also included measures of socioeconomic status, birth outcome history, and maternal stress.\n\nResultsA significant decrease in mean population MSEL measures was observed in 2021 compared to historical references. Infants born during the pandemic exhibited significantly reduced verbal, non-verbal, and overall cognitive performance compared to children born pre-pandemic. Maternal stress was not found to be associated with observed declines but a higher socioeconomic status was found to be protective.\n\nConclusionsResults reveal a striking decline in cognitive performance since the onset of the COVID-19 pandemic with infants born since mid-2020 showing an average decrease of 27-37 points. Further work is merited to understand the underlying causative factors.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sean Deoni", - "author_inst": "Rhode Island Hospital" - }, - { - "author_name": "Jennifer Beauchemin", - "author_inst": "Rhode Island Hospital" - }, - { - "author_name": "Alexandra Volpe", - "author_inst": "Rhode Island Hospital" - }, - { - "author_name": "Viren D'Sa", - "author_inst": "Rhode Island Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.08.10.21261843", "rel_title": "A Comparative Study on the knowledge and attitude of COVID-19 among Urban and Rural populations of Bangladesh.", @@ -626998,6 +627374,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.10.21261847", + "rel_title": "Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021", + "rel_date": "2021-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.10.21261847", + "rel_abs": "BackgroundThe COVID-19 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Eastern Mediterranean Region. Lebanon experienced its largest wave of COVID-19 infections from January to April 2021. Limited genomic surveillance was undertaken, with just twenty six SARS-CoV-2 genomes available for this period, nine of which were from travellers from Lebanon detected by other countries. Additional genome sequencing is thus needed to allow surveillance of variants in circulation.\n\nMethodsNine hundred and five SARS-CoV-2 genomes were sequenced using the ARTIC protocol. The genomes were derived from SARS-CoV-2-positive samples, selected retrospectively from the sentinel COVID-19 surveillance network, to capture diversity of location, sampling time, gender, nationality and age.\n\nResultsAlthough sixteen PANGO lineages were circulating in Lebanon in January 2021, by February there were just four, with the Alpha variant accounting for 97% of samples. In the following two months, all samples contained the Alpha variant. However, this had changed dramatically by June and July, when all samples belonged to the Delta variant.\n\nDiscussionThis study provides a ten-fold increase in the number of SARS-CoV-2 genomes available from Lebanon. The Alpha variant, first detected in the UK, rapidly swept through Lebanon, causing the countrys largest wave to date, which peaked in January 2021. The Alpha variant was introduced to Lebanon multiple times despite travel restrictions, but the source of these introductions remains uncertain. The Delta variant was detected in Gambia in travellers from Lebanon in mid-May, suggesting community transmission in Lebanon several weeks before this variant was detected in the country. Prospective sequencing in June/July 2021 showed that the Delta variant had completely replaced the Alpha variant in under six weeks.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Georgi Merhi", + "author_inst": "Lebanese American University, Department of Natural Sciences, School of Arts and Sciences, Byblos-Lebanon" + }, + { + "author_name": "Alexander J Trotter", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Leonardo de Oliveira Martins", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Jad Koweyes", + "author_inst": "Lebanese American University, Department of Natural Sciences, School of Arts and Sciences, Byblos-Lebanon" + }, + { + "author_name": "Thanh Le-Viet", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Hala Abou Naja", + "author_inst": "Ministry of Public Health, Epidemiologial Surveillance Program, Museum square, Beirut, Lebanon" + }, + { + "author_name": "Mona Al Buaini", + "author_inst": "National Influenza Centre Research Laboratory, Rafic Hariri University Hospital, Beirut, Lebanon" + }, + { + "author_name": "Sophie J Prosolek", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Nabil-Fareed Alikhan", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Martin Lott", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Tatiana Tohmeh", + "author_inst": "Ministry of Public Health, Epidemiologial Surveillance Program, Museum square, Beirut, Lebanon" + }, + { + "author_name": "Bassam Badran", + "author_inst": "Laboratory of Molecular Biology and Cancer Immunology, Faculty of Sciences, Lebanese University" + }, + { + "author_name": "Orla J Jupp", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Sarah Gardner", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Matthew W Felgate", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Kate A Makin", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Janine M Wilkinson", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Rachael Stanley", + "author_inst": "Norfolk and Norwich University Hospital, Norwich, Norfolk, UK" + }, + { + "author_name": "Abdul K Sesay", + "author_inst": "MRC Unit The Gambia at LHSTM, Fajara, Gambia" + }, + { + "author_name": "Mark A Webber", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Rose K Davidson", + "author_inst": "University of East Anglia, Norwich, Norfolk, UK" + }, + { + "author_name": "Nada Ghosn", + "author_inst": "Ministry of Public Health, Epidemiologial Surveillance Program, Museum square, Beirut, Lebanon" + }, + { + "author_name": "Mark Pallen", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Hamad Hasan", + "author_inst": "Ministry of Public Health, Beirut, Lebanon" + }, + { + "author_name": "Andrew J Page", + "author_inst": "Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, UK" + }, + { + "author_name": "Sima Tokajian", + "author_inst": "Lebanese American University, Department of Natural Sciences, School of Arts and Sciences, Byblos-Lebanon" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.10.21261860", "rel_title": "Heterogeneity in COVID-19 Pandemic-Induced Lifestyle Stressors Predicts Mental Health in Adults and Children in the US and UK", @@ -628588,45 +629083,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.09.21261807", - "rel_title": "Ignoring spatial heterogeneity in drivers of SARS-CoV-2 transmission in the US will impede sustained elimination", - "rel_date": "2021-08-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.09.21261807", - "rel_abs": "To dissect the transmission dynamics of SARS-CoV-2 in the United States, we integrate parallel streams of high-resolution data on contact, mobility, seasonality, vaccination and seroprevalence within a metapopulation network. We find the COVID-19 pandemic in the US is characterized by a geographically localized mosaic of transmission along an urban-rural gradient, with many outbreaks sustained by between-county transmission. We detect a dynamic tension between the spatial scale of public health interventions and population susceptibility as pre-pandemic contact is resumed. Further, we identify regions rendered particularly at risk from invasion by variants of concern due to spatial connectivity. These findings emphasize the public health importance of accounting for the hierarchy of spatial scales in transmission and the heterogeneous impacts of mobility on the landscape of contagion risk.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Zachary Susswein", - "author_inst": "Georgetown University" - }, - { - "author_name": "Eugenio Valdano", - "author_inst": "INSERM" - }, - { - "author_name": "Tobias Brett", - "author_inst": "University of Georgia, Athens" - }, - { - "author_name": "Pej Rohani", - "author_inst": "University of Georgia, Athens" - }, - { - "author_name": "Vittoria Colizza", - "author_inst": "INSERM" - }, - { - "author_name": "Shweta Bansal", - "author_inst": "Georgetown University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.09.21261809", "rel_title": "Using Novel, Agent-Based Periodic Mobility Model with Super Spreaders to Analyze Vaccination Strategies for COVID-19", @@ -628839,6 +629295,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.09.21261555", + "rel_title": "Mixed invasive molds among COVID-19 patients", + "rel_date": "2021-08-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.09.21261555", + "rel_abs": "PurposeDue to surge in COVID cases during the second wave of the COVID pandemic, the healthcare system collapsed in India with shortage of hospital beds, injudicious use of steroids and other immunomodulators, and poor glycaemic monitoring among a population with pre-existing risk of diabetes. Fungal epidemic was announced amid COVID pandemic with several cases of COVID-associated mucormycosis and aspergillosis being reported. But, there is no data regarding mixed fungal infections in COVID patients.\n\nMaterials and MethodsThe study presented a series of ten consecutive cases with dual invasive molds in patients infected with SARS-CoV-2. Among patients hospitalized with the diagnosis of COVID in May 2021 at a tertiary care center in North India, ten microbiologically confirmed dual/mixed COVID-associated mucor-aspergillosis (CAMA) were evaluated.\n\nResultsAll patients were diabetics with the majority having severe COVID pneumonia (6/10, 60%) either on admission or in the past one month, whilst two were each of moderate (20%) and mild (20%) categories of COVID. The patients were managed with amphotericin-B along with surgical intervention. In this case series, 70% of all CAMA (Rhizopus arrhizus with Aspergillus flavus in seven and Aspergillus fumigatus in three patients) patients survived, connoting the critical importance of a high index of clinical suspicion and accurate microbiological diagnosis for managing invasive molds.\n\nConclusionsMixed fungal infections i.e. CAMA during COVID and post-COVID periods may be an emerging disease. This outbreak is seen particularly in such patients with uncontrolled diabetes, on steroids, or cocktail therapy, or living in unhygienic environments.We believe that our findings would help gain a better insight into the risk and progression of invasive fungal mixed infections among COVID patients and thus play a pivotal role in diagnosing, classifying, and implementing an effective management strategy for treating similar cases in the future.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Vanya Singh", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Amber Prasad", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Prasan Kumar Panda", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Manjunath Totaganti", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Amit Tyagi", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Abhinav Thaduri", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Shalini Rao", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Mukesh Bairwa", + "author_inst": "AIIMS Rishikesh" + }, + { + "author_name": "Ashok K Singh", + "author_inst": "AIIMS Rishikesh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.05.21261562", "rel_title": "Cryptic Transmission of the Delta Variant AY.3 Sublineage of SARS-CoV-2 among Fully Vaccinated Patients on an Inpatient Ward", @@ -630366,73 +630873,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.08.21261673", - "rel_title": "Limited genomic reconstruction of SARS-CoV-2 transmission history within local epidemiological clusters", - "rel_date": "2021-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.08.21261673", - "rel_abs": "A detailed understanding of how and when SARS-CoV-2 transmission occurs is crucial for designing effective prevention measures. Other than contact tracing, genome sequencing provides information to help infer who infected whom. However, the effectiveness of the genomic approach in this context depends on both (high enough) mutation and (low enough) transmission rates. Today, the level of resolution that we can obtain when describing SARS-CoV-2 outbreaks using just genomic information alone remains unclear. In order to answer this question, we sequenced 49 SARS-CoV-2 patient samples from ten local clusters for which partial epidemiological information was available, and inferred transmission history using genomic variants. Importantly, we obtained high-quality genomic data, sequencing each sample twice and using unique barcodes to exclude cross-sample contamination. Phylogenetic and cluster analyses showed that consensus genomes were generally sufficient to discriminate among independent transmission clusters. However, levels of intrahost variation were low, which prevented in most cases the unambiguous identification of direct transmission events. After filtering out recurrent variants across clusters, the genomic data were generally compatible with the epidemiological information but did not support specific transmission events over possible alternatives. We estimated the effective transmission bottleneck size to be 1-2 viral particles for sample pairs whose donor-recipient relationship was likely. Our analyses suggest that intrahost genomic variation in SARS-CoV-2 might be generally limited and that homoplasy and recurrent errors complicate identifying shared intrahost variants. Reliable reconstruction of direct SARS-CoV-2 transmission based solely on genomic data seems hindered by a slow mutation rate, potential convergent events, and technical artifacts. Detailed contact tracing seems essential in most cases to study SARS-CoV-2 transmission at high resolution.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Pilar Gallego-Garc\u00eda", - "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain" - }, - { - "author_name": "Nair Varela", - "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain" - }, - { - "author_name": "Nuria Est\u00e9vez-G\u00f3mez", - "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain" - }, - { - "author_name": "Loretta De Chiara", - "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain" - }, - { - "author_name": "Iria Fern\u00e1ndez-Silva", - "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain" - }, - { - "author_name": "Diana Valverde", - "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain" - }, - { - "author_name": "Nicolae Sapoval", - "author_inst": "Department of Computer Science, Rice University, Houston, TX, USA" - }, - { - "author_name": "Todd Treangen", - "author_inst": "Department of Computer Science, Rice University, Houston, TX, USA" - }, - { - "author_name": "Benito Regueiro", - "author_inst": "Department of Microbiology, Complexo Hospitalario Universitario de Vigo (CHUVI), Sergas, Vigo, Spain" - }, - { - "author_name": "Jorge Julio Cabrera-Alvargonz\u00e1lez", - "author_inst": "Department of Microbiology, Complexo Hospitalario Universitario de Vigo (CHUVI), Sergas, Vigo, Spain" - }, - { - "author_name": "V\u00edctor del Campo", - "author_inst": "Department of Preventive Medicine, Complexo Hospitalario Universitario de Vigo (CHUVI), Sergas, Vigo, Spai" - }, - { - "author_name": "Sonia P\u00e9rez", - "author_inst": "Department of Microbiology, Complexo Hospitalario Universitario de Vigo (CHUVI), Sergas, Vigo, Spain" - }, - { - "author_name": "David Posada", - "author_inst": "CINBIO, Universidade de Vigo, 36310 Vigo, Spain" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.08.21261357", "rel_title": "High vaccine effectiveness against COVID-19 infection and severe disease among residents and staff of long-term care facilities in Norway, November - June 2021", @@ -630709,6 +631149,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.08.09.455656", + "rel_title": "Reprogramming of the intestinal epithelial-immune cell interactome during SARS-CoV-2 infection", + "rel_date": "2021-08-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.09.455656", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents an unprecedented worldwide health problem. Although the primary site of infection is the lung, growing evidence points towards a crucial role of the intestinal epithelium. Yet, the exact effects of viral infection and the role of intestinal epithelial-immune cell interactions in mediating the inflammatory response are not known. In this work, we apply network biology approaches to single-cell RNA-seq data from SARS-CoV-2 infected human ileal and colonic organoids to investigate how altered intracellular pathways upon infection in intestinal enterocytes leads to modified epithelial-immune crosstalk. We point out specific epithelial-immune interactions which could help SARS-CoV-2 evade the immune response. By integrating our data with existing experimental data, we provide a set of epithelial ligands likely to drive the inflammatory response upon infection. Our integrated analysis of intra- and inter-cellular molecular networks contribute to finding potential drug targets, and suggest using existing anti-inflammatory therapies in the gut as promising drug repurposing strategies against COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Martina Poletti", + "author_inst": "Earlham Institute / Quadram Institute" + }, + { + "author_name": "Agatha Treveil", + "author_inst": "Earlham Institute, Norwich, UK" + }, + { + "author_name": "Leila Gul", + "author_inst": "Earlham Institute, Norwich UK" + }, + { + "author_name": "Dezso Modos", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Matthew Madgwick", + "author_inst": "Earlham Institute" + }, + { + "author_name": "Marton Olbei", + "author_inst": "Earlham Institute, Norwich, UK" + }, + { + "author_name": "Balazs Bohar", + "author_inst": "Earlham Institute, Norwich, UK" + }, + { + "author_name": "Alberto Valdeolivas", + "author_inst": "Heidelberg University, Heidelberg, Germany" + }, + { + "author_name": "Denes Turei", + "author_inst": "Heidelberg University, Heidelberg, Germany" + }, + { + "author_name": "Bram Verstockt", + "author_inst": "KU Leuven, Leuven, Belgium" + }, + { + "author_name": "Sergio Triana", + "author_inst": "European Molecular Biology Laboratory, Heidelberg, Germany" + }, + { + "author_name": "Theodore Alexandrov", + "author_inst": "University of California San Diego, La Jolla, CA, USA" + }, + { + "author_name": "Julio Saez-Rodriguez", + "author_inst": "Heidelberg University, Heidelberg, Germany" + }, + { + "author_name": "Megan L Stanifer", + "author_inst": "Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Steeve Boulant", + "author_inst": "Heidelberg University Hospital, Heidelberg, Germany" + }, + { + "author_name": "Tamas Korcsmaros", + "author_inst": "Earlham Institute / Quadram Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.08.08.455468", "rel_title": "A Tethered Ligand Assay to Probe SARS-CoV-2:ACE2 Interactions", @@ -632424,53 +632943,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.06.21261531", - "rel_title": "Awake Prone Position in Hypoxemic Patients with Coronavirus Disease 19 (COVI-PRONE): A Study protocol and Statistical Analysis Plan for Randomized Clinical Trial", - "rel_date": "2021-08-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.06.21261531", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19), may progress to respiratory failure requiring invasive mechanical ventilation. Due to ventilator shortage and healthcare systems strain, affordable interventions such as awake prone positioning has been used to improve oxygenation, however, the effect of this intervention on patient-important outcomes is uncertain. The COVI-PRONE trial aims to determine if awake prone positioning in hypoxemic COVID-19 patients reduces the need for invasive mechanical ventilation.\n\nStudy designA pragmatic, multicenter, international, parallel-group, and stratified randomized controlled trial, aiming to enrol 400 hospitalized adults with COVID-19.\n\nParticipantsThe target population is hospitalized adults with confirmed or suspected COVID-19, hypoxemia that requires [≥]40% oxygen or [≥] 5 L/min by nasal cannula, and abnormal chest x-ray. We will exclude patients with any of the following: immediate need for intubation; altered mental status; contraindication to prone positioning; hemodynamic instability; body mass index > 40 kg/m2; third trimester pregnancy; do not intubate status; previous enrolment or intubation within the same hospital admission; and prone positioning for more than one day prior to randomization.\n\nStudy intervention and controlFollowing informed a priori or deferred consent, eligible patients will be centrally randomized to either the intervention arm (prone positioning) or standard of care (no prone positioning). Patients randomized to the prone position will be required to either self-prone or assist-prone for a total of eight to ten hours per day until they meet pre-specified stopping criteria.\n\nStudy outcomesThe primary outcome is invasive mechanical ventilation at 30-days of randomization. Other outcomes include mortality at 60 days, invasive and non-invasive mechanical ventilation free days at 30 days, hospital length of stay at 60 days, days alive and outside of the hospital at 60 days, complications of proning, and serious adverse events.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Zainab Al Duhailib", - "author_inst": "King Faisal Specialist Hospital & Research Centre" - }, - { - "author_name": "Yaseen Arabi", - "author_inst": "Ministry of National Guard Health Affairs" - }, - { - "author_name": "Sarah Culgin", - "author_inst": "The Research Institute of St. Joseph's Healthcare Hamilton" - }, - { - "author_name": "Jason Weatherald", - "author_inst": "Libin Cardiovascular Institute, University of Calgary and Alberta Health Services" - }, - { - "author_name": "Ken Kuljit S. Parhar", - "author_inst": "University of Calgary and Alberta Health Services" - }, - { - "author_name": "Kate Nelson", - "author_inst": "The Research Institute of St. Joseph's Healthcare Hamilton" - }, - { - "author_name": "Hani Tamim", - "author_inst": "American University of Beirut Medical Center" - }, - { - "author_name": "Waleed Alhazzani", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.08.05.21261616", "rel_title": "Development and utilization of a surrogate SARS-CoV-2 viral neutralization assay to assess mRNA vaccine responses.", @@ -632811,6 +633283,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.08.05.21261627", + "rel_title": "Systematic review protocol exploring the impact of the COVID-19 pandemic on the wellbeing of general practitioners", + "rel_date": "2021-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261627", + "rel_abs": "BackgroundOver recent years chronic stress and burnout have been reported by doctors working in general practice in the UK NHS and internationally. The COVID-19 pandemic has changed general practitioners working lives - adding potential pressures from avoiding infection and addressing pent-up demand for care, but also changing processes such as rapidly taking up remote consultations. To date, there has been a focus on exploring the impact of the pandemic on the wellbeing of hospital clinicians. No registered systematic reviews currently focus on exploring the impact of the pandemic on the mental health and wellbeing of general practitioners.\n\nAims and objectivesTo synthesise the current international evidence base exploring the impact of COVID-19 on the mental health and wellbeing of general practitioners, and which factors are associated with their reported mental health and wellbeing during the pandemic.\n\nMethodsIn this paper we report a systematic review protocol, following PRISMA guidance. In our search strategy we will identify primary research studies or systematic reviews exploring the mental health and wellbeing of general practitioners during the COVID-19 pandemic in four databases (MEDLINE, Embase, PsychInfo and Medrxiv) and Google Scholar. We will hand-search reference lists and grey literature.\n\nTwo reviewers will undertake all stages including study selection, data extraction and quality assessment, with arbitration by a third reviewer where necessary. We will use standardised quality assessment tools to ensure transparency and reduce bias in quality assessment. Depending on the quality of included studies, we may undertake a sensitivity analysis by excluding studies from narrative synthesis that are rated as low quality using the checklists.\n\nWe will describe the findings across studies using narrative thematic data synthesis, and if sufficiently homogenous data are identified, we will pool quantitative findings through meta-analysis.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Laura Jefferson", + "author_inst": "University of York" + }, + { + "author_name": "Su Golder", + "author_inst": "University of York" + }, + { + "author_name": "Veronica Dale", + "author_inst": "University of York" + }, + { + "author_name": "Holly Essex", + "author_inst": "University of York" + }, + { + "author_name": "Elizabeth McHugh", + "author_inst": "University of York" + }, + { + "author_name": "Karen Bloor", + "author_inst": "University of York" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.08.04.21261576", "rel_title": "When do elementary students need masks in school? Model-estimated risk of in-school SARS-CoV-2 transmission and related infections among household members before and after student vaccination", @@ -634326,97 +634837,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.05.21261610", - "rel_title": "Estimation of Total Immunity to SARS-CoV-2 in Texas", - "rel_date": "2021-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261610", - "rel_abs": "Given the underestimate of seroprevalence in the US due to insufficient testing, accurate estimates of population immunity to SARS-CoV-2 or vaccinations do not exist. Although model-based estimates have been proposed, they require inputting unknown parameters such as viral reproduction number, longevity of immune response, and other dynamic factors. In contrast to a model-based approach for estimating population immunity, or simplistic summing of natural- and vaccine-induced immunity, the current study presents a data-driven statistical procedure for estimating the total immunity rate in a region using prospectively collected serological data along with state-level vaccination data. We present a detailed procedure so that efforts can be replicated regionally to inform policy-making decisions relevant to SARS-CoV-2. Specifically, we conducted a prospective longitudinal statewide cohort serological survey with 10,482 participants and more than 14,000 blood samples beginning on September 30, 2020. Along with Department of State Health Services vaccination data, as of July 4, 2021, the estimated percentage of those with naturally occurring antibodies to SARS-CoV-2 in Texas is 35.3% (95% CI = (33.7%, 36.9%) and total estimated immunity is 69.1%. We conclude the seroprevalence of SARS-CoV-2 is 4 times higher than the state-confirmed COVID-19 cases (8.8%). This methodology is integral to pandemic preparedness.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Stacia M Desantis PhD", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "Luis G Leon-Novelo PhD", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "Michael D Swartz PhD", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "Ashraf Yaseen PhD", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "Melissa A Valerio-Shewmaker PhD, MPH", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Brownsville, Brownsville, TX, USA" - }, - { - "author_name": "Frances A Brito MS", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "Jessica A Ross BS", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "Harold W Kohl PhD", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Austin, Austin, TX, USA" - }, - { - "author_name": "Sarah M Messiah PhD", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Dallas, Dallas, TX, USA" - }, - { - "author_name": "Steven H Kelder PhD", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Austin, Austin, TX, USA" - }, - { - "author_name": "Lequing Wu MS", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "Shiming Zhang MS", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "Kimberly A Aguillard DrPH", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "Michael O Gonzalez MS", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - }, - { - "author_name": "Onyinye S OmegaNjemnobi PhD", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Austin, Austin, TX, USA" - }, - { - "author_name": "David Lakey MD", - "author_inst": "University of Texas System, Austin, TX, USA" - }, - { - "author_name": "Jennifer Shuford MD, MPH", - "author_inst": "Texas Department of State Health Services, Austin, TX USA" - }, - { - "author_name": "Stephen Pont MD, MPH", - "author_inst": "Texas Department of State Health Services, Austin, TX USA" - }, - { - "author_name": "Eric Boerwinkle PhD", - "author_inst": "The University of Texas Health Science Center at Houston, School of Public Health in Houston, Houston, TX, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.05.21258160", "rel_title": "HIF1alpha cardioprotection in COVID-19 patients", @@ -634721,6 +635141,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.06.455424", + "rel_title": "Small-molecule ligands can inhibit -1 programmed ribosomal frameshifting in a broad spectrum of coronaviruses", + "rel_date": "2021-08-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.06.455424", + "rel_abs": "Recurrent outbreaks of novel zoonotic coronavirus (CoV) diseases since 2000 have high-lighted the importance of developing therapeutics with broad-spectrum activity against CoVs. Because all CoVs use -1 programmed ribosomal frameshifting (-1 PRF) to control expression of key viral proteins, the frameshift signal in viral mRNA that stimulates -1 PRF provides a promising potential target for such therapeutics. To test the viability of this strategy, we explored a group of 6 small-molecule ligands, evaluating their activity against the frameshift signals from a panel of representative bat CoVs--the most likely source of future zoonoses--as well as SARS-CoV-2 and MERS-CoV. We found that whereas some ligands had notable activity against only a few of the frameshift signals, the serine protease inhibitor nafamostat suppressed -1 PRF significantly in several of them, while having limited to no effect on -1 PRF caused by frameshift signals from other viruses used as negative controls. These results suggest it is possible to find small-molecule ligands that inhibit -1 PRF specifically in a broad spectrum of CoVs, establishing the frameshift signal as a viable target for developing pan-coronaviral therapeutics.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Sneha Munshi", + "author_inst": "University of Alberta" + }, + { + "author_name": "Krishna Neupane", + "author_inst": "University of Alberta" + }, + { + "author_name": "Sandaru M Ileperuma", + "author_inst": "University of Alberta" + }, + { + "author_name": "Matthew TJ Halma", + "author_inst": "University of Alberta" + }, + { + "author_name": "Jamie A Kelly", + "author_inst": "University of Maryland" + }, + { + "author_name": "Clarissa F Halpern", + "author_inst": "University of Maryland" + }, + { + "author_name": "Jonathan D. Dinman", + "author_inst": "University of Maryland" + }, + { + "author_name": "Sarah Loerch", + "author_inst": "University of California Santa Cruz" + }, + { + "author_name": "Michael T Woodside", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.08.06.455384", "rel_title": "The Inherent Flexibility of Receptor Binding Domains in SARS-CoV-2 Spike Protein", @@ -636088,69 +636559,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.04.21261333", - "rel_title": "Learning about COVID-19 across borders: Public health information and adherence among international travellers to the UK", - "rel_date": "2021-08-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261333", - "rel_abs": "ObjectivePublic health control measures at borders have long been central to national strategies for the prevention and containment of infectious diseases. Travel was inevitably associated with the rapid global transmission of COVID-19. In the UK, public health authorities took action to reduce risks of travel-associated spread by providing public health information at ports of entry. This study aims to understand individual risk assessment processes, decision making, and adherence to official advice among international travellers; to provide evidence to inform future policy on the presentation of public health information to facilitate safer international travel.\n\nStudy designThis study is a qualitative study evaluation.\n\nMethodSemi-structured interviews were conducted to investigate risk assessment processes, decision making, and adherence to official Public Health England (PHE) advice among travellers.\n\nResultsParticipants regarded official advice as adequate at the time, despite observing differences between the intervention measures implemented in the countries of departure. Participants however also described adopting precautionary measures including self-isolation and the use of face coverings that went beyond official advice, and variability in the extent to which they adhered to guidance on contacting health authorities. Adherence to official guidance was informed by the perceived salience of specific transmission possibilities and containment measures assessed in relation to participants social and institutional environments.\n\nConclusionAnalysis of travellers reported motivations demonstrates that responses to public health advice constitute a proactive process of risk assessment and rationalised decision-making that incorporates consideration of living situation, trust in information sources, correspondence with cultural logics, and willingness to accept potential risk to self and significant others in guiding preventive action. Our findings concerning international passengers understanding of, and compliance with, official advice and mitigation measures provide valuable evidence to inform future policy and we provide recommendations on the presentation of public health information to facilitate safer international travel. Access to a central source of regularly updated official information would help minimise confusion between different national guidelines. Greater attention to the differentiated information needs of diverse groups in creating future public-facing guidance would help to minimise the uncertainties generated by receipt of generic information.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Shenghan Cai", - "author_inst": "University of Bristol" - }, - { - "author_name": "Tingting Zhang", - "author_inst": "University of Bristol" - }, - { - "author_name": "Charlotte Robin", - "author_inst": "Public Health England" - }, - { - "author_name": "Clare Sawyer", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Wendy Rice", - "author_inst": "Public Health England" - }, - { - "author_name": "Louise E. Smith", - "author_inst": "King's College London" - }, - { - "author_name": "Richard Aml\u00f4t", - "author_inst": "Public Health England" - }, - { - "author_name": "G. James Rubin", - "author_inst": "King's College London" - }, - { - "author_name": "Lucy Yardley", - "author_inst": "University of Bristol" - }, - { - "author_name": "Matthew Hickman", - "author_inst": "University of Bristol" - }, - { - "author_name": "Isabel Oliver", - "author_inst": "Public Health England" - }, - { - "author_name": "Helen Lambert", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.08.03.21261560", "rel_title": "Increasing Numbers of Non-communicable Disease Co-morbidities: Major Risk Factors for Hospitalization among a Cohort of People with HIV and COVID-19 Coinfection", @@ -636915,6 +637323,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.04.21261538", + "rel_title": "Association between obesity and hospitalization in mild COVID-19 young adult outpatients in Brazil: a prospective cohort study", + "rel_date": "2021-08-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261538", + "rel_abs": "Background/ObjectivesThe aim of this study was to evaluate the association between obesity and hospitalization in mild COVID-19 adult outpatients in Brazil.\n\nSubjects/MethodsAdults with signs and symptoms suggestive of acute SARS-CoV-2 infection who sought two hospitals (one public and one private) emergency department (ED) were prospectively enrolled. Patients with confirmed COVID-19 at inclusion were followed by phone calls at day (D) D7, D14 and D28. Multivariable logistic regression models were employed to explore the association between obesity and other potential predictors for hospitalization.\n\nResultsA total of 1,050 participants were screened, 310 were diagnosed with COVID-19 by RT-PCR. Median age was 37.4 (IQR 29.8-45.0) years, and 186 (60.0%) were female. Duration of symptoms was 3.0 (IQR 2.0-5.0) days, and 10.0 (IQR 8.0-12.0) was the median number of symptoms at inclusion. A total of 98 (31.6%) were obese, and 243 (78.4%) had no previous medical conditions. Twenty three participants (23/310, 7.4%) required hospitalization during the period. After adjusting, obesity (BMI[≥]30.0 kg/m2) (OR=2.69, 95%CI 1.63-4.83, P<0.001) and older age (OR=1.05, 95%CI 1.01-1.09, P<0.001), were significantly associated with higher risks of hospitalization.\n\nConclusionsObesity, followed by aging, was the main factor associated with hospital admission for COVID-19 in a young population in a low-middle income country. Our findings highlighted the need for actions to promote additional protection for obese population, such as vaccination, and to encourage lifestyle changes.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ivaine Tais Sauthier Sartor", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Caroline Nespolo David", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Gabriela Heiden Telo", + "author_inst": "School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre, Brazil" + }, + { + "author_name": "Gabriela Oliveira Zavaglia", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Ingrid Rodrigues Fernandes", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Luciane Beatriz Kern", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Marcia Polese-Bonatto", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Thais Raupp Azevedo", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Amanda Paz Santos", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Walquiria Aparecida Ferreira Almeida", + "author_inst": "General Coordination, National Immunization Program, Brazilian Ministry of Health, Brasilia, Brazil" + }, + { + "author_name": "Victor Bertollo Gomes Porto", + "author_inst": "General Coordination, National Immunization Program, Brazilian Ministry of Health, Brasilia, Brazil" + }, + { + "author_name": "Fernanda Hammes Varela", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil; School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre," + }, + { + "author_name": "Marcelo Comerlato Scotta", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil; School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre," + }, + { + "author_name": "Regis Goulart Rosa", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Renato T Stein", + "author_inst": "Social Responsibility, Hospital Moinhos de Vento, Porto Alegre, Brazil; School of Medicine, Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre," + }, + { + "author_name": "- COVIDa study group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.05.455290", "rel_title": "SARS-CoV-2 variants of concern have acquired mutations associated with an increased spike cleavage", @@ -638290,89 +638777,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.08.03.454782", - "rel_title": "Two-dimensional multiplexed assay for rapid and deep SARS-CoV-2 serology profiling and for machine learning prediction of neutralization capacity", - "rel_date": "2021-08-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.03.454782", - "rel_abs": "Antibody responses serve as the primary protection against SARS-CoV-2 infection through neutralization of viral entry into cells. We have developed a two-dimensional multiplex bead binding assay (2D-MBBA) that quantifies multiple antibody isotypes against multiple antigens from a single measurement. Here, we applied our assay to profile IgG, IgM and IgA levels against the spike antigen, its receptor-binding domain and natural and designed mutants. Machine learning algorithms trained on the 2D-MBBA data substantially improve the prediction of neutralization capacity against the authentic SARS-CoV-2 virus of serum samples of convalescent patients. The algorithms also helped identify a set of antibody isotype-antigen datasets that contributed to the prediction, which included those targeting regions outside the receptor-binding interface of the spike protein. We applied the assay to profile samples from vaccinated, immune-compromised patients, which revealed differences in the antibody profiles between convalescent and vaccinated samples. Our approach can rapidly provide deep antibody profiles and neutralization prediction from essentially a drop of blood without the need of BSL-3 access and provides insights into the nature of neutralizing antibodies. It may be further developed for evaluating neutralizing capacity for new variants and future pathogens.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Akiko Koide", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Tatyana Panchenko", - "author_inst": "New York University Langone Health" - }, - { - "author_name": "Chan Wang", - "author_inst": "NYU Langone Health" - }, - { - "author_name": "Sara A Thannickal", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Larizbeth A Romero", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Kai Wen Teng", - "author_inst": "New York University Langone Health" - }, - { - "author_name": "Francesca-Zhoufan Li", - "author_inst": "New York University Langone Health" - }, - { - "author_name": "Padma Akkapeddi", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Alexis D Corrado", - "author_inst": "New York University Langone Health" - }, - { - "author_name": "Jessica Caro", - "author_inst": "New York University Langone Health" - }, - { - "author_name": "Catherine Diefenbach", - "author_inst": "Perlmutter Cancer Center at NYU Langone Health" - }, - { - "author_name": "Marie I Samanovic", - "author_inst": "New York University Langone Health" - }, - { - "author_name": "Mark J Mulligan", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Takamitsu Hattori", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Kenneth A Stapleford", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Huilin J Li", - "author_inst": "New York University Langone Health" - }, - { - "author_name": "Shohei Koide", - "author_inst": "New York University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.08.04.455134", "rel_title": "GlycoSHIELD: a versatile pipeline to assess glycan impact on protein structures", @@ -638545,6 +638949,177 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.08.02.21261379", + "rel_title": "An adaptive randomized controlled trial of non-invasive respiratory strategies in acute respiratory failure patients with COVID-19", + "rel_date": "2021-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261379", + "rel_abs": "BackgroundBoth continuous positive airway pressure (CPAP) and high-flow nasal oxygenation (HFNO) have been recommended for acute respiratory failure in COVID-19. However, uncertainty exists regarding effectiveness and safety.\n\nMethodsIn the Recovery-Respiratory Support multi-center, three-arm, open-label, adaptive, randomized controlled trial, adult hospitalized patients with acute respiratory failure due to COVID-19, deemed suitable for treatment escalation, were randomly assigned to receive CPAP, HFNO, or conventional oxygen therapy. Comparisons were made between each intervention and conventional oxygen therapy. The primary outcome was a composite of tracheal intubation or mortality within 30-days.\n\nResultsOver 13-months, 1272 participants were randomized and included in the analysis (380 (29.9%) CPAP; 417 (32.8%) HFNO; 475 (37.3%) conventional oxygen therapy). The need for tracheal intubation or mortality within 30-days was lower in the CPAP group (CPAP 137 of 377 participants (36.3%) vs conventional oxygen therapy 158 of 356 participants (44.4%); unadjusted odds ratio 0.72; 95% CI 0.53 to 0.96, P=0.03). There was no difference between HFNO and conventional oxygen therapy (HFNO 184 of 414 participants (44.4%) vs conventional oxygen therapy 166 of 368 participants (45.1%); unadjusted odds ratio 0.97; 95% CI 0.73 to 1.29, P=0.85).\n\nConclusionsCPAP, compared with conventional oxygen therapy, reduced the composite outcome of intubation or death within 30 days of randomisation in hospitalized adults with acute respiratory failure due to COVID-19. There was no effect observed, compared with conventional oxygen therapy, with the use of HFNO.\n\n(Funded by the UK National Institute for Health Research; ISRCTN 16912075).", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Gavin D Perkins", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Chen Ji", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Bronwen A Connolly", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, UK; Lane Fox Cli" + }, + { + "author_name": "Keith Couper", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Ranjit Lall", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh, Midlothian, UK; MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, University of Edinburgh, Edin" + }, + { + "author_name": "Judy M Bradley", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, UK" + }, + { + "author_name": "Paul Dark", + "author_inst": "NIHR Manchester Biomedical Research Centre, University of Manchester, Manchester, UK; Salford Royal Hospital, Northern Care Alliance NHS Group, Manchester, UK" + }, + { + "author_name": "Chirag Dave", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Anthony De Soyza", + "author_inst": "Population and Health Science Institute, NIHR Biomedical Research Centre, Newcastle, University, Newcastle Upon Tyne, UK; Newcastle-Upon-Tyne Hospitals NHS Foun" + }, + { + "author_name": "Anna V Dennis", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Anne Devrell", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK; Research Champion Team, West Midlands Clinical Research Network, Wolv" + }, + { + "author_name": "Sara Fairbairn", + "author_inst": "Grange University Hospital, Aneurin Bevan University Health Board, Cwmbran, UK" + }, + { + "author_name": "Hakim Ghani", + "author_inst": "Watford General Hospital, West Hertfordshire Hospitals NHS Trust, Watford, UK" + }, + { + "author_name": "Ellen A Gorman", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, UK" + }, + { + "author_name": "Christopher A Green", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Nicholas Hart", + "author_inst": "Lane Fox Clinical Respiratory Physiology Research Centre, Guys and St.Thomas NHS Foundation Trust, London, UK; Centre for Human and Applied Physiological Scienc" + }, + { + "author_name": "Siew Wan Hee", + "author_inst": "Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Zoe Kimbley", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Shyam Madathil", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Nicola McGowan", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Benjamin Messer", + "author_inst": "Newcastle-Upon-Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK" + }, + { + "author_name": "Jay Naisbitt", + "author_inst": "Fairfield General Hospital, Pennine Acute Hospitals NHS Trust, Northern Care Alliance NHS Group, Bury, UK" + }, + { + "author_name": "Chloe Norman", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Dhruv Parekh", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Institute of Inflammation and Ageing, School of Medical and Dental Sciences, University of" + }, + { + "author_name": "Emma M Parkin", + "author_inst": "Fairfield General Hospital, Pennine Acute Hospitals NHS Trust, Northern Care Alliance NHS Group, Bury, UK" + }, + { + "author_name": "Jaimin Patel", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK; Institute of Inflammation and Ageing, School of Medical and Dental Sciences, University of" + }, + { + "author_name": "Scott E Regan", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Clare Ross", + "author_inst": "Imperial College Healthcare NHS Trust, London, UK" + }, + { + "author_name": "Anthony J Rostron", + "author_inst": "Sunderland Royal Hospital, South Tyneside and Sunderland NHS Foundation Trust, Sunderland, UK; Translational and Clinical Research Institute, Newcastle Universi" + }, + { + "author_name": "Mohammad Saim", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Anita K Simonds", + "author_inst": "Royal Brompton and Harefield Hospital, Guys and St Thomas NHS Foundation Trust, London, UK" + }, + { + "author_name": "Emma Skilton", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Nigel Stallard", + "author_inst": "Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK" + }, + { + "author_name": "Michael Steiner", + "author_inst": "Institute for Lung Health, NIHR BRC Respiratory Medicine, Department of Respiratory Sciences, University of Leicester, Leicester, UK" + }, + { + "author_name": "Rama Vancheeswaran", + "author_inst": "Watford General Hospital, West Hertfordshire Hospitals NHS Trust, Watford, UK" + }, + { + "author_name": "Joyce Yeung", + "author_inst": "Warwick Clinical Trials Unit, Warwick Medical School, University of Warwick, Coventry, UK; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK" + }, + { + "author_name": "Daniel F McAuley", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Science, Queens University Belfast, Belfast, UK; Royal Victor" + }, + { + "author_name": "- Recovery- RS collaborators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.08.02.21261504", "rel_title": "SARS-CoV-2 antibody binding and neutralization in dried blood spot eluates and paired plasma", @@ -640324,45 +640899,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2021.08.01.454696", - "rel_title": "Allosteric perspective on the mutability and druggability of the SARS-CoV-2 Spike protein", - "rel_date": "2021-08-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.01.454696", - "rel_abs": "Recent developments in the SARS-CoV-2 pandemic point to its inevitable transformation into an endemic disease, urging both diagnostics of emerging variants of concern (VOCs) and design of the variant-specific drugs in addition to vaccine adjustments. Exploring the structure and dynamics of the SARS-CoV-2 Spike protein, we argue that the high mutability characteristic of RNA viruses coupled with the remarkable flexibility and dynamics of viral proteins result in a substantial involvement of allosteric mechanisms. While allosteric effects of mutations should be considered in predictions and diagnostics of new VOCs, allosteric drugs advantageously avoid escaping mutations via non-competitive inhibition originating from many alternative distal locations. The exhaustive allosteric signalling and probing maps provide a comprehensive picture of allostery in the Spike protein, making it possible to locate sites of potential mutations that could work as new VOCs \"drivers\", and to determine binding patches that may be targeted by newly developed allosteric drugs.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Zhen Wah Tan", - "author_inst": "Bioinformatics Institute, A*STAR" - }, - { - "author_name": "Wei-Ven Tee", - "author_inst": "Bioinformatics Institute, A*STAR" - }, - { - "author_name": "Firdaus Samsudin", - "author_inst": "A*STAR" - }, - { - "author_name": "Enrico Guarnera", - "author_inst": "ASTAR" - }, - { - "author_name": "Peter J Bond", - "author_inst": "A*STAR Bioinformatics Institute, Singapore" - }, - { - "author_name": "Igor N. Berezovsky", - "author_inst": "Bioinformatics Institute, A*STAR" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.08.02.454701", "rel_title": "Analysis of B-cell receptor repertoires in COVID-19 patients using deep embedded representations of protein sequences", @@ -640571,6 +641107,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.30.21261383", + "rel_title": "COVID-19 Vaccine Uptake among U.S. Child Care Providers", + "rel_date": "2021-08-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.30.21261383", + "rel_abs": "STRUCUTRED ABSTRACTO_ST_ABSObjectivesC_ST_ABSEnsuring a high COVID-19 vaccine uptake among U.S. child care providers is crucial to mitigating the public health implications of child-to-staff and staff-to-child transmission of SARS-CoV-2; however, the vaccination rate among this group is unknown.\n\nMethodsTo characterize the vaccine uptake among U.S. child care providers, we conducted a cross-sectional survey of the child care workforce. Providers were identified through various national databases and state registries. A link to the survey was sent via email between May 26 and June 23, 2021. Out of 44,771 potential respondents, 21,663 responded (48.4%).\n\nResultsOverall COVID-19 vaccine uptake among U.S. child care providers (78.1%, 95% CI [77.3% to 78.9%]) was higher than that of the U.S. adult population (65%). Vaccination rates varied from 53.5% to 89.4% between states. Vaccine uptake differed significantly (p < .01) based on respondent age (70.0% for ages 25-34, 91.5% for ages 75-84), race (70.0% for Black or African Americans, 92.5% for Asian-Americans), annual household income (70.7% for <$35,000, 85.0% for>$75,000), and childcare setting (72.9% for home-based, 79.7% for center-based).\n\nConclusionsCOVID-19 vaccine uptake among U.S. child care providers was higher than that of the general U.S. adult population. Those who were younger, lower income, Black or African American, resided in states either in the Mountain West or the South, and/or worked in home-based childcare programs reported the lowest rates of vaccination; state public health leaders and lawmakers should prioritize these subgroups for placement on the policy agenda to realize the largest gains in vaccine uptake among providers.\n\nTables of Contents SummaryThis article describes the results of a national survey of childcare providers to determine the overall COVID-19 vaccine uptake and the gaps in vaccine coverage.\n\nWhats Known on This SubjectEnsuring a high COVID-19 vaccine uptake among U.S. child care providers is crucial to mitigating the public health implications of child-to-staff and staff-to-child transmission of SARS-CoV-2; however, the vaccination rate among this group is unknown.\n\nWhat This Study AddsWhile the vaccine uptake among U.S. child care providers was higher than that of U.S. adults, certain subgroups continue to warrant focused attention for outreach and/or placement on the policy agenda.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kavin Patel", + "author_inst": "Yale University" + }, + { + "author_name": "Amyn A. Malik", + "author_inst": "Yale University" + }, + { + "author_name": "Aiden Lee", + "author_inst": "Yale University" + }, + { + "author_name": "Madeline Klotz", + "author_inst": "Yale University" + }, + { + "author_name": "John Eric Humphries", + "author_inst": "Yale University" + }, + { + "author_name": "Thomas Murray", + "author_inst": "Yale University" + }, + { + "author_name": "David Wilkinson", + "author_inst": "Yale University" + }, + { + "author_name": "Mehr Shafiq", + "author_inst": "Yale University" + }, + { + "author_name": "Inci Yildirim", + "author_inst": "Yale University" + }, + { + "author_name": "Jad Elharake", + "author_inst": "Yale University" + }, + { + "author_name": "Rachel Diaz", + "author_inst": "Yale University" + }, + { + "author_name": "Chin Reyes", + "author_inst": "Yale University" + }, + { + "author_name": "Saad Omer", + "author_inst": "Yale University" + }, + { + "author_name": "Walter Gilliam", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.29.21261312", "rel_title": "COVID-ONE-humoral immune: The One-stop Database for COVID-19-specific Antibody Responses and Clinical Parameters", @@ -642262,193 +642869,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.28.21261232", - "rel_title": "An Oral SARS-CoV-2 Mpro Inhibitor Clinical Candidate for the Treatment of COVID-19", - "rel_date": "2021-07-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261232", - "rel_abs": "AbstractThe worldwide outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become an established global pandemic. Alongside vaccines, antiviral therapeutics are an important part of the healthcare response to counter the ongoing threat presented by COVID-19. Here, we report the discovery and characterization of PF-07321332, an orally bioavailable SARS-CoV-2 main protease inhibitor with in vitro pan-human coronavirus antiviral activity, and excellent off-target selectivity and in vivo safety profiles. PF-07321332 has demonstrated oral activity in a mouse- adapted SARS-CoV-2 model and has achieved oral plasma concentrations exceeding the in vitro antiviral cell potency, in a phase I clinical trial in healthy human participants.\n\nClinicalTrials.gov Identifier: NCT04756531\n\nOne-Sentence SummaryPF-07321332 is disclosed as a novel, orally active, investigational small-molecule inhibitor of the SARS-CoV-2 main protease, which is being evaluated in clinical trials for the treatment of COVID-19.", - "rel_num_authors": 43, - "rel_authors": [ - { - "author_name": "Dafydd R Owen", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Cambridge, MA 02139, USA" - }, - { - "author_name": "Charlotte M N Allerton", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Cambridge, MA 02139, USA" - }, - { - "author_name": "Annaliesa S Anderson", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Pearl River, NY 10965, USA" - }, - { - "author_name": "Lisa Aschenbrenner", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Melissa Avery", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Simon Berritt", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Britton Boras", - "author_inst": "Pfizer Worldwide Research, Development & Medical; La Jolla, CA 92121, USA" - }, - { - "author_name": "Rhonda D Cardin", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Pearl River, NY 10965, USA" - }, - { - "author_name": "Anthony Carlo", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Karen Coffman", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Alyssa Dantonio", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Li Di", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Heather Eng", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "RoseAnn Ferre", - "author_inst": "Pfizer Worldwide Research, Development & Medical; La Jolla, CA 92121, USA" - }, - { - "author_name": "Ketan S Gajiwala", - "author_inst": "Pfizer Worldwide Research, Development & Medical; La Jolla, CA 92121, USA" - }, - { - "author_name": "Scott A Gibson", - "author_inst": "Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University; Logan, UT 84322, USA" - }, - { - "author_name": "Samantha E Greasley", - "author_inst": "Pfizer Worldwide Research, Development & Medical; La Jolla, CA 92121, USA" - }, - { - "author_name": "Brett L Hurst", - "author_inst": "Institute for Antiviral Research, Department of Animal, Dairy, and Veterinary Sciences, Utah State University; Logan, UT 84322, USA" - }, - { - "author_name": "Eugene P Kadar", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Amit S Kalgutkar", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Cambridge, MA 02139, USA" - }, - { - "author_name": "Jack C Lee", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Jisun Lee", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Wei Liu", - "author_inst": "Pfizer Worldwide Research, Development & Medical; La Jolla, CA 92121, USA" - }, - { - "author_name": "Stephen W Mason", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Pearl River, NY 10965, USA" - }, - { - "author_name": "Stephen Noell", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Jonathan J Novak", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "R Scott Obach", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Kevin Ogilvie", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Nandini C Patel", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Cambridge, MA 02139, USA" - }, - { - "author_name": "Martin Pettersson", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Cambridge, MA 02139, USA" - }, - { - "author_name": "Devendra K Rai", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Pearl River, NY 10965, USA" - }, - { - "author_name": "Matthew R Reese", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Matthew F Sammons", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Cambridge, MA 02139, USA" - }, - { - "author_name": "Jean G Sathish", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Pearl River, NY 10965, USA" - }, - { - "author_name": "Ravi Shankar P Singh", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Cambridge, MA 02139, USA" - }, - { - "author_name": "Claire M Steppan", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Al E Stewart", - "author_inst": "Pfizer Worldwide Research, Development & Medical; La Jolla, CA 92121, USA" - }, - { - "author_name": "Jamison B Tuttle", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Cambridge, MA 02139, USA" - }, - { - "author_name": "Lawrence Updyke", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Cambridge, MA 02139, USA" - }, - { - "author_name": "Patrick R Verhoest", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Cambridge, MA 02139, USA" - }, - { - "author_name": "Liuqing Wei", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Groton, CT 06340, USA" - }, - { - "author_name": "Qingyi Yang", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Cambridge, MA 02139, USA" - }, - { - "author_name": "Yuao Zhu", - "author_inst": "Pfizer Worldwide Research, Development & Medical; Pearl River, NY 10965, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.28.21261284", "rel_title": "Clinical Determinants and Predictors for Prognosis of SARS-CoV-2 Infected Pediatric Patients in Saudi Arabia", @@ -642657,6 +643077,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.28.21261138", + "rel_title": "Estimates of Single Dose and Full Dose BNT162b2 Vaccine Effectiveness among USAF Academy cadets, 1 Mar - 1 May 2021", + "rel_date": "2021-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261138", + "rel_abs": "Beginning in early March 2021 and continuing through May 2021, the USAF Academy began vaccinating cadets for protection against the SARS-CoV-2 virus with the BNT162b2 (Pfizer-BioNTech) mRNA vaccine. During this period, vaccination of the almost 4200 cadet population increased from 3% to 85% and prevalence of COVID-19 in the cadet population was constant at approximately 0.4% as indicated by weekly surveillance testing. In this study, vaccine effectiveness at preventing infection is estimated by comparing infection risk as a function of time since vaccination. A statistically significant four-fold reduction in infection risk was observed 14 days after the first vaccine dose and an eleven-fold reduction in infection risk was observed in fully vaccinated cadets. Overall, the Pfizer-BioNTech vaccine was 91% (95% confidence interval = 55-99%) effective at preventing infection in healthy young adults (17-26 years of age) in a university setting and military training environment.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Douglas P Wickert", + "author_inst": "USAF Academy" + }, + { + "author_name": "Erin Almand", + "author_inst": "US Air Force Academy" + }, + { + "author_name": "Christopher A Cullenbine", + "author_inst": "USAF Academy" + }, + { + "author_name": "Odaro J Huckstep", + "author_inst": "USAF Academy" + }, + { + "author_name": "Joseph Rohrer", + "author_inst": "USAF Academy" + }, + { + "author_name": "John C Sitko", + "author_inst": "USAF Academy" + }, + { + "author_name": "James Jordan Steel", + "author_inst": "USAF Academy" + }, + { + "author_name": "Steven Hasstedt", + "author_inst": "USAF Academy" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.28.21261286", "rel_title": "Variations in Non-Pharmaceutical Interventions by State Correlate with COVID-19 Disease Outcomes", @@ -644176,49 +644643,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.07.27.21261148", - "rel_title": "Purifying selection determines the short-term time dependency of evolutionary rates in SARS-CoV-2 and pH1N1 influenza", - "rel_date": "2021-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.27.21261148", - "rel_abs": "High throughput sequencing enables rapid genome sequencing during infectious disease outbreaks and provides an opportunity to quantify the evolutionary dynamics of pathogens in near real-time. One difficulty of undertaking evolutionary analyses over short timescales is the dependency of the inferred evolutionary parameters on the timespan of observation. Here, we characterise the molecular evolutionary dynamics of SARS-CoV-2 and 2009 pandemic H1N1 (pH1N1) influenza during the first 12 months of their respective pandemics. We use Bayesian phylogenetic methods to estimate the dates of emergence, evolutionary rates, and growth rates of SARS-CoV-2 and pH1N1 over time and investigate how varying sampling window and dataset sizes affects the accuracy of parameter estimation. We further use a generalised McDonald-Kreitman test to estimate the number of segregating non-neutral sites over time. We find that the inferred evolutionary parameters for both pandemics are time-dependent, and that the inferred rates of SARS-CoV-2 and pH1N1 decline by [~]50% and [~]100%, respectively, over the course of one year. After at least 4 months since the start of sequence sampling, inferred growth rates and emergence dates remain relatively stable and can be inferred reliably using a logistic growth coalescent model. We show that the time-dependency of the mean substitution rate is due to elevated substitution rates at terminal branches which are 2-4 times higher than those of internal branches for both viruses. The elevated rate at terminal branches is strongly correlated with an increasing number of segregating non-neutral sites, demonstrating the role of purifying selection in generating the time-dependency of evolutionary parameters during pandemics.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Mahan Ghafari", - "author_inst": "University of Oxford" - }, - { - "author_name": "Louis du Plessis", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jayna Raghwani", - "author_inst": "University of Oxford" - }, - { - "author_name": "Samir Bhatt", - "author_inst": "Imperial College London" - }, - { - "author_name": "Bo Xu", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Oliver Pybus", - "author_inst": "University of Oxford" - }, - { - "author_name": "Aris Katzourakis", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.26.21260421", "rel_title": "Statistical Analysis Plan for the Helmet Non-Invasive Ventilation for COVID-19 Patients (Helmet-COVID) Randomized Controlled Trial", @@ -644543,6 +644967,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.27.21261221", + "rel_title": "Changes in household food security, access to health services, and income in northern Lao PDR during the COVID-19 pandemic", + "rel_date": "2021-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.27.21261221", + "rel_abs": "BackgroundThe COVID-19 pandemic is expected to exacerbate food insecurity in low- and middle-income countries, through loss of income and disrupted food supply chains. Lao PDR has among the highest rates of malnutrition in Southeast Asia. We assessed the relative difficulty in meeting food needs during the COVID-19 pandemic in rural districts of Luang Prabang Province, Lao PDR compared to before; determined associations between pandemic-associated difficulties in food access and household, maternal and child food security; and identified resiliency-promoting strategies.\n\nMethodsIn November 2020, households (N = 1,122) with children under five years were interviewed. Respondents reported the relative ease of access of food and health care as well as changes in income and expenditures compared to before March 2020. We used generalized linear models with cluster robust standard errors to assess univariate and multivariate associations.\n\nResultsNearly four-fifths (78.5%) found it harder to meet household food needs during the pandemic. The most common reasons were increased food prices (51.2%), loss of income (45.3%), and decreased food availability (36.6%). Adjusting for demographics, households with increased difficulty meeting food needs had lower food consumption scores and child dietary diversity. Over 85% of households lost income during the pandemic. Decreased expenditures was associated with reliance on more extreme coping strategies to meet food needs. The households who experienced no change in meeting food needs produced a greater percentage of their food from homegrown methods (4.22% more, 95% CI: 1.28, 7.15), than households who found it more difficult. We estimated that decreases in child bodyweight by 0.5 - 1% would increase wasting in this population by 1.7 - 2.1 percentage points.\n\nConclusionsPandemic-associated shocks may have large effects on malnutrition prevalence. Action is needed to mitigate consequences of the pandemic on nutrition. Local food production and safety net programs that offset income losses may help.\n\nSummary BoxO_ST_ABSWhat is already known?C_ST_ABSThe COVID-19 pandemic has disrupted food supply chains and livelihoods, causing concerns that a global nutrition crisis is imminent and prompting leaders from United Nations agencies to issue an immediate call to action to direct funds towards prevention of child malnutrition. While documented COVID-19 transmission in Lao PDR was lower than that of surrounding counties, malnutrition rates are high, particularly in the northern province of Luang Prabang, which is heavily reliant on tourism for livelihoods.\n\nWhat are the new findings?Nearly four-fifths of those interviewed in Luang Prabang Province, Lao PDR reported that it was harder to meet their households food needs, compared to before the pandemic, with 51% attributing the reason to increased food prices. Over 85% of households reported losing income. Lower expenditures and increased difficulty obtaining food were both associated with lower household food consumption scores and higher household coping strategies, in adjusted analyses. Households who obtained a greater proportion of their foods through home production appeared more resilient than households who obtained a greater proportion of their foods through purchasing.\n\nWhat do the new findings imply?The pandemic may deeply exacerbate food insecurity in Lao PDR, potentially leading to increases in child wasting. Increased local food production and establishment of safety net programs that offset income losses may be two strategies that address this problem among this population.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jennifer R Head", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Phetsavanh Chanthavilay", + "author_inst": "University of Health Sciences, Vientiane, Lao PDR" + }, + { + "author_name": "Helen Catton", + "author_inst": "Save the Children International, Lao PDR" + }, + { + "author_name": "Ammaline Vongsitthi", + "author_inst": "Save the Children International, Lao PDR" + }, + { + "author_name": "Kelley Khamphouxay", + "author_inst": "Save the Children International, Lao PDR" + }, + { + "author_name": "Niphone Simphaly", + "author_inst": "Luang Prabang Provincial Health Department, Lao PDR" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.28.21261212", "rel_title": "An investigation of spatial-temporal patterns and predictions of the COVID-19 pandemic in Colombia, 2020-2021", @@ -645926,129 +646389,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.28.21261021", - "rel_title": "Benefits and Challenges of Using Virtual Primary Care During the COVID-19 Pandemic: From Key Lessons to a Framework for Implementation", - "rel_date": "2021-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261021", - "rel_abs": "BackgroundWith the onset of COVID-19, general practitioners (GPs) and patients worldwide swiftly transitioned from face-to-face to digital remote consultations. There is a need to evaluate how this global shift has impacted patient care, healthcare providers, patient and carer experience, and health systems.\n\nObjectiveWe explored GPs perspectives on the main benefits and challenges of using digital remote care.\n\nMethodsGPs across 20 countries completed an online questionnaire between June - September 2020. GPs perceptions on main barriers and challenges were explored using free-text questions. Thematic analysis was used to analyse the data.\n\nResults1,605 respondents participated in our survey. The benefits identified included reducing COVID-19 transmission risks, guaranteeing access and continuity of care, improved efficiency, faster access to care, improved convenience and communication with patients, greater work flexibility for providers, and hastening the digital transformation of primary care and the accompanying legal frameworks.\n\nMain challenges included patients preference for face-to-face consultations, digital exclusion, lack of physical examinations, clinical uncertainty, delays in diagnosis and treatment, overuse and misuse of digital remote care, and unsuitability for certain types of consultations. Other challenges include the lack of formal guidance, higher workloads, remuneration issues, organisational culture, technical difficulties, implementation and financial issues, and regulatory weaknesses.\n\nConclusionAt the frontline of care delivery, GPs can provide important insights on what worked well, why, and how. Lessons learned during the emergency phase can be used to inform the stable adoption of virtual care solutions, and co-design processes and platforms that are technologically robust, secure, and supported by a strategic long-term plan.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Edmond C Li", - "author_inst": "Institute of Global Health Innovation, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London" - }, - { - "author_name": "Rosy Tsopra", - "author_inst": "INSERM, Centre de Recherche des Cordeliers, Information Sciences to support Personalized Medicine, Universite de Paris" - }, - { - "author_name": "Geronimo Larrain Gimenez", - "author_inst": "Center for Population Health Sciences, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore" - }, - { - "author_name": "Alice Serafini", - "author_inst": "Local Health Authority of Modena, Italy" - }, - { - "author_name": "Gustavo Gusso", - "author_inst": "Internal Medicine Department, Universidade de Sao Paulo" - }, - { - "author_name": "Heidrun Lingner", - "author_inst": "Center for Public Health and Healthcare, German Center for Lung Research (DZL) BREATH Hannover, Hannover Medical School" - }, - { - "author_name": "Maria Jose Fernandez", - "author_inst": "Galicia South Health Research Institute" - }, - { - "author_name": "Greg Irving", - "author_inst": "Edge Hill University" - }, - { - "author_name": "Davorina Patek", - "author_inst": "Department of Family Medicine, Faculty of Medicine, University of Ljubljana" - }, - { - "author_name": "Robert Hoffman", - "author_inst": "Department of Family Medicine, Sackler Faculty of Medicine, Tel Aviv University" - }, - { - "author_name": "Vanja Lazic", - "author_inst": "University of Zagreb" - }, - { - "author_name": "Ensieh Memarian", - "author_inst": "Department of Clinical Sciences in Malmo, Lund University" - }, - { - "author_name": "Tuomas Koskela", - "author_inst": "General Practice, Faculty of Medicine and Health Technology, Tampere University" - }, - { - "author_name": "Claire Collins", - "author_inst": "Irish College of General Practitioners" - }, - { - "author_name": "Sandra Milena Espitia", - "author_inst": "Department of Public Health and Family Medicine, University of La Sabana Colombia" - }, - { - "author_name": "Ana Claveria", - "author_inst": "Galician South Health Research Institute, Primary Care. Area Sanitaria Vigo, Servizo Galego de Saude, Universidade de Santiago de Compostela" - }, - { - "author_name": "Katarzyna Nessler", - "author_inst": "Department of Family Medicine, Jagiellonian University Medical College" - }, - { - "author_name": "Braden Gregory O'Neill", - "author_inst": "Department of Family and Community Medicine, Temerty Faculty of Medicine, University of Toronto" - }, - { - "author_name": "Kyle Hoedebecke", - "author_inst": "Department of Utilization Management, Oscar Health" - }, - { - "author_name": "Mehmet Ungan", - "author_inst": "Department of Family Medicine, Ankara University School of Medicine" - }, - { - "author_name": "Liliana Laranjo", - "author_inst": "Macquarie University" - }, - { - "author_name": "Saira Ghafur", - "author_inst": "Institute of Global Health Innovation, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London" - }, - { - "author_name": "Gianluca Fontana", - "author_inst": "Institute of Global Health Innovation, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London" - }, - { - "author_name": "Azeem Majeed", - "author_inst": "Department of Primary Care and Public Health, School of Public Health, Imperial College London" - }, - { - "author_name": "Josip Car", - "author_inst": "Department of Primary Care and Public Health, School of Public Health, Imperial College London" - }, - { - "author_name": "Ara Darzi", - "author_inst": "Institute of Global Health Innovation, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London" - }, - { - "author_name": "Ana Luisa Neves", - "author_inst": "Institute of Global Health Innovation, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.07.28.21261300", "rel_title": "The Vaccination Threshold for SARS-CoV-2 Depends on the Indoor Setting and Room Ventilation", @@ -646325,6 +646665,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.25.21260838", + "rel_title": "Doxycycline is a safe alternative to Hydroxychloroquine + Azithromycin to prevent clinical worsening and hospitalization in mild COVID-19 patients: An open label randomized clinical trial (DOXYCOV)", + "rel_date": "2021-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.25.21260838", + "rel_abs": "ObjectiveWe aimed to compare the safety and efficacy of a doxycycline-based regimen against the national standard guidelines (Hydroxychloroquine plus Azithromycin) for the treatment of mild symptomatic COVID-19.\n\nMethodsWe conducted an open-label, randomized, non-inferiority trial, in Cameroon comparing Doxycycline 100mg, twice daily for 7 days versus Hydroxychloroquine, 400 mg daily for 5 days and Azithromycin 500mg at day 1 and 250mg from day 2 through 5, in mild COVID-19 patients. Clinical improvement, biological parameters and adverse events were assessed. The primary outcome was the proportion of clinical cure at day 3, 10 and 30. Non-inferiority was determined by the clinical cure rate between protocols with a 20 percentage points margin.\n\nResults194 participants underwent randomization and were treated with Doxycycline (n=97) or Hydroxychloroquine-Azithromycin (n=97). At day 3, 74/92 (80.4%) participants on Doxycycline versus 77/95 (81.1%) on Hydroxychloroquine-Azithromycin -based protocols were asymptomatic (p=0.91). At day 10, 88/92 (95.7%) participants on Doxycycline versus 93/95 (97.9%) on Hydroxychloroquine-Azithromycin were asymptomatic (p=0.44). At day 30 all participants were asymptomatic. SARS-CoV2 PCR was negative at Day 10 in 60/92 (65.2%) participants allocated to Doxycycline and 63/95 (66.3%) participants allocated to Hydroxychloroquine-Azithromycin. None of the participants were admitted for worsening of the disease after treatment initiation.\n\nConclusionDoxycycline 100 mg twice daily for 7 days is as effective and safe as Hydroxychloroquine-Azithromycin, for preventing clinical worsening of mild symptomatic or asymptomatic COVID-19, and achieving virological suppression.\n\nStrengths and Limitations[tpltrtarr] This study is one of the first randomized trial, assessing the efficacy and tolerance of Doxycycline to treat COVID-19\n[tpltrtarr]It is one of the first to evaluate disease progression and need to hospitalization in mild or asymptomatic COVID-19\n[tpltrtarr]Patients will not receive identical treatments\n[tpltrtarr]Doxycycline has advantages in terms of availability, safety and cost compared to Hydroxychloroquine and Azytromycin\n[tpltrtarr]Though this study has encounter 7 lost to follow-up, this does not have a major influence on our results\n[tpltrtarr]These data will assist clinicians in their daily practice, and provide a new tool for the fight against COVID-19", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Eugene Sobngwi", + "author_inst": "University of Yaounde 1" + }, + { + "author_name": "Sylvain Zemsi", + "author_inst": "RSD Institute" + }, + { + "author_name": "Magellan Guewo-Fokeng", + "author_inst": "RSD Institute" + }, + { + "author_name": "Jean Claude Katte", + "author_inst": "RSD Institute" + }, + { + "author_name": "Charles Kouanfack", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Liliane Mfeukeu-Kuate", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Armel Zemsi", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Yves Wasnyo", + "author_inst": "RSD Institute" + }, + { + "author_name": "Antoinette Assiga-Ntsama", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Jean Arnaud Ndi-Manga", + "author_inst": "RSD Institute" + }, + { + "author_name": "Joelle S Tambekou", + "author_inst": "RSD Institute" + }, + { + "author_name": "William Ngatchou", + "author_inst": "University of Douala, Faculty of Medicine and Pharmaceutical Sciences" + }, + { + "author_name": "Charlotte Moussi-Omgba", + "author_inst": "Ministry of Public Health Cameroon" + }, + { + "author_name": "Jean-Claude Mbanya", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Pierre Ongolo-Zogo", + "author_inst": "Yaounde Central Hospital" + }, + { + "author_name": "Pierre-Joseph Fouda", + "author_inst": "Yaounde Central Hospital" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2021.07.25.21260967", "rel_title": "Influence of Novel Coronavirus COVID-19 and HIV: A Scoping Review of Hospital Course and Symptomatology", @@ -648136,29 +648555,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.27.21260924", - "rel_title": "A Partition-Based Group Testing Algorithm for Estimating the Number of Infected Individuals", - "rel_date": "2021-07-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.27.21260924", - "rel_abs": "The dangers of COVID-19 remain ever-present worldwide. The asymptomatic nature of COVID-19 obfuscates the signs policy makers look for when deciding to reopen public areas or further quarantine. In much of the world, testing resources are often scarce, creating a need for testing potentially infected individuals that prioritizes efficiency. This report presents an advancement to Beigel and Kasifs Approximate Counting Algorithm (ACA). ACA estimates the infection rate with a number of tests that is logarithmic in the population size. Our newer version of the algorithm provides an extra level of efficiency: each subject is tested exactly once. A simulation of the algorithm, created for and presented as part of this paper, can be used to find a linear regression of the results with R2 > 0.999. This allows stakeholders and members of the biomedical community to estimate infection rates for varying population sizes and ranges of infection rates.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Richard Beigel", - "author_inst": "Temple University" - }, - { - "author_name": "Max J Webber", - "author_inst": "Temple University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.21.21260954", "rel_title": "Plasma oxylipin levels may predict Covid-19 patient outcomes. An observational and retrospective study.", @@ -648403,6 +648799,121 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.07.27.453843", + "rel_title": "Molecular Pathophysiology of Cardiac Injury and Cardiac Microthrombi in Fatal COVID-19: Insights from Clinico-histopathologic and Single Nuclei RNA Sequencing Analyses", + "rel_date": "2021-07-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.27.453843", + "rel_abs": "Cardiac injury is associated with critical COVID-19, yet its etiology remains debated. To elucidate the pathogenic mechanisms of COVID-19-associated cardiac injury, we conducted a single-center prospective cohort study of 69 COVID-19 decedents. Of six cardiac histopathologic features, microthrombi was the most commonly detected (n=48, 70%). We tested associations of cardiac microthrombi with biomarkers of inflammation, cardiac injury, and fibrinolysis and with in-hospital antiplatelet therapy, therapeutic anticoagulation, and corticosteroid treatment, while adjusting for multiple clinical factors, including COVID-19 therapies. Higher peak ESR and CRP during hospitalization were independently associated with higher odds of microthrombi. Using single nuclei RNA-sequence analysis, we discovered an enrichment of pro-thrombotic/anti-fibrinolytic, extracellular matrix remodeling, and immune-potentiating signaling amongst cardiac fibroblasts in microthrombi-positive COVID-19 hearts relative to microthrombi-negative COVID-19. Non-COVID-19 non-failing hearts were used as reference controls. Our cumulative findings identify the specific transcriptomic changes in cardiac fibroblasts as salient features of COVID-19-associated cardiac microthrombi.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Nobuaki Fukuma", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Michelle L Hulke", + "author_inst": "Masonic Medical Research Institute" + }, + { + "author_name": "Michael I Brener", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Stephanie Golob", + "author_inst": "Department of Medicine, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Robert Zilinyi", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Zhipeng Zhou", + "author_inst": "Cardiovascular Research Foundation" + }, + { + "author_name": "Christos Tzimas", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Ilaria Russo", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Claire McGroder", + "author_inst": "Division of Pulmonary, Allergy & Critical Care Medicine, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Ryan Pfeiffer", + "author_inst": "Masonic Medical Research Institute" + }, + { + "author_name": "Alexander Chong", + "author_inst": "Division of Infectious Diseases, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Geping Zhang", + "author_inst": "Department of Pathology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Daniel Burkhoff", + "author_inst": "Cardiovascular Research Foundation" + }, + { + "author_name": "Martin B Leon", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Mathew Maurer", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Jeffrey W Moses", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Anne-Catrin Uhlemann", + "author_inst": "Division of Infectious Diseases, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Hanina Hibshoosh", + "author_inst": "Department of Pathology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Nil Uriel", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Matthias J Szabolcs", + "author_inst": "Department of Pathology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Bj\u00f6rn Redfors", + "author_inst": "Cardiovascular Research Foundation" + }, + { + "author_name": "Charles C Marboe", + "author_inst": "Department of Pathology, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Matthew R Baldwin", + "author_inst": "Division of Pulmonary, Allergy & Critical Care Medicine, New York Presbyterian - Columbia University Irving Medical Center" + }, + { + "author_name": "Nathan R Tucker", + "author_inst": "Masonic Medical Research Institute" + }, + { + "author_name": "Emily J Tsai", + "author_inst": "Division of Cardiology, New York Presbyterian - Columbia University Irving Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2021.07.27.453973", "rel_title": "Executable Network of SARS-CoV-2-Host Interaction Predicts Drug Combination Treatments", @@ -650114,65 +650625,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.22.21261000", - "rel_title": "Impact of SARS-CoV-2 variant on the severity of maternal infection and perinatal outcomes: Data from the UK Obstetric Surveillance System national cohort.", - "rel_date": "2021-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.22.21261000", - "rel_abs": "BackgroundIn the UK, the Alpha variant of SARS-CoV-2 became dominant in late 2020, rapidly succeeded by the Delta variant in May 2021. The aim of this study was to compare the impact of these variants on severity of maternal infection and perinatal outcomes within the time-periods in which they predominated.\n\nMethodsThis national, prospective cohort study collated data on hospitalised pregnant women with symptoms of confirmed SARS-CoV-2 infection and compared the severity of infection and perinatal outcomes across the Wildtype (01/03/20-30/11/20), Alpha (01/12/20-15/05/21) and Delta dominant periods (16/05/21-11/07/21), using multivariable logistic regression.\n\nFindingsOf 3371 pregnant women, the proportion that experienced moderate to severe infection significantly increased between Wildtype and Alpha periods (24.4% vs. 35.8%; aOR1.75 95%CI 1.48-2.06), and between Alpha and Delta periods (35.8% vs. 45.0%; aOR1.53, 95%CI 1.07-2.17). Compared to the Wildtype period, symptomatic women admitted in the Alpha period were more likely to require respiratory support (27.2% vs. 20.3%, aOR1.39, 95%CI 1.13-1.78), have pneumonia (27.5% vs. 19.1%, aOR1.65, 95%CI 1.38-1.98) and be admitted to intensive care (11.3% vs. 7.7%, aOR1.61, 95%CI 1.24-2.10). Women admitted during the Delta period had further increased risk of pneumonia (36.8% vs. 27.5%, aOR1.64 95%CI 1.14-2.35). No fully vaccinated pregnant women were admitted between 01/02/2021 when vaccination data collection commenced and 11/07/2021. The proportion of women receiving pharmacological therapies for SARS-CoV-2 management was low, even in those critically ill.\n\nInterpretationSARS-CoV-2 infection during Alpha and Delta dominant periods was associated with more severe infection and worse pregnancy outcomes compared to the Wildtype infection, which itself increased risk compared to women without SARS-CoV-2 infection.1 Clinicians need to be aware and implement COVID-specific therapies in keeping with national guidance. Urgent action to tackle vaccine misinformation and policy change to prioritise uptake in pregnancy is essential.\n\nFundingNational Institute for Health Research HS&DR Programme (11/46/12).", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Nicola Vousden", - "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, UK" - }, - { - "author_name": "Rema Ramakrishnan", - "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, UK" - }, - { - "author_name": "Kathryn Bunch", - "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, UK" - }, - { - "author_name": "Edward Morris", - "author_inst": "Royal College of Obstetricians and Gynaecologists, London, UK" - }, - { - "author_name": "Nigel Simpson", - "author_inst": "Department of Women's and Children's Health, School of Medicine, University of Leeds, UK" - }, - { - "author_name": "Christopher Gale", - "author_inst": "Imperial College London" - }, - { - "author_name": "Patrick O'Brien", - "author_inst": "Institute for Womens Health, University College London, London, UK" - }, - { - "author_name": "Maria Quigley", - "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, UK" - }, - { - "author_name": "Peter Brocklehurst", - "author_inst": "Birmingham Clinical Trials Unit, Institute of Applied Health Research, University of Birmingham, UK" - }, - { - "author_name": "Jennifer J Kurinczuk", - "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, UK" - }, - { - "author_name": "Marian Knight", - "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.07.23.21260970", "rel_title": "Prevention and Control of Acute Respiratory Viral Infections in Adult Population: A Systematic Review and Meta-Analysis on Ginseng-Based Clinical Trials.", @@ -650417,6 +650869,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2021.07.22.21260878", + "rel_title": "Mental Health of HBCU College Students during the COVID-19 Pandemic", + "rel_date": "2021-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.22.21260878", + "rel_abs": "ObjectiveThis study investigated rates and predictors of mental health issues (e.g., depression and anxiety) in a sample of college students currently attending a historically Black college/university (HBCU) during the COVID-19 pandemic.\n\nParticipants/Methods98 undergraduate students (81 female and 17 male) completed an online survey containing questions about demographics, socioeconomic status, academic characteristics, and pandemic-related concerns. The survey also included PHQ-9 and GAD-7 questionnaires to evaluate depression and anxiety, respectively.\n\nResults49% of students met the clinical cutoff for depression, 39% for anxiety, and 52% for depression and/or anxiety. Significant predictors of meeting the cutoffs included parental job loss/hour reduction, being a senior, and feeling that the pandemic negatively impacted daily life, among other factors. Demographic variables (age, gender, etc.) had no effect.\n\nConclusionHBCU students show high rates of depression and anxiety during the COVID-19 pandemic, which may be predicted based on the students academic, socioeconomic, and pandemic-related concerns.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sharron Xuanren Wang", + "author_inst": "Delaware State University" + }, + { + "author_name": "Jarid Goodman", + "author_inst": "Delaware State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.07.22.21260793", "rel_title": "A spatio-temporal study of state-wide case-fatality risks during the first wave of the COVID-19 pandemic in Mexico", @@ -652068,41 +652543,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.15.21260589", - "rel_title": "Preventable deaths from SARS-CoV-2 in England and Wales: a systematic analysis of coroners case reports from the COVID-19 pandemic", - "rel_date": "2021-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260589", - "rel_abs": "ObjectivesTo examine coroners Prevention of Future Deaths reports (PFDs) to identify deaths involving SARS-CoV-2 that coroners deemed preventable.\n\nDesignConsecutive case series.\n\nSettingEngland and Wales.\n\nParticipantsPatients reported in 510 PFDs dated between 01 January 2020 and 28 June 2021, collected from the UKs Courts and Tribunals Judiciary website using web scraping to create an openly available database, https://preventabledeathstracker.net/.\n\nMain outcome measuresConcerns reported by coroners.\n\nPublic and Patient InvolvementPatients and members of the public were not involved in this study.\n\nResultsSARS-CoV-2 was involved in 23 deaths reported by coroners in PFDs. Twelve deaths were indirectly related to the COVID-19 pandemic, defined as those that were not medically caused by SARS-CoV-2, but were associated with mitigation measures. In 11 cases the coroner explicitly reported that COVID-19 had directly caused death. There was geographical variation in the reporting of PFDs; most (39%) were written by coroners in the North-West of England. The coroners raised 56 concerns, problems in communication being the most common (30%), followed by failure to follow protocols (23%). Organizations in the National Health Service (NHS) were sent the most PFDs (51%), followed by the Government (26%), but responses to PFDs by these organizations were poor.\n\nConclusionsPFDs contain a rich source of information on preventable deaths that has previously been difficult to examine systematically. Our openly available tool (https://preventabledeathstracker.net/) streamlines this process and has identified many concerns raised by coroners that should be addressed during the Governments inquiry into the handling of the COVID-19 pandemic, so that mistakes made are less likely to be repeated.\n\nStudy protocol pre-registrationhttps://osf.io/bfypc/\n\nSummary boxO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIThe UK Government has stated that there will be a public inquiry into the handling of the COVID-19 pandemic, to learn lessons for future pandemics.\nC_LIO_LICoroners in England and Wales have a duty to report and communicate information about the deaths they investigate when the coroner believes that action should be taken to prevent future deaths.\nC_LIO_LIThese reports, called Prevention of Future Death reports (PFDs), had not yet been systematically analysed to identify deaths that occurred during the COVID-19 pandemic.\nC_LI\n\nWhat are the new findings?O_LIWe created the Preventable Deaths Database (https://preventabledeathstracker.net/) using web scraping to systematically assess PFDs published on the Courts and Tribunal Judiciary website.\nC_LIO_LIBetween 01 January 2020 and 28 June 2021, one in 20 (4.5%, n=23) PFDs that were published by coroners involved SARS-CoV-2.\nC_LIO_LICoroners raised many concerns about the care of patients in hospitals, care homes, and people in the community during the COVID-19 pandemic, which require action to prevent future deaths.\nC_LI\n\nHow might it affect clinical practice in the foreseeable future?O_LIPreventable deaths that occurred during the COVID-19 pandemic should be referred to the coroner so that an inquest can be performed and a PFD issued, highlightng actions that could be avoided in improving the handling of future pandemics in both the UK and elsewhere.\nC_LIO_LIOur tool, https://preventabledeathstracker.net/, can be used by others to examine preventable deaths in England and Wales, and to identify signals for quality improvement to reduce avoidable harms in clinical practice.\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Bethan Swift", - "author_inst": "University of Oxford" - }, - { - "author_name": "Carl Heneghan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jeffrey K Aronson", - "author_inst": "University of Oxford" - }, - { - "author_name": "David Howard", - "author_inst": "University of Oxford" - }, - { - "author_name": "Georgia C Richards", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.20.21260833", "rel_title": "BNT162b2 Vaccination efficacy is marginally affected by the SARS-CoV-2 B.1.351 variant in fully vaccinated individuals.", @@ -652399,6 +652839,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.19.21260721", + "rel_title": "Present knowledge, attitude, practice, and fear level of Bangladeshi people towards covid-19 after one year of the pandemic situation: a web-based cross-sectional study.", + "rel_date": "2021-07-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260721", + "rel_abs": "In the earlier phase of the pandemic situation, the governments of Bangladesh badly suffered to adhere their people to preventive measures probably due to less knowledge and attitude towards covid-19. To tackle the second wave of coronavirus, the governments again enforced an array of preventive measures, but still encountering the same problem after a year of the pandemic situation. In an attempt to find out the reasons behind this, our study aimed to assess the present knowledge, attitude, practice, and fear level of the people. A cross-sectional study was conducted from 15th to 25th April 2021. A total of 402 participants met all the inclusion criteria and were considered for performing all statistical analyses (Descriptive statistics, Mann-Whitney U test, Kruskal-Wallis H test, Multiple logistic regression, Spearman rank-order correlation). Out of 402 participants, more than 90% participants were students and all were adults aged 16 to 30. 84.6%, 65.7%, 54%, and 21.6% participants had more adequate knowledge, more positive attitude, more frequent practice, and moderate to high fear towards covid-19, respectively. Knowledge, attitude, practice, and fear were interrelated directly or indirectly. It was found knowledgeable participants were more likely to have more positive attitude (OR = 2.12, 95% CI = 1.14-3.95, P < 0.05) and very less fear (OR = 1.98, 95% CI = 1.02-3.82, P < 0.05). More positive attitude was found as a good predictor of more frequent practice (OR = 4.33, 95% CI = 2.66-7.04, P < 0.001), and very less fear had same negative impact on both attitude (OR = 0.48, 95% CI = 0.25-0.91, P < 0.05) and practice (OR = 0.48, 95% CI = 0.27-0.85, P < 0.05). Our findings reflect that knowledge level has elevated but attitude level subsided, and practice level stayed same as was in the earlier phase of pandemic and people are no longer panicked.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Tahsin Ahmed Rupok", + "author_inst": "Department of Pharmacy, University of Rajshahi, Rajshahi-6205, Bangladesh." + }, + { + "author_name": "Sunandan Dey", + "author_inst": "Department of Pharmacy, University of Rajshahi, Rajshahi-6205, Bangladesh." + }, + { + "author_name": "Rashni Agarwala", + "author_inst": "Department of Pharmacy, Islamic University, Kushtia-7003, Bangladesh." + }, + { + "author_name": "Md. Nurnobi Islam", + "author_inst": "Department of Chemistry, Shahjalal University of Science & Technology, Sylhet-3114, Bangladesh." + }, + { + "author_name": "Bayezid Bostami", + "author_inst": "Department of Pharmacy, University of Rajshahi, Rajshahi-6205, Bangladesh." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.21.21260624", "rel_title": "New susceptibility loci for severe COVID-19 by detailed GWAS analysis in European populations", @@ -655086,49 +655561,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.07.23.453393", - "rel_title": "Mesalamine Reduces Intestinal ACE2 Expression Without Modifying SARS-CoV-2 Infection or Disease Severity in Mice.", - "rel_date": "2021-07-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.23.453393", - "rel_abs": "IntroductionCoronavirus Disease 2019 (COVID-19) is an ongoing public health crisis that has sickened or precipitated death in millions. The etiologic agent of COVID-19, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), infects the intestinal epithelium, and can induce GI symptoms similar to the human inflammatory bowel diseases (IBD). An international surveillance epidemiology study (SECURE-IBD) reported that the standardized mortality ratio trends higher in IBD patients (1.5-1.8) and that mesalamine/sulfasalazine therapy correlates with poor outcome. The goal of our study was to experimentally address the relationship between mesalamine and SARS-CoV-2 entry, replication, and/or pathogenesis.\n\nMethodsViral infection was performed with a chimeric vesicular stomatitis virus expressing SARS-CoV-2 spike protein and EGFP (VSV-SARS-CoV-2) and SARS-CoV-2 virus derived from an infectious cDNA clone of 2019n-CoV/USA_WA1/2020. Primary human ileal spheroids derived from healthy donors were grown as 3D spheroids or on 2D transwells. We assessed the effect of 10 mM mesalamine (Millipore Sigma) on viral RNA levels, as well as the expression of the SARS-CoV-2 receptor angiotensin II-converting enzyme 2 (ACE2), Transmembrane Serine Protease 2 (TMPRSS2), TMPRSS4, Cathepsin B (CTSB) and CTSL by qRT-PCR. 8-12 week old K18-ACE2 were treated orally with PBS or mesalamine at 200 mg/kg daily. Mice were inoculated intranasally with 1x103 FFU of SARS-CoV-2. Mice were weighed daily and viral titers were determined 7 days post infection (dpi) by qRT-PCR. For the intestinal viral entry model, VSV-SARS-CoV-2 was injected into a ligated intestinal loop of anesthetized K18-ACE2 mice and tissues were harvested 6 hours post-infection.\n\nResultsWe found no change in viral RNA levels in human intestinal epithelial cells in response to mesalamine. Expression of ACE2 was reduced following mesalamine treatment in enteroids, while CTSL expression was increased. Mice receiving mesalamine lost weight at similar rates compared to mice receiving vehicle control. Mesalamine treatment did not change viral load in the lung, heart, or intestinal tissues harvested at 7 dpi. Pretreatment with mesalamine did not modulate intestinal entry of the chimeric VSV-SARS-CoV-2 in K18-ACE2 mice.\n\nConclusionsMesalamine did not alter viral entry, replication, or pathogenesis in vitro or in mouse models. Mesalamine treatment reduced expression of the viral receptor ACE2 while concurrently increasing CTSL expression in human ileum organoids.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "David M Alvarado", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Juhee Son", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Larissa B. Thackray", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Michael Diamond", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Siyuan Ding", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Matthew A. Ciorba", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "- Washington University IBD Investigators Group", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.07.23.453521", "rel_title": "Probiotic consortia improve anti-viral immunity to SARS-CoV-2 in ferrets", @@ -655273,6 +655705,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.20.21260558", + "rel_title": "Intentions to participate in cervical and colorectal cancer screening during the COVID-19 pandemic: a mixed-methods study", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260558", + "rel_abs": "Worldwide, cancer screening faced significant disruption in 2020 due to the COVID-19 pandemic. If this has led to changes in public attitudes towards screening and reduced intention to participate, there is a risk of long-term adverse impact on cancer outcomes. In this study, we examined previous participation and future intentions to take part in cervical and colorectal cancer (CRC) screening following the first national lockdown in the UK.\n\nOverall, 7543 adults were recruited to a cross-sectional online survey in August-September 2020. Logistic regression analyses were used to identify correlates of strong screening intentions among 2,319 participants eligible for cervical screening and 2,502 eligible for home-based CRC screening. Qualitative interviews were conducted with a sub-sample of 30 participants. Verbatim transcripts were analysed thematically.\n\nOf those eligible, 74% of survey participants intended to attend cervical screening and 84% intended to complete home-based CRC screening when next invited. Thirty percent and 19% of the cervical and CRC samples respectively said they were less likely to attend a cancer screening appointment now than before the pandemic. Previous non-participation was the strongest predictor of low intentions for cervical (aOR 26.31, 95% CI: 17.61-39.30) and CRC (aOR 67.68, 95% CI: 33.91-135.06) screening. Interview participants expressed concerns about visiting healthcare settings but were keen to participate when screening programmes resumed.\n\nIntentions to participate in future screening were high and strongly associated with previous engagement in both programmes. As screening services recover, it will be important to monitor participation and to ensure people feel safe to attend.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Rebecca Wilson", + "author_inst": "Cardiff University" + }, + { + "author_name": "Harriet Quinn-Scoggins", + "author_inst": "Cardiff University" + }, + { + "author_name": "Yvonne Moriarty", + "author_inst": "Cardiff University" + }, + { + "author_name": "Jacqueline Hughes", + "author_inst": "Cardiff University" + }, + { + "author_name": "Mark Goddard", + "author_inst": "Cardiff University" + }, + { + "author_name": "Rebecca Cannings-John", + "author_inst": "Cardiff University" + }, + { + "author_name": "Victoria Whitelock", + "author_inst": "Cancer Research UK" + }, + { + "author_name": "Katriina L Whitaker", + "author_inst": "University of Surrey" + }, + { + "author_name": "Detelina Grozeva", + "author_inst": "Cardiff University" + }, + { + "author_name": "Julia Townson", + "author_inst": "Cardiff University" + }, + { + "author_name": "Kirstie Osborne", + "author_inst": "Cancer Research UK" + }, + { + "author_name": "Stephanie Smits", + "author_inst": "Cardiff University" + }, + { + "author_name": "Michael Robling", + "author_inst": "Cardiff University" + }, + { + "author_name": "Julie Hepburn", + "author_inst": "Public Involvement Community, Health and Care Research Wales" + }, + { + "author_name": "Graham Moore", + "author_inst": "Cardiff University" + }, + { + "author_name": "Ardiana Gjini", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Kate Brain", + "author_inst": "Cardiff University" + }, + { + "author_name": "Jo Waller", + "author_inst": "Kings College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2021.07.19.21260139", "rel_title": "Plasma cell-free DNA promise disease monitoring and tissue injury assessment of COVID-19", @@ -657020,61 +657539,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.19.21260808", - "rel_title": "Delta variants of SARS-CoV-2 cause significantly increased vaccine breakthrough COVID-19 cases in Houston, Texas", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260808", - "rel_abs": "Genetic variants of SARS-CoV-2 have repeatedly altered the course of the COVID-19 pandemic. Delta variants of concern are now the focus of intense international attention because they are causing widespread COVID-19 disease globally and are associated with vaccine breakthrough cases. We sequenced the genomes of 16,965 SARS-CoV-2 from samples acquired March 15, 2021 through September 20, 2021 in the Houston Methodist hospital system. This sample represents 91% of all Methodist system COVID-19 patients during the study period. Delta variants increased rapidly from late April onward to cause 99.9% of all COVID-19 cases and spread throughout the Houston metroplex. Compared to all other variants combined, Delta caused a significantly higher rate of vaccine breakthrough cases (23.7% for Delta compared to 6.6% for all other variants combined). Importantly, significantly fewer fully vaccinated individuals required hospitalization. Individuals with vaccine breakthrough cases caused by Delta had a low median PCR cycle threshold (Ct) value (a proxy for high virus load). This value was closely similar to the median Ct value for unvaccinated patients with COVID-19 caused by Delta variants, suggesting that fully vaccinated individuals can transmit SARS-CoV-2 to others. Patients infected with Alpha and Delta variants had several significant differences. Our integrated analysis emphasizes that vaccines used in the United States are highly effective in decreasing severe COVID-19 disease, hospitalizations, and deaths.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "James M. Musser", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Paul A. Christensen", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Randall J. Olsen", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Scott Wesley Long", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Sishir Subedi", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "James J. Davis", - "author_inst": "Argonne National Laboratories" - }, - { - "author_name": "Parsa Hodjat", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Debbie R. Walley", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Jacob C. Kinskey", - "author_inst": "Houston Methodist Hospital" - }, - { - "author_name": "Jimmy D. Gollihar", - "author_inst": "CCDC Army Research Laboratory-South" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.07.19.21260693", "rel_title": "Effectiveness of Covishield vaccine in preventing Covid-19 -- A test-negative case-control study", @@ -657299,6 +657763,425 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.19.21260779", + "rel_title": "Surveillance of SARS-CoV-2 variants in Argentina: detection of Alpha, Gamma, Lambda, Epsilon and Zeta in locally transmitted and imported cases", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260779", + "rel_abs": "Molecular surveillance of SARS-CoV-2 variants was performed on a total of 2,406 samples from the capital city and nine provinces of Argentina, during 30 epidemiological weeks (EW) that covered the end of the first wave and the beginning of the ongoing second wave of the COVID-19 pandemic in the country (EW 44/2020 to EW 20/2021). The surveillance strategy was mainly based on Sanger sequencing of a Spike coding region that allows the simultaneous identification of signature mutations associated with worldwide circulating variants. In addition, whole SARS-CoV-2 genome sequences were obtained from 456 samples. The main variants found were Gamma, Lambda and Alpha, and to a lesser extent, Zeta and Epsilon. Whereas Gamma dominated in different regions of the country, both Gamma and Lambda prevailed in the most populated area, the metropolitan region of Buenos Aires (MABA), although showing a heterogeneous distribution along this region. This cost-effective surveillance protocol allowed for a rapid response in a limited access to resources scenario, added information on the expansion of the Lambda variant in South America and contributed to the implementation of public health measures to control the disease spread in Argentina.", + "rel_num_authors": 101, + "rel_authors": [ + { + "author_name": "Carolina Torres", + "author_inst": "Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM), Buenos Aires, Arge" + }, + { + "author_name": "Laura Mojsiejczuk", + "author_inst": "Universidad de Buenos Aires, Facultad de Farmacia y Bioquimica, Instituto de Investigaciones en Bacteriologia y Virologia Molecular (IBaViM), Buenos Aires, Arge" + }, + { + "author_name": "Dolores Acuna", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina; Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos" + }, + { + "author_name": "Sofia Alexay", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Ariel Amadio", + "author_inst": "Instituto de Investigacion de la Cadena Lactea (IDICAL) INTA-CONICET. Ruta 34 km 227, Rafaela (2300), Santa Fe, Argentina; Consejo Nacional de Investigaciones C" + }, + { + "author_name": "Paula Aulicino", + "author_inst": "Laboratorio de Biologia Celular y Retrovirus. Hospital de Pediatria Prof. Juan P. Garrahan, CABA, Argentina; Consejo Nacional de Investigaciones Cientificas y T" + }, + { + "author_name": "Humberto Debat", + "author_inst": "Instituto de Patologia Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5" + }, + { + "author_name": "Franco Fernandez", + "author_inst": "Instituto de Patologia Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5" + }, + { + "author_name": "Stephanie Goya", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Guido Konig", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Mercedes Nabaes Jodar", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina; Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos" + }, + { + "author_name": "Luis Pianciola", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina" + }, + { + "author_name": "Sofia Bengoa", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Marco Cacciahue", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Cecilia Camussone", + "author_inst": "Instituto de Investigacion de la Cadena Lactea (IDICAL) INTA-CONICET. Ruta 34 km 227, Rafaela (2300), Santa Fe, Argentina" + }, + { + "author_name": "Maria Jose Dus Santos", + "author_inst": "Instituto de Virologia e Innovaciones Tecnologicas (INTA-CONICET), Hurlingham, Buenos Aires, Argentina; Laboratorio de Diagnostico-UNIDAD COVID- Universidad Nac" + }, + { + "author_name": "Maria Florencia Eberhardt", + "author_inst": "Instituto de Investigacion de la Cadena Lactea (IDICAL) INTA-CONICET. Ruta 34 km 227, Rafaela (2300), Santa Fe, Argentina; Consejo Nacional de Investigaciones C" + }, + { + "author_name": "Ailen Fernandez", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina" + }, + { + "author_name": "Maria Ines Gismondi", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina; Universidad Nacional de Luja" + }, + { + "author_name": "Matias Irazoqui", + "author_inst": "Instituto de Investigacion de la Cadena Lactea (IDICAL) INTA-CONICET. Ruta 34 km 227, Rafaela (2300), Santa Fe, Argentina; Consejo Nacional de Investigaciones " + }, + { + "author_name": "Silvina Lusso", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Nathalie Marquez", + "author_inst": "Instituto de Patologia Vegetal, Centro de Investigaciones Agropecuarias, Instituto Nacional de Tecnologia Agropecuaria (IPAVE-CIAP-INTA), Camino 60 Cuadras Km 5" + }, + { + "author_name": "Marianne Munoz", + "author_inst": "Unidad de Genomica del Instituto de Biotecnologia/Instituto de Agrobiotecnologia y biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Monica Natale", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Belen Pisano", + "author_inst": "Instituto de Virologia Dr. J. M. Vanella, Facultad de Ciencias Medicas, Universidad Nacional de Cordoba; Consejo Nacional de Investigaciones Cientificas y Tecni" + }, + { + "author_name": "Andrea Puebla", + "author_inst": "Instituto de Biotecnologia/Instituto de Agrobiotecnologia y Biologia Molecular (INTA-CONICET), Hurlingham, Buenos Aires, Argentina." + }, + { + "author_name": "Viviana Re", + "author_inst": "Instituto de Virologia Dr. J. M. Vanella, Facultad de Ciencias Medicas, Universidad Nacional de Cordoba; Consejo Nacional de Investigaciones Cientificas y Tecni" + }, + { + "author_name": "Ezequiel Sosa", + "author_inst": "Instituto de Quimica Biologica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina" + }, + { + "author_name": "Jonathan Zaiat", + "author_inst": "Instituto de Quimica Biologica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina" + }, + { + "author_name": "Sebastian Zunino", + "author_inst": "Laboratorio de Virologia Molecular, Hospital Blas L. Dubarry de Mercedes, provincia de Buenos Aires, Argentina; Universidad Nacional de Lujan, Departamento de C" + }, + { + "author_name": "Dario Do porto", + "author_inst": "Instituto de Quimica Biologica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), CONICET, Ciudad de Buenos Aires, Argentina" + }, + { + "author_name": "Maria Elina Acevedo", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Cristina Alvarez Lopez", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Maria Laura Alvarez", + "author_inst": "Laboratorio del Hospital Zonal Dr. Ramon Carrillo, San Carlos De Bariloche, provincia de Rio Negro, Argentina" + }, + { + "author_name": "Patricia Angeleri", + "author_inst": "Comite Operativo de Emergencia COVID, Ministerio de Salud de la Ciudad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Andres Angelletti", + "author_inst": "Laboratorio de salud publica, Facultad de Ciencias Exactas, UNLP, La Plata, Provincia de Buenos Aires, Argentina; Laboratorio de Virologia, HIEAyC San Juan de D" + }, + { + "author_name": "Manuel Arca", + "author_inst": "Laboratorio de Virologia del Hospital JJ Urquiza, Concepcion del Uruguay, provincia de Entre Rios, Argentina" + }, + { + "author_name": "Gabriela Barbas", + "author_inst": "Secretaria de Prevencion y Promocion, Ministerio de Salud de la provincia de Cordoba, Argentina." + }, + { + "author_name": "Ana Bertone", + "author_inst": "Laboratorio de la Direccion de Epidemiologia, Santa Rosa, provincia de La Pampa, Argentina." + }, + { + "author_name": "Agustina Bonnet", + "author_inst": "Laboratorio de Virologia del Hospital JJ Urquiza, Concepcion del Uruguay, provincia de Entre Rios, Argentina" + }, + { + "author_name": "Ignacio Bourlot", + "author_inst": "Laboratorio de biologia molecular del Hospital Centenario, Gualeguaychu, provincia de Entre Rios, Argentina." + }, + { + "author_name": "Alejandro Castello", + "author_inst": "Plataforma de Servicios Biotecnologicos; UTTIPP/PSB, Bernal, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Gonzalo Castro", + "author_inst": "Laboratorio Central de la Provincia de Cordoba, Ministerio de Salud la provincia de Cordoba, Argentina." + }, + { + "author_name": "Carolina Ceriani", + "author_inst": "Laboratorio de Virologia de la Facultad de Veterinaria de la Universidad Nacional del Centro de la provincia de Buenos Aires (UNCPBA), Tandil, provincia de Buen" + }, + { + "author_name": "Carlos Cimino", + "author_inst": "Instituto Nacional de Epidemiologia Dr. Jara (Mar del Plata, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Julian Cipelli", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Maria Colmeiro", + "author_inst": "Laboratorio de Virologia, HIEAyC \"San Juan de Dios\", La Plata, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Andres Cordero", + "author_inst": "Laboratorio de salud publica, Facultad de Ciencias Exactas, UNLP, La Plata, Provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Carolina Cristina", + "author_inst": "Centro de Investigaciones Basicas y Aplicadas, UNNOBA, Junin, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Sofia Di Bella", + "author_inst": "Laboratorio de Virologia, HIEAyC San Juan de Dios, La Plata, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Regina Ercole", + "author_inst": "Laboratorio de Virologia, HIEAyC San Juan de Dios, La Plata, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Yesica Espasandin", + "author_inst": "Laboratorio del Hospital Zonal Dr. Ramon Carrillo, San Carlos De Bariloche, provincia de Rio Negro, Argentina" + }, + { + "author_name": "Carlos Espul", + "author_inst": "Direccion de epidemiologia y Red de Laboratorios del Ministerio de Salud de la provincia de Mendoza, Argentina." + }, + { + "author_name": "Andrea Falaschi", + "author_inst": "Direccion de epidemiologia y Red de Laboratorios del Ministerio de Salud de la provincia de Mendoza, Argentina." + }, + { + "author_name": "Facundo Fernandez Moll", + "author_inst": "Centro de Investigaciones Basicas y Aplicadas, UNNOBA, Junin, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Andrea Gatelli", + "author_inst": "Laboratorio de Virologia, HIEAyC San Juan de Dios, La Plata, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Sandra Goni", + "author_inst": "Plataforma de Servicios Biotecnologicos; UTTIPP/PSB, Bernal, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Maria E Jofre", + "author_inst": "Laboratorio de Biologia Molecular Bolivar, LABBO, Bolivar, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Jose Jaramillo", + "author_inst": "Laboratorio de Virologia Molecular, Hospital Blas L. Dubarry de Mercedes, provincia de Buenos Aires, Argentina" + }, + { + "author_name": "Natalia Labarta", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina" + }, + { + "author_name": "Maria A Lacaze", + "author_inst": "Programa Laboratorio de Salud Publica Dr Dalmiro Perez Laborda, Ministerio de Salud de la provincia de San Luis, Argentina." + }, + { + "author_name": "Rocio Larreche", + "author_inst": "Laboratorio de Biologia Molecular Bolivar, LABBO, Bolivar, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Viviana Leiva", + "author_inst": "Laboratorio de Biologia Molecular Bolivar, LABBO, Bolivar, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Gustavo Levin", + "author_inst": "Laboratorio de biologia molecular del Hospital Centenario, Gualeguaychu, provincia de Entre Rios, Argentina." + }, + { + "author_name": "Erica Luczak", + "author_inst": "Laboratorio del Hospital Interzonal General de Agudos Evita, Lanus, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Marcelo Mandile", + "author_inst": "Plataforma de Servicios Biotecnologicos; UTTIPP/PSB, Bernal, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Carla Massone", + "author_inst": "Laboratorio de Virologia Molecular, Hospital Blas L. Dubarry de Mercedes, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Melina Mazzeo", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina" + }, + { + "author_name": "Carla Medina", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina." + }, + { + "author_name": "Belen Monaco", + "author_inst": "Laboratorio de Virologia Molecular, Hospital Blas L. Dubarry de Mercedes, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Luciana Montoto", + "author_inst": "Laboratorio de Biologia Molecular Hospital Pedro de Elizalde, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Viviana Mugna", + "author_inst": "Laboratorio Central, ciudad de Santa Fe, provincia de Santa Fe. Argentina." + }, + { + "author_name": "Alejandra Musto", + "author_inst": "Laboratorio del Hospital Interzonal General de Agudos Evita, Lanus, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Guillermo Ojeda", + "author_inst": "Laboratorio Central, ciudad de Santa Fe, provincia de Santa Fe. Argentina." + }, + { + "author_name": "Carolina Pintos", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina." + }, + { + "author_name": "Marcia Pozzati", + "author_inst": "Laboratorio de Biologia Molecular, Hospital Cosme Argerich, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Marilina Rahhal", + "author_inst": "Laboratorio de Hospital El Cruce Dr. Nestor C. Kirchner, CEMET, Florencio Varela, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Claudia Rechimont", + "author_inst": "Laboratorio de la Direccion de Epidemiologia, Santa Rosa, provincia de La Pampa, Argentina." + }, + { + "author_name": "Federico Remes Lenicov", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y Sida, CONICET-UBA, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Gabriela Rompato", + "author_inst": "Laboratorio Central, ciudad de Santa Fe, provincia de Santa Fe. Argentina." + }, + { + "author_name": "Vanesa Seery", + "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y Sida, CONICET-UBA, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Leticia Siri", + "author_inst": "Laboratorio de biologia molecular del Hospital Centenario, Gualeguaychu, provincia de Entre Rios, Argentina." + }, + { + "author_name": "Julieta Spina", + "author_inst": "Laboratorio de Biologia Molecular. Hospital Dr. Hector Cura, Olavarria, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Cintia Streitenberger", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina." + }, + { + "author_name": "Ariel Suarez", + "author_inst": "Departamento de Biologia y genetica molecular; IACA Laboratorios, Bahia Blanca, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Jorgelina Suarez", + "author_inst": "Centro de Investigaciones Basicas y Aplicadas, UNNOBA, Junin, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Paula Sujanski", + "author_inst": "Comite Operativo de Emergencia COVID, Ministerio de Salud de la Ciudad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Juan M Talia", + "author_inst": "Programa Laboratorio de Salud Publica Dr Dalmiro Perez Laborda, Ministerio de Salud de la provincia de San Luis, Argentina." + }, + { + "author_name": "Clara Theaux", + "author_inst": "Laboratorio de Biologia molecular del Hospital General de Agudos Dr. Carlos G. Durand, Cuidad Autonoma de Buenos Aires, Argentina." + }, + { + "author_name": "Guillermo Thomas", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina." + }, + { + "author_name": "Marina Ticeira", + "author_inst": "Laboratorio de Biologia Molecular Bolivar, LABBO, Bolivar, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Estefania Tittarelli", + "author_inst": "Departamento de Biologia y genetica molecular; IACA Laboratorios, Bahia Blanca, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Rosana Toro", + "author_inst": "Laboratorio de salud publica, Facultad de Ciencias Exactas, UNLP, La Plata, Provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Osvaldo Uez", + "author_inst": "Instituto Nacional de Epidemiologia Dr. Jara (Mar del Plata, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Maria B Zaffanella", + "author_inst": "Laboratorio de Biologia Molecular. Hospital Dr. Hector Cura, Olavarria, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "Cecilia Ziehm", + "author_inst": "Laboratorio Central ciudad de Neuquen, Ministerio de Salud, Neuquen, Argentina." + }, + { + "author_name": "Martin Zubieta", + "author_inst": "Laboratorio de Hospital El Cruce Dr. Nestor C. Kirchner, CEMET, Florencio Varela, provincia de Buenos Aires, Argentina." + }, + { + "author_name": "- PAIS Consortium", + "author_inst": "-" + }, + { + "author_name": "Alicia Mistchenko", + "author_inst": "Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez, CABA, Argentina; Comision de Investigaciones Cientificas de la provincia de Buenos Aires, Arg" + }, + { + "author_name": "Laura Valinotto", + "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez" + }, + { + "author_name": "Mariana Viegas", + "author_inst": "Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, Argentina; Laboratorio de Virologia, Hospital de Ninos Dr. Ricardo Gutierrez" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.19.21260759", "rel_title": "Development and validation of a prognostic model for COVID-19: a population-based cohort study in Iceland", @@ -658782,105 +659665,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, - { - "rel_doi": "10.1101/2021.07.20.21260849", - "rel_title": "Longitudinal analysis of antibody responses to the Pfizer BNT162b2 vaccine in Patients Undergoing Maintenance Hemodialysis", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260849", - "rel_abs": "BackgroundHemodialyzed patients are at higher risk for COVID-19 and were prioritized in the Portuguese vaccination campaign\n\nMethodsWe performed a prospective, longitudinal, cohort analysis of 143 patients on hemodialysis and 143 age-matched controls along BTN162b2 vaccination. ELISA quantified anti-full-length Spike IgG, IgM and IgA levels prior to the first vaccine dose (t0); 3 weeks later (second dose, t1); and 3 weeks later (t2); 127 patients were re-evaluated140 (t3) and 180 days (t4) after the first dose.\n\nResultsSeroconversion at t1 was remarkably low in patients, with positivity for anti-spike IgG, IgM and IgA antibodies of 29.4%, 12% and 41%, respectively, increasing to 90.9% (IgG) and 83.9% (IgA) in t2, (IgM remained unchanged). Below 70 years of age anti-spike IgG levels at t1 were significantly lower compared to age-matched controls and showed a profile similar to older individuals. Immunosuppression was associated with lower antibody responses (p=0.005 at t1; p=0.008 at t2). Previous unresponsiveness to hepatitis B vaccination (75/129, 58% of patients negative for anti-HBs antibodies) did not correlate with humoral unresponsiveness to BTN162b2. Anti-spike IgG, IgM and IgA positivity and antibody levels significantly decay at t3, with IgG levels showing further waning at t4.\n\nConclusionsThe large majority of hemodialyzed patients showed IgG seroconversion upon BNT162b2 mRNA vaccination, albeit a sizable proportion of patients presented poor responses. Follow-up of antibody responses 180 days post vaccination unveiled significant decay of anti-spike antibodies and warrant close monitoring of COVID-19 infection and further studies on reinforced vaccination schedules in patients undergoing maintenance hemodialysis.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Andr\u00e9 Weigert", - "author_inst": "Davita \u00d3bidos, Casais de Alvito, Portugal" - }, - { - "author_name": "Marie-Louise Bergman", - "author_inst": "IGC, Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal" - }, - { - "author_name": "Ligia Gon\u00e7alves", - "author_inst": "IGC, Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal" - }, - { - "author_name": "Iolanda Godinho", - "author_inst": "Davita \u00d3bidos, Casais de Alvito, Portugal" - }, - { - "author_name": "N\u00e1dia Duarte", - "author_inst": "IGC, Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal" - }, - { - "author_name": "Rita Abrantes", - "author_inst": "Davita \u00d3bidos, Casais de Alvito, Portugal" - }, - { - "author_name": "Patr\u00edcia Borges", - "author_inst": "IGC, Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal" - }, - { - "author_name": "Ana Brennand", - "author_inst": "IGC, Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal" - }, - { - "author_name": "Vanessa Malheiro", - "author_inst": "IGC, Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal" - }, - { - "author_name": "Paula Matoso", - "author_inst": "IGC, Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal" - }, - { - "author_name": "Onome Akpogheneta", - "author_inst": "IGC, Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal" - }, - { - "author_name": "Lindsay Kosack", - "author_inst": "IGC, Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal" - }, - { - "author_name": "Pedro Cruz", - "author_inst": "Davita \u00d3bidos, Casais de Alvito, Portugal" - }, - { - "author_name": "Estela Nogueira", - "author_inst": "Davita \u00d3bidos, Casais de Alvito, Portugal" - }, - { - "author_name": "Magda Pereira", - "author_inst": "Davita \u00d3bidos, Casais de Alvito, Portugal" - }, - { - "author_name": "Ana Ferreira", - "author_inst": "Davita \u00d3bidos, Casais de Alvito, Portugal" - }, - { - "author_name": "Marco Marques", - "author_inst": "Affidea Laborat\u00f3rio Lisboa, Portugal" - }, - { - "author_name": "Telmo Nunes", - "author_inst": "CIISA, Centro de Investiga\u00e7\u00e3o Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterin\u00e1ria, Universidade de Lisboa, Lisboa, Portugal" - }, - { - "author_name": "Jo\u00e3o Viana", - "author_inst": "Servi\u00e7o de Patologia Cl\u00ednica, Centro Hospitalar de Lisboa Ocidental EPE, Carnaxide, Portugal" - }, - { - "author_name": "Jocelyne Demengeot", - "author_inst": "IGC, Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal" - }, - { - "author_name": "Carlos Penha-Gon\u00e7alves", - "author_inst": "IGC, Instituto Gulbenkian de Ci\u00eancia, Oeiras, Portugal" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.21.453304", "rel_title": "Impact of human airway epithelial cellular composition on SARS-CoV-2 infection biology", @@ -659121,6 +659905,65 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.07.22.453287", + "rel_title": "Competent immune responses to SARS-CoV-2 variants in older adults following mRNA vaccination", + "rel_date": "2021-07-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.22.453287", + "rel_abs": "Aging is associated with a reduced magnitude of primary immune responses to vaccination and constriction of immune receptor repertoire diversity. Clinical trials demonstrated high efficacy of mRNA based SARS-CoV-2 vaccines in older adults but concerns about virus variant escape have not been well addressed. We have conducted an in-depth analysis of humoral and cellular immunity against an early-pandemic viral isolate and compared that to the P.1. (Gamma) and B.1.617.2 (Delta) variants in <50 and >55 age cohorts of mRNA vaccine recipients. We have further measured neutralizing antibody titers for B.1.617.1 (Kappa) and B.1.595; a SARS-CoV-2 isolate bearing Spike mutation E484Q. As reported, robust immunity required the second dose of vaccine. Older vaccinees manifested robust cellular immunity against early-pandemic SARS-CoV-2 and more recent variants, which remained statistically comparable to the adult group. The older cohort had lower neutralizing capacity at the first time point following the second dose, but at later time points immunity was indistinguishable between them. While the duration of these immune responses remains to be determined over longer periods of time, these results provide reasons for optimism regarding vaccine protection of older adults against SARS-CoV-2 variants and inform thinking about boost vaccination with variant vaccines.\n\neTOC summaryVaccine responses are often diminished with aging, but we found strong responses to SARS-CoV-2 in older adults following mRNA vaccination. T cell responses were not diminished when confronted by SARS-CoV-2 variants. Neutralizing Ab were reduced but not more than those in adults.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC=\"FIGDIR/small/453287v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@1091655org.highwire.dtl.DTLVardef@1996173org.highwire.dtl.DTLVardef@ccf2f9org.highwire.dtl.DTLVardef@163ed22_HPS_FORMAT_FIGEXP M_FIG C_FIG Created with BioRender.com", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Mladen Jergovi\u0107", + "author_inst": "University of Arizona" + }, + { + "author_name": "Jennifer L. Uhrlaub", + "author_inst": "University of Arizona" + }, + { + "author_name": "Makiko Watanabe", + "author_inst": "University of Arizona" + }, + { + "author_name": "Christine M. Bradshaw", + "author_inst": "University of Arizona" + }, + { + "author_name": "Lisa M. White", + "author_inst": "University of Arizona" + }, + { + "author_name": "Bonnie J. LaFleur", + "author_inst": "University of Arizona" + }, + { + "author_name": "Taylor Edwards", + "author_inst": "University of Arizona" + }, + { + "author_name": "Ryan Sprissler", + "author_inst": "University of Arizona" + }, + { + "author_name": "Michael Worobey", + "author_inst": "University of Arizona" + }, + { + "author_name": "Deepta Bhattacharya", + "author_inst": "University of Arizona" + }, + { + "author_name": "Janko Nikolich-\u017dugich", + "author_inst": "University of Arizona" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.07.20.21260892", "rel_title": "Variation in SARS-CoV-2 bioaerosol production in exhaled breath", @@ -660440,41 +661283,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, - { - "rel_doi": "10.1101/2021.07.15.21259539", - "rel_title": "Medication Use Patterns in COVID-19 Positive Patients in a large state-wide health system by Age Group, Comorbidity, and Month During the Pandemic in 2020", - "rel_date": "2021-07-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21259539", - "rel_abs": "ObjectivesMain objective was to systematically determine most frequently used medications among COVID-19 patients overall and by hospitalization status. Secondary objective was to measure use patterns of medications considered potential therapeutic options\n\nDesignRetrospective cohort study.\n\nSettingThe five academic medical centers of University of California Health.\n\nParticipantsUniversity of California COVID Research Data Set (UC CORDS) patients between March 10, 2020 and December 31, 2020.\n\nExposure(s)Confirmed COVID-19 positive by SARS-CoV-2 nucleic acid amplification.\n\nMain Outcome(s) and Measure(s)Main outcomes were percentages of patients prescribed medications, overall, by age group, and by comorbidity based on hospitalization status. Use percentage by month of COVID-19 diagnosis was measured. Cumulative count of potential therapeutic options was measured over time.\n\nResultsDataset included 22897 unique patients with COVID-19 (mean [SD] age, 42.4 [20.4] years; 12154 [53%] female). Among the sample, 6326 28%) were non-Hispanic White, 8475 (37%) were Hispanic, 1562 (7%) Asian, and 1313 (6%) Black. A COVID-related hospitalization occurred in 3546 patients. Of the hospitalized patients, more than 30% had baseline comorbidities of hypertension (48%), hyperlipidemia (37%), and type 2 diabetes (35%). Most frequently used medications in patients overall were acetaminophen (21.2%), albuterol (14.9%), ondansetron (13.9%), and enoxaparin (10.8%). Medications used were generally similar across ages and comorbidities. Prior to May, dexamethasone was rarely used, with well under 50 COVID-19 patients that had been hospitalized to that point receiving the medication. By mid-August, more than 500 patients to that point had received dexamethasone. Hydroxychloroquine use effectively halted in COVID-19 hospitalized patients after May. Throughout the period of March to December 2020, enoxaparin was used in the most patients to that point at any instance. By mid-December, more than 2000 in the analysis cohort of hospitalized patients had received enoxaparin.\n\nConclusions and RelevanceIn this retrospective cohort study, across age and comorbidity groups, predominant utilization was for supportive care therapy. Dexamethasone and remdesivir experienced large increases in use. Conversely, hydroxychloroquine and azithromycin use markedly dropped. Medication utilization rapidly shifted towards more evidence-concordant treatment of patients with COVID-19 as rigorous study findings emerged.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jonathan H Watanabe", - "author_inst": "UC Irvine School of Pharmacy & Pharmaceutical Sciences" - }, - { - "author_name": "Jimmy Kwon", - "author_inst": "UC Irvine Donald Bren School of Information and Computer Sciences" - }, - { - "author_name": "Bin Nan", - "author_inst": "Department of Statistics UC Irvine Donald Bren School of Information and Computer Sciences" - }, - { - "author_name": "Shira R Abeles", - "author_inst": "UC San Diego School of Medicine" - }, - { - "author_name": "Sanjay Mehta", - "author_inst": "UC San Diego School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.20.452903", "rel_title": "Viral receptor profiles of masked palm civet revealed by single-cell transcriptomics", @@ -660807,6 +661615,49 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.07.20.453118", + "rel_title": "Integrin activation is an essential component of SARS-CoV-2 infection", + "rel_date": "2021-07-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.20.453118", + "rel_abs": "Cellular entry of coronaviruses depends on binding of the viral spike (S) protein to a specific cellular receptor, the angiotensin-converting enzyme 2 (ACE2). Furthermore, the viral spike protein expresses an RGD motif, suggesting that cell surface integrins may be attachment co-receptors. However, using infectious SARS-CoV-2 requires a biosafety level 3 laboratory (BSL-3), which limits the techniques that can be used to study the mechanism of cell entry. Here, we UV-inactivated SARS-CoV-2 and fluorescently labeled the envelope membrane with octadecyl rhodamine B (R18) to explore the role of integrin activation in mediating both cell entry and productive infection. We used flow cytometry and confocal fluorescence microscopy to show that fluorescently labeled SARS-CoV-2R18 particles engage basal-state integrins. Furthermore, we demonstrate that Mn2+, which activates integrins and induces integrin extension, enhances cell binding and entry of SARS-CoV-2R18 in proportion to the fraction of integrins activated. We also show that one class of integrin antagonist, which binds to the I MIDAS site and stabilizes the inactive, closed conformation, selectively inhibits the engagement of SARS-CoV-2R18 with basal state integrins, but is ineffective against Mn2+-activated integrins. At the same time, RGD-integrin antagonists inhibited SARS-CoV-2R18 binding regardless of integrin activity state. Integrins transmit signals bidirectionally: inside-out signaling primes the ligand binding function of integrins via a talin dependent mechanism and outside-in signaling occurs downstream of integrin binding to macromolecular ligands. Outside-in signaling is mediated by G13 and induces cell spreading, retraction, migration, and proliferation. Using cell-permeable peptide inhibitors of talin, and G13 binding to the cytoplasmic tail of an integrins {beta} subunit, we further demonstrate that talin-mediated signaling is essential for productive infection by SARS-CoV-2.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Peter Simons", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Derek Rinaldi", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Virginie Bondu", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Alison Kell", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Steven Bradfute", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Diane Lidke", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Tione Buranda", + "author_inst": "University of New Mexico School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2021.07.20.453054", "rel_title": "Discovery of nanobodies against SARS-CoV-2 and an uncommon neutralizing mechanism", @@ -662410,33 +663261,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.15.21260576", - "rel_title": "Platelet size as a predictor for severity and mortality in COVID-19 patients: a systematic review and meta-analysis", - "rel_date": "2021-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260576", - "rel_abs": "BackgroundParameters reflecting platelet size can be sensitive indicators that circulating platelets are activated and COVID-19 patients are at increased risk of thrombosis. This systematic review aims to assess the association of mean platelet volume (MPV), platelet distribution width (PDW) and platelet-large cell ratio (P-LCR) with disease severity and mortality in COVID-19 patients.\n\nMethodsEnglish and Chinese databases were searched electronically to identify studies reporting data on MPV, PDW or P-LCR in COVID-19 patients. Included articles underwent a quality rating. A meta-analysis was performed using the standard mean difference and interpreted as the common language effect size (CLES).\n\nResultsTwenty-two studies (11,906 patients) were included in the meta-analysis. Of these, 14 were rated poor and eight were fair. The MPV and P-LCR was significantly higher at hospital admission in severe patients compared to non-severe patients. The MPV, PDW and P-LCR were significantly higher at hospital admission in non-survivors compared to survivors. There was a marked increase in the probability of a severe COVID-19 patient presenting with higher P-LCR at hospital admission than a non-severe patient (CLES: 68.7% [95% CI: 59.8%, 76.5%]), when compared with MPV and PDW ((CLES: 59.2% [95% CI: 53.1%, 65.1%]) and (CLES: 55.9% [95% CI: 50.6%, 62.2%]), respectively).\n\nConclusionSevere COVID-19 disease is associated with the increased production of larger, younger platelets. When comparing MPV, PDW and P-LCR, P-LCR is the most important biomarker for evaluating platelet activity. P-LCR testing at hospital admission could identify COVID-19 patients with increased risk for thrombotic events, allowing preventative treatment.\n\nSummary TableO_ST_ABSWhat is known on this topicC_ST_ABSO_LIThe incidence of thrombotic complications is high in COVID-19 patients with severe disease.\nC_LIO_LIParameters reflecting platelet size can be sensitive indicators that circulating platelets are activated and that COVID-19 patients are at increased risk of thrombosis.\nC_LI\n\nWhat does this paper addO_LIWhen compared to MPV and PDW, P-LCR is the most important biomarker for evaluating platelet activity in COVID-19 patients at hospital admission and could be used to identify patients with increased risk for thrombotic events.\nC_LIO_LICurrent evidence is predominantly derived from retrospective design. Prospective studies are warranted to accurately determine cut-off values that may be used in the clinical setting.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sarah A Daniels", - "author_inst": "The University of Manchester" - }, - { - "author_name": "Hua Wei", - "author_inst": "The University of Manchester" - }, - { - "author_name": "David W Denning", - "author_inst": "The University of Manchester" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2021.07.15.21260528", "rel_title": "Analysis, quantification, and visualization of RT-LAMP technique for detection of COVID-19", @@ -662657,6 +663481,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2021.07.15.21260543", + "rel_title": "Understanding Adverse Population Sentiment Towards the Spread of COVID-19 in the United States", + "rel_date": "2021-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260543", + "rel_abs": "BackgroundDuring the ongoing COVID-19 pandemic, the immediate threat of illness and mortality is not the only concern. In the United States, COVID-19 is not only causing physical suffering to patients, but also great levels of adverse sentiment (e.g., fear, panic, anxiety) among the public. Such secondary threats can be anticipated and explained through sentiment analysis of social media, such as Twitter.\n\nMethodsWe obtained a dataset of geotagged tweets on the topic of COVID-19 in the contiguous United States during the period of 11/1/2019 - 9/15/2020. We classified each tweet into \"adverse\" and \"non-adverse\" using the NRC Emotion Lexicon and tallied up the counts for each category per county per day. We utilized the space-time scan statistic to find clusters and a three-stage regression approach to identify socioeconomic and demographic correlates of adverse sentiment.\n\nResultsWe identified substantial spatiotemporal variation in adverse sentiment in our study area/period. After an initial period of low-level adverse sentiment (11/1/2019 - 1/15/2020), we observed a steep increase and subsequent fluctuation at a higher level (1/16/2020 - 9/15/2020). The number of daily tweets was low initially (11/1/2019 - 1/22/2020), followed by spikes and subsequent decreases until the end of the study period. The space-time scan statistic identified 12 clusters of adverse sentiment of varying size, location, and strength. Clusters were generally active during the time period of late March to May/June 2020. Increased adverse sentiment was associated with decreased racial/ethnic heterogeneity, decreased rurality, higher vulnerability in terms of minority status and language, and housing type and transportation.\n\nConclusionsWe utilized a dataset of geotagged tweets to identify the spatiotemporal patterns and the spatial correlates of adverse population sentiment during the first two waves of the COVID-19 pandemic in the United States. The characteristics of areas with high adverse sentiment may be relevant for communication of containment measures. The combination of spatial clustering and regression can be beneficial for understanding of the ramifications of COVID-19, as well as disease outbreaks in general.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alexander Hohl", + "author_inst": "Department of Geography, University of Utah" + }, + { + "author_name": "Moongi Choi", + "author_inst": "Department of Geography, University of Utah" + }, + { + "author_name": "Richard Medina", + "author_inst": "Department of Geography, University of Utah" + }, + { + "author_name": "Neng Wan", + "author_inst": "Department of Geography, University of Utah" + }, + { + "author_name": "Ming Wen", + "author_inst": "Department of Sociology, University of Utah" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.15.21260346", "rel_title": "Elderly acceptance of telemedicine use in Hong Kong during and after the COVID-19 pandemic: a cross-sectional cohort survey", @@ -664272,73 +665131,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.13.21260414", - "rel_title": "COVID-19 convalescent plasma donors: impact of vaccination on antibody levels, breakthrough infections and reinfection rate.", - "rel_date": "2021-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260414", - "rel_abs": "From April 2020 through May 2021 in Padova Province 3395 COVID-19 recovered patients were recruited as potential convalescent plasma donors and tested for SARS-CoV-2 antibodies. Since January 2021 COVID-19 vaccination campaign began in Italy, the impact of vaccination on antibody levels and suspect vaccine breakthrough infections in these subjects were investigated. Post-vaccination anti-Sars-Cov-2 antibody level in 54 previously infected subjects had an exponential increase compared to pre-vaccination level regardless of the number of vaccine doses. However after 100 days from vaccination SARS-CoV-2 antibody level tends to decline. Post-vaccination primary infections were detected in 15 cases, with 3 possible breakthrough infections after a full vaccination course. In these cases, antibody response after infection was present but weaker than the one of subjects vaccinated after natural infection. A trend toward stronger antibody response was observed with increasing distance between natural infection and vaccination. Additionally, 2 cases of asymptomatic reinfections are also discussed.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Massimo La Raja", - "author_inst": "Transfusion Medicine Department of Padova , Azienda Ospedale-Universita' di Padova" - }, - { - "author_name": "Monia Pacenti", - "author_inst": "Microbiologiy and Virology, Azienda Ospedale-Universita' di Padova" - }, - { - "author_name": "Ileana Grimaldi", - "author_inst": "Microbiologiy and Virology, Azienda Ospedale-Universita' di Padova" - }, - { - "author_name": "Caterina Boldrin", - "author_inst": "Microbiologiy and Virology, Azienda Ospedale-Universita' di Padova" - }, - { - "author_name": "Margherita Cattai", - "author_inst": "Microbiologiy and Virology, Azienda Ospedale-Universita' di Padova" - }, - { - "author_name": "Erica Solimbergo", - "author_inst": "Transfusion Medicine Department of Padova, Azienda ULSS 6 Euganea" - }, - { - "author_name": "Anna Battisti", - "author_inst": "Transfusion Medicine Department of Padova, Azienda ULSS 6 Euganea" - }, - { - "author_name": "Michele Scomazzon", - "author_inst": "Transfusion Medicine Department of Padova, Azienda ULSS 6 Euganea" - }, - { - "author_name": "Alberto Roman", - "author_inst": "Transfusion Medicine Department of Padova, Azienda ULSS 6 Euganea" - }, - { - "author_name": "Anna Rosa Lazzaro", - "author_inst": "Transfusion Medicine Department of Padova, Azienda Ospedale-Universita' di Padova" - }, - { - "author_name": "Stefano Vicari", - "author_inst": "Azienda ULSS 6 Euganea" - }, - { - "author_name": "Stefano Terzariol", - "author_inst": "Transfusion Medicine Department of Padova, Azienda Ospedale-Universita' di Padova" - }, - { - "author_name": "Giustina De Silvestro", - "author_inst": "Transfusion Medicine Department of Padova, Azienda Ospedale-Universita' di Padova" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.15.21260600", "rel_title": "Remdesivir for the treatment of COVID-19 disease: A retrospective comparative study of patients treated with and without Remdesivir", @@ -664663,6 +665455,49 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.07.17.452576", + "rel_title": "Mutation-induced Changes in the Receptor-binding Interface of the SARS-CoV-2 Delta Variant B.1.617.2 and Implications for Immune Evasion", + "rel_date": "2021-07-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.17.452576", + "rel_abs": "While the vaccination efforts against SARS-CoV-2 infections are ongoing worldwide, new genetic variants of the virus are emerging and spreading. Following the initial surges of the Alpha (B.1.1.7) and the Beta (B.1.351) variants, a more infectious Delta variant (B.1.617.2) is now surging, further deepening the health crises caused by the pandemic. The sharp rise in cases attributed to the Delta variant has made it especially disturbing and is a variant of concern. Fortunately, current vaccines offer protection against known variants of concern, including the Delta variant. However, the Delta variant has exhibited some ability to dodge the immune system as it is found that neutralizing antibodies from prior infections or vaccines are less receptive to binding with the Delta spike protein. Here, we investigated the structural changes caused by the mutations in the Delta variants receptor-binding interface and explored the effects on binding with the ACE2 receptor as well as with neutralizing antibodies. We find that the receptor-binding {beta}-loop-{beta} motif adopts an altered but stable conformation causing separation in some of the antibody binding epitopes. Our study shows reduced binding of neutralizing antibodies and provides a possible mechanism for the immune evasion exhibited by the Delta variant.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Prabin Baral", + "author_inst": "Florida International University" + }, + { + "author_name": "Nisha Bhattarai", + "author_inst": "Florida International University" + }, + { + "author_name": "Md Lokman Hossen", + "author_inst": "Florida International University" + }, + { + "author_name": "Vitalii Stebliankin", + "author_inst": "Florida International University" + }, + { + "author_name": "Bernard Gerstman", + "author_inst": "Florida International University" + }, + { + "author_name": "Giri Narasimhan", + "author_inst": "Florida International University" + }, + { + "author_name": "Prem P Chapagain", + "author_inst": "Florida International University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.07.16.452733", "rel_title": "One mucosal administration of a live attenuated recombinant COVID-19 vaccine protects non-human primates from SARS-CoV-2", @@ -666194,45 +667029,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.12.21260386", - "rel_title": "Homologous and Variant-Specific Memory B-Cell and Antibody Responses after SARS-CoV-2 mRNA Vaccination", - "rel_date": "2021-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260386", - "rel_abs": "ImportanceA better understanding of the immune memory and functional humoral immunity directed at the emerging Variants of Concern (VoC) strains after SARS-CoV-2 vaccination is essential for predicting the longevity of heterotypic protection.\n\nObjectiveThe aim of our study was to characterize functional humoral immunity (including memory B cell response) after COVID-19 mRNA vaccination and to determine/compare the reactivity of COVID-19 vaccine-induced memory B cells to the emerging SARS-CoV-2 Variants of Concern (VoC).\n\nDesign, setting, participants and interventionsWe designed an exploratory longitudinal observational (convenience sample-based) study at Mayo Clinic, Rochester, MN that enrolled and followed naive subjects and recovered COVID-19 subjects from Olmsted County, MN and surrounding areas after COVID-19 vaccination in January-June 2021. The study enrolled 17 relatively healthy subjects, 59% females and 94% White/Non-Hispanic or Latino with median age at enrollment 41 years. The subjects received either the BNT162b2 (Pfizer/BioNtech) or mRNA-1273 (Moderna) vaccine (n=3) and provided a blood sample at baseline, at [~]3 weeks after their first vaccine dose/before the second dose, and at [~]2 weeks after the receipt of their second vaccine dose.\n\nMain outcomes and measuresSpike-specific humoral and memory B cells responses were assessed over time after vaccination against the original Wuhan-Hu-1/vaccine and against emerging VoC strains/antigens.\n\nResultsWe observed a robust neutralizing antibody response after COVID-19 mRNA vaccination, but a reduction in the functional antibody activity to several of the emerging SARS-CoV-2 VoC. Consistent with this, we also found differences in the number of isotype-switched/IgG+ MBCs responding to homologous and variant receptor-binding domain/RBDs after vaccination. We found a reduction of MBCs reactive to RBDs of Beta, Gamma and Delta SARS-CoV-2 VoC strains.\n\nConclusion and relevanceIn this exploratory study in subjects following receipt of COVID-19 mRNA vaccine, we found differences in antibody titers observed for VoCs after vaccination that are accompanied with, and can partially be explained by, decreased MBC reactivity against the VoCs. This can further attenuate the generated recall humoral immune response upon exposure to these variants.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the reactivity of COVID-19 vaccine-induced memory B cells to the emerging SARS-CoV-2 Variants of Concern (VoC)?\n\nFindingsIn this longitudinal cohort study of subjects receiving COVID-19 mRNA vaccine we assessed memory B cell response and functional antibody titers. We found statistically significant differences between the frequencies of memory B cells responding to homologous and VoC receptor-binding domain/RBDs after vaccination.\n\nMeaningIn concert with the lowered antibody response, the reduced memory B-cell response to VoC could translate to an increased susceptibility to the emerging SARS-CoV-2 variant strains in the face of waning immunity.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Iana H. Haralambieva", - "author_inst": "Mayo Clinic Vaccine Research Group" - }, - { - "author_name": "Jonathon M. Monroe", - "author_inst": "Mayo Clinic Vaccine Research Group" - }, - { - "author_name": "Diane E. Grill", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Inna G Ovsyannikova", - "author_inst": "Mayo Clinic Vaccine Research Group" - }, - { - "author_name": "Gregory A. Poland", - "author_inst": "Mayo Clinic Vaccine Research Group" - }, - { - "author_name": "Richard B. Kennedy", - "author_inst": "Mayo Clinic Vaccine Research Group" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.12.21260227", "rel_title": "Convergent epitope-specific T cell responses after SARS-CoV-2 infection and vaccination", @@ -666689,6 +667485,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.11.21260318", + "rel_title": "Harnessing the Wisdom of the Crowd to Forecast Incident and Cumulative COVID-19 Mortality in the United States", + "rel_date": "2021-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.11.21260318", + "rel_abs": "BackgroundForecasting models have played a pivotal role in health policy decision making during the coronavirus disease-2019 (COVID-19) pandemic. A combined forecast from multiple models will be typically more accurate than an individual forecast, but there are few examples of studies of combined forecasts of COVID-19 data, focusing mainly on simple mean and median ensembles and involving short forecast evaluation periods. We aimed to investigate the accuracy of different ways of combining probabilistic forecasts of weekly COVID-19 mortality data, including two weighted methods that we developed previously, on an extended dataset and new dataset, and evaluate over a period of 52 weeks.\n\nMethodsWe considered 95% interval and point forecasts of weekly incident and cumulative COVID-19 mortalities between 16 May 2020 and 8 May 2021 in multiple locations in the United States. We compared the accuracy of simple and more complex combining methods, as well as individual models.\n\nResultsThe average of the forecasts from the individual models was consistently more accurate than the average performance of these models (the mean combination), which provides a fundamental motivation for combining. Weighted combining performed well for both incident and cumulative mortalities, and for both interval and point forecasting. Our inverse score with tuning method was the most accurate overall. The median combination was a leading method in the last quarter for both mortalities, and it was consistently more accurate than the mean combination for point forecasting. For interval forecasts of cumulative mortality, the mean performed better than the median. The best performance of the leading individual model was in point forecasting.\n\nConclusionsCombining forecasts can improve the contribution of probabilistic forecasting to health policy decision making during epidemics, and, when there are sufficient historical data on forecast accuracy, weighted combining provides the most accurate method.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Kathryn S Taylor", + "author_inst": "University of Oxford" + }, + { + "author_name": "James W Taylor", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.12.21258827", "rel_title": "Olfactory detection of human odorant signatures in Covid patients by trained dogs", @@ -668080,89 +668899,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.14.21260489", - "rel_title": "The Specchio-COVID19 cohort study: a longitudinal follow-up of SARS-CoV-2 serosurvey participants in the canton of Geneva, Switzerland (Study protocol)", - "rel_date": "2021-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.14.21260489", - "rel_abs": "BackgroundThe COVID-19 pandemic has affected billions of people around the world both directly through the infection itself and indirectly through its economic, social and sanitary impact. Collecting data over time is essential for the understanding of the disease spread, the incidence of COVID19-like symptoms, the level and dynamics of immunity, as well as the long-term impact of the pandemic.\n\nObjectiveThe objective of the study was to set up a longitudinal follow-up of adult participants of serosurveys carried out in the Canton of Geneva, Switzerland, during the COVID-19 pandemic.\n\nMethodsSerosurvey participants were invited to create an account on the dedicated digital platform Specchio-COVID19 (https://www.specchio-covid19.ch/). Upon registration, an initial questionnaire assessed socio-demographic and lifestyle characteristics (including housing conditions, physical activity, diet, alcohol and tobacco consumption), anthropometry, general health, and experience related to COVID-19 (symptoms, COVID-19 test results, quarantines, hospitalizations). Weekly, participants were invited to fill in a short questionnaire with updates on self-reported COVID-19-compatible symptoms, SARS-CoV-2 infection testing and vaccination. A more detailed questionnaire about mental health, well-being, risk perception, and changes in working conditions was proposed monthly. Supplementary questionnaires were proposed at regular intervals to assess more in depth the impact of the pandemic on physical and mental health, vaccination adherence, health care consumption and changes in health behaviors. At baseline, serology testing allowed to assess the spread of SARS-CoV-2 infection among the general population and subgroups of workers. Additionally, seropositive participants and a sample of randomly selected participants were invited for serologic testing at regular intervals in order to monitor both the seropersistance of anti-SARS-CoV-2 antibodies and the seroprevalence of anti-SARS-CoV-2 antibodies in the population of the Canton of Geneva.\n\nEthics and disseminationThe study was approved by the Cantonal Research Ethics Commission of Geneva, Switzerland (CCER Project ID 2020-00881). Results will be disseminated in a variety of ways, via the Specchio-COVID19 platform, social media posts, press releases, and through regular scientific dissemination methods (open-access articles, conferences).\n\nArticle summaryO_ST_ABSStrengths and limitationsC_ST_ABSO_LIThis is a large study with a diversified recruitment among the general population and mobilized workers. It will contribute to obtain a clearer picture of the impact of the COVID-19 pandemic, for both the general population and targeted subpopulations.\nC_LIO_LIA major strength of the study is the combined use of serological testing and questionnaires. While regular serological testing will help us to model evolution of the pandemic, self-reported data on socioeconomic characteristics, COVID-19-compatible symptoms, and general and mental health will allow us to monitor the progression of the COVID-19 pandemic as well as to thoroughly analyze its effects on several dimensions of health.\nC_LIO_LIThe longitudinal component of the study will provide insight into the extent and duration of immunity, as well as the long-term impact of the pandemic and the sanitary, social and economic measures associated with it.\nC_LIO_LIThe main limitation is that Specchio-COVID19 is based on self-reports with a risk of information bias. However, considering the pandemic context, participants are generally engaged to participate and to contribute to COVID-19 research. Further, at least half of the sample is based on random selection in the general population.\nC_LIO_LIThe study is primarily being conducted online, which may limit the generalizability of the findings, especially for the elderly and vulnerable populations, although internet access is extensive in Switzerland. Nonetheless, participants can use paper questionnaires to contribute to the major assessments.\nC_LI", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Helene Baysson", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Francesco Pennachio", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Ania Wisniak", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Maria Eugenia Zabella", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Prune Collombet", - "author_inst": "Geneva Univeristy Hospitals" - }, - { - "author_name": "Elsa Lorthe", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Stephane Joost", - "author_inst": "Ecole Polytechnique Federale de Lausanne (EPFL)" - }, - { - "author_name": "Jean-Francois Balavoine", - "author_inst": "University of Geneva" - }, - { - "author_name": "Delphine Bachmann", - "author_inst": "Hirslanden Clinique des Grangettes" - }, - { - "author_name": "Andrew Azman", - "author_inst": "University of Geneva" - }, - { - "author_name": "Didier Pittet", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Francois Chappuis", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Omar Kherad", - "author_inst": "Hopital de la Tour" - }, - { - "author_name": "Laurent Kaiser", - "author_inst": "University of Geneva Hospitals" - }, - { - "author_name": "Idris Guessous", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Silvia Stringhini", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "- Specchio COVID19 study group", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.14.21260495", "rel_title": "SARS-CoV-2 variants of concern, Gamma (P.1) and Delta (B.1.617), sensitive detection and quantification in wastewater employing direct RT-qPCR", @@ -668279,6 +669015,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.07.12.21260345", + "rel_title": "Factors associated with transmission in COVID-19 outbreaks in long-term care facilities", + "rel_date": "2021-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260345", + "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a disproportionate impact on residents in long-term care facilities (LTCFs). Through our experience and data from managing COVID-19 exposures and outbreaks in LTCFs in the Fraser Health region in British Columbia, Canada, we identified risk factors associated with outbreak severity to inform current outbreak management strategies and future pandemic preparedness planning efforts.\n\nMethodsWe used a retrospective cohort study design to evaluate the association between non-modifiable factors (facility building, organization level, and resident population characteristics), modifiable factors (assessments for infection prevention and control (IPC) and public health measures), and severity of COVID-19 outbreaks (attack rate) in LTCFs. We modelled the COVID-19 attack rates in LTCF outbreaks using negative binomial regression models.\n\nResultsFrom March 1, 2020 to January 10, 2021, a total of 145 exposures to at least one confirmed case of COVID-19 in 82 LTCFs occurred. For every item not met in the assessment tool, a 22% increase in the attack rate was observed (rate ratio 1.2 [95% CI 1.1 - 1.4]) after adjusting for other risk factors such as age of the facility, index case type (resident vs. staff) and proportion of single bed rooms.\n\nConclusionOur findings highlight the importance of assessing IPC and public health measures for outbreak management. They also demonstrate the important modifiable and non-modifiable risk factors associated with COVID-19 outbreaks in our jurisdiction. We hope these findings will inform ongoing outbreak management and future pandemic planning efforts.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Rohit Vijh", + "author_inst": "School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada" + }, + { + "author_name": "Carmen H Ng", + "author_inst": "Office of the Medical Health Officer, Fraser Health" + }, + { + "author_name": "Mehdi Shirmaleki", + "author_inst": "Office of the Medical Health Officer, Fraser Health" + }, + { + "author_name": "Aamir Bharmal", + "author_inst": "Office of the Medical Health Officer, Fraser Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.12.21260358", "rel_title": "Increase in SARS-CoV-2 seroprevalence in healthy blood donors after the second wave of COVID-19 pandemic in South-Eastern Italy: evidence for asymptomatic young individuals as potential virus spreaders", @@ -669953,81 +670720,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.13.21260404", - "rel_title": "Pre-existing antibodies targeting a dominant linear antibody epitope on SARS-CoV-2 S2 cross-reacted with commensal gut bacteria and shaped immune responses elicited by a candidate vaccine", - "rel_date": "2021-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260404", - "rel_abs": "The origins of pre-existing SARS-CoV-2 cross-reactive antibodies and their potential impacts on vaccine efficacy have not been fully clarified. In this study, we demonstrated that S2 was the prevailing target of the pre-existing S protein cross-reactive antibodies in both healthy human and SPF mice. A dominant antibody epitope was identified on the connector domain of S2 (1147-SFKEELDKYFKNHT-1160, P144), which could be recognized by pre-existing antibodies in both human and mouse. Through metagenomic sequencing and fecal bacteria transplant, we proved that the generation of S2 cross-reactive antibodies was associated with commensal gut bacteria. Furthermore, six P144 specific monoclonal antibodies were isolated from naive SPF mice and proved to cross-react with commensal gut bacteria collected from both human and mouse. Mice with high levels of pre-existing S2 cross-reactive antibodies mounted higher S protein specific binding antibodies, especially against S2, after being immunized with a SARS-CoV-2 S DNA vaccine. Similarly, we found that levels of pre-existing S2 and P144 reactive antibodies correlated positively with RBD specific binding antibody titers after two doses of inactivated SARS-CoV-2 vaccination in human. Finally, we provided data demonstrating that immunization of a SARS-CoV-2 S DNA vaccine could alter the gut microbiota compositions of mice.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Liqiu Jia", - "author_inst": "Huashan Hospital, Fudan University" - }, - { - "author_name": "Shufeng Weng", - "author_inst": "Fudan University" - }, - { - "author_name": "Jing Wu", - "author_inst": "Huashan hospital, Fudan University" - }, - { - "author_name": "Xiangxiang Tian", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Yifan Zhang", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Xuyang Wang", - "author_inst": "Huashan Hospital, Fudan University" - }, - { - "author_name": "Jing Wang", - "author_inst": "Department of laboratory medicine, Shanghai Public Health Clinical Center" - }, - { - "author_name": "Dongmei Yan", - "author_inst": "Department of Immunology, School of Basic Medical, Jiamusi University" - }, - { - "author_name": "Wanhai Wang", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Fang Fang", - "author_inst": "Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Zhaoqin Zhu", - "author_inst": "Department of laboratory medicine, Shanghai Public Health Clinical Center" - }, - { - "author_name": "Chao Qiu", - "author_inst": "Institutes of biomedical sciences & Shanghai Key Laboratory of Medical Epigenetics, Fudan University" - }, - { - "author_name": "Wenhong Zhang", - "author_inst": "Department of Infectious Diseases, National Medical Center for Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Respo" - }, - { - "author_name": "Ying Xu", - "author_inst": "State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University" - }, - { - "author_name": "Yanmin Wan", - "author_inst": "Fudan University, Huashan hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.13.21260449", "rel_title": "Characterization of long-term patient-reported symptoms of COVID-19: an analysis of social media data", @@ -670360,6 +671052,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.10.21260293", + "rel_title": "Plasma P-selectin is an early marker of thromboembolism in COVID-19", + "rel_date": "2021-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.10.21260293", + "rel_abs": "Coagulopathy and thromboembolism are known complications of SARS-CoV-2 infection. The mechanisms of COVID-19-associated hematologic complications involve endothelial cell and platelet dysfunction and have been intensively studied. We leveraged a prospectively collected acute COVID-19 biorepository to study the association of plasma levels of a comprehensive list of coagulation proteins with the occurrence of venous thromboembolic events (VTE). We included in our analysis 305 subjects with confirmed SARS-CoV-2 infection who presented to an urban Emergency Department with acute respiratory distress during the first COVID-19 surge in 2020; 13 (4.2%) were subsequently diagnosed with venous thromboembolism during hospitalization. Serial samples were obtained and assays were performed on two highly-multiplexed proteomic platforms. Nine coagulation proteins were differentially expressed in patients with thromboembolic events. P-selectin, a cell adhesion molecule on the surface of activated endothelial cells, displayed the strongest association with the diagnosis of VTE, independent of disease severity (p=0.0025). This supports the importance of endothelial activation in the mechanistic pathway of venous thromboembolism in COVID-19. P-selectin together with D-dimer upon hospital presentation provided better discriminative ability for VTE diagnosis than D-dimer alone.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Bank Gabor Fenyves", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA, Department of Emergency Medicine, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Arnav Mehta", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "- MGH COVID-19 Collection & Processing Team", + "author_inst": "-" + }, + { + "author_name": "Kyle Kays", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA" + }, + { + "author_name": "Marcia Goldberg", + "author_inst": "Department of Medicine, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Nir Hacohen", + "author_inst": "Broad Institute and Massachusetts General Hospital" + }, + { + "author_name": "Michael Filbin", + "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.07.11.21260148", "rel_title": "ONLINE QUERIES AS A CRITERION FOR EVALUATION OF THE EPIDEMIOLOGICAL STATUS AND EFFECTIVENESS OF COVID-19 EPIDEMIC CONTROL MEASURES", @@ -671795,69 +672530,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.11.21260336", - "rel_title": "SARS-CoV-2 seroprevalence in asymptomatic or mild symptomatic people and symptomatic patients with negative PCR results: The hidden perspective in epidemiological reports", - "rel_date": "2021-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.11.21260336", - "rel_abs": "BackgroundSARS-CoV-2 has led to the current pandemic of respiratory disease. The reports of confirmed COVID-19 cases based on molecular tests do not completely cover the total number of infected people. These reports do not include the asymptomatic or mildly symptomatic patients and also the patients with false-negative RT-PCR results, while the infection is contagious in all of these conditions.\n\nObjectiveIn this study, we tried to improve our conception of the hidden perspective of SARS-CoV-2 in epidemiological reports.\n\nMethodsFrom May 30 to June 17, 2020, blood samples were collected from two groups of people: asymptomatic or mild symptomatic volunteer participants and severe symptomatic hospitalized patients with negative PCR results. Detection of SARS-CoV-2 antibody was done with ELISA kit targeting N or S proteins.\n\nResultsTotally 716 samples from volunteer participants and 81 samples from symptomatic hospitalized patients with negative PCR were evaluated. The test performance-adjusted seroprevalence (95% CI) of SARS-CoV-2 anti-N IgG was 17.3% (8.8%, 25.8%) for volunteers and 25.5% (12.8%, 39.7%) for anti-N and S IgM in hospitalized group. There was an association between high-risk occupations, high-risk behaviors, or symptomatic diseases with positive SARA-Cov-2 N antibody results. Among anti-N positive infected individuals, 49.2% (21.4%, 78.8%) were anti-S positive.\n\nConclusionThe results showed that SARS-COV-2 infection occurs in asymptomatic or mildly symptomatic individuals, but in more than half of them, the produced antibody is not protective. Findings of hospitalized patients also showed that the combination of IgM assay with real-time PCR improves the detection of the disease by more than 25% in negative molecular cases.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Nazila Hajiahmadi", - "author_inst": "Tarbiat modares university" - }, - { - "author_name": "Faezeh mojtahedzade", - "author_inst": "Tarbiat Modares University" - }, - { - "author_name": "Atefeh Yari", - "author_inst": "Tarbiat Modares University" - }, - { - "author_name": "Mahdi Tat", - "author_inst": "Tarbiat Modares University" - }, - { - "author_name": "Hoorieh Soleimanjahi", - "author_inst": "Tarbiat Modares University" - }, - { - "author_name": "Saeid Amel Jamehdar", - "author_inst": "Mashhad University of Medical Sciences" - }, - { - "author_name": "Mitra Jafari", - "author_inst": "Tarbiat Modares University" - }, - { - "author_name": "Samira Asli", - "author_inst": "Mashhad University of Medical Sciences" - }, - { - "author_name": "Rohollah Dorostkar", - "author_inst": "Baqiyatallah University of Medical Sciences" - }, - { - "author_name": "Maryam Nazemipour", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Mohammad Ali Mansournia", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Taravat Bamdad", - "author_inst": "Tarbiat modares university" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.09.21260224", "rel_title": "A Rapid Saliva Test for Monitoring Immune Protection against SARS-CoV-2 and its Variants", @@ -672138,6 +672810,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.09.21260247", + "rel_title": "Spatiotemporal droplet dispersion measurements demonstrate face masks reduce risks from singing: results from the COvid aNd FacEmaSkS Study (CONFESS)", + "rel_date": "2021-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.09.21260247", + "rel_abs": "BackgroundCOVID-19 has restricted singing in communal worship. We sought to understand variations in droplet transmission and the impact of wearing face masks.\n\nMethodsUsing rapid laser planar imaging, we measured droplets while participants exhaled, said hello or snake, sang a note or Happy Birthday, with and without surgical face masks. We measured mean velocity magnitude (MVM), time averaged droplet number (TADN) and maximum droplet number (MDN). Multilevel regression models were used.\n\nResultsIn 20 participants, sound intensity was 71 Decibels (dB) for speaking and 85 dB for singing (p<0.001). MVM was similar for all tasks with no clear hierarchy between vocal tasks or people and >85% reduction wearing face masks. Droplet transmission varied widely, particularly for singing. Masks decreased TADN by 99% (p<0.001) and MDN by 98% (p<0.001) for singing and 86-97% for other tasks. Masks reduced variance by up to 48%. When wearing a mask, neither singing task transmitted more droplets than exhaling.\n\nConclusionsWide variation exists for droplet production. This significantly reduced when wearing face masks. Singing during religious worship wearing a face mask appears as safe as exhaling or talking. This has implications for UK public health guidance during the COVID-19 pandemic.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Kai Man Alexander Ho", + "author_inst": "University College London" + }, + { + "author_name": "Hywel Davies", + "author_inst": "University College London" + }, + { + "author_name": "Ruth Epstein", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Paul Bassett", + "author_inst": "Statsconsultancy Ltd" + }, + { + "author_name": "Aine Hogan", + "author_inst": "University College London" + }, + { + "author_name": "Yusuf Kabir", + "author_inst": "University College London" + }, + { + "author_name": "John Rubin", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Gee Yen Shin", + "author_inst": "University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Jonathan Reid", + "author_inst": "University of Bristol" + }, + { + "author_name": "Ryo Torii", + "author_inst": "University College London" + }, + { + "author_name": "Manish Tiwari", + "author_inst": "University College London" + }, + { + "author_name": "Ramanarayanan Balachandran", + "author_inst": "University College London" + }, + { + "author_name": "Laurence Lovat", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.12.21259864", "rel_title": "Evidence of SARS-Cov-2-specific memory B cells six months after vaccination with BNT162b2 mRNA vaccine", @@ -673601,61 +674340,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.07.12.452002", - "rel_title": "SARS-CoV-2 Spike Protein Mutations and Escape from Antibodies: a Computational Model of Epitope Loss in Variants of Concern", - "rel_date": "2021-07-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.12.452002", - "rel_abs": "The SARS-CoV-2 spike (S) protein is exposed on the viral surface and is the first point of contact between the virus and the host. For these reasons it represents the prime target for Covid-19 vaccines. In recent months, variants of this protein have started to emerge. Their ability to reduce or evade recognition by S-targeting antibodies poses a threat to immunological treatments and raises concerns for their consequences on vaccine efficacy.\n\nTo develop a model able to predict the potential impact of S-protein mutations on antibody binding sites, we performed unbiased multi-microsecond molecular dynamics of several glycosylated S-protein variants and applied a straightforward structure-dynamics-energy based strategy to predict potential changes in immunogenic regions on each variant. We recover known epitopes on the reference D614G sequence. By comparing our results, obtained on isolated S-proteins in solution, to recently published data on antibody binding and reactivity in new S variants, we directly show that modifications in the S-protein consistently translate into the loss of potentially immunoreactive regions. Our findings can thus be qualitatively reconnected to the experimentally characterized decreased ability of some of the Abs elicited against the dominant S-sequence to recognize variants. While based on the study of SARS-CoV-2 Spike variants, our computational epitope-prediction strategy is portable and could be applied to study immunoreactivity in mutants of proteins of interest whose structures have been characterized, helping the development/selection of vaccines and antibodies able to control emerging variants.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Alice Triveri", - "author_inst": "University of Pavia" - }, - { - "author_name": "Stefano A. Serapian", - "author_inst": "University of Pavia" - }, - { - "author_name": "Filippo Marchetti", - "author_inst": "University of Pavia" - }, - { - "author_name": "Filippo Doria", - "author_inst": "University of Pavia" - }, - { - "author_name": "Silvia Pavoni", - "author_inst": "Department of Physical Chemistry, R&D Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi), Italy" - }, - { - "author_name": "Fabrizio Cinquini", - "author_inst": "Upstream and Technical Services, TECS STES, Eni Spa, via Emilia 1, 20097 San Donato Milanese (Mi), Italy" - }, - { - "author_name": "Eisabetta Moroni", - "author_inst": "SCITEC-CNR, Milano Italy" - }, - { - "author_name": "Andrea Rasola", - "author_inst": "University of Padova" - }, - { - "author_name": "Francesco Frigerio", - "author_inst": "Department of Physical Chemistry, R&D Eni SpA, via Maritano 27, 20097 San Donato Milanese (Mi), Italy" - }, - { - "author_name": "Giorgio Colombo", - "author_inst": "University of Pavia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.07.12.21260208", "rel_title": "Daily sampling of early SARS-CoV-2 infection reveals substantial heterogeneity in infectiousness", @@ -674012,6 +674696,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.11.451855", + "rel_title": "The SARS-CoV-2 spike reversibly samples an open-trimer conformation exposing novel epitopes", + "rel_date": "2021-07-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.11.451855", + "rel_abs": "Current COVID-19 vaccines and many clinical diagnostics are based on the structure and function of the SARS-CoV-2 spike ectodomain. Using hydrogen deuterium exchange mass spectrometry, we have uncovered that, in addition to the prefusion structure determined by cryo-EM, this protein adopts an alternative conformation that interconverts slowly with the canonical prefusion structure. This new conformation--an open trimer-- contains easily accessible RBDs. It exposes the conserved trimer interface buried in the prefusion conformation, thus exposing potential epitopes for pan-coronavirus antibody and ligand recognition. The population of this state and kinetics of interconversion are modulated by temperature, receptor binding, antibody binding, and sequence variants observed in the natural population. Knowledge of the structure and populations of this conformation will help improve existing diagnostics, therapeutics, and vaccines.\n\nOne Sentence SummaryAn alternative conformation of SARS-CoV-2 spike ectodomain modulated by temperature, binding, and sequence variants.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Shawn M Costello", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Sophie R Shoemaker", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Helen T Hobbs", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Annalee W Nguyen", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Ching-Lin Hsieh", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jennifer A Maynard", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Jason S McLellan", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "John E Pak", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Susan Marqusee", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.07.08.21259912", "rel_title": "Efficacy and safety of Andrographis paniculata extract in patients with mild COVID-19: A randomized controlled trial", @@ -675395,81 +676130,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.07.21260101", - "rel_title": "COVID-19 Serology Control Panel Using the Dried Tube Specimen Method", - "rel_date": "2021-07-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21260101", - "rel_abs": "We used the dried tube specimen (DTS) procedure to develop the COVID-19 Serology Control Panel (CSCP). The CSCP contains five well-characterized SARS-CoV-2 pooled plasma samples made available for labs around the world to compare test kits, use for external quality assurance, harmonize laboratory testing, and train laboratory workers.\n\nArticle Summary LineThe dried tube specimen system is a highly effective and resilient way to provide laboratories with well-characterized serology materials. The CSCP can help clinical laboratories inform their choice of diagnostic test to supplement clinical diagnoses of SARS-CoV-2 infection.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "William Jonathan Windsor", - "author_inst": "Colorado School of Public Health" - }, - { - "author_name": "Vijaya Knight", - "author_inst": "Children's Hospital Colorado" - }, - { - "author_name": "Patricia A Merkel", - "author_inst": "Children's Hospital Colorado" - }, - { - "author_name": "Molly M Lamb", - "author_inst": "Colorado School of Public Health" - }, - { - "author_name": "Mario L Santiago", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Mary K McCarthy", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Thomas E Morrison", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Ross M Kedl", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Ashley Frazer-Abel", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Kejun Guo", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Gillian Andersen", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Leah Huey", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Bradley S Barrett", - "author_inst": "University of Colorado Anschutz Medical Campus" - }, - { - "author_name": "Jessica M Colon-Franco", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "May C Chu", - "author_inst": "Colorado School of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.07.21260141", "rel_title": "Myeloid-derived suppressor cells in the blood of Iranian COVID-19 patients", @@ -675698,6 +676358,33 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2021.07.06.21260112", + "rel_title": "COVID-19 Due to Wild-Type SARS-CoV-2 More Prevalent in Adolescents and Youth than in Older Adults Based on 19 US States in Fall 2020 Prior to Vaccine Availability", + "rel_date": "2021-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21260112", + "rel_abs": "PURPOSEIn a prior study, we examined data from six US states during Summer 2020, and found that prevalence of COVID-19 for adolescents and youth was significantly greater than for older adults (p<.00001) as was a prevalence-related measure: Number of cases observed / Number of cases expected (p<.005). We now extended our study to more states in Fall 2020 to confirm the prevalence relationships we found previously. Vaccines were still not available as of Fall 2020. Presumably, the SARS-CoV-2 strain circulating at the time was the wild-type lineage since no variants were reported in the US until the end of December 2020.\n\nMETHODSWe examined data from 19 U.S. states experiencing surges in cases to determine prevalence of COVID-19, and a prevalence-related measure: [Number of cases observed in a given age group] / [Number of cases expected in the age group based on population demographics].\n\nRESULTSIn 16 of the 19 states, we found that: (1) prevalence of COVID-19 for adolescents and youth was significantly greater than for older adults (p-values ranged from p<0.00001 to p = 0.0175; (2) the ratio of cases observed to cases expected was significantly greater in adolescents and youth than in older adults (p-values ranging from p< 0.00001 to p = 0.004).\n\nCONCLUSIONSOur results are consistent with our previous study in Summer 2020. The finding of lower prevalence in older adults cannot be attributed to access to vaccination since our data are from Fall 2020 when vaccinations were not yet available. Our findings with the SARS-CoV-2 wild-type strain are consistent with the findings currently being reported in the UK for the delta variant. In both studies, prevalence in adolescents and youth exceeded that in older adults. The UK findings are more pronounced perhaps because that study transpired following months of vaccinations of older adults whereas ours occurred before vaccinations were available.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Barbara T Rumain", + "author_inst": "New York Medical College" + }, + { + "author_name": "Moshe Schneiderman", + "author_inst": "SUNY Downstate College of Medicine" + }, + { + "author_name": "Allan Geliebter", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.30.21259763", "rel_title": "Which children and young people are at higher risk of severe disease and death after SARS-CoV-2 infection: a systematic review and individual patient meta-analysis", @@ -677357,45 +678044,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.08.21260072", - "rel_title": "Anxiety and Depression among Medical Doctors in Catalonia, Italy, and the UK during the COVID-19 Pandemic", - "rel_date": "2021-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.08.21260072", - "rel_abs": "Healthcare workers have had the longest and most direct exposure to COVID-19 and consequently may suffer from poor mental health. We conducted one of the first repeated multi-country analysis of the mental wellbeing of medical doctors (n=5,275) at two timepoints during the COVID-19 pandemic (June 2020 and November/December 2020) to understand the prevalence of anxiety and depression, as well as associated risk factors. Rates of anxiety and depression were highest in Italy (24.6% and 20.1%, June 2020), second highest in Catalonia (24.6% and 17.4%, June 2020), and lowest in the UK (11.7% and 13.7%, June 2020). Across all countries, higher risk of anxiety and depression symptoms are found among women, individuals below 60 years old, those feeling vulnerable/exposed at work, and those in poor health. We did not find systematic differences in mental health measures between the two rounds of data collection, hence we cannot discard that the mental health repercussions of the pandemic are persistent.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Climent Quintana-Domeque", - "author_inst": "University of Exeter" - }, - { - "author_name": "Ines Lee", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Anwen Zhang", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Eugenio Proto", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Michele Battisti", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Antonia Ho", - "author_inst": "University of Glasgow" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.07.08.21260125", "rel_title": "Automated lung sound analysis using the LungPass platform: A sensitive and specific tool for identifying lower respiratory tract involvement in COVID-19.", @@ -677588,6 +678236,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.07.06.21259473", + "rel_title": "Cross-sectional cycle threshold values reflect epidemic dynamics of COVID-19 in Madagascar", + "rel_date": "2021-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21259473", + "rel_abs": "As the national reference laboratory for febrile illness in Madagascar, we processed samples from the first epidemic wave of COVID-19, between March and September 2020. We fit generalized additive models to cycle threshold (Ct) value data from our RT-qPCR platform, demonstrating a peak in high viral load, low-Ct value infections temporally coincident with peak epidemic growth rates estimated in real time from publicly-reported incidence data and retrospectively from our own laboratory testing data across three administrative regions. We additionally demonstrate a statistically significant effect of duration of time since infection onset on Ct value, suggesting that Ct value can be used as a biomarker of the stage at which an individual is sampled in the course of an infection trajectory. As an extension, the population-level Ct distribution at a given timepoint can be used to estimate population-level epidemiological dynamics. We illustrate this concept by adopting a recently-developed, nested modeling approach, embedding a within-host viral kinetics model within a population-level Susceptible-Exposed-Infectious-Recovered (SEIR) framework, to mechanistically estimate epidemic growth rates from cross-sectional Ct distributions across three regions in Madagascar. We find that Ct-derived epidemic growth estimates slightly precede those derived from incidence data across the first epidemic wave, suggesting delays in surveillance and case reporting. Our findings indicate that public reporting of Ct values could offer an important resource for epidemiological inference in low surveillance settings, enabling forecasts of impending incidence peaks in regions with limited case reporting.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Soa Fy Andriamandimby", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Cara E. Brook", + "author_inst": "Cara Brook" + }, + { + "author_name": "Norosoa H Razanajatovo", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Jean-Marius Rakotondramanga", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Fidisoa Rasambainarivo", + "author_inst": "Princeton University" + }, + { + "author_name": "Vaomalala Raharimanga", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Iony M. Razanajatovo", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Reziky Mangahasimbola", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Richter L Razafindratsimandresy", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Santatra Randrianarisoa", + "author_inst": "University of Antananarivo" + }, + { + "author_name": "Barivola Bernardson", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Joelinotahina H Rabarison", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Mirella Randrianarisoa", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Frederick S Nasolo", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Roger M Rabetombosoa", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Rindra V Randremanana", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Jean-Michel Heraud", + "author_inst": "Institut Pasteur de Madagascar" + }, + { + "author_name": "Philippe G Dussart", + "author_inst": "Institut Pasteur de Madagascar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.08.21259776", "rel_title": "Effectiveness of SARS-CoV-2 mRNA Vaccines for Preventing Covid-19 Hospitalizations in the United States", @@ -679175,93 +679910,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.07.05.21260041", - "rel_title": "High mortality of COVID-19 associated mucormycosis in France: a nationwide retrospective study", - "rel_date": "2021-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21260041", - "rel_abs": "We studied COVID-19 associated mucormycosis based on 17 cases reported nationwide and assessed the differences with India. They differed by frequencies of diabetes mellitus (47% in France versus 95% in India), hematological malignancies (35% versus 1%), anatomical sites (53% lung versus >80% rhino-orbito-cerebral) and prognosis (>80% mortality versus <50%).", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Francois Danion", - "author_inst": "Service de Maladies Infectieuses et Tropicales, CHU de Strasbourg, France" - }, - { - "author_name": "Valerie Letscher-Bru", - "author_inst": "CHU de Strasbourg" - }, - { - "author_name": "Juliette Guitard", - "author_inst": "AP-HP" - }, - { - "author_name": "Karine Sitbon", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sarah Delliere", - "author_inst": "AP-HP" - }, - { - "author_name": "Adela Angoulvant", - "author_inst": "AP-HP" - }, - { - "author_name": "Guillaume Desoubeaux", - "author_inst": "CHU de Tours" - }, - { - "author_name": "Francoise Botterel", - "author_inst": "AP-HP" - }, - { - "author_name": "Anne-Pauline Bellanger", - "author_inst": "CHU de Besancon" - }, - { - "author_name": "Gilles Gargala", - "author_inst": "CHU de Rouen" - }, - { - "author_name": "Fabrice Uhel", - "author_inst": "AP-HP" - }, - { - "author_name": "Marie-Elisabeth Bougnoux", - "author_inst": "AP-HP" - }, - { - "author_name": "Victor Gerber", - "author_inst": "CH de Colmar" - }, - { - "author_name": "Justin Michel", - "author_inst": "AP-HM, Hopital de la Conception, Marseille" - }, - { - "author_name": "Marjorie Cornu", - "author_inst": "CHU de Lille" - }, - { - "author_name": "Stephane Bretagne", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Fanny Lanternier", - "author_inst": "Institut Pasteur, Centre National de Reference des Mycoses Invasives et des Antifongiques, Paris, France" - }, - { - "author_name": "- COVID-Mucor study group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.05.21259867", "rel_title": "Tocilizumab and sarilumab alone or in combination with corticosteroids for COVID-19: A systematic review and network meta-analysis", @@ -679602,6 +680250,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.03.21259953", + "rel_title": "High resolution linear epitope mapping of the receptor binding domain of SARS-CoV-2 spike protein in COVID-19 mRNA vaccine recipients.", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21259953", + "rel_abs": "The prompt rollout of the coronavirus disease (COVID-19) messenger RNA (mRNA) vaccine is facilitating population immunity, which shall become more dominant than natural infection-induced immunity. At the beginning of the vaccine era, understanding the epitope profiles of vaccine-elicited antibodies will be the first step in assessing functionality of vaccine-induced immunity. In this study, the high-resolution linear epitope profiles of Pfizer-BioNTech COVID-19 mRNA vaccine recipients and COVID-19 patients were delineated by using microarrays mapped with overlapping peptides of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein. The vaccine-induced antibodies targeting RBD had broader distribution across the RBD than that induced by the natural infection. Thus, relatively lower neutralizability was observed when a half-maximal neutralization titer measured in vitro by live virus neutralization assays was normalized to a total anti-RBD IgG titer. However, mutation panel assays targeting the SARS-CoV-2 variants of concern have shown that the vaccine-induced epitope variety, rich in breadth, may grant resistance against future viral evolutionary escapes, serving as an advantage of vaccine-induced immunity.\n\nImportanceEstablishing vaccine-based population immunity has been the key factor in attaining herd protection. Thanks to expedited worldwide research efforts, the potency of messenger RNA vaccines against the coronavirus disease 2019 (COVID-19) is now incontestable. The next debate is regarding the coverage of SARS-CoV-2 variants. At the beginning of this vaccine era, it is of importance to describe the similarities and differences between the immune responses of COVID-19 vaccine recipients and naturally infected individuals. In this study, we demonstrated that the antibody profiles of vaccine recipients are richer in variety, targeting a key protein of the invading virus, than those of naturally infected individuals. Yet vaccine-elicited antibodies included more non-neutralizing antibodies than infection-elicited, their breadth in antibody variations suggested possible resilience against future SARS-CoV-2 variants. The antibody profile achieved by vaccinations in naive individuals pose important insight into the first step towards vaccine-based population immunity.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Yuko Nitahara", + "author_inst": "Osaka City University" + }, + { + "author_name": "Yu Nakagama", + "author_inst": "Osaka City University" + }, + { + "author_name": "Natsuko Kaku", + "author_inst": "Osaka City University" + }, + { + "author_name": "Katherine Candray", + "author_inst": "Osaka City University" + }, + { + "author_name": "Yu Michimuko", + "author_inst": "Osaka City University" + }, + { + "author_name": "Evariste Tshibangu-Kabamba", + "author_inst": "Osaka City University" + }, + { + "author_name": "Akira Kaneko", + "author_inst": "Osaka City University" + }, + { + "author_name": "Hiromasa Yamamoto", + "author_inst": "Osaka City University" + }, + { + "author_name": "Yasumitsu Mizobata", + "author_inst": "Osaka City University" + }, + { + "author_name": "Hiroshi Kakeya", + "author_inst": "Osaka City University" + }, + { + "author_name": "Mayo Yasugi", + "author_inst": "Osaka Prefecture University" + }, + { + "author_name": "Yasutoshi Kido", + "author_inst": "Osaka City University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.03.21254541", "rel_title": "Anticoagulants and Antiplatelets in COVID-19: Impact on Survival and Thromboembolism Development", @@ -681025,49 +681736,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.05.21260026", - "rel_title": "Ethnic disparities in hospitalisation and hospital-outcomes during the second wave of COVID-19 infection in east London", - "rel_date": "2021-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21260026", - "rel_abs": "ObjectivesTo determine if changes in public behaviours, developments in COVID-19 treatments, improved patient care, and directed policy initiatives have altered outcomes for minority ethnic groups in the second pandemic wave.\n\nDesignProspectively defined observational study using registry data.\n\nSettingFour acute NHS Hospitals in east London.\n\nParticipantsPatients aged [≥]16 years with an emergency hospital admission with SARS-CoV-2 infection between 1st September 2020 and 17th February 2021.\n\nMain outcome measuresPrimary outcome was 30-day mortality from time of index COVID-19 hospital admission. Secondary endpoints were 90-day mortality and need for ICU admission. Multivariable survival analysis was used to assess associations between ethnicity and mortality accounting for predefined risk factors. Age-standardised rates of hospital admission relative to the local population were compared between ethnic groups.\n\nResultsOf 5533 patients, the ethnic distribution was White (n=1805, 32.6%), Asian/Asian British (n=1983, 35.8%), Black/Black British (n=634, 11.4%), Mixed/Other (n=433, 7.8%), and unknown (n=678, 12.2%). Excluding 678 patients with missing data, 4855 were included in multivariable analysis. Relative to the White population, Asian and Black populations experienced 4.1 times (3.77-4.39) and 2.1 times (1.88-2.33) higher rates of age-standardised hospital admission. After adjustment for various patient risk factors including age, sex, and socioeconomic deprivation, Asian patients were at significantly higher risk of death within 30 days (HR 1.47 [1.24-1.73]). No association with increased risk of death in hospitalised patients was observed for Black or Mixed/Other ethnicity.\n\nConclusionsAsian and Black ethnic groups continue to experience poor outcomes following COVID-19. Despite higher-than-expected rates of admission, Black and Asian patients experienced similar or greater risk of death in hospital, implying a higher overall risk of COVID-19 associated death in these communities.\n\nStrengths and limitations of this studyO_LIThis study represents one of the largest descriptors of outcomes in minority ethnic patients with COVID-19 distinguished by the majority ethnically diverse cohort within a catchment area of approximately one million people in the east of London.\nC_LIO_LILarge absolute numbers of patients drawn from a single geographic region and treated within the same hospital system minimize many of the geographic biases present within other studies including the impact of variation in transmission risk.\nC_LIO_LIOur analyses are strengthened by adherence to a prespecified analysis plan, inclusion of a detailed baseline, comorbidity, and COVID-19 risk factors in multivariable modelling, and sensitivity tests using different measures of comorbidity.\nC_LIO_LIHowever as with all observational studies, not all potential contributing risk factors could be assessed, including other measures of baseline health status such as nutritional or lifestyle influences as well as contextual factors such as household composition and occupation.\nC_LIO_LIWe were not able to include suspected but not proven COVID-19 cases or community cases not requiring hospital admission or the effect of the differing viral strains in the first and second wave.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Yize I Wan", - "author_inst": "William Harvey Research Institute, Queen Mary University of London, UK" - }, - { - "author_name": "Vanessa J Apea", - "author_inst": "Blizard Institute, Queen Mary University of London, UK" - }, - { - "author_name": "Rageshri Dhairyawan", - "author_inst": "Blizard Institute, Queen Mary University of London, UK" - }, - { - "author_name": "Zudin A Puthucheary", - "author_inst": "William Harvey Research Institute, Queen Mary University of London, UK" - }, - { - "author_name": "Rupert M Pearse", - "author_inst": "William Harvey Research Institute, Queen Mary University of London, UK" - }, - { - "author_name": "Chloe M Orkin", - "author_inst": "Blizard Institute, Queen Mary University of London, UK" - }, - { - "author_name": "John R Prowle", - "author_inst": "William Harvey Research Institute, Queen Mary University of London, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.05.21259760", "rel_title": "Spatiotemporal dissemination pattern of SARS-CoV-2 B1.1.28-derived lineages introduced into Uruguay across its southeastern border with Brazil.", @@ -681292,6 +681960,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.07.05.21260050", + "rel_title": "Progressive Increase in Virulence of Novel SARS-CoV-2 Variants in Ontario, Canada, February to June, 2021", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21260050", + "rel_abs": "BackgroundThe period from February to June 2021 was one during which initial wild-type SARS-CoV-2 strains were supplanted in Ontario, Canada, first by variants of concern (VOC) with the N501Y mutation (Alpha/B1.1.17, Beta/B.1.351 and Gamma/P.1 variants), and then by the Delta/B.1.617 variant. The increased transmissibility of these VOCs has been documented but data for increased virulence is limited. We used Ontarios COVID-19 case data to evaluate the virulence of these VOCs compared to non-VOC SARS-CoV-2 infections, as measured by risk of hospitalization, intensive care unit (ICU) admission, and death.\n\nMethodsWe created a retrospective cohort of people in Ontario testing positive for SARS-CoV-2 and screened for VOCs, with dates of test report between February 7 and June 27, 2021 (n=212,332). We constructed mixed effects logistic regression models with hospitalization, ICU admission, and death as outcome variables. Models were adjusted for age, sex, time, vaccination status, comorbidities, and pregnancy status. Health units were included as random intercepts.\n\nResultsCompared to non-VOC SARS-CoV-2 strains, the adjusted elevation in risk associated with N501Y-positive variants was 52% (43-62%) for hospitalization; 89% (67-116%) for ICU admission; and 51% (30-74%) for death. Increases with Delta variant were more pronounced: 108% (80-138%) for hospitalization; 234% (164-331%) for ICU admission; and 132% (47-230%) for death.\n\nInterpretationThe progressive increase in transmissibility and virulence of SARS-CoV-2 VOCs will result in a significantly larger, and more deadly, pandemic than would have occurred in the absence of VOC emergence.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "David Fisman", + "author_inst": "University of Toronto" + }, + { + "author_name": "Ashleigh Tuite", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.06.21260055", "rel_title": "Critical timing for triggering public health interventions to prevent COVID-19 resurgence: a mathematical modelling study", @@ -683155,61 +683846,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2021.07.01.21259869", - "rel_title": "Genomic Surveillance of SARS-CoV-2 in Erie County, New York", - "rel_date": "2021-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.01.21259869", - "rel_abs": "Early in the SAR-CoV-2 pandemic, we established a whole genome sequencing pipeline to assess lineages circulating in Western New York. Initial sequences revealed entry into the region via Europe, similar to observations in New York City. However, as the pandemic progressed and variants of concern emerged, we observed distinct patterns in lineages relative to NYC. Notably, B.1.427 became dominant in Western New York, before it was displaced by B.1.1.7. Our hierarchical cluster analysis of B.1.1.7 lineages, which by May 2021 made up [~] 80% of all cases, indicated both multiple introductions and community spread. Our work highlights the importance of widespread, regional surveillance of SARS-CoV-2 across the United States.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Natalie A Lamb", - "author_inst": "University at Buffalo" - }, - { - "author_name": "Jonathan E Bard", - "author_inst": "University at Buffalo" - }, - { - "author_name": "Alyssa Pohlman", - "author_inst": "University at Buffalo" - }, - { - "author_name": "Amanda Boccolucci", - "author_inst": "University at Buffalo" - }, - { - "author_name": "Donald A Yergeau", - "author_inst": "University at Buffalo" - }, - { - "author_name": "Brandon J Marzullo", - "author_inst": "University at Buffalo" - }, - { - "author_name": "Carleen Pope", - "author_inst": "Erie County Public Health Laboratory" - }, - { - "author_name": "Gale R Burstein", - "author_inst": "Erie County Department of Health and University at Buffalo" - }, - { - "author_name": "John Tomaszewski", - "author_inst": "University at Buffalo and Kaleida Health" - }, - { - "author_name": "Jennifer A Surtees", - "author_inst": "University at Buffalo" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.07.05.21260017", "rel_title": "Attitudes towards a mandatory COVID-19 vaccination in France for the general population or healthcare workers in May 2021", @@ -683386,6 +684022,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.05.21260021", + "rel_title": "Knowledge, attitude, and practice related to the COVID-19 pandemic among undergraduate medical students in Indonesia: a nationwide cross-sectional study", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21260021", + "rel_abs": "IntroductionThe potential role of medical students in raising awareness during public health emergencies has been acknowledged. To further explore their potentials as public educators and role models for the communities during the coronavirus disease 2019 (COVID-19) pandemic, a study is conducted to assess the knowledge, attitude, and practice of these students toward COVID-19.\n\nMethodsAn online cross-sectional survey was conducted among undergraduate medical students in Indonesia. Socio-demographical characteristics, social interaction history, information-seeking behavior, as well as knowledge, attitude, and practice toward COVID-19 were collected through a self-reported questionnaire. A p-value of <0.05 indicated statistical significance.\n\nResultsOut of 4870 respondents, 64.9% and 51.5% had positive attitude and practice toward COVID-19 while only 29.8% had adequate knowledge. Knowledge was slightly positively correlated with attitude and practice ({rho}=0.074 and {rho}=0.054, respectively; both p<0.001), while attitude was weakly correlated with practice ({rho}=0.234, p<0.001). Several factors including age, sex, place of residence, institution type, academic level, family income, history of chronic illness, prior volunteering experience, and perceptual awareness on COVID-19 were significantly associated with either knowledge, attitude, and/or practice toward COVID-19. Furthermore, health institutions and the governments press releases, as well as health expert opinions were deemed as the most reliable sources of COVID-19-related information - yet trivially none of these sources were associated with knowledge, attitude, and practice in the study population.\n\nConclusionMany undergraduate medical students in Indonesia had positive attitude and practice against COVID-19, yet only a few had adequate knowledge. This warrants further interventions to keep them updated with COVID-19 evidence to maximize their potentials in raising public awareness on COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Imam Adli", + "author_inst": "Facullty of Medicine Universitas Indonesia" + }, + { + "author_name": "Indah Suci Widyahening", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Gilbert Lazarus", + "author_inst": "Faculty of Medicine, Universitas Indonesia" + }, + { + "author_name": "Jason Phowira", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Lyanna Azzahra", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Bagas Ariffandi", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Aziz Muhammad Putera", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "David Nugraha", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Nico Gamalliel", + "author_inst": "Faculty of Medicine Universitas Indonesia" + }, + { + "author_name": "Ardi Findyartini", + "author_inst": "Faculty of Medicine Universitas Indonesia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical education" + }, { "rel_doi": "10.1101/2021.07.04.21259985", "rel_title": "Covid-19 Vaccination in Pregnancy: A Systematic Review", @@ -684757,65 +685448,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.07.02.21259886", - "rel_title": "Randomized, double blind, placebo controlled, clinical trial to study co-administration of Ashwagandha on safety, immunogenicity, and protection with COVID-19 vaccine: A Study Protocol", - "rel_date": "2021-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.02.21259886", - "rel_abs": "IntroductionThe government of India has rolled out COVID-19 vaccine program for individuals who are 18 years of age and above and priority is being given to the elderly, and individuals with morbidity. Oxford-AstraZeneca COVID-19 vaccine (COVISHIELD) is most widely used in India. A large number of Indian people have been consuming various traditional medicines in the hope of better protection against COVID-19 infection. Several studies have reported immunological benefits of Ashwagandha and its potential as vaccine adjuvant. We plan to study co-administration of Ashwagandha with COVISHIELD vaccine on safety, immunogenicity and protection.\n\nMethods and analysisWe designed a prospective, randomized, double blind, parallel group, placebo controlled, two arm, exploratory study on healthy volunteers receiving the COVISHIELD vaccine. In addition to the two dose schedule of COVISHIELD vaccine as per national guidelines, participants will be administered 8gm Ashwagandha or placebo tablets respectively per day. Primary outcome measure is immunogenicity as measured by SARS-CoV-2 spike (S1) and RBD-specific IgG antibody titres. Secondary outcome measures are safety, protective immune response and quality of life measures. Adverse event following immunization will be monitored at each time throughout the study. Participants will be tracked on a daily basis with a user friendly mobile phone application. Following power calculation 600 participants will be recruited per arm to demonstrate superiority by a margin of 7% with 80% power. Study duration is 28 weeks with interim analysis at the end of 12 weeks.\n\nEthics and disseminationEthical approval was obtained through the Central and institutional Ethics Committees. Participant recruitment is expected to commence by August 2021. Results will be presented in conferences and published in preprint followed by peer-reviewed medical journals.\n\nRegistration detailsClinical Trial Registry - India (CTRI) Registration Number: CTRI/2021/06/034496. Date of Registration June 30, 2021.\n\nStrengths and limitations of this studyO_LINovel study to demonstrate effect of coadministration of immune adjuvant and COVID-19 vaccine on safety and immunogenicity.\nC_LIO_LIRandomised placebo controlled 28 weeks study with 80 percent power to demonstrate role of putative natural immunomodulator to augment the protection and reduce breakthrough infections\nC_LIO_LIState of art immune assays to measure specific antibodies to SARS-CoV-2 to demonstrate both persistent and late upsurge in immune response\nC_LIO_LIDaily tracking of participants using a study specific designed mobile app\nC_LIO_LIAn interim analysis is planned to provide information on early immune response after first dose of vaccine\nC_LIO_LIParticipants may be reluctant to donate blood repeatedly for immune assays; compliance with the test drug may be a challenge; asymptomatic infections may be missed; the study is not measuring cellular immune response.\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Arvind Chopra", - "author_inst": "Center for Rheumatic Diseases, Pune" - }, - { - "author_name": "Preeti Chavan Gautam", - "author_inst": "Savitribai Phule Pune University, Pune" - }, - { - "author_name": "Girish Tillu", - "author_inst": "Savitribai Phule Pune University, Pune" - }, - { - "author_name": "Manjit Saluja", - "author_inst": "Center for Rheumatic Diseases, Pune" - }, - { - "author_name": "Swapnil Borse", - "author_inst": "Savitribai Phule Pune University, Pune" - }, - { - "author_name": "Sanjeev Sarmukaddam", - "author_inst": "Center for Rheumatic Diseases, Pune" - }, - { - "author_name": "Susmita Chaudhuri", - "author_inst": "Translational Health Science and Technology Institute, Faridabad" - }, - { - "author_name": "BCS Rao", - "author_inst": "Central Council for Research in Ayurvedic Sciences, New Delhi" - }, - { - "author_name": "Babita Yadav", - "author_inst": "Central Council for Research in Ayurvedic Sciences, New Delhi" - }, - { - "author_name": "Narayanam Srikanth", - "author_inst": "Central Council for Research in Ayurvedic Sciences, New Delhi" - }, - { - "author_name": "Bhushan Patwardhan", - "author_inst": "Savitribai Phule Pune University, Pune" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.07.02.21259898", "rel_title": "Comorbidity accounts for severe COVID-19 risk, but how do we measure it? Retrospective assessment of the performance of three measures of comorbidity using 4,607 hospitalizations", @@ -685020,6 +685652,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.06.21259749", + "rel_title": "Application of nasal spray containing dimethyl sulfoxide (DSMO) and ethanol during the COVID-19 pandemic may protect healthcare workers: A randomized controlled trials", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21259749", + "rel_abs": "BackgroundCoronavirus pandemic has affected a large population worldwide. Currently, the standard care for individuals who are exposed is supportive care, symptomatic management, and isolation. The aim of our study was to evaluate effects of combined use of ethanol and DMSO as a nasal spray in preventing COVID-19.\n\nMethodsWe conducted a randomized controlled trial on volunteer healthcare workers of medical centers that were at the forefront of the fight against COVID-19 in Shahroud, Iran. Two hundred and thirty-two participants were randomly assigned to intervention and control groups to receive DMSO/ethanol or routine care, respectively. The subjects were followed for 4 weeks to determine the incidence of COVID-19 infection in each group based on the RT-qPCR test. Finally, absolute risk difference and relative risk were calculated to evaluate the effect of DMSO in prevent COVID-19.\n\nResultsThe results showed that the incidence of COVID-19 in the control group and intervention group were 0.07 and 0.008, respectively. The relative risk (RR) was 0.12 (0.9-0.02) according to the incidence rate in the two groups.\n\nConclusioncombined application of DMSO and ethanol in healthcare providers can considerably prevent COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Ali Hosseinzadeh", + "author_inst": "Shahroud University of medical sciences" + }, + { + "author_name": "Abbas Tavakkolian", + "author_inst": "Islamic Azad University, Shahroud Branch, Shahroud, Iran." + }, + { + "author_name": "Vahid Kia", + "author_inst": "Shahroud University of Medical Sciences" + }, + { + "author_name": "Hossein Ebrahimi", + "author_inst": "Shahroud University School of Medical Sciences" + }, + { + "author_name": "Hossein Sheibani", + "author_inst": "Shahroud University School of Medical Sciences" + }, + { + "author_name": "Ehsan Binesh", + "author_inst": "Shahroud University School of Medical Sciences" + }, + { + "author_name": "Reza Jafari", + "author_inst": "Shahroud University of Medical Sciences" + }, + { + "author_name": "Seyed Mohammad Mirrezaie", + "author_inst": "Shahroud University School of Medical Sciences" + }, + { + "author_name": "Moslem Jafarisani", + "author_inst": "Shahroud University of medical Sciences" + }, + { + "author_name": "Mohammad Hassan Emamian", + "author_inst": "Shahroud University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.05.451222", "rel_title": "Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques", @@ -686395,57 +687082,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.30.21259750", - "rel_title": "SARS-CoV-2 and the role of vertical transmission from infected pregnant women to their fetuses: systematic review.", - "rel_date": "2021-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.30.21259750", - "rel_abs": "BackgroundVertical transmission of SARS-CoV-2 has been reported but does not appear to be common. This study aims to systematically review the evidence for vertical transmission of SARS-CoV-2.\n\nMethodsThis review is part of an Open Evidence Review on the transmission dynamics of SARS-CoV-2 and the role of intrauterine mother to fetus transmission. Literature searches were performed in the WHO Covid-19 Database, LitCovid, medRxiv, and Google Scholar for SARS-CoV-2 using keywords and associated synonyms, search date up to 20 December 2020, no language restrictions.\n\nResultsWe included 106 studies assessing vertical transmission of SARS-CoV-2 from pregnant women to their neonates: these studies comprised 40 reviews (21 fulfilled systematic review methodology, including risk of bias assessment of included studies) and 66 primary studies including 32 case reports (of up to two cases) and 34 prospective and retrospective cohort studies, prospective and retrospective case series, observational studies (including asymptomatic screening), database studies and a quality improvement project. Almost all were conducted in a hospital setting. The 32 case reports were considered to be at high risk of bias, due to the study design; across the 34 remaining primary studies, risk of bias was low to moderate. Sixteen case reports examined vertical transmission, which was not related to maternal symptomatology. For the cohort and case series studies, the percentage of positive neonates ranged from 0% to 22% across the studies. Twenty studies reported no positive vertical transmission. Three studies that reported the highest positivity rates of 11%, 15% and 22% had specifically selected neonates with a positive test (within up to 35 days) within the study population and were therefore more selective populations. Across the cohort and case series studies there were 65/2391 (2.7%) neonates born to mothers with a diagnosis of COVID-19 tested positive for SARS-CoV-2 within 24 hours of birth. No evidence correlated maternal symptomatology to vertical transmission. Mode of delivery did not correlate with rates of vertical transmission. Of 25 studies, 7 identified SARS-CoV-2 in placental tissue; some of these did not demonstrate vertical transmission to the neonate. No study reported the results of viral culture to detect SARS-CoV-2.\n\nConclusionsThe results of these studies indicate that vertical transmission is possible, but is not frequent, and factors that influence when vertical transmission occurs are unknown. Further studies using standardised methods to establish viral infection are needed to establish vertical transmission rates and to assess clinical and other conditions affecting transmission.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Annette Pluddemann", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elizabeth A Spencer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Carl Heneghan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jon Brassey", - "author_inst": "Trip Database" - }, - { - "author_name": "Igho J Onakpoya", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elena Cecilia Rosca", - "author_inst": "Victor Babes University of Medicine and Pharmacy of Timisoara" - }, - { - "author_name": "David H Evans", - "author_inst": "University of Alberta" - }, - { - "author_name": "John M Conly", - "author_inst": "University of Calgary" - }, - { - "author_name": "Tom Jefferson", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.30.21259751", "rel_title": "Monitoring SARS-CoV-2 in sewage: toward sentinels with analytical accuracy", @@ -686666,6 +687302,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.03.21259959", + "rel_title": "Efficacy and safety of cyclosporine in the management of coronavirus disease 2019: A protocol for systematic review and meta-analysis", + "rel_date": "2021-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21259959", + "rel_abs": "IntroductionCyclosporine may improve the clinical course and outcomes of Coronavirus disease 2019 (COVID-19) due to its antiviral and anti-cytokine effects as shown in vitro. A few ongoing trials are exploring the benefit of adding it to the standard of care (SOC) of COVID-19 patients.\n\nObjectivesThe primary objective is to evaluate the severity of COVID-19, determined by oxygen saturation, intensive care unit (ICU) admission, or the World Health Organization COVID-19 clinical severity scale in patients treated with oral or intravenous cyclosporine added to SOC compared SOC alone or placebo. Secondary objectives include mortality, length of hospitalization, length of ICU stay, and laboratory measurements as well as the safety outcomes of cyclosporine.\n\nMethodologyA systematic review and meta-analysis of randomized clinical trials and observational studies that compared cyclosporine to placebo or SOC in COVID-19 patients will be conducted. PubMed, EMBASE, Web of Science, Cochrane Central Register of Controlled Trials, Google Scholar, and ClinicalTrials.gov will be explored for studies that satisfy pre-specified inclusion criteria. Quality assessment of all included studies will be performed. Meta-analyses will be done utilizing random effect models to estimate the effect of cyclosporine on the severity of COVID-19. Heterogeneity will be assessed utilizing Q statistics. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines will be followed.\n\nResultsThe result of this synthesis will inform potential changes in the management of COVID-19 patients, especially regarding the role of calcineurin inhibitors. Additionally, it will serve as hypothesis generating for potential future prospective studies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ibtihal Abdallah", + "author_inst": "Clinical Pharmacy Department, Hamad General Hospital, Hamad Medical Corporation" + }, + { + "author_name": "Mohamed Aabdien", + "author_inst": "Community Medicine Training Program, Medical Education, Hamad Medical Corporation" + }, + { + "author_name": "Mohammed Danjuma", + "author_inst": "Division of General Internal Medicine, Weill Cornell affliated-Hamad General Hospital, Hamad Medical Corporation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.02.21259665", "rel_title": "Assessment and Modeling of COVID-19 Outcomes in a Longitudinal Cohort of Hospitalized Adults", @@ -688129,85 +688792,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.28.21259420", - "rel_title": "Effectiveness of COVID-19 vaccines against variants of concern, Canada", - "rel_date": "2021-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259420", - "rel_abs": "SARS-CoV-2 variants of concern (VOC) are more transmissible and have the potential for increased disease severity and decreased vaccine effectiveness. We estimated the effectiveness of BNT162b2 (Pfizer-BioNTech Comirnaty), mRNA-1273 (Moderna Spikevax), and ChAdOx1 (AstraZeneca Vaxzevria) vaccines against symptomatic SARS-CoV-2 infection and COVID-19 hospitalization or death caused by the Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) VOCs in Ontario, Canada using a test-negative design study. Effectiveness against symptomatic infection [≥]7 days after two doses was 89-92% against Alpha, 87% against Beta, 88% against Gamma, 82-89% against Beta/Gamma, and 87-95% against Delta across vaccine products. The corresponding estimates [≥]14 days after one dose were lower. Effectiveness estimates against hospitalization or death were similar to, or higher than, against symptomatic infection. Effectiveness against symptomatic infection is generally lower for older adults ([≥]60 years) compared to younger adults (<60 years) for most of the VOC-vaccine combinations.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Sharifa Nasreen", - "author_inst": "University of Toronto" - }, - { - "author_name": "Hannah Chung", - "author_inst": "ICES, Toronto" - }, - { - "author_name": "Siyi He", - "author_inst": "ICES, Toronto, Ontario, Canada" - }, - { - "author_name": "Kevin A. Brown", - "author_inst": "Public Health Ontario, ON" - }, - { - "author_name": "Jonathan B. Gubbay", - "author_inst": "Public Health Ontario, ON" - }, - { - "author_name": "Sarah A Buchan", - "author_inst": "Public Health Ontario, ON" - }, - { - "author_name": "Deshayne B. Fell", - "author_inst": "University of Ottawa, ON" - }, - { - "author_name": "Peter C. Austin", - "author_inst": "ICES" - }, - { - "author_name": "Kevin L Schwartz", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Maria E. Sundaram", - "author_inst": "ICES" - }, - { - "author_name": "Andrew Calzavara", - "author_inst": "ICES" - }, - { - "author_name": "Branson Chen", - "author_inst": "ICES" - }, - { - "author_name": "Mina Tadrous", - "author_inst": "ICES" - }, - { - "author_name": "Kumanan Wilson", - "author_inst": "University of Ottawa, Ottawa, ON" - }, - { - "author_name": "Sarah E. Wilson", - "author_inst": "Public Health Ontario, ON" - }, - { - "author_name": "Jeffrey C Kwong", - "author_inst": "ICES" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.29.21259717", "rel_title": "A national survey of attitudes towards and intentions to vaccinate against COVID-19: implications for communications", @@ -688396,6 +688980,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.29.21259605", + "rel_title": "The SARS-CoV-2 receptor-binding domain expressed in Pichia pastoris as a candidate vaccine antigen", + "rel_date": "2021-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.29.21259605", + "rel_abs": "1.The effort to develop vaccines based on economically accessible technological platforms available by developing countries vaccine manufacturers is essential to extend the immunization to the whole world population and to achieve the desired herd immunity, necessary to end the COVID-19 pandemic. Here we report on the development of a SARS-CoV-2 receptor-binding domain (RBD) protein, expressed in yeast Pichia pastoris. The RBD was modified with addition of flexible N- and C-terminal amino acid extensions aimed to modulate the protein/protein interactions and facilitate protein purification. Fermentation with yeast extract culture medium yielded 30-40 mg/L. After purification by immobilized metal ion affinity chromatography and hydrophobic interaction chromatography, the RBD protein was characterized by mass-spectrometry, circular dichroism, and binding affinity to angiotensin-converting enzyme 2 (ACE2) receptor. The recombinant protein shows high antigenicity with convalescent human sera and also with sera from individuals vaccinated with the Pfizer-BioNTech mRNA or Sputnik V adenoviral-based vaccines. The RBD protein stimulates IFN{gamma}, IL-2, IL-6, IL-4, and TNF in mice secreting splenocytes from PBMC and lung CD3+ enriched cells. Immunogenicity studies with 50 {micro}g of the recombinant RBD formulated with alum, induce high levels of binding antibodies in mice and non-human primates, assessed by ELISA plates covered with RBD protein expressed in HEK293T cells. The mouse sera inhibited the RBD binding to ACE2 receptor in an in-vitro test and show neutralization of SARS-CoV-2 infection of Vero E6 cells. These data suggest that the RBD recombinant protein expressed in yeast P. pastoris is suitable as a vaccine candidate against COVID-19.\n\nHighlightsO_LIThe RBD protein (C-RBD-H6 PP) is expressed with high purity in P. pastoris.\nC_LIO_LIPhysico-chemical characterization confirms the right folding of the protein.\nC_LIO_LIThe recombinant protein shows high antigenicity with sera from convalescents.\nC_LIO_LIThe sera from animals inhibit the RBD-ACE2 binding and neutralize the virus.\nC_LIO_LIThe C-RBD-H6 protein stimulates IFN{gamma}, IL-2, IL-6, IL-4, and TNF in mice.\nC_LI", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Miladys Limonta-Fernandez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba" + }, + { + "author_name": "Glay Chinea-Santiago", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Alejandro Miguel Martin-Dunn", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Diamile Gonzalez-Roche", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Monica Bequet-Romero", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Gabriel Marquez-Perera", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Isabel Gonzalez-Moya", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Camila Canaan-Haden-Ayala", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Ania Cabrales-Rico", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Luis Ariel Espinosa-Rodriguez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Yassel Ramos-Gomez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Ivan Andujar-Martinez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Luis Javier Gonzalez-Lopez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Mariela Perez de la Iglesia", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Jesus Zamora-Sanchez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Otto Cruz-Sui", + "author_inst": "Civilian Defense Scientific Research Center, Carretera de Jamaica y Autopista Nacional, San Jose de las Lajas, Mayabeque, Cuba" + }, + { + "author_name": "Gilda Lemos-Perez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Gleysin Cabrera-Herrera", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Jorge Valdes-Hernandez", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Eduardo Martinez-Diaz", + "author_inst": "Biotechnology and Pharmaceutical Industries Group, BioCubaFarma, Ave. Independencia 8126, esq. a Calle 100. Boyeros. La Habana, Cuba." + }, + { + "author_name": "Eulogio Pimentel-Vazquez", + "author_inst": "Biotechnology and Pharmaceutical Industries Group, BioCubaFarma, Ave. Independencia 8126, esq. a Calle 100. Boyeros. La Habana, Cuba." + }, + { + "author_name": "Marta Ayala-Avila", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + }, + { + "author_name": "Gerardo Guillen-Nieto", + "author_inst": "Center for Genetic Engineering and Biotechnology, CIGB, Ave. 31 E/ 158 y 190, La Habana 10600, Cuba." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.28.21259452", "rel_title": "Persistent symptoms following SARS-CoV-2 infection in a random community sample of 508,707 people", @@ -690019,37 +690710,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.26.21259369", - "rel_title": "A Retrospective analysis of DIC score and SIC score in prediction of COVID-19 severity", - "rel_date": "2021-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.26.21259369", - "rel_abs": "BackgroundThe novel Disseminated Intravascular Coagulation (DIC) score [platelet count, prolonged prothrombin time, D-dimer, and fibrinogen] and Sepsis Induced Coagulopathy (SIC) score [platelet count, International normalized ratio, and Sequential organ failure assessment score] are markers of coagulopathy, which, for the first time, are explored in line with the COVID-19 disease outcomes. The correlation of D-dimer with these findings is also studied.\n\nPatients and methodsA retrospective analysis of hospital-based records of 168 COVID-19 patients. Data including D-dimer, routine investigations, DIC and SIC scorings (all within three days of admission) were collected and correlated with the outcomes. The study was conducted in a tertiary care center catering to population of North India.\n\nResultsHigher DIC score (1{middle dot}59 {+/-} 1{middle dot}18 v/s 0{middle dot}96 {+/-} 1{middle dot}18), SIC score (1{middle dot}60 {+/-} 0{middle dot}89 v/s 0{middle dot}63 {+/-} 0{middle dot}99), and D-dimer titers (1321{middle dot}33 {+/-} 1627{middle dot}89 v/s 583{middle dot}66 {+/-} 777{middle dot}71 ng/ml) were significantly associated with severe COVID-19 disease (P<0{middle dot}05). DIC score and SIC score [≥] 1, and D-dimer [≥] 1315 ng/ml for severe disease; DIC score [≥] 1, SIC score [≥] 2, and D-dimer [≥] 600 ng/ml for Pulmonary Embolism (PE); and DIC score and SIC score [≥] 1, and D-dimer level [≥] 990 ng/ml for mortality were the respective cut-off values we found from our study.\n\nConclusionHigher DIC scores, SIC scores, and D-dimer values are associated with severe COVID-19 disease, in-hospital mortality, and PE risk. They can serve as easily accessible early markers of severe disease and prioritize hospital admissions in the presently overburdened scenario, and may be used to develop prognostic prediction models.\n\nHighlightsDIC scores, SIC scores, and D-dimer values are hereby studied in association with COVID-19 disease severity, in-hospital mortality, and PE risk. They serve as easily accessible early markers of severe disease and prioritize hospital admissions in the presently overburdened scenario, and may be used to develop prognostic prediction models.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mayank Kapoor", - "author_inst": "All India Institute of Medical Sciences Rishikesh" - }, - { - "author_name": "Prasan Kumar Panda", - "author_inst": "All India Institute of Medical Sciences Rishikesh" - }, - { - "author_name": "Lokesh Kumar Saini", - "author_inst": "All India Institute of Medical Sciences Rishikesh" - }, - { - "author_name": "Yogesh Arvind Bahurupi", - "author_inst": "All India Institute of Medical Sciences Rishikesh" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.06.27.21258591", "rel_title": "Self-assessment of COVID-19 vaccination efficacy using a simple POCT for SARS-CoV-2 S1 protein antibody IgG-IgM", @@ -690442,6 +691102,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.28.21259384", + "rel_title": "Comparison of Mental Health Symptom Changes from pre-COVID-19 to COVID-19 by Sex or Gender: A Systematic Review and Meta-analysis", + "rel_date": "2021-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259384", + "rel_abs": "ImportanceWomen and gender-diverse individuals have faced disproportionate socioeconomic burden during COVID-19. There have been reports that this has translated into greater negative changes in mental health, but this has been based on cross-sectional research that has not accounted for pre-COVID-19 differences.\n\nObjectiveTo compare mental health symptom changes since pre-COVID-19 by sex or gender.\n\nData SourcesMEDLINE, PsycINFO, CINAHL, EMBASE, Web of Science, China National Knowledge Infrastructure, Wanfang, medRxiv, and Open Science Framework (December 31, 2019 to August 30, 2021).\n\nStudy SelectionEligible studies compared mental health symptom changes from pre-COVID-19 to COVID-19 by sex or gender.\n\nData Extraction and SynthesisData was extracted by a single reviewer with validation by a second reviewer. Adequacy of study methods and reporting was assessed using an adapted version of the Joanna Briggs Institute Checklist for Prevalence Studies. A restricted maximum-likelihood random-effects meta-analyses was conducted.\n\nMain Outcomes and MeasuresAnxiety symptoms, depression symptoms, general mental health, and stress measured continuously or dichotomously.\n\nResults12 studies (10 unique cohorts) were included. All compared females or women to males or men; none included gender-diverse individuals. Continuous symptom change differences were not statistically significant for depression (standardized mean difference [SMD]= 0.12, 95% CI -0.09 to 0.33; 4 studies, 4,475 participants; I2=69.0%) and stress (SMD= - 0.10, 95% CI -0.21 to 0.01; 4 studies, 1,533 participants; I2=0.0%), but anxiety (SMD= 0.15, 95% CI 0.07 to 0.22; 4 studies, 4,344 participants; I2=3.0%) and general mental health (SMD= 0.15, 95% CI 0.12 to 0.18; 3 studies, 15,692 participants; I2=0.0%) worsened more among females or women than males or men during COVID-19. There were no significant differences in changes in proportion above a cut-off: anxiety (difference= -0.05, 95% CI -0.20 to 0.11; 1 study, 217 participants), depression (difference= 0.12, 95% CI -0.03 to 0.28; 1 study, 217 participants), general mental health (difference= -0.03, 95% CI -0.09 to 0.04; 3 studies, 18,985 participants; I2=94.0%), stress (difference= 0.04, 95% CI -0.10 to 0.17; 1 study, 217 participants).\n\nConclusion and RelevanceMental health outcomes did not differ or were worse by amounts below thresholds for clinical significance for women compared to men.\n\nRegistrationPROSPERO (CRD42020179703).\n\nKEY MESSAGESO_ST_ABSQuestionC_ST_ABSDid mental health symptoms worsen more for females or women than males or men in COVID-19?\n\nFindingsWe reviewed almost 65,000 citations and identified 12 studies that provided data to directly compare mental health symptom changes from pre-COVID-19 to during COVID-19 for females or women versus males or men. Statistically significant, but small, sex- or gender-based differences were found in 2 of 8 mental health outcomes.\n\nMeaningMental health changes among females or women were not significantly different from males or men for most outcomes, and differences that were identified were small and less than minimally important difference thresholds.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Tiffany Dal Santo", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Ying Sun", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Yin Wu", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Chen He", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Yutong Wang", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Xiaowen Jiang", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Kexin Li", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Olivia Bonardi", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Ankur Krishnan", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Jill T. Boruff", + "author_inst": "Schulich Library of Physical Sciences, Life Sciences, and Engineering, McGill University" + }, + { + "author_name": "Danielle B. Rice", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Sarah Markham", + "author_inst": "Department of Biostatistics and Health Informatics, King's College London" + }, + { + "author_name": "Brooke Levis", + "author_inst": "Centre for Prognosis Research, School of Medicine, Keele University" + }, + { + "author_name": "Marleine Azar", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Dipika Neupane", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Amina Tasleem", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Anneke Yao", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Ian Thombs-Vite", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + }, + { + "author_name": "Branka Agic", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Christine Fahim", + "author_inst": "Li Ka Shing Knowledge Institute, Unity Health Toronto" + }, + { + "author_name": "Michael S. Martin", + "author_inst": "School of Epidemiology and Public Health, University of Ottawa" + }, + { + "author_name": "Sanjeev Sockalingam", + "author_inst": "Centre for Addiction and Mental Health" + }, + { + "author_name": "Gustavo Turecki", + "author_inst": "Department of Psychology, McGill University" + }, + { + "author_name": "Andrea Benedetti", + "author_inst": "Department of Epidemiology, Biostatistics and Occupational Health, McGill University" + }, + { + "author_name": "Brett B Thombs", + "author_inst": "Lady Davis Institute for Medical Research, Jewish General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.06.27.21259131", "rel_title": "Face mask use and associated factors among students in rural Eastern Uganda amidst the COVID-19 pandemic", @@ -692341,53 +693116,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.28.21259673", - "rel_title": "Infectivity and immune escape of the new SARS-CoV-2 variant of interest Lambda", - "rel_date": "2021-07-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259673", - "rel_abs": "BackgroundThe newly described SARS-CoV-2 lineage C.37 was recently classified as a variant of interest by the WHO (Lambda variant) based on its high circulation rates in South American countries and the presence of critical mutations in the spike protein. The impact of such mutations in infectivity and immune escape from neutralizing antibodies are entirely unknown.\n\nMethodsWe performed a pseudotyped virus neutralization assay and determined the impact of the Lambda variant on infectivity and immune escape using plasma samples from healthcare workers (HCW) from two centers in Santiago, Chile who received the two-doses scheme of the inactivated virus vaccine CoronaVac.\n\nResultsWe observed an increased infectivity mediated by the Lambda spike protein that was even higher than that of the D614G (lineage B) or the Alpha and Gamma variants. Compared to the Wild type (lineage A), neutralization was decreased by 3.05-fold for the Lambda variant while it was 2.33-fold for the Gamma variant and 2.03-fold for the Alpha variant.\n\nConclusionsOur results indicate that mutations present in the spike protein of the Lambda variant of interest confer increased infectivity and immune escape from neutralizing antibodies elicited by CoronaVac. These data reinforce the idea that massive vaccination campaigns in countries with high SARS-CoV-2 circulation must be accompanied by strict genomic surveillance allowing the identification of new isolates carrying spike mutations and immunology studies aimed to determine the impact of these mutations in immune escape and vaccines breakthrough.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "M\u00f3nica L. Acevedo", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Luis Alonso-Palomares", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Andr\u00e9s Bustamante", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Aldo Gaggero", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Fabio Paredes", - "author_inst": "Ministerio de Salud de Chile" - }, - { - "author_name": "Claudia Cort\u00e9s", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Fernando Valiente-Echeverr\u00eda", - "author_inst": "Universidad de Chile" - }, - { - "author_name": "Ricardo Soto-Rifo", - "author_inst": "Universidad de Chile" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.30.450632", "rel_title": "Spike protein cleavage-activation mediated by the SARS-CoV-2 P681R mutation: a case-study from its first appearance in variant of interest (VOI) A.23.1 identified in Uganda", @@ -692640,6 +693368,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.28.21259628", + "rel_title": "Rotation-based schedules in elementary schools to prevent COVID-19 spread: A simulation study", + "rel_date": "2021-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259628", + "rel_abs": "BackgroundRotations of schoolchildren on a weekly basis is one of the nonpharmaceutical interventions often considered in the covid-19 pandemic. This study aims to investigate the impact of different types of rotations in various testing contexts.\n\nMethodsWe built an agent-based model of interactions among pupils and teachers based on an online survey in an elementary school in Prague, Czechia. This model contains 624 schoolchildren and 55 teachers (679 nodes) and about 27 thousands social contacts (edges) in 10 layers. The layers reflect different types of contacts (in classroom, cafeteria etc.) as described in the survey. On this multi-graph structure we run a modified SEIR model of the covid-19 dynamics. The parameters of the model are calibrated on data from the outbreak in the Czech Republic in the period March to June 2020.\n\nFindingsThere are three main findings in our paper.\n\nO_LIWeekly rotations of in-class and distance learning reduce the spread of covid-19 by 75-81% and thus represent an effective preventative measure in school setting.\nC_LIO_LIRegular antigen testing twice a week, or weekly PCR testing, significantly reduces infections even when using tests with a lower sensitivity: tests with a 40% sensitivity reduce infections by more than 50 percent.\nC_LIO_LIThe density of revealed contact graphs for older pupils is 1.5 times higher than the younger pupils graph, the teachers network is yet an order of magnitude denser. Consequently, the infection transmission between teachers is highly overproportional in our school. Moreover, teachers act as bridges connecting clusters of classes, especially in the secondary grade where they are responsible for 14-18% of infections, in comparison to 8-11% in primary grade.\nC_LI\n\nInterpretationWeekly rotations with regular testing are a highly effective non-pharmaceutical intervention for the prevention of covid-19 spread in schools and a way to keep schools open during an epidemic or to reopen them as the epidemiological situation improves.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Cyril Brom", + "author_inst": "Faculty of Mathematics and Physics, Charles University" + }, + { + "author_name": "Tomas Diviak", + "author_inst": "School of Social Sciences, University of Manchester" + }, + { + "author_name": "Jakub Drbohlav", + "author_inst": "Ministry of Education, Youth and Sports of the Czech Republic" + }, + { + "author_name": "Vaclav Korbel", + "author_inst": "CERGE-EI" + }, + { + "author_name": "Rene Levinsky", + "author_inst": "CERGE-EI" + }, + { + "author_name": "Roman Neruda", + "author_inst": "The Czech Academy of Sciences, Institute of Computer Science" + }, + { + "author_name": "Gabriela Suchoparova", + "author_inst": "The Czech Academy of Sciences, Institute of Computer Science" + }, + { + "author_name": "Josef Slerka", + "author_inst": "Faculty of Arts, Charles University" + }, + { + "author_name": "Martin Smid", + "author_inst": "The Czech Academy of Sciences, Institute of Information Theory and Automation" + }, + { + "author_name": "Jan Trnka", + "author_inst": "Third Faculty of Medicine, Charles University" + }, + { + "author_name": "Petra Vidnerova", + "author_inst": "The Czech Academy of Sciences, Institute of Computer Science" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.28.21259620", "rel_title": "The Evolution of Young People's Mental Health during COVID-19: Evidence from four Low-and-Middle-Income-Countries", @@ -694075,65 +694862,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.06.30.450298", - "rel_title": "Pathology and immunity after SARS-CoV-2 infection in male ferrets is affected by age and inoculation route", - "rel_date": "2021-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.30.450298", - "rel_abs": "Improving COVID-19 intervention strategies partly relies on animal models to study SARS-CoV-2 disease and immunity. In our pursuit to establish a model for severe COVID-19, we inoculated young and adult male ferrets intranasally or intratracheally with SARS-CoV-2. Intranasal inoculation established an infection in all ferrets, with viral dissemination into the brain and gut. Upon intratracheal inoculation only adult ferrets became infected. However, neither inoculation route induced observable COVID-19 symptoms. Despite this, a persistent inflammation in the nose was prominent in especially young ferrets and follicular hyperplasia in the bronchi developed 21 days post infection. These effects -if sustained- might resemble long-COVID. Respiratory and systemic cellular responses and antibody responses were induced only in animals with an established infection. We conclude that intranasally-infected ferrets resemble asymptomatic COVID-19 and possibly aspects of long-COVID. Combined with the increasing portfolio to measure adaptive immunity, ferrets are a relevant model for SARS-CoV-2 vaccine research.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Koen van de Ven", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Harry van Dijken", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Lisa Wijsman", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Angela Gomersbach", - "author_inst": "Animal research centre, Poonawalla Science Park" - }, - { - "author_name": "Tanja Schouten", - "author_inst": "Animal research centre, Poonawalla Science Park" - }, - { - "author_name": "Jolanda Kool", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Stefanie Lenz", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Paul Roholl", - "author_inst": "Microscope Consultancy, Weesp, the Netherlands" - }, - { - "author_name": "Adam Meijer", - "author_inst": "National Institute for Public Health and the Environment" - }, - { - "author_name": "Puck van Kasteren", - "author_inst": "National Institute for Public Health and the Environment (RIVM)" - }, - { - "author_name": "Jorgen de Jonge", - "author_inst": "National Institute for Public Health and the Environment" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.30.450483", "rel_title": "Large scale screening discovers clofoctol as an inhibitor of SARS-CoV-2 replication that reduces COVID-19-like pathology", @@ -694350,6 +695078,81 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.06.30.450617", + "rel_title": "Detection of potential new SARS-CoV-2 Gamma-related lineage in Tocantins shows the spread and ongoing evolution of P.1 in Brazil", + "rel_date": "2021-06-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.30.450617", + "rel_abs": "After more than a year of the pandemic situation of COVID-19, the United Kingdom (UK), South Africa, and Brazil became the epicenter of new lineages of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Variants of Concern (VOCs) were identified through a continuous genomic surveillance global effort, the B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), and P.1 (Gamma) harboring a constellation set of mutations. This research aims to: (i) report the predominance of the Gamma (P.1) lineage presenting the epidemiological situation of the SARS-CoV-2 genomic surveillance at the state of Tocantins, and (ii) describe the emergence of possible new mutations and viral variants with the potential new lineage (P1-related) represented by 8 genomes from the Tocantins harboring the mutation L106F in ORF3a. At the moment, 6,687 SARS-CoV-2 genomes from GISAID carry this mutation. The whole-genome sequencing has an important role in understanding the evolution and genomic diversity of SARS-CoV-2, thus, the continuous monitoring will help in the control measures and restrictions imposed by the secretary of health of the state to prevent the spread of variants.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Ueric Jose Borges de Souza", + "author_inst": "Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi, Tocantins, 77410-570, Brazil." + }, + { + "author_name": "Raissa Nunes dos Santos", + "author_inst": "Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi, Tocantins, 77410-570, Brazil." + }, + { + "author_name": "Fernando Lucas Melo", + "author_inst": "Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil." + }, + { + "author_name": "Aline Belmok", + "author_inst": "Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil." + }, + { + "author_name": "Jucimaria Dantas Galvao", + "author_inst": "Central Public Health Laboratory of the State of Tocantins, Palmas, Tocantins, 77054-970, Brazil" + }, + { + "author_name": "Sirlene Borges Damasceno", + "author_inst": "Central Public Health Laboratory of the State of Tocantins, Palmas, Tocantins, 77054-970, Brazil" + }, + { + "author_name": "Tereza Cristina Vieira de Rezende", + "author_inst": "Central Public Health Laboratory of the State of Tocantins, Palmas, Tocantins, 77054-970, Brazil" + }, + { + "author_name": "Miguel de Souza Andrade", + "author_inst": "Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil" + }, + { + "author_name": "Bergmann Morais Ribeiro", + "author_inst": "Baculovirus Laboratory, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasilia, Distrito Federal, 70910-900, Brazil" + }, + { + "author_name": "Jose Carlos Ribeiro Junior", + "author_inst": "Postgraduate Program in Animal Health and Public Health in the Tropics, Federal University of Tocantins, Araguaina, Tocantins, 77804-970, Brazil" + }, + { + "author_name": "Rogerio Fernandes Carvalho", + "author_inst": "Postgraduate Program in Animal Health and Public Health in the Tropics, Federal University of Tocantins, Araguaina, Tocantins, 77804-970, Brazil" + }, + { + "author_name": "Monike da Silva Oliveira", + "author_inst": "Postgraduate Program in Tropical Medicine and Public Health, Federal University of Goias, Goiania, Goias, 74690-900, Brazil." + }, + { + "author_name": "Isac Gabriel Cunha dos Santos", + "author_inst": "Postgraduate Program in Animal Health and Public Health in the Tropics, Federal University of Tocantins, Araguaina, Tocantins, 77804-970, Brazil" + }, + { + "author_name": "Fernando Rosado Spilki", + "author_inst": "One Health Laboratory, Feevale Techpark, Feevale University, Campo Bom, Rio Grande do Sul, 93700-000, Brazil and Molecular Microbiology Laboratory, Feevale Univ" + }, + { + "author_name": "Fabricio Souza Campos", + "author_inst": "Bioinformatics and Biotechnology Laboratory, Campus of Gurupi, Federal University of Tocantins, Gurupi, Tocantins, 77410-570, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.06.30.450547", "rel_title": "Computational saturation mutagenesis of SARS-CoV-1 spike glycoprotein: stability, binding affinity, and comparison with SARS-CoV-2", @@ -696289,57 +697092,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.21.21259104", - "rel_title": "Models of COVID-19 vaccine prioritisation: a systematic literature search and narrative review", - "rel_date": "2021-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.21.21259104", - "rel_abs": "BackgroundHow best to prioritise COVID-19 vaccination within and between countries has been a public health and an ethical challenge for decision-makers globally. We systematically reviewed epidemiological and economic modelling evidence on population priority groups to minimise COVID-19 mortality, transmission and morbidity outcomes.\n\nMethodsWe searched the National Institute of Health iSearch COVID-19 Portfolio (a database of peer-reviewed and pre-print articles), Econlit, the Centre for Economic Policy Research and the National Bureau of Economic Research for mathematical modelling studies evaluating the impact of prioritising COVID-19 vaccination to population target groups. We narratively synthesised the main study conclusions on prioritisation and the conditions under which the conclusions changed.\n\nFindingsThe search identified 1820 studies. 36 studies met the inclusion criteria and were narratively synthesised. 83% of studies described outcomes in high-income countries. We found that for countries seeking to minimise deaths, prioritising vaccination of senior adults was the optimal strategy and for countries seeking to minimise cases the young were prioritised. There were several exceptions to the main conclusion, notably reductions in deaths could be increased, if groups at high risk of both transmission and death could be further identified. Findings were also sensitive to the level of vaccine coverage.\n\nInterpretationThe evidence supports WHO SAGE recommendations on COVID-19 vaccine prioritisation. There is however an evidence gap on optimal prioritisation for low- and middle-income countries, studies that included an economic evaluation, and studies that explore prioritisation strategies if the aim is to reduce overall health burden including morbidity.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Nuru Saadi", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Y-Ling Chi", - "author_inst": "International Decision Support Inititative, Center for Global Health and Development" - }, - { - "author_name": "Srobana Ghosh", - "author_inst": "International Decision Support Inititative, Center for Global Health and Development" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Ciara McCarthy", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Matthew Quaife", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Jeanette Dawa", - "author_inst": "Washington State University - Global Health Program, Nairobi, Kenya. Center for Epidemiological Modelling and Analysis, University of Nairobi, Nairobi, Kenya" - }, - { - "author_name": "Mark Jit", - "author_inst": "Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Anna Vassall", - "author_inst": "London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.22.21258961", "rel_title": "Strong immunogenicity of heterologous prime-boost immunizations with the experimental vaccine GRAd-COV2 and BNT162b2 or ChAdOx1-nCOV19", @@ -696568,6 +697320,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.06.24.21259087", + "rel_title": "Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children", + "rel_date": "2021-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259087", + "rel_abs": "Children are consistently reported to have reduced SARS-CoV-2 infection rates and a substantially lower risk for developing severe COVID-19. However, the molecular mechanisms underlying protection against COVID-19 in younger age groups remain widely unknown. Here, we systematically characterized the single-cell transcriptional landscape in the upper airways in SARS-CoV-2 negative and age-matched SARS-CoV-2 positive children (n=42) and corresponding samples from adults (n=44), covering an age range of four weeks to 77 years. Children displayed higher basal expression of the relevant pattern recognition receptor (PRR) pathways in upper airway epithelial cells, macrophages, and dendritic cells, resulting in stronger innate antiviral responses upon SARS-CoV-2 infection compared to adults. We further detected distinct immune cell subpopulations with an overall dominance of neutrophils and a population of cytotoxic T cells occurring predominantly in children. Our study provides evidence that the airway epithelial and mucosal immune cells of children are pre-activated and primed for virus sensing, resulting in a stronger early innate antiviral responses to SARS-CoV-2 infection compared to adults.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Jennifer Loske", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Jobst R\u00f6hmel", + "author_inst": "Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Soeren Lukassen", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Sebastian Stricker", + "author_inst": "Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Vladimir Gon\u00e7alves Magalh\u00e3es", + "author_inst": "Research group Dynamics of Early Viral Infection and the Innate Antiviral Response, division F170, German Cancer Research Center (DKFZ)" + }, + { + "author_name": "Johannes Liebig", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Robert Lorenz Chua", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Loreen Th\u00fcrmann", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Marey Messingschlager", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Anke Seegebarth", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Bernd Timmermann", + "author_inst": "Max Planck Institute for Molecular Genetics, Berlin" + }, + { + "author_name": "Sven Klages", + "author_inst": "Max Planck Institute for Molecular Genetics, Berlin" + }, + { + "author_name": "Markus Ralser", + "author_inst": "Institute of Biochemistry, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Birgit Sawitzki", + "author_inst": "Institute of Medical Immunology, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Leif Erik Sander", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Victor M Corman", + "author_inst": "Institute of Virology, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Christian Conrad", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Sven Laudi", + "author_inst": "Department of Anesthesiology and Intensive Care, University Hospital Leipzig" + }, + { + "author_name": "Marco Binder", + "author_inst": "Research group Dynamics of Early Viral Infection and the Innate Antiviral Response, division F170, German Cancer Research Center (DKFZ)," + }, + { + "author_name": "Saskia Trump", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin Center for Digital Health, Berlin Institute of Health at Charite" + }, + { + "author_name": "Roland Eils", + "author_inst": "Center for Digital Health, Berlin Institute of Health at Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Marcus Mall", + "author_inst": "Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charite - Universitatsmedizin Berlin" + }, + { + "author_name": "Irina Lehmann", + "author_inst": "Molecular Epidemiology Unit, Berlin Institute of Health at Charite - Universitatsmedizin Berlin Center for Digital Health, Berlin Institute of Health at Charite" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.23.21259394", "rel_title": "Macro-Level Drivers of SARS-CoV-2 Transmission: A Data-Driven Analysis of Factors Contributing to Epidemic Growth During the First Wave of outbreaks in the United States", @@ -698743,85 +699602,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.18.21259162", - "rel_title": "Rapid, large-scale wastewater surveillance and automated reporting system enabled early detection of nearly 85% of COVID-19 cases on a University campus", - "rel_date": "2021-06-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21259162", - "rel_abs": "Wastewater based surveillance has gained prominence and come to the forefront as a leading indicator of forecasting COVID-19 infection dynamics owing to its cost-effectiveness and its ability to inform early public health interventions. A university campus could especially benefit from wastewater surveillance as they are characterized by largely asymptomatic populations and are potential hotspots for transmission that necessitate frequent diagnostic testing. In this study, we employed a large-scale GIS (Geographic information systems) enabled building-level wastewater monitoring system associated with the on-campus residences of 7614 individuals. Sixty-eight automated wastewater samplers were deployed to monitor 239 campus buildings with a focus on residential buildings. Time-weighted composite samples were collected on a daily basis and analyzed within the same day. Sample processing was streamlined significantly through automation, reducing the turnaround time by 20-fold and exceeding the scale of similar surveillance programs by 10 to 100-fold, thereby overcoming one of the biggest bottlenecks in wastewater surveillance. An automated wastewater notification system was developed to alert residents to a positive wastewater sample associated with their residence and to encourage uptake of campus-provided asymptomatic testing at no charge. This system, integrated with the rest of the \"Return to Learn\" program at UC San Diego-led to the early diagnosis of nearly 85% of all COVID-19 cases on campus. Covid-19 testing rates increased by 1.9-13X following wastewater notifications. Our study shows the potential for a robust, efficient wastewater surveillance system to greatly reduce infection risk as college campuses and other high-risk environments reopen.\n\nIMPORTANCEWastewater based epidemiology can be particularly valuable at University campuses where high-resolution spatial sampling in a well-controlled context could not only provide insight into what affects campus community as well as how those inferences can be extended to a broader city/county context. In the present study, a large-scale wastewater surveillance was successfully implemented on a large university campus enabling early detection of 85% of COVID-19 cases thereby averting potential outbreaks. The highly automated sample processing to reporting system enabled dramatically reduced the turnaround time to 5h (sample to result time) for 96 samples. Furthermore, miniaturization of the sample processing pipeline brought down the processing cost significantly ($13/sample). Taken together, these results show that such a system could greatly ameliorate long-term surveillance on such communities as they look to reopen.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Smruthi Karthikeyan", - "author_inst": "University of California - San Diego School of Medicine" - }, - { - "author_name": "Andrew Nguyen", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Daniel McDonald", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Yijian Zong", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Nancy Ronquillo", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Junting Ren", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Jingjing Zou", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Sawyer Farmer", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Greg Humphrey", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Diana Henderson", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Tara Javidi", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Karen Messer", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Cheryl Anderson", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Robert Schooley", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Natasha Martin", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Rob Knight", - "author_inst": "University of California San Diego" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.25.449918", "rel_title": "Progression and Resolution of SARS-1 CoV-2 Infection in Golden Syrian Hamsters", @@ -699334,6 +700114,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.24.21259444", + "rel_title": "Early warning signals predict emergence of COVID-19 waves", + "rel_date": "2021-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259444", + "rel_abs": "Early warning signals (EWSs) aim to predict changes in complex systems from phenomenological signals in time series data. These signals have recently been shown to precede the initial emergence of disease outbreaks, offering hope that policy makers can make predictive rather than reactive management decisions. Here, using daily COVID-19 case data in combination with a novel, sequential analysis, we show that composite EWSs consisting of variance, autocorrelation, and return rate not only pre-empt the initial emergence of COVID-19 in the UK by 14 to 29 days, but also the following wave six months later. We also predict there is a high likelihood of a third wave as of the data available on 9th June 2021. Our work suggests that in highly monitored disease time series such as COVID-19, EWSs offer the opportunity for policy makers to improve the accuracy of time critical decisions based solely upon surveillance data.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Duncan A O'Brien", + "author_inst": "University of Bristol" + }, + { + "author_name": "Christopher F Clements", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.24.21259469", "rel_title": "Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner", @@ -700761,53 +701564,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.24.21259460", - "rel_title": "Analysis of Host Immunological Response of Adenovirus-Based COVID-19 Vaccines", - "rel_date": "2021-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259460", - "rel_abs": "During the SARS-CoV-2 global pandemic, several vaccines, including mRNA and ade-novirus vector approaches, have received emergency or full approval. However, supply chain logistics have hampered global vaccine delivery, which is impacting mass vaccination strategies. Recent studies have identified different strategies for vaccine dose administration so that supply constraints issues are diminished. These include increasing the time between consecutive doses in a two-dose vaccine regimen and reducing the dosage of the second dose. We consider both of these strategies in a mathematical modeling study of a non-replicating viral vector adenovirus vaccine in this work. We investigate the impact of different prime-boost strategies by quantifying their effects on immunological outcomes based on simple ordinary differential equations. The boost dose is administered either at a standard dose (SD) of 1000 or at a low dose (LD) of 500 or 250 vaccine particles. Simulated Second dose fractionation highlights previously shown dose-dependent features of the immune mechanism. In agreement with clinical characteristics of 175 COVID-19 recovered patients, the model predictions for either SD/SD or SD/LD regimens mainly show that by stretching the prime-boost interval until 18 or 20 weeks, the minimum promoted antibody (Nab) response is comparable with the neutralizing antibody level of COVID-19 recovered patients. The minimum stimulated antibody in SD/SD regimen is identical with the high level of clinical trial data. It is at the same range of the medium-high level of Nab in SD/LD, where the second dose is half or quarter of the standard dose.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "suzan farhangsardroodi", - "author_inst": "York university" - }, - { - "author_name": "Chapin Korosec", - "author_inst": "York university" - }, - { - "author_name": "Samaneh Gholami", - "author_inst": "York university" - }, - { - "author_name": "Morgan Craig", - "author_inst": "University of Montreal" - }, - { - "author_name": "Iain R Moyles", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Mohammad Sajjad Ghaemi", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Hsu Kiang Ooi", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Jane M Heffernan", - "author_inst": "York university" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.24.21259294", "rel_title": "Differential pre-pandemic IgA reactivity against SARS-CoV-2 and circulating human coronaviruses measured in milk collected in Uganda and the USA", @@ -700992,6 +701748,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.24.21259218", + "rel_title": "Long-term course of humoral and cellular immune responses in outpatients after SARS-CoV-2 infection", + "rel_date": "2021-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259218", + "rel_abs": "Characterisation of the naturally acquired B and T cell immune responses to SARS-CoV-2 is important for the development of public health and vaccination strategies to manage the burden of COVID-19 disease. We conducted a prospective, longitudinal analysis in COVID-19 recovered patients at various time points over a 10-month period in order to determine how circulating antibody levels and interferon-gamma (IFN-{gamma}) release by peripheral blood cells change over time following natural infection.\n\nFrom March 2020 till January 2021, we enrolled 412 adults mostly with mild or moderate disease course. At each study visit, subjects donated peripheral blood for testing of anti-SARS-CoV-2 IgG antibodies and IFN-{gamma} release after SARS-CoV-2 S-protein stimulation. Anti-SARS-CoV-2 IgG antibodies were identified in 316/412 (76.7%) of the patients and 215/412 (52.2%) had positive neutralizing antibody levels. Likewise, in 274/412 (66.5 %) positive IFN-{gamma} release and IgG antibodies were detected. With respect to time after infection, both IgG antibody levels and IFN-{gamma} concentrations decreased by about half within three hundred days. Statistically, IgG and IFN-{gamma} production were closely associated, but on an individual basis we observed patients with high antibody titres but low IFN-{gamma} levels and vice versa.\n\nOur data suggest that immunological reaction is acquired in most individuals after infection with SARS-CoV-2 and is sustained in the majority of patients for at least 10 months after infection. Since no robust marker for protection against COVID-19 exists so far, we recommend utilizing both, IgG and IFN-{gamma} release for an individual assessment of immunity status.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Julia Schiffner", + "author_inst": "University of Luebeck, Center for Infection and Inflammation Research, Luebeck, Germany" + }, + { + "author_name": "Insa Backhaus", + "author_inst": "Institute of Medical Sociology, Centre for Health and Society, Medical Faculty and University Hospital, Heinrich-Heine-University, Duesseldorf, Germany" + }, + { + "author_name": "Jens Rimmele", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Soeren Schulz", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Till Moehlenkamp", + "author_inst": "Health Protection Authority, Luebeck, Germany" + }, + { + "author_name": "Julia Maria Klemens", + "author_inst": "Institute for Experimental Immunology, affiliated to EUROIMMUN Medizinische Labordiagnostika AG, Luebeck, Germany" + }, + { + "author_name": "Dorinja Zapf", + "author_inst": "Institute for Experimental Immunology, affiliated to EUROIMMUN Medizinische Labordiagnostika AG, Luebeck, Germany" + }, + { + "author_name": "Werner Solbach", + "author_inst": "University of Luebeck, Center for Infection and Inflammation Research, Luebeck, Germany" + }, + { + "author_name": "Alexander Mischnik", + "author_inst": "Health Protection Authority, Luebeck, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.22.21259316", "rel_title": "Investigating phenotypes of pulmonary COVID-19 recovery: a longitudinal observational prospective multicenter trial", @@ -702491,41 +703298,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.15.21259003", - "rel_title": "OVARIAN GRANULOSA CELLS FROM WOMEN WITH PCOS EXPRESS LOW LEVELS OF SARS-COV-2 RECEPTORS AND CO-FACTORS", - "rel_date": "2021-06-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21259003", - "rel_abs": "PurposeSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is global pandemic with more than 3 million deaths so far. Female reproductive tract organs express coronavirus-associated receptors and factors (SCARFs); suggesting they may be susceptible to SARS-CoV-2 infection however the susceptibility of ovary/follicle/oocyte to the same is still elusive. Co-morbidities like obesity, type-2 diabetes mellitus, cardiovascular disease etc. increase the risk of SARS-CoV-2 infection. These features are common in women with polycystic ovary syndrome (PCOS), warranting further scope to study SCARFs expression in ovary of these women.\n\nMaterials and methodsSCARFs expression in ovary and ovarian tissues of women with PCOS and healthy women was explored by analyzing publically available microarray datasets. Transcript expression of SCARFs were investigated in mural and cumulus granulosa cells (MGCs and CGCs) from control and PCOS women undergoing in vitro fertilization (IVF).\n\nResultsMicroarray data revealed that ovary expresses all genes necessary for SARS-CoV-2 infection. PCOS women mostly showed down-regulated/unchanged levels of SCARFs. MGCs and CGCs from PCOS women showed lower expression of receptors ACE2, BSG and DPP4 and protease CTSB than in controls. MGCs showed lower expression of protease CTSL in PCOS than in controls. Expression of TMPRSS2 was not detected in both cell types.\n\nConclusionsHuman ovarian follicle may be susceptible to SARS-CoV-2 infection. Lower expression of SCARFs in PCOS indicate that the risk of SARS-CoV-2 infection to the ovary may be lesser in these women than controls. This knowledge may help in safe practices at IVF settings in the current pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Aalaap Anand Naigaonkar", - "author_inst": "ICMR- National Institute for Research in Reproductive Health, Mumbai, India" - }, - { - "author_name": "Krutika Madhukar Patil", - "author_inst": "ICMR- National Institute for Research in Reproductive Health, Mumbai, India" - }, - { - "author_name": "Shaini Joseph", - "author_inst": "ICMR- National Institute for Research in Reproductive Health, Mumbai, India" - }, - { - "author_name": "Indira Hinduja", - "author_inst": "P. D. Hinduja National Hospital and Medical Research Centre, Mumbai, India" - }, - { - "author_name": "Srabani Mukherjee", - "author_inst": "ICMR-National Institute for Research in Reproductive Health, Mumbai, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "sexual and reproductive health" - }, { "rel_doi": "10.1101/2021.06.16.21259057", "rel_title": "The impact of legislation on Covid-19 mortality in a Brazilian federative unit was mediated by social isolation.", @@ -702786,6 +703558,25 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.06.23.449627", + "rel_title": "E484K and N501Y SARS-CoV 2 Spike Mutants Increase ACE2 Recognition but Reduce Affinity for Neutralizing Antibody", + "rel_date": "2021-06-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.23.449627", + "rel_abs": "SARS-CoV2 mutants emerge as variants of concern (VOC) due to altered selection pressure and rapid replication kinetics. Among them, lineages B.1.1.7, B.1.351, and P.1 contain a key mutation N501Y. B.1.135 and P.1 lineages have another mutation, E484K. Here, we decode the effect of these two mutations on the host receptor, ACE2, and neutralizing antibody (B38) recognition. The gain in binding affinity for the N501Y RBD mutant to the ACE2 is attributed to improved {pi}-{pi} stacking and {pi}-cation interactions. The enhanced receptor affinity of the E484K mutant is caused due to the formation of a specific hydrogen bond and salt-bridge interaction with Glu75 of ACE2. Notably, both the mutations reduce the binding affinity for B38 due to the loss of several hydrogen-bonding interactions. The insights obtained from the study are crucial to interpret the increased transmissibility and reduction in the neutralization efficacy of rapidly emerging SARS-CoV2 VOCs.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Sandipan Chakraborty", + "author_inst": "Amity University, Kolkata" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.06.23.449535", "rel_title": "Integrative COVID-19 Biological Network Inference with Probabilistic Core Decomposition", @@ -704309,25 +705100,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.06.23.449639", - "rel_title": "Comparative Structural Analyses of Selected Spike Protein-RBD Mutations in SARS-CoV-2 Lineages", - "rel_date": "2021-06-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.23.449639", - "rel_abs": "The severity of the covid 19 has been observed throughout the world as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had spread globally claiming more than 2 million lives and left a devastating impact on peoples life. Recently several virulent mutant strains of this virus, such as the B.1.1.7, B.1.351, and P1 lineages have emerged. These strains are predominantly observed in UK, South Africa and Brazil. Another extremely pathogenic B.1.617 lineage and its sub-lineages, first detected in India, are now affecting some countries at notably stronger spread-rates. This paper computationally examines the time-based structures of B.1.1.7, B.1.351, P1 lineages with selected spike protein mutations. Additionally, the mutations in the more recently found B.1.617 lineage and some of its sub-lineages are explored, and the implications for multiple point mutations of the spike proteins receptor-binding domain (RBD) are described.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Urmi Roy", - "author_inst": "Clarkson University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.06.16.21259038", "rel_title": "The statistical analysis of daily data associated with different parameters of the New Coronavirus COVID-19 pandemic in Georgia and their short-term interval prediction in spring 2021", @@ -704492,6 +705264,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.23.449583", + "rel_title": "The Influence of Public Health Faculty on College and University Plans during the COVID-19 Pandemic", + "rel_date": "2021-06-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.23.449583", + "rel_abs": "The purpose of this study was to determine whether the institutional presence of public health faculty within colleges and universities influenced operational plans for the fall semester of 2020. Using cross-sectional data collected by the College Crisis Initiative of Davidson College, six levels of instructional modalities (ranked from least to most restrictive) were compared between Council on Education of Public Health (CEPH)-accredited and non-CEPH-accredited 4-year institutions. Institutions with CEPH-accredited schools and programs were more likely to select some restrictive teaching modalities: 63.8% more likely to use hybrid/hyflex or more restrictive and 66.9% more likely to be primarily online (with some in person) or more restrictive. However, having CEPH-accredited programs did not push institutions to the most restrictive modalities. COVID-19 cases in county, enrollment, and political affiliation of the state governor were also found to influence instructional modality selection. While any ecological study has certain limitations, this study demonstrates that college and university fall plans appear to have been influenced by the presence of CEPH-accredited schools and programs of public health, and/or the input of their faculty. The influence of relevant faculty expertise on institutional decision-making can help inform college and university responses to future crises.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "David A Johnson", + "author_inst": "University of Louisville, School of Public Heath and Information Sciences" + }, + { + "author_name": "Meredith Cahill", + "author_inst": "University of Louisville, School of Public Health and Information Sciences" + }, + { + "author_name": "Sara Choate", + "author_inst": "University of Louisville, School of Public Health and Information Sciences" + }, + { + "author_name": "Dave Roelfs", + "author_inst": "University of Louisville, College of Arts and Sciences, Department of Sociology" + }, + { + "author_name": "Sarah E Walsh", + "author_inst": "Eastern Michigan University, School of Health Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.06.18.21258477", "rel_title": "The polarity and specificity of SARS-CoV2 -specific T lymphocyte responses determine disease susceptibility", @@ -705695,49 +706502,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.06.14.21258906", - "rel_title": "Coverage and effectiveness of mRNA SARS-CoV-2 vaccines among United States Veterans", - "rel_date": "2021-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.14.21258906", - "rel_abs": "ImportanceThe effectiveness of mRNA vaccination in a large and diverse American population, with older age and higher co-morbidity has not been assessed.\n\nObjectiveTo describe the scope of the mRNA vaccination rollout among the diverse U.S. Veterans population, and to study the mRNA COVID-19 vaccine effectiveness (VE) against infection, symptomatic disease, hospitalization, and death.\n\nMethodsVaccination histories were obtained from medical records to determine if patients tested for SARS-CoV-2 were unvaccinated, partially vaccinated (first dose of mRNA COVID-19 vaccine), or fully vaccinated (two doses) at time of testing. First, coverage with any COVID-19 vaccination was described for all Veterans enrolled in Veterans Health Administration (VHA). Second, to evaluate VE, a matched test-negative case-control evaluation was conducted utilizing SARS-CoV-2 positive (cases [n=16,690]) and SARS-CoV-2 negative (controls [n=61,610]) tests from Veterans aged [≥]18 years old who routinely sought care at a VHA facility and were tested from December 14, 2020, through March 14, 2021. VE was calculated from odds ratios (ORs) with 95% confidence intervals (CI).\n\nResultsBy March 7, 2021, among 6,170,750 Veterans, 1,547,045 (23%) received at least one COVID-19 vaccination. mRNA COVID-19 VE against infection, regardless of symptoms, was 94% (95% CI 92-95) and 58% (95%CI 54-62) for full and partial vaccination (vs. no vaccination), respectively. VE against infection was similar across subpopulations, and it was not significantly different from VE against symptomatic disease. VE against COVID-19-related hospitalization and death for full vs. no vaccination was 89% (95%CI 81-93) and 99% (95%CI 87-100), respectively.\n\nConclusions and RelevanceThe VHAs efficient and equitable distribution of effective vaccines decreased COVID-19 infections, hospitalization, and mortality similarly for all Veterans, including Veterans with low income, homeless Veterans, immunocompromised, the elderly, minorities, and rural Veterans thus reducing health inequalities.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Yinong Young-Xu", - "author_inst": "White River Junction Veterans Affairs Medical Center, White River Junction, VT & Geisel School of Medicine at Dartmouth, Hanover, NH" - }, - { - "author_name": "Caroline Korves", - "author_inst": "White River Junction Veterans Affairs Medical Center, White River Junction, VT" - }, - { - "author_name": "Jeff Roberts", - "author_inst": "Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, White Oak, MD" - }, - { - "author_name": "Ethan I Powell", - "author_inst": "White River Junction Veterans Affairs Medical Center, White River Junction, VT" - }, - { - "author_name": "Gabrielle M Zwain", - "author_inst": "White River Junction Veterans Affairs Medical Center, White River Junction, VT" - }, - { - "author_name": "Jeremy Smith", - "author_inst": "White River Junction Veterans Affairs Medical Center, White River Junction, VT" - }, - { - "author_name": "Hector S Izurieta", - "author_inst": "Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, United States Food and Drug Administration, White Oak, MD" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.14.21258875", "rel_title": "Mild Adverse Events of Sputnik V Vaccine Extracted from Russian Language Telegram Posts via BERT Deep Learning Model", @@ -705830,6 +706594,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.19.21258892", + "rel_title": "Breastfeeding mother-child clinical outcomes after COVID-19 vaccination", + "rel_date": "2021-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.19.21258892", + "rel_abs": "This is a prospective cohort study of 88 lactating women in Singapore who received two doses of BNT162b2 vaccination (Pfizer/BioNTech), whereby outcomes of mother-child dyads within 28 days after the second vaccine dose were determined through a structured questionnaire. Minimal effects related to breastfeeding were reported in this cohort; 3 of 88 (3.4%) women had mastitis with 1 of 88 (1.1%) women experiencing breast engorgement. We report an incidence of lymphadenopathy in our cohort at 5 of 88 (5.7%). Reassuringly, there was no change in reported breastmilk supply after vaccination. The most common side effect was pain/redness/swelling at the injection site, which was experienced by 57 of 88 (64.8%) women. There were no serious adverse events of anaphylaxis and hospital admissions. No adverse symptoms were reported in 67 of 88 (76.1%) breastfed children.\n\nWhats known on this subjectTwo studies reported no serious adverse effects in both mother-child dyads after mRNA COVID-19 vaccination in mothers. Up to 61.9-67% lactating women experienced minor side effects.\n\nWhat this study addsWe report an incidence of lymphadenopathy in our cohort at 5.7% as opposed to 0.3% from the Pfizer-BioNTech COVID-19 trial. Reassuringly, there was no change in reported milk supply after vaccination. Minimal effects related to breastfeeding were reported in this cohort; 3 (3.4%) women had mastitis with 1 person experiencing breast engorgement. The most common side effect was pain/redness/swelling at the injection site at 64.8%, which was experienced by 57 of 88 (65%) women. No adverse symptoms were reported in the breastfed children.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jia Ming Low", + "author_inst": "National University Hospital of Singapore" + }, + { + "author_name": "Le Ye Lee", + "author_inst": "National University Hospital of Singapore" + }, + { + "author_name": "Yvonne Peng Mei Ng", + "author_inst": "National University Hospital of Singapore" + }, + { + "author_name": "Youjia Zhong", + "author_inst": "National University Hospital of Singapore" + }, + { + "author_name": "Zubair Amin", + "author_inst": "National University Hospital of Singapore" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.06.21.449352", "rel_title": "Cytoplasmic tail truncation of SARS-CoV-2 Spike protein enhances titer of pseudotyped vectors but masks the effect of the D614G mutation", @@ -707105,113 +707904,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2021.06.15.21258703", - "rel_title": "Common and rare variant analyses combined with single-cell multiomics reveal cell-type-specific molecular mechanisms of COVID-19 severity", - "rel_date": "2021-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258703", - "rel_abs": "The determinants of severe COVID-19 in non-elderly adults are poorly understood, which limits opportunities for early intervention and treatment. Here we present novel machine learning frameworks for identifying common and rare disease-associated genetic variation, which outperform conventional approaches. By integrating single-cell multiomics profiling of human lungs to link genetic signals to cell-type-specific functions, we have discovered and validated over 1,000 risk genes underlying severe COVID-19 across 19 cell types. Identified risk genes are overexpressed in healthy lungs but relatively downregulated in severely diseased lungs. Genetic risk for severe COVID-19, within both common and rare variants, is particularly enriched in natural killer (NK) cells, which places these immune cells upstream in the pathogenesis of severe disease. Mendelian randomization indicates that failed NKG2D-mediated activation of NK cells leads to critical illness. Network analysis further links multiple pathways associated with NK cell activation, including type-I-interferon-mediated signalling, to severe COVID-19. Our rare variant model, PULSE, enables sensitive prediction of severe disease in non-elderly patients based on whole-exome sequencing; individualized predictions are accurate independent of age and sex, and are consistent across multiple populations and cohorts. Risk stratification based on exome sequencing has the potential to facilitate post-exposure prophylaxis in at-risk individuals, potentially based around augmentation of NK cell function. Overall, our study characterizes a comprehensive genetic landscape of COVID-19 severity and provides novel insights into the molecular mechanisms of severe disease, leading to new therapeutic targets and sensitive detection of at-risk individuals.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Sai Zhang", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Johnathan Cooper-Knock", - "author_inst": "University of Sheffield" - }, - { - "author_name": "Annika Weimer", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Calum Harvey", - "author_inst": "University of Sheffield" - }, - { - "author_name": "Thomas Julian", - "author_inst": "University of Sheffield" - }, - { - "author_name": "Cheng Wang", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jingjing Li", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Simone Furini", - "author_inst": "University of Siena" - }, - { - "author_name": "Elisa Frullanti", - "author_inst": "University of Siena" - }, - { - "author_name": "Francesca Fava", - "author_inst": "University of Siena" - }, - { - "author_name": "Alessandra Renieri", - "author_inst": "University of Siena" - }, - { - "author_name": "Cuiping Pan", - "author_inst": "VA Palo Alto Health Care System" - }, - { - "author_name": "Jina Song", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Paul Billing-Ross", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Peng Gao", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Xiaotao Shen", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Ilia Sarah Timpanaro", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "Kevin Kenna", - "author_inst": "University Medical Center Utrecht" - }, - { - "author_name": "- VA Million Veteran Program", - "author_inst": "" - }, - { - "author_name": "- GEN-COVID Network", - "author_inst": "" - }, - { - "author_name": "Mark Davis", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Philip Tsao", - "author_inst": "VA Palo Alto Health Care System" - }, - { - "author_name": "Michael Snyder", - "author_inst": "Stanford University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.06.16.21258691", "rel_title": "App-based COVID-19 surveillance and prediction: The COVID Symptom Study Sweden", @@ -707580,6 +708272,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.15.21258529", + "rel_title": "The impact of temperature on the transmission potential and virulence of COVID-19 in Tokyo, Japan", + "rel_date": "2021-06-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258529", + "rel_abs": "BackgroundAssessing the impact of temperature on COVID-19 epidemiology is critical for implementing non-pharmaceutical interventions. However, few studies have accounted for the nature of contagious diseases, i.e., their dependent happenings.\n\nAimWe aimed to quantify the impact of temperature on the transmissibility and virulence of COVID-19 in Tokyo, Japan. We employed two epidemiological measurements of transmissibility and severity: the effective reproduction number (Rt) and case fatality risk (CFR).\n\nMethodsWe used empirical surveillance data and meteorological data in Tokyo to estimate the Rt and time-delay adjusted CFR and to subsequently assess the nonlinear and delay effect of temperature on Rt and time-delay adjusted CFR.\n\nResultsFor Rt at low temperatures, the cumulative relative risk (RR) at first temperature percentile (3.3{degrees}C) was 1.3 (95% confidence interval (CI): 1.1-1.7). As for the virulence to humans, moderate cold temperatures were associated with higher CFR, and CFR also increased as the temperature rose. The cumulative RR at the 10th and 99th percentiles of temperature (5.8{degrees}C and 30.8{degrees}C) for CFR were 3.5 (95%CI: 1.3-10) and 6.4 (95%CI: 4.1-10.1).\n\nConclusionsThis study provided information on the effects of temperature on the COVID-19 epidemiology using Rt and time-delay adjusted CFR. Our results suggest the importance to take precautions to avoid infection in both cold and warm seasons to avoid severe cases of COVID-19. The results and proposed framework will also help in assessing possible seasonal course of COVID-19 in the future.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lisa Yamasaki", + "author_inst": "Department of Global Health Policy, Graduate School of Medicine, The University of Tokyo" + }, + { + "author_name": "Hiroaki Murayama", + "author_inst": "International University of Health and Welfare" + }, + { + "author_name": "Masahiro Hashizume", + "author_inst": "Department of Global Health Policy, Graduate School of Medicine, The University of Tokyo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.18.21258649", "rel_title": "Large-scale screening of asymptomatic for SARS-CoV-2 variants of concern and rapid P.1 takeover, Curitiba, Brazil", @@ -709526,37 +710245,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.20.448993", - "rel_title": "Selectively expressing SARS-CoV-2 Spike protein S1 subunit in cardiomyocytes induces cardiac hypertrophy in mice.", - "rel_date": "2021-06-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.20.448993", - "rel_abs": "Cardiac injury is common in hospitalized COVID-19 patients and portends poorer prognosis and higher mortality. To better understand how SARS-CoV-2 (CoV-2) damages the heart, it is critical to elucidate the biology of CoV-2 encoded proteins, each of which may play multiple pathological roles. For example, CoV-2 Spike glycoprotein (CoV-2-S) not only engages ACE2 to mediate virus infection, but also directly impairs endothelial function and can trigger innate immune responses in cultured murine macrophages. Here we tested the hypothesis that CoV-2-S damages the heart by activating cardiomyocyte (CM) innate immune responses. HCoV-NL63 is another human coronavirus with a Spike protein (NL63-S) that also engages ACE2 for virus entry but is known to only cause moderate respiratory symptoms. We found that CoV-2-S and not NL63-S interacted with Toll-like receptor 4 (TLR4), a crucial pattern recognition receptor that responsible for detecting pathogen and initiating innate immune responses. Our data show that the S1 subunit of CoV-2-S (CoV-2-S1) interacts with the extracellular leucine rich repeats-containing domain of TLR4 and activates NF-kB. To investigate the possible pathological role of CoV-2-S1 in the heart, we generated a construct that expresses membrane-localized CoV-2-S1 (S1-TM). AAV9-mediated, selective expression of the S1-TM in CMs caused heart dysfunction, induced hypertrophic remodeling, and elicited cardiac inflammation. Since CoV-2-S does not interact with murine ACE2, our study presents a novel ACE2-independent pathological role of CoV-2-S, and suggests that the circulating CoV-2-S1 is a TLR4-recognizable alarmin that may harm the CMs by triggering their innate immune responses.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Steven G. Negron", - "author_inst": "Masonic Medical Research Institute" - }, - { - "author_name": "Chase W. Kessinger", - "author_inst": "Masonic Medical Research Institute" - }, - { - "author_name": "Bing Xu", - "author_inst": "Masonic Medical Research Institute" - }, - { - "author_name": "Zhiqiang Lin", - "author_inst": "Masonic Medical Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.06.19.449100", "rel_title": "SARS-CoV-2 mRNA Vaccine Induces Robust Specific and Cross-reactive IgG and Unequal Strain-specific Neutralizing Antibodies in Nai\u0308ve and Previously Infected Recipients", @@ -709861,6 +710549,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.06.17.448816", + "rel_title": "Structural basis for the interaction of SARS-CoV-2 virulence factor nsp1 with Pol \u03b1 - Primase", + "rel_date": "2021-06-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.17.448816", + "rel_abs": "The molecular mechanisms that drive the infection by the SARS-CoV-2 coronavirus - the causative agent of the COVID-19 (Coronavirus disease-2019) pandemic - are under intense current scrutiny, to understand how the virus operates and to uncover ways in which the disease can be prevented or alleviated.\n\nRecent cell-based analyses of SARS-CoV-2 protein - protein interactions have mapped the human proteins targeted by the virus. The DNA polymerase - primase complex or primosome - responsible for initiating DNA synthesis in genomic duplication - was identified as a target of nsp1 (non structural protein 1), a major virulence factor in the SARS-CoV-2 infection.\n\nHere, we report the biochemical characterisation of the interaction between nsp1 and the primosome and the cryoEM structure of the primosome - nsp1 complex. Our data provide a structural basis for the reported interaction between the primosome and nsp1. They suggest that Pol - primase plays a part in the immune response to the viral infection, and that its targeting by SARS-CoV-2 aims to interfere with such function.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mairi L Kilkenny", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Charlotte E Veale", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Amir Guppy", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Steven W Hardwick", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Dimitri Y Chirgadze", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Neil J Rzechorzek", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Joseph D Maman", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Luca Pellegrini", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.06.18.449086", "rel_title": "Differences in IgG antibody responses following BNT162b2 and mRNA-1273 Vaccines", @@ -711340,77 +712075,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.16.21258960", - "rel_title": "Stable IgG-antibody levels in patients with mild SARS-CoV-2 infection", - "rel_date": "2021-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.16.21258960", - "rel_abs": "More knowledge regarding persistence of antibody response to SARS-CoV-2 infections in the general population with mild symptoms is needed. We measured and compared levels of SARS-CoV-2 spike- and nucleocapsid-specific IgG-antibodies in serum samples from 145 laboratory-confirmed COVID-19 cases and 324 non-cases. The IgG-antibody levels against the spike protein in cases were stable over the time-period studied (14 to 256 days), while antibody levels against the nucleocapsid protein decreased over time.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Thomas Akerlund", - "author_inst": "Public Health Agency of Sweden" - }, - { - "author_name": "Katherina Zakikhany", - "author_inst": "Public Health Agency of Sweden" - }, - { - "author_name": "Charlotta Lofstrom", - "author_inst": "RISE Research Institutes of Sweden" - }, - { - "author_name": "Evelina Lindmark", - "author_inst": "RISE Research Institutes of Sweden" - }, - { - "author_name": "Henrik Kallberg", - "author_inst": "Public Health Agency of Sweden" - }, - { - "author_name": "Ulla Elofsson", - "author_inst": "RISE Research Institutes of Sweden" - }, - { - "author_name": "Karin Cedebrant", - "author_inst": "RISE Research Institutes of Sweden" - }, - { - "author_name": "Erik Nygren", - "author_inst": "RISE Research Institutes of Sweden" - }, - { - "author_name": "Anders Kallin", - "author_inst": "RISE Research Institutes of Sweden" - }, - { - "author_name": "Nina Lagerqvist", - "author_inst": "The Public Health Agency of Sweden" - }, - { - "author_name": "Peter Nilsson", - "author_inst": "KTH Royal Institute of Technology, SciLifeLab, Sweden" - }, - { - "author_name": "Sophia Hober", - "author_inst": "KTH Royal Institute of Technology, SciLifeLab, Sweden" - }, - { - "author_name": "Anna Ridderstad Wollberg", - "author_inst": "RISE Research Institutes of Sweden" - }, - { - "author_name": "Asa Bjorndal", - "author_inst": "Public Health Agency of Sweden" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.16.21258861", "rel_title": "SARS-CoV-2 seroprevalence among Vancouver public school staff in British Columbia, Canada", @@ -711639,6 +712303,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.15.21258928", + "rel_title": "Benefits of Surveillance Testing and Quarantine in a SARS-CoV-2 Vaccinated Population of Students on a University Campus", + "rel_date": "2021-06-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258928", + "rel_abs": "Surveillance testing and quarantine have been effective measures for limiting SARS-CoV-2 transmission on university campuses. However, the importance of these measures needs to be re-evaluated in the context of a complex and rapidly changing environment that includes vaccines, variants, and waning immunity. Also, recent guidelines from the CDC suggest that vaccinated students do not need to participate in surveillance testing. We used an agent-based SEIR model to evaluate the utility of surveillance testing and quarantine in a fully vaccinated student population where vaccine effectiveness may be impacted by the type of vaccination, the presence of variants, and the loss of vaccine-induced or natural immunity over time. We found that weekly surveillance testing at 90% vaccine effectiveness only marginally reduces viral transmission as compared to no testing. However, at 50%-75% effectiveness, surveillance testing can provide over 10-fold reduction in the number of infections on campus over the course of the semester. We also show that a 10-day quarantine protocol for exposures has limited effect on infections until vaccine effectiveness drops to 50%, and that increased surveillance testing for exposures is at least as effective as quarantine at limiting infections. Together these findings provide a foundation for universities to design appropriate mitigation protocols for the 2021-2022 academic year.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Francis C. Motta", + "author_inst": "Department of Mathematical Sciences, Florida Atlantic University" + }, + { + "author_name": "Kevin A. McGoff", + "author_inst": "Department of Mathematics and Statistics, University of North Carolina, Charlotte" + }, + { + "author_name": "Anastasia Deckard", + "author_inst": "Office of Information Technology, Duke University" + }, + { + "author_name": "Cameron R. Wolfe", + "author_inst": "Department of Medicine, Duke University School of Medicine" + }, + { + "author_name": "M. Anthony Moody", + "author_inst": "Department of Pediatrics, Duke University School of Medicine" + }, + { + "author_name": "Kyle Cavanaugh", + "author_inst": "Department of Family Medicine, Duke University School of Medicine" + }, + { + "author_name": "Thomas N. Denny", + "author_inst": "Duke Human Vaccine Institute & Department of Medicine, Duke University School of Medicine" + }, + { + "author_name": "John Harer", + "author_inst": "Department of Mathematics, Duke University" + }, + { + "author_name": "Steven B. Haase", + "author_inst": "Department of Biology, Duke University & Department of Medicine, Duke University School of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.16.21258981", "rel_title": "Remdesivir to treat COVID-19: can dosing be optimized?", @@ -713694,33 +714409,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.12.21258815", - "rel_title": "Intersections between pneumonia, lowered oxygen saturation percentage and immune activation mediate depression, anxiety and chronic fatigue syndrome-like symptoms due to COVID-19: a nomothetic network approach.", - "rel_date": "2021-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.12.21258815", - "rel_abs": "BackgroundCOVID-19 is associated with neuropsychiatric symptoms including increased depressive, anxiety and chronic fatigue-syndrome (CFS)-like physiosomatic (previously known as psychosomatic) symptoms.\n\nAimsTo delineate the associations between affective and CFS-like symptoms in COVID-19 and chest CT-scan anomalies (CCTAs), oxygen saturation (SpO2), interleukin (IL)-6, IL-10, C-Reactive Protein (CRP), albumin, calcium, magnesium, soluble angiotensin converting enzyme (ACE2) and soluble advanced glycation products (sRAGEs).\n\nMethodThe above biomarkers were assessed in 60 COVID-19 patients and 30 heathy controls who had measurements of the Hamilton Depression (HDRS) and Anxiety (HAM-A) and the Fibromyalgia and Chronic Fatigue (FF) Rating Scales.\n\nResultsPartial Least Squares-SEM analysis showed that reliable latent vectors could be extracted from a) key depressive and anxiety and physiosomatic symptoms (the physio-affective or PA-core), b) IL-6, IL-10, CRP, albumin, calcium, and sRAGEs (the immune response core); and c) different CCTAs (including ground glass opacities, consolidation, and crazy paving) and lowered SpO2% (lung lesions). PLS showed that 70.0% of the variance in the PA-core was explained by the regression on the immune response and lung lesions latent vectors. Moreover, one common \"infection-immune-inflammatory (III) core\" underpins pneumonia-associated CCTAs, lowered SpO2 and immune activation, and this III core explains 70% of the variance in the PA core, and a relevant part of the variance in melancholia, insomnia, and neurocognitive symptoms.\n\nDiscussionAcute SARS-CoV-2 infection is accompanied by lung lesions and lowered SpO2 which both may cause activated immune-inflammatory pathways, which mediate the effects of the former on the PA-core and other neuropsychiatric symptoms due to SARS-CoV-2 infection.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Hawraa Al-Jassas", - "author_inst": "Department of Chemistry, College of Science, University of Kufa" - }, - { - "author_name": "Hussein K Al-Hakeim", - "author_inst": "Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Kufa" - }, - { - "author_name": "Michael Maes", - "author_inst": "Chulalongkorn University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.06.16.21259017", "rel_title": "A Novel and Expanding SARS-CoV-2 Variant, B.1.1.318, dominates infections in Mauritius", @@ -714009,6 +714697,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.15.448611", + "rel_title": "SARS-CoV-2 Viral Replication in a High Throughput Human Primary Epithelial Airway Organ Model", + "rel_date": "2021-06-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.15.448611", + "rel_abs": "COVID-19 emerged as a worldwide pandemic early in 2020, and at this writing has caused over 170 million cases and 3.7 million deaths worldwide, and almost 600,000 deaths in the United States. The rapid development of several safe and highly efficacious vaccines stands as one of the most extraordinary achievements in modern medicine, but the identification and administration of efficacious therapeutics to treat patients suffering from COVID-19 has been far less successful. A major factor limiting progress in the development of effective treatments has been a lack of suitable preclinical models for the disease, currently reliant upon various animal models and in vitro culture of immortalized cell lines. Here we report the first successful demonstration of SARS-CoV-2 infection and viral replication in a human primary cell-based organ-on-chip, leveraging a recently developed tissue culture platform known as PREDICT96. This successful demonstration of SARS-CoV-2 infection in human primary airway epithelial cells derived from a living donor represents a powerful new pathway for disease modeling and an avenue for screening therapeutic candidates in a high throughput platform.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Christine R Fisher", + "author_inst": "Draper" + }, + { + "author_name": "Felix Mba Medie", + "author_inst": "Draper" + }, + { + "author_name": "Rebeccah J Luu", + "author_inst": "Draper" + }, + { + "author_name": "Rob Gaibler", + "author_inst": "Draper" + }, + { + "author_name": "Caitlin R Miller", + "author_inst": "Draper" + }, + { + "author_name": "Thomas J Mulhern", + "author_inst": "Draper" + }, + { + "author_name": "Vidhya Vijayakumar", + "author_inst": "Draper" + }, + { + "author_name": "Elizabeth Marr", + "author_inst": "Draper" + }, + { + "author_name": "Jehan Alladina", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Benjamin Medoff", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Jeffrey T Borenstein", + "author_inst": "Draper" + }, + { + "author_name": "Ashley L Gard", + "author_inst": "Draper" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.06.12.21258829", "rel_title": "The Spectre of SARS-CoV-2 in the Ambient Urban Natural Water in Ahmedabad and Guwahati: A Tale of Two Cities", @@ -715679,33 +716430,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2021.06.11.21258766", - "rel_title": "Out-of-Pocket Spending for Health Care Within 90 Days of COVID-19 Hospitalization", - "rel_date": "2021-06-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258766", - "rel_abs": "INTRODUCTIONMillions of U.S. patients have been hospitalized for COVID-19. After discharge, these patients often have extensive health care needs, but out-of-pocket burden for this care is poorly described. We assessed out-of-pocket spending within 90 days of discharge from COVID-19 hospitalization among privately insured and Medicare Advantage patients.\n\nMETHODSIn May 2021, we conducted a cross-sectional analysis of the IQVIA PharMetrics(R) Plus for Academics Database, a national de-identified claims database. Among privately insured and Medicare Advantage patients hospitalized for COVID-19 between March-June 2020, we calculated mean out-of-pocket spending for care within 90 days of discharge. For context, we repeated analyses for patients hospitalized for pneumonia.\n\nRESULTSAmong 1,465 COVID-19 patients included, 516 (35.2%) and 949 (64.8%) were covered by private insurance and Medicare Advantage plans. Among these patients, mean (SD) post-discharge out-of-pocket spending was $534 (1,045) and $680 (1,360); spending exceeded $2,000 for 7.0% and 10.3%. Compared with pneumonia patients, mean post-discharge out-of-pocket spending among COVID-19 patients was higher among the privately insured ($534 vs $445) and lower among Medicare Advantage patients ($680 vs $918).\n\nCONCLUSIONSFor the privately insured, post-discharge out-of-pocket spending was higher among patients hospitalized for COVID-19 than among patients hospitalized for pneumonia. The opposite was true for Medicare Advantage patients, potentially because insurer cost-sharing waivers for COVID-19 treatment covered the costs of some post-discharge care, such as COVID-19 readmissions. Nonetheless, given the high volume of U.S. COVID-19 hospitalizations to date, our findings suggest a large number of Americans have experienced substantial financial burden for post-discharge care.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kao-Ping Chua", - "author_inst": "University of Michigan Medical School" - }, - { - "author_name": "Rena M Conti", - "author_inst": "Questrom Boston University School of Business" - }, - { - "author_name": "Nora V Becker", - "author_inst": "University of Michigan Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.06.10.21258725", "rel_title": "A Warm-start Digital CRISPR-based Method for the Quantitative Detection of Nucleic Acids", @@ -715866,6 +716590,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.15.21258346", + "rel_title": "Antibody response after a single dose of ChAdOx1-nCOV (Covishield) vaccine in subjects with prior SARS-CoV2 infection: Is a single dose sufficient?", + "rel_date": "2021-06-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258346", + "rel_abs": "It is crucial to know whether a single dose of vaccine against SARS-CoV-2 is sufficient to elicit immune response in previously infected people in India. A total of 121 participants (baseline seropositive 46 and seronegative 75) were included to study the immune response to ChAdOx1-nCOV (Covishield) vaccine in previously infected or uninfected people. IgG antibodies were estimated at three different time intervals, i.e. pre-vaccination, 25-35 days post 1st vaccination and 25-35 days post 2nd vaccination. The IgG antibody titre was significantly high among previous seropositive subjects with single dose of vaccine compared to seronegative group with both doses of vaccine respectively (4.59{+/-}1.04 vs 3.08{+/-}1.22, p-value: <0.0001).\n\nIn conclusion, a single dose of Covishield(R) vaccine might be sufficient to induce an effective immune responsein subjects with prior SARS-CoV2 infection. Stratifying vacinees based on their SARS-CoV2 IgG antibody titre before vaccination would help in meeting the increasing vaccine demand and could be effective to circumvent further wave of the pandemic in India.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Biswajyoti Borkakoty", + "author_inst": "ICMR Regional Medical Research Centre NE Region" + }, + { + "author_name": "Mandakini Das Sarmah", + "author_inst": "ICMR Regional Medical Research Centre NE Region" + }, + { + "author_name": "Chandra Kanta Bhattacharjee", + "author_inst": "ICMR Regional Medical Research Centre NE Region" + }, + { + "author_name": "Nargis Bali", + "author_inst": "Sher-i- Kasmir Institute of Medical Science, Jammu and Kasmir, India" + }, + { + "author_name": "Gayatri Gogoi", + "author_inst": "Assam Medical College and Hospital, Dibrugarh, Assam, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.14.21258871", "rel_title": "SARS-CoV-2 Spike protein binding of glycated serum albumin - its potential role in the pathogenesis of the COVID-19 clinical syndromes and bias towards individuals with pre-diabetes/type 2 diabetes & metabolic diseases.", @@ -716758,77 +717517,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.06.10.21258672", - "rel_title": "Reopening International Borders without Quarantine: Contact Tracing Integrated Policy against COVID-19", - "rel_date": "2021-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.10.21258672", - "rel_abs": "With the COVID-19 vaccination widely implemented in most countries, propelled by the need to revive the tourism economy, there is a growing prospect for relieving the social distancing regulation and reopening borders in tourism-oriented countries and regions. The need incentivizes stakeholders to develop border control strategies that fully evaluate health risks if mandatory quarantines are lifted. In this study, we have employed a computational approach to investigate the contact tracing integrated policy in different border reopening scenarios in Hong Kong, China. Built on a modified SEIR epidemic model with a 30% vaccination coverage, the results suggest that scenarios with digital contact tracing and quick isolation intervention can reduce the infectious population by 92.11% compared to those without contact tracing. By further restricting the inbound population with a 10,000 daily quota and applying moderate-to-strong community non-pharmacological interventions (NPIs), the average daily confirmed cases in the forecast period of 60 days can be well controlled at around 9 per day (95% CI: 7-12). Two main policy recommendations are drawn from the study. First, digital contact tracing would be an effective countermeasure for reducing local virus spread, especially when it is applied along with a moderate level of vaccination coverage. Second, implementing a daily quota on inbound travelers and restrictive community NPIs would further keep the local infection under control. This study offers scientific evidence and prospective guidance for developing and instituting plans to lift mandatory border control policies in preparing for the global economic recovery.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Zidong Yu", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Xiaolin Zhu", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Xintao Liu", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Xiang Chen", - "author_inst": "University of Connecticut" - }, - { - "author_name": "Tao Wei", - "author_inst": "Shenzhen University" - }, - { - "author_name": "Hsiang-Yu Yuan", - "author_inst": "City University of Hong Kong" - }, - { - "author_name": "Yang Xu", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Rui Zhu", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Huan He", - "author_inst": "Southwestern University of Finance and Economics" - }, - { - "author_name": "Hui Wang", - "author_inst": "University of Idaho" - }, - { - "author_name": "Man-sing Wong", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Peng Jia", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Wen-zhong Shi", - "author_inst": "The Hong Kong Polytechnic University" - }, - { - "author_name": "Wu Chen", - "author_inst": "The Hong Kong Polytechnic University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.11.21258750", "rel_title": "The prevalence, incidence, prognosis and risk factors for depression and anxiety in a UK cohort during the COVID-19 pandemic", @@ -717121,6 +717809,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.11.21258564", + "rel_title": "Chronic fatigue and post-exertional malaise in people living with long COVID", + "rel_date": "2021-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258564", + "rel_abs": "PurposePeople living with long COVID describe a high symptom burden, and a more detailed assessment of chronic fatigue and post-exertional malaise (PEM) may inform the development of rehabilitation recommendations. The aims of this study were to use validated questionnaires to measure the severity of fatigue and compare this with normative data and thresholds for clinical relevance in other diseases; measure and describe the impact of PEM; and assess symptoms of dysfunctional breathing, self-reported physical activity/sitting time, and health-related quality of life.\n\nMethodsThis was an observational study involving an online survey for adults living with long COVID (data collection from February-April, 2021) following a confirmed or suspected SARS-CoV-2 infection. Questionnaires included the Functional Assessment of Chronic Illness Therapy-Fatigue Scale (FACIT-F) and DePaul Symptom Questionnaire-Post-Exertional Malaise.\n\nResultsAfter data cleaning, n=213 participants were included in the analysis. Participants primarily identified as women (85.5%), aged 40-59 (78.4%), who had been experiencing long COVID symptoms for [≥]6 months (72.3%). The total FACIT-F score was 18{+/-}10 (where the score can range from 0-52, and a lower score indicates more severe fatigue), and 71.4% were experiencing chronic fatigue. Post-exertional symptom exacerbation affected most participants, and 58.7% met the scoring thresholds used in people living with myalgic encephalomyelitis/chronic fatigue syndrome. PEM occurred alongside a reduced capacity to work, be physically active, and function both physically and socially.\n\nConclusionLong COVID is characterized by chronic fatigue that is clinically relevant and is at least as severe as fatigue in several other clinical conditions, including cancer. PEM appears to be a common and significant challenge for the majority of this patient group. Patients, researchers, and allied health professionals are seeking information on safe rehabilitation for people living with long COVID, particularly regarding exercise. Fatigue and post-exertional symptom exacerbation must be monitored and reported in studies involving interventions for people with long COVID.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rosie Twomey", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jessica DeMars", + "author_inst": "Breath Well Physio" + }, + { + "author_name": "Kelli Franklin", + "author_inst": "Patient Partner" + }, + { + "author_name": "S. Nicole Culos-Reed", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jason Weatherald", + "author_inst": "University of Calgary" + }, + { + "author_name": "James G Wrightson", + "author_inst": "University of Calgary" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.11.21258445", "rel_title": "Estimating the Burden of SARS-CoV-2 among the Rohingya Refugees", @@ -718632,49 +719359,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.10.21258693", - "rel_title": "Deaths involving COVID-19 by disability status: a retrospective analysis of 29 million adults during the first two waves of the Coronavirus pandemic in England", - "rel_date": "2021-06-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.10.21258693", - "rel_abs": "ObjectivesTo assess the association between self-reported disability and deaths involving COVID-19 among adults in England.\n\nDesignCohort study of >29 million adults using data from the Office for National Statistics Public Health Data Asset.\n\nSettingPeople living in private households or communal establishments (including care homes) in England.\n\nParticipants29,293,845 adults (47% male) aged 30-100 years (mean age = 56) present at the 2011 Census who were alive on 24 January 2020. The main exposure was self-reported disability from the 2011 Census.\n\nMain outcome measuresDeath involving COVID-19, occurring between 24 January 2020 and 28 February 2021. We estimated the age-standardised mortality rate per 100,000 person-years at-risk, stratified by sex, disability status, and wave of the pandemic. We calculated hazard ratios (HRs) for disabled people compared with non-disabled people, adjusted for geographical factors, socio-demographic characteristics, and pre-pandemic health conditions.\n\nResultsDisabled people made up 17% of the study population, including 7% who were more-disabled and 10% less-disabled. From 24 January 2020 to 28 February 2021, 105,213 people died from causes involving COVID-19 in England, 58% of whom were disabled. Age-adjusted analyses showed that, compared to non-disabled people, mortality involving COVID-19 was higher among both more-disabled people (HR=3.05, 95% CI: 2.98 to 3.11 in males; 3.48, 3.41 to 3.56 in females) and less-disabled people (HR=1.88, 95% CI: 1.84 to 1.92 in males; 2.03, 1.98 to 2.08 in females). Among people aged 30-69, HRs reached 8.47 (8.01 to 8.95) among more-disabled females and 5.42 (5.18 to 5.68) for more-disabled males. Sequential adjustment for residence type, geography, socio-demographics, and health conditions partly explained the associations, indicating that a combination of these factors contributed towards the increased risk.\n\nConclusionDisabled people in England had markedly increased risk of mortality involving COVID-19 compared to non-disabled people and should be prioritised within the pandemic response.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Matthew L Bosworth", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Daniel Ayoubkhani", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Vah\u00e9 Nafilyan", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Josephine Foubert", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Myer Glickman", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Calum Davey", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Hannah Kuper", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.11.448134", "rel_title": "UK B.1.1.7 variant exhibits increased respiratory replication and shedding in nonhuman primates", @@ -718943,6 +719627,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.06.08.21258533", + "rel_title": "The impact of co-circulating pathogens on SARS-CoV-2/COVID-19 surveillance. How concurrent epidemics may decrease true SARS-CoV-2 percent positivity.", + "rel_date": "2021-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258533", + "rel_abs": "BackgroundCirculation of non-SARS-CoV-2 respiratory viruses during the COVID-19 pandemic may alter quality of COVID-19 surveillance, with possible consequences for real-time analysis and delay in implementation of control measures. Here, we assess the impact of an increased circulation of other respiratory viruses on the monitoring of positivity rates of SARS-CoV-2 and interpretation of surveillance data.\n\nMethodsUsing a multi-pathogen Susceptible-Exposed-Infectious-Recovered (SEIR) transmission model formalizing co-circulation of SARS-CoV-2 and another respiratory we assess how an outbreak of secondary virus may inflate the number of SARS-CoV-2 tests and affect the interpretation of COVID-19 surveillance data. Using simulation, we assess to what extent the use of multiplex PCR tests on a subsample of symptomatic individuals can support correction of the observed SARS-CoV-2 percent positive during other virus outbreaks and improve surveillance quality.\n\nResultsModel simulations demonstrated that a non-SARS-CoV-2 epidemic creates an artificial decrease in the observed percent positivity of SARS-CoV-2, with stronger effect during the growth phase, until the peak is reached. We estimate that performing one multiplex test for every 1,000 COVID-19 tests on symptomatic individuals could be sufficient to maintain surveillance of other respiratory viruses in the population and correct the observed SARS-CoV-2 percent positive.\n\nConclusionsThis study highlights that co-circulating respiratory viruses can disrupt SARS-CoV-2 surveillance. Correction of the positivity rate can be achieved by using multiplex PCR, and a low number of samples is sufficient to avoid bias in SARS-CoV-2 surveillance.\n\nSummaryCOVID-19 surveillance indicators may be impacted by increased co-circulation of other respiratory viruses delaying control measure implementation. Continued surveillance through multiplex PCR testing in a subsample of the symptomatic population may play a role in fixing this problem.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Aleksandra Kovacevic", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Marc Baguelin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Matthieu Domenech de Cell\u00e8s", + "author_inst": "Max Planck Institute for Infection Biology" + }, + { + "author_name": "Lulla Opatowski", + "author_inst": "Univ Versailles Saint Quentin / Institut Pasteur / Inserm" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.10.21254528", "rel_title": "NEWS-2 score assessment of inpatient referral during the COVID 19 epidemic", @@ -720462,41 +721181,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.07.21258504", - "rel_title": "Adaptive vaccination may be needed to extirpate COVID-19: Results from a runtime-alterable strain-drift and waning-immunity model", - "rel_date": "2021-06-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258504", - "rel_abs": "In this paper, we present methods for building a Java Runtime-Alterable-Model Platform (RAMP) of complex dynamical systems. We illustrate our methods by building a multivariant SEIR (epidemic) RAMP. Underlying our RAMP is an individual-based model that includes adaptive contact rates, pathogen genetic drift, waning and cross immunity. Besides allowing parameter values, process descriptions, and scriptable runtime drivers to be easily modified during simulations, our RAMP is easily integrated into other computational platforms, such as our illustrated example with R-Studio. Processes descriptions that can be runtime altered within our SEIR RAMP include pathogen variant-dependent host shedding, environmental persistence, host transmission, and within-host pathogen mutation and replication. They also include adaptive social distancing and adaptive application of vaccination rates and variant-valency of vaccines. We present simulation results using parameter values and process descriptions relevant to the current COVID-19 pandemic. Our results suggest that if waning immunity outpaces vaccination rates, then vaccination rollouts may fail to contain the most transmissible variants, particularly if vaccine valencies do not adapt to escape mutations. Our SEIR RAMP is designed for easy-use by individuals and groups involved in formulating social-distancing and adaptive vaccination rollout policies. More generally, our RAMP concept facilitates construction of highly flexible complex systems models of all types, which can then be easily shared among researchers and policymakers as stand alone applications programs.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Wayne M Getz", - "author_inst": "University of California" - }, - { - "author_name": "Richard Salter", - "author_inst": "Numerus Inc." - }, - { - "author_name": "Ludovica Luisa Vissat", - "author_inst": "University of California at Berkeley" - }, - { - "author_name": "James S Koopman", - "author_inst": "University of Michigan" - }, - { - "author_name": "Carl P Simon", - "author_inst": "University of Michigan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.08.21258507", "rel_title": "A year of COVID-19 GWAS results from the GRASP portal reveals potential SARS-CoV-2 modifiers", @@ -720717,6 +721401,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.11.448011", + "rel_title": "B.1.1.7 and B.1.351 SARS-CoV-2 variants display enhanced Spike-mediated fusion", + "rel_date": "2021-06-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.11.448011", + "rel_abs": "Severe COVID-19 is characterized by lung abnormalities, including the presence of syncytial pneumocytes. Syncytia form when SARS-CoV-2 spike protein expressed on the surface of infected cells interacts with the ACE2 receptor on neighbouring cells. The syncytia forming potential of spike variant proteins remain poorly characterized. Here, we first assessed Alpha and Beta spread and fusion in cell cultures. Alpha and Beta replicated similarly to D614G reference strain in Vero, Caco-2, Calu-3 and primary airway cells. However, Alpha and Beta formed larger and more numerous syncytia. Alpha, Beta and D614G fusion was similarly inhibited by interferon induced transmembrane proteins (IFITMs). Individual mutations present in Alpha and Beta spikes differentially modified fusogenicity, binding to ACE2 and recognition by monoclonal antibodies. We further show that Delta spike also triggers faster fusion relative to D614G. Thus, SARS-CoV-2 emerging variants display enhanced syncytia formation.\n\nSynopsisThe Spike protein of the novel SARS-CoV-2 variants are comparative more fusogenic than the earlier strains. The mutations in the variant spike protein differential modulate syncytia formation, ACE2 binding, and antibody escape.\n\nO_LIThe spike protein of Alpha, Beta and Delta, in the absence of other viral proteins, induce more syncytia than D614G\nC_LIO_LIThe ACE2 affinity of the variant spike proteins correlates to their fusogenicity\nC_LIO_LIVariant associated mutations P681H, D1118H, and D215G augment cell-cell fusion, while antibody escape mutation E484K, K417N and {Delta}242-244 hamper it.\nC_LIO_LIVariant spike-mediated syncytia formation is effectively restricted by IFITMs\nC_LI", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Maaran Michael Rajah", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Mathieu Hubert", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Elodie Bishop", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Nell Saunders", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "R\u00e9my Robinot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Ludivine Grzelak", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Delphine Planas", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Jeremy Dufloo", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Stacy Gellenoncourt", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Alice Bongers", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Marija Zivaljic", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Cyril Planchais", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Florence Guivel-Benhassine", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Fran\u00e7oise Porrot", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Hugo Mouquet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Lisa Chakrabarti", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Julian Buchrieser", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.10.447999", "rel_title": "A combination of RBD and NTD neutralizing antibodies limits the generation of SARS-CoV-2 spike neutralization-escape mutants", @@ -722344,73 +723115,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.07.21258114", - "rel_title": "Development of low-cost serological immunoassay to detect antiviral antibodies to Sars-Cov-2 Spike protein", - "rel_date": "2021-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258114", - "rel_abs": "Seroconversion to SARS-CoV-2 has been widely studied to evaluate infection spreading for epidemiological purpose, or even in studies of protective immunity in convalescent or vaccinated individuals. The viral particle has an envelope harboring the spike glycoprotein, which can be used as an antigen for assay development, to detect antiviral antibodies to SARS-CoV-2. Since several vaccines encode a spike subunit, the full length spike-based immunoassay should be a universal tool to evaluate seroconversion. In this manuscript, we propose a low-cost ELISA that can be used to detect antiviral IgG to SARS-CoV-2 in human serum.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Luis Peroni", - "author_inst": "cnpem" - }, - { - "author_name": "Jessica Toscaro", - "author_inst": "cnpem" - }, - { - "author_name": "Camila Canateli", - "author_inst": "cnpem" - }, - { - "author_name": "Gabriel Lima", - "author_inst": "cnpem" - }, - { - "author_name": "ana Pagliarone", - "author_inst": "cnpem" - }, - { - "author_name": "Elaine Cardoso", - "author_inst": "cnpem" - }, - { - "author_name": "Renata Viana", - "author_inst": "Dante Pazzanese" - }, - { - "author_name": "Jessica Bassani", - "author_inst": "Dante Pazzanese" - }, - { - "author_name": "Hui Lin-Wang", - "author_inst": "Dante Pazzanese" - }, - { - "author_name": "Cely Saad Abboud", - "author_inst": "Dante Pazzanese" - }, - { - "author_name": "Carlos Gun", - "author_inst": "Dante Pazzanese" - }, - { - "author_name": "Kleber Franchini", - "author_inst": "cnpem" - }, - { - "author_name": "Marcio Chaim Bajgelman", - "author_inst": "CNPEM" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.07.21258402", "rel_title": "CHA2DS2-VASc score on admission to predict mortality in COVID-19 patients: A meta-analysis", @@ -722647,6 +723351,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.06.21258425", + "rel_title": "Functional dependence of COVID-19 growth rate on lockdown conditions and rate of vaccination.", + "rel_date": "2021-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.06.21258425", + "rel_abs": "It is shown that derived from the solution of differential equations analytical model adequately describes development epidemics with changes in both lockdown conditions and the effective rate of mass vaccination of the population. As in previous studies, the control calculations are in good agreement with observations at all stages of epidemic growth. One of the two model coefficients is uniquely related to the lockdown efficiency parameter. We obtained an approximate correlation between this parameter and the main conditions of lockdown, in particular, physical distancing, reduction in social contacts and strictness of the mask regime.\n\nThe calculation of the incident over a seven-day period using the proposed model is in good agreement with the observational data. Analysis of both curves shows that a better agreement can be obtained by taking into account the lag time of the epidemic response of about 10 days.\n\nFrom the reverse calculation a time-varying curve of the infection rate associated with the \"new\" virus strain under mutation conditions is obtained, which is qualitatively confirmed by the sequencing data.\n\nBased on these studies, it is possible to conclude that the ASILV analytical model developed here can be used to reliably and promptly predict epidemic development under conditions of lockdown and mass vaccination without the use of numerical methods.\n\nThe functional relationships identified allow us to conduct a rapid analysis of the impact of each of the model parameters on the overall process of the epidemic.\n\nIn contrast to previous studies, the calculations of the proposed model were performed using EXCEL, rather than a standard calculator. This is due to the need to account for multiple changes in lockdown conditions and vaccination rates.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Felix Mairanowski", + "author_inst": "Husmann Rus" + }, + { + "author_name": "Denis Below", + "author_inst": "Potsdam Universitet" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.09.21258609", "rel_title": "Depressive and anxiety symptoms and COVID-19-related factors among men and women in Nigeria", @@ -724390,69 +725117,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.06.09.447484", - "rel_title": "DNA damage response at telomeres boosts the transcription of SARS-CoV-2 receptor ACE2 during aging", - "rel_date": "2021-06-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.09.447484", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is known to be more common in the elderly, who show also more severe symptoms and a higher risk of hospitalization and death. Here we show that the expression of the Angiotensin Converting Enzyme 2 (ACE2), the SARS-CoV2 cell receptor, increases during aging in mouse and human lungs, and following telomere shortening or dysfunction in mammalian cells and in mouse models. This increase is regulated at the transcription level, and Ace2 promoter activity is DNA damage response (DDR)-dependent. Indeed, ATM inhibition or the selective inhibition of telomeric DDR, through the use of antisense oligonucleotides, prevents Ace2 upregulation following telomere damage, in cultured cells and in mice.\n\nWe propose that during aging telomeric shortening, by triggering DDR activation, causes the upregulation of ACE2, the SARS-CoV2 cell receptor, thus making the elderly likely more susceptible to the infection.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sara Sepe", - "author_inst": "IFOM Foundation-FIRC Institute of Molecular Oncology Foundation" - }, - { - "author_name": "Francesca Rossiello", - "author_inst": "IFOM Foundation-FIRC Institute of Molecular Oncology Foundation" - }, - { - "author_name": "Valeria Cancila", - "author_inst": "Tumor Immunology Unit, University of Palermo" - }, - { - "author_name": "Fabio Iannelli", - "author_inst": "IFOM Foundation-FIRC Institute of Molecular Oncology Foundation" - }, - { - "author_name": "Valentina Matti", - "author_inst": "IFOM Foundation-FIRC Institute of Molecular Oncology Foundation" - }, - { - "author_name": "Giada Cicio", - "author_inst": "Tumor Immunology Unit, University of Palermo" - }, - { - "author_name": "Matteo Cabrini", - "author_inst": "IFOM Foundation-FIRC Institute of Molecular Oncology Foundation" - }, - { - "author_name": "Eugenia Marinelli", - "author_inst": "IFOM Foundation-FIRC Institute of Molecular Oncology Foundation" - }, - { - "author_name": "Busola Alabi", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Alessia di Lillo", - "author_inst": "IFOM Foundation-FIRC Institute of Molecular Oncology Foundation" - }, - { - "author_name": "Jerry W Shay", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Claudio Tripodo", - "author_inst": "Tumor Immunology Unit, University of Palermo" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.06.09.447656", "rel_title": "Oral subunit SARS-CoV-2 vaccine induces systemic neutralizing IgG, IgA and cellular immune responses and can boost neutralizing antibody responses primed by an injected vaccine", @@ -724701,6 +725365,153 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.06.09.447527", + "rel_title": "Second Generation Antibodies Neutralize Emerging SARS-CoV-2 Variants of Concern", + "rel_date": "2021-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.09.447527", + "rel_abs": "Recently emerged SARS-CoV-2 variants show resistance to some antibodies that were authorized for emergency use. We employed hybridoma technology combined with authentic virus assays to develop second-generation antibodies, which were specifically selected for their ability to neutralize new variants of SARS-CoV-2. AX290 and AX677, two monoclonal antibodies with non-overlapping epitopes, exhibit subnanomolar or nanomolar affinities to the receptor binding domain of the viral Spike protein carrying amino acid substitutions N501Y, N439K, E484K, K417N, and a combination N501Y/E484K/K417N found in the circulating virus variants. The antibodies showed excellent neutralization of an authentic SARS-CoV-2 virus representing strains circulating in Europe in spring 2020 and also the variants of concern B.1.1.7 and B.1.351. Finally, the combination of the two antibodies prevented the appearance of escape mutations of the authentic SARS-CoV-2 virus. The neutralizing properties were fully reproduced in chimeric mouse-human versions, which may represent a promising tool for COVID-19 therapy.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Branislav Kovacech", + "author_inst": "AXON COVIDAX a. s., Slovakia" + }, + { + "author_name": "Lubica Fialova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Peter Filipcik", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Monika Zilkova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Rostislav Skrabana", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Natalia Paulenka-Ivanovova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Andrej Kovac", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Denisa Palova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Gabriela Paulikova Rolkova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Katarina Tomkova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Natalia Turic Csokova", + "author_inst": "Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Karina Markova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Michaela Skrabanova", + "author_inst": "Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Kristina Sinska", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Neha Basheer", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Petra Majerova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Jozef Hanes", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Vojtech Parrak", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Michal Prcina", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Ondrej Cehlar", + "author_inst": "Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Martin Cente", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Juraj Piestansky", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Michal Fresser", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Michal Novak", + "author_inst": "Axon Neuroscience SE, Cyprus" + }, + { + "author_name": "Monika Slavikova", + "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Kristina Borsova", + "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia; Department of Microbiology and Virology, Faculty of Natural" + }, + { + "author_name": "Viktoria Cabanova", + "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Bronislava Brejova", + "author_inst": "Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Slovakia" + }, + { + "author_name": "Tomas Vinar", + "author_inst": "Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Slovakia" + }, + { + "author_name": "Jozef Nosek", + "author_inst": "Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Slovakia" + }, + { + "author_name": "Boris Klempa", + "author_inst": "Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences, Bratislava, Slovakia" + }, + { + "author_name": "Norbert Zilka", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + }, + { + "author_name": "Eva Kontsekova", + "author_inst": "Axon Neuroscience R&D Services SE, Slovakia" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.09.21258553", "rel_title": "Analysis of cell-mediated immunity in people with long Covid.", @@ -726248,41 +727059,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.04.21258344", - "rel_title": "Factors associated with excess all-cause mortality in the first wave of COVID-19 pandemic in the UK: a time-series analysis using the Clinical Practice Research Datalink", - "rel_date": "2021-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.04.21258344", - "rel_abs": "ObjectivesExcess mortality captures the total effect of the COVID-19 pandemic on mortality and is not affected by mis-specification of cause of death. We aimed to describe how health and demographic factors have been associated with excess mortality during the pandemic.\n\nDesignTime-series analysis.\n\nSettingUK primary care data from practices contributing to the Clinical Practice Research Datalink on July 31st 2020.\n\nParticipantsWe constructed a time-series dataset including 9,635,613 adults ([≥]40 years old) who were actively registered at the general practice during the study period.\n\nMain outcome measuresWe extracted weekly numbers of deaths between March 2015 and July 2020, stratified by individual-level factors. Excess mortality during wave 1 of the UK pandemic (5th March to 27th May 2020) compared to pre-pandemic was estimated using seasonally adjusted negative binomial regression models. Relative rates of death for a range of factors were estimated before and during wave 1 by including interaction terms.\n\nResultsAll-cause mortality increased by 43% (95% CI 40%-47%) during wave 1 compared with pre-pandemic. Changes to the relative rate of death associated with most socio-demographic and clinical characteristics were small during wave 1 compared with pre-pandemic. However, the mortality rate associated with dementia markedly increased (RR for dementia vs no dementia pre-pandemic: 3.5, 95% CI 3.4-3.5; RR during wave 1: 5.1, 4.87-5.28); a similar pattern was seen for learning disabilities (RR pre-pandemic: 3.6, 3.4-3.5; during wave 1: 4.8, 4.4-5.3), for Black or South Asian ethnicity compared to white, and for London compared to other regions.\n\nConclusionsThe first UK COVID-19 wave appeared to amplify baseline mortality risk by a relatively constant factor for most population subgroups. However disproportionate increases in mortality were seen for those with dementia, learning disabilities, non-white ethnicity, or living in London.\n\nSummary boxO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIAll-cause mortality during the COVID-19 pandemic was higher than in previous years; this excess mortality was particularly pronounced among elderly people, males, people of non-white ethnicity, people of lower socio-economic status and people living in care-homes.\nC_LIO_LISeveral other papers have studied a wider range of factors associated with mortality due to COVID-19 using cause-of-death data.\nC_LIO_LIThere is little evidence on how all-cause mortality has changed in people with comorbidities.\nC_LI\n\nWhat this study addsO_LIOur study shows that during Wave 1 of the pandemic all cause death rates increased by a similar proportional degree for almost all population subgroups regardless of their health or socio-demographic circumstances; the exceptions were those with a diagnosis of dementia or learning disabilities and those of non-white ethnicity or living in London.\nC_LIO_LIThis suggests that COVID-19 has dialled up the risk of death by a similar proportional degree for everyone except those exposed to a higher risk of infection.\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Helen Strongman", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Helena Carreira", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Bianca L De Stavola", - "author_inst": "UCL" - }, - { - "author_name": "Krishnan Bhaskaran", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "David A Leon", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.05.21258365", "rel_title": "Early epidemiological signatures of novel SARS-CoV-2 variants: establishment of B.1.617.2 in England", @@ -726647,6 +727423,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.06.05.21258407", + "rel_title": "Prediction of severe COVID-19 cases requiring intensive care in Osaka, Japan", + "rel_date": "2021-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.05.21258407", + "rel_abs": "BackgroundTo avoid exhaustion of medical resources by COVID-19 care, policy-makers must predict care needs, specifically estimating the proportion of severe cases likely to require intensive care. In Osaka prefecture, Japan, the number of these severe cases exceeded the capacity of ICU units prepared for COVID-19 from mid-April, 2021.\n\nObjectiveThis study used a statistical model to elucidate dynamics of severe cases in Osaka and validated the model through prospective testing.\n\nMethodsThe study extended from April 3, 2020 through April 26, 2021 in Osaka prefecture, Japan prefecture. We regressed the number of severe cases on the number of severe cases the day prior and the newly onset patients of more than 21 days prior.\n\nResultsWe selected the number of severe cases the day prior and the number of newly onset patients on 21 and 28 days prior as explanatory variables for explaining the number of severe cases based on the adjusted determinant coefficient. The adjusted coefficient of determination was greater than 0.995 and indicated good fit. Prospective out of sample three-week prediction forecast the peak date precisely, but the level was not t.\n\nDiscussion and ConclusionA reason for the gap in the prospective prediction might be the emergence of variant strains.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Junko Kurita", + "author_inst": "Tokiwa University, Ibaraki, Japan" + }, + { + "author_name": "Tamie Sugawara", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Yasushi Ohkusa", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.04.21257951", "rel_title": "Early Epidemiological Evidence of Public Health Value of WA Notify, a Smartphone-based Exposure Notification Tool: Modeling COVID-19 Cases Averted in Washington State", @@ -728062,57 +728865,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.03.21258328", - "rel_title": "NEW CORONAVIRUS IN PREGNANT WOMEN. Maternal and perinatal outcomes.", - "rel_date": "2021-06-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258328", - "rel_abs": "ObjectivesTo report the maternal and neonatal results of patients infected with COVID-19 in Panama.\n\nMethodsThe study is based on the analysis of pregnant women with COVID-19, in 5 hospitals in the Republic of Panama. The inclusion criteria were: Patients with or without symptoms, positive RT-PCR for SARS-CoV-2 in the period from March 23 to 6 months after, whose births were attended in one of those 5 hospitals and who signed the consent. Data was obtained at the time of diagnosis of the infection and at the time of termination of pregnancy for the mother and newborn.\n\nResults253 patients met the inclusion criteria. Most were diagnosed in the third trimester (89.3%). 10.3% of the patients presented in a severe form of COVID-19. The most frequent complication was pre-eclampsia and if we add gestational hypertension they represent 21.2%; most of the patients terminated the pregnancy by caesarean section (58%). 26.9% (95% CI 21.3-32.9%) of the births were premature, and perinatal mortality was 5.4% (95% CI 3.0-9.0%). There was a need for mechanical ventilation in 5.9% (95% CI 3.6-9.6%) of the cohort and there were four maternal deaths (1.6% - 95% CI 0.6-4.0%).\n\nConclusionsThis study of pregnant women infected with COVID-19 and diagnosed with RT-PCR shows serious maternal complications such as high admission to the ICU, need for mechanical ventilation and one death in every 64 infected. Frequent obstetric complications such as hypertension, premature rupture of membranes, high rate of prematurity and perinatal lethality were also seen.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jaime Sanchez", - "author_inst": "Hospital Santo Tomas, Panama" - }, - { - "author_name": "Jorge Espinosa", - "author_inst": "Hospital Santo Tomas, Panama" - }, - { - "author_name": "Luis Carlos Caballero", - "author_inst": "Hospital Luis Chicho Fabrega, Veraguas Panama" - }, - { - "author_name": "Sara Campana", - "author_inst": "Caja de Seguro Social; Panama" - }, - { - "author_name": "Arelys Quintero", - "author_inst": "Hospital Jose Domingo De Obaldia, Chiriqui Panama" - }, - { - "author_name": "Carlos Luo", - "author_inst": "Caja de Seguro Social, Panama" - }, - { - "author_name": "Jorge Ng", - "author_inst": "Caja de Seguro Social, Panama" - }, - { - "author_name": "Rafael de Gracia", - "author_inst": "Hospital San Miguel Arcangel, Panama" - }, - { - "author_name": "Paulino Vigil-De Gracia", - "author_inst": "Complejo Hospitalario Dr. AAM CSS" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.06.03.21258306", "rel_title": "Alcov: Estimating Variant of Concern Abundance from SARS-CoV-2 Wastewater Sequencing Data", @@ -728257,6 +729009,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.03.21258307", + "rel_title": "Loss of recognition of SARS-CoV-2 B.1.351 variant spike epitopes but overall preservation of T cell immunity", + "rel_date": "2021-06-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258307", + "rel_abs": "SARS-CoV-2 variants have emerged that escape neutralization and potentially impact vaccine efficacy. T cell responses play a role in protection from reinfection and severe disease, but the potential for spike mutations to affect T cell immunity is poorly studied. We assessed both neutralizing antibody and T cell responses in 44 South African COVID-19 patients infected either with B.1.351, now dominant in South Africa, or infected prior to its emergence ( first wave), to provide an overall measure of immune evasion. We show for the first time that robust spike-specific CD4 and CD8 T cell responses were detectable in B.1.351-infected patients, similar to first wave patients. Using peptides spanning only the B.1.351 mutated regions, we identified CD4 T cell responses targeting the wild type peptides in 12/22 (54.5%) first wave patients, all of whom failed to recognize corresponding B.1.351-mutated peptides (p=0.0005). However, responses to the mutated regions formed only a small proportion (15.7%) of the overall CD4 response, and few patients (3/44) mounted CD8 responses that targeted the mutated regions. First wave patients showed a 12.7 fold reduction in plasma neutralization of B.1.351. This study shows that despite loss of recognition of immunodominant CD4 epitope(s), overall CD4 and CD8 T cell responses to B.1.351 are preserved. These observations may explain why, despite substantial loss of neutralizing antibody activity against B.1.351, several vaccines have retained the ability to protect against severe COVID-19 disease.\n\nOne Sentence SummaryT cell immunity to SARS-CoV-2 B.1.351 is preserved despite some loss of variant epitope recognition by CD4 T cells.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Catherine Riou", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Roanne Keeton", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Thandeka Moyo-Gwete", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Tandile Hermanus", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Prudence Kgagudi", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Richard Baguma", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Houriiyah Tegally", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP)" + }, + { + "author_name": "Deelan Doolabh", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Arash Iranzadeh", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Lynn Tyers", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Hygon Mutavhatsindi", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Marius Tincho", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Ntombi Benede", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Gert Marais", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Lionel Chinhoyi", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Mathilda Mennen", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Sango Skelem", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Elsa Bruyn", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Cari Stek", + "author_inst": "University of Cape Town" + }, + { + "author_name": "- SA-CIN", + "author_inst": "" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP)" + }, + { + "author_name": "Carolyn Williamson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Penny Moore", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Robert Wilkinson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Ntobeko Ntusi", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Wendy Burgers", + "author_inst": "University of Cape Town" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.04.447160", "rel_title": "Drug Repurposing for the SARS-CoV-2 Papain-Like Protease", @@ -729616,53 +730487,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.01.21258181", - "rel_title": "Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens", - "rel_date": "2021-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.01.21258181", - "rel_abs": "Mutations in emerging SARS-CoV-2 lineages can interfere with the laboratory methods used to generate high-quality genome sequences for COVID-19 surveillance. Here, we identify 46 mutations in current variant of concern lineages affecting the widely used laboratory protocols for SARS-CoV-2 genomic sequencing by Freed et al. and the ARTIC network. We provide laboratory data showing how three of these mutations disrupted sequencing of P.1 lineage specimens during a recent outbreak in British Columbia, Canada, and we also demonstrate how we modified the Freed et al. protocol to restore performance.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Kevin S Kuchinski", - "author_inst": "University of British Columbia/BC Centre for Disease Control" - }, - { - "author_name": "Jason Nguyen", - "author_inst": "British Columbia Centre for Disease Control Public Health Laboratory" - }, - { - "author_name": "Tracy D Lee", - "author_inst": "British Columbia Centre for Disease Control Public Health Laboratory" - }, - { - "author_name": "Rebecca Hickman", - "author_inst": "British Columbia Centre for Disease Control Public Health Laboratory" - }, - { - "author_name": "Agatha N Jassem", - "author_inst": "University of British Columbia/British Columbia Centre for Disease Control Public Health Laboratory" - }, - { - "author_name": "Linda MN Hoang", - "author_inst": "University of British Columbia/British Columbia Centre for Disease Control Public Health Laboratory" - }, - { - "author_name": "Natalie A Prystajecky", - "author_inst": "University of British Columbia/British Columbia Centre for Disease Control Public Health Laboratory" - }, - { - "author_name": "John R Tyson", - "author_inst": "British Columbia Centre for Disease Control Public Health Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.03.21258228", "rel_title": "Persistent SARS-CoV-2 infection and intra-host evolution in association with advanced HIV infection", @@ -729915,6 +730739,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.03.446942", + "rel_title": "Visualization of SARS-CoV-2 infection dynamic", + "rel_date": "2021-06-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.03.446942", + "rel_abs": "Replication-competent recombinant viruses expressing reporter genes provide valuable tools to investigate viral infection. Low levels of reporter gene expressed from previous reporter-expressing rSARS-CoV-2 have jeopardized their use to monitor the dynamics of SARS-CoV-2 infection in vitro or in vivo. Here, we report an alternative strategy where reporter genes were placed upstream of the viral nucleocapsid gene followed by a 2A cleavage peptide. The higher levels of reporter expression using this strategy resulted in efficient visualization of rSARS-CoV-2 in infected cultured cells and K18 hACE2 transgenic mice. Importantly, real-time viral infection was readily tracked using a non-invasive in vivo imaging system and allowed us to rapidly identify antibodies which are able to neutralize SARS-CoV-2 infection in vivo. Notably, these reporter-expressing rSARS-CoV-2 retained wild-type virus like pathogenicity in vivo, supporting their use to investigate viral infection, dissemination, pathogenesis and therapeutic interventions for the treatment of SARS-CoV-2 in vivo.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Kevin Chiem", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jun-Gyu Park", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jesus Silvas", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Desarey Morales Vasquez", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jordi B Torrelles", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "James Kobie", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Mark R Walter", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Juan C de la Torre", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.04.447114", "rel_title": "Sub-Picomolar Detection of SARS-CoV-2 RBD via Computationally-Optimized Peptide Beacons", @@ -731266,49 +732145,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.31.21258111", - "rel_title": "Analytical comparison of nine SARS-CoV-2 antigen-detecting rapid diagnostic tests for emerging SARS-CoV-2 variants", - "rel_date": "2021-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.31.21258111", - "rel_abs": "Several SARS-CoV-2 variants of concern/interest (VOC/VOI) emerged recently, with VOCs outcompeting earlier lineages on a global scale. To date, few data on routine diagnostic performance for VOC/VOIs are available. Here, we investigate the analytical performance of nine commercially available antigen-detecting rapid diagnostic tests (Ag-RDTs) for VOC B.1.1.7, B.1.351, P.1 and VOI P.2 with cultured SARS-CoV-2. Comparable or higher sensitivity was observed for VOC/VOI compared to a non-VOC/VOI early-pandemic virus for all Ag-RDTs.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Meriem Bekliz", - "author_inst": "Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Kenneth Adea", - "author_inst": "Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland." - }, - { - "author_name": "Manel Essaidi", - "author_inst": "Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Jilian A Sacks", - "author_inst": "FIND, Geneva, Switzerland" - }, - { - "author_name": "Camille Escadafal", - "author_inst": "FIND, Geneva, Switzerland" - }, - { - "author_name": "Laurent Kaiser", - "author_inst": "University of Geneva Hospitals" - }, - { - "author_name": "Isabella Eckerle", - "author_inst": "University Hospitals of Geneva" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.02.21258076", "rel_title": "Genomic characterization and Epidemiology of an emerging SARS-CoV-2 variant in Delhi, India", @@ -731849,6 +732685,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.06.01.21258172", + "rel_title": "Humoral and cellular immune response against SARS-CoV-2 variants following heterologous and homologous ChAdOx1 nCoV-19/BNT162b2 vaccination.", + "rel_date": "2021-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.01.21258172", + "rel_abs": "Cerebral venous thrombosis was reported as a rare but serious adverse event in young and middle-aged vaccinees following immunization with AstraZenecas ChAdOx1-nCov-19 vaccine. As a consequence, several European governments recommended using this vaccine only in individuals older than 60 years leaving millions of ChAd primed individuals with the decision to either receive a second shot of ChAd or a heterologous boost with mRNA-based vaccines. However, such combinations have not been tested so far. We used Hannover Medical Schools COVID-19 Contact (CoCo) Study cohort of health care professionals (HCP) to monitor ChAd primed immune responses before and three weeks after booster with ChAd or BioNTech/Pfizers BNT162b2. Whilst both vaccines boosted prime-induced immunity, BNT induced significantly higher frequencies of Spike-specific CD4 and CD8 T cells and, in particular, high titers of neutralizing antibodies against the B.1.1.7, B.1.351 and the P.1 variants of concern of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2).", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Joana Barros-Martins", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Swantje Hammerschmidt", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anne Cossmann", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Ivan Odak", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Metodi V Stankov", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Gema Morillas Ramos", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Alexandra Jablonka", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Annika Heidemann", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Christiane Ritter", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Michaela Friedrichsen", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Christian R Schultze-Florey", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Inga Ravens", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Willenzon Stefanie", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anja Bubke", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Jasmin Ristenpart", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Anika Janssen", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "George Ssebyatika", + "author_inst": "University of Luebeck" + }, + { + "author_name": "Guenter Bernhardt", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Jan R Muench", + "author_inst": "Ulm University" + }, + { + "author_name": "Markus Hoffmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" + }, + { + "author_name": "Stefan Poehlmann", + "author_inst": "Deutsches Primatenzentrum GmbH - Leibniz-Institut fur Primatenforschung" + }, + { + "author_name": "Thomas Krey", + "author_inst": "University of Luebeck" + }, + { + "author_name": "Berislav Bosnjak", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Reinhold Foerster", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Georg MN Behrens", + "author_inst": "Hannover Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.01.21258150", "rel_title": "Ten months of temporal variation in the clinical journey of hospitalised patients with COVID-19: an observational cohort", @@ -733340,129 +734291,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.06.01.446640", - "rel_title": "SARS-CoV-2 infection studies in lung organoids identify TSPAN8 as novel mediator", - "rel_date": "2021-06-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.01.446640", - "rel_abs": "SARS coronavirus-2 (SARS-CoV-2) is causing a global pandemic with large variation in COVID-19 disease spectrum. SARS-CoV-2 infection requires host receptor ACE2 on lung epithelium, but epithelial underpinnings of variation are largely unknown. We capitalized on comprehensive organoid assays to report remarkable variation in SARS-CoV-2 infection rates of lung organoids from different subjects. Tropism is highest for TUBA- and MUC5AC-positive organoid cells, but levels of TUBA-, MUC5A-, or ACE2-positive cells do not predict infection rate. We identify surface molecule Tetraspanin 8 (TSPAN8) as novel mediator of SARS-CoV-2 infection, which is not downregulated by this specific virus. TSPAN8 levels, prior to infection, strongly correlate with infection rate and TSPAN8-blocking antibodies diminish SARS-CoV-2 infection. We propose TSPAN8 as novel functional biomarker and potential therapeutic target for COVID-19.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Lisiena Hysenaj", - "author_inst": "UCSF" - }, - { - "author_name": "Samantha Little", - "author_inst": "UCSF" - }, - { - "author_name": "Kayla R Kulhanek", - "author_inst": "UCSF" - }, - { - "author_name": "Oghenekevwe Gbenedio", - "author_inst": "UCSF" - }, - { - "author_name": "Lauren Rodriguez", - "author_inst": "UCSF" - }, - { - "author_name": "Alan Shen", - "author_inst": "UCSF" - }, - { - "author_name": "Jean-Christophe Lone", - "author_inst": "Essex University" - }, - { - "author_name": "Leonard C Lupin-Jimenez", - "author_inst": "UCSF" - }, - { - "author_name": "Luke Bonser", - "author_inst": "UCSF" - }, - { - "author_name": "Nina K Serwas", - "author_inst": "UCSF" - }, - { - "author_name": "Kriti Bahl", - "author_inst": "UCSF" - }, - { - "author_name": "Eran Mick", - "author_inst": "UCSF" - }, - { - "author_name": "Jack Z Li", - "author_inst": "UCSF" - }, - { - "author_name": "Vivianne Ding", - "author_inst": "UCSF" - }, - { - "author_name": "Shotaro Matsumoto", - "author_inst": "UCSF" - }, - { - "author_name": "Mazharul l Maishan", - "author_inst": "UCSF" - }, - { - "author_name": "Gabriela Fragiadakis", - "author_inst": "UCSF" - }, - { - "author_name": "David M Jablons", - "author_inst": "UCSF" - }, - { - "author_name": "Charles R Langelier", - "author_inst": "UCSF" - }, - { - "author_name": "Michael Matthay", - "author_inst": "UCSF" - }, - { - "author_name": "Melanie Ott", - "author_inst": "UCSF" - }, - { - "author_name": "Anita Sil", - "author_inst": "UCSF" - }, - { - "author_name": "Matthew Krummel", - "author_inst": "UCSF" - }, - { - "author_name": "Alexis J Combes", - "author_inst": "UCSF" - }, - { - "author_name": "David M Erle", - "author_inst": "UCSF" - }, - { - "author_name": "Johannes R Kratz", - "author_inst": "UCSF" - }, - { - "author_name": "Jeroen P Roose", - "author_inst": "UCSF" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.01.446676", "rel_title": "SARS-CoV-2 Infects Syncytiotrophoblast and Activates Inflammatory Responses in the Placenta", @@ -733759,6 +734587,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.05.29.21258010", + "rel_title": "Rapid and sustained decline in CXCL-10 (IP-10) annotates clinical outcomes following TNF-\u03b1 antagonist therapy in hospitalized patients with severe and critical COVID-19 respiratory failure", + "rel_date": "2021-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.29.21258010", + "rel_abs": "BackgroundA feed-forward pathological signaling loop generated by TNF and IFN-{gamma} in inflamed lung tissue, driving CXCL-10 (IP-10) and CXCL-9 chemokine-mediated activated T-cell and monocyte/macrophage tissue recruitment, may define, sustain and amplify the inflammatory biology of lethal COVID-19 respiratory failure.\n\nMethodsTo assess TNF-antagonist therapy, 18 hospitalized adults with hypoxic respiratory failure and COVID-19 pneumonia received single-dose infliximab-abda therapy 5mg/kg intravenously between April and December 2020. The primary endpoint was time to increase in oxygen saturation to fraction of inspired oxygen ratio (SpO2/FiO2) by [≥] 50 compared to baseline and sustained for 48 hours. Secondary endpoints included 28-day mortality, dynamic cytokine profiles (Human Cytokine 48-Plex Discovery Assay, Eve Technologies), secondary infections, duration of supplemental oxygen support and hospitalization.\n\nFindingsPatients were predominantly in critical respiratory failure (15/18, 83%), male (14/18, 78%), above 60 years (median 63 yrs, range 31-80), race-ethnic minorities (13/18, 72%), lymphopenic (13/18, 72%), steroid-treated (17/18, 94%), with a median ferritin of 1953ng/ml. Sixteen patients (89%) met the primary endpoint within a median of 4 days, 15/18 (83%) recovered from respiratory failure, and 14/18 (78%) were discharged in a median of 8 days and were alive at 28-day follow-up. Deaths among three patients [≥] 65yrs age with pre-existing lung disease or multiple comorbidities were attributed to secondary lung infection. Mean plasma IP-10 levels declined sharply from 9183 pg/ml to 483 pg/ml at Day 3 and further to 146 pg/ml at Day 14/discharge. Significant declines in IFN-{gamma}, TNF, IL-27, CRP and ferritin were specifically observed at Day 3 whereas other cytokines were unmodified. IL-6 levels declined sharply among patients with baseline levels >10 pg/ml. Among 13 lymphopenic patients, six (46%) had resolution of lymphopenia by day 3, and 11 by day 14. CXCR3-ligand (IP-10 and CXCL-9) declines were strongly correlated among patients with lymphopenia reversal (Day 3, Pearson r: 0.98, p-value: 0.0006).\n\nInterpretationConsistent with a pathophysiological role of TNF, the clinical and cytokine data indicate that infliximab-abda may rapidly abrogate pathological inflammatory signaling to facilitate clinical recovery in severe and critical COVID-19. Randomized studies are required to formally assess mortality outcomes. Funding: National Center for Advancing Translational Sciences", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Hilal Hachem", + "author_inst": "Tufts Medical Center, Boston MA (current affiliation: Northern Light Cancer Institute,Bangor ME)" + }, + { + "author_name": "Amandeep Godara", + "author_inst": "Tufts Medical Center, Boston MA (current affiliation: University of Utah, Salt Lake City, UT)" + }, + { + "author_name": "Courtney Schroeder", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Daniel Fein", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Hashim Mann", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Christian Lawlor", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Jill Marshall", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Andreas Klein", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Deborah Poutsiaka", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Janis L Breeze", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Raghav Joshi", + "author_inst": "Tufts Medical Center" + }, + { + "author_name": "Paul Mathew", + "author_inst": "Tufts Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.25.21257820", "rel_title": "The Female Predominant Persistent Immune Dysregulation of the Post COVID Syndrome: A Cohort Study", @@ -735182,121 +736073,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.28.21258011", - "rel_title": "SARS-CoV-2 infectious virus, viral RNA in nasopharyngeal swabs, and serostatus of symptomatic COVID-19 outpatients in the United States", - "rel_date": "2021-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21258011", - "rel_abs": "BackgroundWhile SARS-CoV-2 infectious virus isolation in outpatients with COVID-19 has been associated with viral RNA levels and symptom duration, little is known about the host, disease and viral determinants of infectious virus detection.\n\nMethodsCOVID-19 adult outpatients were enrolled within 7 days of symptom onset. Clinical symptoms were recorded via patient diary. Nasopharyngeal swabs were collected to quantitate SARS-CoV-2 RNA by reverse transcriptase polymerase chain reaction and for infectious virus isolation in Vero E6-cells. SARS-CoV-2 antibodies were measured in serum using a validated ELISA assay.\n\nResultsAmong 204 participants with mild-to-moderate symptomatic COVID19, the median nasopharyngeal viral RNA was 6.5 (IQR 4.7-7.6 log10 copies/mL), and 26% had detectable SARS-CoV-2 antibodies (IgA, IgM, IgG, and/or total Ig) at baseline. Infectious virus was recovered in 7% of participants with SARS-CoV-2 antibodies compared to 58% of participants without antibodies (probability ratio (PR)=0.12, 95% CI: 0.04, 0.36; p=0.00016). Infectious virus isolation was also associated with higher levels of viral RNA (mean RNA difference +2.6 log10, 95% CI: 2.2, 3.0; p<0.0001) and fewer days since symptom onset (PR=0.79, 95% CI: 0.71, 0.88 per day; p<0.0001).\n\nConclusionsThe presence of SARS-CoV-2 antibodies is strongly associated with clearance of infectious virus isolation. Seropositivity and viral RNA levels are likely more reliable markers of infectious virus clearance than subjective measure of COVID-19 symptom duration. Virus-targeted treatment and prevention strategies should be administered as early as possible and ideally before seroconversion.\n\nClinicalTrials.gov IdentifierNCT04405570\n\nKey Points (Summary)Among COVID-19 outpatients within 7 days of symptom onset, the presence of SARS-CoV-2-specific antibodies was strongly associated with clearance of infectious virus. Seropositivity appears to be more reliable marker of infectious virus clearance than subjective measure of COVID-19 symptoms.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Katie R. Mollan", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Joseph J. Eron", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Taylor J. Krajewski", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Wendy Painter", - "author_inst": "Ridgeback Biotherapeutics LP, Miami, Florida 33133" - }, - { - "author_name": "Elizabeth R. Duke", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Caryn G. Morse", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "Erin A. Goecker", - "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington" - }, - { - "author_name": "Lakshmanane Premkumar", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Cameron R. Wolfe", - "author_inst": "Duke University Medical Center" - }, - { - "author_name": "Laura J. Szewczyk", - "author_inst": "Ridgeback Biotherapeutics LP, Miami, Florida 33133" - }, - { - "author_name": "Paul L. Alabanza", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Amy James Loftis", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Emily J. Degli-Angeli", - "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington" - }, - { - "author_name": "Ariane J. Brown", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Joan A. Dragavon", - "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington" - }, - { - "author_name": "John J. Won", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Jessica Keys", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Michael G. Hudgens", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Lei Fang", - "author_inst": "Pharstat Inc., Raleigh, NC" - }, - { - "author_name": "David A. Wohl", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Myron S. Cohen", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Ralph S. Baric", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Robert W. Coombs", - "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington" - }, - { - "author_name": "Timothy P. Sheahan", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "William A. Fischer II", - "author_inst": "University of North Carolina at Chapel Hill" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.30.21257382", "rel_title": "Admission criteria in critically ill COVID-19 patients: a physiology-based approach.", @@ -735533,6 +736309,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.28.21258008", + "rel_title": "College Students' COVID-19 Vaccine Beliefs and Intentions: Implications for interventions", + "rel_date": "2021-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21258008", + "rel_abs": "On college campuses, effective management of vaccine-preventable transmissible pathogens requires understanding student vaccination intentions. This is necessary for developing and tailoring health messaging to maximize uptake of health information and vaccines. The current study explored students beliefs and attitudes about vaccines in general, and the new COVID-19 vaccines specifically. This study provides insights into effective health messaging needed to rapidly increase COVID-19 vaccination on college campuses--information that will continue to be informative in future academic years across a broad scope of pathogens. Data were collected via an online cohort survey of college students aged 18 years and older residing on or near the campus of a large public university during fall 2020. Overall, we found COVID-19 vaccine hesitancy in college students correlated strongly with some concerns about vaccines in general as well as with concerns specific to COVID-19 vaccines. Taken together, these results provide further insight for message development and delivery, and can inform more effective interventions to advance critical public health outcomes on college campuses beyond the current pandemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Meg L Small", + "author_inst": "Penn State University" + }, + { + "author_name": "Robert Lennon", + "author_inst": "Penn State University" + }, + { + "author_name": "John Dziak", + "author_inst": "Penn State University" + }, + { + "author_name": "Rachel A Smith", + "author_inst": "Penn State University" + }, + { + "author_name": "Gillian Sommerville", + "author_inst": "Penn State University" + }, + { + "author_name": "Nita Bharti", + "author_inst": "Penn State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.31.21257656", "rel_title": "Acute kidney injury in hospitalized patients due to COVID-19", @@ -736784,45 +737599,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.27.21257032", - "rel_title": "How immunity from and interaction with seasonal coronaviruses can shape SARS-CoV-2 epidemiology", - "rel_date": "2021-05-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.27.21257032", - "rel_abs": "We hypothesised that cross-protection from seasonal epidemics of human coronaviruses (HCoVs) could have affected SARS-CoV-2 transmission, including generating reduced susceptibility in children. To determine what the pre-pandemic distribution of immunity to HCoVs was, we fitted a mathematical model to 6 years of seasonal coronavirus surveillance data from England and Wales. We estimated a duration of immunity to seasonal HCoVs of 7.3 years (95%CI 6.8 - 7.9) and show that, while cross-protection between HCoV and SARS-CoV-2 may contribute to the age distribution, it is insufficient to explain the age pattern of SARS-CoV-2 infections in the first wave of the pandemic in England and Wales. Projections from our model illustrate how different strengths of cross-protection between circulating coronaviruses could determine the frequency and magnitude of SARS-CoV-2 epidemics over the coming decade, as well as the potential impact of cross-protection on future seasonal coronavirus transmission.\n\nSignificance statementCross-protection from seasonal epidemics of human coronaviruses (HCoVs) has been hypothesised to contribute to the relative sparing of children during the early phase of the pandemic. Testing this relies on understanding the pre-pandemic age-distribution of recent HCoV infections, but little is known about their dynamics. Using England and Wales as a case study, we use a transmission model to estimate the duration of immunity to seasonal coronaviruses, and show how cross-protection could have affected the age distribution of susceptibility during the first wave, and alter SARS-CoV-2 transmission patterns over the coming decade.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Naomi R Waterlow", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Edwin Van Leeuwen", - "author_inst": "Public Health England" - }, - { - "author_name": "Nicholas G Davies", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "- CMMID COVID-19 working group", - "author_inst": "" - }, - { - "author_name": "Stefan Flasche", - "author_inst": "LSHTM" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.27.21257909", "rel_title": "The isolated effect of age on the risk of COVID-19 severe outcomes: a systematic review with meta-analysis", @@ -736987,6 +737763,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2021.05.28.21257993", + "rel_title": "The UGT2A1/UGT2A2 locus is associated with COVID-19-related anosmia", + "rel_date": "2021-05-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21257993", + "rel_abs": "Loss of sense of smell is a characteristic symptom of infection with SARS-CoV-2. However, specific mechanisms linking infection with loss of smell are poorly understood. Using self-reported symptom data from the 23andMe COVID-19 study, we describe the demographic patterns associated with COVID-19 related anosmia, and find the symptom is more often reported in women and younger respondents, and less often by those of East Asian and African American ancestry compared to those of European ancestry. We ran a trans-ethnic genome-wide association study (GWAS) comparing loss of smell or taste (n=47,298) with no loss of smell or taste (n=22,543) among those with a positive SARS-CoV-2 test result. We identified an association (rs7688383) in the vicinity of the UGT2A1 and UGT2A2 genes (OR=1.115, p-value=4x10-15), which have been linked to olfactory function. These results may shed light on the biological mechanisms underlying COVID-19 related anosmia.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Janie F. Shelton", + "author_inst": "23andMe" + }, + { + "author_name": "Anjali J. Shastri", + "author_inst": "23andMe" + }, + { + "author_name": "- The 23andMe COVID-19 Team", + "author_inst": "" + }, + { + "author_name": "Stella Aslibekyan", + "author_inst": "23andMe" + }, + { + "author_name": "Adam Auton", + "author_inst": "23andMe" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2021.05.28.21258007", "rel_title": "Temporal stability and detection sensitivity of the dry swab-based diagnosis of SARS-CoV-2", @@ -738329,33 +739140,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.26.21257879", - "rel_title": "Out-of-Pocket Spending for COVID-19 Hospitalizations in 2020", - "rel_date": "2021-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.26.21257879", - "rel_abs": "IMPORTANCEMany insurers waived cost-sharing for COVID-19 hospitalizations during 2020. Nonetheless, patients may have been billed if their plans did not implement waivers or if waivers did not capture all hospitalization-related care, including clinician services. Assessing out-of-pocket spending for COVID-19 hospitalizations in 2020 could demonstrate the financial burden patients may face if insurers allow waivers to expire, as many chose to do during early 2021.\n\nOBJECTIVETo estimate out-of-pocket spending for COVID-19 hospitalizations in 2020\n\nDESIGNCross-sectional analysis\n\nSETTINGIQVIA PharMetrics(R) Plus for Academics Database, a national claims database\n\nPARTICIPANTSCOVID-19 hospitalizations for privately insured and Medicare Advantage patients during March-September 2020\n\nMAIN OUTCOMES/MEASURESMean total out-of-pocket spending, defined as the sum of out-of-pocket spending for facility services billed by hospitals (e.g., accommodation charges) and for professional/ancillary services billed by clinicians and ancillary providers (e.g., clinician inpatient evaluation and management, ambulance transport)\n\nRESULTSAnalyses included 4,075 hospitalizations. Of the 1,377 hospitalizations for privately insured patients and the 2,698 hospitalizations for Medicare Advantage patients, 981 (71.2%) and 1,324 (49.1%) had out-of-pocket spending for facility services, professional/ancillary services, or both. Among these hospitalizations, mean (SD) total out-of-pocket spending was $788 (1,411) and $277 (363). In contrast, 63 (4.6%) and 36 (1.3%) hospitalizations had out-of-pocket spending for facility services. Among these hospitalizations, mean total out-of-pocket spending was $3,840 (3,186) and $1,536 (1,402). Total out-of-pocket spending exceeded $4,000 for 2.5% of privately insured hospitalizations, compared with 0.2% of Medicare Advantage hospitalizations.\n\nCONCLUSIONSFew COVID-19 hospitalizations in this study had out-of-pocket spending for facility services, suggesting most were covered by insurers with cost-sharing waivers. However, many hospitalizations had out-of-pocket spending for professional/ancillary services. Overall, 7 in 10 privately insured hospitalizations and half of Medicare Advantage hospitalizations had any out-of-pocket spending. Findings suggest insurer cost-sharing waivers may not cover all hospitalization-related care. Moreover, high cost-sharing for some hospitalizations suggests out-of-pocket burden could be substantial if waivers expire, particularly for privately insured patients. Rather than rely on voluntary insurer actions to mitigate this burden, federal policymakers should consider mandating insurers to waive cost-sharing for all COVID-19 hospitalization-related care throughout the pandemic.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSHow much were patients billed for COVID-19 hospitalizations in 2020?\n\nFindingsOf 1,377 and 2,698 COVID-19 hospitalizations for privately insured and Medicare Advantage patients, 71.2% and 49.1% had cost-sharing for facility services billed by hospitals, services billed by clinicians or ancillary providers, or both. Among these hospitalizations, mean out-of-pocket spending was $788 and $277. 4.6% and 1.3% had cost-sharing for facility services; among these hospitalizations, mean out-of-pocket spending was $3,840 and $1,536.\n\nMeaningInsurer cost-sharing waivers for COVID-19 hospitalizations may not cover all hospitalization-related care. Patient out-of-pocket burden could be substantial if insurers allow waivers to expire.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kao-Ping Chua", - "author_inst": "University of Michigan Medical School" - }, - { - "author_name": "Rena M Conti", - "author_inst": "Boston University Questrom School of Business" - }, - { - "author_name": "Nora V Becker", - "author_inst": "University of Michigan Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.05.26.21257890", "rel_title": "Use of medicinal plants for COVID-19 prevention and respiratory symptom treatment during the pandemic in Cusco, Peru: A cross-sectional survey", @@ -738608,6 +739392,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.26.21257854", + "rel_title": "Corowa-kun: Impact of a COVID-19 vaccine information chatbot on vaccine hesitancy, Japan 2021", + "rel_date": "2021-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.26.21257854", + "rel_abs": "BackgroundFew studies have assessed how mobile messenger apps affect COVID-19 vaccine hesitancy. We created a COVID-19 vaccine information chatbot in a popular messenger app in Japan to answer commonly asked questions.\n\nMethodsLINE is the most popular messenger app in Japan. Corowa-kun, a free chatbot, was created in LINE on February 6, 2021. Corowa-kun provides instant, automated answers to frequently asked COVID-19 vaccine questions. In addition, a cross-sectional survey assessing COVID-19 vaccine hesitancy was conducted via Corowa-kun during April 5-12, 2021.\n\nResultsA total of 59,676 persons used Corowa-kun during February-April 2021. Of them, 10,192 users (17%) participated in the survey. Median age was 55 years (range 16-97), and most were female (74%). Intention to receive a COVID-19 vaccine increased from 59% to 80% after using Corowa-kun (p < 0.01). Overall, 20% remained hesitant: 16% (1,675) were unsure, and 4% (364) did not intend to be vaccinated. Factors associated with vaccine hesitancy were: age 16 to 34 (odds ratio [OR] = 3.7, 95% confidential interval [CI]: 3.0-4.6, compared to age [≥]65), female sex (OR = 2.4, Cl: 2.1-2.8), and history of a previous vaccine side-effect (OR = 2.5, Cl: 2.2-2.9). Being a physician (OR = 0.2, Cl: 0.1-0.4) and having received a flu vaccine the prior season (OR = 0.4, Cl: 0.3-0.4) were protective.\n\nConclusionsCorowa-kun reduced vaccine hesitancy by providing COVID-19 vaccine information in a messenger app. Mobile messenger apps could be leveraged to increase COVID-19 vaccine acceptance.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Takaaki Kobayashi", + "author_inst": "University of Iowa Hospitals and Clinics" + }, + { + "author_name": "Yuka Nishina", + "author_inst": "Juntendo University Faculty of Medicine" + }, + { + "author_name": "Hana Tomoi", + "author_inst": "MSc Public Health (Cand.), Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Ko Harada", + "author_inst": "Okayama University Graduate School of Medicine" + }, + { + "author_name": "Kyuto Tanaka", + "author_inst": "Kawasaki Municipal Hospital" + }, + { + "author_name": "Eiyu Matsumoto", + "author_inst": "University of Iowa Hospitals & Clinics" + }, + { + "author_name": "Kenta Horimukai", + "author_inst": "Jikei University Katsushika Medical Center" + }, + { + "author_name": "Jun Ishihara", + "author_inst": "Imperial College London" + }, + { + "author_name": "Shugo Sasaki", + "author_inst": "Saitama Medical University Hospital" + }, + { + "author_name": "Kanako Inaba", + "author_inst": "Kanto Central Hospital" + }, + { + "author_name": "Kyosuke Seguchi", + "author_inst": "Kameda Medical Center" + }, + { + "author_name": "Hiromizu Takahashi", + "author_inst": "Juntendo University Faculty of Medicine" + }, + { + "author_name": "Jorge Salinas", + "author_inst": "University of Iowa Hospitals & Clinics" + }, + { + "author_name": "Yuji Yamada", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.29.443900", "rel_title": "Broadening a SARS-CoV-1 neutralizing antibody for potent SARS-CoV-2 neutralization through directed evolution", @@ -739987,109 +740842,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.24.21257744", - "rel_title": "Effectiveness of BNT162b2 and mRNA-1273 COVID-19 vaccines against symptomatic SARS-CoV-2 infection and severe COVID-19 outcomes in Ontario, Canada", - "rel_date": "2021-05-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257744", - "rel_abs": "ObjectivesTo estimate the effectiveness of mRNA COVID-19 vaccines against symptomatic infection and severe outcomes.\n\nDesignWe applied a test-negative design study to linked laboratory, vaccination, and health administrative databases, and used multivariable logistic regression adjusting for demographic and clinical characteristics associated with SARS-CoV-2 and vaccine receipt to estimate vaccine effectiveness (VE) against symptomatic infection and severe outcomes.\n\nSettingOntario, Canada between 14 December 2020 and 19 April 2021.\n\nParticipantsCommunity-dwelling adults aged [≥]16 years who had COVID-19 symptoms and were tested for SARS-CoV-2.\n\nInterventionsPfizer-BioNTechs BNT162b2 or Modernas mRNA-1273 vaccine.\n\nMain outcome measuresLaboratory-confirmed SARS-CoV-2 by RT-PCR; hospitalization/death associated with SARS-CoV-2 infection.\n\nResultsAmong 324,033 symptomatic individuals, 53,270 (16.4%) were positive for SARS-CoV-2 and 21,272 (6.6%) received [≥]1 vaccine dose. Among test-positive cases, 2,479 (4.7%) had a severe outcome. VE against symptomatic infection [≥]14 days after receiving only 1 dose was 60% (95%CI, 57 to 64%), increasing from 48% (95%CI, 41 to 54%) at 14-20 days after the first dose to 71% (95%CI, 63 to 78%) at 35-41 days. VE [≥]7 days after 2 doses was 91% (95%CI, 89 to 93%). Against severe outcomes, VE [≥]14 days after 1 dose was 70% (95%CI, 60 to 77%), increasing from 62% (95%CI, 44 to 75%) at 14-20 days to 91% (95%CI, 73 to 97%) at [≥]35 days, whereas VE [≥]7 days after 2 doses was 98% (95%CI, 88 to 100%). For adults aged [≥]70 years, VE estimates were lower for intervals shortly after receiving 1 dose, but were comparable to younger adults for all intervals after 28 days. After 2 doses, we observed high VE against E484K-positive variants.\n\nConclusionsTwo doses of mRNA COVID-19 vaccines are highly effective against symptomatic infection and severe outcomes. Single-dose effectiveness is lower, particularly for older adults shortly after the first dose.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Hannah Chung", - "author_inst": "ICES, Toronto, ON" - }, - { - "author_name": "Siyi He", - "author_inst": "ICES, Toronto, ON" - }, - { - "author_name": "Sharifa Nasreen", - "author_inst": "ICES, Toronto, ON; University of Toronto" - }, - { - "author_name": "Maria Sundaram", - "author_inst": "ICES, Toronto, ON" - }, - { - "author_name": "Sarah A Buchan", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Sarah E. Wilson", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Branson Chen", - "author_inst": "ICES, Toronto, ON" - }, - { - "author_name": "Andrew Calzavara", - "author_inst": "ICES, Toronto, ON" - }, - { - "author_name": "Deshayne B Fell", - "author_inst": "University of Ottawa, ON" - }, - { - "author_name": "Peter C Austin", - "author_inst": "ICES, Toronto, ON; University of Toronto" - }, - { - "author_name": "Kumanan Wilson", - "author_inst": "University of Ottawa, ON" - }, - { - "author_name": "Kevin L Schwartz", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Kevin A. Brown", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Jonathan Gubbay", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Nicole E. Basta", - "author_inst": "McGill University, Montreal, QC" - }, - { - "author_name": "Salaheddin M. Mahmud", - "author_inst": "University of Manitoba, Winnipeg, MB" - }, - { - "author_name": "Christiaan Righolt", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Lawrence W. Svenson", - "author_inst": "University of Alberta, Edmonton, AB" - }, - { - "author_name": "Shannon E MacDonald", - "author_inst": "University of Alberta" - }, - { - "author_name": "Naveed Z. Janjua", - "author_inst": "University of British Columbia, Vancouver, BC" - }, - { - "author_name": "Mina Tadrous", - "author_inst": "ICES, Toronto, ON" - }, - { - "author_name": "Jeffrey C. Kwong", - "author_inst": "ICES, Toronto, ON" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.27.21257096", "rel_title": "Early Covid-19 Treatment With SARS-CoV-2 Neutralizing Antibody Sotrovimab", @@ -740342,6 +741094,101 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.28.446159", + "rel_title": "SARS-CoV-2 transmission via apical syncytia release from primary bronchial epithelia and infectivity restriction in children epithelia", + "rel_date": "2021-05-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.28.446159", + "rel_abs": "The beta-coronavirus SARS-CoV-2 is at the origin of a persistent worldwide pandemic. SARS-CoV-2 infections initiate in the bronchi of the upper respiratory tract and are able to disseminate to the lower respiratory tract eventually causing acute severe respiratory syndrome with a high degree of mortality in the elderly. Here we use reconstituted primary bronchial epithelia from adult and children donors to follow the infection dynamic following infection with SARS-CoV-2. We show that in bronchial epithelia derived from adult donors, infections initiate in multi-ciliated cells. Then, infection rapidly spread within 24-48h throughout the whole epithelia. Within 3-4 days, large apical syncytia form between multi-ciliated cells and basal cells, which dissipate into the apical lumen. We show that these syncytia are a significant source of the released infectious dose. In stark contrast to these findings, bronchial epithelia reconstituted from children donors are intrinsically more resistant to virus infection and show active restriction of virus spread. This restriction is paired with accelerated release of IFN compared to adult donors. Taken together our findings reveal apical syncytia formation as an underappreciated source of infectious virus for either local dissemination or release into the environment. Furthermore, we provide direct evidence that children bronchial epithelia are more resistant to infection with SARS-CoV-2 providing experimental support for epidemiological observations that SARS-CoV-2 cases fatality is linked to age.\n\nSignificance StatementBronchial epithelia are the primary target for SARS-CoV-2 infections. Our work uses reconstituted bronchial epithelia from adults and children. We show that infection of adult epithelia with SARS-CoV-2 is rapid and results in the synchronized release of large clusters of infected cells and syncytia into the apical lumen contributing to the released infectious virus dose. Infection of children derived bronchial epithelia revealed an intrinsic resistance to infection and virus spread, probably as a result of a faster onset of interferon secretion. Thus, our data provide direct evidence for the epidemiological observation that children are less susceptible to SARS-CoV-2.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Guillaume Beucher", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Marie-Lise Blondot", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Alexis Celle", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France.," + }, + { + "author_name": "Noemie Pied", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France" + }, + { + "author_name": "Patricia Recordon-Pinson", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France" + }, + { + "author_name": "Pauline Esteves", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France.," + }, + { + "author_name": "Muriel Faure", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Mathieu Metifiot", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Sabrina Lacomme", + "author_inst": "University of Bordeaux, CNRS, Institute of Neurodegenerative Diseases, IINS, UMR 5293, Bordeaux, France, University of Bordeaux, CNRS, INSERM, Bordeaux Imaging " + }, + { + "author_name": "Denis Dacheaux", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Derrick Roy Robinson", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France." + }, + { + "author_name": "Gernot Laengst", + "author_inst": "Universitaet Regensburg" + }, + { + "author_name": "Fabien Beaufils", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France.," + }, + { + "author_name": "Marie-Edith Lafon", + "author_inst": "CHU de Bordeaux, Laboratoire de Virologie, 33000 Bordeaux, France" + }, + { + "author_name": "Patrick Berger", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France." + }, + { + "author_name": "Marc Landry", + "author_inst": "University of Bordeaux, CNRS, Institute of Neurodegenerative Diseases, IINS, UMR 5293, Bordeaux, France, University of Bordeaux, CNRS, INSERM, Bordeaux Imaging " + }, + { + "author_name": "Jean-Marie Denis Malvy", + "author_inst": "Department for infectious and tropical d ideales, University Hospital center Pellegrin, Bordeaux, & Inserm 1219, University of Bordeaux, Bordeaux, France" + }, + { + "author_name": "Thomas Trian", + "author_inst": "INSERM, Centre de Recherche Cardio-thoracique de Bordeaux, U1045, CIC 1401, Bordeaux, 33000, France." + }, + { + "author_name": "Marie-Line Andreola", + "author_inst": "Univ. Bordeaux, CNRS, MFP UMR 5234, F-33000 Bordeaux, France" + }, + { + "author_name": "Harald Wodrich", + "author_inst": "Universite de Bordeaux" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.28.446020", "rel_title": "Evaluating the risk of SARS-CoV-2 transmission to bats using a decision analytical framework", @@ -741540,33 +742387,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.05.26.445185", - "rel_title": "Single-Molecule Dynamics of SARS-CoV-2 5' Cap Recognition by Human eIF4F", - "rel_date": "2021-05-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.26.445185", - "rel_abs": "Coronaviruses initiate translation through recognition of the viral RNA 5 m7GpppAm cap by translation factor eIF4F. eIF4F is a heterotrimeric protein complex with cap-binding, RNA-binding, and RNA helicase activities. Modulating eIF4F function through cellular regulation or small-molecule inhibition impacts coronavirus replication, including for SARS-CoV-2. Translation initiation involves highly coordinated dynamics of translation factors with messenger or viral RNA. However, how the eIF4F subunits coordinate on the initiation timescale to define cap-binding efficiency remains incompletely understood. Here we report that translation supported by the SARS-CoV-2 5-UTR is highly sensitive to eIF4A inhibition by rocaglamide. Through a single-molecule fluorescence approach that reports on eIF4E-cap interaction, we dissect how eIF4F subunits contribute to cap-recognition efficiency on the SARS-CoV-2 5 UTR. We find that free eIF4A enhances cap accessibility for eIF4E binding, but eIF4G alone does not change the kinetics of eIF4E-RNA interaction. Conversely, formation of the full eIF4F complex significantly alters eIF4E-cap interaction, suggesting that coordinated eIF4E and eIF4A activities establish the net eIF4F-cap recognition efficiency. Moreover, the eIF4F complex formed with phosphomimetic eIF4E(S209D) binds the viral UTR more efficiently than with wild-type eIF4E. These results highlight a dynamic interplay of eIF4F subunits and mRNA that determines cap-recognition efficiency.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Hea Jin Hong", - "author_inst": "University of California Riverside" - }, - { - "author_name": "Matthew G Guevara", - "author_inst": "University of California Riverside" - }, - { - "author_name": "Eric Lin", - "author_inst": "University of California Riverside" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.05.25.21257780", "rel_title": "Vaccine-Hesitant Parents' Considerations Regarding Covid-19 Vaccination of Adolescents", @@ -741851,6 +742671,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.05.25.21257811", + "rel_title": "Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens", + "rel_date": "2021-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257811", + "rel_abs": "Viral pathogen can rapidly evolve, adapt to novel hosts and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire class of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Zachary R Stromberg", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "James Theiler", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Brian T Foley", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Ad\u00e1n Myers y Guti\u00e9rrez", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Attelia Hollander", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Samantha J Courtney", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Alina Deshpande", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Ebany J Martinez-Finley", + "author_inst": "Presbyterian Healthcare Services" + }, + { + "author_name": "Jason Mitchell", + "author_inst": "Presbyterian Healthcare Services" + }, + { + "author_name": "Harshini Mukundan", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Karina Yusim", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Jessica Z Kubicek-Sutherland", + "author_inst": "Los Alamos National Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.25.21257828", "rel_title": "Correlation of the commercial anti-SARS-CoV-2 receptor binding domain antibody test with the chemiluminescent reduction neutralizing test and possible detection of antibodies to emerging variants", @@ -743738,109 +744621,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2021.05.26.445769", - "rel_title": "Subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells in cynomolgus macaques", - "rel_date": "2021-05-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.26.445769", - "rel_abs": "SARS-CoV-2 infection presents clinical manifestations ranging from asymptomatic to fatal respiratory failure. Despite the induction of functional SARS-CoV-2-specific CD8+ T-cell responses in convalescent individuals, the role of virus-specific CD8+ T-cell responses in the control of SARS-CoV-2 replication remains unknown. In the present study, we show that subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells in cynomolgus macaques. Eight macaques were intranasally inoculated with 105 or 106 TCID50 of SARS-CoV-2, and three of the eight macaques were treated with a monoclonal anti-CD8 antibody on days 5 and 7 post-infection. In these three macaques, CD8+ T cells were undetectable on day 7 and thereafter, while virus-specific CD8+ T-cell responses were induced in the remaining five untreated animals. Viral RNA was detected in nasopharyngeal swabs for 10-17 days post-infection in all macaques, and the kinetics of viral RNA levels in pharyngeal swabs and plasma neutralizing antibody titers were comparable between the anti-CD8 antibody treated and untreated animals. SARS-CoV-2 RNA was detected in the pharyngeal mucosa and/or retropharyngeal lymph node obtained at necropsy on day 21 in two of the untreated group but undetectable in all macaques treated with anti-CD8 antibody. CD8+ T-cell responses may contribute to viral control in SARS-CoV-2 infection, but our results indicate possible containment of subacute viral replication in the absence of CD8+ T cells, implying that CD8+ T-cell dysfunction may not solely lead to viral control failure.\n\nAuthor SummarySARS-CoV-2 infection presents a wide spectrum of clinical manifestations ranging from asymptomatic to fatal respiratory failure. The determinants for failure in viral control and/or fatal disease progression have not been elucidated fully. Both acquired immune effectors, antibodies and CD8+ T cells, are considered to contribute to viral control. However, it remains unknown whether a deficiency in either of these two arms is directly linked to failure in the control of SARS-CoV-2 replication. In the present study, to know the requirement of CD8+ T cells for viral control after the establishment of infection, we examined the effect of CD8+ cell depletion by monoclonal anti-CD8 antibody administration in the subacute phase on SARS-CoV-2 replication in cynomolgus macaques. Unexpectedly, our analysis revealed no significant impact of CD8+ cell depletion on viral replication, indicating that subacute SARS-CoV-2 replication can be controlled in the absence of CD8+ T cells. CD8+ T-cell responses may contribute to viral control in SARS-CoV-2 infection, but this study suggests that CD8+ T-cell dysfunction may not solely lead to viral control failure or fatal disease progression.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Takushi Nomura", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Hiroyuki Yamamoto", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Masako Nishizawa", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Trang Hau", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Shigeyoshi Harada", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Hiroshi Ishii", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Sayuri Seki", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Midori Nakamura-Hoshi", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Midori Okazaki", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Sachie Daigen", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Ai Kawana-Tachikawa", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Noriyo Nagata", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Naoko Iwata-Yoshikawa", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Nozomi Shiwa", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Shun Iida", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Harutaka Katano", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Tadaki Suzuki", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Eun-Sil Park", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Ken Maeda", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Yuriko Suzaki", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Yasushi Ami", - "author_inst": "National Institute of Infectious Diseases: Kokuritsu Kansensho Kenkyujo" - }, - { - "author_name": "Tetsuro Matano", - "author_inst": "National Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.21.21257595", "rel_title": "Ivermectin for the treatment of COVID-19: A systematic review and meta-analysis of randomized controlled trials", @@ -744025,6 +744805,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.24.21257465", + "rel_title": "Psychological factors underpinning vaccine willingness in Israel, Japan and Hungary", + "rel_date": "2021-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257465", + "rel_abs": "The rapid international spread of the SARS-CoV-2 virus 19 led to unprecedented attempts to develop and administer an effective vaccine. However, there is considerable vaccine hesitancy in some countries. We investigated willingness to vaccinate in three nations with historically different levels of vaccine willingness and attitudes: Israel, Japan and Hungary. Employing an ecological-systems approach we analysed associations between demographic factors and health status, individual cognitions, normative pressures, trust in government, belief in COVID-19 myths and willingness to be vaccinated, using data from three nationally representative samples (Israel, N=1011 (Jan 2021); Japan, N= 997 (Feb 2021); Hungary, N=1131 (Apr 2021)). In Israel 74% indicated a willingness to vaccinate, but only 51% in Japan and 31% in Hungary. Multigroup regression analyses indicated greater vaccine willingness amongst those who perceived benefits to vaccination, anticipated regret if not vaccinated and trusted the government. Multi-group latent class analysis of ten COVID-19 (mis)beliefs identified three classes of myths, with concerns about the alteration of DNA (Israel), allergies (Hungary) and catching COVID-19 from the vaccine (Japan) specific to vaccine willingness for each culture. Intervention campaigns should focus on increasing trust and addressing culturally specific myths while emphasising the individual and social group benefits of vaccination.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Robin Goodwin", + "author_inst": "University of Warwick" + }, + { + "author_name": "Menachem Ben-Ezra", + "author_inst": "Ariel University" + }, + { + "author_name": "Masahito Takahashi", + "author_inst": "Yamaguchi University Japan" + }, + { + "author_name": "Lan Anh Nguyen Luu", + "author_inst": "Eotvos Lorand University Budapest" + }, + { + "author_name": "Krisztina Borsfay", + "author_inst": "Eotvos Lorand University Budapest" + }, + { + "author_name": "Monika Kovacs", + "author_inst": "Eotvos Lorand University Budapest" + }, + { + "author_name": "Wai Kai Hou", + "author_inst": "Education University Hong Kong" + }, + { + "author_name": "Yaira Hamama-Raz", + "author_inst": "Ariel University" + }, + { + "author_name": "Yafit Levin", + "author_inst": "University of Zurich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.21.21257612", "rel_title": "COVID-19 vaccination hesitancy model: The impact of vaccine education on controlling the outbreak in the United States", @@ -745232,213 +746063,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.25.21257505", - "rel_title": "Plitidepsin has a positive therapeutic index in adult patients with COVID-19 requiring hospitalization.", - "rel_date": "2021-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257505", - "rel_abs": "Plitidepsin is a marine-derived cyclic-peptide that inhibits SARS-CoV-2 replication at low nanomolar concentrations by the targeting of host protein eEF1A (eukaryotic translation-elongation-factor-1A). We evaluated a model of intervention with plitidepsin in hospitalized COVID-19 adult patients where three doses were assessed (1.5, 2 and 2.5 mg/day for 3 days, as a 90-minute intravenous infusion) in 45 patients (15 per dose-cohort). Treatment was well tolerated, with only two Grade 3 treatment-related adverse events observed (hypersensitivity and diarrhea). The discharge rates by Days 8 and 15 were 56.8% and 81.8%, respectively, with data sustaining dose-effect. A mean 4.2 log10 viral load reduction was attained by Day 15. Improvement in inflammation markers was also noted in a seemingly dose-dependent manner. These results suggest that plitidepsin impacts the outcome of patients with COVID-19.\n\nOne-Sentence SummaryPlitidepsin, an inhibitor of SARS-Cov-2 in vitro, is safe and positively influences the outcome of patients hospitalized with COVID-19.", - "rel_num_authors": 48, - "rel_authors": [ - { - "author_name": "Jose F. Varona", - "author_inst": "Departamento de Medicina Interna, Hospital Universitario HM Monteprincipe, HM Hospitales, Madrid, Spain. Facultad de Medicina, Universidad San Pablo-CEU, Madrid" - }, - { - "author_name": "Pedro Landete", - "author_inst": "Hospital Universitario de La Princesa. Madrid, Spain. Universidad Autonoma de Madrid, Madrid, Spain." - }, - { - "author_name": "Jose A Lopez-Martin", - "author_inst": "PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain." - }, - { - "author_name": "Vicente Estrada", - "author_inst": "Hospital Clinico San Carlos, Madrid, Spain. Universidad Complutense de Madrid, Madrid, Spain." - }, - { - "author_name": "Roger Paredes", - "author_inst": "IrsiCaixa AIDS Research Institute" - }, - { - "author_name": "Pablo Guisado-Vasco", - "author_inst": "Internal Medicine Department, Hospital Universitario Quironsalud, Madrid, Spain. Universidad Europea, Madrid, Spain." - }, - { - "author_name": "Lucia Fernandez de Orueta", - "author_inst": "Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain. European University of Madrid, Madrid, Spain." - }, - { - "author_name": "Miguel Torralba", - "author_inst": "Internal Medicine, Guadalajara University Hospital, Guadalajara, Spain. University of Alcala, Madrid, Spain." - }, - { - "author_name": "Jesus Fortun", - "author_inst": "Hospital Universitario Ramon y Cajal, Madrid, Spain." - }, - { - "author_name": "Roberto Vates", - "author_inst": "Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain." - }, - { - "author_name": "Jose Barberan", - "author_inst": "Hospital Universitario HM Monteprincipe, Madrid, Spain. Facultad de Medicina San Pablo CEU, Madrid, Spain." - }, - { - "author_name": "Bonaventura Clotet", - "author_inst": "Head of Infectious Diseases Department, Director of the Research Lab, IrsiCaixa, Barcelone, Spain. Professor of the UAB and the UVIC-UCC, Barcelone, Spain." - }, - { - "author_name": "Julio Ancochea", - "author_inst": "Hospital Universitario La Princesa, Madrid, Spain. Centro de Investigacion en Red de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III (ISCIII" - }, - { - "author_name": "Daniel Carnevali", - "author_inst": "Hospital Universitario Quironsalud, Madrid, Spain Universidad Europea, Madrid, Spain." - }, - { - "author_name": "Noemi Cabello", - "author_inst": "Infectious Diseases Department, San Carlos University Hospital. Madrid Spain." - }, - { - "author_name": "Lourdes Porras", - "author_inst": "Internal Medicine, Hospital General de Ciudad Real, Ciudad Real, Spain." - }, - { - "author_name": "Paloma Gijon", - "author_inst": "Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio Mara\u00f1on, Instituto de Investigacion Sanitaria Gregorio Mara\u00f1on" - }, - { - "author_name": "Alfonso Monereo", - "author_inst": "Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain" - }, - { - "author_name": "Daniel Abad", - "author_inst": "Internal Medicine Department, Hospital Universitario de Getafe, Madrid, Spain. European University of Madrid, Madrid, Spain." - }, - { - "author_name": "Sonia Zu\u00f1iga", - "author_inst": "Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNBCSIC), Madrid, Spain." - }, - { - "author_name": "Isabel Sola", - "author_inst": "Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNBCSIC), Madrid, Spain." - }, - { - "author_name": "Jordi Rodon", - "author_inst": "IRTA, Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, Bellaterra, Spain" - }, - { - "author_name": "Nuria Izquierdo-Useros", - "author_inst": "IrsiCaixa AIDS Research Institute, 08916, Badalona, Spain. Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, 08916, Badalona, Spain." - }, - { - "author_name": "Salvador Fudio", - "author_inst": "PharmaMar - Clinical Pharmacology Unit. Colmenar Viejo, Madrid, Spain" - }, - { - "author_name": "Maria Jose Pontes", - "author_inst": "PharmaMar - Medical Affairs Unit. Colmenar Viejo. Madrid, Spain." - }, - { - "author_name": "Beatriz de Rivas", - "author_inst": "PharmaMar - Medical Affairs Unit. Colmenar Viejo, Madrid, Spain." - }, - { - "author_name": "Patricia Giron de Velasco", - "author_inst": "PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain." - }, - { - "author_name": "Belen Sopesen", - "author_inst": "PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain. Sylentis, S.A.U., Tres Cantos, Madrid, Spain. Biocross, S.L., Valladolid, Spain." - }, - { - "author_name": "Antonio Nieto", - "author_inst": "PharmaMar - Statistics Unit. Colmenar Viejo, Madrid, Spain." - }, - { - "author_name": "Javier Gomez", - "author_inst": "PharmaMar - Statistics Unit. Colmenar Viejo, Madrid, Spain." - }, - { - "author_name": "Pablo Aviles", - "author_inst": "PharmaMar - Preclinical Unit. Colmenar Viejo, Madrid, Spain" - }, - { - "author_name": "Rubin Lubomirov", - "author_inst": "PharmaMar - Clinical Pharmacology Unit. Colmenar Viejo, Madrid, Spain" - }, - { - "author_name": "Kris M White", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at " - }, - { - "author_name": "Romel Rosales", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at " - }, - { - "author_name": "Soner Yildiz", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at " - }, - { - "author_name": "Ann-Kathrin Reuschl", - "author_inst": "Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom." - }, - { - "author_name": "Lucy G. Thorne", - "author_inst": "Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom." - }, - { - "author_name": "Clare Jolly", - "author_inst": "Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom." - }, - { - "author_name": "Greg J. Towers", - "author_inst": "Division of Infection and Immunity, University College Londo, London, WC1E 6BT, United Kigdom" - }, - { - "author_name": "Lorena Zuliani-Alvarez", - "author_inst": "Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G" - }, - { - "author_name": "Mehdi Bouhaddou", - "author_inst": "Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G" - }, - { - "author_name": "Kirsten Obernier", - "author_inst": "Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. J. David Gladstone Institutes, San Francisco, CA 94158, USA. QBI, Coronavirus Research G" - }, - { - "author_name": "Luis Enjuanes", - "author_inst": "Department of Molecular and Cell Biology, Centro Nacional de Biotecnologia (CNB-CSIC), Madrid, Spain." - }, - { - "author_name": "Jose M Fernandez-Sousa", - "author_inst": "PharmaMar, S.A., Colmenar Viejo, Madrid, Spain." - }, - { - "author_name": "- Plitidepsin COVID Study Group", - "author_inst": "" - }, - { - "author_name": "Nevan J Krogan", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Quantitative Biosciences Institute (QBI), San Francisco, CA 94158, USA. " - }, - { - "author_name": "Jose M. Jimeno", - "author_inst": "PharmaMar. Virology & Inflammation Dept. Colmenar Viejo, Madrid, Spain." - }, - { - "author_name": "Adolfo Garcia-Sastre", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. Global Health Emerging Pathogens Institute, Icahn School of Medicine at " - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.25.445557", "rel_title": "An Issue of Concern: Unique Truncated ORF8 Protein Variants of SARS-CoV-2", @@ -745755,6 +746379,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.05.25.445601", + "rel_title": "Genomic Surveillance of COVID-19 Variants with Language Models and Machine Learning", + "rel_date": "2021-05-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.25.445601", + "rel_abs": "The global efforts to control COVID-19 are threatened by the rapid emergence of novel SARS-CoV-2 variants that may display undesirable characteristics such as immune escape, increased transmissibility or pathogenicity. Early prediction for emergence of new strains with these features is critical for pandemic preparedness. We present Strainflow, a supervised and causally predictive model using unsupervised latent space features of SARS-CoV-2 genome sequences. Strainflow was trained and validated on 0.9 million sequences for the period December, 2019 to June, 2021 and the frozen model was prospectively validated from July, 2021 to December, 2021. Strainflow captured the rise in cases two months ahead of the Delta and Omicron surges in most countries including the prediction of a surge in India as early as beginning of November, 2021. Entropy analysis of Strainflow unsupervised embeddings clearly reveals the explore-exploit cycles in genomic feature-space, thus adding interpretability to the deep learning based model. We also conducted codon-level analysis of our model for interpretability and biological validity of our unsupervised features. Strainflow application is openly available as an interactive web-application for prospective genomic surveillance of COVID-19 across the globe.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sargun Nagpal", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Ridam Pal", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Ashima", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Ananya Tyagi", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Sadhana Tripathi", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Aditya Nagori", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Saad Ahmad", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Hara Prasad Mishra", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Rintu Kutum", + "author_inst": "Indraprastha Institute of Information Technology Delhi, India" + }, + { + "author_name": "Tavpritesh Sethi", + "author_inst": "Indraprastha Institute of Information Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.05.24.445517", "rel_title": "Evolutionary Inference Predicts Novel ACE2 Protein Interactions Relevant to COVID-19 Pathologies", @@ -747302,41 +747981,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.21.21257626", - "rel_title": "COVID-19 Associated Pulmonary Aspergillosis: Systematic Review and Patient-Level Meta-Analysis", - "rel_date": "2021-05-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.21.21257626", - "rel_abs": "RationalePulmonary aspergillosis may complicate COVID-19 and contribute to excess mortality in intensive care unit (ICU) patients. The incidence is unclear because of discordant definitions across studies.\n\nObjectiveWe sought to review the incidence, diagnosis, treatment, and outcomes of COVID-19-associated pulmonary aspergillosis (CAPA), and compare research definitions.\n\nMethodsWe systematically reviewed the literature for ICU cohort studies and case series including [≥] patients with CAPA. We calculated pooled incidence. Patients with sufficient clinical details were reclassified according to 4 standardized definitions (Verweij, White, Koehler, and Bassetti).\n\nMeasurementsCorrelations between definitions were assessed with Spearmans rank test. Associations between antifungals and outcome were assessed with Fishers Exact test.\n\nMain Results38 studies (35 cohort studies and 3 case series) were included. Among 3,297 COVID-19 patients in ICU cohort studies, 313 were diagnosed with CAPA (pooled incidence 9.5%). 197 patients had patient-level data allowing reclassification. Definitions had limited correlation with one another ({rho}=0.330 to 0.621, p<0.001). 38.6% of patients reported to have CAPA did not fulfil any research definitions. Patients were diagnosed after a median of 9 days (interquartile range 5-14) in ICUs. Tracheobronchitis occured in 5.3% of patients examined with bronchoscopy. The mortality rate (50.0%) was high, irrespective of antifungal use (p=0.28); this remained true even when the analysis was restricted to patients meeting standardized definitions for CAPA.\n\nConclusionsThe reported incidence of CAPA is exaggerated by use of non-standard definitions. Further research should focus on identifying patients likely to benefit from antifungals.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ruwandi M. Kariyawasam", - "author_inst": "University of Alberta" - }, - { - "author_name": "Tanis C. Dingle", - "author_inst": "University of Alberta" - }, - { - "author_name": "Brittany E. Kula", - "author_inst": "University of Alberta" - }, - { - "author_name": "Wendy I. Sligl", - "author_inst": "University of Alberta" - }, - { - "author_name": "Ilan S. Schwartz", - "author_inst": "University of Alberta" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.05.20.21257539", "rel_title": "COVID-19 Fatality Rate Classification using Synthetic Minority Oversampling Technique (SMOTE) for Imbalance Class", @@ -747501,6 +748145,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.20.21257542", + "rel_title": "The maladaptive vascular response in COVID-19 acute respiratory distress syndrome and recovery", + "rel_date": "2021-05-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257542", + "rel_abs": "Vascular injury is a menacing element of acute respiratory distress syndrome (ARDS) pathogenesis. To better understand the role of vascular injury in COVID-19 ARDS, we used lung autopsy immunohistochemistry and blood proteomics from COVID-19 subjects at distinct timepoints in disease pathogenesis, including a hospitalized cohort at risk of ARDS development (\"at risk\", N=59), an intensive care unit cohort with ARDS (\"ARDS\", N=31), and a cohort recovering from ARDS (\"recovery\", N=12). COVID-19 ARDS lung autopsy tissue revealed an association between vascular injury and platelet-rich microthrombi. This link guided the derivation of a protein signature in the at risk cohort characterized by lower expression of vascular proteins in subjects who died, an early signal of vascular limitation termed the maladaptive vascular response. These findings were replicated in COVID-19 ARDS subjects, as well as when bacterial and influenza ARDS patients (N=29) were considered, hinting at a common final pathway of vascular injury that is more disease (ARDS) then cause (COVID-19) specific, and may be related to vascular cell death. Among recovery subjects, our vascular signature identified patients with good functional recovery one year later. This vascular injury signature could be used to identify ARDS patients most likely to benefit from vascular targeted therapies.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "David R Price", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Elisa Benedetti", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Katherine Hoffman", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Luis Gomez-Escobar", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Sergio Alvarez-Mulett", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Allyson Capili", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Hina Sarwath", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Christopher N. Parkhurst", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Elyse LaFond", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Karissa Weidman", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Arjun Ravishankar", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jin Gyu Cheong", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Richa Batra", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Mustafa Buyukozkan", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Kelsey Chetnik", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Imaani Easthausen", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Edward J. Schenck", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Alexandra C. Racanelli", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Hasina Outtz Reed", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jeffrey C. Laurence", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Steven Zvi Josefowicz", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Lindsay Lief", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Mary E. Choi", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Shahin Rafii", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Frank Schmidt", + "author_inst": "Weill Cornell Medicine-Qatar" + }, + { + "author_name": "Alain C. Borczuk", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jan Krumsiek", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Augustine M. K. Choi", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.05.20.21256954", "rel_title": "Efficacy and safety of novel probiotic formulation in adult Covid19 outpatients: a randomized, placebo-controlled clinical trial", @@ -749128,113 +749899,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2021.05.19.21257334", - "rel_title": "Reactogenicity of homologous and heterologous prime-boost immunization with BNT162b2 and ChAdOx1-nCoV19: a prospective cohort study", - "rel_date": "2021-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257334", - "rel_abs": "Heterologous prime-boost vaccination is of increasing interest for COVID-19 vaccines. Evidence of rare thrombotic events associated with ChAdOx1-nCoV19 (Vaxzevria, ChAdOx) has lead several European countries to recommend a heterologous booster with mRNA vaccines for certain age groups (e.g. persons <60years in Germany), who have already received one dose of ChAdOx, although data on reactogenicity and safety of this vaccination regimen are still missing. Here we report reactogenicity data of homologous BNT162b2 (Comirnaty, BNT) or heterologous ChAdOx/BNT prime-boost immunisations in a prospective observational cohort study of 326 healthcare workers.\n\nReactogenicity of heterologous ChAdOx/BNT booster vaccination was largely comparable to homologous BNT/BNT vaccination and overall well-tolerated. No major differences were observed in the frequency or severity of local reactions after either of the vaccinations. In contrast, notable differences between the regimens were observed for systemic reactions, which were most frequent after prime immunisation with ChAdOx (86%, 95CI: 79-91), and less frequent after homologous BNT/BNT (65%, 95CI: 56-72), or heterologous ChAdOx/BNT boosters (48%, 95CI: 36-59).\n\nThis interim analysis supports the safety of currently recommended heterologous ChAdOx/BNT prime-boost immunisations with 12-week intervals.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "David Hillus", - "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Unive" - }, - { - "author_name": "Tatjana Schwarz", - "author_inst": "Institute of Virology, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Universit\u00e4 t zu Berlin, and Berlin Institu" - }, - { - "author_name": "Pinkus Tober-Lau", - "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Unive" - }, - { - "author_name": "Hana Hastor", - "author_inst": "Clinical Study Center (CSC), Berlin Institute of Health, and Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, Corporate Member of Freie Universit\u00e4 t Berlin, Humboldt-Univ" - }, - { - "author_name": "Charlotte Thibeault", - "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Unive" - }, - { - "author_name": "Stefanie Kasper", - "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Unive" - }, - { - "author_name": "Elisa T Helbig", - "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Unive" - }, - { - "author_name": "Lena J Lippert", - "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Unive" - }, - { - "author_name": "Patricia Tscheak", - "author_inst": "Institute of Virology, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Universit\u00e4 t zu Berlin, and Berlin Institu" - }, - { - "author_name": "Marie Luisa Schmidt", - "author_inst": "Institute of Virology, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Universit\u00e4 t zu Berlin, and Berlin Institu" - }, - { - "author_name": "Johanna Riege", - "author_inst": "Institute of Virology, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Universit\u00e4 t zu Berlin, and Berlin Institu" - }, - { - "author_name": "Andr Solarek", - "author_inst": "Medical Directorate, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Universit\u00e4 t zu Berlin, and Berlin Institute" - }, - { - "author_name": "Christof von Kalle", - "author_inst": "Clinical Study Center (CSC), Berlin Institute of Health, and Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, Corporate Member of Freie Universit\u00e4 t Berlin, Humboldt-Univ" - }, - { - "author_name": "Chantip Dang-Heine", - "author_inst": "Clinical Study Center (CSC), Berlin Institute of Health, and Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, Corporate Member of Freie Universit\u00e4 t Berlin, Humboldt-Univ" - }, - { - "author_name": "Piotr Kopankiewicz", - "author_inst": "Center for Occupational Medicine, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Universit\u00e4 t zu Berlin, and Ber" - }, - { - "author_name": "Norbert Suttorp", - "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Unive" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Institute of Virology, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Universit\u00e4 t zu Berlin, and Berlin Institu" - }, - { - "author_name": "Harald Bias", - "author_inst": "Center for Occupational Medicine, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Universit\u00e4 t zu Berlin, and Ber" - }, - { - "author_name": "Joachim Seybold", - "author_inst": "Medical Directorate, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Universit\u00e4 t zu Berlin, and Berlin Institute" - }, - { - "author_name": "- COVIM/EICOV Study Group", - "author_inst": "" - }, - { - "author_name": "Florian Kurth", - "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Unive" - }, - { - "author_name": "Victor M Corman", - "author_inst": "Institute of Virology, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Universit\u00e4 t zu Berlin, and Berlin Institu" - }, - { - "author_name": "Leif Erik Sander", - "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 - Universit\u00e4 tsmedizin Berlin, corporate member of Freie Universit\u00e4 t Berlin, Humboldt-Unive" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.19.21257056", "rel_title": "Assessing the Impact of Human Mobility to Predict Regional Excess Death in Ecuador", @@ -749535,6 +750199,201 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.20.21256969", + "rel_title": "Implementation of a qPCR assay coupled with genomic surveillance for real-time monitoring of SARS-CoV-2 variants of concern.", + "rel_date": "2021-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21256969", + "rel_abs": "We developed a genomic surveillance program for real-time monitoring of SARS-CoV-2 variants of concern in Uruguay. Here, we present the first results, including the proposed qPCR-VOC method, the general workflow and the report of the introduction and community transmission of the VOC P.1 in Uruguay in multiple independent events.", + "rel_num_authors": 45, + "rel_authors": [ + { + "author_name": "Natalia Rego", + "author_inst": "Unidad de Bioinformatica, Institut Pasteur de Montevideo." + }, + { + "author_name": "Alicia Costabile", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur Montevideo; Centro de Innovacion en Vigilancia Epidemiologica, Institut Pasteur Montevideo" + }, + { + "author_name": "Mercedes Paz", + "author_inst": "Centro de Innovacion en Vigilancia Epidemiologica, Institut Pasteur Montevideo" + }, + { + "author_name": "Cecilia Salazar", + "author_inst": "Laboratorio de Genomica Microbiana, Institut Pasteur Montevideo" + }, + { + "author_name": "Paula Perbolianachis", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur Montevideo; Laboratorio de Virologia Molecular, Facultad de Ciencias, UdelaR" + }, + { + "author_name": "Lucia Spangemberg", + "author_inst": "Unidad de Bioinformatica, Institut Pasteur de Montevideo" + }, + { + "author_name": "Ignacio Ferres", + "author_inst": "Laboratorio de Genomica Microbiana, Institut Pasteur Montevideo" + }, + { + "author_name": "Rodrigo Arce", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur Montevideo; Laboratorio de Virologia Molecular, Facultad de Ciencias, UdelaR; Laboratorio Biol" + }, + { + "author_name": "Alvaro Fajardo", + "author_inst": "Laboratorio de Evolucion Experimental de Virus, Institut Pasteur Montevideo; Laboratorio de Virologia Molecular, Facultad de Ciencias, UdelaR" + }, + { + "author_name": "Mailen Arleo", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Tania Possi", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Ines Bellini", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Lucia Bilbao", + "author_inst": "Departamento de Genomica, Instituto de Investigaciones Biologicas Clemente Estable. Laboratorio de Biologia Molecular, Sanatorio Americano" + }, + { + "author_name": "Natalia Reyes", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Maria Noel Bentancor", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Andres Lizosain", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Maria Jose Benitez", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Matias Castells", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Matias Victoria", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Leticia Maya", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Viviana Bortagaray", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Ana Moller", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Gonzalo Bello", + "author_inst": "Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz Fiocruz" + }, + { + "author_name": "Ighor Arantes", + "author_inst": "Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz Fiocruz" + }, + { + "author_name": "Mariana Brandes", + "author_inst": "Unidad de Bioinformatica, Institut Pasteur de Montevideo" + }, + { + "author_name": "Pablo Smircich", + "author_inst": "Departamento de Genomica, Instituto de Investigaciones Biologicas Clemente Estable. Laboratorio de Interacciones Moleculares, Facultad de Ciencias, UdelaR." + }, + { + "author_name": "Odhille Chappos", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Melissa Duquia", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Belen Gonzalez", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Luciana Griffero", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Mauricio Mendez", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Maria Pia Techera", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Juan Zanetti", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Bernardina Rivera", + "author_inst": "Laboratorio de Diagnostico Molecular, Institut Pasteur de Montevideo" + }, + { + "author_name": "Matias Maidana", + "author_inst": "Laboratorio de Diagnostico Molecular, Institut Pasteur de Montevideo" + }, + { + "author_name": "Martina Alonso", + "author_inst": "Laboratorio de Diagnostico Molecular, Institut Pasteur de Montevideo" + }, + { + "author_name": "Cecilia Alonso", + "author_inst": "CENUR Este-Sede Rocha-UdelaR" + }, + { + "author_name": "Julio Medina", + "author_inst": "Ministerio de Salud Publica (Uruguay) / Catedra de Enfermedades Infecciosas, Fac. de Medicina, UdelaR." + }, + { + "author_name": "Henry Albornoz", + "author_inst": "Ministerio de Salud Publica (Uruguay)" + }, + { + "author_name": "Rodney Colina", + "author_inst": "Laboratorio de Virologia Molecular. Departamento de Ciencias Biologicas. Centro Universitario Regional del Litoral Norte. UdelaR" + }, + { + "author_name": "Veronica Noya", + "author_inst": "Laboratorio Biologia Molecular Sanatorio Americano" + }, + { + "author_name": "Gregorio Iraola", + "author_inst": "Institut Pasteur de Montevideo" + }, + { + "author_name": "Tamara Fernandez-Calero", + "author_inst": "Unidad de Bioinformatica, Institut Pasteur de Montevideo" + }, + { + "author_name": "Gonzalo Andres Moratorio", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Pilar Moreno", + "author_inst": "Universidad de la Republica. Insitut Pasteur de Montevideo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.19.21257439", "rel_title": "Rapid And high throughput RT-qPCR assay for identification and differentiation between SARS-CoV-2 variants B.1.1.7 and B.1.351", @@ -750950,69 +751809,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.21.445091", - "rel_title": "Identification of a novel lineage bat SARS-related coronaviruses that use bat ACE2 receptor", - "rel_date": "2021-05-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.21.445091", - "rel_abs": "Severe respiratory disease coronavirus-2 (SARS-CoV-2) causes the most devastating disease, COVID-19, of the recent century. One of the unsolved scientific questions around SARS-CoV-2 is the animal origin of this virus. Bats and pangolins are recognized as the most probable reservoir hosts that harbor the highly similar SARS-CoV-2 related viruses (SARSr-CoV-2). Here, we report the identification of a novel lineage of SARSr-CoVs, including RaTG15 and seven other viruses, from bats at the same location where we found RaTG13 in 2015. Although RaTG15 and the related viruses share 97.2% amino acid sequence identities to SARS-CoV-2 in the conserved ORF1b region, but only show less than 77.6% to all known SARSr-CoVs in genome level, thus forms a distinct lineage in the Sarbecovirus phylogenetic tree. We then found that RaTG15 receptor binding domain (RBD) can bind to and use Rhinolophus affinis bat ACE2 (RaACE2) but not human ACE2 as entry receptor, although which contains a short deletion and has different key residues responsible for ACE2 binding. In addition, we show that none of the known viruses in bat SARSr-CoV-2 lineage or the novel lineage discovered so far use human ACE2 efficiently compared to SARSr-CoV-2 from pangolin or some of the SARSr-CoV-1 lineage viruses. Collectively, we suggest more systematic and longitudinal work in bats to prevent future spillover events caused by SARSr-CoVs or to better understand the origin of SARS-CoV-2.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Hua Guo", - "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences." - }, - { - "author_name": "Ben Hu", - "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences" - }, - { - "author_name": "Hao-rui Si", - "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences" - }, - { - "author_name": "Yan Zhu", - "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences" - }, - { - "author_name": "Wei Zhang", - "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences" - }, - { - "author_name": "Bei Li", - "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences" - }, - { - "author_name": "Ang Li", - "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences" - }, - { - "author_name": "Rong Geng", - "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences" - }, - { - "author_name": "Hao-Feng Lin", - "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences" - }, - { - "author_name": "Xing-Lou Yang", - "author_inst": "CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences" - }, - { - "author_name": "Peng Zhou", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" - }, - { - "author_name": "Zhengli Shi", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.20.445077", "rel_title": "6',6'-Difluoro-aristeromycin is a potent inhibitor of MERS-coronavirus replication", @@ -751301,6 +752097,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.05.21.445152", + "rel_title": "The Role of ATP in the RNA Translocation Mechanism of SARS-CoV-2 NSP13 Helicase", + "rel_date": "2021-05-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.21.445152", + "rel_abs": "The COVID-19 pandemic has demonstrated the need to develop potent and transferable therapeutics to treat coronavirus infections. Numerous antiviral targets are being investigated, but non-structural protein 13 (nsp13) stands out as a highly conserved and yet under studied target. Nsp13 is a superfamily 1 (SF1) helicase that translocates along and unwinds viral RNA in an ATP dependent manner. Currently, there are no available structures of nsp13 from SARS-CoV-1 or SARS-CoV-2 with either ATP or RNA bound presenting a significant hurdle to the rational design of therapeutics. To address this knowledge gap, we have built models of SARS-CoV-2 nsp13 in Apo, ATP, ssRNA and ssRNA+ATP substrate states. Using 30 s of Gaussian accelerated molecular dynamics simulation (at least 6 s per substrate state), these models were confirmed to maintain substrate binding poses that are similar to other SF1 helicases. A gaussian mixture model and linear discriminant analysis structural clustering protocol was used to identify key aspects of the ATP-dependent RNA translocation mechanism. Namely, four RNA-nsp13 structures are identified that exhibit ATP-dependent populations and support the inch-worm mechanism for translocation. These four states are characterized by different RNA-binding poses for motifs Ia, IV and V and suggest a powerstroke-like motion of domain 2A relative to domain 1A. This structural and mechanistic insight of nsp13 RNA translocation presents novel targets for the further development of antivirals.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ryan Weber", + "author_inst": "Colorado State University" + }, + { + "author_name": "Martin McCullagh", + "author_inst": "Oklahoma State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.05.21.445090", "rel_title": "Water-triggered, irreversible conformational change of SARS-CoV-2 main protease on passing from the solid state to aqueous solution", @@ -752868,81 +753687,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.19.444875", - "rel_title": "4'-Fluorouridine is a broad-spectrum orally efficacious antiviral blocking respiratory syncytial virus and SARS-CoV-2 replication", - "rel_date": "2021-05-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.19.444875", - "rel_abs": "The COVID-19 pandemic has underscored the critical need for broad-spectrum therapeutics against respiratory viruses. Respiratory syncytial virus (RSV) is a major threat to pediatric patients and the elderly. We describe 4-fluorouridine (4-FlU, EIDD-2749), a ribonucleoside analog that inhibits RSV, related RNA viruses, and SARS-CoV-2 with high selectivity index in cells and well-differentiated human airway epithelia. Polymerase inhibition in in vitro RdRP assays established for RSV and SARS-CoV-2 revealed transcriptional pauses at positions i or i+3/4 post-incorporation. Once-daily oral treatment was highly efficacious at 5 mg/kg in RSV-infected mice or 20 mg/kg in ferrets infected with SARS-CoV-2 WA1/2020 or variant-of-concern (VoC) isolate CA/2020, initiated 24 or 12 hours after infection, respectively. These properties define 4-FlU as a broad-spectrum candidate for the treatment of RSV, SARS-CoV-2 and related RNA virus infections.\n\nOne-Sentence Summary4-Fluorouridine is an orally available ribonucleoside analog that efficiently treats RSV and SARS-CoV-2 infections in vivo.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Julien Sourimant", - "author_inst": "Georgia State University" - }, - { - "author_name": "Carolin Lieber", - "author_inst": "Georgia State University" - }, - { - "author_name": "Megha Aggarwal", - "author_inst": "Georgia State University" - }, - { - "author_name": "Robert Cox", - "author_inst": "Georgia State University" - }, - { - "author_name": "Josef Wolf", - "author_inst": "Georgia State University" - }, - { - "author_name": "Jeong-Joong Yoon", - "author_inst": "Georgia State University" - }, - { - "author_name": "Mart Toots", - "author_inst": "Georgia State University" - }, - { - "author_name": "Chengjin Ye", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Zachary Sticher", - "author_inst": "Emory University" - }, - { - "author_name": "Alexander A Kolykhalov", - "author_inst": "Emory University" - }, - { - "author_name": "Luis Martinez-Sobrido", - "author_inst": "Texas Biomedical Research Institute" - }, - { - "author_name": "Gregory R Bluemling", - "author_inst": "Emory University" - }, - { - "author_name": "Michael G Natchus", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "George R Painter", - "author_inst": "Emory University" - }, - { - "author_name": "Richard K Plemper", - "author_inst": "Georgia State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.20.444952", "rel_title": "A CRISPR/Cas9 genetically engineered organoid biobank reveals essential host factors for coronaviruses", @@ -753243,6 +753987,177 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.05.14.21257058", + "rel_title": "Multicenter cohort study of multisystem inflammatory syndrome in children (MIS-C)", + "rel_date": "2021-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257058", + "rel_abs": "BACKGROUNDSARS-CoV-2 infection can lead to multisystem inflammatory syndrome in children (MIS-C). We investigated risk factors for severe disease and explored changes in severity over time.\n\nMETHODSChildren up to 17 years of age admitted March 1, 2020 through March 7th, 2021 to 15 hospitals in Canada, Iran and Costa Rica with confirmed or probable MIS-C were included. Descriptive analysis and comparison by diagnostic criteria, country, and admission date was performed. Adjusted absolute average risks (AR) and risk differences (RD) were estimated for characteristics associated with ICU admission or cardiac involvement.\n\nRESULTSOf 232 cases (106 confirmed) with median age 5.8 years, 56% were male, and 22% had comorbidities. ICU admission occurred in 73 (31%) but none died. Median length of stay was 6 days (inter-quartile range 4-9). Children 6 to 12 years old had the highest AR for ICU admission (44%; 95% confidence interval [CI] 34-53). Initial ferritin greater than 500 mcg/L was associated with ICU admission. When comparing cases admitted up to October 31, 2020 to those admitted later, the AR for ICU admission increased from 25% (CI 17-33) to 37% (CI 29-46) and for cardiac involvement from 44% (CI 35-53) to 75% (CI 66-84). Risk estimates for ICU admission in the Canadian cohort demonstrated a higher risk in December 2020-March 2021 compared to March-May 2020 (RD 25%; 95%CI 7-44).\n\nINTERPRETATIONMIS-C occurred primarily in previously well children. Illness severity appeared to increase over time. Despite a high ICU admission incidence, most children were discharged within one week.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Joanna Merckx", + "author_inst": "Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal" + }, + { + "author_name": "Suzette Cooke", + "author_inst": "Department of Pediatrics, University of Calgary, Calgary, Alberta" + }, + { + "author_name": "Tala El Tal", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Ronald M. Laxer", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Ari Bitnun", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Shaun K Morris", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "E Ann Yeh", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Carmen Yea", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Peter Gill", + "author_inst": "Department of Pediatrics, University of Toronto, Toronto, Ontario" + }, + { + "author_name": "Jesse Papenburg", + "author_inst": "Department of Pediatrics, McGill University, Montreal, Quebec" + }, + { + "author_name": "Marie-Astrid Lefebvre", + "author_inst": "Department of Pediatrics, McGill University, Montreal, Quebec" + }, + { + "author_name": "Rolando Ulloa-Gutierrez", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Helena Brenes-Chacon", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Adriana Yock-Corrales", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Gabriela Ivankovich-Escoto", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Alejandra Soriano-Fallas", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Marcela Hernandez-de Mezerville", + "author_inst": "Department of Pediatrics, Hospital Nacional de Ninos \"Dr. Carlos Saenz Herrera\", Caja Costarricense de Seguro Social; San Jose, Costa Rica" + }, + { + "author_name": "Tammie Dewan", + "author_inst": "Department of Pediatrics, University of Calgary, Calgary, Alberta" + }, + { + "author_name": "Lea Restivo", + "author_inst": "Department of Pediatrics, University of Calgary, Calgary, Alberta" + }, + { + "author_name": "Alireza Nateghian", + "author_inst": "Department of Pediatrics, Iran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Behzad Haghighi Aski", + "author_inst": "Department of Pediatrics, Iran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Ali Manafi", + "author_inst": "Department of Pediatrics, Iran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Rachel Dwilow", + "author_inst": "Department of Pediatrics, University of Manitoba, Winnipeg, Manitoba" + }, + { + "author_name": "Jared Bullard", + "author_inst": "Department of Pediatrics, University of Manitoba, Winnipeg, Manitoba" + }, + { + "author_name": "Alison Lopez", + "author_inst": "Department of Pediatrics, University of British Columbia, Vancouver, BC" + }, + { + "author_name": "Manish Sadarangani", + "author_inst": "Department of Pediatrics, University of British Columbia; Vaccine Evaluation Center, BC Childrens Hospital Research Institute, Vancouver, BC" + }, + { + "author_name": "Ashley Roberts", + "author_inst": "Department of Pediatrics, University of British Columbia, Vancouver, BC" + }, + { + "author_name": "Michelle Barton", + "author_inst": "Department of Pediatrics, Western University, London, Ontario" + }, + { + "author_name": "Dara Petel", + "author_inst": "Department of Pediatrics, Western University, London, Ontario" + }, + { + "author_name": "Nicole Le Saux", + "author_inst": "Department of Pediatrics, University of Ottawa, Ottawa, Ontario" + }, + { + "author_name": "Jennifer Bowes", + "author_inst": "Department of Pediatrics, University of Ottawa, Ottawa, Ontario" + }, + { + "author_name": "Rupeena Purewal", + "author_inst": "Department of Pediatrics, University of Saskatchewan, Saskatoon, Saskatchewan" + }, + { + "author_name": "Janell Lautermilch", + "author_inst": "Department of Pediatrics, University of Saskatchewan, Saskatoon, Saskatchewan" + }, + { + "author_name": "Sarah Tehseen", + "author_inst": "Department of Pediatrics, University of Saskatchewan, Saskatoon, Saskatchewan" + }, + { + "author_name": "Ann Bayliss", + "author_inst": "Department of Pediatrics, Trillium Health Partners, Mississauga, Ontario" + }, + { + "author_name": "Jacqueline K. Wong", + "author_inst": "Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada" + }, + { + "author_name": "Kirk Leifso", + "author_inst": "Department of Pediatrics, Queens University, Kingston, Ontario" + }, + { + "author_name": "Cheryl Foo", + "author_inst": "Department of Pediatrics, Memorial University, St Johns, Newfoundland and Labrador" + }, + { + "author_name": "Joan Robinson", + "author_inst": "Department of Pediatrics, University of Alberta, Edmonton, Alberta" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.05.13.21257067", "rel_title": "Contact tracing indicators for COVID-19: rapid scoping review and conceptual framework", @@ -754490,73 +755405,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.14.21257204", - "rel_title": "Combined association of obesity and other cardiometabolic diseases with severe COVID-19 outcomes: a nationwide cross-sectional study of 21,773 Brazilian adult and elderly inpatients", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257204", - "rel_abs": "ObjectivesTo investigate the combined association of obesity, diabetes mellitus (DM), and cardiovascular disease (CVD) with severe COVID-19 outcomes in adult and elderly inpatients.\n\nDesignCross-sectional study based on registry data from Brazils influenza surveillance system.\n\nSettingPublic and private hospitals across Brazil.\n\nParticipantsEligible population included 21,942 inpatients aged [≥]20 years with positive RT-PCR test for SARS-CoV-2 until Jun 9th, 2020.\n\nMain outcome measuresSevere COVID-19 outcomes were non-invasive and invasive mechanical ventilation use, ICU admission, and death. Multivariate analyses were conducted separately for adults (20-59 years) and elders ([≥]60 years) to test the combined association of obesity (without and with DM and/or CVD) and degrees of obesity with each outcome.\n\nResultsA sample of 8,848 adults and 12,925 elders were included. Among adults, obesity with DM and/or CVD showed higher prevalence of invasive (PR 3.76, 95%CI 2.82-5.01) and non-invasive mechanical ventilation use (2.06, 1.58-2.69), ICU admission (1.60, 1.40-1.83), and death (1.79, 1.45-2.21) compared with the group without obesity, DM, and CVD. In elders, obesity alone (without DM and CVD) had the highest prevalence of ICU admission (1.40, 1.07-1.82) and death (1.67, 1.00-2.80). In both age groups, obesity alone and combined with DM and/or CVD showed higher prevalence in all outcomes than DM and/or CVD. A dose-response association was observed between obesity and death in adults: class I 1.32 (1.05-1.66), class II 1.41 (1.06-1.87), and class III 1.77 (1.35-2.33).\n\nConclusionsThe combined association of obesity, diabetes, and/or CVD with severe COVID-19 outcomes may be stronger in adults than in elders. Obesity alone and combined with DM and/or CVD had more impact on the risk of COVID-19 severity than DM and/or CVD in both age groups. The study also supports an independent relationship of obesity with severe outcomes, including a dose-response association between degrees of obesity and death in adults.\n\nArticle summaryStrengths and limitations of this study: O_LIThis is the first study that describes the independent and combined relationship of obesity with COVID-19 severity in Brazil, one of the biggest epicenters of the pandemic worldwide.\nC_LIO_LIThe study was based on registry data of a large nationwide sample of patients admitted, due to severe SARS-CoV-2 infection, to public and private hospitals across the country.\nC_LIO_LIThe large sample size and data availability allowed us to analyze the combined association of obesity, diabetes and cardiovascular disease with severe COVID-19 outcomes, separately by age groups and controlled by important confounding variables, e.g. underlying comorbidities.\nC_LIO_LIThe cross-sectional study design does not allow causal inference, and generalization of results must be cautious since only hospitalized cases of severe COVID-19 were included.\nC_LIO_LIAs the study used routinely collected data, which has not been designed primarily for research purposes, it may bring well-known limitations related to missing, underestimation, and potential misclassification.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Natanael J Silva", - "author_inst": "Centre for Data and Knowledge Integration for Health, Oswaldo Cruz Foundation, Salvador, BA, Brazil." - }, - { - "author_name": "Rita C Ribeiro-Silva", - "author_inst": "School of Nutrition, Federal University of Bahia, Salvador, BA, Brazil. Centre for Data and Knowledge Integration for Health, Oswaldo Cruz Foundation, Salvador," - }, - { - "author_name": "Andrea JF Ferreira", - "author_inst": "Institute of Collective Health, Federal University of Bahia, Salvador, BA, Brazil. Centre for Data and Knowledge Integration for Health, Oswaldo Cruz Foundation" - }, - { - "author_name": "Camila SS Teixeira", - "author_inst": "Institute of Collective Health, Federal University of Bahia, Salvador, BA, Brazil. Centre for Data and Knowledge Integration for Health, Oswaldo Cruz Foundation" - }, - { - "author_name": "Aline S Rocha", - "author_inst": "School of Nutrition, Federal University of Bahia, Salvador, BA, Brazil. Centre for Data and Knowledge Integration for Health, Oswaldo Cruz Foundation, Salvador," - }, - { - "author_name": "Flavia Jose O Alves", - "author_inst": "Institute of Collective Health, Federal University of Bahia, Salvador, BA, Brazil. Centre for Data and Knowledge Integration for Health, Oswaldo Cruz Foundation" - }, - { - "author_name": "Ila R Falcao", - "author_inst": "Centre for Data and Knowledge Integration for Health, Oswaldo Cruz Foundation, Salvador, BA, Brazil." - }, - { - "author_name": "Elizabete J Pinto", - "author_inst": "Center for Health Sciences, Federal University of Reconcavo da Bahia, Santo Antonio de Jesus, BA, Brazil. Centre for Data and Knowledge Integration for Health, " - }, - { - "author_name": "Carlos Antonio ST Santos", - "author_inst": "Centre for Data and Knowledge Integration for Health, Oswaldo Cruz Foundation, Salvador, BA, Brazil. Department of Exact Sciences, State University of Feira de " - }, - { - "author_name": "Rosemeire L Fiaccone", - "author_inst": "Institute of Mathematics and Statistics, Federal University of Bahia, Salvador, BA, Brazil. Centre for Data and Knowledge Integration for Health, Oswaldo Cruz F" - }, - { - "author_name": "Maria Yury T Ichihara", - "author_inst": "Centre for Data and Knowledge Integration for Health, Oswaldo Cruz Foundation, Salvador, BA, Brazil." - }, - { - "author_name": "Enny S Paixao", - "author_inst": "Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK. Centre for Data and Knowledge Integration for Health, Oswaldo Cr" - }, - { - "author_name": "Mauricio L Barreto", - "author_inst": "Centre for Data and Knowledge Integration for Health, Oswaldo Cruz Foundation, Salvador, BA, Brazil. Institute of Collective Health, Federal University of Bahia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.13.21257189", "rel_title": "A Time Series Analysis and Forecast of COVID-19 Healthcare Disparity", @@ -754753,6 +755601,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.14.21257224", + "rel_title": "Surveillance of COVID-19 vaccination in US nursing homes, December 2020-April 2021", + "rel_date": "2021-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257224", + "rel_abs": "Unstructured AbstractMonitoring COVID-19 vaccination coverage among nursing home (NH) residents and staff is important to ensure high coverage and guide patient-safety policies. With the termination of the federal Pharmacy Partnership for Long-Term Care Program, another source of facility-based vaccination data is needed. We compared numbers of COVID-19 vaccinations administered to NH residents and staff reported by pharmacies participating in the temporary federal Pharmacy Partnership for Long-Term Care Program with those reported by NHs participating in new COVID-19 vaccination modules of CDCs National Healthcare Safety Network (NHSN). Pearson correlation coefficients comparing the number vaccinated between the two approaches were 0.89, 0.96, and 0.97 for residents and 0.74, 0.90, and 0.90 for staff, in the weeks ending January 3, 10, and 17, respectively. Based on subsequent NHSN reporting, vaccination coverage with [≥]1 vaccine dose reached 77% for residents and 50% for staff the week ending January 31 and plateaued through April 2021.\n\nThree-question summary boxO_LIWhat is the current understanding of the subject?\nBecause of high risk of disease, nursing home residents and staff were prioritized for COVID-19 vaccination when doses were limited.\nC_LIO_LIWhat does this report add to the literature?\nNational monitoring of nursing home residents and staff vaccination coverage through the CDC National Healthcare Safety Network (NHSN) correlated with vaccination administration reports from the federal Pharmacy Partnership for Long-Term Care Program in January 2021. NHSN-reported vaccination coverage rates plateaued from February through April 2021.\nC_LIO_LIWhat are the implications for public health practice?\nNHSN can track COVID-19 vaccination in nursing homes and help guide efforts to increase vaccine uptake in residents and staff.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Andrew I Geller", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Daniel S Budnitz", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Heather Dubendris", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Radhika Gharpure", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Minn Minn Soe", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Hsiu Wu", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Elizabeth J Kalayil", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Andrea L Benin", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Suchita A Patel", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Megan C Lindley", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Ruth Link-Gelles", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.13.21257164", "rel_title": "KL-MOB Automated Covid-19 Recognition Using a Novel Approach Based on Image Enhancement and a Modified MobileNet CNN", @@ -757804,41 +758711,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.16.21257280", - "rel_title": "Predisposing factors associated with the severity of the illness in adults with Covid-19 in Nepal.", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.16.21257280", - "rel_abs": "ObjectiveWe aimed to determine the prevalence of the severity of COVID-19 illness and its associated predisposing factors in Nepal.\n\nDesignCross-sectional, observational study\n\nSettingSingle-centered hospital-based study, conducted at Nepal armed police force (APF) hospital, Kathmandu, Nepal.\n\nParticipantsAll individuals aged [≥]18 years with laboratory-confirmed SARS-Cov-2 (the SARS-CoV-2 specific real-time-RT-PCR result positive), regardless the severity of their disease.\n\nMeasurementsDisease severity was evaluated as a primary outcome and age, sex, BMI, smoking history, alcohol history, Hypertension, diabetes mellitus were evaluated as predictors in the analysis.\n\nResultsMean ages of the patients were 40.79{+/-}16.04 years, and about two-thirds of the patients were male 146 (73.7%). More than half 57.1% (95%CI: 52.42-61.51) of the population had a mild infection, whereas 16.7% (95%CI: 7.4-24.6%) had severe/critical illness. In univariate analysis, each 1-year increase in age (OR: 1.05; 95% CI:1.030-1.081; P<0.001), each 1 unit increase in BMI (OR:1.12; 95% CI:1.02-1.25; P=0.033), comorbid illness (OR: 5.79; 95%CI: 2.51-13.33; P<0.001), hypertension (OR:5.95; 95%CI:2.66-13.30: P<0.001), diabetes mellitus (OR:3.26; 95%CI:1.30-8.15: P<0.005), and fever (OR:34.64; 95% CI:7.98-150.38; P<0.001) were independently associated with severity of the disease, whereas age (OR: 1.049; 95% CI: 1.019-1.080; P=0.02), hypertension (OR: 4.77; 95%CI: 1.62-14.04; P=0.004), and fever (OR: 51.02; 95%CI: 9.56-272.51; P<0.001) remained a significant predictive factors in multivariate analysis.\n\nConclusionThe majority of the patients with COVID-19 had a mild illness, with 16.7% severe illness. Age, BMI, hypertension, diabetes mellitus, comorbidity, and temperature were associated the severity of the illness. Age, hypertension, and fever emerged as an independent predictive factors in multivariate analysis, and thus, these vulnerable groups should be given special protection to the infection and proactive intervention should be initiated at an early stage of the infection to diminish the severity of the illness and improve the clinical outcome of the disease.\n\nStrengths and limitations of the studyO_LIMuch of the studies on COVID-19 in Nepal focus on the describing epidemiology and clinical profile of the disease, however, risk factors that contribute to the severity of the illness are overlooked.\nC_LIO_LIThis study may help estimate the burden of the disease and identify the vulnerable group with poor prognosis, which is vital for clinicians and the public health approach to deal with the disease.\nC_LIO_LIAlthough limiting the study to a single-center with a relatively small sample size, it, however, allows evaluation of the importance of the demographic and geographical variation.\nC_LIO_LISocio-economic factors, lifestyle, and availability of quality medical care may have contributed to the severity of the COVID-19, which needs to be addressed in a further large-scale study.\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Roshan Kumar Jha", - "author_inst": "Nepal Armed Police Force hospital, Balambu, Kathmandu Nepal" - }, - { - "author_name": "Anil Shrestha", - "author_inst": "Nepal Armed Police Force hospital, Balambu, Kathmandu Nepal" - }, - { - "author_name": "Basant Tamang", - "author_inst": "Nepal Armed Police Force hospital, Balambu, Kathmandu Nepal" - }, - { - "author_name": "Indu K.C.", - "author_inst": "Nepal Armed Police Force hospital, Balambu, Kathmandu Nepal" - }, - { - "author_name": "Shiv Kumar Sah", - "author_inst": "Purbanchal University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.16.21257298", "rel_title": "Microsimulation of SARS-CoV-2 Transmission in Society", @@ -757987,6 +758859,161 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.18.21257267", + "rel_title": "Colchicine in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", + "rel_date": "2021-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.18.21257267", + "rel_abs": "BackgroundColchicine has been proposed as a treatment for COVID-19 on the basis of its anti-inflammatory actions.\n\nMethodsIn this randomised, controlled, open-label trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19. Eligible and consenting adults were randomly allocated in a 1:1 ratio to either usual standard of care alone or usual standard of care plus colchicine twice daily for 10 days or until discharge (or one of the other treatment arms) using web-based simple (unstratified) randomisation with allocation concealment. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 27 November 2020 and 4 March 2021, 5610 patients were randomly allocated to receive colchicine and 5730 patients to receive usual care alone. Overall, 1173 (21%) patients allocated to colchicine and 1190 (21%) patients allocated to usual care died within 28 days (rate ratio 1.01; 95% confidence interval [CI] 0.93-1.10; p=0.77). Consistent results were seen in all pre-specified subgroups of patients. There was no significant difference in duration of hospitalisation (median 10 days vs. 10 days) or the proportion of patients discharged from hospital alive within 28 days (70% vs. 70%; rate ratio 0.98; 95% CI 0.94-1.03; p=0.44). Among those not on invasive mechanical ventilation at baseline, there was no significant difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (25% vs. 25%; risk ratio 1.02; 95% CI 0.96-1.09; p=0.47).\n\nInterpretationIn adults hospitalised with COVID-19, colchicine was not associated with reductions in 28-day mortality, duration of hospital stay, or risk of progressing to invasive mechanical ventilation or death.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056). Wellcome Trust (Grant Ref: 222406/Z/20/Z) through the COVID-19 Therapeutics Accelerator.", + "rel_num_authors": 35, + "rel_authors": [ + { + "author_name": "Peter W Horby", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and International Severe Acute Res" + }, + { + "author_name": "Mark Campbell", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King" + }, + { + "author_name": "Enti Spata", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un" + }, + { + "author_name": "Jonathan R Emberson", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un" + }, + { + "author_name": "Natalie Staplin", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un" + }, + { + "author_name": "Guilherme Pessoa-Amorim", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Leon Peto", + "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom and Nuffield Department of Populat" + }, + { + "author_name": "Martin Wiselka", + "author_inst": "Department of Infectious Diseases, University Hospital Leicester, Leicester, United Kingdom" + }, + { + "author_name": "Laura Wiffen", + "author_inst": "Portsmouth Hospitals University NHS Foundation Trust, Portsmouth, United Kingdom" + }, + { + "author_name": "Simon Tiberi", + "author_inst": "Department of Infection, Barts Health NHS Trust, London, United Kingdom" + }, + { + "author_name": "Ben Caplin", + "author_inst": "Department of Renal Medicine, University College London, London, United Kingdom and Royal Free London NHS Trust, London, United Kingdom" + }, + { + "author_name": "Caroline Wroe", + "author_inst": "James Cook University Hospital, Middlesbrough, United Kingdom" + }, + { + "author_name": "Christopher Green", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom" + }, + { + "author_name": "Paul Hine", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom" + }, + { + "author_name": "Benjamin Prudon", + "author_inst": "North Tees and Hartlepool NHS Foundation Trust, Hartlepool, United Kingdom" + }, + { + "author_name": "Tina George", + "author_inst": "Basildon and Thurrock Hospitals NHS Foundation Trust, Basildon, United Kingdom" + }, + { + "author_name": "Andrew Wight", + "author_inst": "Wirral University Teaching Hospital NHS Foundation Trust, Birkenhead, United Kingdom" + }, + { + "author_name": "J Kenneth Baillie", + "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom" + }, + { + "author_name": "Buddha Basnyat", + "author_inst": "Oxford University Clinical Research Unit -Nepal, Patan Academy of Health Sciences, Kathmandu, Nepal" + }, + { + "author_name": "Maya H Buch", + "author_inst": "Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom" + }, + { + "author_name": "Lucy C Chappell", + "author_inst": "School of Life Course Sciences, King?s College London, London, United Kingdom" + }, + { + "author_name": "Jeremy N Day", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer" + }, + { + "author_name": "Saul N Faust", + "author_inst": "NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, " + }, + { + "author_name": "Raph L Hamers", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia and Faculty of Medicine, University of Indonesia, Jakarta, Indonesia and Centre for Tropical Medicine " + }, + { + "author_name": "Thomas Jaki", + "author_inst": "Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom and MRC Biostatistics Unit, University of Cambridge, Cambridge, United" + }, + { + "author_name": "Edmund Juszczak", + "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" + }, + { + "author_name": "Katie Jeffery", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom" + }, + { + "author_name": "Wei Shen Lim", + "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom and Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Notting" + }, + { + "author_name": "Alan Montgomery", + "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" + }, + { + "author_name": "Andrew Mumford", + "author_inst": "School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom" + }, + { + "author_name": "Kathryn Rowan", + "author_inst": "Intensive Care National Audit & Research Centre, London, United Kingdom" + }, + { + "author_name": "Guy Thwaites", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam and Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, Univer" + }, + { + "author_name": "Marion Mafham", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" + }, + { + "author_name": "Richard Haynes", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and Oxford University Hospitals NHS Foundation Trust, Oxford, United King" + }, + { + "author_name": "Martin J Landray", + "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom and MRC Population Health Research Unit, University of Oxford, Oxford, Un" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.16.21257283", "rel_title": "Early Anakinra Treatment for COVID-19 Guided by Urokinase Plasminogen Receptor", @@ -759690,89 +760717,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.13.21257070", - "rel_title": "Tie2 activation protects against prothrombotic endothelial dysfunction in COVID-19", - "rel_date": "2021-05-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21257070", - "rel_abs": "Profound endothelial dysfunction accompanies the microvascular thrombosis commonly observed in severe COVID-19. In the quiescent state, the endothelial surface is anticoagulant, a property maintained at least in part via constitutive signaling through the Tie2 receptor. During inflammation, the Tie2 antagonist angiopoietin-2 (Angpt-2) is released from activated endothelial cells and inhibits Tie2, promoting a prothrombotic phenotypic shift. We sought to assess whether severe COVID-19 is associated with procoagulant dysfunction of the endothelium and alterations in the Tie2-angiopoietin axis. Primary human endothelial cells treated with plasma from patients with severe COVID-19 upregulated the expression of thromboinflammatory genes, inhibited expression of antithrombotic genes, and promoted coagulation on the endothelial surface. Pharmacologic activation of Tie2 with the small molecule AKB-9778 reversed the prothrombotic state induced by COVID-19 plasma in primary endothelial cells. On lung autopsy specimens from COVID-19 patients, we found a prothrombotic endothelial signature as evidenced by increased von Willebrand Factor and loss of anticoagulant proteins. Assessment of circulating endothelial markers in a cohort of 98 patients with mild, moderate, or severe COVID-19 revealed profound endothelial dysfunction indicative of a prothrombotic state. Angpt-2 concentrations rose with increasing disease severity and highest levels were associated with worse survival. These data highlight the disruption of Tie2-angiopoietin signaling and procoagulant changes in endothelial cells in severe COVID-19. Moreover, our findings provide novel rationale for current trials of Tie2 activating therapy with AKB-9778 in severe COVID-19 disease.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Alec A Schmaier", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Gabriel M Pajares Hurtado", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Zachary J Manickas-Hill", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Kelsey D Sack", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Siyu M Chen", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Victoria Bhambhani", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Juweria Quadir", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Anjali K Nath", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Ai-ris M Collier", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Debby Ngo", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Dan H Barouch", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Robert E Gerszten", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Xu G Yu", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard" - }, - { - "author_name": "- MGH COVID-19 Collection and Processing Team", - "author_inst": "" - }, - { - "author_name": "Kevin Peters", - "author_inst": "Aerpio Pharmaceuticals, Inc." - }, - { - "author_name": "Robert Flaumenhaft", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Samir M Parikh", - "author_inst": "Beth Israel Deaconess Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.05.12.21256608", "rel_title": "Susceptibility and infectiousness of children and adults with SARS-CoV-2 variant B.1.1.7 deduced from three daycare centre outbreaks and related household situations; Germany, 2021", @@ -759957,6 +760901,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.15.21256976", + "rel_title": "Excess mortality during the COVID-19 pandemic: a geospatial and statistical analysis in Mogadishu, Somalia", + "rel_date": "2021-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.15.21256976", + "rel_abs": "BackgroundWhile the impact of the COVID-19 pandemic has been well documented in high-income countries, much less is known about its impact in Somalia where health systems are weak and vital registration is under developed.\n\nMethodsWe used remote sensing and geospatial analysis to quantify the number of burials from January 2017 to September 2020 in Mogadishu. We imputed missing grave counts using surface area data. Simple interpolation and a generalised additive mixed growth model were used to predict both actual and counterfactual burial rates by cemetery and across Mogadishu during the most likely period of COVID-19 excess mortality and to compute excess burials. We also undertook a qualitative survey of key informants to determine the drivers of COVID-19 excess mortality.\n\nResultsBurial rates increased during the pandemic period with a ratio to pre-pandemic levels averaging 1.5-fold and peaking at 2.2-fold. When scaled to plausible range of baseline Crude Death Rates (CDR), excess death toll between January and September 2020 ranged between 3,200 and 11,800. When compared to burial records of the Barakaat Cemetery Committee our estimates were found to be lower.\n\nConclusionsOur study points to considerable under estimation of COVID-19 impact in Banadir and an overburdened public health system struggling to deal with the increasing severity of the epidemic in 2020.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Abdihamid Warsame", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Farah Bashiir", + "author_inst": "Somali Disaster Resilience Institute" + }, + { + "author_name": "Terri Freemantle", + "author_inst": "Satellite Applications Catapult" + }, + { + "author_name": "Chris Williams", + "author_inst": "Satellite Applications Catapult" + }, + { + "author_name": "Yolanda Vazquez", + "author_inst": "Satellite Applications Catapult" + }, + { + "author_name": "Chris Reeve", + "author_inst": "Satellite Applications Catapult" + }, + { + "author_name": "Ahmed Aweis", + "author_inst": "Somali Disaster Resilience Institute" + }, + { + "author_name": "Mohamed Ahmed", + "author_inst": "Somali Disaster Resilience Institute" + }, + { + "author_name": "Francesco Checchi", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Abdirisak Dalmar", + "author_inst": "Somali Disaster Resilience Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.12.21257123", "rel_title": "Occupation and COVID-19 mortality in England: a national linked data study of 14.3 million adults", @@ -761672,57 +762671,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.14.21257059", - "rel_title": "Hydroxychloroquine For Prophylaxis Of COVID-19 In Health Workers: A Randomized Clinical Trial.", - "rel_date": "2021-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.14.21257059", - "rel_abs": "Health care workers are at high risk of being infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2). Our aim is to evaluate the efficacy and safety of hydroxychloroquine (HCQ) for prophylaxis of COVID19 in health personnel exposed to patients infected by SARS-COV-2.\n\nMethodsDouble-blind randomized, placebo-controlled single center clinical trial. Included subjects were health care workers caring for severe COVD19 patients. Main outcome was time to symptomatic SARS-CoV2 infection.\n\nResults127 subjects with a confirmed baseline negative RT-PCR SARS-CoV2 test were included in the trial, 62 assigned to HCQ and 65 to placebo. One subject (1.6%) in the HCQ group and 6 (9,2%) subjects in the placebo group developed COVID-19. (Log Rank test p = 0.09). No severe COVID19 cases were observed. The study was suspended because of a refusal to participate and losses to follow up after several trials reported lack of effectiveness of hydroxychloroquine in hospitalized patients with COVID-19.\n\nCONCLUSIONAlthough the number of symptomatic infections in health personnel was lower in the HCQ group, the difference was not statistically significant. The trial is underpowered due to the failure to complete the estimated sample size.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jorge Rojas-Serrano", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Angelica Margarita Portillo-Vasquez", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Ireri Thirion-Romero", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Joel Vazquez-Perez", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Fidencio Mejia-Nepomuceno", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Alejandra Ramirez-Venegas", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Karla Midori Perez-Kawabe", - "author_inst": "Insitituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Rogelio Perez-Padilla", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "- RESEARCH GROUP ON HYDROXYCHLOROQUINE FOR COVID-19", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.15.21257257", "rel_title": "Toxoplasmosis: An important risk factor for acquiring SARS-CoV-2 infection and a severe course of Covid-19 disease", @@ -761898,6 +762846,121 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.13.444010", + "rel_title": "Durability of mRNA-1273-induced antibodies against SARS-CoV-2 variants", + "rel_date": "2021-05-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.13.444010", + "rel_abs": "SARS-CoV-2 mutations may diminish vaccine-induced protective immune responses, and the durability of such responses has not been previously reported. Here, we present a comprehensive assessment of the impact of variants B.1.1.7, B.1.351, P.1, B.1.429, and B.1.526 on binding, neutralizing, and ACE2-blocking antibodies elicited by the vaccine mRNA-1273 over seven months. Cross-reactive neutralizing responses were rare after a single dose of mRNA-1273. At the peak of response to the second dose, all subjects had robust responses to all variants. Binding and functional antibodies against variants persisted in most subjects, albeit at low levels, for 6 months after the primary series of mRNA-1273. Across all assays, B.1.351 had the greatest impact on antibody recognition, and B.1.1.7 the least. These data complement ongoing studies of clinical protection to inform the potential need for additional boost vaccinations.\n\nOne-Sentence SummaryMost mRNA-1273 vaccinated individuals maintained binding and functional antibodies against SARS-CoV-2 variants for 6 months.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Amarendra Pegu", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Stephen D. Schmidt", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Chloe A. Talana", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Jim Albert", + "author_inst": "Emmes Company, Rockville, MD, USA." + }, + { + "author_name": "Evan Anderson", + "author_inst": "Department of Medicine, Center for Childhood Infections and Vaccines (CCIV) of Childrens Healthcare of Atlanta and Emory University Department of Pediatrics, At" + }, + { + "author_name": "Hamilton Bennett", + "author_inst": "Moderna, Inc., Cambridge, MA, USA." + }, + { + "author_name": "Kizzmekia Corbett", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Britta Flach", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Lisa Jackson", + "author_inst": "Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA." + }, + { + "author_name": "Brett Leav", + "author_inst": "Moderna, Inc., Cambridge, MA, USA." + }, + { + "author_name": "Julie E. Ledgerwood", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Catherine J. Luke", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA." + }, + { + "author_name": "Mat Makowski", + "author_inst": "Emmes Company, Rockville, MD, USA." + }, + { + "author_name": "Paul C. Roberts", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA." + }, + { + "author_name": "Mario Roederer", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Paulina Alejandra Rebolledo", + "author_inst": "Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur, GA, USA." + }, + { + "author_name": "Christina A. Rostad", + "author_inst": "Department of Medicine, Center for Childhood Infections and Vaccines (CCIV) of Childrens Healthcare of Atlanta and Emory University Department of Pediatrics, At" + }, + { + "author_name": "Nadine G. Rouphael", + "author_inst": "Hope Clinic, Department of Medicine, Emory University School of Medicine, Decatur, GA, USA." + }, + { + "author_name": "Lingshu Wang", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Eun Sung Yang", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "John H. Beigel", + "author_inst": "Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA." + }, + { + "author_name": "Barney S. Graham", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "John R. Mascola", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Adrian McDermott", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Vaccine Research Center," + }, + { + "author_name": "Nicole A Doria-Rose", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.14.444076", "rel_title": "The Spike Proteins of SARS-CoV-2 B.1.617 and B.1.618 Variants Identified in India Provide Partial Resistance to Vaccine-elicited and Therapeutic Monoclonal Antibodies.", @@ -763809,73 +764872,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.05.14.443968", - "rel_title": "Isolation and characterization of SARS-CoV-2 VOC, 20H/501Y.V2, from UAE travelers", - "rel_date": "2021-05-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.14.443968", - "rel_abs": "Multiple SARS-CoV-2 variants have been emerged and created serious public health in the affected countries. The variant of Concern associated with high transmissibility, disease severity and escape mutations is threat to vaccination program across the globe. Travel has been important factor in spread of SARS-CoV-2 variants worldwide. India has also witnessed the dreadful effect of these SARS-CoV-2 variants. Here, we report the Isolation and characterization of SARS-CoV-2 VOC, 20H/501Y.V2 (B.1.351), from UAE travelers to India. The virus isolate would be useful to determine the efficacy of the currently available vaccines in India.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Pragya Yadav", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021" - }, - { - "author_name": "Prasad Sarkale", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021" - }, - { - "author_name": "Alpana Razdan", - "author_inst": "Genestrings Diagnostic Centre Pvt. Ltd., 3, MMTC, Geetanjali Enclave, New Delhi Pin 110017" - }, - { - "author_name": "Nivedita Gupta", - "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, India Pin-110029" - }, - { - "author_name": "Dimpal Nyayanit", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021" - }, - { - "author_name": "Rima Sahay", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021" - }, - { - "author_name": "Varsha Potdar", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021" - }, - { - "author_name": "Deepak Patil", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021" - }, - { - "author_name": "Shreekant Baradkar", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021" - }, - { - "author_name": "Abhinendra Kumar", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021" - }, - { - "author_name": "Neeraj Aggarwal", - "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, India Pin-110029" - }, - { - "author_name": "Anita Shete", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, Maharashtra, India Pin-411021" - }, - { - "author_name": "Harmanmeet Kaur", - "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, P.O. Box No. 4911, Ansari Nagar, New Delhi, India Pin-110029" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.14.444190", "rel_title": "Glucosidase inhibitors suppress SARS-CoV-2 in tissue culture and may potentiate", @@ -764052,6 +765048,201 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.13.21256639", + "rel_title": "Efficacy of the NVX-CoV2373 Covid-19 Vaccine Against the B.1.1.7 Variant", + "rel_date": "2021-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21256639", + "rel_abs": "BackgroundCovid-19 vaccines are urgently needed, especially against emerging variants. NVX-CoV2373 is a recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 rS) nanoparticle vaccine containing trimeric full-length SARS-CoV-2 spike glycoprotein and Matrix-M adjuvant.\n\nMethodsA phase 3, randomized, observer-blinded, placebo-controlled trial was conducted in adults 18-84 years old who received two intramuscular 5-{micro}g doses, 21 days apart, of NVX-CoV2373 or placebo (1:1) across 33 sites in the United Kingdom. The primary efficacy endpoint was virologically confirmed symptomatic Covid-19 with onset 7 days after second vaccination in serologically negative participants.\n\nResultsA total of 15,187 participants were randomized, of whom 7569 received NVX-CoV2373 and 7570 received placebo; 27.2% were 65 years or older, 44.7% had comorbidities and 4.2% had baseline serological evidence of SARS-CoV-2. There were 10 cases of Covid-19 among NVX-CoV2373 recipients and 96 cases among placebo recipients, with symptom onset at least 7 days after second vaccination; NVX-CoV2373 was 89.7% (95% confidence interval, 80.2 to 94.6) effective in preventing Covid-19, with no hospitalizations or deaths reported. There were five cases of severe Covid-19, all in the placebo group. Post hoc analysis revealed efficacies of 96.4% (73.8 to 99.5) and 86.3% (71.3 to 93.5) against the prototype strain and B.1.1.7 variant, respectively. Vaccine efficacy was similar across subgroups, including participants with comorbidities and those [≥]65 years old. Reactogenicity was generally mild and transient. The incidence of serious adverse events was low and similar in the two groups.\n\nConclusionA two-dose regimen of NVX-CoV2373 conferred 89.7% protection against a blend of prototype and variant Covid-19, demonstrated high efficacy against the B.1.1.7 variant, and had a reassuring safety profile.\n\n(Funded by Novavax, Inc. EudraCT number, 2020-004123-16).", + "rel_num_authors": 45, + "rel_authors": [ + { + "author_name": "Seth Toback", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Paul T. Heath", + "author_inst": "Vaccine Institute, St. George's, University of London and St. Georges University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Eva P. Galiza", + "author_inst": "Vaccine Institute, St. George's, University of London and St. Georges University Hospitals NHS Foundation Trust" + }, + { + "author_name": "David Baxter", + "author_inst": "Stockport NHS Foundation Trust, Stepping Hill Hospital" + }, + { + "author_name": "Marta Boffito", + "author_inst": "Chelsea and Westminster Hospital NHS Foundation Trust and Imperial College London" + }, + { + "author_name": "Duncan Browne", + "author_inst": "Royal Cornwall Hospital NHS Trust" + }, + { + "author_name": "Fiona Burns", + "author_inst": "Institute for Global Health, University College London and Royal Free London NHS Foundation Trust" + }, + { + "author_name": "David R. Chadwick", + "author_inst": "Centre for Clinical Infection, South Tees Hospitals NHS Foundation Trust, James Cook University Hospital" + }, + { + "author_name": "Rebecca Clark", + "author_inst": "Layton Medical Centre" + }, + { + "author_name": "Catherine Cosgrove", + "author_inst": "Vaccine Institute, St. Georges, University of London and St. Georges University Hospitals NHS Foundation Trust" + }, + { + "author_name": "James Galloway", + "author_inst": "Centre for Rheumatic Disease, Kings College London" + }, + { + "author_name": "Anna L. Goodman", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust, University College London" + }, + { + "author_name": "Amardeep Heer", + "author_inst": "Lakeside Healthcare Research, Lakeside Surgeries Corby" + }, + { + "author_name": "Andrew Higham", + "author_inst": "University Hospitals of Morecambe Bay NHS Foundation Trust" + }, + { + "author_name": "Shalini Iyengar", + "author_inst": "Accelerated Enrollment Solutions, Synexus Hexham, Hexham General Hospital" + }, + { + "author_name": "Arham Jamal", + "author_inst": "Accelerated Enrollment Solutions, Synexus Thames Valley" + }, + { + "author_name": "Christopher Jeanes", + "author_inst": "Norfolk and Norwich University Hospital NHS Foundation Trust" + }, + { + "author_name": "Philip A. Kalra", + "author_inst": "Salford Royal NHS Foundation Trust, Northern Care Alliance" + }, + { + "author_name": "Christina Kyriakidou", + "author_inst": "Accelerated Enrolment Solutions, Synexus Midlands" + }, + { + "author_name": "Daniel F. McAuley", + "author_inst": "Wellcome-Wolfson Institute for Experimental Medicine, Queen's University of Belfast & Royal Victoria Hospital" + }, + { + "author_name": "Agnieszka Meyrick", + "author_inst": "Accelerated Enrolment Solutions, Synexus Merseyside" + }, + { + "author_name": "Angela M. Minassian", + "author_inst": "Centre for Clinical Vaccinology and Tropical Medicine, University of Oxford" + }, + { + "author_name": "Jane Minton", + "author_inst": "St James's University Hospital, Leeds Teaching Hospitals NHS Trust" + }, + { + "author_name": "Patrick Moore", + "author_inst": "The Adam Practice, University Hospital Southampton NHS Foundation Trust" + }, + { + "author_name": "Imrozia Munsoor", + "author_inst": "Accelerated Enrolment Solutions, Synexus Glasgow" + }, + { + "author_name": "Helen Nicholls", + "author_inst": "Accelerated Enrolment Solutions, Synexus Wales" + }, + { + "author_name": "Orod Osanlou", + "author_inst": "Bangor University and Betsi Cadwaladr University" + }, + { + "author_name": "Jonathan Packham", + "author_inst": "University of Nottingham and Haywood Hospital, Midlands Partnership NHS Foundation Trust" + }, + { + "author_name": "Carol Pretswell", + "author_inst": "Accelerated Enrolment Solutions, Synexus Lancashire" + }, + { + "author_name": "Alberto San Francisco Ramos", + "author_inst": "Vaccine Institute, St. George's, University of London and St. Georges University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Dinesh Saralaya", + "author_inst": "National Institute for Health Research and Bradford Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Ray P. Sheridan", + "author_inst": "Royal Devon & Exeter Hospital" + }, + { + "author_name": "Richard Smith", + "author_inst": "East Suffolk and North Essex NHS Foundation Trust and University of Essex" + }, + { + "author_name": "Roy L. Soiza", + "author_inst": "Aberdeen Royal Infirmary, NHS Grampian & Ageing Clinical and Experimental Research (ACER) Group, University of Aberdeen" + }, + { + "author_name": "Pauline A. Swift", + "author_inst": "Epsom and St Helier University Hospitals NHS Trust" + }, + { + "author_name": "Emma C Thomson", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Jeremy Turner", + "author_inst": "Norfolk and Norwich University Hospital NHS Foundation Trust" + }, + { + "author_name": "Marianne Elizabeth Viljoen", + "author_inst": "Accelerated Enrolment Solutions, Synexus Manchester" + }, + { + "author_name": "Gary Albert", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Iksung Cho", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Greg Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Joy Rivers", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Andreana Robertson", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Kathy Smith", + "author_inst": "Novavax, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.06.21256757", "rel_title": "COVID-19 outbreak rates and infection attack rates associated with the workplace: a descriptive epidemiological study", @@ -766279,93 +767470,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.05.12.21257083", - "rel_title": "Background rates of five thrombosis with thrombocytopenia syndromes of special interest for COVID-19 vaccine safety surveillance: incidence between 2017 and 2019 and patient profiles from 20.6 million people in six European countries", - "rel_date": "2021-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257083", - "rel_abs": "BackgroundThrombosis with thrombocytopenia syndrome (TTS) has been reported among individuals vaccinated with adenovirus-vectored COVID-19 vaccines. In this study we describe the background incidence of TTS in 6 European countries.\n\nMethodsElectronic medical records from France, Netherlands, Italy, Germany, Spain, and the United Kingdom informed the study. Incidence rates of cerebral venous sinus thrombosis (CVST), splanchnic vein thrombosis (SVT), deep vein thrombosis (DVT), pulmonary embolism (PE), and stroke, all with concurrent thrombocytopenia, were estimated among the general population between 2017 to 2019. A range of additional adverse events of special interest for COVID-19 vaccinations were also studied in a similar manner.\n\nFindingsA total of 25,432,658 individuals were included. Background rates ranged from 1.0 (0.7 to 1.4) to 8.5 (7.4 to 9.9) per 100,000 person-years for DVT with thrombocytopenia, from 0.5 (0.3 to 0.6) to 20.8 (18.9 to 22.8) for PE with thrombocytopenia, from 0.1 (0.0 to 0.1) to 2.5 (2.2 to 2.7) for SVT with thrombocytopenia, and from 0.2 (0.0 to 0.4) to 30.9 (28.6 to 33.3) for stroke with thrombocytopenia. CVST with thrombocytopenia was only identified in one database, with incidence rate of 0.1 (0.1 to 0.2) per 100,000 person-years. The incidence of TTS increased with age, with those affected typically having more comorbidities and greater medication use than the general population. TTS was also more often seen in men than women. A sizeable proportion of those affected were seen to have been taking antithrombotic and anticoagulant therapies prior to their TTS event.\n\nInterpretationAlthough rates vary across databases, TTS has consistently been seen to be a very rare event among the general population. While still very rare, rates of TTS are typically higher among older individuals, and those affected were also seen to generally be male and have more comorbidities and greater medication use than the general population.\n\nFundingThis study was funded by the European Medicines Agency (EMA/2017/09/PE Lot 3).", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Edward Burn", - "author_inst": "Centre for Statistics in Medicine (CSM), NDORMS, University of Oxford, UK. Fundaci\u00f3 Institut Universitari per a la recerca a \u013aAtenci\u00f3 Prim\u00e1ria de Salut Jordi Go" - }, - { - "author_name": "Xintong Li", - "author_inst": "Centre for Statistics in Medicine (CSM), Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDROMS), University of Oxford, UK" - }, - { - "author_name": "Kristin Kostka", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, US. The OHDSI Center at The Roux Institute, Northeastern University, Portland, ME, US" - }, - { - "author_name": "Henry Morgan Stewart", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, US," - }, - { - "author_name": "Christian Reich", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, US," - }, - { - "author_name": "Sarah Seager", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, US," - }, - { - "author_name": "Talita Duarte-Salles", - "author_inst": "Fundaci\u00f3 Institut Universitari per a la recerca a \u013aAtenci\u00f3 Prim\u00e1ria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Sergio Fernandez-Bertolin", - "author_inst": "Fundaci\u00f3 Institut Universitari per a la recerca a \u013aAtenci\u00f3 Prim\u00e1ria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Mar\u00eda Arag\u00f3n", - "author_inst": "Fundaci\u00f3 Institut Universitari per a la recerca a \u013aAtenci\u00f3 Prim\u00e1ria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Carlen Reyes", - "author_inst": "Fundaci\u00f3 Institut Universitari per a la recerca a \u013aAtenci\u00f3 Prim\u00e1ria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Eugenia Martinez-Hernandez", - "author_inst": "Department of Neurology, Hospital Clinic and University of Barcelona, Barcelona, Spain," - }, - { - "author_name": "Edelmira Marti", - "author_inst": "Hemostasis and Thrombosis Unit, Hematology Department, Hospital Cl\u00ednico Universitario de Valencia, Spain," - }, - { - "author_name": "Antonella Delmestri", - "author_inst": "Centre for Statistics in Medicine (CSM), Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDROMS), University of Oxford, UK," - }, - { - "author_name": "Katia Verhamme", - "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" - }, - { - "author_name": "Peter Rijnbeek", - "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" - }, - { - "author_name": "Scott Horban", - "author_inst": "Health Informatics Centre, University of Dundee, Dundee UK" - }, - { - "author_name": "Daniel R Morales", - "author_inst": "Division of Population Health and Genomics, University of Dundee, Dundee, UK. Department of Public Health, University of Southern Denmark, Odense, Denmark" - }, - { - "author_name": "DANIEL PRIETO-ALHAMBRA", - "author_inst": "Centre for Statistics in Medicine (CSM), NDORMS, University of Oxford. Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Neth" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2021.05.11.21257021", "rel_title": "Establishment of an evaluation panel for the decentralized technical evaluation of the sensitivity of 31 rapid detection tests for SARS-CoV-2 diagnostics", @@ -766558,6 +767662,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.06.21256738", + "rel_title": "The evaluation of a novel digital immunochromatographic assay with silver amplification to detect SARS-CoV-2", + "rel_date": "2021-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256738", + "rel_abs": "IntroductionRapid antigen tests are convenient for diagnosing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, they have lower sensitivities than nucleic acid amplification tests. In this study, we evaluated the diagnostic performance of Quick Chaser(R) Auto SARS-CoV-2, a novel digital immunochromatographic assay that is expected to have higher sensitivity than conventional antigen tests.\n\nMethodsA prospective observational study was conducted between February 8 and March 24, 2021. We simultaneously obtained two nasopharyngeal samples, one for evaluation with the QuickChaser(R) Auto SARS-CoV-2 antigen test and the other for assessment with reverse transcription PCR (RT-PCR), considered the gold-standard reference test. The limit of detection (LOD) of the new antigen test was compared with those of four other commercially available rapid antigen tests.\n\nResultsA total of 1401 samples were analyzed. SARS-CoV-2 was detected by reference RT-PCR in 83 (5.9%) samples, of which 36 (43.4%) were collected from symptomatic patients. The sensitivity, specificity, positive predictive value, and negative predictive value were 74.7% (95% confidence interval (CI): 64.0-83.6%), 99.8% (95% CI: 99.5-100%), 96.9% (95% CI: 89.2-99.6%), and 98.4% (95% CI: 97.6-99.0%), respectively. When limited to samples with a cycle threshold (Ct) <30 or those from symptomatic patients, the sensitivity increased to 98.3% and 88.9%, respectively. The QuickChaser(R) Auto SARS-CoV-2 detected 34-120 copies/test, which indicated greater sensitivity than the other rapid antigen tests.\n\nConclusionsQuickChaser(R) Auto SARS-CoV-2 showed sufficient sensitivity and specificity in clinical samples of symptomatic patients. The sensitivity was comparable to RT-PCR in samples with Ct<30.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Yoko Kurihara", + "author_inst": "University of Tsukuba Hospital" + }, + { + "author_name": "Yoshihiko Kiyasu", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Yusaku Akashi", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Yuto Takeuchi", + "author_inst": "University of Tsukuba Hospital" + }, + { + "author_name": "Kenji Narahara", + "author_inst": "Mizuho Medy Co., Ltd." + }, + { + "author_name": "Sunao Mori", + "author_inst": "Mizuho Medy Co., Ltd." + }, + { + "author_name": "Tomonori Takeshige", + "author_inst": "Mizuho Medy Co., Ltd." + }, + { + "author_name": "Shigeyuki Notake", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Atsuo Ueda", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Koji Nakamura", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Hiroichi Ishikawa", + "author_inst": "Tsukuba Medical Center Hospital" + }, + { + "author_name": "Hiromichi Suzuki", + "author_inst": "University of Tsukuba" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.12.21256693", "rel_title": "Nanopore Sequencing of SARS-CoV-2: Comparison of Short and Long PCR-tiling Amplicon Protocols", @@ -767853,49 +769020,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.10.21256423", - "rel_title": "Insights into genetic factors contributing to variability in SARS-CoV-2 susceptibility and COVID-19 disease severity", - "rel_date": "2021-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.10.21256423", - "rel_abs": "Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we applied colocalization to compare summary statistics for 16 GWASs from the COVID-19 Host Genetics Initiative to investigate similarities and differences in their genetic signals. We identified 9 loci associated with susceptibility (one with two independent GWAS signals; one with an ethnicity-specific signal), 14 associated with severity (one with two independent GWAS signals; two with ethnicity-specific signals) and one harboring two discrepant GWAS signals (one for susceptibility; one for severity). Utilizing colocalization we also identified 45 GTEx tissues that had eQTL(s) for 18 genes strongly associated with GWAS signals in eleven loci (1-4 genes per locus). Some of these genes showed tissue-specific altered expression and others showed altered expression in up to 41 different tissue types. Our study provides insights into the complex molecular mechanisms underlying inherited predispositions to COVID-19-disease phenotypes.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Matteo D'Antonio", - "author_inst": "University of California San Diego" - }, - { - "author_name": "- The COVID-19 Host Genetics Initiative", - "author_inst": "-" - }, - { - "author_name": "Timothy D. Arthur", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Jennifer P. Nguyen", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Hiroko Matsui", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Agnieszka D'Antonio-Chronowska", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Kelly A. Frazer", - "author_inst": "University of California, San Diego" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.05.10.21256978", "rel_title": "A Simple Mathematical Tool to Help Distribute Doses of Two-Dose Covid-19 Vaccines among Non-Immunized and Partly-Immunized Population", @@ -768292,6 +769416,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.05.11.21257016", + "rel_title": "Comparative sensitivity evaluation for 122 CE-marked SARS-CoV-2 antigen rapid tests", + "rel_date": "2021-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21257016", + "rel_abs": "ObjectiveIndependent evaluation of the sensitivity of CE-marked SARS-CoV-2 antigen rapid diagnostic tests (Ag RDT) offered in Germany.\n\nMethodThe sensitivity of 122 Ag RDT was adressed using a common evaluation panel. Minimum sensitivity of 75% for panel members with CT<25 was used for differentiation of devices eligible for reimbursement in in the German healthcare system.\n\nResultsThe sensitivity of different SARS-CoV-2 Ag RDT varied over a wide range. The sensitivity limit of 75% for panel members with CT <25 was met by 96 of the 122 tests evaluated; 26 tests exhibited lower sensitivity, few of which were completely failing. Some devices exhibited high sensitivity, e.g. 100% for CT<30.\n\nConclusionThis comparative evaluation succeeded to distinguish less sensitive from better performing Ag RDT. Most of the Ag RDT evaluated appear to be suitable for fast identification of acute infections associated with high viral loads. Market access of SARS-CoV-2 Ag RDT should be based on minimal requirements for sensitivity and specificity.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Heinrich Scheiblauer", + "author_inst": "Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, D-63225 Langen" + }, + { + "author_name": "Angela Filomena", + "author_inst": "Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, D-63225 Langen" + }, + { + "author_name": "Andreas Nitsche", + "author_inst": "Robert Koch-Institute, Seestrasse 10, D-13353 Berlin" + }, + { + "author_name": "Andreas Puyskens", + "author_inst": "Robert Koch-Institute, Seestrasse 10, D-13353 Berlin" + }, + { + "author_name": "Victor Corman", + "author_inst": "Institute of Virology, Charite, Chariteplatz 1, D-10117 Berlin" + }, + { + "author_name": "Christian Drosten", + "author_inst": "Institute of Virology, Charite, Chariteplatz 1, D-10117 Berlin" + }, + { + "author_name": "Katrin Zwirglmaier", + "author_inst": "Bundeswehr Institute of Microbiology, Neuherbergstr 11, D-80937 Munich" + }, + { + "author_name": "Constanze Lange", + "author_inst": "LADR GmbH, Lauenburger Str. 67, D-21502 Geesthacht" + }, + { + "author_name": "Petra Emmerich", + "author_inst": "Bernhard-Nocht Institute, Dep.Virology, Bernhard-Nocht Str. 74, D-20359 Hamburg" + }, + { + "author_name": "Michael Mueller", + "author_inst": "MVZ Labor 28 GmbH, Mecklenburgische Str. 2, D-14197 Berlin" + }, + { + "author_name": "Olivia Knauer", + "author_inst": "Paul-Ehrlich-Institute, Paul-Ehrlich-Str. 51-59, D-63225 Langen" + }, + { + "author_name": "Micha Nuebling", + "author_inst": "Paul-Ehrlich-Institut" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.10.21256996", "rel_title": "Quantifying the potential for dominant spread of SARS-CoV-2 variant B.1.351 in the United States", @@ -770159,41 +771346,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.05.11.21256886", - "rel_title": "Lack of evidence for infectious SARS-CoV-2 in feces and sewage", - "rel_date": "2021-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21256886", - "rel_abs": "PurposeThe SARS-CoV-2 coronavirus is a respiratory virus whose primary route of transmission is airborne. However, it has been shown that the virus can replicate in gastrointestinal cells, can be excreted in feces, and can reach sewage systems. Although viral RNA has been found in patient feces and sewage, little is known about the potential fecal-oral transmission of the coronavirus. Determining the presence of infective viral particles in feces and sewage is necessary to take adequate control measures and to discover new routes of coronavirus transmission.\n\nMethodsFeces and urine of COVID-19 patients, and wastewater samples at the time of high prevalence in the region under study (Valencia, Spain), have been analyzed both by molecular methods and cell culture.\n\nResultsPresence of SARS-CoV-2 in feces of COVID-19 patients has been detected, even in patients without gastrointestinal symptoms, suggesting that viral shedding though stool is common. In addition, we have developed a sample concentration methodology that allows us to maintain the infectivity of the viral particles present in the samples. Finally, inoculation of cell cultures with fecal and sewage concentrated samples do not evidence the presence of infective viral particles.\n\nConclusionThere is no evidence of the presence of infectious SARS-CoV-2 in feces and sewage, suggesting that fecal-oral transmission is not a primary route. However, larger-scale efforts are needed to elucidate whether the fecal-oral transmission should be considered, especially with the emergence of new viral variants.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sandra Albert", - "author_inst": "Instituto de Biologia Integrativa de Sistemas, Universitat de Valencia-CSIC, Paterna, Spain" - }, - { - "author_name": "Alba Ruiz", - "author_inst": "Instituto de Investigacion Sanitaria La Fe, Hospital Universitari i Politecnic La Fe, Valencia, Spain" - }, - { - "author_name": "Javier Peman", - "author_inst": "Instituto de Investigacion Sanitaria La Fe, Hospital Universitari i Politecnic La Fe, Valencia, Spain" - }, - { - "author_name": "Miguel Salavert", - "author_inst": "Instituto de Investigacion Sanitaria La Fe, Hospital Universitari i Politecnic La Fe, Valencia, Spain" - }, - { - "author_name": "Pilar Domingo-Calap", - "author_inst": "Instituto de Biologia Integrativa de Sistemas, Universitat de Valencia-CSIC, Paterna, Spain and Department of Genetics, Universitat de Valencia, Burjassot, Spai" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.10.21256935", "rel_title": "Identifying risk factors for COVID-19 severity and mortality in the UK Biobank", @@ -770434,6 +771586,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.11.21256479", + "rel_title": "Communicable and non-communicable co-morbidities and the presentation of COVID-19 in an African setting of high HIV-1 and tuberculosis prevalence", + "rel_date": "2021-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21256479", + "rel_abs": "ObjectivesTo describe the presentation and outcome of SARS-CoV2 infection in an African setting of high non-communicable co-morbidity and also HIV-1 and tuberculosis prevalence.\n\nDesignCase control analysis with cases stratified by HIV-1 and tuberculosis status.\n\nSettingA single-centre observational case-control study of adults admitted to a South African hospital with proven SARS-CoV-2 infection or alternative diagnosis.\n\nParticipants104 adults with RT-PCR-proven SARS-CoV2 infection of which 55 (52.9%) were male and 31 (29.8%) HIV-1 co-infected. 40 adults (35.7% male, 30.9% HIV-1 co-infected) admitted during the same period with no RT-PCR or serological evidence of SARS-CoV2 infection and assigned alternative diagnoses. Additional in vitro data from prior studies of 72 healthy controls and 118 HIV-1 uninfected and infected persons participants enrolled to a prior study with either immune evidence of tuberculosis sensitization but no symptoms or microbiologically confirmed pulmonary tuberculosis.\n\nResultsTwo or more co-morbidities were present in 57.7% of 104 RT-PCR proven COVID-19 presentations, the commonest being hypertension (48%), type 2 diabetes mellitus (39%), obesity (31%) but also HIV-1 (30%) and active tuberculosis (14%). Amongst patients dually infected by tuberculosis and SARS-CoV-2, clinical features could be dominated by either SARS-CoV-2 or tuberculosis: lymphopenia was exacerbated, and some markers of inflammation (D-dimer and ferritin) elevated in singly SARS-CoV-2 infected patients were even further elevated (p < 0.05). HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, with those in the lowest peripheral CD4 percentage strata exhibiting absent or lower antibody responses against SARS-CoV2. Death occurred in 30/104 (29%) of all COVID-19 patients and in 6/15 (40%) of patients with coincident SARS-CoV-2 and tuberculosis.\n\nConclusionsIn this South African setting, HIV-1 and tuberculosis are common co-morbidities in patients presenting with COVID-19. In environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease. Clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high.\n\nWhat is already known on this topic?It has been quite widely thought that Africa has been spared the worst effects of the COVID-19 pandemic. There are very few reported case series and no case-control studies comparing COVID-19 patients admitted to hospital to those admitted for other reasons. However several studies have indicated both HIV-1 and tuberculosis co-infection that are endemic in Africa constitute risk factors for poor outcome. In addition Africa is subject to demographic transition and the prevalence of non-communicable co-morbidities such as type 2 diabetes, hypertension and cardiovascular disease is rising rapidly. No study from Africa has described the clinical impact on the presentation of COVID-19 infection.\n\nWhat this study addsTwo or more co-morbidities were present in over half COVID-19 presentations, including HIV-1 (30%) and active tuberculosis (14%). Patients dually infected by tuberculosis and SARS-CoV-2, presented as either SARS-CoV-2 or tuberculosis. HIV-1 and SARS-CoV2 co-infection resulted in lower absolute number and proportion of CD4 lymphocytes, and those with low CD4 counts had absent or lower antibody responses against SARS-CoV2. Death occurred 29% of all COVID-19 patients and in 40% of patients with coincident SARS-CoV-2 and tuberculosis. Thus in environments in which tuberculosis is common, SARS-CoV-2 and tuberculosis may co-exist with clinical presentation being typical of either disease and clinical suspicion of exacerbation of co-existent tuberculosis accompanying SARS-CoV-2 should be high.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Elsa du Bruyn", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Cari Stek", + "author_inst": "University of Cape Town and Imperial College London" + }, + { + "author_name": "Remy Daroowala", + "author_inst": "Imperial College London and University of Cape Town" + }, + { + "author_name": "Qonita Said-Hartley", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Marvin Hsiao", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Rene Tina Goliath", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Fatima Abrahams", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Amanda Jackson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Sean Wasserman", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Brian Allwood", + "author_inst": "University of Stellenbosch" + }, + { + "author_name": "Angharad G Davis", + "author_inst": "University College London, Francis Crick Institute, and University of Cape Town" + }, + { + "author_name": "Rachel Lai", + "author_inst": "Imperial College London and Francis Crick Institute" + }, + { + "author_name": "Anna Kathleen Coussens", + "author_inst": "Walter and Eliza Hall Institute and University of Cape Town" + }, + { + "author_name": "Katalin Andrea Wilkinson", + "author_inst": "The Francis Crick Institute and University of Cape Town" + }, + { + "author_name": "Jantina De Vries", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Nicki Tiffin", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Maddalena Cerrone", + "author_inst": "Imperial College London and Francis Crick Institute" + }, + { + "author_name": "Ntobeko Ntusi", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Catherine Riou", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Robert J Wilkinson", + "author_inst": "University of Cape Town" + }, + { + "author_name": "- HIATUS investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.05.11.21256877", "rel_title": "A blood atlas of COVID-19 defines hallmarks of disease severity and specificity", @@ -772729,161 +773980,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.07.21256388", - "rel_title": "SARS-CoV-2 antibody prevalence among homeless people, sex workers and shelter workers in Denmark: a nationwide cross-sectional study", - "rel_date": "2021-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256388", - "rel_abs": "BackgroundPeople experiencing homelessness (PEH) and associated shelter workers may be at higher risk of infection with \"Severe acute respiratory syndrome coronavirus 2\" (SARS-CoV-2). The aim of this study was to determine the prevalence of SARS-CoV-2 among PEH and shelter workers in Denmark.\n\nDesign and methodsIn November 2020, we conducted a nationwide cross-sectional seroprevalence study among PEH and shelter workers at 21 recruitment sites in Denmark. The assessment included a point-of-care test for antibodies against SARS-CoV-2, followed by a questionnaire. The seroprevalence was compared to that of geographically matched blood donors considered as a proxy for the background population, tested using a total Ig ELISA assay.\n\nResultsWe included 827 participants in the study, of whom 819 provided their SARS-CoV-2 antibody results. Of those, 628 were PEH (median age 50.8 (IQR 40.9-59.1) years, 35.5% female) and 191 were shelter workers (median age 46.6 (IQR 36.1-55.0) years and 74.5% female). The overall seroprevalence was 6.7% and was similar among PEH and shelter workers (6.8% vs 6.3%, p=0.87); and 12.2% among all participants who engaged in sex work. The overall participant seroprevalence was significantly higher than that of the background population (2.9%, p <0.001). When combining all participants who reported sex work or were recruited at designated safe havens, we found a significantly increased risk of seropositivity compared to other participants (RR 2.1, 95% CI 1.16-3.75, p=0.02). Seropositive and seronegative participants reported a similar presence of at least one SARS-CoV-2 associated symptom (49% and 54%, respectively).\n\nInterpretationsThe prevalence of SARS-CoV-2 antibodies was more than twice as high among PEH and associated shelter workers, compared to the background population. The subset of the study participants who were also sex workers were at particularly high risk of COVID-19 infection.\n\nFundingTrygFonden and HelseFonden.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Alexandra R. Roethlin Eriksen", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark" - }, - { - "author_name": "Kamille Fogh", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark" - }, - { - "author_name": "Rasmus Bo Hasselbalch", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark" - }, - { - "author_name": "Henning Bundgaard", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Rigshospitalet, Denmark" - }, - { - "author_name": "Susanne Dam Nielsen", - "author_inst": "Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Denmark" - }, - { - "author_name": "Charlotte Svaerke Joergensen", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Bibi FSS Scharff", - "author_inst": "Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Denmark" - }, - { - "author_name": "Christian Erikstrup", - "author_inst": "Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark" - }, - { - "author_name": "Susanne G Saekmose", - "author_inst": "Department of Clinical Immunology, Zealand University Hospital, Koege, Denmark" - }, - { - "author_name": "Dorte K Holm", - "author_inst": "Department of Clinical Immunology, Odense University Hospital, Odense, Denmark" - }, - { - "author_name": "Bitten Aagaard", - "author_inst": "Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark" - }, - { - "author_name": "Jonas H Kristensen", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark" - }, - { - "author_name": "Cecilie A Boedker", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark" - }, - { - "author_name": "Jakob B Norsk", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark" - }, - { - "author_name": "Pernille B Nielsen", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark" - }, - { - "author_name": "Lars Oestergaard", - "author_inst": "Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark" - }, - { - "author_name": "Svend Ellermann-Eriksen", - "author_inst": "Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark" - }, - { - "author_name": "Berit Andersen", - "author_inst": "University Research Clinic for Cancer Screening, Randers Regional Hospital, Randers, Denmark" - }, - { - "author_name": "Henrik Nielsen", - "author_inst": "Department of Infectious Diseases, Aalborg University Hospital, Aalborg, Denmark" - }, - { - "author_name": "Isik S Johansen", - "author_inst": "Department of Infectious Diseases, Odense University Hospital, Odense, Denmark" - }, - { - "author_name": "Lothar Wiese", - "author_inst": "Department of Infectious Diseases, Zealand University Hospital, Roskilde, Denmark" - }, - { - "author_name": "Lone Simonsen", - "author_inst": "Department of Science and Environment, University of Roskilde, Denmark" - }, - { - "author_name": "Thea K Fischer", - "author_inst": "Department of Clinical Research, North Zealand Hospital, Hilleroed, Denmark" - }, - { - "author_name": "Fredrik Folke", - "author_inst": "Copenhagen Emergency Medical Services, Copenhagen, Denmark" - }, - { - "author_name": "Freddy Lippert", - "author_inst": "Copenhagen Emergency Medical Services, Copenhagen, Denmark" - }, - { - "author_name": "Sisse R Ostrowski", - "author_inst": "Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Denmark" - }, - { - "author_name": "Steen Ethelberg", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Anders Koch", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Anne-Marie Vangsted", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Tyra Krause", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Anders Fomsgaard", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Claus Nielsen", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Henrik Ullum", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Robert Skov", - "author_inst": "Statens Serum Institut, Copenhagen, Denmark" - }, - { - "author_name": "Kasper K Iversen", - "author_inst": "Department of Cardiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.08.21256845", "rel_title": "Association of Obesity with COVID-19 Severity and Mortality: A Systemic Review and Meta-Regression", @@ -773096,6 +774192,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.07.21256743", + "rel_title": "Effect of using personal protective equipment during the COVID-19 pandemic on the quality indicators of screening colonoscopies.", + "rel_date": "2021-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256743", + "rel_abs": "BackgroundCoronavirus Disease 2019 (COVID-19) has affected many facets of the practice of medicine including screening colonoscopies.\n\nAimsOur study looks to observe if there has been an effect on the quality of colonoscopies, as indicated by quality measures such as cecal intubation rate (CIR), cecal intubation time (CIT), scope withdrawal time (SWT) and adenoma detection rate (ADR) with the adoption of standard COVID-19 precautions.\n\nMethodsWe conducted a retrospective chart review to analyze the effects of the COVID-19 pandemic on screening colonoscopies. The study utilized data on CIR, CIT, SWT and ADR from outpatient, non-emergent procedures conducted at 3 endoscopy suites of St Lukes University Health Network. All inpatient and emergent procedures were excluded.\n\nResultsOur study demonstrated that the total number of screening colonoscopies was decreased between 2019 to 2020 (318 in 2019 vs 157 in 2020, p= 0.005). CIT (320{+/-}105 seconds in 2019 vs 392{+/-}107 seconds in 2020, p=0.001) and SWT (706{+/-}232 seconds in 2019 vs 830{+/-}241 seconds in 2020, p=0.001) were increased while CIR (98.2% in 2019 vs 96.6% in 2020, p=0.04) was decreased between 2019 and 2020 likely due to PPE introduction. ADR was similar between the two groups (38.23 (12.50-66.66) in 2019 vs 38.18(16.66-66.00) in 2020, p=0.8).\n\nConclusionOur study showed that quality indices for screening colonoscopies like CIR, CIT, and SWT were negatively impacted during the COVID-19 time period. ADR, however, were similar. Thus, the efficiency of the procedures was affected by the use of PPE but it did not affect the colonoscopys clinical benefit.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Subin G Chirayath", + "author_inst": "St. Luke's University Hospital" + }, + { + "author_name": "Janak Bahirwani", + "author_inst": "St. Luke's University Hospital" + }, + { + "author_name": "Parampreet Kaur", + "author_inst": "St. Luke's University Hospital" + }, + { + "author_name": "Noel Martins", + "author_inst": "St. Luke's University Hospital" + }, + { + "author_name": "Ronak Modi", + "author_inst": "St. Luke's University Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2021.05.08.21256792", "rel_title": "Yet another lockdown? A large-scale study on people's unwillingness to be confined during the first 5 months of the COVID-19 pandemic in Spain", @@ -774863,217 +775994,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.09.442808", - "rel_title": "A human antibody that broadly neutralizes betacoronaviruses protects against SARS-CoV-2 by blocking the fusion machinery", - "rel_date": "2021-05-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.09.442808", - "rel_abs": "The repeated spillovers of {beta}-coronaviruses in humans along with the rapid emergence of SARS-CoV-2 escape variants highlight the need to develop broad coronavirus therapeutics and vaccines. Five monoclonal antibodies (mAbs) were isolated from COVID-19 convalescent individuals and found to cross-react with multiple {beta}-coronavirus spike (S) glycoproteins by targeting the stem helix. One of these mAbs, S2P6, cross-reacts with more than twenty human and animal {beta}-coronavirus S glycoproteins and broadly neutralizes SARS-CoV-2 and pseudotyped viruses from the sarbecovirus, merbecovirus and embecovirus subgenera. Structural and functional studies delineate the molecular basis of S2P6 cross-reactivity and broad neutralization and indicate that this mAb blocks viral entry by inhibiting membrane fusion. S2P6 protects hamsters challenged with SARS-CoV-2 (including the B.1.351 variant of concern) through direct viral neutralization and Fc-mediated effector functions. Serological and B cell repertoire analyses indicate that antibodies targeting the stem helix are found in some convalescent donors and vaccinees but are predominantly of narrow specificity. Germline reversion of the identified cross-reactive mAbs revealed that their unmutated ancestors are specific for the endemic OC43 or HKU1 viruses and acquired enhanced affinity and breadth through somatic mutations. These data demonstrate that conserved epitopes in the coronavirus fusion machinery can be targeted by protective antibodies and provide a framework for structure-guided design of pan-{beta}-coronavirus vaccines eliciting broad protection.", - "rel_num_authors": 49, - "rel_authors": [ - { - "author_name": "Dora Pinto", - "author_inst": "Humabs BioMed SA" - }, - { - "author_name": "Maximilian M. Sauer", - "author_inst": "University of Washington" - }, - { - "author_name": "Nadine Czudnochowski", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Jun Siong Low", - "author_inst": "Institute for Research in Biomedicine" - }, - { - "author_name": "M. Alejandra Tortorici", - "author_inst": "University of Washington" - }, - { - "author_name": "Michael P. Housley", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Julia Noack", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Alexandra C. Walls", - "author_inst": "University of Washington" - }, - { - "author_name": "John E. Bowen", - "author_inst": "University of Washington" - }, - { - "author_name": "Barbara Guarino", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Laura E. Rosen", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Julia di Iulio", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Josipa Jerak", - "author_inst": "Institute for Research in Biomedicine" - }, - { - "author_name": "Hanna Kaiser", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Saiful Islam", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Stefano Jaconi", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Nicole Sprugasci", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Katja Culap", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Rana Abdelnabi", - "author_inst": "Rega Institute, KU Leuven" - }, - { - "author_name": "Caroline Shi-Yan Foo", - "author_inst": "Katholieke Universiteit Leuven" - }, - { - "author_name": "Lotte Coelmont", - "author_inst": "KU Leuven" - }, - { - "author_name": "Istvan Bartha", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Siro Bianchi", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Chiara Silacci-Fregni", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Jessica Bassi", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Roberta Marzi", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Eneida Vetti", - "author_inst": "Humans Biomed SA" - }, - { - "author_name": "Antonino Cassotta", - "author_inst": "Institute for Research in Biomedicine" - }, - { - "author_name": "Alessandro Ceschi", - "author_inst": "Ente Ospedaliero Cantonale" - }, - { - "author_name": "Paolo Ferrari", - "author_inst": "Universita della Svizzera italiana" - }, - { - "author_name": "Samuele Ceruti", - "author_inst": "Clinica Luganese Moncucco" - }, - { - "author_name": "Agostino Riva", - "author_inst": "Luigi Sacco Hospital" - }, - { - "author_name": "Fabio Benigni", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Elisabetta Cameroni", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Luca Piccoli", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Matteo Samuele Pizzuto", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Meghan Smithey", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "David Hong", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Amalio Telenti", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Florian A. Lempp", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Johan Neyts", - "author_inst": "Rega Institute" - }, - { - "author_name": "Colin Havenar-Daughton", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Antonio Lanzavecchia", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Federica Sallusto", - "author_inst": "Institute for Research in Biomedicine" - }, - { - "author_name": "Gyorgy Snell", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Herbert W. Virgin", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Martina Beltramello", - "author_inst": "Humabs Biomed SA" - }, - { - "author_name": "Davide Corti", - "author_inst": "Humabs Biomed SA, subsidiary of Vir Biotechnology" - }, - { - "author_name": "David Veesler", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.05.09.443299", "rel_title": "Infection and vaccine-induced neutralizing antibody responses to the SARS-CoV-2 B.1.617.1 variant", @@ -775350,6 +776270,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.05.21256668", + "rel_title": "COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland", + "rel_date": "2021-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256668", + "rel_abs": "The COVID-19 pandemic has led to unprecedented restrictions in peoples lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring peoples psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively.\n\nClinical relevanceIn 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sofia de la Fuente Garcia", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Fasih Haider", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Saturnino Luz", + "author_inst": "The University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.05.05.21256677", "rel_title": "SARS-CoV-2 RNA in urban wastewater samples to monitor the COVID-19 epidemic in Lombardy, Italy (March - June 2020)", @@ -777317,37 +778264,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.05.04.21256613", - "rel_title": "Meta-Analysis of Risk of Vaccine-Induced Immune Thrombotic Thrombocytopenia Following ChAdOx1-S Recombinant Vaccine", - "rel_date": "2021-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256613", - "rel_abs": "ContextVaccine-induced immune thrombotic thrombocytopenia (VITT) has been reported after administering ChAdOx1-S recombinant COVID-19 vaccine (marketed as Vaxzevira by Astra-Zeneca, Covishield). Estimates of incidence vary between countries, due to different age distributions chosen, case definitions and choice of denominator (persons vaccinated vs immunizations given). This study clarifies these estimates by pooling data from ten countries and examining differences by age group.\n\nMethodsWe examined case reports, press releases and immunization data and calculated pooled estimates of VITT incidence using random effects models. Sensitivity analyses considered different combinations of countries and varying assumptions on time between vaccination and reporting of cases.\n\nResultsPooling all countries, VITT incidence was 0.73 per 100,000 persons receiving first dose of Covishield/Vaxzevira [95% CI .43,1.23]. Incidence for age 65 and over was 0.11 per 100,000 persons [95% CI .05-.26], and significantly higher among those under age 55: 1.67 per 100,000 persons [95% CI 1.30-2.14] in the UK, 5.06 per 100,000 persons in Norway [95% CI 2.16, 11.86]. The latter had the best data on counts of persons vaccinated. Incidence for age 55 to 64 years was 0.34 [95% CI 0.13, 0.85] in the UK, lower than for under age 55.\n\nConclusionVITT is a rare vaccine-associated adverse event. Incidence estimates vary between jurisdictions. However, even the highest reported incidence from Norway is low - and in settings with high community transmission, lower than risk of serious outcomes associated with Covid-19. Policymakers and individuals can use these data to calculate risk-benefit ratios and better target vaccine distribution.\n\nEssentialsO_LIThis paper measures risk of vaccine-induced immune thrombotic thrombocytopenia (VITT) after ChAdOx1-S recombinant COVID-19 vaccine\nC_LIO_LIPooled estimates of incidence were calculated with a random effects model based on data from 10 countries\nC_LIO_LIOverall risk is 1 in 139,000; for age 65 and over, about 1 in 1,000,000; for age under 55, between 1 in 20,000 to 60,000\nC_LIO_LIVITT risk is low and varies by age. These data can inform policies around vaccination distribution.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Benjamin T.B. Chan", - "author_inst": "Institute for Healthcare Policy, Management & Evaluation, University of Toronto" - }, - { - "author_name": "Pavlos Bobos", - "author_inst": "Applied Health Research Centre (AHRC), Li Ka Shing Knowledge Institute of St. Michael's Hospital, Toronto, Canada" - }, - { - "author_name": "Ayodele Odutayo", - "author_inst": "Division of Nephrology, Department of Medicine, University of Toronto" - }, - { - "author_name": "Menaka Pai", - "author_inst": "Division of Hematology & Thromboembolism, Department of Medicine, McMaster University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2021.05.04.21256611", "rel_title": "Effect of storage conditions on SARS-CoV-2 RNA quantification in wastewater solids", @@ -777500,6 +778416,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.05.04.21256655", + "rel_title": "COVID-19 cases from the first local outbreak of SARS-CoV-2 B.1.1.7 variant in China presented more serious clinical features: a prospective, comparative cohort study", + "rel_date": "2021-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256655", + "rel_abs": "BackgroundThe SARS-CoV-2 B.1.1.7 variant which was first identified in the United Kingdom (U.K.) has increased sharply in numbers worldwide and was reported to be more contagious. On January 17, 2021, a COVID-19 clustered outbreak caused by B.1.1.7 variant occurred in a community in Daxing District, Beijing, China. Three weeks prior, another non-variant (lineage B.1.470) COVID-19 outbreak occurred in Shunyi District, Beijing. This study aimed to investigate the clinical features of B.1.1.7 variant infection.\n\nMethodsA prospective cohort study was conducted on COVID-19 cases admitted to Ditan hospital since January 2020. Data of 74 COVID-19 cases from two independent COVID-19 outbreaks in Beijing were extracted as study subjects from a Cloud Database established in Ditan hospital, which included 41 Shunyi cases (Shunyi B.1.470 group) and 33 Daxing cases (Daxing B.1.1.7 group) that have been hospitalized since December 25, 2020 and January 17, 2021, respectively. We conducted a comparison of the clinical characteristics, RT-qPCR results and genomic features between the two groups.\n\nFindingsCases from Daxing B.1.1.7 group (15 [45.5%] male; median age, 39 years [range, 30.5, 62.5]) and cases from Shunyi B.1.470 group (25 [61.0%] male; median age, 31 years [range, 27.5, 41.0]) had a statistically significant difference in median age (P =0.014). Seven clinical indicators of Daxing B.1.1.7 group were significantly higher than Shunyi B.1.470 group including patients having fever over 38{degrees}C (14/33 [46.43%] in Daxing B.1.1.7 group vs. 9/41 (21.95%) in Shunyi B.1.470 group [P = 0 .015]), C-reactive protein ([CRP, mg/L], 4.30 [2.45, 12.1] vs. 1.80, [0.85, 4.95], [P = 0.005]), Serum amyloid A ([SAA, mg/L], 21.50 [12.50, 50.70] vs. 12.00 [5.20, 26.95], [P = 0.003]), Creatine Kinase ([CK, U/L]), 110.50 [53.15,152.40] vs. 70.40 [54.35,103.05], [P = 0.040]), D-dimer ([DD, mg/L], 0.31 [0.20, 0.48] vs. 0.24 [0.17,0.31], [P = 0.038]), CD4+ T lymphocyte ([CD4+ T, mg/L], [P = 0.003]), and Ground-glass opacity (GGO) in lung (15/33 [45.45%] vs. 5/41 [12.20%], [P =0.001]). After adjusting for the age factor, B.1.1.7 variant infection was the risk factor for CRP (P = 0.045, Odds ratio [OR] 2.791, CI [1.025, 0.8610]), SAA (0.011, 5.031, [1.459, 17.354]), CK (0.034, 4.34, [0.05, 0.91]), CD4+ T (0.029, 3.31, [1.13, 9.71]), and GGO (0.005, 5.418, [1.656, 17.729]) of patients. The median Ct value of RT-qPCR tests of the N-gene target in the Daxing B.1.1.7 group was significantly lower than the Shunyi B.1.470 group (P=0.036). The phylogenetic analysis showed that only 2 amino acid mutations in spike protein were detected in B.1.470 strains while B.1.1.7 strains had 3 deletions and 7 mutations.\n\nInterpretationClinical features including a more serious inflammatory response, pneumonia and a possible higher viral load were detected in the cases infected with B.1.1.7 SARS-CoV-2 variant. It could therefore be inferred that the B.1.1.7 variant may have increased pathogenicity.\n\nFundingThe study was funded by the National Key Research and Development Program (grant nos.2020YFC0846200 and 2020YFC0848300) and National Natural Science Foundation of China (grant no. 82072295).", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Yang Song M.D.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Ziruo Ge M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Shuping Cui M.Sc.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China and Peking University, Ditan Teaching Hospital, Beijing, Ch" + }, + { + "author_name": "Di Tian M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Gang Wan M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Shuangli Zhu B.Sc.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Xianbo Wang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Yu Wang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Xiang Zhao M.D.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Pan Xiang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Yanli Xu M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Tingyu Zhang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Long Liu M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Gang Liu M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Yanhai Wang M.Sc.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Jianbo Tan M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Wei Zhang M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + }, + { + "author_name": "Wenbo Xu M.D.", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Zhihai Chen M.D.", + "author_inst": "Emergency department of COVID-19, Beijing Ditan Hospital, Capital Medical University, Beijing, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.04.21256635", "rel_title": "Visual Exploratory Analysis of COVID-19 Pandemic: One Year After the Outbreak", @@ -779267,69 +780274,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.05.06.442903", - "rel_title": "A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2", - "rel_date": "2021-05-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.06.442903", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019 and spread globally to cause the COVID-19 pandemic. Despite the constant accumulation of genetic variation in the SARS-CoV-2 population, there was little evidence for the emergence of significantly more transmissible lineages in the first half of 2020. Starting around November 2020, several more contagious and possibly more virulent Variants of Concern (VoCs) were reported in various regions of the world. These VoCs share some mutations and deletions that haven arisen recurrently in distinct genetic backgrounds. Here, we build on our previous work modelling the association of mutations to SARS-CoV-2 transmissibility and characterise the contribution of individual recurrent mutations and deletions to estimated viral transmissibility. We then assess how patterns of estimated transmissibility in all SARS-CoV-2 clades have varied over the course of the COVID-19 pandemic by summing transmissibility estimates for all individual mutations carried by any sequenced genome analysed. Such an approach recovers the Delta variant (21A) as the most transmissible clade currently in circulation, followed by the Alpha variant (20I). By assessing transmissibility over the time of sampling, we observe a tendency for estimated transmissibility within clades to slightly decrease over time in most clades. Although subtle, this pattern is consistent with the expectation of a decay in transmissibility in mainly non-recombining lineages caused by the accumulation of weakly deleterious mutations. SARS-CoV-2 remains a highly transmissible pathogen, though such a trend could conceivably play a role in the turnover of different global viral clades observed over the pandemic so far.\n\nCaveatsO_LIThis work is not about the severity of disease. We do not analyse the severity of disease. We do not present any evidence that SARS-CoV-2 has decreased in severity.\nC_LIO_LILineage replacement dynamics are affected by many factors. The trend we recover for a decrease in inferred transmissibility of a clade over time is a small effect. We caution against over-interpretation. This result would not affect the management of the SARS-CoV-2 pandemic: for example, we make no claims about any impact on the efficacy of particular non-pharmaceutical interventions (NPIs).\nC_LIO_LIOur phylogeny-based method to infer changes in estimated transmissibility due to recurrent mutations and deletions makes a number of simplifying assumptions. These may not all be valid. The consistent trend for the slight decrease we report might be due to an as-yet-unidentified systematic bias.\nC_LI", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Damien Richard", - "author_inst": "University College London" - }, - { - "author_name": "Liam P. Shaw", - "author_inst": "Oxford University" - }, - { - "author_name": "Robert Lanfear", - "author_inst": "Australian National University: Canberra, AU" - }, - { - "author_name": "Russell Corbett-Detig", - "author_inst": "UC Santa Cruz" - }, - { - "author_name": "Yatish Turakhia", - "author_inst": "University of California, Santa Cruz" - }, - { - "author_name": "Angie S Hinrichs", - "author_inst": "University of California at Santa Cruz" - }, - { - "author_name": "Jakob McBroome", - "author_inst": "UC Santa Cruz" - }, - { - "author_name": "Mislav Acman", - "author_inst": "University College London" - }, - { - "author_name": "Christopher Owen", - "author_inst": "University College London" - }, - { - "author_name": "Cedric C.S. Tan", - "author_inst": "University College London" - }, - { - "author_name": "Lucy van Dorp", - "author_inst": "UCL Genetics Institute" - }, - { - "author_name": "Francois Balloux", - "author_inst": "UCL Genetics Institute" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.05.07.443115", "rel_title": "Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques", @@ -779554,6 +780498,57 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.05.01.21256182", + "rel_title": "Modelling upper respiratory viral load dynamics of SARS-CoV-2", + "rel_date": "2021-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.01.21256182", + "rel_abs": "Relationships between viral load, severity of illness, and transmissibility of virus, are fundamental to understanding pathogenesis and devising better therapeutic and prevention strategies for COVID-19. Here we present within-host modelling of viral load dynamics observed in the upper respiratory tract (URT), drawing upon 2172 serial measurements from 605 subjects, collected from 17 different studies. We developed a mechanistic model to describe viral load dynamics and host response, and contrast this with simpler mixed-effects regression analysis of peak viral load and its subsequent decline. We observed wide variation in URT viral load between individuals, over 5 orders of magnitude, at any given point in time since symptom onset. This variation was not explained by age, sex, or severity of illness, and these variables were not associated with the modelled early or late phases of immune-mediated control of viral load. We explored the application of the mechanistic model to identify measured immune responses associated with control of viral load. Neutralizing antibody correlated strongly with modelled immune-mediated control of viral load amongst subjects who produced neutralizing antibody. Our models can be used to identify host and viral factors which control URT viral load dynamics, informing future treatment and transmission blocking interventions.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Joseph D Challenger", + "author_inst": "Imperial College London" + }, + { + "author_name": "Cher Y Foo", + "author_inst": "Imperial College London" + }, + { + "author_name": "Yue Wu", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ada WC Yan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Mahdi Moradi Marjaneh", + "author_inst": "Imperial College London" + }, + { + "author_name": "Felicity Liew", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ryan S Thwaites", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lucy C Okell", + "author_inst": "Imperial College London" + }, + { + "author_name": "Aubrey J Cunnington", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.03.21256520", "rel_title": "The BNT162b2 mRNA vaccine against SARS-CoV-2 reprograms both adaptive and innate immune responses", @@ -781377,41 +782372,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.05.04.442634", - "rel_title": "Single-virus fusion measurements yield an opportunistic model for SARS-CoV-2 fusion", - "rel_date": "2021-05-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.04.442634", - "rel_abs": "SARS-CoV-2 binds to cell-surface receptors and is activated for membrane fusion and cell entry via proteolytic cleavage. Phenomenological data have shown that SARS-CoV-2 can be activated for entry at either the cell surface or in endosomes, but the relative roles in different cell types and mechanisms of entry have been debated. Here we use single-virus fusion experiments and exogenously controlled proteases to probe activation directly. We find that plasma membrane and an appropriate protease are sufficient to support SARS-CoV-2 pseudovirus fusion. Furthermore, fusion kinetics of SARS-CoV-2 pseudoviruses are indistinguishable no matter which of a broad range of proteases was used to activate the virus. This suggests that fusion mechanism is insensitive to protease identity or even whether activation occurs before or after receptor binding. These data support a model for opportunistic fusion by SARS-CoV-2, where subcellular location of entry likely depends on the differential activity of airway, cell-surface, and endosomal proteases, but all support infection. Inhibiting any single host protease may thus reduce infection in some cells but may be less clinically robust.\n\nImportanceSARS-CoV-2 can use multiple pathways to infect cells, as demonstrated recently when new viral variants switched dominant infection pathways. Here, we use single-virus fusion experiments together with biochemical reconstitution to show that these multiple pathways coexist simultaneously and specifically that the virus can be activated by different proteases in different cellular compartments with mechanistically identical effect. The consequences of this are that the virus is evolutionarily plastic and that therapies targeting viral entry should address multiple pathways at once to achieve optimal clinical effects.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Anjali Sengar", - "author_inst": "University of Virginia" - }, - { - "author_name": "Marcos Cervantes", - "author_inst": "University of Virginia" - }, - { - "author_name": "Sai T Bondalapati", - "author_inst": "University of Virginia" - }, - { - "author_name": "Tobin Hess", - "author_inst": "University of Virginia" - }, - { - "author_name": "Peter Kasson", - "author_inst": "University of Virginia and Uppsala University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.05.442784", "rel_title": "SARS-CoV-2 B.1.1.7 and B.1.351 variants of concern induce lethal disease in K18-hACE2 transgenic mice despite convalescent plasma therapy", @@ -781607,6 +782567,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.05.442782", + "rel_title": "Combination Respiratory Vaccine Containing Recombinant SARS-CoV-2 Spike and QuadrivalentSeasonal Influenza Hemagglutinin Nanoparticles with Matrix-M Adjuvant", + "rel_date": "2021-05-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.05.442782", + "rel_abs": "The 2019 outbreak of a severe respiratory disease caused by an emerging coronavirus, SARS-CoV-2, has spread globally with high morbidity and mortality. Co-circulating seasonal influenza has greatly diminished recently, but expected to return with novel strains emerging, thus requiring annual strain adjustments. We have developed a recombinant hemagglutinin (HA) quadrivalent nanoparticle influenza vaccine (qNIV) produced using an established recombinant insect cell expression system to produce nanoparticles. Influenza qNIV adjuvanted with Matrix-M was well-tolerated and induced robust antibody and cellular responses, notably against both homologous and drifted A/H3N2 viruses in Phase 1, 2, and 3 trials. We also developed a full-length SARS-CoV-2 spike protein vaccine which is stable in the prefusion conformation (NVX-CoV2373) using the same platform technology. In phase 3 clinical trials, NVX-CoV2373 is highly immunogenic and protective against the prototype strain and B.1.1.7 variant. Here we describe the immunogenicity and efficacy of a combination quadrivalent seasonal flu and COVID-19 vaccine (qNIV/CoV2373) in ferret and hamster models. The combination qNIV/CoV2373 vaccine produces high titer influenza hemagglutination inhibiting (HAI) and neutralizing antibodies against influenza A and B strains. The combination vaccine also elicited antibodies that block SARS-CoV-2 spike protein binding to the human angiotensin converting enzyme-2 (hACE2) receptor. Significantly, hamsters immunized with qNIV/CoV2373 vaccine and challenged with SARS-CoV-2 were protected against weight loss and were free of replicating SARS-CoV-2 in the upper and lower respiratory tract with no evidence of viral pneumonia. This study supports evaluation of qNIV/CoV2373 combination vaccine as a preventive measure for seasonal influenza and CoVID-19.\n\nHighlightsO_LICombination qNIV/CoV2373 vaccine induced protective hemagglutination inhibition (HAI) responses to seasonal influenza A and B unchanged when formulated with recombinant spike.\nC_LIO_LICombination qNIV/CoV2373 vaccine maintained clinical and virologic protection against experimental challenge with SARS-CoV-2.\nC_LIO_LICombination qNIV/CoV2373 vaccine showed no clinical or histological sign of enhanced disease following experimental challenge with SARS-CoV-2.\nC_LIO_LICombination qNIV/CoV2373 vaccine induced antibodies against SARS-CoV-2 neutralizing epitopes common between US-WA and B.1.352 variant.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Micheal J Massare", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Nita Patel", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Bin Zhou", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Sonia Maciejewski", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Rhonda Flores", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Mimi Guebre-Xabier", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Jing-Hui Tian", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Alyse D Portnoff", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Louis Fries", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Vivek Shinde", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Larry R Ellingsworth", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Greg Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.04.442701", "rel_title": "SARS-CoV-2 cell-to-cell infection is resistant to neutralizing antibodies", @@ -783362,41 +784389,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.03.21256503", - "rel_title": "Protocol of the COVID-19 Health Adherence Research in Scotland Vaccination (CHARIS-V) study: Understanding the influence of vaccination decisions on adherence to transmission-reducing behaviours in a prospective longitudinal study of the Scottish Population.", - "rel_date": "2021-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.03.21256503", - "rel_abs": "IntroductionThe global population has been asked to live under tight restrictions to slow the spread of SARS-CoV-2. Transmission-reducing behaviours (TRBs), (physical distancing, hand washing, wearing a face covering) were introduced by governments in 2020 prior to vaccine availability. People should maintain TRBs throughout the vaccination programme, because there is much uncertainty about the vaccine efficacy, immunity duration, whether there will be the requirement for booster vaccines, and whether vaccinated individuals can be carriers of the virus. This study will explore the effect of the vaccination programme in Scotland on adherence to TRBs.\n\nMethods and analysisTelephone interviews will be conducted with participants from the nationally representative CHARIS project that agreed to be contacted for further research. Approximately 200, ten-minute telephone interviews will be conducted. Data will be collected on vaccine uptake or intention and adherence to TRBs. Univariate and multivariate logistic regression analyses and moderation analyses will be used to analyse the data collected. Ethical approval was granted by the Life Sciences and Medicine School Ethics Review Board (SERB) at the University of Aberdeen.\n\nDiscussionCHARIS-V will provide an understanding of the effect of the vaccination programme on adherence to TRBs in Scotland. Findings should be useful to governments and public health agencies for the current COVID-19 pandemic and vaccination programme and assist in the management of any future outbreaks.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Marina Maciver", - "author_inst": "University of Aberdeen, University of the Highlands and Islands" - }, - { - "author_name": "Chantal Den Daas", - "author_inst": "University of Aberdeen" - }, - { - "author_name": "Marie Johnston", - "author_inst": "University of Aberdeen" - }, - { - "author_name": "Diane Dixon", - "author_inst": "University of Aberdeen" - }, - { - "author_name": "Gill Hubbard", - "author_inst": "University of the Highlands and Islands" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.02.21256329", "rel_title": "Investigating the relationship between serum ACE 2 level and COVID-19 patients' prognosis: a cross-sectional study", @@ -783545,6 +784537,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.30.21256377", + "rel_title": "Disordered eating and self-harm as risk factors for poorer mental health during the COVID-19 pandemic: A population-based cohort study", + "rel_date": "2021-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256377", + "rel_abs": "BackgroundYoung adults and especially those with pre-existing mental health conditions, such as disordered eating and self-harm, appear to be at greater risk of developing metal health problems during the COVID-19 pandemic. However, it is unclear whether this increased risk is affected by any changes in lockdown restrictions, and whether any lifestyle changes could moderate this increased risk.\n\nMethodsIn a longitudinal UK-based birth cohort (The Avon Longitudinal Study of Parents and Children, ALSPAC) we assessed the relationship between pre-pandemic measures of disordered eating and self-harm and mental health during the COVID-19 pandemic in 2,657 young adults. Regression models examined the relationship between self-reported disordered eating, self-harm, and both disordered eating and self-harm at age 25 years and depressive symptoms, anxiety symptoms and mental wellbeing during a period of eased restrictions in the COVID-19 pandemic (May-July 2020) when participants were aged 27-29 years. Analyses were adjusted for sex, questionnaire completion date, pre-pandemic socioeconomic disadvantage and pre-pandemic mental health and wellbeing. We also examined whether lifestyle changes (sleep, exercise, alcohol, visiting green space, eating, talking with family/friends, hobbies, relaxation) in the initial UK lockdown (April-May 2020) moderated these associations.\n\nResultsPre-existing disordered eating, self-harm and comorbid disordered eating and self-harm were all associated with the reporting of a higher frequency of depressive symptoms and anxiety symptoms, and poorer mental wellbeing during the pandemic compared to individuals without disordered eating and self-harm. Associations remained when adjusting for pre-pandemic mental health measures. There was little evidence that interactions between disordered eating and self-harm exposures and lifestyle change moderators affected pandemic mental health and wellbeing.\n\nConclusionsYoung adults with pre-pandemic disordered eating, self-harm and comorbid disordered eating and self-harm were at increased risk for developing symptoms of depression, anxiety and poor mental wellbeing during the COVID-19 pandemic, even when accounting for pre-pandemic mental health. Lifestyle changes during the pandemic do not appear to alter this risk. A greater focus on rapid and responsive service provision is essential to reduce the impact of the pandemic on the mental health of these already vulnerable individuals.\n\nPlain English summaryThe aim of this project was to explore the mental health of young adults with disordered eating behaviours (such as fasting, vomiting/taking laxatives, binge-eating and excessive exercise) and self-harm during the COVID-19 pandemic. We analysed data from an established study that has followed children from birth (in 1991 and 1992) up to present day, including during the pandemic when participants were 28 years old. We looked at the relationship between disordered eating and/or self-harm behaviours from before the pandemic and mental health problems (symptoms of depression and anxiety) and mental wellbeing during the pandemic. We also explored whether there were any lifestyle changes (such as changes in sleep, exercise, visiting green space) that might be linked to better mental health and wellbeing in young adults with disordered eating and self-harm. We found that young adults with prior disordered eating and/or self-harm had more symptoms of depression and anxiety, and worse mental wellbeing than individuals without prior disordered eating or self-harm. However, lifestyle changes did not appear to affect mental health and wellbeing in these young adults. Our findings suggest that people with a history of disordered eating and/or self-harm were at high risk for developing mental health problems during the pandemic, and they will need help from mental health services.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Naomi Warne", + "author_inst": "University of Bristol" + }, + { + "author_name": "Jon Heron", + "author_inst": "University of Bristol" + }, + { + "author_name": "Becky Mars", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alex Siu Fung Kwong", + "author_inst": "University of Bristol" + }, + { + "author_name": "Francesca Solmi", + "author_inst": "UCL" + }, + { + "author_name": "Rebecca Pearson", + "author_inst": "Univeristy of Bristol" + }, + { + "author_name": "Paul Moran", + "author_inst": "University of Bristol" + }, + { + "author_name": "Helen Bould", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.04.442648", "rel_title": "Immunolocalization studies of vimentin and ACE2 on the surface of cells exposed to SARS-CoV-2 Spike proteins", @@ -784968,97 +786007,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.03.442357", - "rel_title": "Mouse Adapted SARS-CoV-2 protects animals from lethal SARS-CoV challenge", - "rel_date": "2021-05-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.03.442357", - "rel_abs": "The emergence of SARS-CoV-2 has resulted in a worldwide pandemic causing significant damage to public health and the economy. Efforts to understand the mechanisms of COVID-19 disease have been hampered by the lack of robust mouse models. To overcome this barrier, we utilized a reverse genetic system to generate a mouse-adapted strain of SARS-CoV-2. Incorporating key mutations found in SARSCoV-2 variants, this model recapitulates critical elements of human infection including viral replication in the lung, immune cell infiltration, and significant in vivo disease. Importantly, mouse-adaptation of SARS-CoV-2 does not impair replication in human airway cells and maintains antigenicity similar to human SARS-CoV-2 strains. Utilizing this model, we demonstrate that SARS-CoV-2 infected mice are protected from lethal challenge with the original SARS-CoV, suggesting immunity from heterologous CoV strains. Together, the results highlight the utility of this mouse model for further study of SARS-CoV-2 infection and disease.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Antonio Muruato", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Michelle Vu", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Bryan A Johnson", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Meredith Davis-Gardner", - "author_inst": "Emory University" - }, - { - "author_name": "Abigail Rose Vanderheiden", - "author_inst": "Emory University" - }, - { - "author_name": "Kumari Lokugamage", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Craig Schindewolf", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Patricia A Crocquet-Valdes", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Rose M Langsjoen", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jessica A Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kenneth S Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Scott C Weaver", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kari Debbink", - "author_inst": "Bowies State" - }, - { - "author_name": "Andrew L Routh", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "David H Walker", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Mehul S Suthar", - "author_inst": "Emory University" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Xuping Xie", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Vineet D Menachery", - "author_inst": "University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.04.21255938", "rel_title": "Longitudinal Changes in COVID-19 Associated In-Hospital Mortality", @@ -785115,6 +786063,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.04.21256298", + "rel_title": "Fatal cytokine release syndrome by an aberrant FLIP/STAT3 axis", + "rel_date": "2021-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256298", + "rel_abs": "Inflammatory responses rapidly detect pathogen invasion and mount a regulated reaction. However, dysregulated anti-pathogen immune responses can provoke life-threatening inflammatory pathologies collectively known as cytokine release syndrome (CRS), exemplified by key clinical phenotypes unearthed during the SARS-Cov-2 pandemic. The underlying pathophysiology of CRS remains elusive. We found that FLIP, a protein that controls caspase-8 death pathways, was highly expressed in myeloid cells of COVID-19 lungs. FLIP controlled CRS by fueling a STAT3-dependent inflammatory program. Indeed, constitutive expression of a viral FLIP homologue in myeloid cells triggered a STAT3-linked, progressive and fatal inflammatory syndrome in mice, characterized by elevated cytokine output, lymphopenia, lung injury and multiple organ dysfunctions that mimicked human CRS. As STAT3-targeting approaches relieved inflammation, immune disorders, and organ failures in these mice, targeted intervention towards this pathway could suppress the lethal CRS inflammatory state.\n\nOne sentence summaryFLIP-expressing myeloid cells are key drivers of CRS through aberrant overexpression of STAT3 pathway. STAT3-targeting is effective in mitigating CRS like severe COVID-19.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.05.04.21256489", "rel_title": "COVID-19 VACCINE PERCEPTIONS AND DIFFERENCES BY SEX, AGE, AND EDUCATION: FINDINGS FROM A CROSS-SECTIONAL ASSESSMENT OF 1367 COMMUNITY ADULTS IN ONTARIO", @@ -786321,53 +787283,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.30.442194", - "rel_title": "SARS-CoV-2 spike protein induces brain pericyte immunoreactivity in absence of productive viral infection", - "rel_date": "2021-05-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.30.442194", - "rel_abs": "COVID-19 is a respiratory disease caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). COVID-19 pathogenesis causes vascular-mediated neurological disorders via still elusive mechanisms. SARS-CoV-2 infects host cells by binding to angiotensin-converting enzyme 2 (ACE2), a transmembrane receptor that recognizes the viral spike (S) protein. Brain pericytes were recently shown to express ACE2 at the neurovascular interface, outlining their possible implication in microvasculature injury in COVID-19. Yet, pericyte responses to SARS-CoV-2 is still to be fully elucidated. Using cell-based assays, we report that ACE2 expression in human brain vascular pericytes is highly dynamic and is increased upon S protein stimulation. Pericytes exposed to S protein underwent profound phenotypic changes translated by increased expression of contractile and myofibrogenic proteins, namely -smooth muscle actin (-SMA), fibronectin, collagen I, and neurogenic locus notch homolog protein-3 (NOTCH3). These changes were associated to an altered intracellular calcium (Ca2+) dynamic. Furthermore, S protein induced lipid peroxidation, oxidative and nitrosative stress in pericytes as well as triggered an immune reaction translated by activation of nuclear factor-kappa-B (NF-{kappa}B) signalling pathway, which was potentiated by hypoxia, a condition associated to vascular comorbidities, which exacerbate COVID-19 pathogenesis. S protein exposure combined to hypoxia enhanced the production of pro-inflammatory cytokines involved in immune cell activation and trafficking, namely interleukin-8 (IL-8), IL-18, macrophage migration inhibitory factor (MIF), and stromal cell-derived factor-1 (SDF-1). Finally, we found that S protein could reach the mouse brain via the intranasal route and that reactive ACE2-expressing pericytes are recruited to the damaged tissue undergoing fibrotic scarring in a mouse model of cerebral multifocal micro-occlusions, a main reported vascular-mediated neurological condition associated to COVID-19. Our data demonstrate that the released S protein is sufficient to mediate pericyte immunoreactivity, which may contribute to microvasculature injury in absence of a productive viral infection. Our study provides a better understanding for the possible mechanisms underlying cerebrovascular disorders in COVID-19, paving the way to develop new therapeutic interventions.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Rayan Khaddaj-Mallat", - "author_inst": "Universit\u00e9 Laval" - }, - { - "author_name": "Natija Aldib", - "author_inst": "Universit\u00e9 Laval" - }, - { - "author_name": "Anne-Sophie Paquette", - "author_inst": "Universit\u00e9 Laval" - }, - { - "author_name": "Aymeric Ferreira", - "author_inst": "Universit\u00e9 Laval" - }, - { - "author_name": "Sarah Lecordier", - "author_inst": "Universit\u00e9 Laval" - }, - { - "author_name": "Maxime Bernard", - "author_inst": "Universit\u00e9 Laval" - }, - { - "author_name": "Armen Saghatelyan", - "author_inst": "Universit\u00e9 Laval" - }, - { - "author_name": "Ayman ElAli", - "author_inst": "Universit\u00e9 Laval" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2021.05.02.441948", "rel_title": "Inhibiting LSD1 suppresses coronavirus-induced inflammation but spares innate antiviral activity", @@ -786680,6 +787595,165 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.01.442279", + "rel_title": "Signaling through Fc\u03b3RIIA and the C5a-C5aR pathway mediates platelet hyperactivation in COVID-19", + "rel_date": "2021-05-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.01.442279", + "rel_abs": "Patients with COVID-19 present with a wide variety of clinical manifestations. Thromboembolic events constitute a significant cause of morbidity and mortality in patients infected with SARS-CoV-2. Severe COVID-19 has been associated with hyperinflammation and pre-existing cardiovascular disease. Platelets are important mediators and sensors of inflammation and are directly affected by cardiovascular stressors. In this report, we found that platelets from severely ill, hospitalized COVID-19 patients exhibit higher basal levels of activation measured by P-selectin surface expression, and have a poor functional reserve upon in vitro stimulation. Correlating clinical features to the ability of plasma from COVID-19 patients to stimulate control platelets identified ferritin as a pivotal clinical marker associated with platelet hyperactivation. The COVID-19 plasma-mediated effect on control platelets was highest for patients that subsequently developed inpatient thrombotic events. Proteomic analysis of plasma from COVID-19 patients identified key mediators of inflammation and cardiovascular disease that positively correlated with in vitro platelet activation. Mechanistically, blocking the signaling of the Fc{gamma}RIIa-Syk and C5a-C5aR pathways on platelets, using antibody-mediated neutralization, IgG depletion or the Syk inhibitor fostamatinib, reversed this hyperactivity driven by COVID-19 plasma and prevented platelet aggregation in endothelial microfluidic chamber conditions, thus identifying these potentially actionable pathways as central for platelet activation and/or vascular complications in COVID-19 patients. In conclusion, we reveal a key role of platelet-mediated immunothrombosis in COVID-19 and identify distinct, clinically relevant, targetable signaling pathways that mediate this effect. These studies have implications for the role of platelet hyperactivation in complications associated with SARS-CoV-2 infection.\n\nCover illustration O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY\n\nOne-sentence summaryThe Fc{gamma}RIIA and C5a-C5aR pathways mediate platelet hyperactivation in COVID-19", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Sokratis A. Apostolidis", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Amrita Sarkar", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Heather M. Giannini", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Rishi R. Goel", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Divij Mathew", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Aae Suzuki", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Amy E. Baxter", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Allison R. Greenplate", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Cecile Alanio", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Mohamed Abdel-Hakeem", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Derek A. Oldridge", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Josephine R. Giles", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jennifer E. Wu", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Zeyu Chen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Yinghui Jane Huang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ajinkya Pattekar", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sasikanth Manne", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Oliva Kuthuru", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jeanette Dougherty", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Brittany Weiderhold", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ariel R. Weisman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Caroline A.G. Ittner", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sigrid Gouma", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Debora Dunbar", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ian Frank", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alexander C. Huang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Laura A. Vella", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "- The UPenn COVID Processing Unit", + "author_inst": "-" + }, + { + "author_name": "John P. Reilly", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Scott E. Hensley", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Lubica Rauova", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Liang Zhao", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Nuala J. Meyer", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Mortimer Poncz", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Charles S. Abrams", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "E John Wherry", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.03.441080", "rel_title": "Human organoid systems reveal in vitro correlates of fitness for SARS-CoV-2 B.1.1.7", @@ -788235,61 +789309,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.28.21256245", - "rel_title": "Transmission dynamics of SARS-CoV-2 in the hospital setting", - "rel_date": "2021-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.28.21256245", - "rel_abs": "BackgroundSARS-CoV-2 can spread efficiently in hospitals, but the transmission pathways amongst patients and healthcare workers are unclear.\n\nMethodsWe analysed data from four teaching hospitals in Oxfordshire, UK, from January to October 2020. Associations between infectious SARS-CoV-2 individuals and infection risk were quantified using logistic, generalised additive and linear mixed models. Cases were classified as community- or hospital-acquired using likely incubation periods.\n\nResultsNine-hundred and twenty of 66184 patients who were hospitalised during the study period had a positive SARS-CoV-2 PCR test within the same period (1%). Out of these, 571 patients had their first positive PCR tests while hospitalised (62%), and 97 of these occurred at least seven days after admission (11%). Amongst the 5596 healthcare workers, 615 (11%) tested positive during the study period using PCR or serological tests. For susceptible patients, one day in the same ward with another patient with hospital-acquired SARS-CoV-2 was associated with an additional eight infections per 1000 susceptible patients (95%CrI 6-10). Exposure to an infectious patient with community-acquired COVID-19 or to an infectious healthcare worker was associated with substantially lower infection risks (2/1000 susceptible patients/day, 95%CrI 1-2). As for healthcare worker infections, exposure to an infectious patient with hospital-acquired SARS-CoV-2 or to an infectious healthcare worker were both associated with an additional one infection per 1000 susceptible healthcare workers per day (95%CrI 1-2). Exposure to an infectious patient with community-acquired SARS-CoV-2 was associated with half this risk (0.5/1000 susceptible healthcare workers/day, 95%CrI 0.3-0.7).\n\nInterpretationExposure to patients with hospital-acquired SARS-CoV-2 poses a substantial infection risk. Infection control measures to limit nosocomial transmission must be optimised to protect both staff and patients from SARS-CoV-2 infection.\n\nFundingNational Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Healthcare Associated Infections and Antimicrobial Resistance at Oxford University in partnership with Public Health England (PHE) (NIHR200915). Medical Research Council, Nosocomial transmission of SARS-CoV-2 (MR/V028456/1).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched the PubMed database using the search terms (\"COVID-19\" OR \"SARS-CoV-2\") AND (\"nosocomial\" OR \"hospital\") AND (\"transmission\") in either the abstracts or titles, for English-language articles published up to March 31, 2021. This returned 748 results, out of which ten reported transmission events in the hospital setting quantitatively. These publications can be broadly categorised to epidemiological descriptions of isolated outbreaks (5) or contact tracing of patients exposed to infected healthcare workers (1), retrospective cohort studies involving a particular group of patients, e.g., patients who underwent surgical procedures (2), and using genomic sequencing to identify transmission clusters (2). None of the studies reported the comparative transmission rates of SARS-CoV-2 amongst patients and staff.\n\nAdded value of this studyThis study reports the analysis of a large observational dataset collected from a group of hospitals in the UK over eight months, consisting of both hospitalised patients and healthcare workers. Based on these detailed individual-level data, we quantified the associations between patient and healthcare worker characteristics and risks for acquiring nosocomial SARS-CoV-2 infection after adjusting for their exposures to SARS-CoV-2. Over the study period, we describe how risk of acquisition changes both with calendar time and over a patients hospital stay. By linking the presence of infected and susceptible patients and healthcare workers by time and ward locations, we quantify the relative importance of the transmission pathways for both the susceptible patients and healthcare workers.\n\nImplications of all the available evidenceNosocomial transmission of SARS-CoV-2 is common. Identifying the drivers of SARS-CoV-2 transmissions in the hospital setting is essential for designing infection prevention and control policies to minimise the added pressure from such events on our health systems. We found that newly infected patients who acquired SARS-CoV-2 in the hospital pose the highest risk of onward transmission to other patients and healthcare workers. Infection control and prevention efforts need to be enhanced around these patients to prevent further transmissions and studies assessing the effectiveness of these policies are needed.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Yin Mo", - "author_inst": "National University Hospital" - }, - { - "author_name": "David W Eyre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sheila Lumley", - "author_inst": "Oxford University Hospitals, NHS Foundation Trust, Oxford, United Kingdom" - }, - { - "author_name": "Timothy Walker", - "author_inst": "Oxford University Hospitals, NHS Foundation Trust, Oxford, United Kingdom" - }, - { - "author_name": "Robert Shaw", - "author_inst": "Oxford University Hospitals, NHS Foundation Trust, Oxford, United Kingdom" - }, - { - "author_name": "Lisa Butcher", - "author_inst": "Oxford University Hospitals, NHS Foundation Trust, Oxford, United Kingdom" - }, - { - "author_name": "Katie Jeffery", - "author_inst": "Oxford University Hospitals, NHS Foundation Trust, Oxford, United Kingdom" - }, - { - "author_name": "Christl A. Donnelly", - "author_inst": "Department of Statistics, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "- Oxford COVID infection review team", - "author_inst": "" - }, - { - "author_name": "Ben S. Cooper", - "author_inst": "Oxford Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.28.21256242", "rel_title": "Sustained seroprevalence of anti SARS-CoV-2 total immunoglobulins in asymptomatic blood donors", @@ -788454,6 +789473,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.28.21256146", + "rel_title": "The causal effects of chronic air pollution on the intensity of COVID-19 disease: Some answers are blowing in the wind", + "rel_date": "2021-04-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.28.21256146", + "rel_abs": "The threats posed by COVID-19 have catalyzed a search by researchers across multiple disciplines for policy-relevant findings about critical risk factors. We contribute to this effort by providing causal estimates of the link between increased chronic ambient pollutant concentrations and the intensity of COVID-19 disease, as measured by deaths and hospitalizations in New York City from March through August, 2020. Given concerns about unobservable characteristics that contribute to both ambient air pollutant concentrations and the impacts of COVID-19 disease, we instrument for pollutant concentrations using the time spent downwind of nearby highways and estimate key causal relationships using two-stage least squares models. The causal links between increases in concentrations of our traffic-related air pollutants (PM2.5, NO2, and NO) and COVID-19 deaths are much larger than the correlations presented in recent observational studies. We find that a 0.16 g/m3 increase in average ambient PM2.5 concentration leads to an approximate 30% increase in COVID-19 deaths. This is the change in concentration associated with being downwind of a nearby highway. We see that this effect is mostly driven by residents with at least 75 years of age. In addition to emphasizing the importance of searching for causal relationships, our analysis highlights the value of increasing the density of pollution-monitoring networks and suggests potential benefits of further tightening of Clean Air Act amendments, as our estimated effects occur at concentrations well below thresholds set by the National Ambient Air Quality Standards.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Marc N Conte", + "author_inst": "Fordham University" + }, + { + "author_name": "Matthew Gordon", + "author_inst": "Yale University" + }, + { + "author_name": "Nicole Swartwood", + "author_inst": "Harvard T.H. Chan School" + }, + { + "author_name": "Rachel Wilwerding", + "author_inst": "Fordham University" + }, + { + "author_name": "Chu A. (Alex) Yu", + "author_inst": "Wake Forest University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.27.21256210", "rel_title": "U.S. Regional Differences in Physical Distancing: Evaluating Racial and Socioeconomic Divides During the COVID-19 Pandemic", @@ -789831,37 +790885,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.04.30.441434", - "rel_title": "N440K variant of SARS-CoV-2 has Higher Infectious Fitness", - "rel_date": "2021-04-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.30.441434", - "rel_abs": "Several variants of SARS-CoV-2 have been emerging across the globe, continuing to threaten the efforts to end COVID-19 pandemic. Recent data indicate the prevalence of variants with N440K Spike substitution in several parts of India, which is under the second wave of the pandemic. Here, we first analyze the prevalence of N440K variants within the sequences submitted from India and identify a rising trend of its spread across various clusters. We then compare the replicative fitness and infectivity of a prototype of this variant with two other previously prevalent strains. The N440K variant produced ten times higher infectious viral titers than a prevalent A2a strain, and over 1000 folds higher titers than a much less prevalent A3i strain prototype in Caco2 cells. Similar results were detected in Calu-3 cells as well, confirming the increased potency of the N440K variant. Interestingly, A3i strain showed the highest viral RNA levels, but the lowest infectious titers in the culture supernatants, indicating the absence of correlation between the RNA content and the infectivity of the sample. N440K mutation has been reported in several viral sequences across India and based on our results, we predict that the higher infectious titers achieved by N440K variant could possibly lead to its higher rate of transmission. Availability of more sequencing data in the immediate future would help understand the potential spread of this variant in more detail.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Dixit Tandel", - "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" - }, - { - "author_name": "Divya Gupta", - "author_inst": "Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Vishal Sah", - "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" - }, - { - "author_name": "Krishnan Harinivas Harshan", - "author_inst": "Centre for Cellular and Molecular Biology, Academy of Scientific and Innovative Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.29.442060", "rel_title": "SARS-CoV-2 bearing a mutation at the S1/S2 cleavage site exhibits attenuated virulence and confers protective immunity", @@ -790050,6 +791073,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.04.28.21255760", + "rel_title": "SARS-CoV-2 infections in nasal epithelial cells from smokers versus non-smokers", + "rel_date": "2021-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.28.21255760", + "rel_abs": "Whether smoking exacerbates Coronavirus disease 2019 is still debated. Ex-vivo Infection of reconstituted epithelial tissues from smoker versus non-smoker donors suggested comparable susceptibility to SARS-CoV-2 in epithelia from both groups.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Manel Essaidi-Laziosi", + "author_inst": "University of Geneva - Faculty of Medicine 1 rue Michel-Servet CH-1211 Geneva 4" + }, + { + "author_name": "Giulia Torriani", + "author_inst": "University of Geneva - Faculty of Medicine 1 rue Michel-Servet CH-1211 Geneva 4" + }, + { + "author_name": "Catia Alvarez", + "author_inst": "University of Geneva - Faculty of Medicine 1 rue Michel-Servet CH-1211 Geneva 4" + }, + { + "author_name": "Laurent Kaiser", + "author_inst": "University of Geneva Hospitals" + }, + { + "author_name": "Isabella Eckerle", + "author_inst": "University Hospitals of Geneva" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.27.21255023", "rel_title": "Large university with high COVID-19 incidence did not increase risk to non-student population", @@ -791677,157 +792735,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.27.21256133", - "rel_title": "From first to second wave: follow-up of the prospective Covid-19 cohort (KoCo19) in Munich (Germany)", - "rel_date": "2021-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21256133", - "rel_abs": "BackgroundIn the 2nd year of the Covid-19 pandemic, knowledge about the dynamics of the infection in the general population is still limited. Such information is essential for health planners, as many of those infected show no or only mild symptoms and thus, escape the surveillance system. We therefore aimed to describe the course of the pandemic in the Munich general population living in private households from April 2020 to January 2021.\n\nMethodsThe KoCo19 baseline study took place from April to June 2020 including 5313 participants (age 14 years and above). From November 2020 to January 2021, we could again measure SARS-CoV-2 antibody status in 4,433 of the baseline participants (response 83%). Participants were offered a self-sampling kit to take a capillary blood sample (dry blood spot; DBS). Blood was analysed using the Elecsys(R) Anti-SARS-CoV-2 assay (Roche). Questionnaire information on socio-demographics and potential risk factors assessed at baseline was available for all participants. In addition, follow-up information on health-risk taking behaviour and number of personal contacts outside the household (N=2768) as well as leisure time activities (N=1263) were collected in summer 2020.\n\nResultsWeighted and adjusted (for specificity and sensitivity) SARS-CoV-2 sero-prevalence at follow-up was 3.6% (95% CI 2.9-4.3%) as compared to 1.8% (95% CI 1.3-3.4%) at baseline. 91% of those tested positive at baseline were also antibody-positive at follow-up. While sero-prevalence increased from early November 2021 to January 2021, no indication of geospatial clustering across the city of Munich was found, although cases clustered within households. Taking baseline result and time to follow-up into account, men and participants in the age group 20-34 years were at the highest risk of sero-positivity. In the sensitivity analyses, differences in health-risk taking behaviour, number of personal contacts and leisure time activities partly explained these differences.\n\nConclusionThe number of citizens in Munich with SARS-CoV-2 antibodies was still below 5% during the 2nd wave of the pandemic. Antibodies remained present in the majority of baseline participants. Besides age and sex, potentially confounded by differences in behaviour, no major risk factors could be identified. Non-pharmaceutical public health measures are thus still important.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Katja Radon", - "author_inst": "LMU University Hospital Munich" - }, - { - "author_name": "Abhishek Bakuli", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany" - }, - { - "author_name": "Peter Puetz", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health" - }, - { - "author_name": "Ronan Le Gleut", - "author_inst": "5Institute of Computational Biology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health" - }, - { - "author_name": "Jessica Michelle Guggenbuehl Noller", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany" - }, - { - "author_name": "Laura Olbrich", - "author_inst": "University Hospital, LMU Munich" - }, - { - "author_name": "Elmar Saathoff", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich, Germany" - }, - { - "author_name": "Merce Gari", - "author_inst": "Helmholtz Zentrum for Environmental Health" - }, - { - "author_name": "Yannik Schaelte", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health" - }, - { - "author_name": "Turid Frahnow", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health" - }, - { - "author_name": "Roman Woelfel", - "author_inst": "Bundeswehr Institute of Microbiology, Munich" - }, - { - "author_name": "Michael Pritsch", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Camilla Rothe", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Michel Pletschette", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Raquel Rubio-Acero", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Jessica Beyerl", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Dafni Metaxa", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Felix Forster", - "author_inst": "Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich" - }, - { - "author_name": "Verena Thiel", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Noemi Castelletti", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Friedrich Riess", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Maximilian N Diefenbach", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Guenter Froeschl", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Jan Marius Bruger", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Simon Michael Winter", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Jonathan Leon Frese", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Kerstin Puchinger", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Isabel Brand", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Inge Kroidl", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Andreas Wieser", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Michael Hoelscher", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, 80802 Munich" - }, - { - "author_name": "Jan Hasenauer", - "author_inst": "University of Bonn" - }, - { - "author_name": "Christiane Fuchs", - "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health" - }, - { - "author_name": "- KoCo19 study group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.28.21256052", "rel_title": "Clinical Risk, Sociodemographic Factors, and SARS-CoV-2 Infection Over Time in Ontario, Canada", @@ -792036,6 +792943,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.04.26.21255732", + "rel_title": "Deprivation and Exposure to Public Activities during the COVID-19 Pandemic in England and Wales", + "rel_date": "2021-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21255732", + "rel_abs": "BackgroundDifferential exposure to public activities and non-household contacts may contribute to stark deprivation-related inequalities in SARS-CoV-2 infection and outcomes, but has not been directly investigated. We set out to investigate whether participants in Virus Watch - a large community cohort study based in England and Wales - reported different levels of exposure to public activities and non-household contacts during the Autumn-Winter phase of the COVID-19 pandemic according to postcode-level socioeconomic deprivation.\n\nMethodsParticipants (n=20120-25228 across surveys) reported their daily activities during three weekly periods in late November 2020, late December 2020, and mid-February 2021. Deprivation was quantified based on participants postcode of residence using English or Welsh Indices of Multiple Deprivation quintiles. We used Poisson mixed effect models with robust standard errors to estimate the relationship between deprivation and risk of exposure to public activities during each survey period.\n\nResultsRelative to participants in the least deprived areas, participants in the most deprived areas persistently exhibited elevated risk of exposure to vehicle sharing (aRR range across time points 1.73-8.52), public transport (aRR 3.13-5.73), work or education outside of the household (aRR 1.09-1.21), essential shops (aRR 1.09-1.13) and non-household contacts (aRR 1.15-1.19) across multiple survey periods.\n\nConclusionDifferential exposure to essential public activities in deprived communities is likely to contribute to inequalities in infection risk and outcomes during the COVID-19 pandemic. Public health interventions to reduce exposure during essential activities and financial and practical support to enable low-paid workers to stay at home during periods of intense transmission may reduce COVID-related inequalities.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Sarah Beale", + "author_inst": "University College London" + }, + { + "author_name": "Isobel Braithwaite", + "author_inst": "University College London" + }, + { + "author_name": "Annalan MD Navaratnam", + "author_inst": "University College London" + }, + { + "author_name": "Pia Hardelid", + "author_inst": "University College London" + }, + { + "author_name": "Alison Rodger", + "author_inst": "University College London; Royal Free London NHS Foundation Trust," + }, + { + "author_name": "Anna Aryee", + "author_inst": "University College London" + }, + { + "author_name": "Thomas Edward Byrne", + "author_inst": "University College London" + }, + { + "author_name": "Wing Lam Erica Fong", + "author_inst": "University College London" + }, + { + "author_name": "Ellen Fragaszy", + "author_inst": "University College London" + }, + { + "author_name": "Cyril Geismar", + "author_inst": "University College London" + }, + { + "author_name": "Jana Kovar", + "author_inst": "University College London" + }, + { + "author_name": "Vincent Nguyen", + "author_inst": "University College London" + }, + { + "author_name": "Parth Patel", + "author_inst": "University College London" + }, + { + "author_name": "Madhumita Shrotri", + "author_inst": "University College London" + }, + { + "author_name": "Robert W Aldridge", + "author_inst": "University College London" + }, + { + "author_name": "Andrew C Hayward", + "author_inst": "University College London" + }, + { + "author_name": "- Virus Watch Collaborative", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.25.21256067", "rel_title": "Trends of SARS-CoV-2 antibody prevalence in selected regions across Ghana", @@ -793483,205 +794473,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/092619", - "rel_title": "Resolving the Functional Significance of BRCA1 RING Domain Missense Substitutions", - "rel_date": "2021-04-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/092619", - "rel_abs": "Part 1Development and calibration of suitably accurate functional assays for BRCA1 RING domain and BRCT domain missense substitutions could dramatically accelerate clinical classification of rare missense substitutions observed in that gene. Leveraging data from 68,000 full sequence tests of BRCA1 and BRCA2, plus data from the limited number of already classified BRCA1 RING domain missense substitutions, we used logistic regression and related techniques to evaluate three BRCA1 RING domain assays. These were recently described high throughput yeast 2-hybrid and E3 ubiquitin ligase assays, plus a newly developed mammalian 2-hybrid assay. While there were concerns about the accuracy of the yeast 2-hybrid assay and the indirect nature of the ubiquitin ligase assay, the mammalian 2-hybrid assay had excellent correlation with existing missense substitution classifications. After calibration, this assay contributed to classification of one newly reported BRCA1 missense substitution. In principal, the mammalian 2-hybrid assay could be converted to a high-throughput format that would likely retain suitable accuracy.\n\nPart 2How does one achieve clinically applicable classification of the vast majority of all possible sequence variants in disease susceptibility genes? BRCA1 is a high-risk susceptibility gene for breast and ovarian cancer. Pathogenic protein truncating variants are scattered across the open reading frame, but all known missense substitutions that are pathogenic because of missense dysfunction are located in either the amino-terminal RING domain or the carboxy-terminal BRCT domain. Heterodimerization of the BRCA1 and BARD1 RING domains is a molecularly defined obligate activity. Hence, we tested every BRCA1 RING domain missense substitution that can be created by a single nucleotide change for heterodimerization with BARD1 in a Mammalian 2-hybrid (M2H) assay. Downstream of the M2H laboratory assay, we addressed three additional challenges: assay calibration, validation thereof, and integration of the calibrated results with other available data such as computational evidence and patient/population observational data to achieve clinically applicable classification. Overall, we found that about 20% of BRCA1 RING domain missense substitutions are pathogenic. Using a Bayesian point system for data integration and variant classification, we achieved clinical classification of about 89% of observed missense substitutions. Moreover, among missense substitutions not present in the human observational data used here, we find an additional 47 with concordant computational and functional assay evidence in favor of pathogenicity; these are particularly likely to be classified as Likely Pathogenic once human observational data become available.", - "rel_num_authors": 46, - "rel_authors": [ - { - "author_name": "Davide F. Robbiani", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Christian Gaebler", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Julio Cetrulo Lorenzi", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Zijun Wang", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Alice Cho", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Marianna Agudelo", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Christopher Barnes", - "author_inst": "Caltech" - }, - { - "author_name": "Shlomo Finkin", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Thomas Hagglof", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Thiago Oliveira", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Charlotte Viant", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Arlene Hurley", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Katrina Millard", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Rhonda Kost", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Melissa Cipolla", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Anna Gazumyan", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Kristie Gordon", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Filippo Bianchini", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Spencer Chen", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Victor Ramos", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Roshni Patel", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Juan Dizon", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Irina Shimeliovich", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Pilar Mendoza", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Harald Hartweger", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Lilian Nogueira", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Maggi Pack", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Jill Horowitz", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Fabian Schmidt", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Yiska Weisblum", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Hans-Heinrich Hoffmann", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Eleftherios Michailidis", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Alison Ashbrook", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Eric F. Waltari", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "John Pak", - "author_inst": "Chan Zuckerberg Biohub" - }, - { - "author_name": "Kathryn Huey-Tubman", - "author_inst": "Caltech" - }, - { - "author_name": "Nicholas Koranda", - "author_inst": "Caltech" - }, - { - "author_name": "Pauline Hoffman", - "author_inst": "Caltech" - }, - { - "author_name": "Anthony West", - "author_inst": "Caltech" - }, - { - "author_name": "Charles Rice", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Pamela Bjorkman", - "author_inst": "Caltech" - }, - { - "author_name": "Paul Bieniasz", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Marina Caskey", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Michel Nussenzweig", - "author_inst": "Rockefeller University" - } - ], - "version": "2", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2021.04.19.21255726", "rel_title": "Re-emergence of COVID-19 in Beijing was triggered by frozen virus: evidence from molecular clock", @@ -793934,6 +794725,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.19.21255709", + "rel_title": "Perceived public health threat a key factor for willingness to get the COVID-19 vaccine in Australia", + "rel_date": "2021-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255709", + "rel_abs": "BackgroundVaccination rollout against COVID-19 has begun across multiple countries worldwide. Although the vaccine is free, rollout might still be compromised by hesitancy or concerns about COVID-19 vaccines.\n\nMethodsWe conducted two online surveys of Australian adults in April (during national lockdown; convenience cross-sectional sample) and November (virtually no cases of COVID-19; nationally representative sample) 2020, prior to vaccine rollout. We asked about intentions to have a potential COVID-19 vaccine (If a COVID-19 vaccine becomes available, I will get it) and free-text responses (November only).\n\nResultsAfter adjustment for differences in sample demographics, the estimated proportion agreeing to a COVID-19 vaccine if it became available in April (n=1146) was 76.2%. In November (n=2034) this was estimated at 71.4% of the sample; additional analyses identified that the variation was driven by differences in perceived public health threat between April and November. Across both surveys, female gender, being younger, having inadequate health literacy and lower education were associated with reluctance to be vaccinated against COVID-19. Lower perceived susceptibility to COVID-19, belief that data on the efficacy of vaccines is largely made up, having lower confidence in government, and lower perception of COVID-19 as a public health threat, were also associated with reluctance to be vaccinated against COVID-19. The top three reasons for agreeing to vaccinate (November only) were to protect myself and others, moral responsibility, and having no reason not to get it. For those who were indifferent or disagreeing to vaccinate, safety concerns were the top reason, followed by indecision and lack of trust in the vaccine respectively.\n\nCONCLUSIONSThese findings highlight some factors related to willingness to accept a COVID-19 vaccine prior to one being available in Australia. Now that the vaccine is being offered, this study identifies key issues that can inform public health messaging to address vaccine hesitancy.\n\nHIGHLIGHTSO_LIPerceived public health threat is associated with intentions to vaccinate\nC_LIO_LIThose believing the efficacy of vaccines is made up were less willing to get vaccinated\nC_LIO_LITo protect myself and others was the top reason for getting the vaccine\nC_LIO_LISafety concerns was the top reason against getting the vaccine\nC_LI", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Rachael H Dodd", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Kristen Pickles", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Erin Cvejic", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Samuel Cornell", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Jennifer MJ Isautier", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Tessa Copp", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Brooke Nickel", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Carissa Bonner", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Carys Batcup", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Danielle M Muscat", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Julie Ayre", + "author_inst": "The University of Sydney" + }, + { + "author_name": "Kirsten J McCaffery", + "author_inst": "The University of Sydney" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.19.21255714", "rel_title": "Antibody response after COVID-19 mRNA vaccination in relation to age, sex, and side effects", @@ -795276,41 +796130,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.27.441512", - "rel_title": "Iota-carrageenan prevents the replication of SARS-CoV-2 on an in vitro respiratory epithelium model", - "rel_date": "2021-04-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.27.441512", - "rel_abs": "There are, except for remdesivir, no approved antivirals for the treatment or prevention of SARS-CoV-2 infections. Iota-carrageenan formulated into a nasal spray has already been proven safe and effective in viral respiratory infections. We explored this antiviral activity in Calu-3, a human respiratory model cell line. A formula of iota-carrageenan and sodium chloride, as a nasal spray, already approved for human use, effectively inhibited SARS-CoV-2 infection in vitro, providing a more substantial reference for further clinical studies or developments.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Augusto Varese", - "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, Buenos Aires, Argentina" - }, - { - "author_name": "Ana Ceballos", - "author_inst": "Instituto de Investigaciones Biomedicas en Retrovirus y SIDA (INBIRS), Universidad de Buenos Aires, Buenos Aires, Argentina" - }, - { - "author_name": "Carlos Adolfo Palacios", - "author_inst": "Respiratory Research Group, Instituto de Ciencia y Tecnologia Dr. Cesar Milstein - (Consejo Nacional de Investigaciones Cientificas y Tecnicas CONICET- Fundacio" - }, - { - "author_name": "Juan Manuel Figueroa", - "author_inst": "Respiratory Research Group, Instituto de Ciencia y Tecnologia Dr. Cesar Milstein - (Consejo Nacional de Investigaciones Cientificas y Tecnicas CONICET- Fundacio" - }, - { - "author_name": "Andrea Vanesa Dugour", - "author_inst": "Respiratory Research Group, Instituto de Ciencia y Tecnologia Dr. Cesar Milstein - (Consejo Nacional de Investigaciones Cientificas y Tecnicas CONICET- Fundacio" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.26.21255437", "rel_title": "Curating and translating the evidence about SARS-CoV-2 and COVID-19 for frontline public health and clinical care: The Novel Coronavirus Research Compendium (NCRC)", @@ -795571,6 +796390,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.24.21256054", + "rel_title": "High proportion of post-acute sequelae of SARS-CoV-2 infection in individuals 1-6 months after illness and association with disease severity in an outpatient telemedicine population", + "rel_date": "2021-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.24.21256054", + "rel_abs": "BackgroundIndividuals with coronavirus disease 2019 (COVID-19) may have persistent symptoms following their acute illness. The prevalence and predictors of these symptoms, termed post-acute sequelae of SARS-CoV-2 (PASC), are not fully described.\n\nMethodsParticipants discharged from an outpatient telemedicine program for COVID-19 were emailed a survey (1-6 months after discharge) about ongoing symptoms, acute illness severity, and quality of life. Standardized telemedicine notes from acute illness were used for covariates (comorbidities and provider-assessed symptom severity). Bivariate and multivariable analyses were performed to assess predictors of persistent symptoms.\n\nResultsTwo hundred and ninety patients completed the survey, of whom 115 (39.7%) reported persistent symptoms including fatigue (n= 59, 20.3%), dyspnea on exertion (n=41, 14.1%), and mental fog (n=39, 13.5%) among others. Proportion of persistent symptoms did not differ based on duration since illness (<90 days: n=32, 37.2% versus >90 days: n=80, 40.4%, p = 0.61). Predictors of persistent symptoms included provider-assessed moderate-severe illness (aOR 3.24, 95% CI 1.75, 6.02), female sex (aOR 1.99 95% 0.98, 4.04; >90 days out: aOR 2.24 95% CI 1.01, 4.95), and middle age (aOR 2.08 95% CI 1.07, 4.03). Common symptoms associated with reports of worse physical health included weakness, fatigue, myalgias, and mental fog.\n\nConclusionsSymptoms following acute COVID-19 are common and may be predicted by factors during the acute phase of illness. Fatigue and neuropsychiatric symptoms figured prominently. Select symptoms seem to be particularly associated with perceptions of physical health following COVID-19 and warrant specific attention on future studies of PASC.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "James B O'Keefe", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "H. Caroline Minton", + "author_inst": "Rollins School of Public Health, Emory University" + }, + { + "author_name": "Mary Morrow", + "author_inst": "Emory Healthcare" + }, + { + "author_name": "Colin Johnson", + "author_inst": "Emory Healthcare" + }, + { + "author_name": "Miranda A Moore", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Ghazala A. D. O'Keefe", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Karima Benameur", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Jason Higdon", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Jessica K. Fairley", + "author_inst": "Emory University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.26.21256131", "rel_title": "SARS-CoV-2 subgenomic RNA kinetics in longitudinal clinical samples", @@ -797034,77 +797904,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2021.04.23.21255940", - "rel_title": "Indirect Effects of COVID-19 on Maternal, Neonatal, Child, Sexual and Reproductive Health Services in Kampala, Uganda", - "rel_date": "2021-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21255940", - "rel_abs": "BackgroundCOVID-19 impacted global maternal, neonatal and child health outcomes. We hypothesised that the early, strict lockdown which restricted individuals movements in Uganda limited access to services.\n\nMethodsAn observational study, using routinely collected data from Electronic Medical Records was carried out, in Kawempe district, Kampala. An interrupted time series analysis assessed the impact on maternal, neonatal, child, sexual and reproductive health services from July 2019 to December 2020. Descriptive statistics summarised the main outcomes before (July 2019 - March 2020), during (April 2020 - June 2020) and after the national lockdown (July 2020 - December 2020).\n\nResultsBetween 1st July 2019 and 31st December 2020 there were 14,401 antenatal clinic attendances, 33,499 deliveries, 111,658 childhood service attendances and 57,174 for sexual health. All antenatal and vaccination services ceased in lockdown for four weeks. During the three-month lockdown, the number of antenatal attendances significantly decreased, and remain below pre-COVID levels (370 fewer/month). Attendances for prevention of mother-to-child transmission of HIV dropped then stabilised. Increases during lockdown and immediately postlockdown included the number of women treated for high blood pressure, eclampsia and pre-eclampsia (218 more/month), adverse pregnancy outcomes (stillbirths, low-birth-weight and premature infant births), the rate of neonatal unit admissions, neonatal deaths and abortions. Maternal mortality remained stable. Immunisation clinic attendance declined whilst neonatal death rate rose (from 39-49/1000 livebirths). The number of children treated for pneumonia, diarrhoea and malaria decreased during lockdown.\n\nConclusionThe Ugandan response to COVID-19 negatively impacted maternal, child and neonatal health, with an increase seen in pregnancy complications, and fetal and infant outcomes, likely due to delayed care-seeking behaviour. Decreased vaccination clinic attendance leaves a cohort of infants unprotected, affecting all vaccine-preventable diseases. Future pandemic responses must consider impacts of movement restrictions and access to preventative services to protect maternal and child health.\n\nO_TEXTBOXKEY QUESTIONS\n\nWhat is already known?O_LIThe response to COVID-19 has been shown to have indirectly impacted on maternal, child, neonatal, sexual, and reproductive health.\nC_LIO_LIThis is largely related to access to services and fear of contracting COVID-19 in outpatient departments.\nC_LIO_LIThere has been very little data published on the health impacts of the COVID-19 response in Uganda.\nC_LI\n\nWhat are the new findings?O_LIAntenatal attendances decreased dramatically in April, followed by increased numbers low-birthweight infants and neonatal deaths.\nC_LIO_LINewborn immunisations against polio, tetanus, diphtheria, hepatitis B, haemophilus influenzae, rotavirus and pneumococcus decreased significantly.\nC_LIO_LISexual, and reproductive health services were reduced in number.\nC_LI\n\nWhat do the new findings imply?O_LIAlthough Uganda has been less affected directly by COVID-19 infections in the first wave, the indirect impacts are far-reaching and will have future influences on population health.\nC_LIO_LIThere is a degree of resilience within the healthcare service, but many services were adversely affected by the lockdown leading to poorer pregnancy and neonatal outcomes.\nC_LIO_LIAntenatal and vaccination services are of particular importance in ensuring the safety of mother and child and must be prioritised in the responses to future pandemics.\nC_LI\n\nC_TEXTBOX", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jessica Florence Burt Miss", - "author_inst": "School of Medicine, University of Leeds, Leeds, UK" - }, - { - "author_name": "Joseph Ouma", - "author_inst": "Makarere University Johns Hopkins University, Kampala, Uganda" - }, - { - "author_name": "Lawrence Lubyayi", - "author_inst": "MRC/UVRI and LSHTM Uganda Research Unit" - }, - { - "author_name": "Alexander Amone Dr", - "author_inst": "Makarere University Johns Hopkins University, Kampala, Uganda" - }, - { - "author_name": "Lorna Aol Ms", - "author_inst": "Makarere University Johns Hopkins University, Kampala, Uganda" - }, - { - "author_name": "Musa Sekikubo Dr", - "author_inst": "Department of Obstetrics and Gynaecology, Makarere University, Kampala, Uganda" - }, - { - "author_name": "Annettee Nakimuli Prof", - "author_inst": "Department of Obstetrics and Gynaecology, Makarere University, Kampala, Uganda" - }, - { - "author_name": "Eve Nakabembe Dr", - "author_inst": "Department of Obstetrics and Gynaecology, Makarere University, Kampala, Uganda" - }, - { - "author_name": "Robert Mboizi Dr", - "author_inst": "Makarere University Johns Hopkins University, Kampala, Uganda" - }, - { - "author_name": "Philippa Musoke Prof", - "author_inst": "Makarere University Johns Hopkins University, Kampala, Uganda" - }, - { - "author_name": "Mary Kyohere Dr", - "author_inst": "Makarere University Johns Hopkins University, Kampala, Uganda" - }, - { - "author_name": "Emily Namara Dr", - "author_inst": "Makarere University Johns Hopkins University, Kampala, Uganda" - }, - { - "author_name": "Asma Khalil Prof", - "author_inst": "Infection and Immunity, St Georges, University of London, London, UK" - }, - { - "author_name": "Kirsty Le Doare Prof", - "author_inst": "Maternal Vaccines Programme, Medical Research Council/Uganda Virus Institute at the London School of Hygiene and Tropical Medicine, Entebbe, Uganda; Infection" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.23.21255958", "rel_title": "Estimation of local time-varying reproduction numbers in noisy surveillance data", @@ -797381,6 +798180,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.23.21255995", + "rel_title": "Regional opening strategies with commuter testing and containment of new SARS-CoV-2 variants", + "rel_date": "2021-04-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.23.21255995", + "rel_abs": "BackgroundDespite the vaccination process in Germany, a large share of the population is still susceptible to SARS-CoV-2. In addition, we face the spread of novel variants. Until we overcome the pandemic, reasonable mitigation and opening strategies are crucial to balance public health and economic interests.\n\nMethodsWe model the spread of SARS-CoV-2 over the German counties by a graph-SIR-type, metapopulation model with particular focus on commuter testing. We account for political interventions by varying contact reduction values in private and public locations such as homes, schools, workplaces, and other. We consider different levels of lockdown strictness, commuter testing strategies, or the delay of intervention implementation. We conduct numerical simulations to assess the effectiveness of the different intervention strategies after one month. The virus dynamics in the regions (German counties) are initialized randomly with incidences between 75-150 weekly new cases per 100,000 inhabitants (red zones) or below (green zones) and consider 25 different initial scenarios of randomly distributed red zones (between 2 and 20 % of all counties). To account for uncertainty, we consider an ensemble set of 500 Monte Carlo runs for each scenario.\n\nResultsWe find that the strength of the lockdown in regions with out of control virus dynamics is most important to avoid the spread into neighboring regions. With very strict lockdowns in red zones, commuter testing rates of twice a week can substantially contribute to the safety of adjacent regions. In contrast, the negative effect of less strict interventions can be overcome by high commuter testing rates. A further key contributor is the potential delay of the intervention implementation. In order to keep the spread of the virus under control, strict regional lockdowns with minimum delay and commuter testing of at least twice a week are advisable. If less strict interventions are in favor, substantially increased testing rates are needed to avoid overall higher infection dynamics.\n\nConclusionsOur results indicate that local containment of outbreaks and maintenance of low overall incidence is possible even in densely populated and highly connected regions such as Germany or Western Europe. While we demonstrate this on data from Germany, similar patterns of mobility likely exist in many countries and our results are, hence, generalizable to a certain extent.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Martin J Kuehn", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Daniel Abele", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Sebastian Binder", + "author_inst": "Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany" + }, + { + "author_name": "Kathrin Rack", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Margrit Klitz", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Jan Kleinert", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Jonas Gilg", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Luca Spataro", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Wadim Koslow", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Martin Siggel", + "author_inst": "German Aerospace Center, Institute for Software Technology" + }, + { + "author_name": "Michael Meyer-Hermann", + "author_inst": "Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology (BRICS), Helmholtz Centre for Infection Research, Braunschweig, Germany." + }, + { + "author_name": "Achim Basermann", + "author_inst": "German Aerospace Center, Institute for Software Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.22.21255941", "rel_title": "Predicting the end of Covid-19 infection for various countries using a stochastic agent-based model taking into account vaccination rates and the new mutant", @@ -798660,41 +799522,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.21.21255861", - "rel_title": "Longitudinal changes in physical activity during and after the first national lockdown due to the COVID-19 pandemic in England", - "rel_date": "2021-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255861", - "rel_abs": "BackgroundRecent studies have shown reduced physical activity at early stages of the COVID-19 pandemic. However, there is a lack of investigation on longitudinal changes in physical activity beyond lockdowns and stay at home orders. Moreover, it is unclear if there is heterogeneity in physical activity growth trajectories. This study aimed to explore longitudinal patterns of physical activity and factors associated with them.\n\nMethodsData were from the UCL COVID -19 Social Study. The analytical sample consisted of 35,915 adults in England who were followed up for 22 weeks from 24th March to 23rd August 2020. Data were analysed using growth mixture models.\n\nFindingsOur analyses identified six classes of growth trajectories, including three stable classes showing little change over time (62.4% in total), two classes showing decreasing physical activity (28.6%), and one class showing increasing physical activity over time (9%). A range of factors were found to be associated the class membership of physical activity trajectories, such as age, gender, education, income, employment status, and health.\n\nInterpretationThere is substantial heterogeneity in longitudinal changes in physical activity during the COVID-19 pandemic. However, a substantial proportion of our sample showed persistent physical inactivity or decreasing physical activity. Given the well-established linked between physical activity and health, persistent or increased physical inactivity is likely to have both immediate and long-term implications for peoples physical and mental health, as well as general wellbeing. More efforts are needed to promote physical activity during the pandemic and beyond.\n\nFundingNuffield Foundation, UK Research and Innovation, Wellcome Trust", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Feifei Bu", - "author_inst": "University College London" - }, - { - "author_name": "Jessica K Bone", - "author_inst": "University College London" - }, - { - "author_name": "John Mitchell", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Steptoe", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.21.21255872", "rel_title": "Immunogenetics of resistance to SARS-CoV-2 infection in discordant couples", @@ -798979,6 +799806,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.21.21255874", + "rel_title": "Evaluation of the sensitivity, accuracy and currency of the Cochrane COVID-19 Study Register for supporting rapid evidence synthesis production", + "rel_date": "2021-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.21.21255874", + "rel_abs": "IntroductionThe Cochrane COVID-19 Study Register (CCSR) is a public, continually updated, curated database of COVID-19 study references. The aim of this study-based register is to support rapid and living evidence synthesis, including a project to build an evidence ecosystem of COVID-19 research (CEOsys). In November and December 2020 we conducted an evaluation of the CCSR for CEOsys, measured its performance and identified areas for improvement.\n\nMethodsFor the evaluation we generated a purposive sample of 286 studies from 20 reviews to calculate the CCSRs sensitivity (comprehensiveness), accuracy (correctly classified and linked studies) and currency (time to publish and process references).\n\nResultsThe CCSR had an overall sensitivity of 77.2%, with the highest sensitivity for interventional studies (94.4%) and lowest sensitivity for modelling studies (63.6%). The study register had 100% sensitivity for trial registry records, 86.5% for journal articles and 52.4% for preprints. 98.3% of references were correctly classified with regard to study type, and 93.4% with regard to study aim. 89% of studies were correctly linked. 81.4% of references were published to the register in under 30 days, with 0.5 day (median) for trial registry records, 2 days for journal articles and 56 days for preprints.\n\nConclusionThe CCSR had high sensitivity, accurate study classifications and short publishing times for journal articles and trial registry records. We identified that the CCSRs coverage and publishing times for preprints needed improvement. Finally, the evaluation illustrated the value of a study-based register for identifying additional study references for analysis in evidence synthesis.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Maria-Inti Metzendorf", + "author_inst": "Cochrane Metabolic and Endocrine Disorders Group, Institute of General Practice, Medical Faculty of the Heinrich-Heine-University Duesseldorf" + }, + { + "author_name": "Robin M Featherstone", + "author_inst": "Cochrane, Editorial and Methods Department, London, United Kingdom" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.22.21255631", "rel_title": "Risk Profile of Thanksgiving Gatherers and Subsequent SARS-CoV2 Testing and Diagnosis", @@ -800274,37 +801124,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.20.21255821", - "rel_title": "COVID-19 vaccine hesitancy January-March 2021 among 18-64 year old US adults by employment and occupation", - "rel_date": "2021-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255821", - "rel_abs": "COVID-19 vaccine hesitancy threatens pandemic control efforts. We evaluated vaccine hesitancy in the US by employment status and occupation category during the COVID-19 vaccine rollout. US adults 18-64 years completed an online COVID-19 survey 3,179,174 times from January 6-May 19, 2021. Data was aggregated by month. Survey weights matched the sample to the US population age, gender, and state profile. Weighted percentages and 95% confidence intervals (95%CI) were calculated. Changes in vaccine hesitancy from January-May varied widely by employment status (e.g., -7.8% [95%CI, -8.2--7.5] among those working outside the home, a 26.6% decrease; -13.3% [95%CI, -13.7--13.0] among those not working for pay, a 44.9% decrease), and occupation category (e.g., -15.9% [95%CI, -17.7--14.2] in production, a 39.3% decrease; -1.4% [95%CI, -3.8--1.0] in construction/extraction, a 3.0% decrease). April 20-May 19, 2021, vaccine hesitancy ranged from 7.3% (95%CI, 6.7-7.8) in computer/mathematical professions to 45.2% (95%CI, 43.2-46.8) in construction/extraction. Hesitancy was 9.0% (95%CI, 8.6-9.3) among educators and 14.5% (95%CI, 14.0-15.0) among healthcare practitioners/technicians. While the prevalence of reasons for hesitancy differed by occupation, over half of employed hesitant participants reported concern about side effects (51.7%) and not trusting COVID-19 vaccines (51.3%), whereas only 15.0% didnt like vaccines in general. Over a third didnt believe they needed the vaccine, didnt trust the government, and/or were waiting to see if it was safe. In this massive national survey of adults 18-64 years, vaccine hesitancy varied widely by occupation. Reasons for hesitancy indicate messaging about safety and addressing trust are paramount.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Wendy C King", - "author_inst": "Graduate School of Public Health University of Pittsburgh" - }, - { - "author_name": "Max Rubinstein", - "author_inst": "Heinz College and Department of Statistics & Data Science, Carnegie Mellon University" - }, - { - "author_name": "Alex Reinhart", - "author_inst": "Department of Statistics & Data Science, Carnegie Mellon University" - }, - { - "author_name": "Robin J Mejia", - "author_inst": "Department of Statistics & Data Science, Carnegie Mellon University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.21.21255621", "rel_title": "Saliva Is Comparable to Nasopharyngeal Swabs for Molecular Detection of SARS-CoV-2", @@ -800509,6 +801328,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.22.21255952", + "rel_title": "COVID-19 pandemic: Analyzing of different pandemic control strategies using saturation models", + "rel_date": "2021-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255952", + "rel_abs": "Since December 2019, the world is confronted with the outbreak of the respiratory disease COVID-19. At the beginning of 2020, the COVID-19 epidemic evolved into a pandemic, which continues to this day. Within many countries, several control strategies or combinations of them, like restrictions (e.g. lockdown actions), medical care (e.g. development of vaccine or medicaments) and medical prevention (e.g. hygiene concept), were established with the goal to control the pandemic. Depending on the chosen control strategy, the COVID-19 spreading behavior slowed down or approximately stopped for a defined time range. This phenomenon is called saturation effect and can be described by saturation models: E.g. a fundamental approach is Verhulst (1838). The model parameter allows the interpretation of the spreading speed (growth) and the saturation effect in a sound way. This paper shows results of a research study of the COVID-19 spreading behavior and saturation effects depending on different pandemic control strategies in different countries and time phases based on Johns Hopkins University data base (2020). The study contains the analyzing of saturation effects related to short time periods, e.g. possible caused by lockdown strategies, geographical influences and medical prevention activities. The research study is focusing on reference countries like Germany, Japan, Denmark, Iceland, Ireland and Israel.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Stefan Bracke", + "author_inst": "University of Wuppertal, Germany" + }, + { + "author_name": "Lars Grams", + "author_inst": "University of Wuppertal, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.22.21255953", "rel_title": "COVID-19 pandemic: Analyzing of spreading behavior, the impact of restrictions and prevention measures in Germany and Japan.", @@ -802228,37 +803070,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.17.21255513", - "rel_title": "A Caveat to Using Wearable Sensor Data for COVID-19 Detection: The Role of Behavioral Change after Receipt of Test Results", - "rel_date": "2021-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.17.21255513", - "rel_abs": "Recent studies indicate that wearable sensors have the potential to capture subtle within-person changes that signal SARS-CoV-2 infection. However, it remains unclear the extent to which observed discriminative performance is attributable to behavioral change after receiving test results. We conducted a retrospective study in a sample of medical interns who received COVID-19 test results from March to December 2020. Our data confirmed that sensor data were able to differentiate between symptomatic COVID-19 positive and negative individuals with good accuracy (area under the curve (AUC) = 0.75). However, removing post-result data substantially reduced discriminative capacity (0.75 to 0.63; delta= -0.12, p=0.013). Removing data in the symptomatic period prior to receipt of test results did not produce similar reductions in discriminative capacity. These findings suggest a meaningful proportion of the discriminative capacity of wearable sensor data for SARS-CoV-2 infection may be due to behavior change after receiving test results.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jennifer L Cleary", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Yu Fang", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Srijan Sen", - "author_inst": "University of Michigan, Ann Arbor" - }, - { - "author_name": "Zhenke Wu", - "author_inst": "University of Michigan, Ann Arbor" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.18.21255687", "rel_title": "Short time effect of Covid 19 pandemic on HbA1c and acute metabolic complications in children with type 1 diabetes", @@ -802459,6 +803270,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.19.21255727", + "rel_title": "Prolonged activation of nasal immune cell populations and development of tissue-resident SARS-CoV-2 specific CD8 T cell responses following COVID-19", + "rel_date": "2021-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255727", + "rel_abs": "The immune system plays a major role in Coronavirus Disease 2019 (COVID-19) pathogenesis, viral clearance and protection against re-infection. Immune cell dynamics during COVID-19 have been extensively documented in peripheral blood, but remain elusive in the respiratory tract. We performed minimally-invasive nasal curettage and mass cytometry to characterize nasal immune cells of COVID-19 patients during and 5-6 weeks after hospitalization. Contrary to observations in blood, no general T cell depletion at the nasal mucosa could be detected. Instead, we observed increased numbers of nasal granulocytes, monocytes, CD11c+ NK cells and exhausted CD4+ T effector memory cells during acute COVID-19 compared to age-matched healthy controls. These pro-inflammatory responses were found associated with viral load, while neutrophils also negatively correlated with oxygen saturation levels. Cell numbers mostly normalized following convalescence, except for persisting CD127+ granulocytes and activated T cells, including CD38+ CD8+ tissue-resident memory T cells. Moreover, we identified SARS-CoV-2 specific CD8+ T cells in the nasal mucosa in convalescent patients. Thus, COVID-19 has both transient and long-term effects on the immune system in the upper airway.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Anna H.E. Roukens", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Marion Konig", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Tim Dalebout", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Tamar Tak", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Shohreh Azimi", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Yvonne Kruize", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Cilia R. Pothast", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Renate S. Hagedoorn", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Sesmu M. Arbous", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Jaimie L.H. Zhang", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Maaike Verheij", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Corine Prins", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Anne M. Does van der", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Pieter S. Hiemstra", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Jutte J.C. Vries de", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Jacqueline J. Janse", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Meta Roestenberg", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Sebenzile K. Myeni", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Marjolein Kikkert", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Mirjam H.M. Heemskerk", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Maria Yazdanbakhsh", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Hermelijn H. Smits", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Simon P. Jochems", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "- BEAT-COVID group", + "author_inst": "" + }, + { + "author_name": "- COVID-19 LUMC group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.19.21255723", "rel_title": "B and T cell immune responses elicited by the BNT162b2 (Pfizer BioNTech) COVID-19 vaccine in nursing home residents", @@ -803913,145 +804839,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.04.21.440862", - "rel_title": "Rapid induction of antigen-specific CD4+ T cells guides coordinated humoral and cellular immune responses to SARS-CoV-2 mRNA vaccination", - "rel_date": "2021-04-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.21.440862", - "rel_abs": "The SARS-CoV-2 mRNA vaccines have shown remarkable clinical efficacy, but questions remain about the nature and kinetics of T cell priming. We performed longitudinal antigen-specific T cell analyses in healthy individuals following mRNA vaccination. Vaccination induced rapid near-maximal antigen-specific CD4+ T cell responses in all subjects after the first vaccine dose. CD8+ T cell responses developed gradually after the first and second dose and were variable. Vaccine-induced T cells had central memory characteristics and included both Tfh and Th1 subsets, similar to natural infection. Th1 and Tfh responses following the first dose predicted post-boost CD8+ T cell and neutralizing antibody levels, respectively. Integrated analysis of 26 antigen-specific T cell and humoral responses revealed coordinated features of the immune response to vaccination. Lastly, whereas booster vaccination improved CD4+ and CD8+ T cell responses in SARS-CoV-2 naive subjects, the second vaccine dose had little effect on T cell responses in SARS-CoV-2 recovered individuals. Thus, longitudinal analysis revealed robust T cell responses to mRNA vaccination and highlighted early induction of antigen-specific CD4+ T cells.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC=\"FIGDIR/small/440862v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (52K):\norg.highwire.dtl.DTLVardef@db812dorg.highwire.dtl.DTLVardef@fdc549org.highwire.dtl.DTLVardef@a34663org.highwire.dtl.DTLVardef@1621e52_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Mark M Painter", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Divij Mathew", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Rishi R Goel", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Sokratis A Apostolidis", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Ajinkya Pattekar", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Oliva Kuthuru", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Amy E Baxter", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Ramin S Herati", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Derek A Oldridge", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Sigrid Gouma", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Philip Hicks", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Sarah Dysinger", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Kendall A Lundgreen", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Leticia Kuri-Cervantes", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Sharon Adamski", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Amanda Hicks", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Scott Korte", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Josephine R Giles", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Madison E Weirick", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Christopher M McAllister", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Jeanette Dougherty", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Sherea Long", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Jacob T Hamilton", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Michael R Betts", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Paul Bates", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Scott E Hensley", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Alba Grifoni", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Allison R Greenplate", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "E. John Wherry", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.21.21255772", "rel_title": "Measuring Oxygen Access: lessons from health facility assessments in Nigeria", @@ -804392,6 +805179,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.20.21255350", + "rel_title": "When can we safely return to normal? A novel method for identifying safe levels of NPIs in the context of COVID-19 vaccinations", + "rel_date": "2021-04-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255350", + "rel_abs": "Over the course of the COVID-19 pandemic, governing bodies and individuals have relied on a variety of non-pharmaceutical interventions (NPIs) to control the transmission of SARS-CoV-2, which posed an acute threat to individuals well-being and consistently impacted economic activities in many countries worldwide. NPIs have been implemented at varying levels of severity and in response to widely-divergent perspectives of risk tolerance. Now, concurrently with the introduction of multiple SARS-CoV-2 vaccines, the world looks optimistically to a \"return to normality\". In this work, we propose a multi-disciplinary approach, combining transmission modeling with control and optimization theory, to examine how risk tolerance and vaccination rates will impact the safe return to normal behavior over the next few months. To this end, we consider a version of the Susceptible-Exposed-Infected-Recovered transmission model that accounts for hospitalizations, vaccinations, and loss of immunity. We then propose a novel control approach to calibrate the necessary level of NPIs at various geographical levels to guarantee that the number of hospitalizations does not exceed a given risk tolerance (i.e., a maximum allowable threshold). Our model and control objectives are calibrated and tailored for the state of Colorado, USA. Our results suggest that: (i) increasing risk tolerance can decrease the number of days required to discontinue all NPIs; (ii) increasing risk tolerance inherently increases COVID-19 deaths even in the context of vaccination; (iii) if the vaccination uptake in the population is 70% or less, then return to normal behavior within the next year may newly stress the healthcare system. Furthermore, by using a multi-region model accounting for travel, our simulations predict that: (iv) relaxation should take into account regional heterogeneity in transmission and travel; and (v) premature relaxation of NPIs, even if restricted only to low-density regions, will lead to exceeding hospitalization limits even when highly-populated regions implement full-closures. Although the simulations are performed for the state of Colorado, the proposed model of transmission and control methods are applicable to any area worldwide and can be utilized at any geographical granularity.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Gianluca Bianchin", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Emiliano Dall'Anese", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Jorge Ivan Poveda", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Andrea Buchwald", + "author_inst": "University of Colorado Anschutz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.21.440801", "rel_title": "Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania", @@ -805927,41 +806745,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.14.21255436", - "rel_title": "COVID-19 epidemic scenarios into 2021 based on observed key superdispersion events", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255436", - "rel_abs": "Key high transmission dates for the year 2020 are used to create scenarios of the evolution of the COVID-19 pandemic in several states of Mexico for 2021. These scenarios are obtained through the estimation of a time-dependent contact rate, where the main assumption is that disease behavior is heavily determined by the mobility and social activity of the population during holidays and other important calendar dates. First, changes in the effective contact rate on predetermined dates of 2020 are estimated. Then, this information is used to propose different scenarios for the number of cases and deaths for 2021. The fundamental assumptions behind this methodology are that the effective contact rate incorporates the main superspreading transmission events during last year, that each region has an independent epidemic not explicitly interconnected with other regions and, finally, that there are no new highly transmissible SARS-CoV-2 variants active during the timeline of the forecasts. Also, several levels of vaccination are considered to analyze their impact on the projections of the epidemic curve. The objective is to generate a range of scenarios that could be useful to evaluate the possible evolution of the epidemic and its likely impact on incidence and mortality.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mario Santana-Cibrian", - "author_inst": "CONACYT - Instituto de Matematicas UNAM-Juriquilla" - }, - { - "author_name": "M. Adrian Acu\u00f1a-Zegarra", - "author_inst": "Universidad de Sonora" - }, - { - "author_name": "Carlos E. Rodr\u00edguez", - "author_inst": "IIMAS-UNAM" - }, - { - "author_name": "Jorge X. Velasco-Hernandez", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Rams\u00e9s H. Mena", - "author_inst": "IIMAS-UNAM" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.13.21255418", "rel_title": "Forecast of the covid19 epidemic in France", @@ -806142,6 +806925,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.14.21255448", + "rel_title": "Gender Differences in Health Protective Behaviors During the COVID-19 Pandemic in Taiwan: An Empirical Study", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255448", + "rel_abs": "IntroductionSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection produces more severe symptoms and a higher mortality in men than in women. The role of biological sex in the immune response to SARS-CoV-2 is believed to explain this sex disparity. However, the contribution of gender factors that influence health protective behaviors and therefore health outcomes, remains poorly explored.\n\nMethodsWe assessed the contributions of gender in attitudes towards the COVID-19 pandemic, using a hypothetical influenza pandemic data from the 2014 Taiwan Social Change Survey. Participants were selected through a stratified, three-stage probability proportional-to-size sampling from across the nation, to fill in questionnaires that asked about their perception of the hypothetical pandemic, and intention to adopt health protective behaviors.\n\nResultsA total of 1,990 participants (median age 45.92 years, 49% women) were included. Significant gender disparities (p<0.001) were observed. The risk perception of pandemic (OR=1.28, 95% CI=1.21-1.35, p<0.001), older age (1.06, 95%=1.05-1.07, p<0.001), female gender (OR = 1.18, 95% CI = 1.09{square}1.27, p<0.001), higher education (OR=1.10, 95% CI=1.06-1.13, p<0.001), and larger family size (OR=1.09, 95% CI=1.06-1.15, p<0.001) were positively associated with health protective behaviors. The risk perception of pandemic (OR=1.25, 95% CI=1.15-1.36), higher education (OR=1.07, 95% CI=1.02-1.13, p<0.05), being married (OR=1.17, 95% CI=1.01-1.36, p<0.05), and larger family size (OR=1.33, 95% CI=1.25-1.42, p<0.001), were positively associated with intention to receive a vaccine. However, female gender was negatively associated with intention to receive a vaccine (OR=0.85, 95% CI=0.75-0.90, p<0.01) and to comply with contact-tracing (OR=0.95, 95% CI=0.90-1.00, p<0.05) compared to men. Living with children was also negatively associated with intention to receive vaccines (OR=0.77, 95% CI=0.66-0.90, p<0.001).\n\nConclusionThis study unveils gender differences in risk perception, health protective behaviors, vaccine hesitancy, and compliance with contact-tracing using a hypothetical viral pandemic. Gender-specific health education raising awareness of health protective behaviors may be beneficial to prevent future pandemics.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jasmine Tan", + "author_inst": "School of Medicine, National Taiwan University, Taipei, Taiwan" + }, + { + "author_name": "Yilin Yoshida", + "author_inst": "Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA" + }, + { + "author_name": "Kevin Sheng-Kai Ma", + "author_inst": "Department of Life Science, National Taiwan University, Taipei, Taiwan" + }, + { + "author_name": "Franck Mauvais-Jarvis", + "author_inst": "Tulane Center of Excellence in Sex-Based Biology & Medicine, New Orleans, LA, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.14.21255490", "rel_title": "Expectant parents' perceptions of healthcare and support during COVID-19 in the UK: A thematic analysis.", @@ -807557,97 +808371,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.17.21255540", - "rel_title": "Thromboembolism risk is higher among patients with diabetes and COVID-19 and is associated to poor clinical outcome", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.17.21255540", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSPurposeC_ST_ABSIndividuals with diabetes/stress hyperglycemia carry an increased risk for adverse clinical outcome in case of SARS-CoV-2 infection. The purpose of this study was to evaluate whether this risk is, at least in part, modulated by an increase of thromboembolic complications.\n\nMethodsWe prospectively followed 180 hospitalized patients with confirmed COVID-19 pneumonia admitted to the Internal Medicine Units of San Raffaele Hospital. Data from 11 out of 180 patients were considered incomplete and excluded from the analysis. We analysed inflammation, tissue damage biomarkers, hemostatic parameters, thrombotic events (TEs) and clinical outcome according to the presence of diabetes/stress hyperglycemia.\n\nResultsAmong 169 patients, 51 (30.2%) had diabetes/stress hyperglycemia. Diabetes/stress hyperglycemia and fasting blood glucose (FBG) were associated with increased inflammation and tissue damage circulating markers, higher D-dimer levels, increased prothrombin time and lower antithrombin III activity. Forty-eight venous and 10 arterial TEs were identified in 49 (29%) patients. Diabetes/stress hyperglycemia (HR 2.71, p=0.001), fasting blood glucose (HR 4.32, p<0.001) and glucose variability (HR 1.6, p < 0.009) were all associated with an increased risk of thromboembolic complication. TEs significantly increased the risk for an adverse clinical outcome only in the presence of diabetes/stress hyperglycemia (HR 3.05, p=0.01) or fasting blood glucose [≥] 7 mmol/l (HR 3.07, p=0.015).\n\nConclusionsThromboembolism risk is higher among patients with diabetes/stress hyperglycemia and COVID-19 pneumonia and is associated to poor clinical outcome. In case of SARS-Cov-2 infection patients with diabetes/stress hyperglycemia could be considered for a more intensive prophylactic anticoagulation regimen.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Calvisi Laura Stefania", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Giuseppe Alvise Ramirez", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Marina Scavini", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Valentina Da Prat", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Giuseppe Di Lucca", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Andrea Laurenzi", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Gabriele Gallina", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Ludovica Cavallo", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Giorgia Borio", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Federica Farolfi", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Maria Pascali", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Jacopo Castellani", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Vito Lampasona", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Armando D'Angelo", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Giovanni Landoni", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Fabio Ciceri", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Patrizia Rovere Querini", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Moreno Tresoldi", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Lorenzo Piemonti", - "author_inst": "IRCCS Ospedale San Raffaele" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2021.04.19.21255755", "rel_title": "The Mental Health Under the COVID-19 Crisis in Africa: A Systematic Review and Meta-Analysis", @@ -807876,6 +808599,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.14.21255512", + "rel_title": "Assessing the Mortality Impact of the COVID-19 Pandemic in Florida State Prisons", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255512", + "rel_abs": "BackgroundThe increased risk of COVID-19 infection among incarcerated individuals due to environmental hazards is well known and recent studies have highlighted the higher rates of infection and mortality prisoners in the United States face due to COVID-19. However, the impact of COVID-19 on all-cause mortality rates in incarcerated populations has not been studied.\n\nMethodsUsing data reported by the Florida Department of Corrections on prison populations and mortality events we conducted a retrospective cohort study of all individuals incarcerated in Florida state prisons between 2015 and 2020. We calculated excess deaths by estimating age-specific expected deaths from mortality trends in 2015 through 2019 and taking the difference between observed and expected deaths during the pandemic period. We calculated life table measures using standard demographic techniques and assessed significant yearly changes using bootstrapping.\n\nFindingsThe Florida Department of Corrections reported 510 total deaths from March 1, 2020 to December 31, 2020 among the state prison population. This was 42% higher (rate ratio 1.42, 95% CI 1.15 to 1.89) than the expected number of deaths in light of mortality rates for previous years. Reported COVID-19 deaths in a month were positively correlated with estimated excess deaths (80.4%, p <.01). Using age-specific mortality estimates, we found that life expectancy at age 20 declined by 4 years (95% CI 2.06-6.57) between 2019 and 2020 for the Florida prison population.\n\nInterpretationThe Florida prison population saw a significant increase in all-cause mortality during the COVID-19 pandemic period, leading to a decrease in life expectancy of more than four years. Life years lost by the Florida prison population were likely far greater than those lost by the general United States population, as reported by other studies. This difference in years lost highlights the need for increased interventions to protect vulnerable incarcerated populations during pandemics.\n\nFundingVital Projects Fund, Arnold Ventures, US Centers for Disease Control, Eunice Kennedy Shriver National Institute of Child Health and Human Development", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Neal Marquez", + "author_inst": "University of Washington" + }, + { + "author_name": "Aaron Littman", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Victoria Rossi", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Michael Everett", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Erika Tyagi", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Hope Johnson", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Sharon Dolovich", + "author_inst": "University of California Los Angeles" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.14.21255476", "rel_title": "Geographic and demographic heterogeneity of SARS-CoV-2 diagnostic testing in Illinois, USA, March to December 2020", @@ -809795,61 +810561,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.13.21255379", - "rel_title": "Effect of multiple freeze-thaw cycles on detection of anti-SARS-CoV-2 IgG antibodies", - "rel_date": "2021-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255379", - "rel_abs": "Several studies have investigated the effect of repeated freeze-thaw (F/T) cycles on RNA detection for SARS-CoV-2. However, no data is available regarding the effect of repeated F/T cycles on SARS-CoV-2 antibody detection in serum. We investigated the effect of multiple F/T cycles on anti-SARS-CoV-2 IgG detection using an ELISA test targeting the nucleocapsid antibodies. Ten positive and one negative SARS-CoV-2 IgG sera from 11 participants, in replicates of five were subjected to a total of 16 F/T cycles and stored at 4{degrees}C until tested by ELISA. Statistical analysis was done to test for F/T cycle effect. Non-of the 10 positive sera turned into negative after 16 F/T cycles. There was no significant difference in the OD average reading between the first and last F/T cycles, except for one serum with a minimal decline in the OD. The random-effect linear regression of log (OD) on the number of cycles showed no significant trend with a slope consistent with zero (B=-0.0001; 95% CI -0.0008; 0.0006; p-value=0.781). These results suggest that multiple F/T cycles had no effect on the ability of the ELISA assay to detect the SARS-CoV-2 IgG antibodies.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Farah M. Shurrab", - "author_inst": "Qatar University" - }, - { - "author_name": "Duaa W. Al-Sadeq", - "author_inst": "Qatar University" - }, - { - "author_name": "Fathima Amanullah", - "author_inst": "Qatar University" - }, - { - "author_name": "Salma N. Younes", - "author_inst": "Qatar University" - }, - { - "author_name": "Hadeel Al-Jighefee", - "author_inst": "Qatar University" - }, - { - "author_name": "Nadin Younes", - "author_inst": "Qatar University" - }, - { - "author_name": "Soha R. Dargham", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "HADI M. YASSINE", - "author_inst": "Qatar University" - }, - { - "author_name": "Laith J Abu-Raddad", - "author_inst": "Weill Cornell Medicine-Qatar" - }, - { - "author_name": "Gheyath K. Nasrallah", - "author_inst": "Qatar University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.12.21255327", "rel_title": "The impact of the COVID-19 pandemic on health service utilisation in Sierra Leone", @@ -810206,6 +810917,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.13.21255396", + "rel_title": "Ultra-fast, high throughput and inexpensive detection of SARS-CoV-2 seroconversion", + "rel_date": "2021-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255396", + "rel_abs": "A technique allowing high throughput, fast and low-cost quantitative analysis of human IgG antibodies reacting to SARS-CoV-2 antigens will be required to understand the levels of protecting antibodies in the population raised in response to infections and/or to immunization. We described previously a fast, simple, and inexpensive Ni2+ magnetic bead immunoassay which allowed detection of human antibodies reacting against the SARS-CoV-2 nucleocapsid protein using a minimal amount of serum or blood. A major drawback of the previously described system was that it only processed 12 samples simultaneously. Here we describe a manually operating inexpensive 96 well plate magnetic extraction / homogenization process which allows high throughput analysis delivering results of 96 samples in chromogenic format in 12 minutes or in fluorescent ultrafast format which takes only 7 minutes. We also show that His tag antigen purification can be performed on the fly while loading antigens to the Ni2+ magnetic beads in a process which takes only 12 min reducing the pre analytical time and cost. Finally, we show that the magnetic bead immunoassay is antigen flexible and can be performed using either Nucleocapsid, Spike or Spike RBD. The method performed with low inter and intra assay variability using different antigens and detection modes and was able to deliver >99.5% specificity and >95% sensitivity for a cohort of 203 pre pandemic and 63 COVID-19 positive samples.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Marcelo S Conzentino Sr.", + "author_inst": "UFPR" + }, + { + "author_name": "Tatiele P.C. Santos Sr.", + "author_inst": "UFPR" + }, + { + "author_name": "Khaled Selim", + "author_inst": "Tubingen University" + }, + { + "author_name": "Berenike Wagner", + "author_inst": "Tubingen University" + }, + { + "author_name": "Janette T Alford", + "author_inst": "Tubingen University" + }, + { + "author_name": "Nelli Deobald", + "author_inst": "Tubingen University" + }, + { + "author_name": "Nigella M Paula", + "author_inst": "UFPR" + }, + { + "author_name": "Fabiane G.M Rego Sr.", + "author_inst": "UFPR" + }, + { + "author_name": "Dalila L Zanette", + "author_inst": "Fiocruz" + }, + { + "author_name": "Mateus N Aoki", + "author_inst": "Fiocruz" + }, + { + "author_name": "Jeanine M Nardin", + "author_inst": "Hospital Erasto Gaerthener" + }, + { + "author_name": "Maria C.C Huergo", + "author_inst": "Prefeitura Municipal de Guaratuba" + }, + { + "author_name": "Rodrigo A Reis", + "author_inst": "UFPR" + }, + { + "author_name": "Luciano Huergo Sr.", + "author_inst": "UFPR" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.12.21255330", "rel_title": "Identification of natural SARS-CoV-2 infection in seroprevalence studies among vaccinated populations", @@ -811641,201 +812423,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.12.21255275", - "rel_title": "Children develop strong and sustained cross-reactive immune responses against spike protein following SARS-CoV-2 infection", - "rel_date": "2021-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.12.21255275", - "rel_abs": "SARS-CoV-2 infection is generally mild or asymptomatic in children but the biological basis for this is unclear. We studied the profile of antibody and cellular immunity in children aged 3-11 years in comparison with adults. Antibody responses against spike and receptor binding domain (RBD) were high in children and seroconversion boosted antibody responses against seasonal Beta-coronaviruses through cross-recognition of the S2 domain. Seroneutralisation assays against alpha, beta and delta SARS-CoV-2 variants demonstrated comparable neutralising activity between children and adults. T cell responses against spike were >2-fold higher in children compared to adults and displayed a TH1 cytokine profile. SARS-CoV-2 spike-specific T cells were also detected in many seronegative children, revealing pre-existing responses that were cross-reactive with seasonal Alpha and Beta-coronaviruses. Importantly, all children retained high antibody titres and cellular responses at 6 months after infection whilst relative antibody waning was seen in adults. Spike-specific responses in children also remained broadly stable beyond 12 months. Children thus distinctly generate robust, cross-reactive and sustained immune responses after SARS-CoV-2 infection with focussed specificity against spike protein. These observations demonstrate novel features of SARS-CoV-2-specific immune responses in children and may provide insight into their relative clinical protection. Furthermore, this information will help to guide the introduction of vaccination regimens in the paediatric population.", - "rel_num_authors": 45, - "rel_authors": [ - { - "author_name": "Alexander C Dowell", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Megan S. Butler", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Elizabeth Jinks", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Gokhan Tut", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Tara Lancaster", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Panagiota Sylla", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Jusnara Begum", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Rachel Bruton", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Hayden Pearce", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Kriti Verma", - "author_inst": "University of Birmingham" - }, - { - "author_name": "Nicola Logan", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61-1QH, UK" - }, - { - "author_name": "Grace Tyson", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61-1QH, UK" - }, - { - "author_name": "Eliska Spalkova", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Sandra Margielewska-Davies", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Graham S. Taylor", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Eleni Syrimi", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Frances Baawuah", - "author_inst": "Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK" - }, - { - "author_name": "Joanne Beckmann", - "author_inst": "East London NHS Foundation Trust, 9 Allie Street, London E1 8DE, UK" - }, - { - "author_name": "Ifeanyichukwu Okike", - "author_inst": "Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK 4.\tUniversity Hospitals of Derby and Burton NHS Foundation Trust, Uttoxeter New Road, Derby" - }, - { - "author_name": "Shazaad Ahmad", - "author_inst": "Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9WL, UK" - }, - { - "author_name": "Joanna Garstang", - "author_inst": "Birmingham Community Healthcare NHS Trust, Holt Street, Aston B7 4BN, UK" - }, - { - "author_name": "Andrew Brent", - "author_inst": "Oxford University Hospitals NHS Foundation Trust, Old Road, Oxford OX3 7HE University of Oxford, Wellington Square, Oxford OX1 2JD, UK" - }, - { - "author_name": "Bernadette Brent", - "author_inst": "Oxford University Hospitals NHS Foundation Trust, Old Road, Oxford OX3 7HE" - }, - { - "author_name": "Georgina Ireland", - "author_inst": "Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK" - }, - { - "author_name": "Felicity Aiano", - "author_inst": "Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK" - }, - { - "author_name": "Zahin Amin-Chowdhury", - "author_inst": "Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK" - }, - { - "author_name": "Samuel Jones", - "author_inst": "Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK" - }, - { - "author_name": "Ray Borrow", - "author_inst": "Public Health England, Manchester Royal Infirmary, Manchester, United Kingdom" - }, - { - "author_name": "Ezra Linley", - "author_inst": "Public Health England, Manchester Royal Infirmary, Manchester, United Kingdom" - }, - { - "author_name": "Rafaq Azad", - "author_inst": "Bradford Teaching Hospitals NHS Foundation Trust" - }, - { - "author_name": "John Wright", - "author_inst": "Bradford Teaching Hospitals NHS Foundation Trust" - }, - { - "author_name": "Dagmar Waiblinger", - "author_inst": "Bradford Teaching Hospitals NHS Foundation Trust" - }, - { - "author_name": "Chris Davis", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Emma C Thomson", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Massimo Palmarini", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Brian James Willett", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Wendy S Barclay", - "author_inst": "Imperial College, London" - }, - { - "author_name": "John Poh", - "author_inst": "Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK" - }, - { - "author_name": "Vanessa Saliba", - "author_inst": "Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK" - }, - { - "author_name": "Gayatri Amirthalingam", - "author_inst": "Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK" - }, - { - "author_name": "Kevin Brown", - "author_inst": "Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK" - }, - { - "author_name": "Mary Ramsay", - "author_inst": "Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK" - }, - { - "author_name": "Jianmin Zuo", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Paul Moss", - "author_inst": "Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK" - }, - { - "author_name": "Shamez Ladhani", - "author_inst": "Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.04.13.21255404", "rel_title": "SARS-CoV-2 transmission dynamics in Belarus revealed by genomic and incidence data analysis", @@ -812024,6 +812611,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.13.21255384", + "rel_title": "Outcomes of COVID-19 infection in patients treated with Clozapine.", + "rel_date": "2021-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255384", + "rel_abs": "BackgroundClozapine, an antipsychotic, is associated with increased susceptibility to infection with COVID-19, compared to other antipsychotics.\n\nAimsTo investigate associations between clozapine treatment and increased risk of adverse outcomes of COVID-19, namely COVID-related hospitalisation and intensive care treatment, and death, among patients taking antipsychotics with schizophrenia-spectrum disorders.\n\nMethodUsing data from South London and Maudsley NHS Foundation Trust (SLAM) clinical records, via the Clinical Record Interactive Search system, we identified 157 individuals who had an ICD-10 diagnosis of schizophrenia-spectrum disorders, were taking antipsychotics at the time of the COVID-19 pandemic in the UK, and had a laboratory-confirmed COVID-19 infection. The following health outcomes were measured: COVID-related hospitalisation, COVID-related intensive care treatment death. We tested associations between clozapine treatment and each outcome using logistic regression models, adjusting for gender, age, ethnicity, neighbourhood deprivation, obesity, smoking status, diabetes, asthma, bronchitis and hypertension using propensity scores.\n\nResultsIn the 157 individuals who developed COVID while on antipsychotics, there were 44 COVID-related hospitalisations, 13 COVID-related intensive care treatments and 13 deaths of any cause during the follow-up period. In the unadjusted analysis, there was no significant association between clozapine and any of the outcomes and there remained no associations following adjusting for the confounding variables.\n\nConclusionsIn our sample of patients with COVID-19 and schizophrenia-spectrum disorders, we found no evidence that clozapine treatment puts patients at increased risk of hospitalisation, intensive care treatment or death, compared to any other antipsychotic treatment. However, further research should be considered in larger samples to confirm this.\n\nConflict of interestRDH has received research funding from Roche, Pfizer, Janssen, and Lundbeck. DFF has received research funding from Janssen and Lundbeck. JHM has received research funding from Lundbeck. JTT has received research funding from Bristol-Meyers-Squibb. RS declares research support in the last 36 months from Janssen, GSK and Takeda.\n\nEthics statementThe research was conducted under ethical approval reference 18/SC/0372 from Oxfordshire Research Ethics Committee C.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Risha Govind", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Daniela Fonseca de Freitas", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Megan Pritchard", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Mizanur Khondoker", + "author_inst": "Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich, UK." + }, + { + "author_name": "James T Teo", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Robert Stewart", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "Richard D. Hayes", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + }, + { + "author_name": "James H. MacCabe", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.04.13.21255413", "rel_title": "The impact of population mobility on COVID-19 incidence and socioeconomic disparities at the sub-city level in 314 Latin American cities", @@ -813411,37 +814045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.11.21255290", - "rel_title": "The Actual Conditions of Person-to-Object Contact and a Proposal for Prevention Measures During the COVID-19 Pandemic", - "rel_date": "2021-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.11.21255290", - "rel_abs": "The novel coronavirus disease (COVID-19) is currently spreading worldwide, resulting in widespread infections. Although infection control measures for maintaining physical distance between people and decreasing opportunities for close contact are effective, the global infection rate continues to increase. Conversely, data concerning potentially effective countermeasures related to person-to-object contact are sparse. This study focused on human contact behavior with objects and discussed control measures against infection at various locations where contact between people and objects occurs based on the relationship between human behavior and the objects in question. In this study, 1,260 subjects residing in Tokyo and the Kanagawa prefecture, Japan, were surveyed regarding their activities on days when they went outside (between December 3 [Thursday] and December 7 [Monday], 2020) and the objects they touched during this period. The survey results revealed that, depending on the location, the types and numbers of objects that were touched differed, and the respective mean values of contact objects differed significantly. Previous studies have particularly noted the remnants of viruses on doorknobs and toilets; however, the general dynamics of these contact numbers indicated that the percentage of people coming into contact with these objects is small. Although it is impossible to disinfect all objects and spaces, our findings will provide insights into human behavior and contact with objects. These findings are expected to contribute to the prioritization of disinfection during periods of widespread infection.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Teruaki Hayashi", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Daisuke Hase", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Hikaru Suenaga", - "author_inst": "The University of Tokyo" - }, - { - "author_name": "Yukio Ohsawa", - "author_inst": "The University of Tokyo" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.10.21255248", "rel_title": "Retrospective cohort study of Ivermectin as a SARS-CoV-2 pre-exposure prophylaxis method in Healthcare Workers", @@ -813786,6 +814389,129 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.04.13.21255139", + "rel_title": "Strong anti-viral responses in pediatric COVID-19 patients in South Brazil", + "rel_date": "2021-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255139", + "rel_abs": "Epidemiological evidence that COVID-19 manifests as a milder disease in children compared to adults has been reported by numerous studies, but the mechanisms underlying this phenomenon have not been characterized. It is still unclear how frequently children get infected, and/or generate immune responses to SARS-CoV-2. We have performed immune profiling of pediatric and adult COVID-19 patients in Brazil, producing over 38 thousand data points, asking if cellular or humoral immune responses could help explain milder disease in children. In this study, pediatric COVID-19 patients presented high viral titers. Though their non-specific immune profile was dominated by naive, non-activated lymphocytes, their dendritic cells expressed high levels of HLA-DR and were low in CX3CR1, indicating competence to generate immune responses that are not targeted to inflamed tissue. Finally, children formed strong specific antibody and T cell responses for viral structural proteins. Childrens T cell responses differed from adults in that their CD8+ TNF+ T cell responses were low for S peptide but significantly higher against N and M peptide pools. Altogether, our data support a scenario in which SARS-CoV-2 infected children may contribute to transmission, though generating strong and differential responses to the virus that might associate with protection in pediatric COVID-19 presentation.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Tiago Fazolo", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Karina Lima", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Julia C. Fontoura", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Priscila Oliveira de Souza", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Gabriel Hilario", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Renata Zorzetto", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Luiz Rodrigues Jr.", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Veridiane Maria Pscheidt", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Jayme Ferreira Neto", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Alisson F. Haubert", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Izza Gambin", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Aline C. Oliveira", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Raissa S. Mello", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Matheus Gutierrez", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + }, + { + "author_name": "Rodrigo Benedetti Gassen", + "author_inst": "Center for Transplantation Sciences, Department of Surgery, Massachusetts" + }, + { + "author_name": "Ivaine Tais Sauthier Sartor", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Gabriela Oliveira Zavaglia", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Ingrid Rodrigues Fernandes", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Fernanda Hammes Varela", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "M\u00e1rcia Polese-Bonatto", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Thiago J. Borges", + "author_inst": "Center for Transplantation Sciences, Department of Surgery, Massachusetts" + }, + { + "author_name": "Sidia Maria Callegari-Jacques", + "author_inst": "Departamento de Estat\u00edstica, Universidade Federal do Rio Grande do Sul" + }, + { + "author_name": "Marcela Santos Correa da Costa", + "author_inst": "Coordena\u00e7\u00e3o-Geral do Programa Nacional de Imuniza\u00e7\u00f5es - Departamento de Imuniza\u00e7\u00f5es e Doen\u00e7as Transmiss\u00edveis - Secretaria de Vigil\u00e2ncia em Sa\u00fade - Minist\u00e9rio da" + }, + { + "author_name": "Jaqueline de Araujo Schwartz", + "author_inst": "Coordena\u00e7\u00e3o-Geral do Programa Nacional de Imuniza\u00e7\u00f5es - Departamento de Imuniza\u00e7\u00f5es e Doen\u00e7as Transmiss\u00edveis - Secretaria de Vigil\u00e2ncia em Sa\u00fade - Minist\u00e9rio da" + }, + { + "author_name": "Marcelo Comerlato Scotta", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Renato T. Stein", + "author_inst": "Social responsibility - PROADI-SUS, Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Cristina Bonorino", + "author_inst": "Departamento de Ci\u00eancias B\u00e1sicas da Sa\u00fade, Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre - UFCSPA. Porto Alegre RS Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.04.10.21254878", "rel_title": "Preparations of Dutch emergency departments for the COVID-19 pandemic: a questionnaire-based study", @@ -815233,33 +815959,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.11.21255138", - "rel_title": "Continuing COVID-19 Vaccination of Front-Line Workers in British Columbia with the AstraZeneca Vaccine: Benefits in the Face of Increased Risk for Prothrombotic Thrombocytopenia", - "rel_date": "2021-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.11.21255138", - "rel_abs": "BackgroundOn March 29th, 2021, Canadas National Advisory Committee on Immunization (NACI) recommended against using the AstraZeneca COVID-19 vaccine in younger adults pending further review of the risk for Vaccine-Induced Pro-thrombotic Immune Thrombocytopenia (VIPIT). As a result, the province of British Columbia halted its front-line workers vaccination program which used the AstraZeneca vaccine. The province is expected to receive an additional 246,700 doses of AstraZeneca vaccine through US and COVAX until April 11th, enough to provide the first dose of vaccine to all unvaccinated front-line workers. It is unclear whether the alternative, mRNA vaccines can be immediately made available to front-line workers. We evaluated the harms and benefits of delaying vaccination of front-line workers in BC.\n\nMethodsWe reviewed the latest available evidence and used compartmental modelling to 1) compare the expected number of deaths due to COVID-19 and VIPIT under the scenarios of immediately continuing vaccination of front-line workers with the AstraZeneca vaccine or delaying it in favour of mRNA vaccines, and 2) compare the individual mortality risk of immediately receiving the AstraZeneca vaccine with waiting to receive an mRNA vaccine later for different age groups.\n\nResultsWe estimate that if British Columbia continues the front-line worker vaccination program with the AstraZeneca vaccine, we expect to see approximately 27,000 fewer cases of COVID-19, 500 fewer hospitalizations, 80 fewer COVID-related deaths, and 1,400 fewer cases of Long COVID from April 1st to October 1st, 2021, for an expected number of VIPIT-related deaths of 0.674 [95% CI 0.414-0.997]. In the same period and in areas of high transmission, the projected excess risk of mortality due to COVID-19 and VIPIT was significantly higher in the delayed vaccination with the mRNA vaccine scenario (3.23 to 4.44 times higher risk) than that of immediate vaccination with the AstraZeneca vaccine for those between 30 and 69 years of age. For those under 30, immediate vaccination with the AstraZeneca vaccine posed a higher risk than delayed vaccination with an mRNA vaccine.\n\nConclusionsThe benefits of immediately continuing immunization of front-line workers with the AstraZeneca vaccine far outweigh the risk both at a societal level and at an individual risk level for those over 40, and those over 30 in high-risk areas.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Amin Adibi", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Mohammad Mozafarihashjin", - "author_inst": "1- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario. 2-Department of Microbiology, Sinai Health System, Toronto, Ontario" - }, - { - "author_name": "Mohsen Sadatsafavi", - "author_inst": "The University of British Columbia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.09.21255190", "rel_title": "IL-1\u03b1 Mediates Tissue Specific Inflammation and Severe Respiratory Failure In Covid-19: Clinical And Experimental Evidence", @@ -815476,6 +816175,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.08.21255118", + "rel_title": "The association between loneliness during the COVID-19 pandemic and psychological distress", + "rel_date": "2021-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255118", + "rel_abs": "The purpose of this study was to examine the association between loneliness and psychological distress during the COVID-19 pandemic in Japan. We conducted a cross-sectional, online study from 22 to 26 December 2020. A total of 27,036 participants, all employed at the time of the survey, were included in the analysis. Participants were asked if they felt loneliness in a single-item question. The Kessler 6 (K6) was used to assess psychological distress defined as K6 scores of 5 or higher, and 13 or higher. The odds ratios (ORs) of psychological distress associated with loneliness were estimated using a multilevel logistic model nested in the prefecture of residence, with adjustment for age, sex, marital status, equivalent income, educational level, smoking, alcohol consumption, job type, number of workplace employees, and cumulative incidence rate of COVID-19 in the prefecture. Communication with friends, acquaintances, and family was strongly associated with psychological distress, so we adjusted for these factors and eating meals alone. Results showed a significant association between loneliness and psychological distress (OR = 36.62, 95%CI = 32.95-40.69). Lack of friends to talk to, lack of acquaintances to ask for help, and lack of people to communicate with through social networking sites were all strongly associated with psychological distress, as were family time and solitary eating. Even after adjusting for these factors, loneliness was still strongly associated with psychological distress (OR = 29.36, 95%CI = 26.44-32.98). The association between loneliness during the COVID-19 pandemic and psychological distress indicates the need for intervention.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yusuke Konno", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Masako Nagata", + "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" + }, + { + "author_name": "Ayako Hino", + "author_inst": "Department of Mental Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Seiichiro Tateishi", + "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Mayumi Tsuji", + "author_inst": "Department of Environmental Health, School of Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Akira Ogami", + "author_inst": "Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Japa" + }, + { + "author_name": "Reiji Yoshimura", + "author_inst": "Department of Psychiatry, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Shinya Matsuda", + "author_inst": "Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan" + }, + { + "author_name": "Yoshihisa Fujino", + "author_inst": "University of Occupational and Environmental Health, Japan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.04.09.21255215", "rel_title": "Impacts of COVID-19 on sick leave", @@ -816879,121 +817629,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.11.21255153", - "rel_title": "Vaccination boosts protective responses and counters SARS-CoV-2-induced pathogenic memory B cells", - "rel_date": "2021-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.11.21255153", - "rel_abs": "Given the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the recent implementation of SARS-CoV-2 vaccination, we have much to learn about the duration of immune protection and the interface between the immune responses to infection and to vaccination. To address these questions, we monitored immune responses to SARS-CoV-2 infection in convalescent individuals over seven months and following mRNA vaccination. Spike Receptor-Binding-Domain (RBD)-specific circulating antibodies and plasma neutralizing activity generally decreased over time, whereas RBD-specific memory B cells persisted. Additionally, using antibody depletion techniques, we showed that the neutralizing activity of plasma specifically resides in the anti-RBD antibodies. More vigorous antibody and B cell responses to vaccination were observed in previously infected subjects relative to uninfected comparators, presumably due to immune priming by infection. SARS-CoV-2 infection also led to increased numbers of double negative B memory cells, which are described as a dysfunctional B cell subset. This effect was reversed by SARS-CoV-2 vaccination, providing a potential mechanistic explanation for the vaccination-induced reduction in symptoms in patients with \"Long-COVID\".", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Pankaj K Mishra", - "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA." - }, - { - "author_name": "Natalie Bruiners", - "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA." - }, - { - "author_name": "Rahul Ukey", - "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA." - }, - { - "author_name": "Pratik Datta", - "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA." - }, - { - "author_name": "Alberta Onyuka", - "author_inst": "Global Tuberculosis Institute,New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA" - }, - { - "author_name": "Deborah Handler", - "author_inst": "Global Tuberculosis Institute,New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA" - }, - { - "author_name": "Sabiha Hussain", - "author_inst": "Department of Medicine, 7Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901" - }, - { - "author_name": "William Honnen", - "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA." - }, - { - "author_name": "Sukhwinder Singh", - "author_inst": "NJMS Flow Cytometry and Immunology Core Laboratory,New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA." - }, - { - "author_name": "Valentina Guerrini", - "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA." - }, - { - "author_name": "Yue Yin", - "author_inst": "Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA" - }, - { - "author_name": "Hannah Dewald", - "author_inst": "Department of Medicine,New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA." - }, - { - "author_name": "Alok Choudhary", - "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA." - }, - { - "author_name": "Daniel B Horton", - "author_inst": "Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ" - }, - { - "author_name": "Emily S Barret", - "author_inst": "Environmental and Occupational Health Sciences Institute,Rutgers University, Piscataway, NJ" - }, - { - "author_name": "Jason Roy", - "author_inst": "Department of Biostatistics and Epidemiology, School of Public Health, Rutgers University, Piscataway, NJ" - }, - { - "author_name": "Stanley H Weiss", - "author_inst": "Department of Medicine,New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA." - }, - { - "author_name": "Patricia Fitzgerald-Bocarsly", - "author_inst": "Department of Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA." - }, - { - "author_name": "Martin J Blaser", - "author_inst": "Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA" - }, - { - "author_name": "Jeffrey L Carson", - "author_inst": "Department of Medicine,Rutgers University, Piscataway, NJ" - }, - { - "author_name": "Reynold A. Panettieri Jr.", - "author_inst": "Rutgers Institute for Translational Medicine & Science, New Brunswick, NJ." - }, - { - "author_name": "Alfred Lardizabal", - "author_inst": "Global Tuberculosis Institute,New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA" - }, - { - "author_name": "Theresa L Chang", - "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA" - }, - { - "author_name": "Abraham Pinter", - "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA." - }, - { - "author_name": "Maria L Gennaro", - "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.14.21255468", "rel_title": "Using high effective risk of Adult-Senior duo in multigenerational homes to prioritize COVID-19 vaccination", @@ -817282,6 +817917,109 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.04.13.439641", + "rel_title": "Spike Protein Targeting \"Nano-Glue\" that Captures and Promotes SARS-CoV-2 Elimination", + "rel_date": "2021-04-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.13.439641", + "rel_abs": "The global emergency caused by the SARS-CoV-2 pandemics can only be solved with adequate preventive and therapeutic strategies, both currently missing. The electropositive Receptor Binding Domain (RBD) of SARS-CoV-2 spike protein with abundant {beta}-sheet structure serves as target for COVID-19 therapeutic drug design. Here, we discovered that ultrathin 2D CuInP2S6 (CIPS) nanosheets as a new agent against SARS-CoV-2 infection, which also able to promote viral host elimination. CIPS exhibits extremely high and selective binding capacity with the RBD of SARS-CoV-2 spike protein, with consequent inhibition of virus entry and infection in ACE2-bearing cells and human airway epithelial organoids. CIPS displays nano-viscous properties in selectively binding with spike protein (KD < 1 pM) with negligible toxicity in vitro and in vivo. Further, the CIPS-bound SARS-CoV-2 was quickly phagocytosed and eliminated by macrophages, suggesting CIPS could be successfully used to capture and facilitate the virus host elimination with possibility of triggering anti-viral immunization. Thus, we propose CIPS as a promising nanodrug for future safe and effective anti-SARS-CoV-2 therapy, as well as for use as disinfection agent and surface coating material to constrain the SARS-CoV-2 spreading.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Guofang Zhang", + "author_inst": "Laboratory of Immunology and Nanomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Yalin Cong", + "author_inst": "University of Chinese Academy of Science" + }, + { + "author_name": "Guoli Cao", + "author_inst": "Laboratory of Immunology and Nanomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Liang Li", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Peng Yu", + "author_inst": "School of Materials Science and Engineering, Sun Yat-sen University" + }, + { + "author_name": "Qingle Song", + "author_inst": "Laboratory of Immunology and Nanomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Ke Liu", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Jing Qu", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Jing Wang", + "author_inst": "State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University" + }, + { + "author_name": "Wei Xu", + "author_inst": "CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and Natio" + }, + { + "author_name": "Shumin Liao", + "author_inst": "Department of Otolaryngology, The Seventh Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Yunping Fan", + "author_inst": "Department of Otolaryngology, The Seventh Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Yufeng Li", + "author_inst": "CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and Natio" + }, + { + "author_name": "Guocheng Wang", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Lijing Fang", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Yanzhong Chang", + "author_inst": "College of Life Science, Hebei Normal University" + }, + { + "author_name": "Yuliang Zhao", + "author_inst": "Research Unit of Nanoscience and Technology, Chinese Academy of Medical Sciences" + }, + { + "author_name": "Diana Boraschi", + "author_inst": "The Institute of Biochemistry and Cell Biology, National Research Council" + }, + { + "author_name": "Hongchang Li", + "author_inst": "Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences" + }, + { + "author_name": "Chunying Chen", + "author_inst": "CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and Natio" + }, + { + "author_name": "Liming Wang", + "author_inst": "CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety & CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and Natio" + }, + { + "author_name": "Yang Li", + "author_inst": "Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.14.439793", "rel_title": "Neuropilin-1 Mediates SARS-CoV-2 Infection in Bone Marrow-derived Macrophages", @@ -818665,85 +819403,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.08.21255163", - "rel_title": "COLI-NET: Fully Automated COVID-19 Lung and Infection Pneumonia Lesion Detection and Segmentation from Chest CT Images", - "rel_date": "2021-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255163", - "rel_abs": "BackgroundWe present a deep learning (DL)-based automated whole lung and COVID-19 pneumonia infectious lesions (COLI-Net) detection and segmentation from chest CT images.\n\nMethodsWe prepared 2358 (347259, 2D slices) and 180 (17341, 2D slices) volumetric CT images along with their corresponding manual segmentation of lungs and lesions, respectively, in the framework of a multi-center/multi-scanner study. All images were cropped, resized and the intensity values clipped and normalized. A residual network (ResNet) with non-square Dice loss function built upon TensorFlow was employed. The accuracy of lung and COVID-19 lesions segmentation was evaluated on an external RT-PCR positive COVID-19 dataset (7333, 2D slices) collected at five different centers. To evaluate the segmentation performance, we calculated different quantitative metrics, including radiomic features.\n\nResultsThe mean Dice coefficients were 0.98{+/-}0.011 (95% CI, 0.98-0.99) and 0.91{+/-}0.038 (95% CI, 0.90-0.91) for lung and lesions segmentation, respectively. The mean relative Hounsfield unit differences were 0.03{+/-}0.84% (95% CI, -0.12 - 0.18) and -0.18{+/-}3.4% (95% CI, -0.8 - 0.44) for the lung and lesions, respectively. The relative volume difference for lung and lesions were 0.38{+/-}1.2% (95% CI, 0.16-0.59) and 0.81{+/-}6.6% (95% CI, -0.39-2), respectively. Most radiomic features had a mean relative error less than 5% with the highest mean relative error achieved for the lung for the Range first-order feature (- 6.95%) and least axis length shape feature (8.68%) for lesions.\n\nConclusionWe set out to develop an automated deep learning-guided three-dimensional whole lung and infected regions segmentation in COVID-19 patients in order to develop fast, consistent, robust and human error immune framework for lung and pneumonia lesion detection and quantification.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Isaac Shiri", - "author_inst": "Geneva University Hospital" - }, - { - "author_name": "Hossein Arabi", - "author_inst": "Geneva University Hospital" - }, - { - "author_name": "Yazdan Salimi", - "author_inst": "Geneva University Hospital" - }, - { - "author_name": "Amir Hossein Sanaat", - "author_inst": "Geneva University Hospital" - }, - { - "author_name": "Azadeh Akhavanalaf", - "author_inst": "Geneva University Hospital" - }, - { - "author_name": "Ghasem Hajianfar", - "author_inst": "Iran University of Medical Science" - }, - { - "author_name": "Dariush Askari", - "author_inst": "Shahid Beheshti University of Medical" - }, - { - "author_name": "Shakiba Moradi", - "author_inst": "Med Fanavarn Plus" - }, - { - "author_name": "Zahra Mansouri", - "author_inst": "Shahid Beheshti University of medical sciences" - }, - { - "author_name": "Masoumeh Pakbin", - "author_inst": "Qom university of medical sciences" - }, - { - "author_name": "Saleh Sandoughdaran", - "author_inst": "Shahid Beheshti University of medical sciences" - }, - { - "author_name": "Hamid Abdollahi", - "author_inst": "Kerman University of Medical sciences" - }, - { - "author_name": "Amir Reza Radmard", - "author_inst": "Tehran University of Medical Sciences" - }, - { - "author_name": "Kiara Rezaei-Kalantari", - "author_inst": "Iran University of Medical Science" - }, - { - "author_name": "Mostafa Ghelich Oghli", - "author_inst": "KU Leuven" - }, - { - "author_name": "Habib Zaidi", - "author_inst": "Geneva University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2021.04.09.21255184", "rel_title": "Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus", @@ -818880,6 +819539,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.11.21253563", + "rel_title": "Impact of COVID -19 on Depression and Anxiety among Healthcare Professionals in Abu Dhabi", + "rel_date": "2021-04-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.11.21253563", + "rel_abs": "COVID-19 have affected Healthcare workers is many ways. One of the important areas is the psychological impact. The aim of this study is to examine the effects of the COVID-19 outbreak on the mental health of healthcare Professionals (HCP). A cross-sectional study was conducted between April 11th, and July 23rd, 2020, to assess depression and anxiety of healthcare workers, during the COVID-19 pandemic. An online, self-administered, anonymous questionnaire evaluated 1,268 HCP. More than half of the participants reported symptoms of anxiety (51.5%). Mild anxiety was reported in 28.8% of participating HCP, and 12.68 % of the participants registered moderate anxiety scores, while 9.95 % reported severe anxiety. Depression symptoms were revealed in 38.3 % of participating providers. Among all participates, 4.3 % and 2.7 % reported moderately severe and severe depression, accordingly, while 22.5%, and 8.8 % of the participating health care providers documented mild and moderate depression. The high prevalence of anxiety and depression recorded among HCP during the pandemic suggests that mental health intervention and support are necessary to ensure the psychological well-being of HCP.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Amal Alzarooni", + "author_inst": "Ambulatory health care,Abu Dhabi Health Services Company, UAE" + }, + { + "author_name": "Aljazia Alghfeli", + "author_inst": "Ambulatory health care, Abu Dhabi Health Services Company, AE" + }, + { + "author_name": "Hamda Alremeithi", + "author_inst": "Ambulatory health care,Abu Dhabi Health Services Company , UAE" + }, + { + "author_name": "Roqayah Al Madhaani,", + "author_inst": "Ambulatory Healthcare Services,Abu Dhabi Health Services Company, UAE" + }, + { + "author_name": "Latifa Al Ketbi,", + "author_inst": "Ambulatory Healthcare Services, Abu Dhabi Health Services Company, UAE" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.09.21255179", "rel_title": "SARS-CoV-2 UK, South African and Brazilian Variants in Karachi- Pakistan", @@ -820551,49 +821245,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.07.21255078", - "rel_title": "Antibody Response after First-dose of ChAdOx1-nCOV (Covishield) and BBV-152 (Covaxin) amongst Health Care Workers in India: Preliminary Results of Cross-sectional Coronavirus Vaccine-induced Antibody Titre (COVAT) study", - "rel_date": "2021-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.07.21255078", - "rel_abs": "BackgroundTwo vaccines are currently being administered in India to prevent the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We assessed the humoral immune response after the first dose of two vaccines ChAdOx1-nCOV (Covishield) and BBV-152 (Covaxin) in Indian health care workers (HCW).\n\nMethodsThis ongoing, Pan-India, Cross-sectional, Coronavirus Vaccine-induced Antibody Titre (COVAT) study is being conducted amongst HCW, with or without past history of SARS-CoV-2 infection. SARS-CoV-2 anti-spike binding antibody is being assessed quantitatively at four timepoints between 21 days or more after the first dose to 6 months after the second dose. Primary aim is to analyze antibody response following each dose of both vaccines and its correlation to age, sex, body mass index (BMI) and comorbidities. Here we report the preliminary results of anti-spike antibody response after the first dose.\n\nResultsAmongst the 552 HCW (325 Male, 227 Female), 456 and 96 received first dose of Covishield and Covaxin respectively. Overall, 79.3% showed seropositivity after the first dose. Responder rate and median (IQR) rise in anti-spike antibody was significantly higher in Covishield vs. Covaxin recipient (86.8 vs. 43.8%; 61.5 vs. 6 AU/ml; both p<0.001). This difference persisted in propensity-matched (age, sex and BMI) analysis in 172 subjects. No difference was observed with age, gender and BMI. History of hypertension had lower responder rate (65.7 vs. 82.3%, p=0.001). Covishield recipient had more adverse event vs. Covaxin arm (46.7 vs. 31.2%, p=0.006). Presence of comorbidities, past SARS-CoV-2 infection and vaccine types used were independent predictors for seropositivity after the first dose, in multiple logistic regression analysis.\n\nConclusionsWhile both vaccines elicited immune response, seropositivity rates to anti-spike antibody were significantly higher in Covishield recipient compared to Covaxin after the first dose. Ongoing COVAT study will further enlighten the immune response between two vaccines after the second dose.\n\nHighlightsO_LIThis study evaluated the humoral antibody response of two SARS-CoV-2 vaccines Covishield and Covaxin in Indian health-care workers.\nC_LIO_LIBoth vaccines showed seropositivity to anti-spike antibody, 21 days or more after the first dose.\nC_LIO_LIResponder rates were higher in Covishield recipient compared to Covaxin in propensity-matched cohorts.\nC_LIO_LIPast SARS-CoV-2 infection, presence of comorbidities and vaccine type received were independent predictors of antibody response after the first dose.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "AWADHESH KUMAR SINGH", - "author_inst": "GD Hospital & Diabetes Institute, Kolkata, India" - }, - { - "author_name": "Sanjeev Phatak", - "author_inst": "Vijayratna Diabetes Centre, Ahmedabad, Gujarat, India." - }, - { - "author_name": "Nagendra Kumar Singh", - "author_inst": "Diabetes and Heart Research Centre, Dhanbad, Jharkhand, India" - }, - { - "author_name": "Arvind Gupta", - "author_inst": "Rajasthan Hospital, Opposite, Jaipur, India" - }, - { - "author_name": "Arvind Sharma", - "author_inst": "Dept. of Community Medicine, Mahatma Gandhi Medical College & Hospital, Jaipur, India" - }, - { - "author_name": "Kingshuk Bhattacharjee", - "author_inst": "Independent Biostatistician, Kolkata, India" - }, - { - "author_name": "RITU SINGH", - "author_inst": "G.D Hospital & Diabetes Institute, Kolkata, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.08.21255150", "rel_title": "A multiplexed high-throughput neutralization assay reveals a lack of activity against multiple variants after SARS-CoV-2 infection", @@ -820862,6 +821513,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.09.21255161", + "rel_title": "The PUPPY Study - Protocol for a Longitudinal Mixed Methods Study Exploring Problems Coordinating and Accessing Primary Care for Attached and Unattached Patients Exacerbated During the COVID-19 Pandemic Year", + "rel_date": "2021-04-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255161", + "rel_abs": "BackgroundThe COVID-19 pandemic significantly disrupted primary care in Canada, with many walk-in clinics and family practices initially closing or being perceived as inaccessible, pharmacies remaining open with restrictions on patient interactions, rapid uptake of virtual care, and reduced referrals for lab tests, diagnostics, and specialist care. The PUPPY Study (Problems Coordinating and Accessing Primary Care for Attached and Unattached Patients Exacerbated During the COVID-19 Pandemic Year) seeks to understand the impact of COVID-19 across the quadruple aim of primary care, with particular focus on the impacts on patients without attachment to a regular provider and those with chronic health conditions.\n\nObjectiveThe PUPPY Study objective is to understand the impact of COVID-19 across the quadruple aim of primary care.\n\nMethodsThe PUPPY study builds on an existing research program exploring patients access and attachment to primary care, pivoted to adapt to the emerging COVID-19 context. We will undertake a longitudinal mixed methods study to understand critical gaps in primary care access and coordination, comparing data pre- and post-pandemic in three Canadian provinces (Quebec, Ontario, and Nova Scotia). Multiple data sources will be used including: a policy review; qualitative interviews with primary care policymakers, providers (i.e., family physicians, nurse practitioners, and pharmacists), and patients (N=120); and medication prescribing and healthcare billings. The findings will inform the strengthening of primary care during and beyond the COVID-19 pandemic.\n\nResultsFunding was provided by the Canadian Institutes of Health Research COVID-19 Rapid Funding Opportunity Grant. Ethical approval to conduct this study was granted in Ontario (Queens Health Sciences & Affiliated Teaching Hospitals Research Ethics Board, file number 6028052; Western University Health Sciences Research Ethics Board, project 116591; University of Toronto Health Sciences Research Ethics Board, protocol number 40335), Quebec (Centre integre universitaire de sante et de services sociaux de lEstrie, project number 2020-3446) and Nova Scotia (Nova Scotia Health Research Ethics Board, file number 1024979).\n\nConclusionsThis is the first study of its kind exploring the impacts of COVID-19 on primary care systems, with particular focus on the issues of patients attachment and access to primary care. Through a multi-stakeholder, cross-jurisdictional approach, the PUPPY Study will generate findings and implications for future policy and practice.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Emily Gard Marshall", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Mylaine Breton", + "author_inst": "Universite de Sherbrooke" + }, + { + "author_name": "Benoit Cossette", + "author_inst": "Universite de Sherbrooke" + }, + { + "author_name": "Jennifer Isenor", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Maria Mathews", + "author_inst": "Western University" + }, + { + "author_name": "Caitlyn Ayn", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Melanie Ann Smithman", + "author_inst": "Universite de Sherbrooke" + }, + { + "author_name": "David Stock", + "author_inst": "Dalhousie University" + }, + { + "author_name": "Eliot Frymire", + "author_inst": "Queen's University" + }, + { + "author_name": "Lynn Edwards", + "author_inst": "Nova Scotia Health" + }, + { + "author_name": "Michael Green", + "author_inst": "Queen's University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2021.04.08.21255046", "rel_title": "COVID-19 and mortality risk in patients with psychiatric disorders", @@ -822225,181 +822935,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.08.21255115", - "rel_title": "Program and patient characteristics for the United States Expanded Access Program to COVID-19 convalescent plasma", - "rel_date": "2021-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255115", - "rel_abs": "BackgroundThe United States (US) Expanded Access Program (EAP) to COVID-19 convalescent plasma was initiated in response to the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease-2019 (COVID-19). While randomized clinical trials were in various stages of development and enrollment, there was an urgent need for widespread access to potential therapeutic agents particularly for vulnerable racial and ethnic minority populations who were disproportionately affected by the pandemic. The objective of this study is to report on the demographic, geographic, and chronological access to COVID-19 convalescent plasma in the US via the EAP.\n\nMethods and findingsMayo Clinic served as the central IRB for all participating facilities and any US physician could participate as local physician-principal investigator. Registration occurred through the EAP central website. Blood banks rapidly developed logistics to provide convalescent plasma to hospitalized patients with COVID-19. Demographic and clinical characteristics of all enrolled patients in the EAP were summarized. Temporal trends in access to COVID-19 convalescent plasma were investigated by comparing daily and weekly changes in EAP enrollment in response to changes in infection rate on a state level. Geographical analyses on access to convalescent plasma included assessing EAP enrollment in all national hospital referral regions as well as assessing enrollment in metropolitan and less populated areas which did not have access to COVID-19 clinical trials.\n\nFrom April 3 to August 23, 2020, 105,717 hospitalized patients with severe or life-threatening COVID-19 were enrolled in the EAP. A majority of patients were older than 60 years of age (57.8%), male (58.4%), and overweight or obese (83.8%). There was substantial inclusion of minorities and underserved populations, including 46.4% of patients with a race other than White, and 37.2% of patients were of Hispanic ethnicity. Severe or life-threatening COVID-19 was present in 61.8% of patients and 18.9% of patients were mechanically ventilated at time of convalescent plasma infusion. Chronologically and geographically, increases in enrollment in the EAP closely followed confirmed infections across all 50 states. Nearly all national hospital referral regions enrolled patients in the EAP, including both in metropolitan and less populated areas.\n\nConclusionsThe EAP successfully provided widespread access to COVID-19 convalescent plasma in all 50 states, including for underserved racial and ethnic minority populations. The efficient study design of the EAP may serve as an example framework for future efforts when broad access to a treatment is needed in response to a dynamic disease affecting demographic groups and areas historically underrepresented in clinical studies.", - "rel_num_authors": 40, - "rel_authors": [ - { - "author_name": "Jonathon W Senefeld", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Patrick W Johnson", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Katie L Kunze", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Noud van Helmond", - "author_inst": "Cooper Medical School of Rowan University" - }, - { - "author_name": "Stephen A Klassen", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Chad C Wiggins", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Katelyn A Bruno", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Michael A Golafshar", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Molly M Petersen", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Matthew R Buras", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Allan M Klompas", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Matthew A Sexton", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Juan C Diaz Soto", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Sarah E Baker", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "John R.A. Shepherd", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Nicole C Verdun", - "author_inst": "U.S. Food and Drug Administration" - }, - { - "author_name": "Peter Marks", - "author_inst": "U.S. Food and Drug Administration" - }, - { - "author_name": "Camille M van Buskirk", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Jeffrey L Winters", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "James R Stubbs", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Robert F Rea", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Vitaly Herasevich", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Emily R Whelan", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Andrew J Clayburn", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Kathryn F Larson", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Juan G Ripoll", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Kylie J Andersen", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Matthew N.P. Vogt", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Joshua J Dennis", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Riley J Regimbal", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Philippe R Bauer", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Janis E Blair", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Katherine Wright", - "author_inst": "Arizona State University" - }, - { - "author_name": "Joel T Greenshields", - "author_inst": "Indiana University" - }, - { - "author_name": "Nigel S Paneth", - "author_inst": "Michigan State University" - }, - { - "author_name": "DeLisa Fairweather", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "R. Scott Wright", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Arturo Casadevall", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Rickey E Carter", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Michael J Joyner", - "author_inst": "Mayo Clinic" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.08.21255148", "rel_title": "COVID-19 outcomes among hospitalized men with or without exposure to alpha-1-adrenergic receptor blocking agents", @@ -822640,6 +823175,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.09.439260", + "rel_title": "Nosocomial Pseudomonas aeruginosaregulates alginate biosynthesis and Type VI secretion system during adaptive and convergent evolution for coinfection in critically ill COVID-19 patients", + "rel_date": "2021-04-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.09.439260", + "rel_abs": "COVID-19 pandemic has caused millions of death globally and caused huge impact on the health of infected patients. Shift in the lung microbial ecology upon such viral infection often worsens the disease and increases host susceptibility to secondary infections. Recent studies have indicated that bacterial coinfection is an unignorable factor contributing to the aggravation of COVID-19 and posing great challenge to clinical treatments. However, there is still a lack of in-depth investigation on the coinfecting bacteria in COVID-19 patients for better treatment of bacterial coinfection. With the knowledge that Pseudomonas aeruginosa is one of the top coinfecting pathogens, we analyzed the adaptation and convergent evolution of nosocomial P. aeruginosa isolated from two critical COVID-19 patients in this study. We sequenced and compared the genomes and transcriptomes of P. aeruginosa isolates longitudinally and parallelly for its evolutionary traits. P. aeruginosa overexpressed alginate and attenuated Type VI secretion system (T6SS) during coinfection for excessive biofilm formation and suppressed virulence. Results of bacterial competition assay and macrophage cytotoxicity test indicated that P. aeruginosa reduced its virulence towards both prokaryotic competitors and eukaryotic host through inhibiting its T6SS during evolution. P. aeuginosa T6SS is thus one of the reasons for its advantage to cause coinfection in COVID-19 patients while the attenuation of T6SS could cause a shift in the microecological composition in the lung. Our study will contribute to the development of therapeutic measures and the discovery of novel drug target to eliminate P. aeruginosa coinfection in COVID-19 patient.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Zhao Cai", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Xiangke Duan", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Han Zhang", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Shuhong Han", + "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, China" + }, + { + "author_name": "Kaiwei Yu", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Yingdan Zhang", + "author_inst": "School of Medicine, Southern University of Science and Technology" + }, + { + "author_name": "Yang Liu", + "author_inst": "Medical Research Center, Southern University of Science and Technology Hospital" + }, + { + "author_name": "Liang Yang", + "author_inst": "School of Medicine, Southern University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.10.439275", "rel_title": "CoVac501, a self-adjuvanting peptide vaccine conjugated with TLR7 agonists, against SARS-CoV-2 induces protective immunity", @@ -824159,53 +824741,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.08.21255128", - "rel_title": "Changing patterns of sickness absence among healthcare workers in England during the COVID-19 pandemic.", - "rel_date": "2021-04-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255128", - "rel_abs": "ObjectiveTo explore impacts of the COVID-19 pandemic on patterns of sickness absence among staff employed by the National Health Service (NHS) in England.\n\nMethodsWe analysed prospectively collected, pseudonymised data on 959,356 employees who were continuously employed by NHS trusts during 1 January 2019 to 31 July 2020, comparing the frequency of new sickness absence in 2020 with that at corresponding times in 2019.\n\nResultsAfter exclusion of episodes directly related to COVID-19, the overall incidence of sickness absence during the initial 10 weeks of the pandemic (March-May 2020) was more than 20% lower than in corresponding weeks of 2019, but trends for specific categories of illness varied. Marked increases were observed for asthma (122%), infectious diseases (283%) and mental illness (42.3%), while reductions were apparent for gastrointestinal problems (48.4%), genitourinary/gynaecological disorders (33.8%), eye problems (42.7%), injury and fracture (27.7%), back problems (19.6%), other musculoskeletal disorders (29.3%), disorders of ear, nose and throat (32.7%), cough/flu (24.5%) and cancer (24.1%). A doubling of new absences for pregnancy-related disorders during 18 May to 19 July of 2020 was limited to women with earlier COVID-19 sickness absence.\n\nConclusionsVarious factors will have contributed to the large and divergent changes that were observed. The findings add to concerns regarding delays in diagnosis and treatment of cancers, and support a need to plan for a large backlog of treatment for many other diseases. Further research should explore the rise in absence for pregnancy-related disorders among women with earlier COVID-19 sickness absence.\n\nO_TEXTBOX1. What is already known about this subject?\n\nHistorically, rates of sickness absence among the NHS workforce in England have been relatively high but stable. Reports of a marked increase during the first wave of the COVID-19 pandemic have not distinguished between different categories of underlying illness.\n\n2. What are the new findings?\n\nDuring the first wave of COVID-19, incidence of sickness-absence changed markedly when compared to the previous year, with major increases for some categories of illness, and large declines for many others, including cancer.\n\n3. How might this impact on policy or clinical practice in the foreseeable future?\n\nThe findings support a need to plan for effects from delayed diagnosis and treatment of cancer, and to manage a large backlog of treatment for many other diseases.\n\nC_TEXTBOX", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Rhiannon Edge", - "author_inst": "Lancaster University" - }, - { - "author_name": "Diana A van der Plaat", - "author_inst": "National Heart and Lung Institute (NHLI), Imperial College London" - }, - { - "author_name": "Vaughan Parsons", - "author_inst": "Guys and St Thomas NHS Foundation Trust" - }, - { - "author_name": "David Coggon", - "author_inst": "MRC Lifecourse Epidemiology Unit, University of Southampton" - }, - { - "author_name": "Martie J van Tongeren", - "author_inst": "Centre for Occupational and Environmental Health, University of Manchester" - }, - { - "author_name": "Rupert Muiry", - "author_inst": "Guys and St Thomas NHS Foundation Trust" - }, - { - "author_name": "Ira Madan", - "author_inst": "Guy's and St Thomas' NHS Foundation Trust" - }, - { - "author_name": "Paul Cullinan", - "author_inst": "National Heart and Lung Institute (NHLI), Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.04.08.438924", "rel_title": "Genome-wide CRISPR activation screen identifies novel receptors for SARS-CoV-2 entry", @@ -824418,6 +824953,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.04.05.21254834", + "rel_title": "Performance of Repeat BinaxNOW SARS-CoV-2 Antigen Testing in a Community Setting, Wisconsin, November-December 2020", + "rel_date": "2021-04-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254834", + "rel_abs": "Repeating the BinaxNOW antigen test for SARS-CoV-2 by two groups of readers within 30 minutes resulted in high concordance (98.9%) in 2,110 encounters. BinaxNOW test sensitivity was 77.2% (258/334) compared to real-time reverse transcription-polymerase chain reaction. Repeating antigen testing on the same day did not significantly improve test sensitivity while specificity remained high.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Melisa M. Shah", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Phillip P. Salvatore", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Laura Ford", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Emiko Kamitani", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Melissa J. Whaley", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Kaitlin Mitchell", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Dustin W. Currie", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Clint N. Morgan", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Hannah E. Segaloff", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Shirley Lecher", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Tarah Somers", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Miriam E. Van Dyke", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "John Paul Bigouette", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Augustina Delaney", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Juliana DaSilva", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Michelle O'Hegarty", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Lauren Boyle-Estheimer", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Fatima Abdirizak", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Sandor E. Karpathy", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jennifer Meece", + "author_inst": "Marshfield Clinic Research Institute" + }, + { + "author_name": "Lynn Ivanic", + "author_inst": "Marshfield Clinic Research Institute" + }, + { + "author_name": "Kimberly Goffard", + "author_inst": "Winnebago County Health Department" + }, + { + "author_name": "Doug Gieryn", + "author_inst": "Winnebago County Health Department" + }, + { + "author_name": "Alana Sterkel", + "author_inst": "Wisconsin State Laboratory of Hygiene" + }, + { + "author_name": "Allen Bateman", + "author_inst": "Wisconsin State Laboratory of Hygiene" + }, + { + "author_name": "Juliana Kahrs", + "author_inst": "University of Wisconsin-Oshkosh" + }, + { + "author_name": "Kimberly Langolf", + "author_inst": "University of Wisconsin-Oshkosh" + }, + { + "author_name": "Tara Zochert", + "author_inst": "University of Wisconsin-Oshkosh" + }, + { + "author_name": "Nancy W. Knight", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Christopher H. Hsu", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Hannah L. Kirking", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jacqueline E. Tate", + "author_inst": "Centers for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.04.21254881", "rel_title": "Neutralization of SARS-CoV-2 variants by convalescent and vaccinated serum", @@ -825637,101 +826315,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2021.04.09.439147", - "rel_title": "Nasal delivery of single-domain antibodies improve symptoms of SARS-CoV-2 infection in an animal model", - "rel_date": "2021-04-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.09.439147", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes the disease COVID-19 can lead to serious symptoms, such as severe pneumonia, in the elderly and those with underlying medical conditions. While vaccines are now available, they do not work for everyone and therapeutic drugs are still needed particularly for treating life-threatening conditions. Here, we showed nasal delivery of a new, unmodified camelid single-domain antibody (VHH), termed K-874A, effectively inhibited SARS-CoV-2 titers in infected lungs of Syrian hamsters without causing weight loss and cytokine induction. In vitro studies demonstrated that K-874A neutralized SARS-CoV-2 in both VeroE6/TMPRSS2 and human lung-derived alveolar organoid cells. Unlike other drug candidates, K-874A blocks viral membrane fusion rather than viral attachment. Cryo-electron microscopy revealed K-874A bound between the receptor binding domain and N-terminal domain of the virus S protein. Further, infected cells treated with K-874A produced fewer virus progeny that were less infective. We propose that direct administration of K-874A to the lung via a nebulizer could be a new treatment for preventing the reinfection of amplified virus in COVID-19 patients.\n\nAuthor summaryVaccines for COVID-19 are now available but therapeutic drugs are still needed to treat life-threatening cases and those who cannot be vaccinated. We discovered a new heavy-chain single-domain antibody that can effectively neutralize the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19. Unlike other drug candidates, which prevent the virus from attaching to the receptor on the host cell, this new antibody acts by blocking the virus membrane from fusing with the host cell membrane. We studied the behavior of the new antibody in vitro using VeroE6/TMPRSS2 cells and human lung organoids. When delivered through the nose to infected Syrian hamsters, we found that this antibody could prevent the typical symptoms caused by SARS-CoV-2. Our results are significant because delivering simple drugs directly to infected lungs using a nebulizer could increase the potency of the drugs while reducing the risk of immune reaction that could occur if the drugs escape or are delivered through the blood stream.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Kei Haga", - "author_inst": "Kitasato University: Kitasato Daigaku" - }, - { - "author_name": "Reiko Takai-Todaka", - "author_inst": "Kitasato University: Kitasato Daigaku" - }, - { - "author_name": "Yuta Matsumura", - "author_inst": "Kao Corporation" - }, - { - "author_name": "Tomomi Takano", - "author_inst": "Kitasato University School of Veterinary Medicine Graduate School of Veterinary Medicine: Kitasato Daigaku Juigakubu Daigakuin Juigakukei Kenkyuka" - }, - { - "author_name": "Takuto Tojo", - "author_inst": "Kao Corporation" - }, - { - "author_name": "Atsushi Nagami", - "author_inst": "Kao Corporation" - }, - { - "author_name": "Yuki Ishida", - "author_inst": "Kao Corporation" - }, - { - "author_name": "Hidekazu Masaki", - "author_inst": "Epsilon Molecular Engineering, Inc" - }, - { - "author_name": "Masayuki Tsuchiya", - "author_inst": "Epsilon Molecular Engineering, Inc" - }, - { - "author_name": "Toshiki Ebisudani", - "author_inst": "Keio University - Shinanomachi Campus: Keio Gijuku Daigaku - Shinanomachi Campus" - }, - { - "author_name": "Shinya Sugimoto", - "author_inst": "Keio University - Shinanomachi Campus: Keio Gijuku Daigaku - Shinanomachi Campus" - }, - { - "author_name": "Toshiro Sato", - "author_inst": "Keio University - Shinanomachi Campus: Keio Gijuku Daigaku - Shinanomachi Campus" - }, - { - "author_name": "Hiroyuki Yasuda", - "author_inst": "Keio University - Shinanomachi Campus: Keio Gijuku Daigaku - Shinanomachi Campus" - }, - { - "author_name": "Koichi Fukunaga", - "author_inst": "Keio University - Shinanomachi Campus: Keio Gijuku Daigaku - Shinanomachi Campus" - }, - { - "author_name": "Akihito Sawada", - "author_inst": "Kitasato University: Kitasato Daigaku" - }, - { - "author_name": "Naoto Nemoto", - "author_inst": "Epsilon Molecular Engineering, Inc" - }, - { - "author_name": "Chihong Song", - "author_inst": "National institutes of Natural Sciences" - }, - { - "author_name": "Kazuyoshi Murata", - "author_inst": "National Institutes of Natural Sciences" - }, - { - "author_name": "Takuya Morimoto", - "author_inst": "Kao Corpolation" - }, - { - "author_name": "Kazuhiko Katayama", - "author_inst": "Kitasato University: Kitasato Daigaku" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.08.439006", "rel_title": "Intranasal HD-Ad Vaccine Protects the Upper and Lower Respiratory Tracts of hACE2 Mice against SARS-CoV-2", @@ -825984,6 +826567,205 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.06.438709", + "rel_title": "Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape", + "rel_date": "2021-04-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.06.438709", + "rel_abs": "An ideal anti-SARS-CoV-2 antibody would resist viral escape1-3, have activity against diverse SARS-related coronaviruses4-7, and be highly protective through viral neutralization8-11 and effector functions12,13. Understanding how these properties relate to each other and vary across epitopes would aid development of antibody therapeutics and guide vaccine design. Here, we comprehensively characterize escape, breadth, and potency across a panel of SARS-CoV-2 antibodies targeting the receptor-binding domain (RBD), including S3094, the parental antibody of the late-stage clinical antibody VIR-7831. We observe a tradeoff between SARS-CoV-2 in vitro neutralization potency and breadth of binding across SARS-related coronaviruses. Nevertheless, we identify several neutralizing antibodies with exceptional breadth and resistance to escape, including a new antibody (S2H97) that binds with high affinity to all SARS-related coronavirus clades via a unique RBD epitope centered on residue E516. S2H97 and other escape-resistant antibodies have high binding affinity and target functionally constrained RBD residues. We find that antibodies targeting the ACE2 receptor binding motif (RBM) typically have poor breadth and are readily escaped by mutations despite high neutralization potency, but we identify one potent RBM antibody (S2E12) with breadth across sarbecoviruses closely related to SARS-CoV-2 and with a high barrier to viral escape. These data highlight functional diversity among antibodies targeting the RBD and identify epitopes and features to prioritize for antibody and vaccine development against the current and potential future pandemics.", + "rel_num_authors": 46, + "rel_authors": [ + { + "author_name": "Tyler N Starr", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA" + }, + { + "author_name": "Nadine Czudnochowski", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Fabrizia Zatta", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Young-Jun Park", + "author_inst": "Department of Biochemistry, University of Washington, Seattle, WA 98195, USA" + }, + { + "author_name": "Zhuoming Liu", + "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA" + }, + { + "author_name": "Amin Addetia", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA" + }, + { + "author_name": "Dora Pinto", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Martina Beltramello", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Patrick Hernandez", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Allison J Greaney", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98" + }, + { + "author_name": "Roberta Marzi", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "William G Glass", + "author_inst": "Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA" + }, + { + "author_name": "Ivy Zhang", + "author_inst": "Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional PhD Pro" + }, + { + "author_name": "Adam S Dingens", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA" + }, + { + "author_name": "John E Bowen", + "author_inst": "Department of Biochemistry, University of Washington, Seattle, WA 98195, USA" + }, + { + "author_name": "Jason A Wojcechowskyj", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Anna De Marco", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Laura E Rosen", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Jiayi Zhou", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Martin Montiel-Ruiz", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Hannah Kaiser", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Heather Tucker", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Michael P. Housley", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Julia Di Iulio", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Gloria Lombardo", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Maria Agostini", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Nicole Sprugasci", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Katja Culap", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Stefano Jaconi", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Marcel Meury", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Exequiel Dellota", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Elisabetta Cameroni", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Tristan I Croll", + "author_inst": "Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, CB2 0XY, UK" + }, + { + "author_name": "Jay C Nix", + "author_inst": "Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA" + }, + { + "author_name": "Colin Havenar-Daughton", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Amalio Telenti", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Florian A Lempp", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Matteo Samuele Pizzuto", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "John D Chodera", + "author_inst": "Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA" + }, + { + "author_name": "Christy M Hebner", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + }, + { + "author_name": "Sean PJ Whelan", + "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA" + }, + { + "author_name": "Herbert W Virgin", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA; Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO 63110, USA; D" + }, + { + "author_name": "David Veesler", + "author_inst": "Department of Biochemistry, University of Washington, Seattle, WA 98195, USA" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs BioMed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98" + }, + { + "author_name": "Gyorgy Snell", + "author_inst": "Vir Biotechnology, San Francisco, CA 94158, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.07.438806", "rel_title": "Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of nsp5 Main Protease", @@ -828235,37 +829017,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.04.03.21254871", - "rel_title": "Evolving SARS-CoV-2 variants and mutational cascades", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.03.21254871", - "rel_abs": "The emergence of novel SARS-CoV-2 variants of concern (VOC), in late 2020, with selective transmission advantage and partial immunity escape potential, threatens a pandemic resurgence. The timing of mutational evolution and its limits are thus of paramount importance in preparedness planning. Here, we present a model predicting the pattern of epidemic growth including the emergence of variants through mutation. It is based on the SEIR (Susceptible, Exposed, Infected, Removed) model, but its equations are modifiable according to the transmission parameters of novel variants. Since more transmissible strains will drive a further increase in the number of cases, they will also lead to further novel mutations. As one cannot predict whether there is a viral mutational evolutionary limit, we model a cascade that could lead to hyper-exponential growth involving the emergence of even more transmissible mutants that could overwhelm systemic response. Our results are consistent with the timing, since the beginning of the pandemic, of the concurrent and independent emergence of the VOCs. We examine conditions that favor the expected appearance of similar variants, thus enabling better preparedness and relevant research.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "John M Halley", - "author_inst": "University of Ioannina" - }, - { - "author_name": "Despoina Vokou", - "author_inst": "Aristotle University of Thessaloniki" - }, - { - "author_name": "Georgios Pappas", - "author_inst": "Institute of Continuing Medical Education of Ioannina" - }, - { - "author_name": "Ioannis Sainis", - "author_inst": "University of Ioannina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.03.21254727", "rel_title": "Study of the effectiveness of partial quarantines applied to control the spread of the Covid-19 virus", @@ -828358,6 +829109,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.01.21254798", + "rel_title": "Female-male differences in COVID vaccine adverse events have precedence in seasonal flu shots: a potential link to sex-associated baseline gene expression patterns", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.01.21254798", + "rel_abs": "Nearly 150 million doses of FDA-authorized COVID vaccines have been administered in the United States. Sex-based differences of adverse events remain poorly understood, mandating the need for real-world investigation from Electronic Health Records (EHRs) and broader epidemiological data sets. Based on an augmented curation of EHR clinical notes of 31,064 COVID-vaccinated individuals (19,321 females and 11,743 males) in the Mayo Clinic, we find that nausea and vomiting were documented significantly more frequently in females than males after both vaccine doses (nausea: RRDose 1 = 1.67, pDose 1 <0.001, RRDose 2 = 2.2, pDose 1 < 0.001; vomiting: RRDose 1 = 1.58, pDose 1 < 0.001, RRDose 2 = 1.88, pDose 1 = 3.4x10-2). Conversely, fever, fatigue, and lymphadenopathy were more common in males after the first dose vaccination (fever RR = 0.62; p = 8.65x10-3; fatigue RR = 0.86, p = 2.89x10-2; lymphadenopathy RR = 0.61, p = 3.45x10-3). Analysis of the Vaccine Adverse Events Reporting System (VAERS) database further confirms that nausea comprises a larger fraction of total reports among females than males (RR: 1.58; p<0.001), while fever comprises a larger fraction of total reports among males than females (RR: 0.84; p<0.001). Importantly, increased reporting of nausea and fever among females and males, respectively, is also observed for prior influenza vaccines in the VAERS database, establishing that these differences are not unique to the recently developed COVID-19 vaccines. Investigating the mechanistic basis underlying these clinical findings, an analysis of bulk RNA-sequencing data from 12,158 human blood samples (8626 female, 3532 male) reveals 85 genes that are not only significantly different in their gene expression between females and males at baseline, but also have established literature-based associations to COVID-19 as well as the vaccine-related adverse events of clinical consequence. The NLRP3 inflammasome and the NR3C1 glucocorticoid receptor emerge as particularly promising baseline links to sex-associated vaccine adverse events, warranting targeted investigation of these signaling pathways and associated cell types. From a public health standpoint, our clinical findings shall aid in educating patients on the sex-associated risks they should expect for COVID-19 vaccines and also promote better clinical management of vaccine-associated adverse events.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "AJ Venkatakrishnan", + "author_inst": "nference" + }, + { + "author_name": "Praveen Kumar-M", + "author_inst": "nference" + }, + { + "author_name": "Eli Silvert", + "author_inst": "nference" + }, + { + "author_name": "Enrique Garcia-Rivera", + "author_inst": "nference" + }, + { + "author_name": "Mariola Szenk", + "author_inst": "nference" + }, + { + "author_name": "Rohit Suratekar", + "author_inst": "nference Labs" + }, + { + "author_name": "Patrick Lenehan", + "author_inst": "nference" + }, + { + "author_name": "Emily Lindemer", + "author_inst": "nference" + }, + { + "author_name": "John C OHoro", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Amy W Williams", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew D Badley", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Abinash Virk", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Melanie D Swift", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Gregory J Gores", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Venky Soundararajan", + "author_inst": "nference" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.05.21254897", "rel_title": "No Evidence of Infectious SARS-CoV-2 in Human Milk: Analysis of a Cohort of 110 Lactating Women", @@ -829813,49 +830639,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.04.21254906", - "rel_title": "Impact of a nighttime curfew on overnight mobility", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.04.21254906", - "rel_abs": "BackgroundAmong non-pharmaceutical interventions, individual movement restrictions have been among the most impactful methods for controlling COVID-19 case growth. While nighttime curfews to control COVID-19 case growth have been implemented in certain regions and cities, few studies have examined their impacts on mobility or COVID-19 incidence. In the second wave of COVID-19, Canadas two largest and adjacent provinces implemented lockdown restrictions with (Quebec) and without (Ontario) a nighttime curfew, providing a natural experiment to study the association between curfews and mobility.\n\nMethodsThis study spanned from December 1, 2020 to January 23, 2021 and included the populations of Ontario (including Toronto) and Quebec (including Montreal). The intervention of interest was a nighttime curfew implemented across Quebec on January 9, 2021. Unadjusted and adjusted difference-in-differences models (DID) were used to measure the incremental impact of the curfew on nighttime mobility in Quebec as compared to Ontario.\n\nResultsThe implementation of the curfew was associated with an immediate reduction in nighttime mobility. The adjusted DID analysis indicated that Quebec experienced a 31% relative reduction in nighttime mobility (95%CI: -36% to -25%) compared to Ontario, and that Montreal experienced a 39% relative reduction compared to Toronto (95%CI: -43, -34).\n\nDiscussionHowever, this natural experiment among two neighbouring provinces provides useful evidence that curfews lead to an immediate and substantial decrease nighttime mobility, particularly in these provinces largest urban areas hardest hit by COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Amir Ghasemi", - "author_inst": "Communications Research Centre Canada" - }, - { - "author_name": "Nick Daneman", - "author_inst": "Sunnybrook Hospital" - }, - { - "author_name": "Isha Berry", - "author_inst": "Dalla Lana School of Public Health, University of Toronto" - }, - { - "author_name": "Sarah A Buchan", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Jean-Paul Soucy", - "author_inst": "Dalla Lana School of Public Health, University of Toronto" - }, - { - "author_name": "Shelby Sturrock", - "author_inst": "Dalla Lana School of Public Health, University of Toronto" - }, - { - "author_name": "Kevin Antoine Brown", - "author_inst": "Public Health Ontario" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.01.21254744", "rel_title": "Industry and workplace characteristics associated with the use of a COVID-19 contact tracing app in Japan: a nation-wide employee survey", @@ -830136,6 +830919,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.02.21254809", + "rel_title": "Risk factors for severity on admission and the disease progression during hospitalization in a large cohort of COVID-19 patients in Japan", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.02.21254809", + "rel_abs": "ObjectivesTo investigate the risk factors contributing to severity on admission. Additionally, risk factors on worst severity and fatality were studied. Moreover, factors were compared based on three points: early severity, worst severity, and fatality.\n\nDesignA observational cohort study utilizing data entered in a Japan nationwide COVID-19 inpatient registry, COVIREGI-JP.\n\nSettingAs of August 31, 2020, 7,546 cases from 780 facilities have been registered. Participating facilities cover a wide range of hospitals where COVID-19 patients are admitted in Japan.\n\nParticipantsParticipants who had a positive test result on any applicable SARS-CoV-2 diagnostic tests, and were admitted to participating healthcare facilities. A total of 3,829 cases were identified from January 16 to May 31, 2020, of which 3,376 cases were included in this study.\n\nPrimary and secondary outcoe measuresPrimary outcome was severe or non-severe on admission, determined by the requirement of mechanical ventilation or oxygen therapy, SpO2, or respiratory rate. Secondary outcome was the worst severity during hospitalization, judged by the requirement of oxygen and/or IMV/ECMO.\n\nResultsRisk factors for severity on admission were older age, male, cardiovascular disease, chronic respiratory disease, diabetes, obesity, and hypertension. Cerebrovascular disease, liver disease, renal disease or dialysis, solid tumor, and hyperlipidemia did not influence severity on admission; however it influenced worst severity. Fatality rates for obesity, hypertension, and hyperlipidemia were relatively lower.\n\nConclusionsThis study segregated the comorbidities driving severity and death. It is possible that risk factors for severity on admission, worst severity, and fatality are not consistent and may be propelled by different factors. Specifically, while hypertension, hyperlipidemia, and obesity had major effect on worst severity, their impact was mild on fatality in the Japanese population. Some studies contradict our results; therefore, detailed analyses, considering in-hospital treatments, are needed for validation.\n\nTrial registrationUMIN000039873. https://upload.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000045453\n\nStrengths and limitations of this studyO_LIIn this article, we studied the disease progression of COVID-19, by comparing the risk factors on three points: early severity, worst severity, and fatality.\nC_LIO_LIOur results are useful from a public health perspective, as we provide risk factors for predicting the severity on admission and disease progression from patients background factors.\nC_LIO_LIThis study pointed out the possibility that risk factors of the severity on admission, worst severity, and fatality are not consistent and may be propelled by different factors.\nC_LIO_LIOur data were collected from hundreds of healthcare facilities; thus data accuracy may be questionable.\nC_LIO_LIAlso, treatment type, dosage, duration, and combination varied immensely across the facilities and we did not consider treatments prior to and during hospitalization in the analysis.\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Mari Terada", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Hiroshi Ohtsu", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Sho Saito", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Kayoko Hayakawa", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Shinya Tsuzuki", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Yusuke Asai", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Nobuaki Matsunaga", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Satoshi Kutsuna", + "author_inst": "National Centre for Global Health and Medicine" + }, + { + "author_name": "Wataru Sugiura", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "National Center for Global Health and Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.01.21254755", "rel_title": "Rapid screening for variants of concern in routine SARS-CoV-2 PCR diagnostics", @@ -831551,69 +832389,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.04.06.438579", - "rel_title": "Interactions of SARS-CoV-2 envelope protein with amilorides correlate with antiviral activity", - "rel_date": "2021-04-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.06.438579", - "rel_abs": "SARS-CoV-2 is the novel coronavirus that is the causative agent of COVID-19, a sometimes-lethal respiratory infection responsible for a world-wide pandemic. The envelope (E) protein, one of four structural proteins encoded in the viral genome, is a 75-residue integral membrane protein whose transmembrane domain exhibits ion channel activity and whose cytoplasmic domain participates in protein-protein interactions. These activities contribute to several aspects of the viral replication-cycle, including virion assembly, budding, release, and pathogenesis. Here, we describe the structure and dynamics of full-length SARS-CoV-2 E protein in hexadecylphosphocholine micelles by NMR spectroscopy. We also characterized its interactions with four putative ion channel inhibitors. The chemical shift index and dipolar wave plots establish that E protein consists of a long transmembrane helix (residues 8-43) and a short cytoplasmic helix (residues 53-60) connected by a complex linker that exhibits some internal mobility. The conformations of the N-terminal transmembrane domain and the C-terminal cytoplasmic domain are unaffected by truncation from the intact protein. The chemical shift perturbations of E protein spectra induced by the addition of the inhibitors demonstrate that the N-terminal region (residues 6-18) is the principal binding site. The binding affinity of the inhibitors to E protein in micelles correlates with their antiviral potency in Vero E6 cells: HMA {approx} EIPA > DMA >> Amiloride, suggesting that bulky hydrophobic groups in the 5 position of the amiloride pyrazine ring play essential roles in binding to E protein and in antiviral activity. An N15A mutation increased the production of virus-like particles, induced significant chemical shift changes from residues in the inhibitor binding site, and abolished HMA binding, suggesting that Asn15 plays a key role in maintaining the protein conformation near the binding site. These studies provide the foundation for complete structure determination of E protein and for structure-based drug discovery targeting this protein.\n\nAuthor SummaryThe novel coronavirus SARS-CoV-2, the causative agent of the world-wide pandemic of COVID-19, has become one of the greatest threats to human health. While rapid progress has been made in the development of vaccines, drug discovery has lagged, partly due to the lack of atomic-resolution structures of the free and drug-bound forms of the viral proteins. The SARS-CoV-2 envelope (E) protein, with its multiple activities that contribute to viral replication, is widely regarded as a potential target for COVID-19 treatment. As structural information is essential for drug discovery, we established an efficient sample preparation system for biochemical and structural studies of intact full-length SARS-CoV-2 E protein and characterized its structure and dynamics. We also characterized the interactions of amilorides with specific E protein residues and correlated this with their antiviral activity during viral replication. The binding affinity of the amilorides to E protein correlated with their antiviral potency, suggesting that E protein is indeed the likely target of their antiviral activity. We found that residue asparagine15 plays an important role in maintaining the conformation of the amiloride binding site, providing molecular guidance for the design of inhibitors targeting E protein.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sang Ho Park", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Haley Siddiqi", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Daniela Castro", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Anna De Angelis", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Aaron L. Oom", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Charlotte Stoneham", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Mary Lewinski", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Alex Clark", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Ben Croker", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Aaron Carlin", - "author_inst": "University of California San Diego" - }, - { - "author_name": "John Guatelli", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Stanley J. Opella", - "author_inst": "University of California San Diego" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.04.06.438584", "rel_title": "Mutations in the B.1.1.7 SARS-CoV-2 spike protein reduce receptor-binding affinity and induce a flexible link to the fusion peptide", @@ -831906,6 +832681,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.05.438465", + "rel_title": "The Up state of the SARS-COV-2 Spike homotrimer favors an increased virulence for new variants", + "rel_date": "2021-04-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.05.438465", + "rel_abs": "The COVID-19 pandemic has spread widely worldwide. However, as soon as the vaccines were released - the only scientifically verified and efficient therapeutic option thus far - a few mutations combined into variants of SARS-CoV-2 that are more transmissible and virulent emerged raising doubts about their efficiency. Therefore, this work aims to explain possible molecular mechanisms responsible for the increased transmissibility and the increased rate of hospitalizations related to the new variants. A combination of theoretical methods was employed. Constant-pH Monte Carlo simulations were carried out to quantify the stability of several spike trimeric structures at different conformational states and the free energy of interactions between the receptor binding domain (RBD) and Angiotensin Converting Enzyme 2 (ACE2) for the most worrying variants. Electrostatic epitopes were mapped using the PROCEEDpKa method. These analyses showed that the increased virulence is more likely to be due to the improved stability to the S trimer in the opened state (the one in which the virus can interact with the cellular receptor ACE2) than due to alterations in the complexation RBD-ACE2, once the increased observed in the free energy values is small. Conversely, the South African variant (B.1.351), when compared with the wild type SARS-CoV-2, is much more stable in the opened state (either with one or two RBDs in the up position) than in the closed state (with the three RBDs in the down position). Such results contribute to the understanding of the natural history of disease and also to indicate possible strategies to both develop new therapeutic molecules and to adjust the vaccine doses for a higher production of B cells antibodies.\n\nGraphical Abstract O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Carolina Correa Giron", + "author_inst": "Universidade Federal do Triangulo Mineiro" + }, + { + "author_name": "Aatto Laaksonen", + "author_inst": "Stockholm University" + }, + { + "author_name": "Fernando Luis Barroso da Silva", + "author_inst": "University of Sao Paulo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.04.05.438500", "rel_title": "An Autoantigen-ome from HS-Sultan B-Lymphoblasts Offers a Molecular Map for Investigating Autoimmune Sequelae of COVID-19", @@ -833513,97 +834315,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.31.21254683", - "rel_title": "Immunogenicity of COVID-19 Tozinameran Vaccination in Patients on Chronic Dialysis", - "rel_date": "2021-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254683", - "rel_abs": "ObjectivePatients with kidney failure have notoriously weak responses to common vaccines. Thus, immunogenicity of novel SARS-CoV-2 vaccines might be impaired in this group. To determine immunogenicity of SARS-CoV-2 vaccination in patients with chronic dialysis, we analyzed the humoral and T-cell response after two doses of mRNA vaccine Tozinameran (BNT162b2 BioNTech/Pfizer).\n\nDesign, Settings, and ParticipantsThis observational study included 43 patients on dialysis before vaccination with two doses of Tozinameran 21 days apart. Overall, 36 patients completed the observation period. Serum samples were analyzed by SARS-CoV-2 specific antibodies [~]1 and [~]3-4 weeks after the second vaccination. In addition, SARS-CoV-2-specific T-cell responses were assessed at the later time point by an interferon-gamma release assay (IGRA). Outcomes at later timepoints were compared to a group of 44 elderly patients with no dialysis after immunization with Tozinameran.\n\nExposuresBlood drawings during regular laboratory routine assessment right before start of dialysis therapy or at the time of vaccination and at follow-up study visits.\n\nMain Outcomes and MeasuresAssessment of immunogenicity after vaccination against SARS-CoV-2 in patients on and without dialysis.\n\nResultsMedian age of patients on chronic dialysis was 74.0 years (IQR 66.0, 82.0). The proportion of males was higher (69.4%) than females. Only 20/36 patients (55.6%, 95%CI: 38.29-71.67) developed SARS-CoV-2-IgG antibodies at first sampling, whereas 32/36 patients (88.9%, 95%CI:73.00-96.38) demonstrated seropositivity at the second sampling. Seroconversion rates and antibody titers were significantly lower compared to a cohort of vaccinees with similar age but no chronic dialysis (>90% seropositivity). SARS-CoV-2-specific T-cell responses 3 weeks after second vaccination were detected in 21/31 vaccinated dialysis patients (67.7%, 95%CI: 48.53-82.68) compared to 42/44 (93.3%, 95%CI: 76.49-98.84) in controls of similar age.\n\nConclusion and RelevancePatients on dialysis demonstrate a delayed, but robust immune response three weeks after the second dose, which indicates effective vaccination of this vulnerable group. However, the lower immunogenicity of Tozinameran in these patients needs further attention to develop potential countermeasures such as an additional booster vaccination.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Eva Vanessa Schrezenmeier", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Leon Bergfeld", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "David Hillus", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Joerg-Detlev Lippert", - "author_inst": "Nierenzentrum Koethen" - }, - { - "author_name": "Ulrike Weber", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Pinkus Tober-Lau", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Irmgard Landgraf", - "author_inst": "Hausarztpraxis am Agaplesion Bethanien Sophienhaus" - }, - { - "author_name": "Tatjana Schwarz", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Kai Kappert", - "author_inst": "Labor Berlin - Charite Vivantes GmbH" - }, - { - "author_name": "Ana-Luisa Stefanski", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Arne Sattler", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Katja Kotsch", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Thomas Doerner", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Leif Erik Sander", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Klemens Budde", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Fabian Halleck", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Florian Kurth", - "author_inst": "Charite-Universitaetsmedizin Berlin" - }, - { - "author_name": "Victor M Corman", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Mira Choi", - "author_inst": "Charite-Universitaetsmedizin Berlin" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.31.21254689", "rel_title": "Covid-19 and excess mortality rates not comparable across countries", @@ -833784,6 +834495,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.06.438634", + "rel_title": "Plasma microbiome in COVID-19 subjects: an indicator of gut barrier defects and dysbiosis", + "rel_date": "2021-04-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.06.438634", + "rel_abs": "The gut is a well-established route of infection and target for viral damage by SARS-CoV-2. This is supported by the clinical observation that about half of COVID-19 patients exhibit gastrointestinal (GI) symptoms. We asked whether the analysis of plasma could provide insight into gut barrier dysfunction in patients with COVID-19 infection. Plasma samples of COVID-19 patients (n=30) and healthy control (n=16) were collected during hospitalization. Plasma microbiome was analyzed using 16S rRNA sequencing, metatranscriptomic analysis, and gut permeability markers including FABP-2, PGN and LPS in both patient cohorts. Almost 65% (9 out 14) COVID-19 patients showed abnormal presence of gut microbes in their bloodstream. Plasma samples contained predominately Proteobacteria, Firmicutes, and Actinobacteria. The abundance of gram-negative bacteria (Acinetobacter, Nitrospirillum, Cupriavidus, Pseudomonas, Aquabacterium, Burkholderia, Caballeronia, Parabhurkholderia, Bravibacterium, and Sphingomonas) was higher than the gram-positive bacteria (Staphylococcus and Lactobacillus) in COVID-19 subjects. The levels of plasma gut permeability markers FABP2 (1282{+/-}199.6 vs 838.1{+/-}91.33; p=0.0757), PGN (34.64{+/-}3.178 vs 17.53{+/-}2.12; p<0.0001), and LPS (405.5{+/-}48.37 vs 249.6{+/-}17.06; p=0.0049) were higher in COVID-19 patients compared to healthy subjects. These findings support that the intestine may represent a source for bacteremia and may contribute to worsening COVID-19 outcomes. Therapies targeting the gut and prevention of gut barrier defects may represent a strategy to improve outcomes in COVID-19 patients.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Ram Prasad", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Michael John Patton", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Jason L Floyd", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Cristiano P Vieira", + "author_inst": "Univeristy of Alabama at Birmingham" + }, + { + "author_name": "Seth D. Fortmann", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Mariana DuPont", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Angie Harbour", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Jeremy R Chen See", + "author_inst": "WrightLabs LLC" + }, + { + "author_name": "Justin Wright", + "author_inst": "Wright Labs LLC" + }, + { + "author_name": "Regina Lamendella", + "author_inst": "Juniata College" + }, + { + "author_name": "Bruce R. Stevens", + "author_inst": "University of Florida College of Medicine" + }, + { + "author_name": "Maria B. Grant", + "author_inst": "University of Alabama- Birmingham" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.05.438537", "rel_title": "High-Potency Polypeptide-based Interference for Coronavirus Spike Glycoproteins", @@ -835387,33 +836161,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.04.438417", - "rel_title": "Substitutions and codon usage in SARS-CoV-2 in mammals indicate natural selection and host adaptation", - "rel_date": "2021-04-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.04.438417", - "rel_abs": "The outbreak of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, rapidly spread to create a global pandemic and has continued to spread across hosts from humans to animals, transmitting particularly effectively in mink. How SARS-CoV-2 evolves in animals and humans and the differences in the separate evolutionary processes remain unclear. We analyzed the composition and codon usage bias of SARS-CoV-2 in infected humans and animals. Compared with other animals, SARS-CoV-2 in mink had the most substitutions. The substitutions of cytidine in SARS-CoV-2 in mink account for nearly 50% of the substitutions, while those in other animals represent only 30% of the substitutions. The incidence of adenine transversion in SARS-CoV-2 in other animals is threefold higher than that in mink-CoV (the SARS-CoV-2 virus in mink). A synonymous codon usage analysis showed that SARS-CoV-2 is optimized to adapt in the animals in which it is currently reported, and all the animals showed decreased adaptability relative to that of humans, except for mink. A binding affinity analysis indicated that the spike protein of the SARS-CoV-2 variant in mink showed a greater preference for binding with the mink receptor ACE2 than with the human receptor, especially as the mutation Y453F and F486L in mink-CoV lead to improvement of binding affinity for mink receptor. Our study focuses on the divergence of SARS-CoV-2 genome composition and codon usage in humans and animals, indicating possible natural selection and current host adaptation.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Zhixiong Lei Sr.", - "author_inst": "Hubei University of Medicine" - }, - { - "author_name": "Dan Zhang Sr.", - "author_inst": "Hubei University of Medicine" - }, - { - "author_name": "Long Liu", - "author_inst": "Hubei University of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2021.04.04.438404", "rel_title": "COVID-19 mRNA vaccines drive differential Fc-functional profiles in pregnant, lactating, and non-pregnant women", @@ -835770,6 +836517,121 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.02.438288", + "rel_title": "An emerging SARS-CoV-2 mutant evading cellular immunity and increasing viral infectivity", + "rel_date": "2021-04-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.02.438288", + "rel_abs": "During the current SARS-CoV-2 pandemic that is devastating the modern societies worldwide, many variants that naturally acquire multiple mutations have emerged. Emerging mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has recently been investigated, that to human leukocyte antigen (HLA)-restricted cellular immunity remains unaddressed. Here we demonstrate that two recently emerging mutants in the receptor binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429) and Y453F (in B.1.298), can escape from the HLA-24-restricted cellular immunity. These mutations reinforce the affinity to viral receptor ACE2, and notably, the L452R mutation increases protein stability, viral infectivity, and potentially promotes viral replication. Our data suggest that the HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes, and the escape from cellular immunity can be a further threat of the SARS-CoV-2 pandemic.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=198 SRC=\"FIGDIR/small/438288v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@153428forg.highwire.dtl.DTLVardef@136ca5aorg.highwire.dtl.DTLVardef@1ee490org.highwire.dtl.DTLVardef@2fe478_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Chihiro Motozono", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Mako Toyoda", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Jiri Zahradnik", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Terumasa Ikeda", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Akatsuki Saito", + "author_inst": "University of Miyazaki" + }, + { + "author_name": "Toong Seng Tan", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Isaac Ngare", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Hesham Nasser", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Izumi Kimura", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Keiya Uriu", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Yusuke Kosugi", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Shiho Torii", + "author_inst": "Osaka University" + }, + { + "author_name": "Akiko Yonekawa", + "author_inst": "Kyushu University" + }, + { + "author_name": "Nobuyuki Shimono", + "author_inst": "Kyushu University" + }, + { + "author_name": "Yoji Nagasaki", + "author_inst": "Kyushu Medical Center" + }, + { + "author_name": "Rumi Minami", + "author_inst": "Kyushu Medical Center" + }, + { + "author_name": "Takashi Toya", + "author_inst": "Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital" + }, + { + "author_name": "Noritaka Sekiya", + "author_inst": "Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital" + }, + { + "author_name": "Takasuke Fukuhara", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Yoshiharu Matsuura", + "author_inst": "Osaka University" + }, + { + "author_name": "Gideon Schreiber", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) consortium", + "author_inst": "-" + }, + { + "author_name": "So Nakagawa", + "author_inst": "Tokai University School of Medicine" + }, + { + "author_name": "Takamasa Ueno", + "author_inst": "Kumamoto University" + }, + { + "author_name": "Kei Sato", + "author_inst": "Institute of Medical Science, The University of Tokyo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.04.438420", "rel_title": "Rational Selection of PCR Primer/Probe Design Sites for SARS-CoV-2", @@ -837317,69 +838179,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.03.31.21254660", - "rel_title": "Qualitatively distinct modes of Sputnik V vaccine-neutralization escape by SARS-CoV-2 Spike variants", - "rel_date": "2021-04-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254660", - "rel_abs": "The novel pandemic betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected at least 120 million people since its identification as the cause of a December 2019 viral pneumonia outbreak in Wuhan, China. Despite the unprecedented pace of vaccine development, with six vaccines already in use worldwide, the emergence of SARS-CoV-2 variants of concern (VOC) across diverse geographic locales suggests herd immunity may fail to eliminate the virus. All three officially designated VOC carry Spike (S) polymorphisms thought to enable escape from neutralizing antibodies elicited during initial waves of the pandemic. Here, we characterize the biological consequences of the ensemble of S mutations present in VOC lineages B.1.1.7 (501Y.V1) and B.1.351 (501Y.V2). Using a replication-competent EGFP-reporter vesicular stomatitis virus (VSV) system, rcVSV-CoV2-S, which encodes S from SARS coronavirus 2 in place of VSV-G, and coupled with a clonal HEK-293T ACE2 TMPRSS2 cell line optimized for highly efficient S-mediated infection, we determined that 8 out of 12 (75%) of serum samples from 12 recipients of the Russian Sputnik V Ad26 / Ad5 vaccine showed dose response curve slopes indicative of failure to neutralize rcVSV-CoV2-S: B.1.351. The same set of sera efficiently neutralized S from B.1.1.7 and showed only moderately reduced activity against S carrying the E484K substitution alone. Taken together, our data suggest that control of emergent SARS-CoV-2 variants may benefit from updated vaccines.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Satoshi Ikegame", - "author_inst": "Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA" - }, - { - "author_name": "Mohammed N. A. Siddiquey", - "author_inst": "Department of Microbiology and Immunology, Louisiana State University Health Shreveport, Shreveport, LA 71103, USA" - }, - { - "author_name": "Chuan-Tien Hung", - "author_inst": "Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA" - }, - { - "author_name": "Griffin Haas", - "author_inst": "Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA" - }, - { - "author_name": "Luca Brambilla", - "author_inst": "Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA" - }, - { - "author_name": "Kasopefoluwa Y. Oguntuyo", - "author_inst": "Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA" - }, - { - "author_name": "Shreyas Kowdle", - "author_inst": "Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA" - }, - { - "author_name": "Ariel Esteban Vilardo", - "author_inst": "National Administration of Laboratories and Health Institutes of Argentina (ANLIS) Dr. Carlos G. Malbran, Buenos Aires, Argentina" - }, - { - "author_name": "Alexis Edelstein", - "author_inst": "National Administration of Laboratories and Health Institutes of Argentina (ANLIS) Dr. Carlos G. Malbran, Buenos Aires, Argentina" - }, - { - "author_name": "Claudia Perandones", - "author_inst": "National Administration of Laboratories and Health Institutes of Argentina (ANLIS) Dr. Carlos G. Malbran, Buenos Aires, Argentina" - }, - { - "author_name": "Jeremy P. Kamil", - "author_inst": "Department of Microbiology and Immunology, Louisiana State University Health Shreveport, Shreveport, LA 71103, USA" - }, - { - "author_name": "Benhur Lee", - "author_inst": "Department of Microbiology at the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.02.438182", "rel_title": "A realistic touch-transfer method reveals low risk of transmission for SARS-CoV-2 by contaminated coins and bank notes", @@ -837616,6 +838415,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.02.438155", + "rel_title": "An immunoinformatics approach to study the epitopes contributed by Nsp13 of SARS-CoV-2", + "rel_date": "2021-04-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.02.438155", + "rel_abs": "The on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2 has infected hundreds of millions of people and killed more than two million people worldwide. Currently, there are no effective drugs available for treating SARS-CoV-2 infections; however, vaccines are now being administered worldwide to control this virus. In this study, we have studied SARS-CoV-2 helicase, Nsp13, which is critical for viral replication. We compared the Nsp13 sequences reported from India with the first reported sequence from Wuhan province, China to identify and characterize the mutations occurring in this protein. To correlate the functional impact of these mutations, we characterised the most prominent B cell and T cell epitopes contributed by Nsp13. Our data revealed twenty-one epitopes, which exhibited high antigenicity, stability and interactions with MHC class-I and class-II molecules. Subsequently, the physiochemical properties of these epitopes were also analysed. Furthermore, several of these Nsp13 epitopes harbour mutations, which were further characterised by secondary structure and per-residue disorderness, stability and dynamicity predictions. Altogether, we report the candidate epitopes of Nsp13 that may help the scientific community to understand the evolution of SARS-CoV-2 variants and their probable implications.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sushant Kumar", + "author_inst": "Patna University" + }, + { + "author_name": "Gajendra Kumar Azad", + "author_inst": "Patna University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.04.02.438204", "rel_title": "Discovery and in-vitro evaluation of potent SARS-CoV-2 entry inhibitors", @@ -839523,37 +840345,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.29.21254517", - "rel_title": "Upregulated miR-200c may increase the risk of obese individuals to severe COVID-19", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254517", - "rel_abs": "Obesity is a risk factor for coronavirus disease 2019 (COVID-19) infection, the prevalence of obese individuals admitted with COVID-19 ranging between 30 and 60%. Herein we determined whether early changes in microRNAs (miRNAs) could be the underlying molecular mechanism increasing the risk of obese individuals to COVID-19 infection. Quantitative real-time PCR analysis of plasma samples for circulating miRNAs showed a significant upregulation of miR-200c and a small increase in miR-let-7b obese individuals. This was associated with significant downregulation of angiotensin-converting enzyme 2 (ACE2). Both the miRNAs are the direct targets of ACE2, the specific functional receptor for severe acute respiratory syndrome coronavirus 2. Correlation analysis confirmed a significant negative correlation between ACE2 and both the miRNAs. Recent studies showed that despite being the functional receptor, inhibition/downregulation of ACE2 did not reduce the severity of COVID-19 infection. In contrast, increased angiotensin II following inhibition of ACE2 may increase the severity of the disease. Taken together, our novel results identify that upregulation of miR-200c may increase the susceptibility of obese individuals to COVID-19. Considering miRNA are the earliest molecular regulators, circulating miR-200c could be a potential biomarker in the early identification of those at the risk of severe COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jayanthi Bellae Papannarao", - "author_inst": "University of Otago" - }, - { - "author_name": "Daryl Schwenke", - "author_inst": "University of Otago" - }, - { - "author_name": "Patrick J Manning", - "author_inst": "University of Otago" - }, - { - "author_name": "Rajesh Katare", - "author_inst": "University of Otago" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2021.03.29.21254599", "rel_title": "Assessing the impact of multiple comorbidities on fatal outcome in young COVID-19", @@ -839770,6 +840561,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.28.21254496", + "rel_title": "SARS-CoV-2 infections in children and adolescents with rheumatic musculoskeletal diseases: data from the National Pediatric Rheumatology Database in Germany", + "rel_date": "2021-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.28.21254496", + "rel_abs": "ObjectivesDue to their underlying disease as well as therapeutic immunosuppression, children and adolescents with rheumatic and musculoskeletal diseases (RMD) may be at higher risk for a severe course or worse outcome of COVID-19, and SARS-CoV2 infection may trigger a flare of the RMD. To address these issues, a specific SARS-CoV-2 questionnaire was implemented in the National Pediatric Rheumatology Database (NPRD) in Germany.\n\nMethodsDemographic, clinical and treatment data from juvenile patients with RMD as well as data about SARS-CoV-2 infection like test date and method, clinical characteristics, disease course, outcome and impact on the disease activity of the RMD documented on this questionnaire were analyzed.\n\nResultsFrom April 17th, 2020, to February 14th, 2021, data were collected from 79 patients (53% female) with RMD with median age of 14 years, diagnosed with juvenile idiopathic arthritis (57%), autoinflammatory (23%) and connective tissue disease (8%). Sixty-one patients (77%) received disease-modifying antirheumatic drugs (DMARDs), 43% biologic DMARDs, and 9% systemic glucocorticoids. Sixty patients (76%) developed symptoms of COVID-19. Disease severity was mild and outcome was good in the majority of patients. Two patients were hospitalized, one of whom required intensive care and died of cardiorespiratory failure. In 84% of SARS-CoV-2-positive patients, no relevant increase in disease activity of the RMD was observed.\n\nConclusionsIn our cohort, COVID-19 in juvenile patients with RMD under various medications was mild with good outcome in the majority of cases. SARS-CoV-2 infection does not appear to have a relevant impact on disease activity of the underlying condition.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Claudia Sengler", + "author_inst": "German Rheumatism Research Center, Epidemiology Unit, Berlin, Germany" + }, + { + "author_name": "Sascha Eulert", + "author_inst": "German Rheumatism Research Center, Epidemiology Unit, Berlin, Germany" + }, + { + "author_name": "Martina Niewerth", + "author_inst": "German Rheumatism Research Center, Epidemiology Unit, Berlin, Germany" + }, + { + "author_name": "Kirsten Minden", + "author_inst": "German Rheumatism Research Center, Epidemiology Unit, Berlin, Germany" + }, + { + "author_name": "Gerd Horneff", + "author_inst": "Asklepios Klinik St. Augustin, Allgemeine Kinder- und Jugendmedizin, Sankt Augustin, Germany" + }, + { + "author_name": "Jasmin B Kuemmerle-Deschner", + "author_inst": "Tuebingen University Hospital, Department of Pediatric and Adolescent Medicine, Tuebingen, Germany" + }, + { + "author_name": "Caroline Siemer", + "author_inst": "Deutsches Zentrum fuer Kinder- und Jugendrheumatologie, Garmisch-Partenkirchen, Germany" + }, + { + "author_name": "Rainer Berendes", + "author_inst": "Kinderkrankenhaus St. Marien, Landshut, Germany" + }, + { + "author_name": "Hermann Girschick", + "author_inst": "Krankenhaus im Friedrichshain, Klinik fuer Kinder- und Jugendmedizin, Berlin, Germany" + }, + { + "author_name": "Regina Huehn", + "author_inst": "Universitaetsklinikum Halle (Saale), Klinik fuer Kinder- und Jugendmedizin, Haale (Saale), Germany" + }, + { + "author_name": "Michael Borte", + "author_inst": "Klinikum St. Georg, Klinik fuer Kinder- und Jugendmedizin, Leipzig, Germany" + }, + { + "author_name": "Anton Hospach", + "author_inst": "Olgahospital and Women`s Clinic, Paediatrie 2 - Allgemeine und spezielle Paediatrie, Stuttgart, Germany" + }, + { + "author_name": "Wolfgang Emminger", + "author_inst": "Universitaetskinderklinik Wien, Wien, Austria" + }, + { + "author_name": "Jakob Peter Armann", + "author_inst": "University Hospital and Medical Faculty Carl Gustav Carus, Technische Uni" + }, + { + "author_name": "Ariane Klein", + "author_inst": "Asklepios Klinik St. Augustin, Allgemeine Kinder- und Jugendmedizin, Sankt Augustin, Germany" + }, + { + "author_name": "Tilmann Kallinich", + "author_inst": "Charite - Universitaetsmedizin Berlin, Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Berlin, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2021.03.29.21254538", "rel_title": "Half year longitudinal seroprevalence of SARS-CoV-2-antibodies and rule compliance in German hospital employees", @@ -840961,53 +841831,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.29.21254588", - "rel_title": "Post-acute sequelae of COVID-19 in a non-hospitalized cohort: results from the Arizona CoVHORT", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254588", - "rel_abs": "Clinical presentation, outcomes, and duration of COVID-19 has ranged dramatically. While some individuals recover quickly, others suffer from persistent symptoms, collectively known as post-acute sequelae of SAR-CoV-2 (PASC). Most PASC research has focused on hospitalized COVID-19 patients with moderate to severe disease. We used data from a diverse population-based cohort of Arizonans to estimate prevalence of various symptoms of PASC, defined as experiencing at least one symptom 30 days or longer. There were 303 non-hospitalized individuals with a positive lab-confirmed COVID-19 test who were followed for a median of 61 days (range 30-250). COVID-19 positive participants were mostly female (70%), non-Hispanic white (68%), and on average 44 years old. Prevalence of PASC at 30 days post-infection was 68.7% (95%CI 63.4, 73.9). The most common symptoms were fatigue (37.5%), shortness-of-breath (37.5%), brain fog (30.8%), and stress (30.8%). The median number of symptoms was 3 (range 1-20). Amongst 157 participants with longer follow-up ([≥]60 days), PASC prevalence was 77.1%.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Melanie L Bell", - "author_inst": "Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson, AZ, USA" - }, - { - "author_name": "Collin J Catalfamo", - "author_inst": "Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson, AZ, USA" - }, - { - "author_name": "Leslie V Farland", - "author_inst": "Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson, AZ, USA" - }, - { - "author_name": "Kacey C Ernst", - "author_inst": "Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson, AZ, USA" - }, - { - "author_name": "Elizabeth T Jacobs", - "author_inst": "Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson, AZ, USA" - }, - { - "author_name": "Yann C Klimentidis", - "author_inst": "Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson, AZ, USA" - }, - { - "author_name": "Megan Jehn", - "author_inst": "School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA" - }, - { - "author_name": "Kristen Pogreba-Brown", - "author_inst": "Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson, AZ, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.30.437757", "rel_title": "Supramolecular cylinders target bulge structures in the 5-prime UTR of the RNA genome of SARS-CoV-2 and inhibit viral replication", @@ -841296,6 +842119,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.29.21254590", + "rel_title": "Use of portable air cleaners to reduce aerosol transmission on a hospital COVID-19 ward", + "rel_date": "2021-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254590", + "rel_abs": "ObjectiveTo study the airflow, transmission and clearance of aerosols in the clinical spaces of a hospital ward that had been used to care for patients with COVID-19, and to examine the impact of portable air cleaners on aerosol clearance.\n\nDesignObservational study\n\nSettingA single ward of a tertiary public hospital in Melbourne Australia\n\nInterventionGlycerine-based aerosol was used as a surrogate for respiratory aerosols. The transmission of aerosols from a single patient room into corridors and a nurses station in the ward was measured. The rate of clearance of aerosols was measured over time from the patient room, nurses station and ward corridors with and without air cleaners (also called portable HEPA filters).\n\nResultsAerosols rapidly travelled from the patient room into other parts of the ward. Air cleaners were effective in increasing the clearance of aerosols from the air in clinical spaces and reducing their spread to other areas. With two small domestic air cleaners in a single patient room of a hospital ward, 99% of aerosols could be cleared within 5.5 minutes.\n\nConclusionAir cleaners may be useful in clinical spaces to help reduce the risk of healthcare acquired acquisition of respiratory viruses that are transmitted via aerosols. They are easy to deploy and are likely to be cost effective in a variety of healthcare settings", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Kirsty Lee Buising", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Robyn Schofield", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Louis Irving", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Melita Keywood", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Ashley Stevens", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Nick Keogh", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Grant Skidmore", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Imogen Wadlow", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Kevin Kevin", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Behzad Rismanchi", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Amanda Wheeler", + "author_inst": "Australian Catholic University" + }, + { + "author_name": "Ruhi Humphries", + "author_inst": "Commonwealth Scientific and Industrial research Organization" + }, + { + "author_name": "Marion Kainer", + "author_inst": "Western Health" + }, + { + "author_name": "Forbes McGain", + "author_inst": "Western Health" + }, + { + "author_name": "Jason Monty", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Caroline Marshall", + "author_inst": "The University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.29.21254509", "rel_title": "Genetic associations with severe COVID-19", @@ -842775,29 +843677,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.26.21254433", - "rel_title": "A randomized controlled trial of a video intervention shows evidence of increasing COVID-19 vaccination intention", - "rel_date": "2021-03-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254433", - "rel_abs": "Increasing acceptance of COVID-19 vaccines is imperative for public health, as unvaccinated individuals may impede the ability to reach herd immunity. Previous research on educational interventions to overcome vaccine hesitancy have shown mixed effects in increasing vaccination intention, although much of this work has focused on parental attitudes toward childhood vaccination. In this study, we conducted a randomized controlled trial to investigate whether vaccination intention changes after viewing an animated YouTube video explaining how COVID-19 mRNA vaccines work. We exposed participants to one of four interventions - watching the video with a male narrator, watching the same video with a female narrator, reading the text of the transcript of the video, or receiving no information (control group). We found that participants who watched the version of the video with a male narrator expressed statistically significant increased vaccination intention compared to the control group. The video with a female narrator had more variation in results. As a whole, there was a non-significant increased vaccination intention when analyzing all participants who saw the video with a female narrator; however, for politically conservative participants there was decreased vaccination intention for this intervention, particularly at a threshold between being currently undecided and expressing probable interest. These results are encouraging for the ability of interventions as simple as YouTube videos to increase vaccination propensity, although the inconsistent response to the video with a female narrator demonstrates the potential for bias to affect how certain groups respond to different messengers.\n\nSignificance StatementWidespread vaccination is important for ending the COVID-19 pandemic. This study investigates whether communicating the science behind new COVID-19 vaccines can increase peoples willingness to get vaccinated. We examined the effectiveness of an eight-minute animated video explaining how COVID-19 mRNA vaccines work, varying between a male narrator, a female narrator, and a control group. Participants who saw the video with a male narrator expressed a greater intent to get vaccinated than the control group. Participants who saw the video with a female narrator had more varied responses, including a decreased intent to get vaccinated among political conservatives. These findings indicate that science education may help increase vaccine uptake, but that beliefs about gender may influence how people receive such information.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Leah S Witus", - "author_inst": "Macalester College" - }, - { - "author_name": "Erik Larson", - "author_inst": "Macalester College" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.25.21252076", "rel_title": "De novo Powered Air-Purifying Respirator Design and Fabrication for Pandemic Response", @@ -843122,6 +844001,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.27.21254480", + "rel_title": "Assessing the impact of widespread respirator use in curtailing COVID-19 transmission in the United States", + "rel_date": "2021-03-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.27.21254480", + "rel_abs": "Dynamic models are used to assess the impact of three types of face masks-cloth masks, surgical/procedure masks and respirators-in controlling the COVID-19 pandemic in the United States. We showed that the pandemic would have failed to establish in the US if a nationwide mask mandate, based on using respirators with moderately-high compliance, had been implemented during the first two months of the pandemic. The other mask types would fail to prevent the pandemic from becoming established. When mask usage compliance is low to moderate, respirators are far more effective in reducing disease burden. Using data from the third wave, we showed that the epidemic could be eliminated in the US if at least 40% of the population consistently wore respirators in public. Surgical masks can also lead to elimination, but requires compliance of at least 55%. Daily COVID-19 mortality could be eliminated in the US by June or July 2021 if 95% of the population opted for either respirators or surgical masks from the beginning of the third wave. We showed that the prospect of effective control or elimination of the pandemic using mask-based strategy is greatly enhanced if combined with other nonpharmaceutical interventions (NPIs) that significantly reduce the baseline community transmission. By slightly modifying the model to include the effect of a vaccine against COVID-19 and waning vaccine-derived and natural immunity, this study shows that the waning of such immunity could trigger multiple new waves of the pandemic in the US. The number, severity and duration of the projected waves depend on the quality of mask type used and the level of increase in the baseline levels of other NPIs used in the community during the onset of the third wave of the pandemic in the US. Specifically, no severe fourth or subsequent wave of the pandemic will be recorded in the US if surgical masks or respirators are used, particularly if the mask-use strategy is combined with an increase in the baseline levels of other NPIs. This study further emphasizes the role of human behavior towards masking on COVID-19 burden, and highlights the urgent need to maintain a healthy stockpile of highly-effective respiratory protection, particularly respirators, to be made available to the general public in times of future outbreaks or pandemics of respiratory diseases that inflict severe public health and socio-economic burden on the population.\n\nAuthor summaryWe developed and used dynamic models to assess the role of highly-effective face coverings on the control and mitigation of the COVID-19 pandemic in the US. The study indicates that implementing and sustaining mask mandates is useful in containing diseases like COVID-19. Additionally, the study suggests that prioritizing the use of respirators is more effective in combating the disease than using other mask types. Specifically, the COVID-19 pandemic would have been prevented from being established in the US if four in every five Americans started wearing respirators during the first two months of the pandemic. The study further shows that COVID-19 can be eliminated in the US if a universal masking strategy that emphasizes respirators, requiring only 23% compliance, is combined with other nonpharmaceutical interventions that can reduce community transmission by 20%. Furthermore, the daily COVID-19 death rate can be completely suppressed by June 2021 if 95% of the population consistently use respirators. The elimination will extend to January 2022 if cloth masks were adopted instead. We conclude that stockpiling and distributing highly-efficient face coverings, notably respirators, will be vital in effectively curtailing future epidemics and pandemics of respiratory diseases.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Calistus N Ngonghala", + "author_inst": "University of Florida" + }, + { + "author_name": "James R Knitter", + "author_inst": "The University of Arizona, College of Medicine, Tucson" + }, + { + "author_name": "Lucas Marinacci", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Matthew H Bonds", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Abba B Gumel", + "author_inst": "Arizona State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.26.21254429", "rel_title": "Forecasting the Spreading Trajectory of the COVID-19 Pandemic", @@ -844609,145 +845523,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2021.03.26.21253645", - "rel_title": "Monozygotic twins discordant for severe clinical recurrence of COVID-19 show drastically distinct T cell responses to SARS-Cov-2", - "rel_date": "2021-03-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21253645", - "rel_abs": "BackgroundClinical recurrence of COVID-19 in convalescent patients has been reported, which immune mechanisms have not been thoroughly investigated. Presence of neutralizing antibodies suggests other types of immune response are involved.\n\nMethodsWe assessed the innate type I/III IFN response, T cell responses to SARS-CoV-2 with IFN{gamma} ELISPOT, binding and neutralizing antibody assays, in two monozygotic twin pairs with one COVID-19 recurrence case.\n\nResultsIn pair 1, four months after a first mild episode of infection for both siblings, one displayed severe clinical recurrence of COVID-19. Twin pair 2 of siblings underwent non-recurring asymptomatic infection. All fours individuals presented similar overall responses, except for remarkably difference found in specific cellular responses. Recurring sibling presented a reduced number of recognized T cell epitopes as compared to the other three including her non-recurring sibling.\n\nConclusionsOur results suggest that an effective SARS-CoV-2-specific T cell immune response is key for complete viral control and avoidance of clinical recurrence of COVID-19. Besides, adaptive immunity can be distinct in MZ twins. Given the rising concern about SARS-CoV-2 variants that evade neutralizing antibodies elicited by vaccination or infection, our study stresses the importance of T cell responses in protection against recurrence/reinfection.\n\nKey pointsImmune parameters leading to COVID-19 recurrence/reinfection are incompletely understood. A COVID-19 recurrence case in a monozygotic twin pair is described with an intact antibody and innate type I/III Interferon response and drastically reduced number of recognized SARS-CoV-2 T cell epitopes.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Mateus V. Castro", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Keity S. Santos", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Juliana S. Apostolico", - "author_inst": "Federal University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Edgar R. Fernandes", - "author_inst": "Federal University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Rafael R. Almeida", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Gabriel Levin", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Jhosiene Y. Magawa", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Joao Paulo S. Nunes", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Mirian Bruni", - "author_inst": "Federal University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Marcio M. Yamamoto", - "author_inst": "Federal University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Ariane C. Lima", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Monize V. R. Silva", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Larissa R. B. Matos", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Vivian R. Coria", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Erick C. Castelli", - "author_inst": "Sao Paulo State University - Botucatu, SP, Brazil" - }, - { - "author_name": "Marilia O. Scliar", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Andreia Kuramoto", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Fernanda R. Bruno", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Lucas C. Jacintho", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Kelly Nunes", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Jaqueline Y. T. Wang", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Veronica P. Coelho", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Miguel Mitne Neto", - "author_inst": "Fleury Laboratory - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Rui M. B. Maciel", - "author_inst": "Fleury Laboratory - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Michel S. Naslavsky", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Maria Rita Passos-Bueno", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Silvia B. Boscardin", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Daniela S. Rosa", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Jorge Kalil", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Mayana Zatz", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - }, - { - "author_name": "Edecio Cunha-Neto", - "author_inst": "University of Sao Paulo - Sao Paulo, SP, Brazil" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.26.21254424", "rel_title": "Mental health in relation to changes in sleep, exercise, alcohol and diet during the COVID-19 pandemic: examination of five UK cohort studies", @@ -844908,6 +845683,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.26.21254427", + "rel_title": "Assessment of serological assays for identifying high titer convalescent plasma", + "rel_date": "2021-03-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254427", + "rel_abs": "The COVID-19 pandemic has been accompanied by the largest mobilization of therapeutic convalescent plasma (CCP) in over a century. Initial identification of high titer units was based on dose-response data using the Ortho VITROS IgG assay. The proliferation of SARS-CoV-2 serological assays and non-uniform application has led to uncertainty about their interrelationships. The purpose of this study was to establish correlations and analogous cutoffs between commercially available serological tests (Ortho, Abbott, Roche), a spike ELISA, and a virus neutralization assay using convalescent plasma from a cohort of 79 donors from April 2020. Relationships relative to FDA-approved cutoffs under the CCP EUA were identified by linear regression and receiver operator characteristic curves. Relative to the Ortho VITROS assay, the r2 of the Abbott, Roche, the anti-Spike ELISA and the neutralizing assay were 0.58, 0.5, 0.82, and 0.44, respectively. The best correlative index for establishing high-titer units was 3.82 S/C for the Abbott, 10.89 COI for the Roche, 1:1,202 for the anti-Spike ELISA, and 1:200 by the neutralization assay. The overall agreement using derived cutoffs compared to the CCP EUA Ortho VITROS cutoff of 9.5 was 92.4% for Abbott, 84.8% for Roche, 87.3% for the anti-S ELISA and 78.5% for the neutralization assay. Assays based on antibodies against the nucleoprotein (Roche, Abbott) and neutralizing antibody tests were positively associated with the Ortho assay, although their ability to distinguish FDA high-titer specimens was imperfect. The resulting relationships help reconcile results from the large body of serological data generated during the COVID-19 pandemic.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Christopher W. Farnsworth", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Brett Case", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Karl Hock", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Rita E Chen", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Jane O'Halloran", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Rachel Presti", + "author_inst": "Wash U" + }, + { + "author_name": "Charles William Goss", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Adriana M Rauseo", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Ali Ellebedy", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Elitza S Theel", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Michael Diamond", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Jeffrey P Henderson", + "author_inst": "Washington University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.27.21254471", "rel_title": "Estimation of SARS-CoV-2 antibody prevalence through integration of serology and incidence data", @@ -846379,61 +847217,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2021.03.22.21253818", - "rel_title": "Viability RT-PCR for SARS-CoV-2: a step forward to solve the infectivity quandary", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21253818", - "rel_abs": "BackgroundIsolation, contact tracing and restrictions on social movement are being globally implemented to prevent and control onward spread of SARS-CoV-2, even though the infection risk modelled on RNA detection by RT-qPCR remains biased as viral shedding and infectivity are not discerned. Thus, we aimed to develop a rapid viability RT-qPCR procedure to infer SARS-CoV-2 infectivity in clinical specimens and environmental samples.\n\nMethodsWe screened monoazide dyes and platinum compounds as viability molecular markers on five SARS-CoV-2 RNA targets. A platinum chloride-based viability RT-qPCR was then optimized using genomic RNA, and inactivated SARS-CoV-2 particles inoculated in buffer, stool, and urine. Our results were finally validated in nasopharyngeal swabs from persons who tested positive for COVID-19 and in wastewater samples positive for SARS-CoV-2 RNA.\n\nFindingsWe established a rapid viability RT-qPCR that selectively detects potentially infectious SARS-CoV-2 particles in complex matrices. In particular, the confirmed positivity of nasopharyngeal swabs following the viability procedure suggests their potential infectivity, while the complete prevention of amplification in wastewater indicated either non-infectious particles or free RNA.\n\nInterpretationThe viability RT-qPCR approach provides a more accurate ascertainment of the infectious viruses detection and it may complement analyses to foster risk-based investigations for the prevention and control of new or re-occurring outbreaks with a broad application spectrum.\n\nFundingsThis work was supported by Spanish Scientific Research Council (CSIC), Generalitat Valenciana, and MICINN co-founded by AEI/FEDER, UE.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Enric Cuevas-Ferrando", - "author_inst": "Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology" - }, - { - "author_name": "Walter Randazzo", - "author_inst": "Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology" - }, - { - "author_name": "Alba Perez-Cataluna", - "author_inst": "Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology" - }, - { - "author_name": "Irene Falco", - "author_inst": "Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology" - }, - { - "author_name": "David Navarro", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute" - }, - { - "author_name": "Sandra Martin-Latin", - "author_inst": "Universite Paris-Est, ANSES Laboratory for Food Safety, Maisons-Alfort, F-94700, France" - }, - { - "author_name": "Azahara Diaz-Reolid", - "author_inst": "Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology" - }, - { - "author_name": "Ines Giron-Guzman", - "author_inst": "Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology" - }, - { - "author_name": "Ana Allende", - "author_inst": "Research Group on Quality and Safety of Fruits and Vegetables, Department of Food Science and Technology, CEBAS-CSIC, Campus Universitario de Espinardo, 25, 301" - }, - { - "author_name": "Gloria Sanchez", - "author_inst": "Department of Preservation and Food Safety Technologies, Institute of Agrochemistry and Food Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.22.21254032", "rel_title": "Vitamin D-related polymorphisms and vitamin D levels as risk biomarkers of COVID-19 infection severity", @@ -846794,6 +847577,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.17.21253847", + "rel_title": "Femtomolar SARS-CoV-2 Antigen Detection Using the Microbubbling Digital Assay with Smartphone Readout Enables Antigen Burden Quantitation and Dynamics Tracking", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253847", + "rel_abs": "BackgroundLittle is known about the dynamics of SARS-CoV-2 antigen burden in respiratory samples in different patient populations at different stages of infection. Current rapid antigen tests cannot quantitate and track antigen dynamics with high sensitivity and specificity in respiratory samples.\n\nMethodsWe developed and validated an ultra-sensitive SARS-CoV-2 antigen assay with smartphone readout using the Microbubbling Digital Assay previously developed by our group, which is a platform that enables highly sensitive detection and quantitation of protein biomarkers. A computer vision-based algorithm was developed for microbubble smartphone image recognition and quantitation. A machine learning-based classifier was developed to classify the smartphone images based on detected microbubbles. Using this assay, we tracked antigen dynamics in serial swab samples from COVID patients hospitalized in ICU and immunocompromised COVID patients.\n\nResultsThe limit of detection (LOD) of the Microbubbling SARS-CoV-2 Antigen Assay was 0.5 pg/mL (10.6 fM) recombinant nucleocapsid (N) antigen or 4000 copies/mL inactivated SARS-CoV-2 virus in nasopharyngeal (NP) swabs, comparable to many rRT-PCR methods. The assay had high analytical specificity towards SARS-CoV-2. Compared to EUA-approved rRT-PCR methods, the Microbubbling Antigen Assay demonstrated a positive percent agreement (PPA) of 97% (95% confidence interval (CI), 92-99%) in symptomatic individuals within 7 days of symptom onset and positive SARS-CoV-2 nucleic acid results, and a negative percent agreement (NPA) of 97% (95% CI, 94-100%) in symptomatic and asymptomatic individuals with negative nucleic acid results. Antigen positivity rate in NP swabs gradually decreased as days-after-symptom-onset increased, despite persistent nucleic acid positivity of the same samples. The computer vision and machine learning-based automatic microbubble image classifier could accurately identify positives and negatives, based on microbubble counts and sizes. Total microbubble volume, a potential marker of antigen burden, correlated inversely with Ct values and days-after-symptom-onset. Antigen was detected for longer periods of time in immunocompromised patients with hematologic malignancies, compared to immunocompetent individuals. Simultaneous detectable antigens and nucleic acids may indicate the presence of replicating viruses in patients with persistent infections.\n\nConclusionsThe Microbubbling SARS-CoV-2 Antigen Assay enables sensitive and specific detection of acute infections, and quantitation and tracking of antigen dynamics in different patient populations at various stages of infection. With smartphone compatibility and automated image processing, the assay is well-positioned to be adapted for point-of-care diagnosis and to explore the clinical implications of antigen dynamics in future studies.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Hui Chen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Zhao Li", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sheng Feng", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Anni Wang", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Melissa Richard-Greenblatt", + "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" + }, + { + "author_name": "Emily Hutson", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Stefen Andrianus", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Laurel Glaser", + "author_inst": "Raymond and Ruth Perelman School of Medicine at the University of Pennsylvania" + }, + { + "author_name": "Kyle G Rodino", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jianing Qian", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Dinesh Jayaraman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ronald Collman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Abigail L Glascock", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Frederic Bushman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Jae Seung Lee", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Sara Cherry", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alejandra Fausto", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Susan R Weiss", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Hyun Koo", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Patricia M Corby", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Una ODoherty", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alfred L Garfall", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Dan T Vogl", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Edward A Stadtmauer", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ping Wang", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.21.21254061", "rel_title": "Quantitative SARS-CoV-2 anti-spike responses to Pfizer-BioNTech and Oxford-AstraZeneca vaccines by previous infection status", @@ -848365,153 +849263,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.03.23.21254158", - "rel_title": "The polymorphism L412F in TLR3 inhibits autophagy and is a marker of severe COVID-19 in males.", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254158", - "rel_abs": "The polymorphism L412F in TLR3 has been associated with several infectious diseases. However, the mechanism underlying this association is still unexplored. Here, we show that the L412F polymorphism in TLR3 is a marker of severity in COVID-19. This association increases in the sub-cohort of males. Impaired autophagy and reduced TNF production was demonstrated in HEK293 cells transfected with TLR3-L412F plasmid and stimulated with specific agonist poly(I:C). A statistically significant reduced survival at 28 days was shown in L412F COVID-19 patients treated with the autophagy-inhibitor hydroxychloroquine (P=0.038). An increased frequency of autoimmune disorders as co-morbidity was found in L412F COVID-19 males with specific class II HLA haplotypes prone to autoantigen presentation. Our analyses indicate that L412F polymorphism makes males at risk of severe COVID-19 and provides a rationale for reinterpreting clinical trials considering autophagy pathways.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Susanna Croci", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Mary Anna Venneri", - "author_inst": "Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy" - }, - { - "author_name": "Stefania Mantovani", - "author_inst": "Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy" - }, - { - "author_name": "Chiara Fallerini", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Elisa Benetti", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Nicola Picchiotti", - "author_inst": "University of Siena, DIISM-SAILAB, Siena, Italy; Department of Mathematics, University of Pavia, Pavia, Italy" - }, - { - "author_name": "Federica Campolo", - "author_inst": "Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy" - }, - { - "author_name": "Francesco Imperatore", - "author_inst": "Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Via Fiorentina, 1 53100 Siena, Italy; Consiglio Nazionale delle Ricerche, Istituto di Fisio" - }, - { - "author_name": "Maria Palmieri", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Sergio Daga", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Chiara Gabbi", - "author_inst": "Independent Medical Scientist, Milan, Italy" - }, - { - "author_name": "Francesca Montagnani", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Department of Medical Sciences, Infectious and Tropica" - }, - { - "author_name": "Giada Beligni", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Ticiana D.J. Farias", - "author_inst": "Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aur" - }, - { - "author_name": "Miriam L. Carriero", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Laura Di Sarno", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Diana Alaverdian", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Sigrid Aslaksen", - "author_inst": "Department of Clinical Science, University of Bergen and K.G. Jebsen Center for Autoimmune Diseases, University of Bergen, Bergen, Norway." - }, - { - "author_name": "Maria Vittoria Cubellis", - "author_inst": "Department of Biology, Universita degli Studi di Napoli \"Federico II\", Napoli, Italy" - }, - { - "author_name": "Ottavia Spiga", - "author_inst": "Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Siena 53100, Italy" - }, - { - "author_name": "Margherita Baldassarri", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Francesca Fava", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Paul J. Norman", - "author_inst": "Division of Biomedical Informatics and Personalized Medicine, and Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aur" - }, - { - "author_name": "Elisa Frullanti", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Andrea M. Isidori", - "author_inst": "Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy" - }, - { - "author_name": "Antonio Amoroso", - "author_inst": "Department of Medical Sciences, University of Turin, Italy; Immunogenetics and Transplant Biology, Azienda Ospedaliera Universitaria Citta della Salute e della " - }, - { - "author_name": "Francesca Mari", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Simone Furini", - "author_inst": "Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - }, - { - "author_name": "Mario Mondelli", - "author_inst": "Division of Infectious Diseases and Immunology, Department of Medical Sciences and Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy; 1" - }, - { - "author_name": "- GEN-COVID Multicenter Study", - "author_inst": "-" - }, - { - "author_name": "Mario Chiariello", - "author_inst": "Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Via Fiorentina, 1 53100 Siena, Italy; Consiglio Nazionale delle Ricerche, Istituto di Fisio" - }, - { - "author_name": "Alessandra Renieri", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy; Genetica" - }, - { - "author_name": "Ilaria Meloni", - "author_inst": "Medical Genetics, University of Siena, Italy; Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.03.24.21253517", "rel_title": "Improving COVID-19 vaccination centre operation through computer modelling and simulation", @@ -848768,6 +849519,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.23.21254169", + "rel_title": "COVID-19 antibody seroprevalence in Duhok, Kurdistan Region, Iraq: A population-based study", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254169", + "rel_abs": "ObjectiveThis population-based study aimed to evaluate the seroprevalence of antibodies to SARS-CoV-2 in Duhok City, Kurdistan Region of Iraq.\n\nMethodsWe analyzed the national COVID-19 database that contains data regarding COVID-19 testing, management, and clinical outcomes in Duhok. For this study, different subdistricts within each district of Duhok were considered distinct clusters. Blood samples were collected from and questionnaires were administered to eligible and consenting participants who were members of different families from the subdistricts. Immunoassays were conducted to detect antibodies against SARS-CoV-2, and the associations between certain variables were investigated.\n\nResultsThe average number cases of COVID-19 before November 2020 was 23141 {+/-} 4364, which was significantly higher than the average number of cases between November 2020 and February 2021 (3737 {+/-} 2634; P = 0.001). A total of 743 individuals agreed to participate and were enrolled in the study. Among the participants, 465/743 (62.58%) were found to have antibodies against severe acute respiratory syndrome coronavirus 2. Among the participants with antibodies, 262/465 (56.34%) denied having any history of COVID-19-related symptoms. The most common symptom was fever (81.77%), followed by myalgia (81.28%). We found that antibody levels increased steadily with age (Pearson correlation coefficient = 0.117; P = 0.012). A significant association was found between antibody levels and the presence of symptoms (P = 0.023; odds ratio = 1.0023; 95% confidence interval = 1.0002-1.0061).\n\nConclusionsA significant reduction in the number of COVID-19 cases was observed. This might be due to the high prevalence of SARS-CoV-2 antibodies in Duhok. However, infection-prevention measures should be followed as it remains unclear whether acquired immunity is protective against reinfection. It expected that the infection rates during the next wave will not be as high as the first wave due to the high infection rate in the society.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Nawfal R Hussein", + "author_inst": "Department of Biomolecular Sciences, College of Medicine, University of Zakho" + }, + { + "author_name": "Amer Balatay", + "author_inst": "Department of pharmacology and clinical pharmacy, College of pharmacy, University of Duhok, Kurdistan Region, Iraq" + }, + { + "author_name": "Ibrahim A Naqid", + "author_inst": "Department of Biomedical Sciences, College of Medicine, University of Zakho, Kurdistan Region, Iraq" + }, + { + "author_name": "Shakir A Jamal", + "author_inst": "Department of Biomedical Sciences, College of Medicine, University of Zakho, Kurdistan Region, Iraq" + }, + { + "author_name": "Narin A Rasheed", + "author_inst": "Akre Technical Institute, Duhok Polytechnic University, Duhok, Kurdistan Region, Iraq" + }, + { + "author_name": "Alind N Ahmed", + "author_inst": "Azadi Teaching Hospital, Duhok, Kurdistan Region of Iraq" + }, + { + "author_name": "Reving S Salih", + "author_inst": "Azadi Teaching Hospital, Duhok, Kurdistan Region of Iraq" + }, + { + "author_name": "Ahmed S Mahdi", + "author_inst": "Childhood Friends Hospital of Amedi, Kurdistan Region of Iraq" + }, + { + "author_name": "Sabeeha A Mansour", + "author_inst": "Azadi Teaching Hospital, Duhok, Kurdistan Region of Iraq" + }, + { + "author_name": "Shaveen Mahdi", + "author_inst": "Duhok Maternity Hospital, Duhok, Kurdistan Region of Iraq" + }, + { + "author_name": "Nashwan Ibrahim", + "author_inst": "Department of Surgery, College of Medicine, University of Duhok, Kurdistan Region, Iraq" + }, + { + "author_name": "Dildar H Musa", + "author_inst": "Department of Surgery, College of Medicine, University of Duhok, Kurdistan Region, Iraq" + }, + { + "author_name": "Zana SM Saleem", + "author_inst": "Department of Medicine, College of Medicine, University of Duhok, Duhok, Kurdistan Region of Iraq" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.23.21253460", "rel_title": "Serological profiles of pan-coronavirus-specific responses in COVID-19 patients using a multiplexed electro-chemiluminescence-based testing platform", @@ -849947,65 +850765,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.26.21254388", - "rel_title": "Relationship between teaching modality and COVID-19, well-being, and teaching satisfaction (Campus & Corona): a cohort study among students in higher education", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254388", - "rel_abs": "BackgroundAfter lock-down during the first wave of the COVID-19 pandemic, higher education institutions globally struggled to balance the need for infection control and educational requirements as they prepared to reopen. A particularly difficult choice was whether to offer for in-person or online teaching, since there was little or no empirical research to inform this decision. Norwegian universities and university colleges opted for a hybrid model when they reopened for the autumn semester, with some students offered more in-person teaching than others. This gave us an opportunity to study the association between different teaching modalities and COVID-19 risk, quality of life (subjective well-being), and teaching satisfaction.\n\nMethodsWe conducted a prospective, observational cohort study among students in higher education institutions in Norway. Participants were surveyed biweekly from September to December in 2020.\n\nFindings26 754 students from 14 higher education institutions provided data to our analyses. Our best estimate for the association between two weeks of in-person teaching and COVID-19 risk was -22% (95% CI -77% to 33%), compared to online teaching. Quality of life was positively associated with in-person teaching (3% relative risk difference; 95% CI 2% to 4%), as was teaching satisfaction (10%; 95% CI 8% to 11%).\n\nInterpretationThe association between COVID-19 infection and teaching modality was highly uncertain. Shifting from in-person to online teaching seems to have a negative impact on the well-being of students in higher education.\n\nFundingNone.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Atle Fretheim", - "author_inst": "Oslo Metropolitan University and Norwegian Institute of Public Health" - }, - { - "author_name": "Arnfinn Helleve", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Borghild Loyland", - "author_inst": "Oslo Metropolitan University" - }, - { - "author_name": "Ida Hellum Sandbekken", - "author_inst": "Oslo Metropolitan University" - }, - { - "author_name": "Martin Flato", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kjetil Telle", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Sara Sofie Viksmoen Watle", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Alexander Schjoll", - "author_inst": "Oslo Metropolitan University" - }, - { - "author_name": "Solvi Helseth", - "author_inst": "Oslo Metropolitan University" - }, - { - "author_name": "Gro Jamtvedt", - "author_inst": "Oslo Metropolitan University" - }, - { - "author_name": "Rannveig Kaldager Hart", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.24.21254124", "rel_title": "Understanding and Addressing Vaccine Hesitancy in the Context of COVID-19: Development of a Digital intervention", @@ -850310,6 +851069,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2021.03.23.21254207", + "rel_title": "Association between the physical work environment and work functioning impairment while working from home under the COVID-19 pandemic in Japanese workers", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254207", + "rel_abs": "ObjectiveThis study examined the relationship between the physical work environment and work functioning impairment while working from home in the context of rapid changes associated with the COVID-19 pandemic.\n\nMethodsThis cross-sectional study of internet monitors was conducted between December 22 and 26, 2020. Of a total of 33,302 participants, 5,760 who worked from home at least 1 day a month, excluding those who met the exclusion criteria, were included in the analysis. A binary subjective assessment of the physical work environment while working from home was used as an exposure factor. We examined 9 items related to the physical work environment, including level of illuminance and use of suitable desks and chairs, traditionally recommended for health and safety management when working at a desk. The number of non-conformities to 7 items was also used as an exposure factor. The presence of severe work functioning impairment was measured using the Work Functioning impairment Scale (WFun), a self-reported outcome measure of the degree of work functioning impairment. Odds ratios of severe work functioning impairment were estimated using mixed-effects logistic regression analysis with the prefecture of residence as a random effect.\n\nResultsMultivariate analysis showed that the odds ratio of severe work functioning impairment was significantly higher among those who indicated \"No\" to all recommended items except for \"I work at a desk/chair for office use.\" The highest odds ratio of work functioning impairment was associated with a \"No\" response to \"There is enough light to do my work\" (aOR: 2.02, 95%CI: 1.73-2.35, p<0.01). Our results also suggest the presence of a dose-response relationship between the number of non-conformities to recommendations for work environments while working from home and work functioning impairment.\n\nConclusionsOur findings suggest that it is important for both companies and individual workers to create a work environment that prevents negative health outcomes and improves productivity while working from home.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Makoto Okawara", + "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Tomohiro Ishimaru", + "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Seiichiro Tateishi", + "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Ayako Hino", + "author_inst": "Department of Mental Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Mayumi Tsuji", + "author_inst": "Department of Environmental Health, School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Kazunori Ikegami", + "author_inst": "Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Masako Nagata", + "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" + }, + { + "author_name": "Shinya Matsuda", + "author_inst": "Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Yoshihisa Fujino", + "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.03.25.21254314", "rel_title": "Automatic identification of risk factors for SARS-CoV-2 positivity and severe clinical outcomes of COVID-19 using Data Mining and Natural Language Processing", @@ -851605,33 +852415,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, - { - "rel_doi": "10.1101/2021.03.26.21254377", - "rel_title": "Why COVID-19 is not so spread in Africa: How does Ivermectin affect it?", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254377", - "rel_abs": "BackgroundScientists have so far been unable to determine the reason for the low number of COVID-19 cases in Africa.\n\nObjectiveTo evaluate the impact of ivermectin interventions for onchocerciasis on the morbidity, mortality, recovery, and fatality rates caused by COVID-19.\n\nMethodA retrospective statistical analysis study of the impact of ivermectin against COVID-19 between the 31 onchocerciasis-endemic countries using the community-directed treatment with ivermectin (CDTI) and the non-endemic 22 countries in Africa. The morbidity, mortality, recovery rate, and fatality rate caused by COVID-19 were calculated from the WHO situation report in Africa. We investigated the onchocerciasis endemic 31 countries and the non-endemic 22 countries. Statistical comparisons used by the Welch test of them in the two groups were made.\n\nResultsThe morbidity and mortality were statistically significantly less in the 31 countries using CDTI. The recovery and fatality rates were not statistically significant difference. The average life expectancy was statistically significantly higher in the non-endemic countries.\n\nConclusionsThe morbidity and mortality in the onchocerciasis endemic countries are lesser than those in the non-endemic ones. The community-directed onchocerciasis treatment with ivermectin is the most reasonable explanation for the decrease in morbidity and fatality rate in Africa. In areas where ivermectin is distributed to and used by the entire population, it leads to a significant reduction in mortality.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Hisaya Tanioka", - "author_inst": "Tanioka Clinic" - }, - { - "author_name": "Sayaka Tanioka", - "author_inst": "Tanioka Clinic" - }, - { - "author_name": "Kimitaka Kaga", - "author_inst": "National Institute of Sensory Organs National Tokyo Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.25.21253802", "rel_title": "Emergence of N antigen SARS-CoV-2 genetic variants escaping detection of antigenic tests", @@ -851804,6 +852587,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.24.21254046", + "rel_title": "Sudden rise in COVID-19 case fatality among young and middle-aged adults in the south of Brazil after identification of the novel B.1.1.28.1 (P.1) SARS-CoV-2 strain: analysis of data from the state of Parana", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254046", + "rel_abs": "Brazil is currently suffering a deadly surge of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections, which has been attributed to the spread of a new strain known as P.1 (B.1.1.28.1). In this investigation, we analyzed coronavirus disease 2019 (COVID-19) public health data from Parana, the largest state in southern half of Brazil, between September 1, 2020 and March 17, 2021, to evaluate recent trends in case fatality rates in different age groups. A total of 553,518 cases of SARS-CoV-2, 8,853 currently registered as fatal, were finally included in our analysis. All age groups showed either decline or stabilization of the case fatality rates (CFRs) between September 2020 and January 2021. In February 2021, an increase in CFR for almost all age groups could be instead observed. All groups above 20 years of age showed statistically significant increases in CFR when diagnosed in February 2021 as opposed to January 2021. Patients aged 20-29 years experienced a tripling of their CFR, from 0.04% to 0.13%, while those aged 30-39, 40-49, 50-59 experienced approximate CFR doubling. Individuals between 20 and 29 years of age whose diagnosis was made in February 2021 had an over 3-fold higher risk of death compared to those diagnosed in January 2021 (Risk Ratio (RR): 3.15 [95%CI: 1.52-6.53], p<0.01), while those aged 30-39, 40-49, 50-59 years experienced 93% (1.93 [95%CI:1.31-2.85], p<0.01), 110% (RR: 2.10 [95%CI:1.62-2.72], p<0.01), and 80% (RR: 1.80 [95%CI:1.50-2.16], p<0.01) increases in risk of death, respectively. Notably, the observed CFR increase coincided with the second consecutive month of declining number of diagnosed SARS-CoV-2 cases. Taken together, these preliminary findings suggest significant increases in CFR in young and middle-aged adults after identification of a novel SARS-CoV-2 strain circulating in Brazil, and this should raise public health alarms, including the need for more aggressive local and regional public health interventions and faster vaccination.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Maria Helena Santos de Oliveira", + "author_inst": "Federal University of Parana" + }, + { + "author_name": "Giuseppe Lippi", + "author_inst": "University of Verona" + }, + { + "author_name": "Brandon Michael Henry", + "author_inst": "Cincinnati Children's Hospital Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.24.21254254", "rel_title": "Dental mitigation strategies to reduce aerosolization of SARS-CoV-2", @@ -853459,85 +854269,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.22.21253577", - "rel_title": "Demographic and clinical features associated with in-hospital mortality in Egyptian COVID-19 patients: A retrospective cohort study", - "rel_date": "2021-03-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21253577", - "rel_abs": "IntroductionSince the worldwide emergence of the COVID-19, several protocols were used by different healthcare organisations. We evaluated in this study the demographic and clinical characteristics of COVID-19 disease in Egyptian population with special consideration for its mortality predictors.\n\nMethodology8162 participants (mean age 48.7{+/-}17.3 years,54.5% males) with RT-PCR positive COVID-19 were included. The electronic medical records were reviewed for demographic, clinical, laboratory, and radiologic features. The primary outcome was the in-hospital mortality rate.\n\nResultsThe in-hospital mortality was 11.2%. There was a statistically significant strong association of in-hospital mortality with age >60 years old (OR:4.7; 95% CI 4.1-5.4;p<0.001), diabetes mellitus (OR:4.6; 95% CI 3.99-5.32;p<0.001), hypertension (OR:3.9; 95% CI 3.4-4.5;p<0.001), coronary artery disease (OR:2.7; 95% CI 2.2-3.2;p<0.001), chronic obstructive pulmonary disease (OR:2.1; 95% CI 1.7-2.5;p<0.001), chronic kidney disease (OR:4.8; 95% CI 3.9-5.9;p<0.001), malignancy (OR:3.7; 95% CI 2.3-5.75;p<0.001), neutrophil-lymphocyte ratio >3.1 (OR:6.4; 95% CI 4.4-9.5;P< 0.001), and ground glass opacities (GGOs) in CT chest (OR:3.5; 95% CI 2.84-4.4;P<0.001), respectively. There was a statistically significant moderate association of in-hospital mortality with male gender (OR:1.6; 95% CI 1.38-1.83;p<0.001) and smoking (OR:1.6; 95% CI 1.3-1.9;p<0.001). GGOs was reported as the most common CT finding (occurred in 73.1% of the study participants).\n\nConclusionsThis multicenter, retrospective study ascertained the higher in-hospital mortality rate in Egyptian COVID-19 patients with different comorbidities.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Noha Asem", - "author_inst": "Ministry of Health and Population and Faculty of Medicine, Cairo University" - }, - { - "author_name": "Mohamed Hassany", - "author_inst": "Hepatology and Tropical Medicine Department, National Hepatology and Tropical Medicine Research Institute, Cairo, Egypt, Ministry of Health and Population, Cair" - }, - { - "author_name": "Khaled Taema", - "author_inst": "Critical care medicine, Cairo University, Egypt" - }, - { - "author_name": "Hossam Masoud", - "author_inst": "Professor of pulmonology, Cairo University" - }, - { - "author_name": "Gehan Elassal", - "author_inst": "Professor of pulmonology, Ain Shams University" - }, - { - "author_name": "Ehab Kamal", - "author_inst": "Medical research division. National research centre. Giza Egypt. Minster of health assistant for continuous medical education, head of fever hospitals directora" - }, - { - "author_name": "Wagdy Amin", - "author_inst": "Director General for chest diseases, MOHP" - }, - { - "author_name": "Akram Abdelbary", - "author_inst": "Professor of critical care medicine, Cairo University" - }, - { - "author_name": "Amin Abdel-Baki", - "author_inst": "Hepatology, Gastroenterology and Infectious diseases department. National Hepatology and Tropical Medicine Research Institute (NHTMRI), Cairo, Egypt." - }, - { - "author_name": "Samy Zaky", - "author_inst": "Professor of Hepatogastroenterology and infectious diseases, Alazhar University" - }, - { - "author_name": "Ahmad Abdalmohsen", - "author_inst": "Critical care medicine, Cairo University, Egypt" - }, - { - "author_name": "Hamdy Ibrahim", - "author_inst": "National Hepatology and Tropical Medicine Research Institute (NHTMRI), Cairo, Egypt" - }, - { - "author_name": "Mohamed Elnady", - "author_inst": "Professor of pulmonology, Cairo University" - }, - { - "author_name": "Ahmed Mohamed", - "author_inst": "Professor of chest diseases and Bronchscopy, Tanta university" - }, - { - "author_name": "Ehab Attia", - "author_inst": "Ministry of Health and Population" - }, - { - "author_name": "Hala Zaid", - "author_inst": "Ministry of Health and Population" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.24.436523", "rel_title": "Efficacy of a Broadly Neutralizing SARS-CoV-2 Ferritin Nanoparticle Vaccine in Nonhuman Primates", @@ -853921,6 +854652,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.25.436930", + "rel_title": "Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India", + "rel_date": "2021-03-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.25.436930", + "rel_abs": "Emergence of distinct viral clades has been observed in SARS-CoV2 variants across the world and India. Identification of the genomic diversity and the phylodynamic profiles of the prevalent strains of the country are critical to understand the evolution and spread of the variants. We performed whole-genome sequencing of 54 SARS-CoV2 strains collected from COVID-19 patients in Kolkata, West Bengal during August to October 2020. Phylogeographic and phylodynamic analyses were performed using these 54 and other sequences from India and abroad available in GISAID database. Spatio-temporal evolutionary dynamics of the pathogen across various regions and states of India over three different time periods in the year 2020 were analyzed. We estimated the clade dynamics of the Indian strains and compared the clade specific mutations and the co-mutation patterns across states and union territories of India over the time course. We observed that GR, GH and G (GISAID) or 20B and 20A (Nextstrain) clades were the prevalent clades in India during middle and later half of the year 2020. However, frequent mutations and co-mutations observed within the major clades across time periods do not show much overlap, indicating emergence of newer mutations in the viral population prevailing in the country. Further, we explored the possible association of specific mutations and co-mutations with the infection outcomes manifested within the Indian patients.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Nupur Biswas", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Priyanka Mallick", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Sujay Krishna Maity", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Debaleena Bhowmik", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Arpita Ghosh Mitra", + "author_inst": "MEDICA Superspeciality Hospital, Kolkata, West Bengal, India" + }, + { + "author_name": "Soumen Saha", + "author_inst": "MEDICA Superspeciality Hospital, Kolkata, West Bengal, India" + }, + { + "author_name": "Aviral Roy", + "author_inst": "MEDICA Superspeciality Hospital, Kolkata, West Bengal, India" + }, + { + "author_name": "Partha Chakrabarti", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "Sandip Paul", + "author_inst": "CSIR-IICB" + }, + { + "author_name": "Saikat Chakrabarti", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.03.25.437046", "rel_title": "Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring", @@ -855236,85 +856022,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.16.21251286", - "rel_title": "Transcriptome analysis of PBMCs reveals distinct immune response in the asymptomatic and re-detectable positive COVID-19 patients", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21251286", - "rel_abs": "The existence of asymptomatic and re-detectable positive COVID-19 patients presents the disease control challenges of COVID-19. Most studies on immune response of COVID-19 have focused on the moderately or severely symptomatic patients, however little is known about the immune response in asymptomatic and re-detectable positive patients. Here we performed a comprehensive analysis of the transcriptomic profiles of PBMCs from 48 COVID-19 patients which include 8 asymptomatic, 13 symptomatic, 15 recovering and 12 RP patients. Our analysis revealed a down-regulation of IFN response and complement activation in the asymptomatic patients compared with the symptomatic, indicating a weaker immune response of the PBMCs in the asymptomatic patients. In addition, we observed a lower expression of the cytokines and chemokines in the PBMC of asymptomatic and symptomatic patients. In contrast, the cytokines and chemokines level in the RP patients are higher than the recovering. GSEA analysis showed the enrichment of TNFa/NF-{kappa}B and influenza infection in the RP patients compared with the recovering patients, indicating a flu-like, hyper-inflammatory immune response in the PBMC of RP patients. Thus our findings could extend our understanding of host immune response during the progression COVID-19 disease and help the clinical management and the immunotherapy development for COVID-19.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jiaqi Zhang", - "author_inst": "Shunde Hospital of Guangzhou University of Chinese Medicine" - }, - { - "author_name": "Dongzi Lin", - "author_inst": "The Forth People's Hospital of Foshan" - }, - { - "author_name": "Kui Li", - "author_inst": "Guangzhou Huayin Medical Laboratory Center. Ltd" - }, - { - "author_name": "Xiangming Ding", - "author_inst": "Guangzhou Geneseed Biotech Co.,Ltd" - }, - { - "author_name": "Lin Li", - "author_inst": "Shunde Hospital of Guangzhou University of Chinese Medicine" - }, - { - "author_name": "Yuntao Liu", - "author_inst": "The Second Affiliated Hospital of Guangzhou University of Chinese Medicine" - }, - { - "author_name": "Dongdong Liu", - "author_inst": "The Second Affiliated Hospital of Guangzhou University of Chinese Medicine" - }, - { - "author_name": "Jing Lin", - "author_inst": "The First People's Hospital of Foshan" - }, - { - "author_name": "Xiangyun Teng", - "author_inst": "Shunde Hospital of Guangzhou University of Chinese Medicine" - }, - { - "author_name": "Yizhe Li", - "author_inst": "Shunde Hospital of Guangzhou University of Chinese Medicine" - }, - { - "author_name": "Ming Liu", - "author_inst": "Guangzhou Geneseed Biotech Co.,Ltd" - }, - { - "author_name": "Xiaodan Wang", - "author_inst": "Guangzhou Huayin Medical Laboratory Center. Ltd" - }, - { - "author_name": "Dan He", - "author_inst": "Guangzhou Huayin Medical Laboratory Center. Ltd" - }, - { - "author_name": "Yaling Shi", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University" - }, - { - "author_name": "Dawei Wang", - "author_inst": "Shunde Hospital of Guangzhou University of Chinese Medicine" - }, - { - "author_name": "Jianhua Xu", - "author_inst": "Shunde Hospital of Guangzhou University of Chinese Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.03.17.21253773", "rel_title": "Weak humoral immune reactivity among residents of long-term care facilities following one dose of the BNT162b2 mRNA COVID-19 vaccine", @@ -855587,6 +856294,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.22.21254134", + "rel_title": "Relationship between COVID-19 pandemic and ecological, economic, and social characteristics", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21254134", + "rel_abs": "COVID-19 pandemic had huge impacts on the global world, with both a negative impact on society and economy, but a positive one on nature. But this universal effect resulted in different infection rates from country to country. We analyzed the relationship between the pandemic and ecological, economic, and social characteristics. All of these data were collected in 140 countries at 6 time points. Correlations were studied using univariate and multivariate regression models.\n\nThe world was interpreted as a single global ecosystem consisting of ecosystem units representing countries. We first studied 140 countries around the world together, and infection rates were related to per capita GDP, Ecological Footprint, median age, urban population, and Biological Capacity, globally. We then ranked 140 countries by infection rate and created 4 equal groups, each with 35 countries. In the first group, the infection rate was very high and was related to the Ecological Footprint (consumption) and GDP per capita (production). This group is dominated by developed countries and their ecological characteristics have proven to be particularly significant. In groups 2, 3, and 4, infection rates were high, moderate, and low, and were primarily associated with median age and urban population.\n\nIn the scientific discussion, we have interpreted why infection is high in developed countries. Sustainable ecosystems are balanced, unlike the ecosystems of developed countries. According to science, the resilience and health of both natural ecosystems and humans are closely linked to the world of microbial communities. Our results suggest that both the economy and society need to be in harmony with nature, creating sustainable ecosystems in developed countries as well.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Attila Muranyi", + "author_inst": "Institute for Soil Science and Agricultural Chemistry, Hungarian Academy of Sciences" + }, + { + "author_name": "Balint Varga", + "author_inst": "Department of Computer Science, Institute of Mathematics, Eotvos Lorand University, Budapest, Hungary" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.20.21253892", "rel_title": "Intention of Healthcare Workers to Receive COVID-19 Vaccine: A Cross-Sectional Survey in 10 Countries in Eastern Mediterranean Region", @@ -856892,57 +857622,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, - { - "rel_doi": "10.1101/2021.03.22.21253621", - "rel_title": "COVID-19 therapeutics for low- and middle-income countries: a review of re-purposed candidate agents with potential for near-term use and impact", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21253621", - "rel_abs": "Low- and middle-income countries (LMICs) face significant challenges in the control of COVID-19, given limited resources, especially for inpatient care. In a parallel effort to that for vaccines, the identification of therapeutics that have near-term potential to be available and easily administered is critical. Using the United States, European Union, and World Health Organization clinical trial registries, we reviewed COVID-19 therapeutic agents currently under investigation. The search was limited to oral or potentially oral agents, with at least a putative anti-SARS-CoV-2 virus mechanism, and with at least 3 registered trials. We describe the available evidence regarding agents that met these criteria and additionally discuss the need for additional investment by the global scientific community in large well-coordinated trials of accessible agents and their combinations in LMICs. The search yielded 636, 175, and 930 trials, in the US, EU, and WHO trial registers, respectively. These trials covered 17 oral or potentially oral repurposed agents that are currently used as antimicrobials and immunomodulatory therapeutics and therefore have established safety. The available evidence regarding proposed mechanism of actions, clinical efficacy, and potential limitations is summarized. We also identified the need for large well-coordinated trials of accessible agents and their combinations in LMICs. Several repurposed agents have potential to be safe, available, and easily administrable to treat COVID-19. To prevent COVID-19 from becoming a neglected tropical disease, there is critical need for rapid and coordinated effort in their evaluation and the deployment of those found to be efficacious.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Daniel Maxwell", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Kelly C. Sanders", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Oliver Sabot", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Ahmad Hachem", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Alejandro Llanos-Cuentas", - "author_inst": "Universidad Peruana Cayetano Heredia" - }, - { - "author_name": "Ally Olotu", - "author_inst": "Ifakara Health Institute" - }, - { - "author_name": "Roly Gosling", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "James Cutrell", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Michelle S. Hsiang", - "author_inst": "University of Texas Southwestern Medical Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.14.21253537", "rel_title": "The Effect of Famotidine on Hospitalized Patients with COVID-19: a Systematic Review and Meta-Analysis", @@ -857219,6 +857898,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.14.21253532", + "rel_title": "Epicardial adipose tissue thickness is associated with increased severity and mortality related to SARS-CoV-2 infection", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.14.21253532", + "rel_abs": "BACKGROUNDIncreased adiposity and visceral obesity have been linked to adverse COVID-19 outcomes. The amount of epicardial adipose tissue (EAT) may have relevant implications given its proximity to the heart and lungs. Here, we explored the role of EAT in increasing the risk for COVID-19 adverse outcomes.\n\nMETHODSWe included 748 patients with COVID-19 attending a reference center in Mexico City. EAT thickness, sub-thoracic and extra-pericardial fat were measured using thoracic CT scans. We explored the association of each thoracic adipose tissue compartment with COVID-19 mortality and severe COVID-19 (defined as mortality and need for invasive mechanical ventilation), according to the presence or absence of obesity. Mediation analyses evaluated the role of EAT in facilitating the effect of age, body mass index and cardiac troponin levels with COVID-19 outcomes.\n\nRESULTSEAT thickness was associated with increased risk of COVID-19 mortality (HR 1.18, 95%CI 1.01-1.39) independent of age, gender, comorbid conditions and BMI. Increased EAT was associated with lower SpO2 and PaFi index and higher levels of cardiac troponins, D-dimer, fibrinogen, C-reactive protein, and 4C severity score, independent of obesity. EAT mediated 13.1% (95%CI 3.67-28.0%) and 5.1% (95%CI 0.19-14.0%) of the effect of age and 19.4% (95%CI 4.67-63.0%) and 12.8% (95%CI 0.03-46.0%) of the effect of BMI on requirement for intubation and mortality, respectively. EAT also mediated the effect of increased cardiac troponins on myocardial infarction during COVID-19.\n\nCONCLUSIONEAT is an independent risk factor for severe COVID-19 and mortality independent of obesity. EAT partly mediates the effect of age and BMI and increased cardiac troponins on adverse COVID-19 outcomes.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Roopa Mehta", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Omar Yaxmehen Bello-Chavolla", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Leonardo Mancillas-Adame", + "author_inst": "Facultad de Medicina, Universidad Autonoma de Nuevo Leon" + }, + { + "author_name": "Marcela Rodr\u00edguez-Flores", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Natalia Ram\u00edrez-Pedraza", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Bethsabel Rodr\u00edguez-Encinas", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Carolina Isabel P\u00e9rez-Carri\u00f3n", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Mar\u00eda Isabel Jasso-\u00c1vila", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Jorge Valladares-Garcia", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Pablo Esteban Vanegas-Cedillo", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Diana Hern\u00e1ndez-Ju\u00e1rez", + "author_inst": "dianaheez@hotmail.com" + }, + { + "author_name": "Arsenio Vargas-V\u00e1zquez", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Neftali Eduardo Antonio-Villa", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Monica Chapa-Ibarguengoitia", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Paloma Almeda-Vald\t\u00e9s", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Daniel Elias-Lopez", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Arturo Galindo-Fraga", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Alfonso Gulias-Herrero", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Alfredo Ponce de Leon", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Jose Sifuentes-Osornio", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + }, + { + "author_name": "Carlos A. Aguilar-Salinas", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "endocrinology" + }, { "rel_doi": "10.1101/2021.03.16.21253652", "rel_title": "Within-Day Variability of SARS-CoV-2 RNA in Municipal Wastewater Influent During Periods of Varying COVID-19 Prevalence and Positivity", @@ -858810,161 +859588,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.19.21253328", - "rel_title": "Accelerated RNA detection using tandem CRISPR nucleases", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253328", - "rel_abs": "Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided recognition of RNA that triggers cleavage and release of a fluorescent reporter molecule1,2, but long reaction times hamper sensitivity and speed when applied to point-of-care testing. Here we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of [~]30 RNA copies/microliter in 20 minutes. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that detected SARS-CoV-2 RNA from nasopharyngeal samples with PCR-derived Ct values up to 29 in microfluidic chips, using a compact imaging system. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables direct RNA detection in a format amenable to point-of-care infection diagnosis, as well as to a wide range of other diagnostic or research applications.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Tina Y. Liu", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Gavin J. Knott", - "author_inst": "Monash University, VIC 3800, Australia" - }, - { - "author_name": "Dylan C.J. Smock", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "John J. Desmarais", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Sungmin Son", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Abdul Bhuiya", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Shrutee Jakhanwal", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Noam Prywes", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Shreeya Agrawal", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Mar\u00eda D\u00edaz de Le\u00f3n Derby", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Neil A. Switz", - "author_inst": "San Jos\u00e9 State University, San Jos\u00e9, CA, USA" - }, - { - "author_name": "Maxim Armstrong", - "author_inst": "Lawrence Berkeley National Laboratory, Berkeley, CA, USA" - }, - { - "author_name": "Andrew R. Harris", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Emeric J. Charles", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Brittney W. Thornton", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Parinaz Fozouni", - "author_inst": "Gladstone Institutes, San Francisco, CA, USA" - }, - { - "author_name": "Jeffrey Shu", - "author_inst": "Gladstone Institutes, San Francisco, CA, USA" - }, - { - "author_name": "Stephanie I. Stephens", - "author_inst": "Gladstone Institutes, San Francisco, CA, USA" - }, - { - "author_name": "G. Renuka Kumar", - "author_inst": "Gladstone Institutes, San Francisco, CA, USA" - }, - { - "author_name": "Chunyu Zhao", - "author_inst": "Chan-Zuckerberg Biohub, San Francisco, CA, USA" - }, - { - "author_name": "Amanda Mok", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Anthony T. Iavarone", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Arturo M. Escajeda", - "author_inst": "Wainamics Inc., Pleasanton, CA, USA" - }, - { - "author_name": "Roger McIntosh", - "author_inst": "Wainamics Inc., Pleasanton, CA, USA" - }, - { - "author_name": "Shin E. Kim", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Eli J. Dugan", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "- IGI Testing Consortium", - "author_inst": "" - }, - { - "author_name": "Katherine S. Pollard", - "author_inst": "Gladstone Institutes, San Francisco, CA, USA" - }, - { - "author_name": "Ming X. Tan", - "author_inst": "Wainamics Inc., Pleasanton, CA, USA" - }, - { - "author_name": "Melanie Ott", - "author_inst": "Gladstone Institutes, San Francisco, CA, USA" - }, - { - "author_name": "Daniel A. Fletcher", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Liana F. Lareau", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Patrick D. Hsu", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "David F. Savage", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Jennifer A. Doudna", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.15.21253542", "rel_title": "Comparison between one and two dose SARS-CoV-2 vaccine prioritisation for a fixed number of vaccine doses", @@ -859185,6 +859808,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.21.21254047", + "rel_title": "Factors influencing COVID-19 vaccination uptake in an elderly sample in Poland", + "rel_date": "2021-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.21.21254047", + "rel_abs": "BackgroundsThis research represents an investigation into potential predictors for the uptake of the COVID-19 vaccination in Poland, following the instigation of policies to encourage the over-seventies to be vaccinated.\n\nMethodsIndividuals participated in cross-sectional structured interviews. 1427 respondents were questioned for determining vaccination uptake, revealing attitudes regarding vaccination, where information was sourced from, health status and behavior, demographics and socio-economic profiles.\n\nResultsSelected predictors for acceptance of the vaccination were: being talked through the importance of the vaccination and potential side-effects by a medical professional; sharing living space with others; having a high ranking occupation; suffering from chronic illnesses; being able to access medical services by driving or walking rather than using public transport or relying on others. Those who opted not to be vaccinated most frequently justify their decision by saying that they were concerned about the efficacy of the vaccine or that they were worried about side-effects.\n\nConclusionsIt appears that the current nationwide campaign has successfully raised awareness regarding the vaccine, but this research indicates that a more information-based campaign, focusing on evidence of the vaccines efficacy and the non-serious nature of all side-effects, could lead to improved uptake of the COVID-19 vaccine.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Marta Malesza", + "author_inst": "University of Economics and Human Sciences in Warsaw" + }, + { + "author_name": "Magdalena Bozym", + "author_inst": "Military Academy Hospital, Warsaw, Poland" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.21.21254068", "rel_title": "Determinants of COVID-19 outcomes: A systematic review.", @@ -861108,53 +861754,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.19.21254000", - "rel_title": "Evaluating the neutralizing ability of a CpG-adjuvanted S-2P subunit vaccine against SARS-CoV-2 Variants of Concern", - "rel_date": "2021-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21254000", - "rel_abs": "Vaccination is currently the best weapon to control the COVID-19 pandemic. However, an alarming number of novel variants termed Variants of Concern (VoC) were found to harbor mutations that diminished the neutralizing capacity of antibodies elicited by the vaccines. We have investigated the neutralizing titers of antibodies from sera of humans and rats immunized with the MVC-COV1901 vaccine against pseudoviruses coated with the wildtype, D614G, B.1.1.7, or B.1.351 spike proteins. Rats vaccinated with two doses of adjuvanted S-2P retained neutralization activities against the B.1.351 variant, albeit with a slight reduction compared to wildtype. Phase 1 vaccinated subjects showed more reduced neutralization abilities against the B.1.351 variant. The study is among the first, to our knowledge, to demonstrate dose-dependent neutralizing responses against VoCs, particularly against B.1.351, from different doses of antigen in a clinical trial for a subunit protein COVID-19 vaccine. The appearance of vaccine escape variants is a growing concern facing many current COVID-19 vaccines and therapeutics. Strategies should be adopted against the ever-changing nature of these variants. The observations of this study grant us valuable insight into preemptive strikes against current and future variants.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Chia-En Lien", - "author_inst": "Medigen Vaccine Biologics Corporation; Institute of Public Health, National Yang-Ming Chiao Tung University" - }, - { - "author_name": "Tsun-Yung Kuo", - "author_inst": "Medigen Vaccine Biologics Corporation; Department of Biotechnology and Animal Science, National Ilan University" - }, - { - "author_name": "Yi-Jiun Lin", - "author_inst": "Medigen Vaccine Biologics Corporation" - }, - { - "author_name": "Wei-Cheng Lian", - "author_inst": "Medigen Vaccine Biologics Corporation" - }, - { - "author_name": "Meei-Yun Lin", - "author_inst": "Medigen Vaccine Biologics Corporation" - }, - { - "author_name": "Luke Tzu Chi Liu", - "author_inst": "Medigen Vaccine Biologics Corp" - }, - { - "author_name": "Yu-Chi Chou", - "author_inst": "Biomedical Translation Research Center (BioTReC), Academia Sinica" - }, - { - "author_name": "Charles Chen", - "author_inst": "Medigen Vaccine Biologics Corporation" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.03.19.21253991", "rel_title": "Lives Saved from Age-Prioritised COVID-19 Vaccination", @@ -861283,6 +861882,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.03.19.21253425", + "rel_title": "COVID 19 Vaccine Perceptions in the New York State Intellectual and Developmental Disabilities Community", + "rel_date": "2021-03-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253425", + "rel_abs": "BackgroundPeople with intellectual and developmental disabilities (IDD) are at disproportionate risk for severe COVID-19 outcomes, particularly those living in congregate care settings. Yet, there is limited data on vaccine perceptions in the disability community.\n\nObjectiveTo explore COVID-19 vaccine perceptions in individuals with IDD, their family members, and those who work with them, to inform a statewide vaccine information and messaging project.\n\nMethodsA national survey, adapted for the IDD community, was distributed to a convenience sample of IDD organizations throughout New York State, in five languages. Constructs included vaccine intention, reasons for vaccine hesitancy, and trusted sources of vaccine information. Zip code data were used to map respondent location and vaccine preferences.\n\nResultsOf n= 825 respondents, approximately 75% intended to or had received the vaccine, across roles (i.e., people with disabilities, family members, direct care workers) and racial/ethnic groups. Greater vaccine hesitancy was reported in younger individuals and those making decisions on behalf of a person with IDD. Concerns included side effects and the swiftness of vaccine development. Black and Hispanic participants had heightened concerns about being an \"experiment\" for the vaccine. Trusted sources of information included healthcare providers and family members. Respondents who intended/got the vaccine were distributed throughout the state.\n\nConclusionsVaccine preferences in this New York State disability community sample align with national data. Identified concerns suggest the need for community education that addresses misperceptions. Age and race differences in perspectives highlight the need for tailored education, delivered by trusted messengers.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Suzannah Iadarola", + "author_inst": "University of Rochester Medical Center, Director, Strong Center for Developmental Disabilities" + }, + { + "author_name": "Joanne Siegel", + "author_inst": "Einstein College of Medicine-Montefiore Medical Center" + }, + { + "author_name": "Qi Gao", + "author_inst": "Einstein College of Medicine" + }, + { + "author_name": "Kathleen McGrath", + "author_inst": "Einstein College of Medicine" + }, + { + "author_name": "Karen Bonuck", + "author_inst": "Einstein College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.21.21254048", "rel_title": "Factors informing healthcare workers' willingness to work during the COVID-19 pandemic", @@ -863273,6 +863907,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2021.03.19.21253962", + "rel_title": "The effects of physical distancing and lockdown to restrain SARS-CoV-2 outbreak in the Italian Municipality of Cogne", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253962", + "rel_abs": "The outbreak of SARS-CoV-2 started in Wuhan, China, and is now a pandemic. An understanding of the prevalence and contagiousness of the disease, and of whether the strategies used to contain it to date have been successful, is important for understanding future containment strategies. One strategy for controlling the spread of SARS-CoV-2 is to adopt strong social distancing policies. The Municipality of Cogne (I), adopted strict lockdown rules from March 4, 2020 up to May 18, 2020. This first wave of the pandemic impressed by the extremely low impact of the SARS-CoV-2 on the locals, compared to the number accused on all the Italian territory. Starting from October 2020 up to the end of December, when the second wave hit Italy and Cogne territory, heavier effects were observed. In order to cast light on the effectiveness of the adopted strategy 74,5% of the local population underwent to a blood screening to detect IgM and IgG antibodies and after six months all the people tested positive were again investigated to establish the longitudinal changes in antibodies level. Moreover, within the context of this survey a rare and interesting case of secondary infection has been identified and here presented.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Gianpiero Gervino", + "author_inst": "University of Torino" + }, + { + "author_name": "Fabio Truc", + "author_inst": "University of Torino" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.03.18.21253881", "rel_title": "A Prospective Study of Long-Term Outcomes Among Hospitalized COVID-19 Patients with and without Neurological Complications", @@ -865129,33 +865786,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.19.21253980", - "rel_title": "Analysis of Thrombotic Adverse Reactions of COVID-19 AstraZeneca Vaccine reported to EudraVigilance database", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253980", - "rel_abs": "The development of safe, effective, affordable vaccines against COVID-19 remains the cornerstone to mitigating this pandemic. Early December 2020, multiple research groups had designed potential vaccines. From 11 March 2021, several European countries temporarily suspended the use of the Oxford-AstraZeneca vaccine amid reports of blood clot events and death of a vaccinated person, despite the European Medicines Agency and the World Health Organization assurance that there was no indication that vaccination was linked. This study aimed to identify and analyse the thrombotic adverse reactions associated with Oxford-AstraZeneca vaccine. This was a retrospective descriptive study using spontaneous reports submitted to the EudraVigilance database in the period from 17 February to 12 March 2021. There were 54,571 adverse reaction reports of which 28 were associated with thrombotic adverse reactions. Three fatalities were related to Pulmonary Embolism; 1 fatality to Thrombosis. With 17 million people having had the AstraZeneca vaccine, these are extremely rare events. The EMAs Pharmacovigilance Risk Assessment Committee (18 March 2021) concluded that the vaccine was safe, effective and the benefits outweighed the risks. Conducting further analyses based on more detailed thrombotic adverse event reports, including patients characteristics and comorbidities, may enable assessment of the causality with higher specificity.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mansour Tobaiqy", - "author_inst": "Associate Professor, Department of Pharmacology, College of Medicine, University of Jeddah, Jeddah, Saudi Arabia" - }, - { - "author_name": "Hajer Elkout", - "author_inst": "Department of Family and Community Medicine, Medical faculty, University of Tripoli, Tripoli, Libya" - }, - { - "author_name": "Katie MacLure", - "author_inst": "Independent Research Consultant, Aberdeen, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.16.21251969", "rel_title": "COVID-19 IN IRAQ, THE RURAL INITIATION (AL-MUTHANNA PROVINCE AS AN EXAMPLE)", @@ -865803,6 +866433,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.19.21253974", + "rel_title": "Data-driven estimate of SARS-CoV-2 herd immunity threshold in populations with individual contact pattern variations", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253974", + "rel_abs": "The development of efficacious vaccines has made it possible to envision mass vaccination programs aimed at suppressing SARS-CoV-2 transmission around the world. Here we use a data-driven age-structured multilayer representation of the population of 34 countries to estimate the disease induced immunity threshold, accounting for the contact variability across individuals. We show that the herd immunization threshold of random (un-prioritized) mass vaccination programs is generally larger than the disease induced immunity threshold. We use the model to test two additional vaccine prioritization strategies, transmission-focused and age-based, in which individuals are inoculated either according to their behavior (number of contacts) or infection fatality risk, respectively. Our results show that in the case of a sterilizing vaccine the behavioral strategy achieves herd-immunity at a coverage comparable to the disease-induced immunity threshold, but it appears to have inferior performance in averting deaths than the risk vaccination strategy. The presented results have potential use in defining the effects that the heterogeneity of social mixing and contact patterns has on herd immunity levels and the deployment of vaccine prioritization strategies.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Dan Lu", + "author_inst": "University of Zaragoza" + }, + { + "author_name": "Alberto Aleta", + "author_inst": "ISI Foundation" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Department of Epidemiology and Biostatistics, Indiana University School of Public Health, Bloomington" + }, + { + "author_name": "Romualdo Pastor-Satorras", + "author_inst": "Universitat Politecnica de Catalunya" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Northeastern University" + }, + { + "author_name": "Yamir Moreno", + "author_inst": "University of Zaragoza" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.18.21253931", "rel_title": "A convergence based assessment of relative differences in age-stratified susceptibility and infectiousness for SARS-CoV-2 variants of B.1.1.7 lineage", @@ -866991,53 +867660,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.17.20200246", - "rel_title": "Evidence for antibody as a protective correlate for COVID-19 vaccines", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.20200246", - "rel_abs": "Though eleven novel COVID-19 vaccines have demonstrated efficacy, additional affordable, scalable, and deliverable vaccines are needed to meet unprecedented global demand. With placebo-controlled efficacy trials becoming infeasible due to the roll out of licensed vaccines, a correlate of protection is urgently needed to provide a path for regulatory approval of novel vaccines. To assess whether antibody titers may reasonably predict efficacy, we evaluated the relationship between efficacy and in vitro neutralizing and binding antibodies of 7 vaccines for which sufficient data have been generated. Once calibrated to titers of human convalescent sera reported in each study, a robust correlation was seen between neutralizing titer and efficacy ({rho}= 0.79) and binding antibody titer and efficacy ({rho} = 0.93), despite geographically diverse study populations subject to different forces of infection and circulating variants, and use of different endpoints, assays, convalescent sera panels and manufacturing platforms. This correlation is strengthened by substituting post-hoc analyses for efficacy against the ancestral strain (D614G), where available. Together with an accumulating body of evidence from natural history studies and animal models, these results support the use of post-immunization antibody titers as the basis for establishing a correlate of protection for COVID-19 vaccines.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Kristen A Earle", - "author_inst": "Bill and Melinda Gates Foundation" - }, - { - "author_name": "Donna M Ambrosino", - "author_inst": "Independent Advisor" - }, - { - "author_name": "Andrew Fiore-Gartland", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "David Goldblatt", - "author_inst": "University College London" - }, - { - "author_name": "Peter B Gilbert", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "George R Siber", - "author_inst": "Independent Advisor" - }, - { - "author_name": "Peter Dull", - "author_inst": "Bill and Melinda Gates Foundation" - }, - { - "author_name": "Stanley A Plotkin", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.16.21253248", "rel_title": "Household transmission of SARS-CoV-2 R.1 lineage with spike E484K mutation in Japan", @@ -867345,6 +867967,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.16.21253731", + "rel_title": "The Spike-specific IgA in milk commonly-elicited after SARS-Cov-2 infection is concurrent with a robust secretory antibody response, exhibits neutralization potency strongly correlated with IgA binding, and is highly durable over time", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253731", + "rel_abs": "Approximately 10% of infants will experience COVID-19 illness requiring advanced care (1). A potential mechanism to protect this population could be provided by passive immunity through the milk of a previously infected mother. We and others have reported on the presence of SARS-CoV-2-specific antibodies in human milk (2-5). We now report the prevalence of SARS-CoV-2 IgA in the milk of 75 COVID-19-recovered participants, and find that 88% of samples are positive for Spike-specific IgA. In a subset of these samples, 95% exhibited robust IgA activity as determined by endpoint binding titer, with 50% considered high-titer. These IgA positive specimens were also positive for Spike-specific antibodies bearing the secretory component. Levels of IgA antibodies and antibodies bearing secretory component were shown to be strongly positively correlated. The secretory IgA response was dominant among the milk samples tested compared to the IgG response, which was present in 75% of samples and found to be of high-titer in only 13% of cases. Our IgA durability analysis using 28 paired samples, obtained 4-6 weeks and 4-10 months after infection, found that all samples exhibited persistently significant Spike-specific IgA, with 43% of donors exhibiting increasing IgA titers over time. Finally, COVID-19 and pre-pandemic control milk samples were tested for the presence of neutralizing antibodies; 6 of 8 COVID-19 samples exhibited neutralization of Spike-pseudotyped VSV (IC50 range, 2.39 - 89.4ug/mL) compared to 1 of 8 controls. IgA binding and neutralization capacities were found to be strongly positively correlated. These data are highly relevant to public health, not only in terms of the protective capacity of these antibodies for breastfed infants, but also for the potential use of such antibodies as a COVID-19 therapeutic, given that secretory IgA is highly stable not only in milk and the infant mouth and gut, but in all mucosa including the gastrointestinal tract, upper airway, and lungs (6).", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alisa Fox", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jessica Marino", + "author_inst": "University of California, Merced" + }, + { + "author_name": "Fatima Amanat", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kasopefoluwa Y. Oguntuyo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jennifer Hahn-Holbrook", + "author_inst": "University of California, Merced" + }, + { + "author_name": "Benhur Lee", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Susan Zolla-Pazner", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Rebecca L Powell", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.03.17.21252673", "rel_title": "Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, Greece", @@ -868941,45 +869614,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2021.03.15.21253509", - "rel_title": "Lessons learned from the resilience of Chinese hospitals to the COVID-19 pandemic: a scoping review.", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253509", - "rel_abs": "As the SARS-CoV-2 pandemic has brought huge strain on hospitals worldwide, the resilience shown by Chinas hospitals appears to have been a critical factor in their successful response to the pandemic. This paper aims to determine the key findings, recommendations and lessons learned in terms of hospital resilience during the pandemic, as well as the quality and limitations of research in this field at present.\n\nWe conducted a scoping review of evidence on the resilience of hospitals in China during the COVID-19 crisis in the first half of 2020. Two online databases (the CNKI and WHO databases) were used to identify papers meeting the eligibility criteria, from which we selected 59 publications (English: n= 26; Chinese: n= 33). After extracting the data, we present an information synthesis using a resilience framework.\n\nWe found that much research was rapidly produced in the first half of 2020, describing certain strategies used to improve hospital resilience, particularly in three key areas: human resources; management and communication; and security, hygiene and planning. Our search revealed that considerable attention was focused on interventions related to training, healthcare worker well-being, e-health/ telemedicine, and work organization, while other areas, such as hospital financing, information systems and healthcare infrastructure, were less well represented in the literature.\n\nWe identified a number of lessons learned regarding how Chinas hospitals have maintained resilience when confronted with the SARS-CoV-2 pandemic. However, we also noted that the literature was dominated by descriptive case studies, often lacking consideration of methodological limitations, and that there was a lack of both highly-focused research on individual interventions and holistic research that attempted to unite the topics within a resilience framework. Research on Chinese hospitals would benefit from a greater range of analysis in order to draw more nuanced and contextualised lessons from the responses to the crisis.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jack Stennett", - "author_inst": "CEPED, Institute for Research on Sustainable Development, IRD-Universite de Paris" - }, - { - "author_name": "Renyou Hou", - "author_inst": "CEPED, Institute for Research on Sustainable Development, IRD-Universite de Paris" - }, - { - "author_name": "Lola Traverson", - "author_inst": "CEPED, Institute for Research on Sustainable Development, IRD-Universite de Paris" - }, - { - "author_name": "Valery Ridde", - "author_inst": "CEPED, Institute for Research on Sustainable Development, IRD-Universite de Paris" - }, - { - "author_name": "Kate Zinszer", - "author_inst": "Centre de recherche en sante publique, Montreal, Canada / Universite de Montreal" - }, - { - "author_name": "Fanny Chabrol", - "author_inst": "CEPED, Institute for Research on Sustainable Development, IRD-Universite de Paris" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.03.15.21253646", "rel_title": "Real-World Effectiveness and Tolerability of Monoclonal Antibodies for Ambulatory Patients with Early COVID-19", @@ -869295,6 +869929,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.13.21253527", + "rel_title": "PD-1highCXCR5-CD4+ Peripheral Helper T (Tph) cells Promote Tissue-Homing Plasmablasts in COVID-19", + "rel_date": "2021-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.13.21253527", + "rel_abs": "A dysregulated immune response against coronavirus-2 (SARS-CoV-2) plays a critical role in the outcome of patients with coronavirus disease 2019 (COVID-19). A significant increase in circulating plasmablasts is characteristic of COVID-19 though the underlying mechanisms and its prognostic implications are not known. Here, we demonstrate that in the acute phase of COVID-19, activated PD-1highCXCR5-CD4+ T cells, peripheral helper T cells, (Tph) are significantly increased and promote inflammatory tissue-homing plasmablasts in patients with stable but not severe COVID-19. Analysis of scRNA-seq data revealed that plasmablasts in stable patients express higher levels of tissue-homing receptors including CXCR3. The increased Tph cells exhibited \"B cell help\" signatures similar to that of circulating T follicular helper (cTfh) cells and promoted B cell differentiation in vitro. Compared with cTfh cells, Tph cells produced more IFN{gamma}, inducing tissue-homing chemokine receptors on plasmablasts. Finally, expansion of activated Tph cells was correlated with the frequency of CXCR3+ plasmablasts in the acute phase of patients with stable disease. Our results demonstrate a novel role for Tph cells in acute viral immunity by inducing ectopic, antibody secreting plasmablasts.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Hiromitsu Asashima", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Subhasis Mohanty", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Michela Comi", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "William E Ruff", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Kenneth B Hoehn", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Patrick Wong", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Inessa Cohen", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Sarah Coffey", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Khadir Raddassi", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Omkar Chaudhary", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Avraham Unterman", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Brinda Emu", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Steven H Kleinstein", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Ruth R Montgomery", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Charles S Dela Cruz", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Naftali Kaminski", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Albert C Shaw", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "David A Hafler", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Tomokazu S Sumida", + "author_inst": "Yale School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.03.15.21253619", "rel_title": "COVID-19 with early neurological and cardiac thromboembolic phenomena--timeline of incidence and clinical features", @@ -870543,129 +871272,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.05.21251413", - "rel_title": "THE EFFECTIVENESS OF ACB-IP 1.0 UNIVERSAL PATHOGEN FREE CONCENTRATED COCKTAIL CONVALESCENT PLASMA IN COVID-19 INFECTION", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21251413", - "rel_abs": "IntroductionThe efficacy of SARS-CoV2 standard single donor convalescent plasma varied according to the application time and most importantly the amount of antibody that is administered. Single donor plasma has some drawbacks; such as the insufficient levels of neutralizing antibody activities, the requirements of blood group compatibility, and the risk of infection transmission. In this study, the efficacy and safety of pathogen inactivated, isohemagglutinin-depleted (concentrated) and pooled convalescent plasma was investigated.\n\nMethodsIn this study, ACB-IP 1.0 convalescent plasma product was prepared as follows; first, convalescent plasma was collected from different donors, then pathogen-inactivation was carried-out, and isohemagglutinins were cryodepleted, respectively. Finally, concentrated convalescent plasma product was pooled and stored until use.\n\nA total of sixteen patients were treated with two different convalescent plasma products. Nine patients were treated with standard single donor convalescent plasma and seven were treated with pathogen-free, concentrated, pooled convalescent plasma (ACB-IP 1.0) between 01 March 2020 and 31 December 2020.\n\nThe outcomes of these two plasma products were compared regarding SARS-CoV2 antibody titers, neutralizing antibody activities, length of hospitalization and mortality rates.\n\nResultsFive out of six single donor plasma SARS-CoV2 antibody titers remained below 12 s/co, but the antibody titers of all ACB-IP 1.0 plasma were above 12 s/co. SARS-CoV2 total antibody titers of ACB-IP 1.0 plasma were statistically higher than the antibody titers of single donor plasma. Mean total plasma neutralizing antibody activity of ACB-IP 1.0 plasma (1.5421) was found statistically higher than single donor plasma (0.9642) in 1:256 dilution ({rho}=0.0087)\n\nThe mortality rate of the patients treated with ACB-IP 1.0 plasma showed statistically lower (p: 0,033) than the patients treated with single donor plasma. The administration of either single donor plasma or ACB-IP 1.0 plasma to the patients within eight days significantly shortened the length of hospitalization compared to administration of either plasma to the patients later than eight days ({rho}= 0,0021)\n\nDiscussionPathogen-free, concentrated, pooled convalescent plasma may resolve the bias in SARS-CoV2 antibody titers and neutralizing antibody activities, without requiring blood group compatibility that allows patient accessibility in a shorter time and has safe plasma characteristic. This study indicates that ACB-IP 1.0 may be a superior product compared to standard single donor plasma.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Cansu Hemsinlioglu", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Nil Banu Pelit", - "author_inst": "Acibadem Labmed Blood Banks" - }, - { - "author_name": "Koray Yalcin", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Omur Selin Gunaydin", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Nihal Ozturk Sahin", - "author_inst": "Acibadem Labmed Blood Banks" - }, - { - "author_name": "Esra Savas Karagacli", - "author_inst": "Acibadem Altunizade Hospital, Apheresis Center" - }, - { - "author_name": "Omer Elibol", - "author_inst": "Acibadem Altunizade Hospital, Apheresis Center" - }, - { - "author_name": "Sefa Onur Demir", - "author_inst": "Acibadem Altunizade Hospital, Apheresis Center" - }, - { - "author_name": "Evren Safak", - "author_inst": "Acibadem Altunizade Hospital, Apheresis Center" - }, - { - "author_name": "Raife Dilek Turan", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Goncagul Celebi", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Miyase Ezgi Kocaoglu", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Gozde Sir Karakus", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Bulut Yurtsever", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Cihan Tastan", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Selen Abanuz", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Didem Cakirsoy", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Derya Dilek Kancagi", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Zeynep Torun", - "author_inst": "Acibadem Altunizade Hospital, Apheresis Center" - }, - { - "author_name": "Utku Seyis", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Muhammer Elek", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - }, - { - "author_name": "Rehile Zengin", - "author_inst": "Acibadem Altunizade Hospital Infectious Disease Unit, Istanbul" - }, - { - "author_name": "Ayse Sesin Kocagoz", - "author_inst": "Acibadem Altunizade Hospital Infectious Disease Unit, Istanbul" - }, - { - "author_name": "Caglar Cuhadaroglu", - "author_inst": "Acibadem Altunizade Hospital Intensive Care Unit" - }, - { - "author_name": "Nur Birgen", - "author_inst": "Acibadem Altunizade Hospital" - }, - { - "author_name": "Siret Ratip", - "author_inst": "Acibadem Altunizade Hospital Bone Marrow Transplantation Unit" - }, - { - "author_name": "Ercument Ovali", - "author_inst": "Acibadem Labcell Cellular Therapy Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.17.21253788", "rel_title": "High risk of patient self-inflicted lung injury in COVID-19 with frequently encountered spontaneous breathing patterns: a computational modelling study", @@ -871041,6 +871647,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.16.435705", + "rel_title": "Identification of ACE2 mutations that modulate SARS-CoV-2 spike binding across multiple mammalian species", + "rel_date": "2021-03-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.16.435705", + "rel_abs": "Understanding how SARS-CoV-2 interacts with different mammalian angiotensin-converting enzyme II (ACE2) cell entry receptors elucidates determinants of virus transmission and facilitates development of vaccines for humans and animals. Yeast display-based directed evolution identified conserved ACE2 mutations that increase spike binding across multiple species. Gln42Leu increased ACE2-spike binding for human and four of four other mammalian ACE2s; Leu79Ile had a effect for human and three of three mammalian ACE2s. These residues are highly represented, 83% for Gln42 and 56% for Leu79, among mammalian ACE2s. The above findings can be important in protecting humans and animals from existing and future SARS-CoV-2 variants.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Pete Heinzelman", + "author_inst": "UW-Madison" + }, + { + "author_name": "Jonathan Greenhalgh", + "author_inst": "University of Wisconsin--Madison" + }, + { + "author_name": "Philip A Romero", + "author_inst": "UW-Madison" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.03.16.434488", "rel_title": "SARS-CoV-2 Spike receptor-binding domain with a G485R mutation in complex with human ACE2", @@ -872813,29 +873446,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.13.21253485", - "rel_title": "Impact of School Reopening on Pandemic Spread: A Case Study using an Agent-Based Model for COVID-19", - "rel_date": "2021-03-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.13.21253485", - "rel_abs": "This article examines the impact of partial/full reopening of school/college campuses on the spread of a pandemic using COVID-19 as a case study. The study uses an agent-based simulation model that replicates community spread in an urban region of U.S.A. via daily social mixing of susceptible and infected individuals. Data representing population demographics, SARS-CoV-2 epidemiology, and social interventions guides the models behavior, which is calibrated and validated using data reported by the government. The model indicates a modest but significant increase (8.15 %) in the total number of reported cases in the region for a complete (100%) reopening compared to keeping schools and colleges fully virtual. For partial returns of 75% and 50%, the percent increases in the number of reported cases are shown to be small (2.87% and 1.26%, respectively) and statistically insignificant. The AB model also predicts that relaxing the stringency of the school safety protocol for sanitizing, use of mask, social distancing, testing, and quarantining and thus allowing the school transmission coefficient to double may result in a small increase in the number of reported infected cases (2.14%). Hence for pandemic outbreaks from viruses with similar characteristics as for SARS-CoV-2, keeping the schools and colleges open with a modest campus safety protocol and in-person attendance below a certain threshold may be advisable.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Hanisha Anand Tatapudi", - "author_inst": "University of South Florida" - }, - { - "author_name": "Tapas K Das", - "author_inst": "University of South Florida" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.09.21253012", "rel_title": "The local and systemic response to SARS-CoV-2 infection in children and adults", @@ -873267,6 +873877,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.11.21253404", + "rel_title": "COVID-19 Underreporting and its Impact on Vaccination Strategies", + "rel_date": "2021-03-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253404", + "rel_abs": "We present a novel methodology for the stable rate estimation of hospitalization and death related to the Corona Virus Disease 2019 (COVID-19) using publicly available reports from various distinct communities. These rates are then used to estimate underreported infections on the corresponding areas by making use of reported daily hospitalizations and deaths. The impact of underreporting infections on vaccination strategies is estimated under different disease-transmission scenarios using a Susceptible-Exposed-Infective-Removed-like (SEIR) epidemiological model.\n\nOne sentence SummaryUsing a novel methodology, we estimate COVID-19 underreporting from public data, quantifying its impact on vaccination.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vinicius V. L. Albani", + "author_inst": "Universidade Federal de Santa Catarina" + }, + { + "author_name": "Jennifer Loria", + "author_inst": "Instituto Nacional de Matematica Pura e Aplicada and Universidad de Costa Rica" + }, + { + "author_name": "Eduardo Massad", + "author_inst": "Fundacao Getulio Vargas" + }, + { + "author_name": "Jorge P. Zubelli", + "author_inst": "Khalifa University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.12.21253000", "rel_title": "Novel highly divergent SARS-CoV-2 lineage with the Spike substitutions L249S and E484K", @@ -875271,53 +875912,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.13.21253500", - "rel_title": "Engagement with daily testing instead of self-isolating in contacts of confirmed cases of SARS-CoV-2.", - "rel_date": "2021-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.13.21253500", - "rel_abs": "BackgroundIn December 2020, Public Health England with NHS Test and Trace initiated a pilot study in which close contacts of people with confirmed COVID-19 were given the option to carryout lateral flow device antigen tests at home, as an alternative to self-isolation for 10-14 days. In this study, we evaluated acceptability of and engagement with daily testing, and assessed levels of adherence to the rules relating to behaviour following positive or negative test results.\n\nMethodsWe conducted a service evaluation of a pilot study, involving an online cross-sectional survey offered to adult (> 18 years) contacts of confirmed COVID-19 cases who were invited to participate in seven days of daily testing instead of isolation. We used a comparison group of contacts who were not offered testing and performed self-isolation. Herein, we examine survey responses from a subset of those who took part in the pilot study and who responded to the evaluation questionnaire.\n\nResultsAcceptability of daily testing was lower among survey respondents who were not offered the option of having it and among people from ethnic minority groups. Overall, 52% of respondents reported being more likely to share details of people that they had been in contact with following a positive test result, if they knew that their contacts would be offered the option of daily testing. Only 2% reported that they would be less likely to provide details of their contacts. On the days that they were trying to self-isolate, 19% of participants reported that they left the house, with no significant demographic group differences. Following a negative test, 13% of respondents reported that they increased their contacts, but most (58%) reported having fewer risky contacts.\n\nConclusionsOur data suggest that daily testing is potentially acceptable, and may facilitate sharing contact details of close contacts among those who test positive for COVID-19, and promote adherence to self-isolation. A better understanding is needed of how to make this option more acceptable for all households. The impact of receiving a negative test on behaviour remains a risk that needs to be monitored and mitigated by appropriate messaging. Future research should examine attitudes and behaviour in a context where infection levels are lower, testing is more familiar, much of the population has been vaccinated and restrictions on activity have been reduced.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Alex F Martin", - "author_inst": "King's College London" - }, - { - "author_name": "Sarah Denford", - "author_inst": "University of Bristol" - }, - { - "author_name": "Nicola Love", - "author_inst": "Public Health England" - }, - { - "author_name": "Derren Ready", - "author_inst": "Public Health England" - }, - { - "author_name": "Isabel Oliver", - "author_inst": "Public Health England" - }, - { - "author_name": "Richard Amlot", - "author_inst": "Public Health England" - }, - { - "author_name": "G. James Rubin", - "author_inst": "King's College London" - }, - { - "author_name": "Lucy Yardley", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.08.21252901", "rel_title": "The causal effect of serum vitamin D concentration on COVID-19 susceptibility, severity and hospitalization traits: a Mendelian randomization study", @@ -875601,6 +876195,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.12.21253484", + "rel_title": "Limits of lockdown: characterising essential contacts during strict physical distancing", + "rel_date": "2021-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253484", + "rel_abs": "COVID-19 has exposed health inequalities within countries and globally. The fundamental determining factor behind an individuals risk of infection is the number of social contacts they make. In many countries, physical distancing measures have been implemented to control transmission of SARS-CoV-2, reducing social contacts to a minimum. Characterising unavoidable social contacts is key for understanding the inequalities behind differential risks and planning vaccination programmes. We utilised an existing English longitudinal birth cohort, which is broadly representative of the wider population (n=6807), to explore social contact patterns and behaviours when strict physical distancing measures were in place during the UKs first lockdown in March-May 2020. Essential workers, specifically those in healthcare, had 4.5 times as many contacts as non-essential workers [incident rate ratio = 4.42 (CI95%: 3.88-5.04)], whilst essential workers in other sectors, mainly teaching and the police force had three times as many contacts [IRR = 2.84 (2.58-3.13)]. The number of individuals in a household, which is conflated by number of children, increases essential social contacts by 40%. Self-isolation effectively reduces numbers of contacts outside of the home, but not entirely. Together, these findings will aid the interpretation of epidemiological data and impact the design of effective SARS-CoV-2 control strategies, such as vaccination, testing and contact tracing.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Amy C Thomas", + "author_inst": "University of Bristol" + }, + { + "author_name": "Leon Danon", + "author_inst": "University of Bristol" + }, + { + "author_name": "Hannah Christensen", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kate Northstone", + "author_inst": "University of Bristol" + }, + { + "author_name": "Daniel Smith", + "author_inst": "University of Bristol" + }, + { + "author_name": "Emily J Nixon", + "author_inst": "University of Bristol" + }, + { + "author_name": "Adam Trickey", + "author_inst": "University of Bristol" + }, + { + "author_name": "Gibran Hemani", + "author_inst": "University of Bristol" + }, + { + "author_name": "Sarah Sauchelli", + "author_inst": "NIHR Bristol Biomedical Research Centre, University of Bristol" + }, + { + "author_name": "Adam Finn", + "author_inst": "University of Bristol" + }, + { + "author_name": "Nicholas J Timpson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Ellen Brooks-Pollock", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.12.21253493", "rel_title": "Seroprevalence of Antibodies to SARS-CoV-2 among Health Care Workers in Kenya", @@ -877305,37 +877962,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.03.08.21253150", - "rel_title": "Maximisation of open hospital capacity under shortage of SARS-CoV-2 vaccines", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253150", - "rel_abs": "MotiveThe Covid-19 pandemic has led to the novel situation that hospitals must prioritise staff for a vaccine rollout while there is acute shortage of the vaccine. In spite of the availability of guidelines from state agencies, there is partial confusion about what an optimal rollout plan is. This study investigates effects in a hospital model under different rollout schemes.\n\nMethodsA simulation model is implemented in VBA and studied for parameter variation. The implemented code is available as open access supplement.\n\nMain resultsA rollout scheme assigning vaccine doses to staff primarily by staffs pathogen exposure maximises the predicted open hospital capacity when compared to a rollout based on hierarchical prioritisation. The effect increases under resource scarcity and increasing disease activity. Nursing staff benefits most from an exposure focused rollout.\n\nConclusionsThe model employs SARS-CoV-2 parameters; nonetheless, effects observable in the model are transferable to other infectious diseases. Necessary future prioritisation plans need to consider pathogen characteristics and social factors.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Wolfram A Bosbach", - "author_inst": "Justus Liebig University of Giessen (Germany)" - }, - { - "author_name": "Martin Heinrich", - "author_inst": "Justus Liebig University of Giessen (Germany)" - }, - { - "author_name": "Rainer Kolisch", - "author_inst": "Technical University of Munich (Germany)" - }, - { - "author_name": "Christian Heiss", - "author_inst": "Justus Liebig University of Giessen (Germany)" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2021.03.10.21252242", "rel_title": "Quantified Flu: an individual-centered approach to gaining sickness-related insights from wearable data", @@ -877603,6 +878229,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.10.21253260", + "rel_title": "Analytical and clinical performances of a SARS-CoV-2 S-RBD IgG assay: comparison with neutralization titers", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253260", + "rel_abs": "BackgroundSARS-CoV-2 serology presents an important role in understanding the virus epidemiology, in vaccine prioritization strategies and in convalescent plasma therapy. Immunoassays performances have to be accurately evaluated and correlated with neutralizing antibodies to be used as a surrogate measure of neutralizing activity. We investigate the analytical and clinical performance of a SARS-CoV-2 RBD IgG assay, automated on a high throughput platform, and the correlation of the antibodies (Ab) levels with the plaque reduction neutralization (PRNT50) Ab titers.\n\nMethodsA series of 546 samples were evaluated by SARS-CoV-2 RBD IgG assay (Snibe diagnostics), including 171 negative and 168 positive SARS-CoV-2 subjects and a further group of 207 subjects of the COVID-19 family clusters follow-up cohort.\n\nResultsAssay precision was acceptable at low and medium levels; linearity was excellent in all the measurement range. Considering specimens collected after 14 days post symptoms onset, overall sensitivity and specificity were 99.0% and 92.5%, respectively. A total of 281 leftover samples results of the PRNT50 test were available. An elevated correlation was obtained between the SARS-CoV-2 RBD IgG assay and the PRNT50 titer at univariate (rho = 0.689) and multivariate (rho = 0.712) analyses.\n\nConclusionsSARS-CoV-2 S-RBD IgG assay achieves elevated analytical and clinical performances, and a strong correlation with sera neutralization activity.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Andrea Padoan", + "author_inst": "university of padova" + }, + { + "author_name": "Francesco Bonfante", + "author_inst": "Istituto Zooprofilattico sperimentale delle venezie, legnaro, italy" + }, + { + "author_name": "Chiara Cosma", + "author_inst": "Department of Laboratory medicine, University-hospital of padova, italy" + }, + { + "author_name": "Costanza Di Chiara", + "author_inst": "Department of women's and children's health, university of padova" + }, + { + "author_name": "Laura Sciacovelli", + "author_inst": "Department of Laboratory Medicine, University-Hospital of Padova" + }, + { + "author_name": "Matteo Pagliari", + "author_inst": "Istituto zooprofilattico sperimentale delle venezie, legnaro, italy" + }, + { + "author_name": "Alessio Bortolami", + "author_inst": "Istituto zooprofilattico sperimentale delle venezie, legnaro, italy" + }, + { + "author_name": "Paola Costenaro", + "author_inst": "Department for Women's and Children's Health, University of Padova, Italy" + }, + { + "author_name": "Giulia Musso", + "author_inst": "Department of Laboratory Medicine, University-Hospital of Padova, Italy" + }, + { + "author_name": "Daniela Basso", + "author_inst": "University of Padova" + }, + { + "author_name": "Mario Plebani", + "author_inst": "University of Padova" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.10.21252711", "rel_title": "An In-House ELISA for SARS-CoV-2 RBD uncovers elevatedimmune response at higher altitudes", @@ -879119,77 +879804,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2021.03.10.21252851", - "rel_title": "Spread and sources of information and misinformation about COVID-19 early during the pandemic in a U.S. national cohort study", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21252851", - "rel_abs": "BackgroundEarly in the pandemic, misinformation about COVID-19 was spread on social media. The purpose of this study was to describe trusted sources of COVID-19 information and claims seen and believed about COVID-19 early in the pandemic among U.S. adults. Then, we assessed the impact of believing such claims on engaging in personal protective actions (PPA).\n\nMethodsWe used baseline data from the CHASING COVID Cohort (n = 7,070) collected March 28, 2020 to April 20, 2020 to describe trusted sources of COVID-19 information as well as claims circulating on social media that had been seen and believed. We used Poisson regression to determine the association of believing certain claims with engaging in a higher number of PPA.\n\nResultsThe top three trusted sources of COVID-19 information were the CDC (67.9%), the WHO (53.7%), and State Health Departments (53.0%). Several COVID-19 claims circulated on social media had been seen, e.g., that the virus was created in a laboratory (54.8%). Moreover, substantial proportions of participants indicated agreement with some of these claims. In multivariable regression, we found that belief in certain claims was associated with engaging in a higher number of PPA. For example, believing that paper masks would prevent transmission of the virus was associated with engaging in a higher number of protective actions ({beta} = 0.02, 95% CI: 0.004 - 0.046).\n\nConclusionsResults suggest the need for public health leadership on social media platforms to combat misinformation and supports social media as a tool to further public health interventions.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Drew A Westmoreland", - "author_inst": "CUNY Institute for Implementation Science in Population Health" - }, - { - "author_name": "Amanda Berry", - "author_inst": "CUNY Institute for Implementation Science in Population Health" - }, - { - "author_name": "Rebecca Zimba", - "author_inst": "CUNY Institute for Implementation Science in Population Health" - }, - { - "author_name": "Sarah Gorrell Kulkarni", - "author_inst": "CUNY Institute for Implementation Science in Population Health" - }, - { - "author_name": "Angela Parcesepe", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Andrew R Maroko", - "author_inst": "CUNY Graduate School of Public Health and Health Policy" - }, - { - "author_name": "Emily Poehlein", - "author_inst": "CUNY Institute for Implementation Science in Population Health" - }, - { - "author_name": "William You", - "author_inst": "CUNY Institute for Implementation Science in Population Health" - }, - { - "author_name": "Chloe Mirzayi", - "author_inst": "CUNY Institute for Implementation Science in Population Health; CUNY Graduate School of Public Health" - }, - { - "author_name": "Shivani Kochhar", - "author_inst": "CUNY Institute for Implementation Science in Population Health" - }, - { - "author_name": "McKaylee Robertson", - "author_inst": "CUNY Institute for Implementation Science in Population Health" - }, - { - "author_name": "Levi Waldron", - "author_inst": "CUNY Institute for Implementation Science in Population Health; CUNY Graduate School of Public Health" - }, - { - "author_name": "Christian Grov", - "author_inst": "CUNY Institute for Implementation Science in Population Health; CUNY Graduate School of Public Health" - }, - { - "author_name": "Denis Nash", - "author_inst": "City University of New York School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.10.21253280", "rel_title": "The impact of headache disorders on COVID-19 survival: a world population-based analysis", @@ -879429,6 +880043,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.10.21253322", + "rel_title": "A Dynamical Map to Describe Covid-19 Epidemics", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253322", + "rel_abs": "Nonlinear dynamics perspective is an interesting approach to describe COVID-19 epidemics, providing information to support strategic decisions. This paper proposes a dynamical map to describe COVID-19 epidemics based on the classical susceptible-exposed-infected-recovered (SEIR) differential model, incorporating vaccinated population. On this basis, the novel map represents COVID-19 discrete-time dynamics by adopting three populations: infected, cumulative infected and vaccinated. The map promotes a dynamical description based on algebraic equations with a reduced number of variables and, due to its simplicity, it is easier to perform parameter adjustments. In addition, the map description allows analytical calculations of useful information to evaluate the epidemic scenario, being important to support strategic decisions. In this regard, it should be pointed out the estimation of the number death cases, infectious rate and the herd immunization point. Numerical simulations show the model capability to describe COVID-19 dynamics, capturing the main features of the epidemic evolution. Reported data from Germany, Italy and Brazil are of concern showing the map ability to describe different scenario patterns that include multi-wave and plateaus behaviors. The effect of vaccination is analyzed considering different campaign strategies, showing its importance to control the epidemics.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Eduardo Villela M. dos Reis", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Marcelo A. Savi", + "author_inst": "Universidade Federal do Rio de Janeiro" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.10.21253259", "rel_title": "Evaluation of Measles Surveillance System amidst Covid 19 pandemic in Asutifi North District, Ahafo Region, Ghana.", @@ -880701,29 +881338,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.11.21253306", - "rel_title": "COVID-19 and Medical Education in Ghana: Assessing the Impact", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253306", - "rel_abs": "Medical education in Ghana has been affected in many ways by the onslaught of the COVID-19 pandemic. Though the pandemic has affected both preclinical and clinical segments of medical education, the effect has been felt more at the clinical stage. Medical students on vacation who started their clinical training abroad could not return to their destination of study to complete their programme because of COVID-19 linked travel restrictions. This qualitative study examined how COVID-19 impacted on teaching and learning at a public higher education institution offering clinical medical education in Ghana for over 200 medical students. These medical students were from three different higher education institutions with varied curriculum outcomes. Thus, for them to be considered as a single group required innovativeness on the part of administrators. Open-ended interviews were held with administrators and the outcome indicated that salient aspects of the clinical training process had been impacted. These included administration of clinical education, curriculum, student learning, student assessment and code of practice. As a result of the pandemic, student learning shifted from traditional face to face interaction to online learning at the beginning. Some of the administrative challenges that ensued included the need for reduced number of students per tutor and introduction of afternoon sessions with a limited budget. The paper concludes that COVID-19 has been disruptive to traditional medical education in Ghana. However, the novel learning processes may provide opportunities to increase access to medical education using a phased system of learning. The findings from this study should have implications for policy and contribute to the discourse on blended learning in medical education in Ghana while ensuring that quality is maintained in all instances.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Edward Asumanu", - "author_inst": "37 Military Hospital, Neghelli Barracks, Accra, Ghana" - }, - { - "author_name": "Linda Tsevi", - "author_inst": "School of Continuing and Distance Education, College of Education, University of Ghana," - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2021.03.11.21253384", "rel_title": "Automated Production of Research Data Marts from a Canonical Fast Healthcare Interoperability Resource (FHIR) Data Repository: Applications to COVID-19 Research", @@ -880959,6 +881573,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.11.21253367", + "rel_title": "SARS-CoV-2 specific immune-signature in direct contacts of COVID-19 cases protect them from contracting disease: A Retrospective Study", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253367", + "rel_abs": "The response to SARS-CoV-2 is largely impacted by the level of exposure and the status of immunity. The nature of protection shown by direct contacts of COVID-19 positive patients is quite intriguing to note. We aimed to study the immune differences reinforcing contact individuals in circumventing the disease. Our observation showed direct contacts of PCR positive patients developed elevated neutralizing antibody titres and cytokine levels. On the other hand, single cell data revealed differential usage of V(D)J genes and unique BCR clonotypes imparting protective immune signatures.\n\nTopicsserologic tests, immunoglobulin a, immunoglobulin g, immunoglobulin m, antibody titre; cytokine levels; virus neutralization; V(D)J sequencing; BCR clonotypes", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Sunil K. Raghav", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Kaushik Sen", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Arup Ghosh", + "author_inst": "Institute of Life Sciences" + }, + { + "author_name": "Sudeshna Datta", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Abdul Ahad", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Atimukta Jha", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Sanchari Chatterjee", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Sandhya Suranjika", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Soumya Sengupta", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Gargee Bhattacharya", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Omprakash Shriwas", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Kiran Avula", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Jayasingh Kshatri", + "author_inst": "ICMR-Regional Medical Research Center" + }, + { + "author_name": "Punit Prasad", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + }, + { + "author_name": "Ajay K. Parida", + "author_inst": "Institute of Life Sciences, Bhubaneswar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.09.21253218", "rel_title": "An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status", @@ -882271,29 +882960,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.12.21253136", - "rel_title": "I was facilitating everybody else's life. And mine had just ground to a halt: the COVID-19 pandemic and its impact on women in the UK", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253136", - "rel_abs": "A growing body of research has highlighted the disproportionately negative impact of the COVID-19 pandemic on women globally. This paper contributes to this work by interrogating the lived realities of 64 women in the UK through semi-structured interviews, undertaken during the first and second periods of lockdown associated with COVID-19 in 2020. Categorising the data by theme and type of gendered disadvantage, this paper explores the normative and policy-imposed constraints experienced by women in 2020, highlighting the role that government can and should proactively play in attending to gender inequalities throughout its COVID-19 response.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Asha Herten-Crabb", - "author_inst": "London School of Economics and Political Science" - }, - { - "author_name": "Clare Wenham", - "author_inst": "London School of Economics and Political Science (LSE)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.11.434872", "rel_title": "Chimeric spike mRNA vaccines protect against sarbecovirus challenge in mice", @@ -882612,6 +883278,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.03.11.434841", + "rel_title": "Antibody responses to SARS-CoV-2 mRNA vaccines are detectable in saliva", + "rel_date": "2021-03-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.11.434841", + "rel_abs": "Vaccines are critical for curtailing the COVID-19 pandemic (1, 2). In the USA, two highly protective mRNA vaccines are available: BNT162b2 from Pfizer/BioNTech and mRNA-1273 from Moderna (3, 4). These vaccines induce antibodies to the SARS-CoV-2 S-protein, including neutralizing antibodies (NAbs) predominantly directed against the Receptor Binding Domain (RBD) (1-4). Serum NAbs are induced at modest levels within [~]1 week of the first dose, but their titers are strongly boosted by a second dose at 3 (BNT162b2) or 4 weeks (mRNA-1273) (3, 4). SARS-CoV-2 is most commonly transmitted nasally or orally and infects cells in the mucosae of the respiratory and to some extent also the gastrointestinal tract (5). Although serum NAbs may be a correlate of protection against COVID-19, mucosal antibodies might directly prevent or limit virus acquisition by the nasal, oral and conjunctival routes (5). Whether the mRNA vaccines induce mucosal immunity has not been studied. Here, we report that antibodies to the S-protein and its RBD are present in saliva samples from mRNA-vaccinated healthcare workers (HCW). Within 1-2 weeks after their second dose, 37/37 and 8/8 recipients of the Pfizer and Moderna vaccines, respectively, had S-protein IgG antibodies in their saliva, while IgA was detected in a substantial proportion. These observations may be relevant to vaccine-mediated protection from SARS-CoV-2 infection and disease.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Thomas J. Ketas", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Devidas Chaturbhuj", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Victor Cruz Portillo", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Erik Francomano", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Encouse Golden", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Sharanya Chandrasekhar", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Gargi Debnath", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Randy Diaz Tapia", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Anila Yasmeen", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Wilhem Leconet", + "author_inst": "Genmab" + }, + { + "author_name": "Zhen Zhao", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Philip J.M. Brouwer", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Melissa M. Cushing", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Rogier Sanders", + "author_inst": "Amsterdam University Medical Center" + }, + { + "author_name": "Albert Cupo", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Per Johan Klasse", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Silvia C. Formenti", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "John P. Moore", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.11.434937", "rel_title": "SARS-CoV-2 comprehensive receptor profiling: mechanistic insight to drive new therapeutic strategies", @@ -884079,105 +884832,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.08.21252775", - "rel_title": "High levels of common cold coronavirus antibodies in convalescent plasma are associated with improved survival in COVID-19 patients", - "rel_date": "2021-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21252775", - "rel_abs": "BackgroundCOVID-19 Convalescent plasma (CCP) is safe and effective, particularly if given at an early stage of the disease. Our study aimed to identify an association between survival and specific antibodies found in CCP.\n\nPatients and MethodsPatients [≥]18 years of age who were hospitalized with moderate to severe COVID-19 infection and received CCP at the MD Anderson Cancer Center between 4/30/2020 and 8/20/2020 were included in the study. We quantified the levels of anti-SARS-CoV-2 antibodies, as well as antibodies against antigens of other coronavirus strains, in the CCP units and compared antibody levels with patient outcomes. For each antibody, a Bayesian exponential survival time regression model including prognostic variables was fit, and the posterior probability of a beneficial effect (PBE) of higher antibody level on survival time was computed.\n\nResultsCCP was administered to 44 cancer patients. The median age was 60 years (range 37-84) and 19 (43%) were female. Twelve patients (27%) died of COVID-19-related complications. Higher levels of two non-SARS-CoV-2-specific antibodies, anti-HCoV-OC43 spike IgG and anti-HCoV-HKU1 spike IgG, had PBE = 1.00, and 4 SARS-CoV-2-specific antibodies had PBEs between 0.90 and 0.95. Other factors associated with better survival were shorter time to CCP administration, younger age, and female sex.\n\nConclusionsCommon cold coronavirus spike IgG antibodies anti-HCoV-OC43 and anti-HCoV-HKU1 may target a common domain for SARS-CoV-2 and other coronaviruses. They provide a promising therapeutic target for monoclonal antibody production.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Uri Greenbaum", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Kimberly Klein", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Fernando Martinez", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Juhee Song", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Peter F. Thall", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Jeremy L. Ramdial", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Cristina Knape", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Fleur M Aung", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Jamie Scroggins", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Adriana Knopfelmacher", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Victor Mulanovich", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Jovan Borjan", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Javier Adachi", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Mayoora Muthu", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Cerena Leung", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Mayrin Correa Medina", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Richard Champlin", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Amanda Olson", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Amin Alousi", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Katayoun Rezvani", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Elizabeth J. Shpall", - "author_inst": "The University of Texas MD Anderson Cancer Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.08.21253090", "rel_title": "Trends over time in the risk of adverse outcomes among patients with SARS-CoV-2 infection", @@ -884565,6 +885219,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.09.21252764", + "rel_title": "A High Rate of COVID-19 Vaccine Hesitancy Among Arabs: Results of a Large-scale Survey", + "rel_date": "2021-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21252764", + "rel_abs": "In this study, we present the results of the first large-scale multinational study (36,220 participants) that measures vaccine hesitancy among Arab-speaking subjects. Our analysis shows a significant rate of vaccine hesitancy among Arabs in and outside the Arab region (83% and 81%, respectively). The most cited reasons for hesitancy are concerns about side effects and distrust in healthcare policies, vaccine expedited production, published studies and vaccine producing companies. We also found that female participants, participants 30-59 year-old, those with no chronic diseases, those with lower-level of academic education, and those who do not know the type of vaccine authorized in their countries are more hesitant to receive COVID-19 vaccination. On the other hand, participants who regularly receive the influenza vaccine, health care workers, and those from countries with higher rates of COVID-19 infections showed more vaccination willingness. Interactive representation of our results is posted on our project website at https://mainapp.shinyapps.io/CVHAA.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Eyad A. Qunaibi", + "author_inst": "Department of Pharmaceutical Sciences, Jerash Private University, Jerash, Jordan" + }, + { + "author_name": "Mohamed Helmy", + "author_inst": "Agency for Science, Research and Technology" + }, + { + "author_name": "Iman Basheti", + "author_inst": "Department of Clinical Pharmacy and Therapeutics, Faculty of Pharmacy, Applied Science Private University, Amman, Jordan" + }, + { + "author_name": "Iyad Sultan", + "author_inst": "King Hussein Cancer Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.08.21253141", "rel_title": "COVID-19 is associated with multiple sclerosis exacerbations that are prevented by disease modifying therapies", @@ -886681,65 +887366,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.08.21253007", - "rel_title": "Effectiveness of a telerehabilitation program for COVID-19 survivors (TERECO) on exercise capacity, pulmonary function, lower limb muscle strength, and quality of life: a randomised controlled trial", - "rel_date": "2021-03-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253007", - "rel_abs": "ObjectivesTo investigate superiority of a telerehabilitation program for Covid-19 (TERECO) over no rehabilitation with regard to functional exercise capacity, lower-limb muscle strength (LMS), pulmonary function, health-related quality of life (HRQOL), and perceived dyspnoea.\n\nDesignParallel-group randomised controlled-trial with 1:1 block-randomisation.\n\nSettingThree major hospitals from Jiangsu and Hubei provinces, China.\n\nParticipants120 Covid-19 survivors with modified Medical Research Council (mMRC) dyspnoea score of 2-3 who had been discharged from hospital were randomised. 61 were allocated to the control group and 59 to the TERECO group.\n\nInterventionThe control group received educational instructions. The TERECO group participated in a 6-week home-based, pulmonary rehabilitation program delivered via smartphone and monitored with chest-worn heart rate telemetry. Exercise types comprised breathing control and thoracic expansion, aerobic exercise, and LMS exercise.\n\nOutcomesPrimary outcome was 6-minute walking distance (6MWD) in metres. Secondary outcomes were LMS measured as squat time in seconds; pulmonary function assessed by spirometry with parameters being forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), FEV1/FVC, maximum voluntary ventilation (MVV), and peak expiratory flow; HRQOL measured with SF-12 physical component score (PCS) and mental component score (MCS); and mMRC dyspnoea, favourable outcome (no dyspnoea). Outcomes were assessed at 6 weeks (post-treatment) and 28 weeks (follow-up).\n\nResults120 patients were randomised, 15 (12.5%) were lost to follow-up at study endpoint. No serious adverse events occurred. 38 participants in the TERECO group complied with the exercise protocol (64.41% of randomized). The adjusted between-group difference in change in 6MWD from baseline was 65.45 metres (95% CI 43.8-87.1, p<0.001) at post-treatment and 68.62 metres (95% CI 46.39-90.85, p<0.001) at follow-up. Treatment effects for LMS were 20.12 seconds (95% CI 12.34-27.9, p<0.001) post-treatment and 22.23 seconds (95% CI 14.24-30.21, p<0.001) at follow-up. No group differences were found for lung function apart from post-treatment MVV (10.57 litres/minute, 95% CI 0.26-17.88, p=0.005). Increase in SF-12 PCS was greater in the TERECO group with treatment effects estimated as 3.79 (95% CI 1.24-6.35, p=0.004) at post-treatment and 2.69 (95% CI 0.06-5.32, p=0.045) at follow-up. No significant between-group differences were found for improvements in SF-12 MCS. At post-treatment 90.4% endorsed a favourable outcome for mMRC dyspnoea in the TERECO group vs. 61.7% in control (adjusted RR 1.46, 1.17-1.82, p=0.001).\n\nConclusionsThis trial demonstrated superiority of TERECO over no rehabilitation for 6MWD, LMS, and SF-12 PCS. We found no persistent effects on pulmonary function, SF-12 MCS, and perceived dyspnoea.\n\nTrial registrationChinese Clinical Trial Registry: ChiCTR2000031834, 11 Apr 2020, URL: http://www.chictr.org.cn/showproj.aspx?proj=52216\n\nKEY POINTSO_ST_ABSWhat is already knownC_ST_ABSMany Covid-19 survivors discharged from hospital have reduced exercise capacity, impaired pulmonary function, muscle weakness, and reduced quality of life, all of which might be addressed with pulmonary rehabilitation.\n\nHowever, evidence on effective pulmonary rehabilitation measures for this population is currently lacking. As delivery of conventional rehabilitation services is furthermore limited due to pandemic control measures, telerehabilitation programs represent a possible alternative.\n\nWhat the study addsWe developed a telerehabilitation program for Covid-19 survivors (TERECO program) that is delivered via smartphone and can be carried out at home.\n\nOur study suggests that TERECO was safe and participants of the TERECO program had improved exercise capacity, lower-limb muscle strength, and physical quality of life. No relevant group differences were found for lung function, self-reported breathlessness, and mental quality of life.\n\nThe TERECO program is inexpensive and could be implemented on a large scale to improve physical health of Covid-19 survivors after discharge from hospital.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Jian'an Li", - "author_inst": "The First Affiliated Hospital of Nanjing Medical University" - }, - { - "author_name": "Wenguang Xia", - "author_inst": "Hubei Province Hospital of integrated Chinese and Western Medicine" - }, - { - "author_name": "Chao Zhan", - "author_inst": "Huangshi Traditional Chinese Medicine Hospital" - }, - { - "author_name": "Shouguo Liu", - "author_inst": "The First Affiliated Hospital of Nanjing Medical University" - }, - { - "author_name": "Zhifei Yin", - "author_inst": "The First Affiliated Hospital of Nanjing Medical University" - }, - { - "author_name": "Jiayue Wang", - "author_inst": "The First Affiliated Hospital of Nanjing Medical University" - }, - { - "author_name": "Yufei Chong", - "author_inst": "Hubei Province Hospital of integrated Chinese and Western Medicine" - }, - { - "author_name": "Chanjuan Zheng", - "author_inst": "Hubei Province Hospital of integrated Chinese and Western Medicine" - }, - { - "author_name": "Xiaoming Fang", - "author_inst": "Huangshi Traditional Chinese Medicine Hospital" - }, - { - "author_name": "Wei Cheng", - "author_inst": "Huangshi Traditional Chinese Medicine Hospital" - }, - { - "author_name": "Jan D. Reinhardt", - "author_inst": "Sichuan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.03.08.21253109", "rel_title": "Predicting vaccine hesitancy from area-level indicators: A machine learning approach", @@ -887023,6 +887649,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.08.21252839", + "rel_title": "Transmission of SARS-CoV-2 by children attending school. Interim report on an observational, longitudinal sampling study of infected children, contacts, and the environment", + "rel_date": "2021-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21252839", + "rel_abs": "BackgroundAssessing transmission of SARS-CoV-2 by children in schools is of critical importance to inform public health action. We assessed frequency of acquisition of SARS-CoV-2 by contacts of children with COVID-19 in schools and households, as well as the amount of virus shed into the air and onto fomites in both settings.\n\nMethodsCases of COVID-19 in children in London schools were identified via notification. Weekly sampling for 3-4 weeks and PCR testing for SARS-CoV-2 of immediate classroom contacts (the \"bubble\"), non-bubble school contacts, and household contacts was undertaken supported by genome sequencing, along with surface and air sampling in the school and home environment.\n\nResultsWithin schools, secondary transmission was not detected in 28 individual bubble contacts, representing 10 distinct bubble classes. Across 8 non-bubble classes, 3/62 pupils tested positive- all three were asymptomatic and tested positive in one setting on the same day, unrelated to the original index case. In contrast, the secondary attack rate in naive household contacts was 14.3% (5/35) rising to 19.1% (9/47) when considering all household contacts. Environmental contamination with SARS-CoV-2 was rare in schools, regardless of school type; fomite SARS-CoV-2 RNA was identified in 4/189 (2.1%) samples in bubble classrooms, 2/127 (1.6%) samples in non-bubble classrooms, and 5/130 (3.8%) samples in washrooms. This contrasted with fomites in households, where SARS-CoV-2 RNA was identified in 60/248 (24.2%) bedroom samples, 66/241 (27.4%) communal room samples, and 21/188 (11.2%) bathroom samples. Air sampling identified SARS-CoV-2 RNA in just 1/68 (1.5%) of school air samples, compared with 21/85 (24.7%) of air samples taken in homes.\n\nSummaryThe low levels of environmental contamination in schools are consistent with low transmission frequency and adequate levels of cleaning and ventilation in schools during the period of study. Secondary transmission in schools was rare. The high frequency of secondary transmission in households associated with evident viral shedding throughout the home suggests a need to improve advice to households with infection in children in order to prevent onward community spread by sibling and adult contacts. The data highlight that transmission from children is very likely to occur when precautions are reduced.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Rebecca Cordery", + "author_inst": "Public Health England" + }, + { + "author_name": "Lucy Reeves", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jie Zhou", + "author_inst": "Imperial College London" + }, + { + "author_name": "Aileen G. Rowan", + "author_inst": "Imperial College London" + }, + { + "author_name": "Patricia Watber", + "author_inst": "Imperial College London" + }, + { + "author_name": "Carolina Rosadas", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michael Andrew Crone", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marko Storch", + "author_inst": "Imperial College London" + }, + { + "author_name": "Paul Freemont", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lucy Mosscrop", + "author_inst": "Imperial College London" + }, + { + "author_name": "Alice Cowley", + "author_inst": "Public Health England" + }, + { + "author_name": "Gina Zelent", + "author_inst": "Public Health England" + }, + { + "author_name": "Kate Bisset", + "author_inst": "Public Health England" + }, + { + "author_name": "Holly LeBlond", + "author_inst": "Public Health England" + }, + { + "author_name": "Sadie Regmi", + "author_inst": "Public Health England" + }, + { + "author_name": "Christian Buckingham", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ramlah Junaideen", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nadia Abdulla", + "author_inst": "Imperial College London" + }, + { + "author_name": "Joseph Eliahoo", + "author_inst": "Imperial College London" + }, + { + "author_name": "Miranda Mindlin", + "author_inst": "Public Health England" + }, + { + "author_name": "Theresa Lamagni", + "author_inst": "Public Health England" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Imperial College London" + }, + { + "author_name": "Graham P Taylor", + "author_inst": "Imperial College London" + }, + { + "author_name": "Shiranee Sriskandan", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.08.21252200", "rel_title": "Vaccine effectiveness after 1st and 2nd dose of the BNT162b2 mRNA Covid-19 Vaccine in long-term care facility residents and healthcare workers - a Danish cohort study", @@ -889127,49 +889864,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.07.434287", - "rel_title": "A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic", - "rel_date": "2021-03-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.07.434287", - "rel_abs": "The SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Simon Pollett", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Matthew A Conte", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Mark A Sanborn", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Richard G Jarman", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Grace M Lidl", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Kayvon Modjarrad", - "author_inst": "Walter Reed Army Institute of Research" - }, - { - "author_name": "Irina Maljkovic Berry", - "author_inst": "Walter Reed Army Institute of Research" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.03.08.434404", "rel_title": "Human nasal and lung tissues infected ex vivo with SARS-CoV-2 provide insights into differential tissue-specific and virus-specific innate immune responses in the upper and lower respiratory tract", @@ -889461,6 +890155,33 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.03.06.434059", + "rel_title": "Structural Analysis of Spike Protein Mutations in an Emergent SARS-CoV-2 Variant from the Philippines", + "rel_date": "2021-03-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.06.434059", + "rel_abs": "A SARS-CoV-2 lineage designated as P.3 with multiple signature mutations in the Spike protein region was recently reported with cases from the Central Visayas Region of the Philippines. Whole genome sequencing revealed that the 33 samples under this lineage all contain the E484K, N501Y, and P681H Spike mutations previously found in variants of concern (VOC) such as the B.1.351, the P.1 and B.1.1.7 variants first reported in South Africa, Brazil, and the United Kingdom, respectively. The possible implications of the mutations found in the Spike protein of P.3 were analyzed for their potential effects on structure, stability, and molecular surface character. The analysis suggests that these mutations could significantly impact the possible interactions of the Spike protein with the ACE2 receptor and neutralizing antibodies, and warrants further clinical investigation. Some of the mutations affecting the N and C terminal domains may have effects on Spike monomer and trimer stability. This report provides insights on relevant targets for the design of future diagnostics, therapeutics and vaccines against the evolving SARS-CoV-2 variants in the Philippines.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Neil Andrew David Bascos", + "author_inst": "University of the Philippines Diliman" + }, + { + "author_name": "Denise Mirano-Bascos", + "author_inst": "University of the Philippines Diliman" + }, + { + "author_name": "Cynthia Palmes Saloma", + "author_inst": "University of the Philippines" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.03.08.434390", "rel_title": "Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses", @@ -890745,41 +891466,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.04.21252943", - "rel_title": "Comparative analysis of policies and programs to support families and children during COVID-19", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252943", - "rel_abs": "BackgroundPolicies and programs that promote positive social environments for young children and their families have the potential to improve early childhood development and long-term health. However, due to the community-wide public health measures implemented to reduce transmission of COVID-19, many families are experiencing health and socio-economic challenges and pre-existing supports and services may no longer be available. In this study, we compared the policies and programs countries have implemented to support maternal and child health during the first wave of COVID-19.\n\nMethodsWe compared the policies and programs implemented to support child health and well-being during the first wave of COVID-19 in Australia, Canada, the Netherlands, Singapore, the UK, and the USA. A grey literature review was performed to identify policies, announcements, and guidelines released from governmental and public health organizations within each country related to children, parents, families, early childhood development, adverse childhood experiences, child welfare, pre-school, or daycares. We also performed a manual search of government websites. Both provincial and federal government policies were included for Canada.\n\nResultsThe main policies identified were focused on prenatal care, well-baby visit and immunization schedules, financial supports, domestic violence and housing, childcare supports, child protective services, and food security. All of the included countries implemented some of these policies, but there was a large variation in the number, size, and barriers to access these supports. None of the countries implemented supports in all of the potential areas identified.\n\nConclusionPolitical legacy and previous redistributive policies might have influenced the variation in policies and programs introduced by governments. As the COVID-19 pandemic continues, further opportunity for governments to implement supportive programs and policies for children and families exists.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Joanne Kearon", - "author_inst": "McMaster University" - }, - { - "author_name": "Mark Cachia", - "author_inst": "McMaster University" - }, - { - "author_name": "Sarah Carsley", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Meta van den Heuvel", - "author_inst": "Hospital for Sick Children" - }, - { - "author_name": "Jessica Hopkins", - "author_inst": "Public Health Ontario" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.05.21252963", "rel_title": "Diagnostic accuracy and predictive value of clinical symptoms for the diagnosis of mild COVID 19", @@ -891019,6 +891705,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.04.21252658", + "rel_title": "SARS-CoV-2-specific T Cell Memory is Sustained in COVID-19 Convalescents for 8 Months with Successful Development of Stem Cell-like Memory T Cells", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252658", + "rel_abs": "Memory T cells contribute to rapid viral clearance during re-infection, but the longevity and differentiation of SARS-CoV-2-specific memory T cells remain unclear. We conducted direct ex vivo assays to evaluate SARS-CoV-2-specific CD4+ and CD8+ T cell responses in COVID-19 convalescents up to 254 days post-symptom onset (DPSO). Here, we report that memory T cell responses were maintained during the study period. In particular, we observed sustained polyfunctionality and proliferation capacity of SARS-CoV-2-specific T cells. Among SARS-CoV-2-specific CD4+ and CD8+ T cells detected by activation-induced markers, the proportion of stem cell-like memory T (TSCM) cells increased, peaking at approximately 120 DPSO. Development of TSCM cells was confirmed by SARS-CoV-2-specific MHC-I multimer staining. Considering the self-renewal capacity and multipotency of TSCM cells, our data suggest that SARS-CoV-2-specific T cells are long-lasting after recovery from COVID-19. The current study provides insight for establishing an effective vaccination program and epidemiological measurement.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Jae Hyung Jung", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Min-Seok Rha", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Moa Sa", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Hee Kyoung Choi", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Ji Hoon Jeon", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Hyeri Seok", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Dae Won Park", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Su-Hyung Park", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Hye Won Jeong", + "author_inst": "Chungbuk National University College of Medicine" + }, + { + "author_name": "Won Suk Choi", + "author_inst": "Korea University College of Medicine, Ansan Hospital" + }, + { + "author_name": "Eui-Cheol Shin", + "author_inst": "Korea Advanced Institute of Science and Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.04.21252528", "rel_title": "Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England", @@ -892423,49 +893168,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2021.03.07.21252959", - "rel_title": "The relationship between new PCR positive cases and going out in public during the COVID-19 epidemic in Japan", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.07.21252959", - "rel_abs": "Suppression of the first wave of COVID-19 in Japan is assumedly attributable to peoples increased risk perception by acquiring information from the government and media reports. In this study, going out in public amidst the spread of COVID-19 infections was investigated by examining new polymerase chain reaction (PCR) positive cases of COVID-19 and its relationship to four indicators of people going out in public (the people flow, the index of web searches for going outside, the number of times people browse restaurants, and the number of hotel guests), from the Regional Economic and Social Analysis System (V-RESAS). Two waves of COVID-19 infections were examined with cross-correlation analysis. In the first wave, all four indicators of going out reacted oppositely with the change in new PCR positive cases, showing a lag period of -1 to +6 weeks. In the second wave, the same relationship was only observed for the index of web searches for going outside. These results suggest that going out in public could not be described by new PCR positive cases alone in the second wave, even though they could explain people going out to some extent in the first wave.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Hiromichi Takahashi", - "author_inst": "Department of Healthcare Economics and Quality Management, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan" - }, - { - "author_name": "Iori Terada", - "author_inst": "Department of Healthcare Economics and Quality Management, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan" - }, - { - "author_name": "Takuya Higuchi", - "author_inst": "Department of Healthcare Economics and Quality Management, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan" - }, - { - "author_name": "Daisuke Takada", - "author_inst": "Department of Healthcare Economics and Quality Management, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan" - }, - { - "author_name": "Jung-ho Shin", - "author_inst": "Department of Healthcare Economics and Quality Management, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan" - }, - { - "author_name": "Susumu Kunisawa", - "author_inst": "Department of Healthcare Economics and Quality Management, Graduate School of Medicine, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan" - }, - { - "author_name": "Yuichi Imanaka", - "author_inst": "Kyoto University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.03.08.21253112", "rel_title": "OpenSAFELY: Risks of COVID-19 hospital admission and death for people with learning disabilities - a cohort study.", @@ -892953,6 +893655,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.03.06.21253058", + "rel_title": "Low Dose Regimens of BNT162b2 mRNA Vaccine Exceed SARS-Cov-2 Correlate of Protection Estimates for Symptomatic Infection, in those 19-55 Years of Age", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.06.21253058", + "rel_abs": "BackgroundAn exact correlate of protection (CoP) is not yet known for symptomatic COVID-19. However, it is still possible to show a new vaccine regimen exceeds an unknown CoP, provided the regimen shows an equivalent or greater immunological response in all measured indicators relative to the immunological response elicited by a clinically proven vaccine regimen. The principle of comparing immunogenicity between regimens is what the FDA, EMA, and Access Consortium use to authorize modifications to the vaccines for VOC, without requiring clinical efficacy studies before implementation. It is logical to apply the same principle to modifying vaccine doses if the data is available to do so. A two dose 30ug regimen of BNT162b2 has strong clinical evidence of efficacy, as does a single dose 30 ug regimen. The immunological markers for these regimens have been profiled in detail in Phase 1 and 2 trial data.\n\nMethodsThe immunological profile (including binding antibodies, viral neutralization, cytokine profiles, and CD4 and 8 expansion) of the 2 dose 30ug BNT162b2 vaccine is examined, referred to as a highly conservative CoP estimate. The single dose 30 ug BNT162b2 immunological profile is also examined, a tenable CoP estimate. Data from the phase 1 and 2 trials are examined to see if alternate regimens meet or exceed the level of each immune marker measured, relative to the regimens listed above that have proven clinical efficacy.\n\nResultsFor adults aged 19-55, a 2 dose 10ug BNT162b2 regimen elicits a comparable response to the standard 30 ug dose for each immune indicator, with viral neutralization nearly an order of magnitude greater than the tenable CoP estimate. Similarly, a single dose 10ug BNT 162b2 regimen or a two dose 1ug BNT 162b2 regimen equals or exceeds the immunogenicity of a single 30 ug dose.\n\nConclusionIf it is reasonable for the FDA, EMA, and Access Consortium to approve vaccine modifications without a clinical trial based on immunogenicity data, three alternate low dose regimens were identified that meet the requirements of having comparable immunogenicity relative to a protocol that has proven clinical efficacy. Immediate implementation of these lower dose regimens should be considered as they have major implications in alleviating vaccine supply, as well as improving vaccine side effect profile, and lowering total cost of vaccination.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Graham Jurgens", + "author_inst": "Unaffiliated" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.03.06.21252964", "rel_title": "Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data", @@ -894701,29 +895422,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.04.21252540", - "rel_title": "COVID Seroprevalence, Symptoms and Mortality During the First Wave of SARS-CoV-2 in Canada", - "rel_date": "2021-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252540", - "rel_abs": "BackgroundEfforts to stem Canadas SARS-CoV-2 pandemic can benefit from direct understanding of the prevalence, infection fatality rates (IFRs), and information on asymptomatic infection.\n\nMethodsWe surveyed a representative sample of 19,994 adult Canadians about COVID symptoms and analyzed IgG antibodies against SARS-CoV-2 from self-collected dried blood spots (DBS) in 8,967 adults. A sensitive and specific chemiluminescence ELISA detected IgG to the spike trimer. We compared seroprevalence to deaths to establish IFRs and used mortality data to estimate infection levels in nursing home residents.\n\nResultsThe best estimate (high specificity) of adult seroprevalence nationally is 1.7%, but as high as 3.5% (high sensitivity) depending on assay cut-offs. The highest prevalence was in Ontario (2.4-3.9%) and in younger adults aged 18-39 years (2.5-4.4%). Based on mortality, we estimated 13-17% of nursing home residents became infected. The first viral wave infected 0.54-1.08 million adult Canadians, half of whom were <40 years old. The IFR outside nursing homes was 0.20-0.40%, but the COVID mortality rate in nursing home residents was >70 times higher than that in comparably-aged adults living in the community. Seropositivity correlated with COVID symptoms, particularly during March. Asymptomatic adults constituted about a quarter of definite seropositives, with a greater proportion in the elderly.\n\nInterpretationCanada had relatively low infection prevalence and low IFRs in the community, but not in nursing homes, during the first viral wave. Self-collected DBS for antibody testing is a practicable strategy to monitor the ongoing second viral wave and, eventually, vaccine-induced immunity among Canadian adults.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "- Action to beat coronavirus/Action pour battre le coronavirus (Ab-C) Study Investigators", - "author_inst": "" - }, - { - "author_name": "Prabhat Jha", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.24.21251989", "rel_title": "Virological and serological characterization of critically ill patient with COVID-19 in the UK: a special focus on variant detection", @@ -895059,6 +895757,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.02.21252766", + "rel_title": "Self-reported symptoms, self-reported viral testing result and seroprevalence of SARS CoV-2 among a community sample in Essex County New Jersey: A brief report.", + "rel_date": "2021-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252766", + "rel_abs": "BackgroundSARS-CoV-2, the virus that causes COVID-19, has rapidly spread globally beginning in late 2019. Early areas impacted by this pandemic in the US include Essex County, New Jersey. Beyond understanding the prevalence of active infections and deaths, it is important to understand the true burden of infection in the community, as indicated by seroprevalence of antibodies directed to the virus. Understanding the spectrum of disease is key to the effectiveness of primary prevention and control measures and the design of interventions against transmission of infection.\n\nMethodsWe utilized venue-based-sampling (VBS), implemented by a community partner, to sample members of the community in Essex County. In VBS the venues are randomized as a proxy for randomizing the attendees of the venues. We asked standard demographic questions, questions about symptoms and PCR testing and previous antibody testing. Participants provide a blood sample collected by finger stick with the Neoteryx Mitra Collection device. Samples were tested using a novel ELISA based approached developed by our team.\n\nResultsFrom September 15, 2020 to December 22, 2020, we conducted 92 randomly selected sampling events where we approached 1349 individuals for screening. Of these, 924 consented and had complete data for analysis. Only 6.5% of the sample reported any COVID-19 like symptoms while 45.9% had sought out a COVID-19 test. In total 13 (1.4%) participants received a positive SARS-CoV-2 PCR test result. While 33 participants (2.6%) sought a SARS-CoV-2 antibody test, only 0.5% of the sample reported a positive antibody result. Testing in this study identified 83 (9.0%) participants positive for SARS-CoV-2 antibodies.\n\nConclusionWe recruited a large sample of the population of Essex County, New Jersey using VBS, electronic surveys, novel sample collection and lab methods. Our findings suggest that the burden of SARS-Cov-2 is slightly more than six times than that suggested by PCR testing. This burden is higher than most estimates obtained through studies of remnant blood samples from hospitals (4.2%), samples from staff at a public-school system (2.9%), and residents of a California county recruited with targeted Facebook ads (1.5%). (9-11) Moreover, with only 6.5% of the sample reporting any COVID-19-like symptoms, our finding suggests that the number of asymptomatic persons may be close to 1.5 times greater than anyone reporting symptoms.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Henry F Raymond", + "author_inst": "School of Public Health, Rutgers University" + }, + { + "author_name": "Pratik Datta", + "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark NJ" + }, + { + "author_name": "Rahul Ukey", + "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark NJ" + }, + { + "author_name": "Peng Wang", + "author_inst": "School of Public Health, Rutgers University, Piscataway, NJ" + }, + { + "author_name": "Richard J Martino", + "author_inst": "School of Public Health, Rutgers University, Piscataway, NJ" + }, + { + "author_name": "Kristen D Krause", + "author_inst": "School of Public Health, Rutgers University, Piscataway, NJ" + }, + { + "author_name": "Corey Rosmarin-DeStefano", + "author_inst": "North Jersey Community Research Initiative, Newark, NJ" + }, + { + "author_name": "Abraham Pinter", + "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark NJ" + }, + { + "author_name": "Perry N Halkitis", + "author_inst": "School of Public Health, Rutgers University, Piscataway, NJ" + }, + { + "author_name": "Maria L Gennaro", + "author_inst": "Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark NJ" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.03.21252809", "rel_title": "Sharing positive changes made during COVID-19 national lockdown: a multi-method co-production study", @@ -896379,29 +897132,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.02.21252801", - "rel_title": "A Two-Sample Robust Bayesian Mendelian Randomization Method Accounting for Linkage Disequilibrium and Idiosyncratic Pleiotropy With Applications to the COVID-19 Outcome", - "rel_date": "2021-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252801", - "rel_abs": "Mendelian randomization (MR) is a statistical method exploiting genetic variants as instrumental variables to estimate the causal effect of modifiable risk factors on an outcome of interest. Despite wide uses of various popular two-sample MR methods based on genome-wide association study summary level data, however, those methods could suffer from potential power loss or/and biased inference when the chosen genetic variants are in linkage disequilibrium (LD), and also have relatively large direct effects on the outcome whose distribution might be heavy-tailed which is commonly referred to as the idiosyncratic pleiotropy phenomenon. To resolve those two issues, we propose a novel Robust Bayesian Mendelian Randomization (RBMR) model that uses the more robust multivariate generalized t-distribution (Arellano-Valle and Bolfarine, 1995) to model such direct effects in a probabilistic model framework which can also incorporate the LD structure explicitly. The generalized t-distribution can be represented as a Gaussian scaled mixture so that our model parameters can be estimated by the EM-type algorithms. We compute the standard errors by calibrating the evidence lower bound using the likelihood ratio test. Through extensive simulation studies, we show that our RBMR has robust performance compared to other competing methods. We also apply our RBMR method to two benchmark data sets and find that RBMR has smaller bias and standard errors. Using our proposed RBMR method, we find that coronary artery disease is associated with increased risk of critically ill coronavirus disease 2019 (COVID-19). We also develop a user-friendly R package RBMR (https://github.com/AnqiWang2021/RBMR) for public use.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Anqi Wang", - "author_inst": "Department of Statistics and Actuarial Science, University of Hong Kong, Hong Kong SAR, China" - }, - { - "author_name": "Zhonghua Liu", - "author_inst": "Department of Statistics and Actuarial Science, University of Hong Kong, Hong Kong SAR, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.05.434000", "rel_title": "Inhibition of amyloid formation of the Nucleoprotein of SARS-CoV-2", @@ -896793,6 +897523,77 @@ "type": "confirmatory results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.03.05.434152", + "rel_title": "Scalable, Micro-Neutralization Assay for Qualitative Assessment of SARS-CoV-2 (COVID 19) Virus-Neutralizing Antibodies in Human Clinical Samples", + "rel_date": "2021-03-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.05.434152", + "rel_abs": "As the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic was expanding, it was clear that effective testing for the presence of neutralizing antibodies in the blood of convalescent patients would be critical for development of plasma-based therapeutic approaches. To address the need for a high-quality neutralization assay against SARS-CoV-2, a previously established fluorescence reduction neutralization assay (FRNA) against Middle East respiratory syndrome coronavirus (MERS-CoV) was modified and optimized. The SARS-CoV-2 FRNA provides a quantitative assessment of a large number of infected cells through use of a high-content imaging system. Because of this approach, and the fact that it does not involve subjective interpretation, this assay is more efficient and more accurate than other neutralization assays. In addition, the ability to set robust acceptance criteria for individual plates and specific test wells provided further rigor to this assay. Such agile adaptability avails use with multiple virus variants. By February 2021, the SARS-CoV-2 FRNA had been used to screen over 5,000 samples, including acute and convalescent plasma or serum samples and therapeutic antibody treatments, for SARS-CoV-2 neutralizing titers.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Michael R Holbrook", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Richard S Bennett", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Elena N Postnikova", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Janie Liang", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Robin Gross", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Dawn Gerhardt", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Shalamar Georgia-Clark", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Yingyun Cai", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Shuiqinq Yu", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Lindsay Marron", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Greg Kocher", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Steven Mazur", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Saurabh Dixit", + "author_inst": "NIAID IRF-Frederick" + }, + { + "author_name": "Vladimir V Lukin", + "author_inst": "Kearney" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.05.434119", "rel_title": "SARS-CoV-2-host chimeric RNA-sequencing reads do not necessarily signify virus integration into the host DNA", @@ -898333,101 +899134,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.02.21252437", - "rel_title": "Day by day symptoms following positive and negative PCR tests for SARS-CoV-2 in non-hospitalized health-care workers: a 90-day follow-up study", - "rel_date": "2021-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252437", - "rel_abs": "BackgroundLittle is known about the long-term course of symptoms for mild coronavirus disease 2019 (COVID-19) when accounting for symptoms due to other causes. We aimed to compare symptoms day by day for non-hospitalised individuals who tested positive and negative with polymerase chain reaction for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).\n\nMethodsWe followed 210 test-positive and 630 individually matched test-negative health-care workers of the Central Denmark Region up to 90 days after the test, April-June 2020. They daily reported seven COVID-19 related symptoms. Symptom courses were compared graphically and by conditional multivariable logistic regression.\n\nResultsThirty % of test-positive and close to zero of test-negative participants reported a reduced sense of taste and smell during all 90 days of follow-up (adjusted odds ratio [aOR] 86.07, 95% CI 22.86-323). Dyspnoea was reported by an initial 20% of test-positive with a gradual decline to about 5% after 30 days without ever reaching the level of the test-negative participants (aOR 6.88, 95% CI 2.41-19.63). Cough, headache, sore throat, muscle aches, and fever were temporarily more prevalent among the test positive participants, but after 30 days, no increases were seen. Women and participants aged 45 years or older tended to be more susceptible to SARS-CoV-2 infection.\n\nConclusionPrevalence of long-lasting reduced sense of taste and smell is highly increased after being diagnosed with mild COVID-19. This pattern is also seen for dyspnoea at a low level but not for cough, sore throat, headache, muscle ache or pain, or fever.\n\nKey messagesO_LIReduced sense of taste and smell is present at a highly increased level of 30% during 90 days after testing positive for severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2).\nC_LIO_LITest-positive participants experience dyspnoea persistently more often than test-negative participants but affect only few.\nC_LIO_LIThe prevalence of cough, sore throat, headache, muscle ache or pain, and fever following a positive test reach the level seen after a negative test within 30 days.\nC_LIO_LIWomen and participants aged 45 years or older tend to be more susceptible to symptoms following SARS-CoV-2 infection.\nC_LI", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Kent J Nielsen", - "author_inst": "Department of Occupational Medicine, Danish Ramazzini Centre, Herning Regional Hospital, DK-7400 Herning, Denmark" - }, - { - "author_name": "Jesper Medom Vestergaard", - "author_inst": "Department of Occupational Medicine, Danish Ramazzini Centre, Aarhus University Hospital, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Vivi Schl\u00fcnssen", - "author_inst": "Department of Public Health, Work, Environment and Health, Danish Ramazzini Centre, Aarhus University, DK-8000 Aarhus C, Denmark" - }, - { - "author_name": "Jens Peter Bonde", - "author_inst": "Department of Occupational and Environmental Medicine, Bispebjerg and Frederiksberg Hospital, University of Copenhagen, DK-2400, Copenhagen, Denmark" - }, - { - "author_name": "Kathrine A Kaspersen", - "author_inst": "Department of Clinical Immunology, Aarhus University Hospital, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Karin Biering", - "author_inst": "Department of Occupational Medicine, Danish Ramazzini Centre, Herning Regional Hospital, DK-7400 Herning, Denmark" - }, - { - "author_name": "Ole Carstensen", - "author_inst": "Department of Occupational Medicine, Danish Ramazzini Centre, Herning Regional Hospital, DK-7400 Herning, Denmark" - }, - { - "author_name": "Thomas Greve", - "author_inst": "Department of Clinical Microbiology, Aarhus University Hospital, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Karoline K Hansen", - "author_inst": "Department of Occupational Medicine, Danish Ramazzini Centre, Aarhus University Hospital, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Annett Dalb\u00f8ge", - "author_inst": "Department of Occupational Medicine, Danish Ramazzini Centre, Aarhus University Hospital, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Esben Meulengracht Flachs", - "author_inst": "Department of Occupational and Environmental Medicine, Bispebjerg and Frederiksberg Hospital, University of Copenhagen, DK-2400, Copenhagen, Denmark" - }, - { - "author_name": "Sanne Jespersen", - "author_inst": "Department of Infectious Diseases, Aarhus University Hospital, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Mette Lausten Hansen", - "author_inst": "Department of Occupational Medicine, Danish Ramazzini Centre, Aarhus University Hospital, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Susan Mikkelsen", - "author_inst": "Department of Clinical Immunology, Aarhus University Hospital, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Marianne Kragh Thomsen", - "author_inst": "Department of Clinical Microbiology, Aarhus University Hospital, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Jacob Dvinge Redder", - "author_inst": "Business Intelligence, Central Denmark Region, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Else Toft W\u00fcrtz", - "author_inst": "Department of Occupational Medicine, Danish Ramazzini Centre, Aarhus University Hospital, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Lars \u00d8stergaard", - "author_inst": "Department of Infectious Diseases, Aarhus University Hospital, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Christian Erikstrup", - "author_inst": "Department of Clinical Immunology, Aarhus University Hospital, DK-8200 Aarhus N, Denmark" - }, - { - "author_name": "Henrik A. Kolstad", - "author_inst": "Aarhus University Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.03.02.21252747", "rel_title": "redBERT: A Topic Discovery and Deep SentimentClassification Model on COVID-19 OnlineDiscussions Using BERT NLP Model", @@ -898703,6 +899409,197 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.02.21252420", + "rel_title": "Delayed rise of oral fluid antibodies, elevated BMI, and absence of early fever correlate with longer time to SARS-CoV-2 RNA clearance in an longitudinally sampled cohort of COVID-19 outpatients", + "rel_date": "2021-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252420", + "rel_abs": "BackgroundSustained molecular detection of SARS-CoV-2 RNA in the upper respiratory tract (URT) in mild to moderate COVID-19 is common. We sought to identify host and immune determinants of prolonged SARS-CoV-2 RNA detection.\n\nMethodsNinety-five outpatients self-collected mid-turbinate nasal, oropharyngeal (OP), and gingival crevicular fluid (oral fluid) samples at home and in a research clinic a median of 6 times over 1-3 months. Samples were tested for viral RNA, virus culture, and SARS-CoV-2 and other human coronavirus antibodies, and associations were estimated using Cox proportional hazards models.\n\nResultsViral RNA clearance, as measured by SARS-CoV-2 RT-PCR, in 507 URT samples occurred a median (IQR) 33.5 (17-63.5) days post-symptom onset. Sixteen nasal-OP samples collected 2-11 days post-symptom onset were virus culture positive out of 183 RT-PCR positive samples tested. All participants but one with positive virus culture were negative for concomitant oral fluid anti-SARS-CoV-2 antibodies. The mean time to first antibody detection in oral fluid was 8-13 days post-symptom onset. A longer time to first detection of oral fluid anti-SARS-CoV-2 S antibodies (aHR 0.96, 95% CI 0.92-0.99, p=0.020) and BMI [≥] 25kg/m2 (aHR 0.37, 95% CI 0.18-0.78, p=0.009) were independently associated with a longer time to SARS-CoV-2 viral RNA clearance. Fever as one of first three COVID-19 symptoms correlated with shorter time to viral RNA clearance (aHR 2.06, 95% CI 1.02-4.18, p=0.044).\n\nConclusionsWe demonstrate that delayed rise of oral fluid SARS-CoV-2-specific antibodies, elevated BMI, and absence of early fever are independently associated with delayed URT viral RNA clearance.", + "rel_num_authors": 44, + "rel_authors": [ + { + "author_name": "Annukka A. R. Antar", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Tong Yu", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Nora Pisnic", + "author_inst": "The Johns Hopkins University Bloomberg School of Medicine" + }, + { + "author_name": "Razvan Azamfirei", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jeffrey A Tornheim", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Diane M. Brown", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Kate Kruczynski", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Justin P. Hardick", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Thelio Sewell", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Minyoung Jang", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Taylor Church", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Samantha N. Walch", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Carolyn Reuland", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Vismaya S. Bachu", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Kirsten Littlefield", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Han-Sol Park", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Rebecca L. Ursin", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Abhinaya Ganesan", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Oyinkansola Kusemiju", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Brittany Barnaba", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Curtisha Charles", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Michelle Prizzi", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jaylynn R. Johnstone", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Christine Payton", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Weiwei Dai", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Joelle Fuchs", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Guido Massaccesi", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Derek T. Armstrong", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jennifer L. Townsend", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Sara C. Keller", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Zoe O Demko", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Chen Hu", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Mei-Cheng Wang", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Lauren M. Sauer", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Heba H. Mostafa", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Jeanne C. Keruly", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Shruti H. Mehta", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Sabra L. Klein", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Andrea L. Cox", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Andrew Pekosz", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "Christopher D. Heaney", + "author_inst": "The Johns Hopkins University Bloomberg School of Public Health" + }, + { + "author_name": "David L. Thomas", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Paul W. Blair", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "Yukari C. Manabe", + "author_inst": "The Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.01.21252243", "rel_title": "On the Environmental Determinants of COVID-19 Seasonality", @@ -900563,41 +901460,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.02.21252750", - "rel_title": "SARS-CoV-2 Sequence Characteristics of COVID-19 Persistence and Reinfection", - "rel_date": "2021-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252750", - "rel_abs": "BackgroundBoth SARS-CoV-2 reinfection and persistent infection have been described, but a systematic assessment of mutations is needed. We assessed sequences from published cases of COVID-19 reinfection and persistence, characterizing the hallmarks of reinfecting sequences and the rate of viral evolution in persistent infection.\n\nMethodsA systematic review of PubMed was conducted to identify cases of SARS-CoV-2 reinfection and persistent infection with available sequences. Amino acid changes in the reinfecting sequence were compared to both the initial and contemporaneous community variants. Time-measured phylogenetic reconstruction was performed to compare intra-host viral evolution in persistent COVID-19 to community-driven evolution.\n\nResultsFourteen reinfection and five persistent infection cases were identified. Reports of reinfection cases spanned a broad distribution of ages, baseline health status, reinfection severity, and occurred as early as 1.5 months or >8 months after the initial infection. The reinfecting viral sequences had a median of 9 amino acid changes with enrichment of changes in the S, ORF8 and N genes. The number of amino acid changes did not differ by the severity of reinfection and reinfecting variants were similar to the contemporaneous sequences circulating in the community. Patients with persistent COVID-19 demonstrated more rapid accumulation of mutations than seen with community-driven evolution with continued viral changes during convalescent plasma or monoclonal antibody treatment.\n\nConclusionsSARS-CoV-2 reinfection does not require an unusual set of circumstances in the host or virus, while persistent COVID-19 is largely described in immunosuppressed individuals and is associated with accelerated viral evolution as measured by clock rates.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Manish Chandra Choudhary", - "author_inst": "Brigham & Women's Hospital" - }, - { - "author_name": "Charles R Crain", - "author_inst": "Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Xueting Qiu", - "author_inst": "Harvard T.H. Chan School of Public Health, Boston, MA, USA" - }, - { - "author_name": "William Hanage", - "author_inst": "Harvard T.H. Chan School of Public Health, Boston, MA, USA" - }, - { - "author_name": "Jonathan Z. Li", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.03.21252814", "rel_title": "Upper respiratory tract SARS-CoV-2 RNA loads in symptomatic and asymptomatic children and adults", @@ -900913,6 +901775,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.23.21252328", + "rel_title": "SARS-CoV-2 antibodies detected in human breast milk post-vaccination", + "rel_date": "2021-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252328", + "rel_abs": "ImportanceThe SARS-CoV-2 pandemic has infected over a hundred million people worldwide, with almost 2.5 million deaths at the date of this publication. In the United States, Pfizer-BioNTech and Moderna vaccines were first administered to the public starting in December 2020, and no lactating women were included in the initial trials of safety/efficacy. Research on SARS-CoV-2 vaccination in lactating women and the potential transmission of passive immunity to the infant through breast milk is needed to guide patients, clinicians and policy makers during the worldwide effort to curb the spread of this virus.\n\nObjectiveTo determine whether SARS-CoV-2 specific immunoglobins are found in breast milk post-vaccination, and to characterize the time course and types of immunoglobulins present.\n\nDesignProspective cohort study\n\nSettingProvidence Portland Medical Center, Oregon, USA\n\nParticipantsSix lactating women who planned to receive both doses of the Pfizer-BioNTech or Moderna vaccine between December 2020 and January 2021. Breast milk samples were collected pre-vaccination and at 11 additional timepoints, with last sample at 14 days post 2nd dose of vaccine.\n\nExposureTwo doses of Pfizer-BioNTech or Moderna SARS-CoV-2 vaccine.\n\nMain Outcome(s) and Measure(s)Levels of SARS-CoV-2 specific IgA and IgG immunoglobulins in breast milk.\n\nResultsIn this cohort of 6 lactating women who received 2 doses of SARS-CoV-2 vaccine, we observed significantly elevated levels of SARS-CoV-2 specific IgG and IgA antibodies in breast milk beginning at Day 7 after the initial vaccine dose, with an IgG-dominant response.\n\nConclusions and RelevanceWe are the first to show that maternal vaccination results in SARS-CoV-2 specific immunoglobulins in breast milk that may be protective for infants.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jill K Baird", + "author_inst": "Legacy Medical Group, Portland OR USA" + }, + { + "author_name": "Shawn M Jensen", + "author_inst": "Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, USA" + }, + { + "author_name": "Walter J Urba", + "author_inst": "Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, USA" + }, + { + "author_name": "Bernard A Fox", + "author_inst": "Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, USA" + }, + { + "author_name": "Jason R Baird", + "author_inst": "Earle A. Chiles Research Institute, Providence Cancer Institute, Providence Portland Medical Center, Portland, OR, USA" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.26.21252555", "rel_title": "Introductions and evolutions of SARS-CoV-2 strains in Japan", @@ -902385,77 +903282,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2021.03.02.433522", - "rel_title": "High resolution profiling of MHC-II peptide presentation capacity, by Mammalian Epitope Display, reveals SARS-CoV-2 targets for CD4 T cells and mechanisms of immune-escape", - "rel_date": "2021-03-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.02.433522", - "rel_abs": "Understanding the mechanisms of immune evasion is critical for formulating an effective response to global threats like SARS-CoV2. We have fully decoded the immune synapses for multiple TCRs from acute patients, including cognate peptides and the presenting HLA alleles. Furthermore, using a newly developed mammalian epitope display platform (MEDi), we determined that several mutations present in multiple viral isolates currently expanding across the globe, resulted in reduced presentation by multiple HLA class II alleles, while some increased presentation, suggesting immune evasion based on shifting MHC-II peptide presentation landscapes. In support, we found that one of the mutations present in B1.1.7 viral strain could cause escape from CD4 T cell recognition in this way. Given the importance of understanding such mechanisms more broadly, we used MEDi to generate a comprehensive analysis of the presentability of all SARS-CoV-2 peptides in the context of multiple common HLA class II molecules. Unlike other strategies, our approach is sensitive and scalable, providing an unbiased and affordable high-resolution map of peptide presentation capacity for any MHC-II allele. Such information is essential to provide insight into T cell immunity across distinct HLA haplotypes across geographic and ethnic populations. This knowledge is critical for the development of effective T cell therapeutics not just against COVID-19, but any disease.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Franz Josef Obermair", - "author_inst": "Repertoire Immune Medicine, Cambridge, USA - Tepthera subsidiary, Schlieren, Switzerland" - }, - { - "author_name": "Florian Renoux", - "author_inst": "Repertoire Immune Medicine, Cambridge, USA - Tepthera subsidiary, Schlieren, Switzerland" - }, - { - "author_name": "Sebastian Heer", - "author_inst": "Repertoire Immune Medicine, Cambridge, USA - Tepthera subsidiary, Schlieren, Switzerland" - }, - { - "author_name": "Chloe Lee", - "author_inst": "Institute of Molecular Health Sciences, ETH Zurich, Switzerland" - }, - { - "author_name": "Nastassja Cereghetti", - "author_inst": "Repertoire Immune Medicine, Cambridge, USA - Tepthera subsidiary, Schlieren, Switzerland" - }, - { - "author_name": "Giulia Maestri", - "author_inst": "Repertoire Immune Medicine, Cambridge, USA - Tepthera subsidiary, Schlieren, Switzerland" - }, - { - "author_name": "Yannick Haldner", - "author_inst": "Repertoire Immune Medicine, Cambridge, USA - Tepthera subsidiary, Schlieren, Switzerland" - }, - { - "author_name": "Robin Wuigk", - "author_inst": "Repertoire Immune Medicine, Cambridge, USA - Tepthera subsidiary, Schlieren, Switzerland" - }, - { - "author_name": "Ohad Iosefson", - "author_inst": "Repertoire Immune Medicine, Cambridge, USA" - }, - { - "author_name": "Pooja Patel", - "author_inst": "Repertoire Immune Medicine, Cambridge, USA" - }, - { - "author_name": "Katherine Triebel", - "author_inst": "Repertoire Immune Medicine, Cambridge, USA" - }, - { - "author_name": "Manfred Kopf", - "author_inst": "Institute of Molecular Health Sciences, ETH Zurich, Switzerland" - }, - { - "author_name": "Joanna Swain", - "author_inst": "Repertoire Immune Medicine, Cambridge, USA" - }, - { - "author_name": "Jan Kisielow", - "author_inst": "Repertoire Immune Medicine, Cambridge, USA - Tepthera subsidiary, Schlieren, Switzerland" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.02.433390", "rel_title": "Vaccination with SARS-CoV-2 Spike Protein and AS03 Adjuvant Induces Rapid Anamnestic Antibodies in the Lung and Protects Against Virus Challenge in Nonhuman Primates", @@ -902919,6 +903745,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.01.21252598", + "rel_title": "Investigation of ventilation conditions associated with CO2 concentration changes in ultrasonographic exam room from the perspective of COVID-19 infection control", + "rel_date": "2021-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.01.21252598", + "rel_abs": "ObjectivesVentilation is an important factor in preventing COVID-19 infection. To clarify the state of ventilation in ultrasonic exam rooms, as an index of ventilation rate, the carbon dioxide (CO2) concentration in our exam rooms was measured.\n\nMethodsWe measured the CO2 concentration in each exam room before the examination and 0-15 minutes after end of the exam.\n\nThe subjects were 70 cases (abdomen: 24, breast: 16, neck: 16, and musculoskeletal: 14). In infant cases, one parent accompanied the patient during the examination.\n\nResultsThe highest CO2 concentration was 2261 ppm, observed after the breast examination. In all cases, the CO2 concentration in the exam room was highest immediately after the examination or two minutes after. Almost all cases had recovered to within 120% of the pre-examination CO2 concentrations within 15 minutes after the examination. The average CO2 concentration after ultrasonography was significantly higher for breast examinations than others.\n\nConclusionsEven in a hospital with modern ventilation equipment, the CO2 concentration in the ultrasound room was high after the exam and it takes 15 minutes to recover to the pre-exam state. Care must be taken to ensure adequate ventilation in ultrasonographic facilities.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Roka Namoto Matsubayashi", + "author_inst": "National Hospital Organization Kyushu Medical Center" + }, + { + "author_name": "Shino Harada", + "author_inst": "National Hospital Organization Kyushu Medical Center" + }, + { + "author_name": "Mitsuhiro Tominaga", + "author_inst": "National Hospital Organization Kyushu Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.03.01.21252330", "rel_title": "Does Telemedicine Reduce health disparities? Longitudinal Evidence during the COVID-19 Pandemic in the US", @@ -904199,85 +905052,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.01.433110", - "rel_title": "Ultrapotent miniproteins targeting the receptor-binding domain protect against SARS-CoV-2 infection and disease in mice", - "rel_date": "2021-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.01.433110", - "rel_abs": "Despite the introduction of public health measures and spike protein-based vaccines to mitigate the COVID-19 pandemic, SARS-CoV-2 infections and deaths continue to rise. Previously, we used a structural design approach to develop picomolar range miniproteins targeting the SARS-CoV-2 receptor binding domain. Here, we investigated the capacity of modified versions of one lead binder, LCB1, to protect against SARS-CoV-2-mediated lung disease in human ACE2-expressing transgenic mice. Systemic administration of LCB1-Fc reduced viral burden, diminished immune cell infiltration and inflammation, and completely prevented lung disease and pathology. A single intranasal dose of LCB1v1.3 reduced SARS-CoV-2 infection in the lung even when given as many as five days before or two days after virus inoculation. Importantly, LCB1v1.3 protected in vivo against a historical strain (WA1/2020), an emerging B.1.1.7 strain, and a strain encoding key E484K and N501Y spike protein substitutions. These data support development of LCB1v1.3 for prevention or treatment of SARS-CoV-2 infection.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "James Brett Case", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Rita E. Chen", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Longxing Cao", - "author_inst": "Institute for Protein Design" - }, - { - "author_name": "Boaling Ying", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Emma S Winkler", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Inna Goreshnik", - "author_inst": "University of Washington" - }, - { - "author_name": "Swathi Shrihari", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Natasha M Kafai", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Adam L Bailey", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Xuping Xie", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Rashmi Ravichandran", - "author_inst": "Institute for Protein Design" - }, - { - "author_name": "Lauren Carter", - "author_inst": "Institute for Protein Design" - }, - { - "author_name": "Lance Stewart", - "author_inst": "University of Washington" - }, - { - "author_name": "David Baker", - "author_inst": "University of Washington" - }, - { - "author_name": "Michael S. Diamond", - "author_inst": "Washington University School of Medicine" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.02.27.433186", "rel_title": "Effect of SARS-CoV-2 proteins on vascular permeability", @@ -904633,6 +905407,137 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.03.01.433314", + "rel_title": "Reduced antibody cross-reactivity following infection with B.1.1.7 than with parental SARS-CoV-2 strains", + "rel_date": "2021-03-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.01.433314", + "rel_abs": "We examined the immunogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant B.1.1.7 that arose in the United Kingdom and spread globally. Antibodies elicited by B.1.1.7 infection exhibited significantly reduced recognition and neutralisation of parental strains or of the South Africa B.1.351 variant, than of the infecting variant. The drop in cross-reactivity was more pronounced following B.1.1.7 than parental strain infection, indicating asymmetric heterotypic immunity induced by SARS-CoV-2 variants.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Nikhil Faulkner", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Kevin Ng", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Mary Wu", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Ruth Harvey", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Saira Hussain", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Maria Greco", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "William Bolland", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Scott Warchal", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Marios Margaritis", + "author_inst": "UCL" + }, + { + "author_name": "Stavroula Paraskevopoulou", + "author_inst": "UCL" + }, + { + "author_name": "Judith Heaney", + "author_inst": "UCL" + }, + { + "author_name": "Hannah Rickman", + "author_inst": "UCL" + }, + { + "author_name": "Catherine Houlihan", + "author_inst": "UCL" + }, + { + "author_name": "Moria Spyer", + "author_inst": "UCL" + }, + { + "author_name": "Daniel Frampton", + "author_inst": "UCL" + }, + { + "author_name": "Matthew Byott", + "author_inst": "UCL" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "University of KwaZulu-Natal,SA" + }, + { + "author_name": "Alex Sigal", + "author_inst": "University of KwaZulu-Natal,SA" + }, + { + "author_name": "Svend Kjaer", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Charles Swanton", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Sonia Gandhi", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Rupert Beale", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Steve Gamblin", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "John Mccauley", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Rodney Daniels", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Michael Howell", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "David Bauer", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Eleni Nastouli", + "author_inst": "UCL" + }, + { + "author_name": "George Kassiotis", + "author_inst": "The Francis Crick Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.27.433180", "rel_title": "Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees.", @@ -905945,73 +906850,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.25.21252447", - "rel_title": "Seroepidemiology of SARS-CoV-2 infections in an urban Nicaraguan population", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252447", - "rel_abs": "In a Nicaraguan population-based cohort, SARS-CoV-2 seroprevalence was 34%, with higher prevalence in children compared to adults. Having a seropositive household member was associated with a two-fold probability of individual seropositivity, suggesting a role for household transmission. Co-morbidities and preventive behaviors were not associated with SARS-CoV-2 seroprevalence.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Fredman Gonz\u00e1lez", - "author_inst": "National Autonomous University of Nicaragua - Le\u00f3n" - }, - { - "author_name": "Nadja Alexandra Vielot", - "author_inst": "University of North Carolina at Chapel Hill School of Medicine" - }, - { - "author_name": "Michael Sciaudone", - "author_inst": "University of North Carolina at Chapel Hill Schoolof Medicine" - }, - { - "author_name": "Christian Toval-Ru\u00edz", - "author_inst": "National Autonomous University of Nicaragua - Le\u00f3n" - }, - { - "author_name": "LAKSHMANANE PREMKUMAR", - "author_inst": "University of North Carolina School of Medicine" - }, - { - "author_name": "Lester Gutierrez", - "author_inst": "National Autonomous University of Nicaragua - Le\u00f3n" - }, - { - "author_name": "Eduing Centeno Cuadra", - "author_inst": "National Autonomous University of Nicaragua - Le\u00f3n" - }, - { - "author_name": "Patricia Bland\u00f3n", - "author_inst": "National Autonomous University of Nicaragua - Le\u00f3n" - }, - { - "author_name": "Aravinda de Silva", - "author_inst": "University of North Carolina at Chapel Hill School of Medicine" - }, - { - "author_name": "Rebecca Rubinstein", - "author_inst": "University of North Carolina at Chapel Hill School of Medicine" - }, - { - "author_name": "Natalie Bowman", - "author_inst": "University of North Carolina at Chapel Hill School of Medicine" - }, - { - "author_name": "Sylvia Becker-Dreps", - "author_inst": "University of North Carolina at Chapel Hill School of Medicine" - }, - { - "author_name": "Filemon Bucardo", - "author_inst": "National Autonomous University of Nicaragua - Le\u00f3n" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.25.21252454", "rel_title": "RT-qPCR assay for detection of British (B.1.1.7) and South Africa (B.1.351) variants of SARS-CoV-2", @@ -906207,6 +907045,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.25.21252451", + "rel_title": "Muscle Strength Explains the Protective Effect of Physical Activity against COVID-19 Hospitalization among Adults aged 50 Years and Older", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252451", + "rel_abs": "ObjectivesPhysical activity has been proposed as a protective factor for COVID-19 hospitalization. However, the mechanisms underlying this association are unclear. Here, we examined the association between physical activity and COVID-19 hospitalization and whether this relationship was explained by other risk factors for severe COVID-19.\n\nMethodWe used data from adults aged 50 years and older from the Survey of Health, Ageing and Retirement in Europe. The outcome was self-reported hospitalization due to COVID-19 measured before August 2020. The main exposure was usual physical activity, self-reported between 2004 and 2017. Data were analyzed using logistic regression models.\n\nResultsAmong the 3139 participants included in the study (69.3 {+/-} 8.5 years, 1763 women), 266 were tested positive for COVID-19 and 66 were hospitalized. Results showed that individuals who engaged in physical activity more than once a week had lower odds of COVID-19 hospitalization than individuals who hardly ever or never engaged in physical activity (odds ratios = 0.41, 95% confidence interval = 0.22-0.74, p = .004). This association between physical activity and COVID-19 hospitalization was explained by muscle strength, but not by other risk factors.\n\nConclusionThese findings suggest that, after 50 years of age, engaging in physical activity more than once a week is associated with lower odds of COVID-19 hospitalization. The protective effect of physical activity on COVID-19 hospitalization is explained by muscle strength.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Silvio Maltagliati", + "author_inst": "Universite Grenoble Alpes" + }, + { + "author_name": "Stefan Sieber", + "author_inst": "University of Geneva" + }, + { + "author_name": "Philippe Sarrazin", + "author_inst": "Universite Grenoble Alpes" + }, + { + "author_name": "Stephane Cullati", + "author_inst": "University of Fribourg" + }, + { + "author_name": "Aina Chalabaev", + "author_inst": "Universite Grenoble Alpes" + }, + { + "author_name": "Gregoire P Millet", + "author_inst": "University of Lausanne" + }, + { + "author_name": "Matthieu P Boisgontier", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Boris Cheval", + "author_inst": "University of Geneva" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2021.02.26.21252552", "rel_title": "The Charitable Feeding System helps Food Insecure Participants maintain Fruit and Vegetable intake during COVID-19.", @@ -907407,65 +908292,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.21.21251691", - "rel_title": "Laboratory-Developed Test for SARS-CoV-2 Using Saliva Samples at the University of California, Riverside", - "rel_date": "2021-02-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.21.21251691", - "rel_abs": "Here we describe a relatively quick, simple, economical and accurate laboratory developed test (LDT) for detection of SARS-CoV-2 in heated and diluted saliva samples without RNA extraction. Our protocol is a variation of the University of Illinois Urbana-Champaign SHIELD LDT. Differences include chilling of the samples during dilution and using a reduced volume for the qRT-PCR reactions. The level of detection for our LDT is 3125 copies/ml, which compares favorably with other saliva-based tests. Initial validation studies with a limited number of patient samples have demonstrated excellent agreement between results using our LDT and those obtained from external laboratories. The cost of consumables for our test is under $8 and a throughput of 1000 tests/day can be achieved with 3-4 personnel.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Rong Hai", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Matthew Collin", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Sophia Tsau", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Daniel Raygoza", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Juliet Morrison", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Alexander J. Carrillo", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Logan A Collier", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Walter Bayubay", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Kenneth Han", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Isgouhi Kaloshian", - "author_inst": "University of California, Riverside" - }, - { - "author_name": "Katherine A Borkovich", - "author_inst": "University of California, Riverside" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.23.21252143", "rel_title": "Risk of death among teachers in England and Wales during the Covid19 pandemic", @@ -907693,6 +908519,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.23.21252319", + "rel_title": "Control of COVID-19 transmission on an urban university campus during a second wave of the pandemic", + "rel_date": "2021-02-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252319", + "rel_abs": "ImportanceThe COVID-19 pandemic had a wide-ranging impact on educational institutions across the United States. Given potential financial challenges and adverse psychosocial effects of campus closure, as done in the spring of 2020 in response to the first wave, many institutions of higher education developed strategies to allow campuses to reopen and operate in the fall despite the ongoing threat of COVID-19. Many however opted to have limited campus re-opening in order to minimize potential risk of spread of SARS-CoV-2.\n\nObjectiveTo analyze how Boston University (BU) fully reopened its campus in the fall of 2020 and controlled COVID-19 transmission despite worsening transmission in the city of Boston.\n\nDesignMulti-faceted intervention case study.\n\nSettingLarge urban university campus.\n\nInterventionsThe BU response included a high-throughput SARS-CoV-2 PCR testing facility with capacity to delivery results in less than 24 hours; routine asymptomatic screening for COVID-19; daily health attestations; compliance monitoring and feedback; robust contact tracing, quarantine and isolation in on campus facilities; face mask use; enhanced hand hygiene; social distancing recommendations; de-densification of classrooms and public places; and enhancement of all building air systems.\n\nMain Outcomes and MeasuresBetween August and December 2020, BU conducted >500,000 COVID-19 tests and identified 719 individuals with COVID-19: 627 (87.2%) students, 11 (1.5%) faculty, and 212 (25.5%) staff. Overall, about 1.8% of the BU community tested positive. Infections among faculty and staff were mostly acquired off campus, while undergraduate infections were more likely acquired in non-classroom campus settings. Of 837 close contacts traced, 86 (10.3%) tested positive for COVID-19. BU contact tracers identified a source of transmission for 51.5% of cases with 55.7% identifying a source outside of BU. Among infected faculty and staff with a known source of infection, the majority reported a transmission source outside of BU (100% for faculty and 79.8% for staff).\n\nConclusions and RelevanceBU was successful in containing COVID-19 transmission on campus while minimizing off campus acquisition of COVID-19 from the greater Boston area. A coordinated strategy of testing, contact tracing, isolation and quarantine, with robust management and oversight, can control COVID-19 transmission, even in an urban university setting.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Davidson H Hamer", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Laura White", + "author_inst": "Boston University" + }, + { + "author_name": "Helen E Jenkins", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "christopher J gill", + "author_inst": "boston university school of public health" + }, + { + "author_name": "Hannah N. Landsberg", + "author_inst": "Boston University" + }, + { + "author_name": "Catherine Klapperich", + "author_inst": "Boston University" + }, + { + "author_name": "Katia Bulekova", + "author_inst": "Boston University" + }, + { + "author_name": "Judy Platt", + "author_inst": "Boston University" + }, + { + "author_name": "Linette Decarie", + "author_inst": "Boston University" + }, + { + "author_name": "Wayne Gilmore", + "author_inst": "Boston University" + }, + { + "author_name": "Megan Pilkington", + "author_inst": "Boston University" + }, + { + "author_name": "Trevor L. McDowell", + "author_inst": "Boston University" + }, + { + "author_name": "Mark A. Fari", + "author_inst": "Boston University" + }, + { + "author_name": "Douglas M. Densmore", + "author_inst": "Boston University" + }, + { + "author_name": "Lena Landaverde", + "author_inst": "Boston University" + }, + { + "author_name": "Wenrui Li", + "author_inst": "Boston University" + }, + { + "author_name": "Tom Rose", + "author_inst": "Boston University" + }, + { + "author_name": "Stephen P. Burgay", + "author_inst": "Boston University" + }, + { + "author_name": "Candice Miller", + "author_inst": "Boston University" + }, + { + "author_name": "Lynn Doucette-Stamm", + "author_inst": "Boston University" + }, + { + "author_name": "Kelly Lockard", + "author_inst": "Boston University" + }, + { + "author_name": "Kenneth Elmore", + "author_inst": "Boston University" + }, + { + "author_name": "Tracy Schroeder", + "author_inst": "Boston University" + }, + { + "author_name": "Ann M. Zaia", + "author_inst": "Boston University" + }, + { + "author_name": "Eric D. Kolaczyk", + "author_inst": "Boston University" + }, + { + "author_name": "Gloria Waters", + "author_inst": "Boston University" + }, + { + "author_name": "Robert A. Brown", + "author_inst": "Boston University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.23.21252299", "rel_title": "The Public Health Impact of Delaying a Second Dose of the BNT162b2 or mRNA-1273 COVID-19 Vaccine", @@ -909493,101 +910442,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.23.21251975", - "rel_title": "The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers (UK-REACH): Protocol for a prospective longitudinal cohort study of healthcare and ancillary workers in UK healthcare settings", - "rel_date": "2021-02-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21251975", - "rel_abs": "IntroductionThe COVID-19 pandemic has resulted in significant morbidity and mortality, and has devastated economies in many countries. Amongst the groups identified as being at increased risk from COVID-19 are healthcare workers (HCWs) and ethnic minority groups. Emerging evidence suggests HCWs from ethnic minority groups are at increased risk of adverse COVID-19-related physical and mental health outcomes. To date there has been no large-scale analysis of these risks in UK healthcare workers or ancillary workers in healthcare settings, stratified by ethnicity or occupation type, and adjusted for potential confounders. This paper reports the protocol for a prospective longitudinal questionnaire study of UK HCWs, as part of the UK-REACH programme (The United Kingdom Research study into Ethnicity And COVID-19 outcomes in Healthcare workers).\n\nMethods and analysisA baseline questionnaire with follow-up questionnaires at 4 and 8 months will be administered to a national cohort of UK healthcare workers and ancillary workers in healthcare settings, and those registered with UK healthcare regulators. With consent, data will be linked to health records, and participants followed up for 25 years.\n\nUnivariate associations between ethnicity and primary outcome measures (clinical COVID-19 outcomes, and physical and mental health) and key confounders/explanatory variables will be tested, followed by multivariable analyses to test for associations between ethnicity and key outcomes adjusted for the confounder/explanatory variables, with interactions included as appropriate. Using follow-up data, multilevel models will be used to model changes over time by ethnic group, facilitating understanding of absolute and relative risks in different ethnic groups, and generalisability of findings.\n\nEthics and disseminationThe study is approved by Health Research Authority (reference 20/HRA/4718), and carries minimal risk to participants. We aim to manage the small risk of participant distress due to being asked questions on sensitive topics by clearly indicating on the participant information sheet that the questionnaire covers sensitive topics and that participants are under no obligation to answer these, or indeed any other, questions, and by providing links to support organisations. Results will be disseminated with reports to Government and papers uploaded to pre-print servers and submitted to peer reviewed journals.\n\nRegistration detailsTrial ID: ISRCTN11811602\n\nSTRENGTHS AND LIMITATIONS OF THIS STUDYO_LINational, UK-wide, study, aiming to capture variety of healthcare worker job roles including ancillary workers in healthcare settings.\nC_LIO_LILongitudinal study including three waves of questionnaire data collection, and linkage to administrative data over 25 years, with consent.\nC_LIO_LIUnique support from all major UK healthcare worker regulators, relevant healthcare worker organisations, and a Professional Expert Panel to increase participant uptake and the validity of findings.\nC_LIO_LIPotential for self-selection bias and low response rates, and the use of electronic invitations and online data collection makes it harder to reach ancillary workers without regular access to work email addresses.\nC_LI", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Katherine Woolf", - "author_inst": "University College London" - }, - { - "author_name": "Carl Melbourne", - "author_inst": "University of Leicester" - }, - { - "author_name": "Luke Bryant", - "author_inst": "University of Leicester" - }, - { - "author_name": "Anna Louise Guyatt", - "author_inst": "University of Leicester" - }, - { - "author_name": "Ian Christopher McManus", - "author_inst": "University College London" - }, - { - "author_name": "Amit Gupta", - "author_inst": "University Hospitals Oxford NHS Foundation Trust" - }, - { - "author_name": "Robert C Free", - "author_inst": "University of Leicester" - }, - { - "author_name": "Laura Nellums", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Sue Carr", - "author_inst": "General Medical Council, University Hospitals Leicester NHS Trust" - }, - { - "author_name": "Catherine John", - "author_inst": "University of Leicester" - }, - { - "author_name": "Christopher A Martin", - "author_inst": "University of Leicester" - }, - { - "author_name": "Louise V Wain", - "author_inst": "University of Leicester" - }, - { - "author_name": "Laura J Gray", - "author_inst": "University of Leicester" - }, - { - "author_name": "Claire Garwood", - "author_inst": "University of Leicester" - }, - { - "author_name": "Vishant Modhwadia", - "author_inst": "University of Leicester" - }, - { - "author_name": "Keith Abrams", - "author_inst": "University of York" - }, - { - "author_name": "Martin D Tobin", - "author_inst": "University of Leicester" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "University of Leicester" - }, - { - "author_name": "Manish Pareek", - "author_inst": "University of Leicester" - }, - { - "author_name": "- UK-REACH Study Collaborative Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.23.21252231", "rel_title": "Outcomes of Percutaneous Tracheostomy for Patients with SARS-CoV-2 Respiratory Failure", @@ -909819,6 +910673,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.23.21252294", + "rel_title": "Evaluation of COVID-19 as a risk factor for maternal-fetal and neonatal complications: protocol of a systematic review and meta-analysis of cohort and case-control studies.", + "rel_date": "2021-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252294", + "rel_abs": "BackgroundCOVID-19 in pregnant women has been suggested to impair maternal-fetal and neonatal outcomes. We then designed the present systematic review with meta-analysis to evaluate the repercussion of such disease over maternal fetal and neonatal mortality, need for intensive care, way of delivery, premature delivery, birth weight, Apgar score, presence of intrauterine growth restriction (IGR), and presence of amniotic fluid change.\n\nMethodsWe will conduct a computerized search through MEDLINE/PubMed, LILACS/BIREME, Web of science, Biorxiv, Medrxiv, and Embase on July 23, 2020. We will include cohort and case-control studies fully reported comparing pregnant women with COVID-19 with those not affected by the disease for maternal fetal and neonatal mortality, need for intensive care, way of delivery, premature delivery occurrence, birth weight, Apgar scores, presence of intrauterine growth restriction, and presence of amniotic fluid change. Three doubles of reviewers will perform in duplicate and independently all steps on screening, risk of bias judgments, and data extraction with ability to discuss disagreements with supervising authors. Pooled effects will be estimated by both fixed and random-effects models and presented according to qualitative and quantitative heterogeneity assessment. Sensitivity analyses will be performed as well as a priori subgroup, meta-regression and multiple meta-regression analyses. Well also evaluate the risk of selective publication by assessing funnel plot asymmetry and the quality of the evidence by the application of the GRADE recommendations.\n\nDiscussionThis systematic review with meta-analysis aims to assess the repercussion of COVID-19 in pregnant women over maternal-fetal and neonatal outcomes and to help clinicians and health systems improve such population outcomes throughout the current pandemic.\n\nSystematic review registrationThis review protocol was also submitted to PROSPERO registration on February 9, 2021.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Priscila Bezerra", + "author_inst": "Instituto de Medicina Integral professor Fernando Figueira" + }, + { + "author_name": "Fernanda Gabriella de Siqueira Barros Nogueira Sr.", + "author_inst": "Instituto de Medicina Integral Prof. Fernando Figueira (IMIP)" + }, + { + "author_name": "Alan Chaves dos Santos", + "author_inst": "Instituto de medicina integral professor Fernando Figueira" + }, + { + "author_name": "Anna Katharina Souza Lima", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "David Emanuel Ribeiro", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Elias Almeida Silva Barbosa", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Suellen Casado dos Santos", + "author_inst": "Universidade Federal de Pernambuco" + }, + { + "author_name": "Clistenes Cristian de Carvalho", + "author_inst": "Instituto de Medicina Integral Professor Fernando Figueira" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2021.02.23.21251915", "rel_title": "Clinical evaluation of the molecular-based BD SARS-CoV-2/Flu for the BD MAX\u2122 System", @@ -911407,37 +912308,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.23.21252284", - "rel_title": "Depression and anxiety before and during the COVID-19 lockdown: a longitudinal cohort study with university students", - "rel_date": "2021-02-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252284", - "rel_abs": "BackgroundFor young people, just as in the general population, COVID-19 caused many changes in their lives, including an increased risk for mental illness symptoms. We aimed to study the impact of the COVID-19 pandemic in anxiety and depression symptoms in a cohort of university students.\n\nMethodsThis study is part of broader longitudinal research on university students mental health with data of the Portuguese version of The Patient Health Questionnaire (PHQ-9) and the Portuguese version of the Generalised Anxiety Disorder (GAD-7) with evaluations on January, May and October 2019 and June 2020, as well as socio-demographic information.\n\nResults341 university students (257 females and 84 males) were included, with a mean age of 19.91 (SD=1.58). In June 2020, the mean for perceived wellbeing loss was 60.47% (SD=26.56) and 59.54% (SD=28.95) for mental health loss. The proportion of students with scores equal to or above 15 in the PHQ-9 ranged between 22.6% and 25.5% in 2019 and 37.0% in June 2020. The proportion of GAD-7 scores above cut-off ten ranged between 46.0% and 47.8% in 2019 and 64.5% in 2020. Compared with preceding trends, PHQ-9 scores were 3.11 (CI=2.40-3.83) higher than expected, and GAD-7 scores were 3.56 (CI=2.75-5.37) higher.\n\nDiscussionCOVID-19 impacted negatively depressive and anxiety symptoms, confirming previous studies and young peoples vulnerability in such uncertain times.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Virginia Conceicao", - "author_inst": "EPIUnit - Institute of Public Health, University of Porto, Portugal" - }, - { - "author_name": "Ines Rothes", - "author_inst": "Faculty of Psychology and Education Science, University of Porto, Portugal" - }, - { - "author_name": "Ricardo Gusmao", - "author_inst": "EPIUnit - Institute of Public Health, University of Porto, Portugal" - }, - { - "author_name": "Henrique Barros", - "author_inst": "EPIUnit - Institute of Public Health, University of Porto, Portugal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.02.23.21249481", "rel_title": "A longitudinal study of healthcare workers' surveillance during the ongoing COVID-19 Epidemics in Italy: is SARS-CoV-2 still a threat for the Health-care System?", @@ -911829,6 +912699,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.22.21252254", + "rel_title": "Associations Between Google Search Trends for Symptoms and COVID-19 Confirmed and Death Cases in the United States", + "rel_date": "2021-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252254", + "rel_abs": "We utilize functional data analysis techniques to investigate patterns of COVID-19 positivity and mortality in the US and their associations with Google search trends for COVID-19 related symptoms. Specifically, we represent state-level time series data for COVID-19 and Google search trends for symptoms as smoothed functional curves. Given these functional data, we explore the modes of variation in the data using functional principal component analysis (FPCA). We also apply functional clustering analysis to identify patterns of COVID-19 confirmed case and death trajectories across the US. Moreover, we quantify the associations between Google COVID-19 search trends for symptoms and COVID-19 confirmed case and death trajectories using dynamic correlation. Finally, we examine the dynamics of correlations for the top nine Google search trends of symptoms commonly associated with COVID-19 confirmed case and death trajectories. Our results reveal and characterize distinct patterns for COVID-19 spread and mortality across the US. The dynamics of these correlations suggest the feasibility of using Google queries to forecast COVID-19 cases and mortality for up to three weeks in advance. Our results and analysis framework set the stage for the development of predictive models for forecasting COVID-19 confirmed cases and deaths using historical data and Google search trends for nine symptoms associated with both outcomes.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Mostafa Abbas", + "author_inst": "Geisinger" + }, + { + "author_name": "Thomas B. Morland", + "author_inst": "Geisinger" + }, + { + "author_name": "Eric S. Hall", + "author_inst": "Geisinger" + }, + { + "author_name": "Yasser El-Manzalawy", + "author_inst": "Geisinger" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.23.21252230", "rel_title": "Prior COVID-19 Infection and Antibody Response to Single Versus Double Dose mRNA SARS-CoV-2 Vaccination", @@ -913389,41 +914290,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.02.20.21252129", - "rel_title": "Impact of the COVID-19 pandemic on mental health among Greek adults: a cross-sectional survey.", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.20.21252129", - "rel_abs": "ObjectivesThe coronavirus disease 2019 (COVID-19) pandemic and mitigation measures based on social distancing are expected to have serious adverse effects on mental health. This cross-sectional study aimed to examine self-reported changes in the mental health status of Greek adults.\n\nStudy designThe current study is a primary research conducted on Greek adults during the first wave of the epidemic (March to April 2020).\n\nMethodsA total of 527 individuals participated in an online survey using a validated questionnaire (State-Trait Anxiety Inventory-STAI and DASS-21).\n\nResultsThe respondents had a moderate mental health status based on the following scores: STAI-S, 45.8; STAI-T, 40.7; depression, 4.6; anxiety, 3.1; and stress, 6.1. Women, younger respondents, those from lower income households, and those living in smaller apartments experienced increased depression, anxiety, and stress. Additionally, infection control practices during the COVID-19 pandemic such as the use of masks, gloves, and antiseptic can drastically decrease the prevalence of mental health illnesses.\n\nConclusionsThese findings can be used by the Greek State to reduce the effects of COVID-19 on the mental health of the population and protect socially vulnerable groups.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Efthimios Dragotis", - "author_inst": "Department of Business Management and Administration, University of Patras, Greece" - }, - { - "author_name": "Korina Atsopardi", - "author_inst": "Laboratory of Molecular Biology and Immunology, Department of Pharmacy, University of Patras, Greece" - }, - { - "author_name": "Anastasia Barbouni", - "author_inst": "Department of Public and Community Health, University of West Attica" - }, - { - "author_name": "Konstantinos Farsalinos", - "author_inst": "University of West Attica" - }, - { - "author_name": "Konstantinos Poulas", - "author_inst": "Laboratory of Mol. Biology and Immunology" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.19.21252089", "rel_title": "Follow-up study in the ski-resort Ischgl: Antibody and T cell responses to SARS-CoV-2 persisted for up to 8 months after infection and transmission of virus was low even during the second infection wave in Austria", @@ -913751,6 +914617,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.19.21252073", + "rel_title": "Health-related quality of life of adult COVID-19 patients following one-month illness experience since diagnosis: findings of a cross-sectional study in Bangladesh", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.19.21252073", + "rel_abs": "BackgroundThe pandemic coronavirus disease 2019 (COVID-19) stances an incredible impact on the quality of life of the patients. The disease not only denigrates the physical health of the patients but also affects their mental health. This cross-sectional study aimed to assess the health-related quality of life (HRQOL) of patients.\n\nMethodsThe study was conducted at the National Institute of Preventive and Social Medicine (NIPSOM), Dhaka, Bangladesh during the period from June to November 2020. The study enrolled 1204 adult (>18 years) COVID-19 patients diagnosed by real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay and completed the one-month duration of illness. The patients were interviewed with the CDC HRQOL-14 questionnaire to assess their HRQOL. Data were collected by telephone-interview and reviewing medical records using a semi-structured questionnaire and checklist respectively. Informed consent was obtained from each patient before data collection.\n\nResultsThe majority of the COVID-19 patients were males (72.3%), urban residents (50.2%), and diverse service holders (49.6%). More than one-third (35.5%) of patients had comorbidity including hypertension (55.6%), diabetes mellitus (55.6%), ischaemic heart disease (16.4%), chronic lung (12.4%), kidney (2.8%), and liver (4.2%) diseases. The mean{+/-}SD duration of physical illness was 9.83({+/-}7.09) days, and it was 7.97({+/-}8.12) days for mental illness. During the one-month disease course, the general health condition was excellent/very good/good in 70.1% of the patients while it was fair/poor in 29.8% of the patients. Older age, sex, and marital status were significantly associated with at least one dimension of HRQOL. Patients having symptoms of COVID-19 and comorbidity had significantly poorer HRQOL.\n\nConclusionCOVID-19 pretenses a significant impact on the HRQOL of the patients including physical and mental illness during the clinical course. Our findings suggest more pragmatic preventive, promotive, and curative measures considering illness experiences of the COVID-19 patients to restore their quality of life.\n\nHighlightsSince COVID-19 was identified first in china in 2019, it has been transmitted globally and caused a significant impact on human health. A few studies have been carried out on HRQOL of COVID-19 patients and struggled with an accurate estimation of the severity of their physical and mental illness. Most of the studies recognized the poor quality of life of COVID-19 patients after the one-month disease course. Our study provides new insights on the HRQOL of the COVID-19 patients using the CDC HRQOL-14 questionnaire. We measured the HRQOL following one-month illness experience of the patients using three modules: the healthy days core; the activity limitations; and the healthy days symptoms. The study adds information regarding general health conditions including both the physical and mental health of COVID-19 patients. The study also complements information regarding the activity limitations of the patients. The study findings could contribute to designing an efficient clinical algorithm to alleviate the illness sufferings of the COVID-19 patients using a more pragmatic approach. The study conserves decisive policy implications to concoct effective interventions for improving the HRQOL of COVID-19 patients in the country and elsewhere in other countries world-wide.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Md. Ziaul Islam", + "author_inst": "National Institute of Preventive and Social Medicine (NIPSOM)" + }, + { + "author_name": "Baizid Khoorshid Riaz", + "author_inst": "National Institute of Preventive and Social Medicine" + }, + { + "author_name": "Syeda Sumaiya Efa", + "author_inst": "Diabetic Association of Bangladesh" + }, + { + "author_name": "Sharmin Farjana", + "author_inst": "Shaheed Suhrawardy Medical College Hospital" + }, + { + "author_name": "Fahad Mahmood", + "author_inst": "National Institute of Preventive and Social Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.20.21251855", "rel_title": "Transmission of SARS-CoV-2 Considering Shared Chairs in Outpatient Dialysis: A Real-World Case-Control Study", @@ -915427,69 +916328,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.21.21252163", - "rel_title": "COVID-19 Vaccine Hesitancy in Underserved Communities of North Carolina", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.21.21252163", - "rel_abs": "BackgroundIn the United States, underserved communities including Blacks and Latinx are disproportionately affected by COVID-19, and widespread vaccination is critical for curbing this pandemic. This study sought to estimate the prevalence of COVID-19 vaccine hesitancy, describe attitudes related to vaccination, and identify correlates among racial minority and marginalized populations across 9 counties in North Carolina.\n\nMethodsWe conducted a cross-sectional survey with a self-administered questionnaire distributed at free COVID-19 testing events in underserved rural and urban communities from August 27 - December 15, 2020. Vaccine hesitancy was defined as the response of \"no\" or \"dont know/not sure\" to whether the participant would get the COVID-19 vaccine as soon as it became available.\n\nResultsThe sample comprised 948 participants including 27.7% Whites, 59.6% Blacks, 12.7% Latinx, and 63% female. Thirty-two percent earned <$20K annually, 60% owned a computer and [~]80% had internet access at home. The prevalence of vaccine hesitancy was 68.9% including 62.7%, 74%, and 59.5% among Whites, Blacks, and Latinx, respectively. Between September and December, the largest decline in vaccine hesitancy occurred among Whites (27.5 percentage points), followed by Latinx (17.6) and the smallest decline was among Black respondents (12.0). 51.2% of the respondents reported vaccine safety concerns, 23.7% wanted others to get of the respondents reported they would trust health care providers with information about the COVID-19 vaccine. Factors associated with hesitancy in multivariable logistic regression included being female (OR=1.90 95%CI[1.36, 2.64]), being Black (OR=1.68 [1.106 2.45]), calendar month (OR=0.76 [0.63, 0.92]), safety concerns (OR=4.28 [3.06, 5.97]), and government distrust (OR=3.57 [2.26, 5.63]).\n\nConclusionsThis study reached underserved minority populations in a number of different locations to investigate COVID-19 vaccine hesitancy. We built on existing relationships and further engaged the community, stake holders and health department to provide free COVID-19 testing. This direct approach permitted assessment of vaccine hesitancy (which was much higher than national estimates), distrust, and safety concerns.\n\nHighlightsO_LIThis study surveyed 948 adults at COVID-19 testing sites in 9 counties of North Carolina between August 27 and December 15, 2020 where vaccine hesitancy was widespread including 74% in Blacks, 62.7% in Whites and 59.5% in Latinx.\nC_LIO_LIVaccine hesitancy declined over time but remained high for Blacks.\nC_LIO_LIOn-site surveys conducted in underserved areas that were paper-based and self-administered permitted reaching adults with no internet (17%), no cell phone (20%), no computer (40%) and yearly incomes less than 20K (31%).\nC_LIO_LIWidespread vaccine hesitancy in predominately minority communities of NC must be addressed to successfully implement mass COVID-19 vaccination programs.\nC_LI", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Irene Doherty", - "author_inst": "North Carolina Central University" - }, - { - "author_name": "William Pilkington", - "author_inst": "North Carolina Central University" - }, - { - "author_name": "Laurin Brown", - "author_inst": "North Carolina Central University" - }, - { - "author_name": "Victoria Billings", - "author_inst": "North Carolina Central University" - }, - { - "author_name": "Undi Hoffler", - "author_inst": "North Carolina Central University" - }, - { - "author_name": "Lisa Paulin", - "author_inst": "North Carolina Central University" - }, - { - "author_name": "Sean K Kimbro", - "author_inst": "North Carolina Central University" - }, - { - "author_name": "Brittany Baker", - "author_inst": "North Carolina Central University" - }, - { - "author_name": "Tianduo Zhang", - "author_inst": "North Carolina Central University" - }, - { - "author_name": "Tracie Locklear", - "author_inst": "North Carolina Central University" - }, - { - "author_name": "Seronda Robinson", - "author_inst": "North Carolina Central University" - }, - { - "author_name": "Deepak Kumar", - "author_inst": "North Carolina Central University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.19.21251739", "rel_title": "A Prospective Clinical Evaluation of a Patient Isolation Hood During the COVID-19 Pandemic", @@ -915697,6 +916535,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.19.21252106", + "rel_title": "Impact of environmental temperature on Covid-19 spread: Model and analysis of measurements recorded during the second pandemic in Cyprus", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.19.21252106", + "rel_abs": "The paper investigates the effect of the environmental temperature on the spread of COVID-19. We study the daily numbers of the cases infected and deaths caused by Covid-19 during the second wave of the pandemic within 2020, and how they were affected by the daily average-high temperature for the districts of the Republic of Cyprus. Among the findings of the paper, we show that (i) the average ratio of the PCR to rapid positive tests is [~]2.57{+/-}0.25, as expected from the tests responses, indicating that PCR overestimates positivity by [~]2.5 times; (ii) the average age of deaths caused by Covid-19 increases with rate about a year of age per week; (iii) the probability of a person infected by Covid-19 to develop severe symptoms leading to death is strongly depended on the persons age, while the probability of having a death on the age of [~]67 or younger is less than 1/1000; (iv) the number of infected cases and deaths declined dramatically when the environmental temperature reaches and/or climbs above the critical temperature of TC=30.1{+/-}2.4 C0; (v) the observed negative correlation between the exponential growth rate of the infected cases and the environmental temperature can be described within the framework of chemical kinetics, with at least two competing reactions, the connection of the coronavirus towards the receptor and the dissolution of the coronavirus; the estimated activation energy difference corresponding to the competing chemical reactions, 0.212{+/-}0.25 eV, matches the known experimental value; and (vi) the infected cases will decline to zero, when the environmental temperature climbs above the critical temperature within the summery days of 2021, which is expected for the Republic of Cyprus by the 16th of May, 2021.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "George Livadiotis", + "author_inst": "Southwest Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.22.21252208", "rel_title": "Vaccination efforts in Brazil: scenarios and perspectives under a mathematical modeling approach", @@ -917185,33 +918042,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.21.21252147", - "rel_title": "A Second Wave? What Do People Mean By COVID Waves?- A Working Definition of Epidemic Waves", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.21.21252147", - "rel_abs": "Policymakers and researchers describe the COVID-19 epidemics by waves without a common vocabulary on what constitutes an epidemic wave, either in terms of a working definition or operationalization, causing inconsistencies and confusions. A working definition and operationalization can be helpful to characterize and communicate about epidemics. We propose a working definition of epidemic waves in the ongoing COVID-19 pandemic and an operationalization based on the public data of the effective reproduction number R. Our operationalization characterizes the numbers and durations of waves (upward and downward) in 178 countries and reveals patterns that can enable healthcare organizations and policymakers to make better description and assessment of the COVID crisis to make more informed resource planning, mobilization, and allocation temporally in the continued COVID-19 pandemic.\n\nOne Sentence SummaryA working definition and operationalization of waves to enable common ground to understand and communicate COVID-19 crisis.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Stephen X. Zhang", - "author_inst": "University of Adelaide" - }, - { - "author_name": "Francisc Arroyo Marioli", - "author_inst": "Central Bank of Chile" - }, - { - "author_name": "Renfei Gao", - "author_inst": "University of Manchester" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.23.432450", "rel_title": "The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation", @@ -917523,6 +918353,153 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.02.20.432046", + "rel_title": "Reduced binding and neutralization of infection- and vaccine-induced antibodies to the B.1.351 (South African) SARS-CoV-2 variant", + "rel_date": "2021-02-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.20.432046", + "rel_abs": "The emergence of SARS-CoV-2 variants with mutations in the spike protein is raising concerns about the efficacy of infection- or vaccine-induced antibodies to neutralize these variants. We compared antibody binding and live virus neutralization of sera from naturally infected and spike mRNA vaccinated individuals against a circulating SARS-CoV-2 B.1 variant and the emerging B.1.351 variant. In acutely-infected (5-19 days post-symptom onset), convalescent COVID-19 individuals (through 8 months post-symptom onset) and mRNA-1273 vaccinated individuals (day 14 post-second dose), we observed an average 4.3-fold reduction in antibody titers to the B.1.351-derived receptor binding domain of the spike protein and an average 3.5-fold reduction in neutralizing antibody titers to the SARS-CoV-2 B.1.351 variant as compared to the B.1 variant (spike D614G). However, most acute and convalescent sera from infected and all vaccinated individuals neutralize the SARS-CoV-2 B.1.351 variant, suggesting that protective immunity is retained against COVID-19.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Venkata Viswanadh Edara", + "author_inst": "Emory University" + }, + { + "author_name": "Carson Norwood", + "author_inst": "Emory University" + }, + { + "author_name": "Katharine Floyd", + "author_inst": "Emory University" + }, + { + "author_name": "Lilin Lai", + "author_inst": "Emory University" + }, + { + "author_name": "Meredith E Davis-Gardner", + "author_inst": "Emory University" + }, + { + "author_name": "William H Hudson", + "author_inst": "Emory University" + }, + { + "author_name": "Grace Mantus", + "author_inst": "Emory University" + }, + { + "author_name": "Lindsay E Nyhoff", + "author_inst": "Emory University" + }, + { + "author_name": "Max W Adelman", + "author_inst": "Emory University" + }, + { + "author_name": "Rebecca Fineman", + "author_inst": "Emory University" + }, + { + "author_name": "Shivan Patel", + "author_inst": "Emory University" + }, + { + "author_name": "Rebecca Byram", + "author_inst": "Emory University" + }, + { + "author_name": "Dumingu Nipuni Gomes", + "author_inst": "Emory University" + }, + { + "author_name": "Garett Michael", + "author_inst": "Emory University" + }, + { + "author_name": "Hayatu Abdullahi", + "author_inst": "Emory University" + }, + { + "author_name": "Nour Beydoun", + "author_inst": "Emory University" + }, + { + "author_name": "Bernadine Panganiban", + "author_inst": "Emory University" + }, + { + "author_name": "Nina McNair", + "author_inst": "Emory University" + }, + { + "author_name": "Kieffer Hellmeister", + "author_inst": "Emory University" + }, + { + "author_name": "Jamila Pitts", + "author_inst": "Emory University" + }, + { + "author_name": "Joy Winters", + "author_inst": "Emory University" + }, + { + "author_name": "Jennifer Kleinhenz", + "author_inst": "Emory University" + }, + { + "author_name": "Jacob Usher", + "author_inst": "Emory University" + }, + { + "author_name": "Anne Piantadosi", + "author_inst": "Emory University" + }, + { + "author_name": "Jesse J Waggoner", + "author_inst": "Emory University" + }, + { + "author_name": "Ahmed Babiker", + "author_inst": "Emory University" + }, + { + "author_name": "David S Stephens", + "author_inst": "Emory University" + }, + { + "author_name": "Evan J Anderson", + "author_inst": "Emory University" + }, + { + "author_name": "Srilatha Edupuganti", + "author_inst": "Emory University" + }, + { + "author_name": "Nadine Rouphael", + "author_inst": "Emory University" + }, + { + "author_name": "Rafi Ahmed", + "author_inst": "Emory University" + }, + { + "author_name": "Jens Wrammert", + "author_inst": "Emory University" + }, + { + "author_name": "Mehul S Suthar", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.20.432110", "rel_title": "A novel glucocorticoid and androgen receptor modulator reduces viral entry and innate immune inflammatory responses in the Syrian Hamster model of SARS-CoV-2", @@ -918843,33 +919820,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.15.21251772", - "rel_title": "Evaluation of rapid antibody test and chest computed tomography results of COVID-19 patients: A retrospective study", - "rel_date": "2021-02-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251772", - "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) continues to spread around the world. Therefore, rapid, simpler, and more accurate diagnostic tests are urgently needed to diagnose the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection. The purpose of this study was to evaluate the SARS-CoV-2 IgM/ IgG rapid antibody test results in symptomatic patients with COVID-19 and their chest computed tomography (CT) data.\n\nMethodsA total of 320 patients admitted to our hospital for different durations due to COVID-19 were included in the study. Serum samples were obtained within 0 to 7 days from COVID-19 patients confirmed by RT-PCR and chest CT scan. According to the SARS-CoV-2 RT-PCR results, the patients included in the study were divided into two groups: PCR positive group (n=46), and PCR negative group (n=274).\n\nResultsOf the 320 COVID-19 serum samples, IgM, IgG, and IgM/IgG were detected in 9.4%, 3.1%, and 17.8% within one week respectively. IgG/IgM antibodies were not detected in 69.7% of the patients. In the study, it was determined that 249 (77.8%) of 320 patients had positive chest CT scans. Four (5.6%) of 100 patients with negative chest CT scan had IgM positive and 2 (2.8%) had both IgM/ IgG positive. IgM was detected in 23 (9.2%), IgG in 1 (0.4%) and IgM/IgG in 35 (14%) of chest CT scan positive patients. The rate of CT findings in patients with antibody positivity (n=97) was found to be significantly higher than those with antibody negativity.\n\nConclusionsThe results of the present study show the accurate and equivalent performance of serological antibody assays and chest CT in detecting SARS-CoV-2 0 to 7 days from the onset of COVID19 symptoms. When the RT-PCR is not available, we believe that the combination of immunochromatographic test and chest CT scan can increase diagnostic sensitivity for COVID-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ali Ozturk", - "author_inst": "Department of Medical Microbiology, Nigde Omer Halisdemir University Faculty of Medicine, Nigde, Turkey" - }, - { - "author_name": "Taylan Bozok", - "author_inst": "Department of Medical Microbiology, Nigde Omer Halisdemir University Training and Research Hospital, Nigde, Turkey" - }, - { - "author_name": "Tugce Simsek Bozok", - "author_inst": "Department of Infectious Diseases and Clinical Microbiology, Nigde Omer Halisdemir University Training and Research Hospital, Nigde, Turkey" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.20.431155", "rel_title": "Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19", @@ -919165,6 +920115,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.16.21251838", + "rel_title": "Profile of SARS-CoV-2-specific CD4 T cell response: Relationship with disease severity and impact of HIV-1 and active Mycobacterium tuberculosis co-infection", + "rel_date": "2021-02-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251838", + "rel_abs": "T cells are involved in control of COVID-19, but limited knowledge is available on the relationship between antigen-specific T cell response and disease severity. Here, we assessed the magnitude, function and phenotype of SARS-CoV-2-specific CD4 T cells in 95 hospitalized COVID-19 patients (38 of them being HIV-1 and/or tuberculosis (TB) co-infected) and 38 non-COVID-19 patients, using flow cytometry. We showed that SARS-CoV-2-specific CD4 T cell attributes, rather than magnitude, associates with disease severity, with severe disease being characterized by poor polyfunctional potential, reduced proliferation capacity and enhanced HLA-DR expression. Moreover, HIV-1 and TB co-infection skewed the SARS-CoV-2 T cell response. HIV-1 mediated CD4 T cell depletion associated with suboptimal T cell and humoral immune responses to SARS-CoV-2; and a decrease in the polyfunctional capacity of SARS-CoV-2-specific CD4 T cells was observed in COVID-19 patients with active TB. Our results also revealed that COVID-19 patients displayed reduced frequency of Mtb-specific CD4 T cells, with possible implications for TB disease progression. There results corroborate the important role of SARS-CoV-2-specific T cells in COVID-19 pathogenesis and support the concept of altered T cell functions in patients with severe disease.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Catherine Riou", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Elsa du Bruyn", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Cari Stek", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Remy Daroowala", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Rene T Goliath", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Fatima Abrahams", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Qonita Said-Hartley", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Brian W Allowed", + "author_inst": "Stellenbosch University and Tygerberg Hospital" + }, + { + "author_name": "Marvin Hsiao", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Katalin A Wilkinson", + "author_inst": "University of Cape Town and The Francis Crick Institute" + }, + { + "author_name": "Cecilia S Lindestam Arlehamn", + "author_inst": "La Jolla Institute for Immunology" + }, + { + "author_name": "Alessandro Sette", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Sean Wasserman", + "author_inst": "University of Cape Town" + }, + { + "author_name": "Robert J Wilkinson", + "author_inst": "University of Cape Town, Imperial College London and The Francis Crick Institute" + }, + { + "author_name": "- the HIATUS consortium", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.18.21251939", "rel_title": "Applicability of Neighborhood and Building Scale Wastewater-Based Genomic Epidemiology to Track the SARS-CoV-2 Pandemic and other Pathogens.", @@ -920281,73 +921306,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.02.16.21251850", - "rel_title": "A comparison of performance metrics for cloth face masks as source control devices for simulated cough and exhalation aerosols", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251850", - "rel_abs": "Universal mask wearing is recommended by the Centers for Disease Control and Prevention to help control the spread of COVID-19. Masks reduce the expulsion of respiratory aerosols (called source control) and offer some protection to the wearer. However, masks vary greatly in their designs and construction materials, and it is not clear which are most effective. Our study tested 15 reusable cloth masks (which included face masks, neck gaiters, and bandanas), two medical masks, and two N95 filtering facepiece respirators as source control devices for aerosols [≤] 7 {micro}m produced during simulated coughing and exhalation. These measurements were compared with the mask filtration efficiencies, airflow resistances, and fit factors. The source control collection efficiencies for the cloth masks ranged from 17% to 71% for coughing and 35% to 66% for exhalation. The filtration efficiencies of the cloth masks ranged from 1.4% to 98%, while the fit factors were 1.3 to 7.4 on an elastomeric manikin headform and 1.0 to 4.0 on human test subjects. The correlation coefficients between the source control efficacies and the other performance metrics ranged from 0.31 to 0.66 and were significant in all but one case. However, none of the alternative metrics were strong predictors of the source control performance of cloth masks. Our results suggest that a better understanding of the relationships between source control performance and metrics like filtration efficiency, airflow resistance, and fit factor are needed to develop simple methods to estimate the effectiveness of masks as source control devices for respiratory aerosols.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "William G Lindsley", - "author_inst": "National Institute for Occupational Safety and Health" - }, - { - "author_name": "Francoise M Blachere", - "author_inst": "National Institute for Occupational Safety and Health" - }, - { - "author_name": "Donald H Beezhold", - "author_inst": "National Institute for Occupational Safety and Health" - }, - { - "author_name": "Brandon F Law", - "author_inst": "National Institute for Occupational Safety and Health" - }, - { - "author_name": "Raymond C Derk", - "author_inst": "National Institute for Occupational Safety and Health" - }, - { - "author_name": "Justin M Hettick", - "author_inst": "National Institute for Occupational Safety and Health" - }, - { - "author_name": "Karen Woodfork", - "author_inst": "West Virginia University" - }, - { - "author_name": "William T Goldsmith", - "author_inst": "West Virginia University" - }, - { - "author_name": "James R Harris", - "author_inst": "National Institute for Occupational Safety and Health" - }, - { - "author_name": "Matthew G Duling", - "author_inst": "National Institute for Occupational Safety and Health" - }, - { - "author_name": "Brenda Boutin", - "author_inst": "National Institute for Occupational Safety and Health" - }, - { - "author_name": "Timothy Nurkiewicz", - "author_inst": "West Virginia University" - }, - { - "author_name": "John D Noti", - "author_inst": "National Institute for Occupational Safety and Health" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.15.21251762", "rel_title": "Clustering of Countries for COVID-19 Cases based on Disease Prevalence, Health Systems and Environmental Indicators", @@ -920543,6 +921501,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.16.21251625", + "rel_title": "Healthcare-associated COVID-19 in England: a national data linkage study", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251625", + "rel_abs": "ObjectivesNosocomial transmission was an important aspect of SARS-CoV-1 and MERS-CoV outbreaks. Healthcare-associated SARS-CoV-2 infection has been reported in single and multi-site hospital-based studies in England, but not nationally.\n\nMethodsAdmission records for all hospitals in England were linked to SARS-CoV-2 national test data for the period 01/03/2020 to 31/08/2020. Case definitions were: community-onset community-acquired (CO.CA), first positive test (FPT) <14 days pre-admission, up to day 2 of admission; hospital-onset indeterminate healthcare-associated (HO.iHA), FPT on day 3-7; hospital-onset probable healthcare-associated (HO.pHA), FPT on day 8-14; hospital-onset definite healthcare-associated (HO.HA), FPT from day 15 of admission until discharge; community-onset possible healthcare-associated (CO.pHA), FPT [≤]14 days post-discharge.\n\nResultsOne-third (34.4%, 100,859/293,204) of all laboratory-confirmed COVID-19 cases were linked to a hospital record. HO.pHA and HO.HA cases represented 5.3% (15,564/293,204) of all laboratory-confirmed cases and 15.4% (15,564/100,859) of laboratory-confirmed cases among hospital patients. CO.CA and CO.pHA cases represented 86.5% (253,582/293,204) and 5.1% (14,913/293,204) of all laboratory-confirmed cases, respectively.\n\nConclusionsUp to 1 in 6 SARS-CoV-2 infections among hospitalised patients with COVID-19 in England during the first 6 months of the pandemic could be attributed to nosocomial transmission, but these represent less than 1% of the estimated 3 million COVID-19 cases in this period.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Alex Bhattacharya", + "author_inst": "Public Health England" + }, + { + "author_name": "Simon M Collin", + "author_inst": "Public Health England" + }, + { + "author_name": "James Stimson", + "author_inst": "Public Health England" + }, + { + "author_name": "Simon Thelwall", + "author_inst": "Public Health England" + }, + { + "author_name": "Olisaeloka Nsonwu", + "author_inst": "Public Health England" + }, + { + "author_name": "Sarah Gerver", + "author_inst": "Public Health England" + }, + { + "author_name": "Julie Robotham", + "author_inst": "Public Health England" + }, + { + "author_name": "Mark Wilcox", + "author_inst": "University of Leeds" + }, + { + "author_name": "Susan Hopkins", + "author_inst": "Public Health England" + }, + { + "author_name": "Russell Hope", + "author_inst": "Public Health England" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.16.21251844", "rel_title": "An exploratory study on the correlation of population SARS-CoV-2 cycle threshold values to local disease dynamics", @@ -921751,149 +922764,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.17.21251895", - "rel_title": "Risk factors for long-term consequences of COVID-19 in hospitalised adults in Moscow using the ISARIC Global follow-up protocol: StopCOVID cohort study", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21251895", - "rel_abs": "BackgroundThe long-term sequalae of COVID-19 remain poorly characterised. In this study, we aimed to assess long-standing symptoms (LS) (symptoms lasting from the time of discharge) in previously hospitalised patients with COVID-19 and assess associated risk factors.\n\nMethodsThis is a longitudinal cohort study of adults ([≥]18 years of age) with clinically diagnosed or laboratory-confirmed COVID-19 admitted to Sechenov University Hospital Network in Moscow, Russia. Data were collected from patients discharged between April 8 and July 10, 2020. Participants were interviewed via telephone using Tier 1 ISARIC Long-term Follow-up Study CRF and the WHO CRF for Post COVID conditions. Reported symptoms were further categorised based on the system(s) involved. Additional information on dyspnoea, quality of life and fatigue was collected using validated instruments. Multivariable logistic regressions were performed to investigate risk factors for development of LS categories.\n\nFindingsOverall, 2,649 of 4,755 patients discharged from the hospitals were available for the follow-up and included in the study. The median age of the patients was 56 years (IQR, 46-66) and 1,353 (51.1%) were women. The median follow-up time since hospital discharge was 217.5 (200.4-235.5) days. At the time of the follow-up interview 1247 (47.1%) participants reported LS. Fatigue (21.2%, 551/2599), shortness of breath (14.5%, 378/2614) and forgetfulness (9.1%, 237/2597) were the most common LS reported. Chronic fatigue (25%, 658/2593) and respiratory (17.2% 451/2616) were the most common LS categories. with reporting of multi-system involvement (MSI) less common (11.3%; 299). Female sex was associated with LS categories of chronic fatigue with an odds ratio of 1.67 (95% confidence interval 1.39 to 2.02), neurological (2.03, 1.60 to 2.58), mood and behaviour (1.83, 1.41 to 2.40), dermatological (3.26, 2.36 to 4.57), gastrointestinal (2.50, 1.64 to 3.89), sensory (1.73, 2.06 to 2.89) and respiratory (1.31, 1.06 to 1.62). Pre-existing asthma was associated with neurological (1.95, 1.25 to 2.98) and mood and behavioural changes (2.02, 1.24 to 3.18) and chronic pulmonary disease was associated with chronic fatigue (1.68, 1.21 to 2.32).\n\nInterpretation6 to 8 months after acute infection episode almost a half of patients experience symptoms lasting since hospital discharge. One in ten individuals experiences MSI. Female sex is the main risk factor for majority of the LS categories. chronic pulmonary disease is associated with a higher risk of chronic fatigue development, and asthma with neurological and mood and behaviour changes. Individuals with LS and MSI should be the main target for future research and intervention strategies.\n\nFundingThis study is supported by Russian Fund for Basic Research and UK Embassy in Moscow. The ISARIC work is supported by grants from: the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with Public Health England (PHE), in collaboration with Liverpool School of Tropical Medicine and the University of Oxford [award 200907], Wellcome Trust and Department for International Development [215091/Z/18/Z], and the Bill and Melinda Gates Foundation [OPP1209135], EU Platform for European Preparedness Against (Re-) emerging Epidemics (PREPARE) [FP7 project 602525] This research was funded in part, by the Wellcome Trust. The views expressed are those of the authors and not necessarily those of the DID, NIHR, Wellcome Trust or PHE.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSEvidence suggests that COVID-19 may result in short- and long-term consequences to health. Most studies do not provide definitive answers due to a combination of short follow-up (2-3 months), small sample size, and use of non-standardised tools. There is a need to study the longer-term health consequences of previously hospitalised patients with COVID-19 infection and to identify risk factors for sequalae.\n\nAdded value of this studyTo our knowledge, this is the largest cohort study (n=2,649) with the longest follow-up since hospital discharge (6-8 months) of previously hospitalised adult patients. We found that 6-8 months after discharge from the hospital, around a half (47.1%) of patients reported at least one long-standing symptom since discharge. Once categories of symptoms were assessed, chronic fatigue and respiratory problems were the most frequent clusters of long-standing symptoms in our patients. Of those patients having long-term symptoms, a smaller proportion (11.3%) had multisystem involvement, with three or more categories of long-standing symptoms present. Although most patients developed symptoms since discharge, a smaller number of individuals experienced symptom beginning symptom appearing weeks or months after the acute phase. Female sex was a predictor for most of the symptom categories at the time of the follow-up interview, with chronic pulmonary disease associated with chronic fatigue-related symptoms, and asthma with a higher risk of neurological symptoms, mood and behaviour problems.\n\nImplications of all the available evidenceThe majority of patients experienced long-lasting symptoms 6 to 8 months after hospital discharge and almost half reported at least one long-standing symptom, with chronic fatigue and respiratory problems being the most frequent. A smaller number reported multisystem impacts with three or more long-standing categories present at follow-up. A higher risk was found for women, for chronic pulmonary disease with chronic fatigue, and neurological symptoms and mood and behaviour problems with asthma. Patterns of the symptom development following COVID-19 should be further investigated in future research.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Daniel Munblit", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia, Imperial College London, London, United Kingdom, Research and Clinical Cen" - }, - { - "author_name": "Polina Bobkova", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Ekaterina Spiridonova", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Anastasia Shikhaleva", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Aysylu Gamirova", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Oleg Blyuss", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia School of Physics, Astronomy and Mathematics, University of Hertfordshire, " - }, - { - "author_name": "Nikita A Nekliudov", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Polina Bugaeva", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Margarita Andreeva", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Audrey DunnGalvin", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia School of Applied Psychology, University College Cork, Cork City, Ireland" - }, - { - "author_name": "Pasquale Comberiati", - "author_inst": "University of Pisa, Pisa, Italy" - }, - { - "author_name": "Christian Apfelbacher", - "author_inst": "Institute of Social Medicine and Health Systems Research, Faculty of Medicine, Otto von Guericke University Magdeburg, Magdeburg, Germany" - }, - { - "author_name": "Jon Genuneit", - "author_inst": "Pediatric Epidemiology, Department of Pediatrics, Medical Faculty, Leipzig University, Leipzig, Germany" - }, - { - "author_name": "Sergey Avdeev", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Valentina Kapustina", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Alla Guekht", - "author_inst": "Research and Clinical Center for Neuropsychiatry, Moscow, Russia" - }, - { - "author_name": "Victor Fomin", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Andrey A Svistunov", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Peter Timashev", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Thomas M Drake", - "author_inst": "Centre for Medical Informatics, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Sarah Wulf Hanson", - "author_inst": "Institute for Health Metrics and Evaluation, University of Washington, Seattle, USA" - }, - { - "author_name": "Laura Merson", - "author_inst": "ISARIC Global Support Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Peter Horby", - "author_inst": "ISARIC Global Support Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Louise Sigfrid", - "author_inst": "ISARIC Global Support Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Janet T Scott", - "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK" - }, - { - "author_name": "Malcolm G Semple", - "author_inst": "Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Scie" - }, - { - "author_name": "John O Warner", - "author_inst": "Inflammation, Repair and Development Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom" - }, - { - "author_name": "Theo Vos", - "author_inst": "Institute for Health Metrics and Evaluation, University of Washington, Seattle, USA" - }, - { - "author_name": "Piero Olliaro", - "author_inst": "ISARIC Global Support Centre, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Petr Glybochko", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "Denis Butnaru", - "author_inst": "Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia" - }, - { - "author_name": "- Sechenov StopCOVID Research Team", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.17.21251732", "rel_title": "Harnessing recombinase polymerase amplification for rapid detection of SARS-CoV-2 in resource-limited settings", @@ -922181,6 +923051,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.17.21251758", + "rel_title": "Prediction of Mortality in hospitalized COVID-19 patients in a statewide health network", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.17.21251758", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSImportanceC_ST_ABSA predictive model to automatically identify the earliest determinants of both hospital discharge and mortality in hospitalized COVID-19 patients could be of great assistance to caregivers if the predictive information is generated and made available in the immediate hours following admission.\n\nObjectiveTo identify the most important predictors of hospital discharge and mortality from measurements at admission for hospitalized COVID-19 patients.\n\nDesignObservational cohort study.\n\nSettingElectronic records from hospitalized patients.\n\nParticipantsPatients admitted between March 3rd and August 24th with COVID-19 in Johns Hopkins Health System hospitals.\n\nExposures216 phenotypic variables collected within 48 hours of admission.\n\nMain OutcomesWe used age-stratified (<60 and >=60 years) random survival forests with competing risks to identify the most important predictors of death and discharge. Fine-Gray competing risk regression (FGR) models were then constructed based on the most important RSF-derived covariates.\n\nResultsOf 2212 patients, 1913 were discharged (age 57{+/-}19, time-to-discharge 9{+/-}11 days) while 279 died (age 75{+/-}14, time to death 14{+/-}15 days). Patients >= 60 years were nearly 10 times as likely to die within 60 days of admission as those <60. As the pandemic evolved, the rate of hospital discharge increased in both older and younger patients. Incident death and hospital discharge were accurately predicted by measures of respiratory distress, inflammation, infection, renal function, red cell turn over and cardiac stress. FGR models for each of hospital discharge and mortality as outcomes based on these variables performed well in the older (AUC 0.80-0.85 at 60-days) and younger populations (AUC >0.90 at 60-days).\n\nConclusions and RelevanceWe identified markers collected within 2 days of admission that predict hospital discharge and mortality in COVID-19 patients and provide prediction models that may be used to guide patient care. Our proposed model suggests that hospital discharge and mortality can be forecasted with high accuracy based on 8-10 variables at this stage of the COVID-19 pandemic. Our findings also point to several specific pathways that could be the focus of future investigations directed at reducing mortality and expediting hospital discharge among COVID-19 patients. Probability of hospital discharge increased over the course of the pandemic.\n\nKO_SCPLOWEYC_SCPLOW PO_SCPLOWOINTSC_SCPLOWO_ST_ABSQuestionC_ST_ABSCan we predict the likelihood of hospital discharge as well as mortality from data obtained in the first 48 hours from admission in hospitalized COVID-19 patients?\n\nFindingsModels based on extensive phenotyping mined directly from electronic medical records followed by variable selection, accounted for the competing events of hospital death versus discharge, predicted both death and discharge with area under the receiver operating characteristic curves of >0.80.\n\nMeaningHospital discharge and mortality can be forecasted with high accuracy based on just 8-10 variables, and the probability of hospital discharge increased over the course of the pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Bharath Ambale Venkatesh", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Thiago Quinaglia", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Mahsima Shabani", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Jaclyn Sesso", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Karan Kapoor", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "Matthew Matheson", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Colin O Wu", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Christopher Cox", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Joao A Lima", + "author_inst": "Johns Hopkins Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.16.21251849", "rel_title": "Convalescent plasma for preventing critical illness in COVID-19: A phase 2 trial and immune profile", @@ -923525,93 +924446,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2021.02.18.21250737", - "rel_title": "Viral genetic sequencing identifies staff transmission of COVID-19 is important in a community hospital outbreak", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21250737", - "rel_abs": "BackgroundWe have successfully used whole-genome sequencing to provide additional information for transmission pathways in infectious spread. We report and interpret genomic sequencing results in clinical context from a large outbreak of COVID-19 with 46 cases across staff and patients in a community hospital in the UK.\n\nMethodsFollowing multiple symptomatic cases within a two-week period, all staff and patients were screened by RT-PCR and staff subsequently had serology tests.\n\nResultsThirty staff (25%) and 16 patients (62%) tested positive for COVID-19. Genomic sequencing data showed significant overlap of viral haplotypes in staff who had overlapping shift patterns. Patient haplotypes were more distinct from each other but had overlap with staff haplotypes.\n\nConclusionsThis study includes clinical and genomic epidemiological detail that demonstrates the value of a combined approach. Viral genetic sequencing has identified that staff transmission of COVID-19 was important in this community hospital outbreak.\n\nKey pointsO_LIDetailed analysis of a large community hospital outbreak in older adults and staff with concurrent clinical and genomic data, including working patterns.\nC_LIO_LIStaff transmission was important in this community hospital outbreak.\nC_LIO_LIWe found plausible associations between staff and patient cases.\nC_LI", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Jane Masoli", - "author_inst": "University of Exeter" - }, - { - "author_name": "Aaron Jeffries", - "author_inst": "University of Exeter" - }, - { - "author_name": "Ben Temperton", - "author_inst": "University of Exeter" - }, - { - "author_name": "Cressida Auckland", - "author_inst": "Royal Devon and Exeter NHS Trust" - }, - { - "author_name": "Michelle Michelsen", - "author_inst": "University of Exeter" - }, - { - "author_name": "Joanna Warwick-Dugdale", - "author_inst": "University of Exeter" - }, - { - "author_name": "Robyn Manley", - "author_inst": "University of Exeter" - }, - { - "author_name": "Audrey Farbos", - "author_inst": "University of Exeter" - }, - { - "author_name": "Sian Ellard", - "author_inst": "Royal Devon and Exeter NHS Trust" - }, - { - "author_name": "Beatrice Knight", - "author_inst": "Royal Devon and Exeter NHS Trust" - }, - { - "author_name": "Claire Bewshea", - "author_inst": "University of Exeter" - }, - { - "author_name": "Christine Sambles", - "author_inst": "University of Exeter" - }, - { - "author_name": "James W Harrison", - "author_inst": "University of Exeter" - }, - { - "author_name": "Benjamin Bunce", - "author_inst": "University of Exeter" - }, - { - "author_name": "Alexis Carr", - "author_inst": "Royal Devon and Exeter NHS Trust" - }, - { - "author_name": "Andrew T Hattersley", - "author_inst": "University of Exeter" - }, - { - "author_name": "Steven Ll Michell", - "author_inst": "University of Exeter" - }, - { - "author_name": "David Studholme", - "author_inst": "University of Exeter" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.19.431973", "rel_title": "Efficiency Improvements and Discovery of New Substrates for a SARS-CoV-2 Main Protease FRET Assay", @@ -923911,6 +924745,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.15.21249420", + "rel_title": "COVID-19 Associated Stroke--A Single Centre Experience", + "rel_date": "2021-02-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21249420", + "rel_abs": "Background and PurposeVarious neurological complications have been reported in association with COVID-19. We report our experience of COVID-19 with stroke at a single center over a period of eight months spanning 1 March to 31 October 2020.\n\nMethodsWe recruited all patients admitted to Internal Medicine with an acute stroke, who also tested positive for COVID-19 on RTPCR. We included all stroke cases in our analysis for prediction of in-hospital mortality, and separately analyzed arterial infarcts for vascular territory of ischemic strokes.\n\nResultsThere were 62 stroke cases among 3923 COVID-19 admissions (incidence 1.6%). Data was available for 58 patients {mean age 52.6 years; age range 17-91; F/M=20/38; 24% (14/58) aged [≤]40; 51% (30/58) hypertensive; 36% (21/58) diabetic; 41% (24/58) with O2 saturation <95% at admission; 32/58 (55.17 %) in-hospital mortality}. Among 58 strokes, there were 44 arterial infarcts, seven bleeds, three arterial infarcts with associated cerebral venous sinus thrombosis, two combined infarct and bleed, and two of indeterminate type. Among the total 49 infarcts, Carotid territory was the commonest affected (36/49; 73.5%), followed by vertebrobasilar (7/49; 14.3%) and both (6/49; 12.2%). Concordant arterial block was seen in 61% (19 of 31 infarcts with angiography done). Early stroke (within 48 hours of respiratory symptoms) was seen in 82.7% (48/58) patients. Patients with poor saturation at admission were older (58 vs 49 years) and had more comorbidities and higher mortality (79% vs 38%). Mortality was similar in young strokes and older patients, although the latter required more intense respiratory support. Logistic regression analysis showed that low GCS and requirement for increasing intensity of respiratory support predicted in-hospital mortality.\n\nConclusionsWe had a 1.6% incidence of COVID-19 related stroke of which the majority were carotid territory infarcts. In-hospital mortality was 55.17%, predicted by low GCS at admission.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Uma Sundar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Niteen Karnik", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Amita Mukhopadhyay", + "author_inst": "Dr Chandramma Dayananda Sagar Institute of Medical Education and Research, Kanakapura 562112, Ramanagara District, Karnataka, India" + }, + { + "author_name": "Pramod Darole", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Shaonak Kolte", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Ashank Bansal", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Yojana Gokhale", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Dnaneshwar Asole", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Anagha Joshi", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Sangeeta Pednekar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Swati Chavan", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Trupti Trivedi", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Namita Padwal", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Lalana Kalekar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Charulata Londhe", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Rupal Padhiyar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Dharmendra Pandey", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Dhirendra Yadav", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Sonal Honrao", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Prerana Bhavsar", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Priyanshu Shah", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Satish Gosavi", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Aniket Wadal", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Awesh Shingare", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Mayuri Trivedi", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + }, + { + "author_name": "Gauri Pathak Oak", + "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.13.21251670", "rel_title": "Excess Mortality in Suicide caused by COVID-19 in Japan", @@ -925227,37 +926180,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.02.16.21251807", - "rel_title": "Impacts of COVID-19 on long-term health and health care use", - "rel_date": "2021-02-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251807", - "rel_abs": "AimTo explore the temporal impact of mild COVID-19 on need for primary and specialist health care services.\n\nMethodsIn all persons tested for SARS-CoV-2 in Norway March 1st 2020 to February 1st 2021 (N=1 401 922), we contrasted the monthly all-cause health care use before and up to 6 months after the test (% relative difference), for patients with a positive test for SARS-CoV-2 (non-hospitalization, i.e. mild COVID-19) and patients with a negative test (no COVID-19).\n\nResultsWe found a substantial short-term elevation in primary care use in all age groups, with men generally having a higher relative increase (men 20-44 years: 522%, 95%CI=509-535, 45-69 years: 439%, 95%CI=426-452, [≥] 70 years: 199%, 95%CI=180-218) than women (20-44 years: 342, 95%CI=334-350, 45-69 years=375, 95%CI=365-385, [≥] 70 years: 156%, 95%CI=141-171) at 1 month following positive test. At 2 months, this sex difference was less pronounced, with a (20-44 years: 21%, 95%CI=13-29, 45-69 years=38%, 95%CI=30-46, [≥] 70 years: 15%, 95%CI=3-28) increase in primary care use for men, and a (20-44 years: 30%, 95%CI=24-36, 45-69 years=57%, 95%CI=50-64, [≥] 70 years: 14%, 95%CI=4-24) increase for women. At 3 months after test, only women aged 45-70 years still had an increased primary care use (14%, 95%CI=7-20). The increase was due to respiratory- and general/unspecified conditions. We observed no long-term (4-6 months) elevation in primary care use, and no elevation in specialist care use.\n\nConclusionMild COVID-19 gives an elevated need for primary care that vanishes 2-3 months after positive test. Middle-aged women had the most prolonged increased primary care use.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Katrine Damgaard Skyrud", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kjersti Helene Hernaes Jr.", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kjetil Elias Telle", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Karin Magnusson", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.16.21251824", "rel_title": "Use of Convalescent Plasma Therapy among Hospitalized Coronavirus Disease 2019 (COVID-19) Patients: A Single-Center Experience", @@ -925689,6 +926611,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.15.21251781", + "rel_title": "Epidemiological dynamics of the incidence of COVID-19 in children and the relationship with the opening of schools in Catalonia (Spain)", + "rel_date": "2021-02-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251781", + "rel_abs": "Here we analyse the epidemiological trend of the incidence of COVID-19 in children in Catalonia (Spain) during the first 20 weeks of the 2020-2021 school year. This study demonstrates that while schools were open the incidence rate among children remained significantly lower than in general population, despite a greater diagnostic effort in children. These results suggest that schools have not played a significant role in the SARS-CoV-2 dissemination in Catalonia.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Aida Perramon", + "author_inst": "Universitat Pompeu Fabra, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Antoni Soriano-Arandes", + "author_inst": "Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain" + }, + { + "author_name": "David Pino", + "author_inst": "Department of Physics, Universitat Politecnica de Catalunya (UPC BarcelonaTech), Barcelona, Catalonia, Spain" + }, + { + "author_name": "Uxue Lazcano", + "author_inst": "Agencia de Qualitat i Avaluacio Sanitaries de Catalunya (AQuAS), Barcelona, Catalonia, Spain" + }, + { + "author_name": "Cristina Andres", + "author_inst": "Respiratory Viruses Unit, Department of Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Marti Catala", + "author_inst": "Comparative Medicine and Bioimage Centre of Catalonia (CMCiB), Fundacio Institut d'Investigacio en Ciencies de la Salut Germans Trias i Pujol (IGTP), Badalona, " + }, + { + "author_name": "Anna Gatell", + "author_inst": "Equip Pediatria Territorial Alt Penedes-Garraf, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Mireia Carulla", + "author_inst": "ABS Pla d'Urgell (Mollerussa), Lleida, Catalonia, Spain" + }, + { + "author_name": "Dolors Canadell", + "author_inst": "CAP Barbera del Valles, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Gemma Ricos", + "author_inst": "CAP Drassanes, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Maria Teresa Riera-Bosch", + "author_inst": "EAP Vic Nord, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Silvia Burgaya", + "author_inst": "EAP Manlleu, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Olga Salvado", + "author_inst": "CAP Llibertat Reus, Tarragona, Catalonia, Spain" + }, + { + "author_name": "Javier Cantero", + "author_inst": "Corporacio del Maresme i la Selva, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Monica Vila", + "author_inst": "EAP Horta, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Miriam Poblet", + "author_inst": "Equip Territorial Pediatric Sabadell Nord, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Almudena Sanchez", + "author_inst": "CAP Les Hortes, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Anna Maria Ristol", + "author_inst": "CAP Can Serra Hospitalet de Llobregat, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Pepe Serrano", + "author_inst": "Equip Pediatria Territorial Alt Penedes-Garraf, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Andres Anton", + "author_inst": "Respiratory Viruses Unit, Department of Microbiology, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain" + }, + { + "author_name": "Clara Prats", + "author_inst": "Department of Physics, Universitat Politecnica de Catalunya (UPC BarcelonaTech), Barcelona, Catalonia, Spain" + }, + { + "author_name": "Pere Soler-Palacin", + "author_inst": "Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Barcelona, Catalonia, Spain" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.15.21251788", "rel_title": "COVID-19 European Regional Tracker", @@ -927104,29 +928129,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.16.21251803", - "rel_title": "An early assessment of the epidemiological effects of SARS-CoV-2 variants of concern in Germany", - "rel_date": "2021-02-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251803", - "rel_abs": "Growing evidence on higher transmissibility of novel variants of the SARS-CoV-2 coronavirus is raising alarm in many countries. We provide near-time estimates of the statistical association between reported cases of SARS-CoV-2 variants of concern (VOC) and epidemiological indicators at the local area level in Germany. Our findings indicate that the 7-day incidence rates in regions with confirmed VOC cases increased by up to 35%, on average, after VOC reporting compared to regions without confirmed cases by February 4. The hospitalization rate for COVID-19 patients in intensive care increased by up to 40%, but only for regions with most reported VOC cases. Both indicators further show a clear upward trend in regions with reported VOC cases vis-a-vis those without cases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Timo Friedel Mitze", - "author_inst": "Department of Business and Economics, University of Southern Denmark" - }, - { - "author_name": "Johannes Rode", - "author_inst": "Department of Law and Economics, Technische Universitaet Darmstadt" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.15.21251738", "rel_title": "Changes in health behaviors, mental and physical health among older adults under severe lockdown restrictions during the COVID-19 pandemic in Spain", @@ -927494,6 +928496,137 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.15.431291", + "rel_title": "Favourable antibody responses to human coronaviruses in children and adolescents with autoimmune rheumatic diseases", + "rel_date": "2021-02-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.15.431291", + "rel_abs": "Differences in humoral immunity to coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), between children and adults remain unexplained and the impact of underlying immune dysfunction or suppression unknown. Here, we examined the antibody immune competence of children and adolescents with prevalent inflammatory rheumatic diseases, juvenile idiopathic arthritis (JIA), juvenile dermatomyositis (JDM) and juvenile systemic lupus erythematosus (JSLE), against the seasonal human coronavirus (HCoV)-OC43 that frequently infects this age group. Despite immune dysfunction and immunosuppressive treatment, JIA, JDM and JSLE patients mounted comparable or stronger responses than healthier peers, dominated by IgG antibodies to HCoV-OC43 spike, and harboured IgG antibodies that cross-reacted with SARS-CoV-2 spike. In contrast, responses to HCoV-OC43 and SARS-CoV-2 nucleoproteins exhibited delayed age-dependent class-switching and were not elevated in JIA, JDM and JSLE patients, arguing against increased exposure. Consequently, autoimmune rheumatic diseases and their treatment were associated with a favourable ratio of spike to nucleoprotein antibodies.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Claire Deakin", + "author_inst": "UCL" + }, + { + "author_name": "Georgina Cornish", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Kevin Ng", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Nikhil Faulkner", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "William Bolland", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Veera Panova", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Joshua Hope", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Annachiara Rosa", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Ruth Harvey", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Saira Hussain", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Chris Earl", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Bethany Jebson", + "author_inst": "UCL" + }, + { + "author_name": "Merry Wilkinson", + "author_inst": "UCL" + }, + { + "author_name": "Lucy Marshall", + "author_inst": "UCL" + }, + { + "author_name": "Lizzy Rosser", + "author_inst": "UCL" + }, + { + "author_name": "Ania Radziszewska", + "author_inst": "UCL" + }, + { + "author_name": "Hannah Peckham", + "author_inst": "UCL" + }, + { + "author_name": "Judith Heaney", + "author_inst": "UCL" + }, + { + "author_name": "Hannah Rickman", + "author_inst": "UCL" + }, + { + "author_name": "Stavroula Paraskevopoulou", + "author_inst": "UCL" + }, + { + "author_name": "Catherine Houlihan", + "author_inst": "UCL" + }, + { + "author_name": "Moria Spyer", + "author_inst": "UCL" + }, + { + "author_name": "Steve Gamblin", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "John Mccauley", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Eleni Nastouli", + "author_inst": "UCL" + }, + { + "author_name": "Peter Cherepanov", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Coziana Ciurtin", + "author_inst": "UCL" + }, + { + "author_name": "Lucy Wedderburn", + "author_inst": "UCL" + }, + { + "author_name": "George Kassiotis", + "author_inst": "The Francis Crick Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.15.430863", "rel_title": "Live attenuated SARS-CoV-2 vaccine candidate: Protective immunity without serious lung lesions in Syrian hamsters", @@ -928645,73 +929778,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.10.21250915", - "rel_title": "ImplemeNting SARS-CoV-2 Rapid antigen testing in the Emergency wArd of a Swiss univErsity hospital: the INCREASE study", - "rel_date": "2021-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21250915", - "rel_abs": "BackgroundWhile facing a second wave in SARS-CoV-2 pandemic, in November 2020 the Swiss Federal Office of Public Health (FOPH) authorized the use of rapid antigen tests (RATs) in addition to the gold-standard reverse transcription-polymerase chain reaction (RT-PCR).\n\nMethodsWe implemented the use of RAT in the emergency ward of our university hospital for rapid patients triaging and compared performances of four different antigen tests. All results were compared to SARS-CoV-2 specific RT-PCR (reference standard).\n\nResultsTriaging patients using RAT in association with RT-PCR allowed us to isolate promptly positive patients and to save resources, in a context of rapid RT-PCR reagents shortage. Among 532 patients with valid results, overall sensitivities were 48.3% for One Step Exdia and 41.2% for Standard Q(R), Panbio-and BD Veritor. All four antigen tests exhibited specificity above 99%. Sensitivity increased up to 74.6%, 66.2%, 66.2% and 64.8% for One Step Exdia, Standard Q, Panbio, and BD Veritor respectively, when considering viral loads above 105copies/ml, up to 100%, 97.8%, 96.6% and 95.6% for viral loads above 106 copies/ml and 100% (for all tests) when considering viral loads above 107 copies/ml. Sensitivity was significantly higher for patients presenting with symptoms onset within 4 days (74.3%, 69.2%, 69.2% and 64%, respectively) versus patients with evolution of symptoms for more than 4 days (36.8%, 21.1%, 21.1% and 23.7%, respectively). Sensitivities of all RAT assays were of only 33% among hospitalized patients without COVID-19 symptoms.\n\nConclusionRAT might represent a useful epidemiological resource in selected clinical settings as a complementary tool to the molecular tests for rapid patients triaging, but the lower sensitivity compared to RT-PCR, especially in late presenters and subjects without COVID-19 symptoms, must be taken into account in order to correctly use RAT for triaging.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Giorgia Caruana", - "author_inst": "Lausanne University Hospital and University of Lausanne" - }, - { - "author_name": "Antony Croxatto", - "author_inst": "Lausanne University Hospital and University of Lausanne" - }, - { - "author_name": "Eleftheria Kampouri", - "author_inst": "Lausanne University Hospital and University of Lausanne" - }, - { - "author_name": "Antonios Kritikos", - "author_inst": "Lausanne University Hospital and University of Lausanne" - }, - { - "author_name": "Onya Opota", - "author_inst": "Lausanne University Hospital and University of Lausanne" - }, - { - "author_name": "Marylin Foerster", - "author_inst": "Lausanne University Hospital" - }, - { - "author_name": "Rene Brouillet", - "author_inst": "Lausanne University Hospital" - }, - { - "author_name": "Laurence Senn", - "author_inst": "Lausanne University Hospital and University of Lausanne" - }, - { - "author_name": "Reto Lienhard", - "author_inst": "ADMED" - }, - { - "author_name": "Adrian Egli", - "author_inst": "University Hospital Basel" - }, - { - "author_name": "Giuseppe Pantaleo", - "author_inst": "Lausanne University Hospital" - }, - { - "author_name": "Pierre-Nicolas Carron", - "author_inst": "Lausanne University Hospital" - }, - { - "author_name": "Gilbert Greub", - "author_inst": "Lausanne University Hospital and University of Lausanne" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.09.21251464", "rel_title": "Pooled Surveillance Testing Program for Asymptomatic SARS-CoV-2 Infections in K-12 Schools and Universities", @@ -929139,6 +930205,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.12.431032", + "rel_title": "Pulsed broad-spectrum UV light effectively inactivates SARS-CoV-2 on multiple surfaces", + "rel_date": "2021-02-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.12.431032", + "rel_abs": "The ongoing SARS-CoV-2 pandemic has resulted in an increased need for technologies capable of efficiently disinfecting public spaces as well as personal protective equipment. UV light disinfection is a well-established method for inactivating respiratory viruses. Here, we have determined that broad-spectrum, pulsed UV light is effective at inactivating SARS-CoV-2 on multiple surfaces. For hard, non-porous surfaces we observed that SARS-CoV-2 was inactivated to undetectable levels on plastic and glass with a UV dose of 34.9 mJ/cm2 and stainless steel with a dose of 52.5 mJ/cm2. We also observed that broad-spectrum, pulsed UV light is effective at reducing SARS-CoV-2 on N95 respirator material to undetectable levels with a dose of 103 mJ/cm2. We included UV dosimeter cards that provide a colorimetric readout of UV dose and demonstrated their utility as a means to confirm desired levels of exposure were reached. Together, the results present here demonstrate that broad-spectrum, pulsed UV light is an effective technology for the inactivation of SARS-CoV-2 on multiple surfaces.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Alexander S Jureka", + "author_inst": "Georgia State University" + }, + { + "author_name": "Caroline G Williams", + "author_inst": "Georgia State University" + }, + { + "author_name": "Christopher F Basler", + "author_inst": "Georgia State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.12.431026", "rel_title": "Jumper Enables Discontinuous Transcript Assembly in Coronaviruses", @@ -930303,69 +931396,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "ophthalmology" }, - { - "rel_doi": "10.1101/2021.02.11.20196766", - "rel_title": "Deep learning models for COVID-19 chest x-ray classification: Preventing shortcut learning using feature disentanglement", - "rel_date": "2021-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.20196766", - "rel_abs": "In response to the COVID-19 global pandemic, recent research has proposed creating deep learning based models that use chest radiographs (CXRs) in a variety of clinical tasks to help manage the crisis. However, the size of existing datasets of CXRs from COVID-19+ patients are relatively small, and researchers often pool CXR data from multiple sources, for example, using different x-ray machines in various patient populations under different clinical scenarios. Deep learning models trained on such datasets have been shown to overfit to erroneous features instead of learning pulmonary characteristics - a phenomenon known as shortcut learning. We propose adding feature disentanglement to the training process, forcing the models to identify pulmonary features from the images while penalizing them for learning features that can discriminate between the original datasets that the images come from. We find that models trained in this way indeed have better generalization performance on unseen data; in the best case we found that it improved AUC by 0.13 on held out data. We further find that this outperforms masking out non-lung parts of the CXRs and performing histogram equalization, both of which are recently proposed methods for removing biases in CXR datasets.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Caleb Robinson", - "author_inst": "Microsoft AI for Good" - }, - { - "author_name": "Anusua Trivedi", - "author_inst": "Microsoft AI for Good" - }, - { - "author_name": "Marian Blazes", - "author_inst": "University of Washington" - }, - { - "author_name": "Anthony Ortiz", - "author_inst": "Microsoft AI for Good" - }, - { - "author_name": "Jocelyn Desbiens", - "author_inst": "Intelligent Retinal Imaging Systems" - }, - { - "author_name": "Sunil Gupta", - "author_inst": "Intelligent Retinal Imaging Systems" - }, - { - "author_name": "Rahul Dodhia", - "author_inst": "Microsoft AI for Good" - }, - { - "author_name": "Pavan K Bhatraju", - "author_inst": "Department of Medicine and Sepsis Center of Research Excellence, University of Washington (SCORE-UW)" - }, - { - "author_name": "W. Conrad Liles", - "author_inst": "Department of Medicine and Sepsis Center of Research Excellence, University of Washington (SCORE-UW)" - }, - { - "author_name": "Aaron Lee", - "author_inst": "University of Washington" - }, - { - "author_name": "Jayashree Kalpathy-Cramer", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Juan M Lavista Ferres", - "author_inst": "Microsoft AI for Good" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2021.02.14.431129", "rel_title": "ALG-097111, a potent and selective SARS-CoV-2 3-chymotrypsin-like cysteine protease inhibitor exhibits in vivo efficacy in a Syrian Hamster model", @@ -930689,6 +931719,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.02.10.21251478", + "rel_title": "CATALYST trial protocol: A multicentre, open-label, phase II, multi-arm trial for an early and accelerated evaluation of the potential treatments for COVID-19 in hospitalised adults", + "rel_date": "2021-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251478", + "rel_abs": "IntroductionSevere SARS-CoV-2 infection is associated with a dysregulated immune response. Inflammatory monocytes and macrophages are crucial, promoting injurious, pro-inflammatory sequelae. Immunomodulation is, therefore, an attractive therapeutic strategy and we sought to test licensed and novel candidate drugs.\n\nMethods and analysisThe CATALYST trial is a multi-arm, open-label, multi-centre, phase II platform trial designed to identify candidate novel treatments to improve outcomes of patients hospitalised with COVID-19 compared with usual care. Treatments with evidence of biomarker improvements will be put forward for larger-scale testing by current national phase III platform trials. Hospitalised patients >16 years with a clinical picture strongly suggestive of SARS-CoV-2 pneumonia (confirmed by chest X-ray or CT scan, with or without a positive reverse transcription polymerase chain reaction (RT-PCR) assay) and a C-Reactive Protein (CRP) [≥]40 mg/L are eligible. The primary outcome measure is CRP, measured serially from admission to day 14, hospital discharge or death. Secondary outcomes include the WHO Clinical Progression Improvement Scale as a principal efficacy assessment.\n\nEthics and disseminationThe protocol was approved by the East Midlands - Nottingham 2 Research Ethics Committee (20/EM/0115) and given Urgent Public Health status; initial approval was received on 05-May-2020, current protocol version (v6.0) approval on 12-Oct-2020. The MHRA also approved all protocol versions. The results of this trial will be disseminated through national and international presentations and peer-reviewed publications.\n\nTrial registration numberEudraCT Number: 2020-001684-89\n\nISRCTN Number: 40580903\n\nStrengths and limitations of this trialO_LICATALYST will provide a rapid readout on the safety and proof-of-concept of candidate novel treatments\nC_LIO_LICATALYST will enable phase III trial resources to be focussed and allocated for agents with a high likelihood of success\nC_LIO_LICATALYST uses Bayesian multi-level models to allow for nesting of repeated measures data, with factors for each individual patient and treatment arm, and allowing for non-linear responses\nC_LIO_LICATALYST is not designed to provide a definitive signal on clinical outcomes\nC_LI", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Tonny Veenith", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Benjamin A Fisher", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Daniel Slade", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Anna Rowe", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Rowena Sharpe", + "author_inst": "University of Birmingham" + }, + { + "author_name": "David R Thickett", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Tony Whitehouse", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Matthew Rowland", + "author_inst": "University of Oxford" + }, + { + "author_name": "James Scriven", + "author_inst": "University Hospitals Birmingham NHS Trust" + }, + { + "author_name": "Dhruv Parekh", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Sarah J Bowden", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Joshua S Savage", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Duncan Richards", + "author_inst": "University of Oxford" + }, + { + "author_name": "Julian Bion", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Pamela Kearns", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Simon Gates", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.02.11.21251581", "rel_title": "A genetically-informed study disentangling the relationships between tobacco smoking, cannabis use, alcohol consumption, substance use disorders and respiratory infections, including COVID-19", @@ -932215,36 +933324,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.09.21251416", - "rel_title": "Accounting for imported cases in estimating the time-varying reproductive number of COVID-19", - "rel_date": "2021-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21251416", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Tim Tsang", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Peng Wu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Eric Lau", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Benjamin J Cowling", - "author_inst": "The University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.09.21251440", "rel_title": "Explaining COVID-19 Outbreaks with Reactive SEIRD Models", @@ -932427,6 +933506,232 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.10.21251247", + "rel_title": "Safety and efficacy of the ChAdOx1 nCoV-19 (AZD1222) Covid-19 vaccine against the B.1.351 variant in South Africa", + "rel_date": "2021-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251247", + "rel_num_authors": 53, + "rel_authors": [ + { + "author_name": "Shabir Ahmed Madhi", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Vicky Lynne Baillie", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Clare Louise Cutland", + "author_inst": "Wits- Alive: African Leadership in Vaccinology Expertise, University of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Merryn Voysey", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" + }, + { + "author_name": "Anthonet L Koen", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Lee Fairlie", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Sherman D Padayachee", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Keertan Dheda", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute University of Cape Town, South Africa" + }, + { + "author_name": "Shaun L Barnabas", + "author_inst": "Family Centre for Research with Ubuntu, Department of Paediatrics, University of Stellenbosch, Cape Town, South Africa" + }, + { + "author_name": "Qasim Ebrahim Bhorat", + "author_inst": "Soweto Clinical Trials Centre" + }, + { + "author_name": "Carmen Briner", + "author_inst": "Perinatal HIV Research Unit, Faculty of Health Science, University of the Witwatersrand, South Africa" + }, + { + "author_name": "Gaurav Kwatra", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Khatija Ahmed", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Parvinder Aley", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" + }, + { + "author_name": "Sutika Bhikha", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Jinal N Bhiman", + "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa." + }, + { + "author_name": "As'ad Ebrahim Bhorat", + "author_inst": "Soweto Clinical Trials Centre, Soweto, South Africa" + }, + { + "author_name": "Jeanine du plessis", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Aliasgar Esmail", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute University of Cape Town, South Africa" + }, + { + "author_name": "Marisa Groenewald", + "author_inst": "Family Centre for Research with Ubuntu, Department of Paediatrics, University of Stellenbosch, Cape Town, South Africa" + }, + { + "author_name": "Elizea Horne", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Shi-Hsia Hwa", + "author_inst": "Africa Health Research Institute, Durban 4001, South Africa." + }, + { + "author_name": "Aylin Jose", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Teresa Lambe", + "author_inst": "Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK" + }, + { + "author_name": "Matt Laubscher", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Mookho Malahleha", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Masebole Masenya", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Mduduzi Masilela", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Shakeel McKenzie", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Kgaogelo Molapo", + "author_inst": "Setshaba Research Centre, Tshwane, South Africa" + }, + { + "author_name": "Andrew Moultrie", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Suzette Oelofse", + "author_inst": "Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute University of Cape Town, South Africa" + }, + { + "author_name": "Faeezah Patel", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Sureshnee Pillay", + "author_inst": "KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban South Africa" + }, + { + "author_name": "Sarah Rhead", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" + }, + { + "author_name": "Hylton Rodel", + "author_inst": "Africa Health Research Institute, Durban 4001, South Africa." + }, + { + "author_name": "Lindie Rossouw", + "author_inst": "Family Centre for Research with Ubuntu, Department of Paediatrics, University of Stellenbosch, Cape Town, South Africa" + }, + { + "author_name": "Carol Taoushanis", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Houryiah Tegally", + "author_inst": "KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban South Africa" + }, + { + "author_name": "Asha Thombrayil", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "Samuel van Eck", + "author_inst": "Wits Reproductive Health and HIV Institute, Faculty of Health Sciences, University of the Witwatersrand, Johanesburg, South Africa" + }, + { + "author_name": "Constantinos Wibmer", + "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa." + }, + { + "author_name": "Nicholas M Durham", + "author_inst": "Astra Zeneca Biopharmaceuticals, Cambridge, UK" + }, + { + "author_name": "Elizabeth J Kelly", + "author_inst": "Astra Zeneca Biopharmaceuticals, Cambridge, UK" + }, + { + "author_name": "Tonya Villafana", + "author_inst": "Astra Zeneca Biopharmaceuticals, Cambridge, UK" + }, + { + "author_name": "Sarah Gilbert", + "author_inst": "Jenner Institute, Nuffield Department of Medicine, University of Oxford, UK" + }, + { + "author_name": "Andrew J Pollard", + "author_inst": "Oxford Vaccine Group, Department of Paediatrics, University of Oxford, UK" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "KwaZulu-Natal Research and Innovation Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban South Africa" + }, + { + "author_name": "Penny L Moore", + "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa." + }, + { + "author_name": "Alex Sigal", + "author_inst": "Africa Health Research Institute, Durban 4001, South Africa." + }, + { + "author_name": "Alane Izu", + "author_inst": "Wits-VIDA - Vaccines and infectious diseases analytical research unit, Universtiy of the Witwatersrand, Johannesburg, South Africa" + }, + { + "author_name": "- Network for Genomic Surveillance in South Africa (NGS-SA)", + "author_inst": "" + }, + { + "author_name": "- Wits VIDA COVID vaccine trial group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.10.21251392", "rel_title": "COVID-19 and Influenza: Vaccination Before and During the Pandemic among the Lebanese Adult Population", @@ -933991,57 +935296,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.08.21250899", - "rel_title": "Combinatorial analysis of phenotypic and clinical risk factors associated with hospitalized COVID-19 patients", - "rel_date": "2021-02-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21250899", - "rel_abs": "1Characterization of the risk factors associated with variability in the clinical outcomes of COVID-19 is important. Our previous study using genomic data identified a potential role of calcium and lipid homeostasis in severe COVID-19. This study aimed to identify similar combinations of features (disease signatures) associated with severe disease in a separate patient population with purely clinical and phenotypic data.\n\nThe PrecisionLife combinatorial analytics platform was used to analyze features derived from de-identified health records in the UnitedHealth Group COVID-19 Data Suite. The platform identified and analyzed 836 disease signatures in two cohorts associated with increased risk of COVID-19 hospitalization. Cohort 1 was formed of cases hospitalized with COVID-19 and a set of controls who developed mild symptoms. Cohort 2 included Cohort 1 individuals for whom additional laboratory test data was available.\n\nWe found several disease signatures where lower levels of lipids were found co-occurring with lower levels of serum calcium and leukocytes. Many of the low lipid signatures were independent of statin use and 50% of cases with hypocalcemia signatures were reported with vitamin D deficiency. These signatures may be attributed to similar mechanisms linking calcium and lipid signaling where changes in cellular lipid levels during inflammation and infection affect calcium signaling in host cells.\n\nThis study and our previous genomics analysis demonstrate that combinatorial analysis can identify disease signatures associated with the risk of developing severe COVID-19 separately from genomic or clinical data in different populations. Both studies suggest associations between calcium and lipid signalling in severe COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sayoni Das", - "author_inst": "PrecisionLife Ltd" - }, - { - "author_name": "Matthew Pearson", - "author_inst": "PrecisionLife Ltd" - }, - { - "author_name": "Krystyna Taylor", - "author_inst": "PrecisionLife Ltd" - }, - { - "author_name": "Veronique Bouchet", - "author_inst": "PrecisionLife Ltd" - }, - { - "author_name": "Gert Lykke M\u00f8ller", - "author_inst": "PrecisionLife Ltd" - }, - { - "author_name": "Taryn O. Hall", - "author_inst": "OptumLabs at UnitedHealth Group" - }, - { - "author_name": "Mark Strivens", - "author_inst": "PrecisionLife Ltd" - }, - { - "author_name": "Kathy T.H. Tzeng", - "author_inst": "OptumLabs at UnitedHealth Group" - }, - { - "author_name": "Steve Gardner", - "author_inst": "PrecisionLife Ltd" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.02.05.21251139", "rel_title": "Estimating real-world COVID-19 vaccine effectiveness in Israel", @@ -934237,6 +935491,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2021.02.08.21250309", + "rel_title": "Hospitalizations for emergency-sensitive conditions in Germany during the Covid-19 pandemic - Insights from the German-wide Helios hospital network", + "rel_date": "2021-02-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21250309", + "rel_abs": "BackgroundWhile there are numerous reports that describe emergency care during the early Covid-19 pandemic, there is scarcity of data for later stages. This study analyzes hospitalization rates for 37 emergency-sensitive conditions in the largest German-wide hospital network during different pandemic phases.\n\nMethodsUsing claims data of 80 hospitals, consecutive cases between January 1 and November 17, 2020 were analyzed and compared to a corresponding period in 2019. Incidence-rate ratios (IRR) comparing the both periods were calculated using Poisson regression to model the number of hospitalizations per day.\n\nResultsThere was a hospitalization deficit between March 12 and June 13, 2020 (coinciding with the 1st pandemic wave) with 32,807 hospitalizations as opposed to 39,379 in 2019 (IRR 0.83, 95% CI 0.82 - 0.85, P<0.01). During the following period (June 14 to November 17, 2020, including the start of 2nd wave), hospitalizations were reduced from 63,799 in 2019 to 59,910 in 2020, but this reduction was not that pronounced (IRR 0.94, 95% CI 0.93 - 0.95, P<0.01). There was an increase in hospitalizations for acute myocardial infarction, aortic aneurism/dissection and pulmonary embolism after the 1st wave during which hospitalizations had been reduced for those conditions. In contrast, hospitalizations for sepsis, pneumonia, obstructive pulmonary disease, and intracranial injuries were reduced during the entire pandemic.\n\nConclusionsThere was an overall reduction of hospitalizations for emergency-sensitive conditions in Germany during the Covid-19 pandemic with heterogeneous effects on different disease categories. The increase of hospitalizations for acute myocardial infarction, aortic aneurism/dissection and pulmonary embolism is an alarming signal that requires attention and further studies.\n\nKEY MESSAGESO_ST_ABSWhat is already known on this subjectC_ST_ABSO_LIThere has been a reduction in emergency room visits and hospital admissions for several emergent medical and surgical conditions during the early Covid-19 pandemic (1st wave).\nC_LI\n\nWhat this study addsO_LIUsing claims data of 80 German-wide Helios hospitals, we found an overall reduction of hospitalizations for emergency-sensitive conditions in Germany during the Covid-19 pandemic until mid November 2020 with heterogeneous effects on different disease categories. While hospitalizations for sepsis, pneumonia, obstructive pulmonary disease, and intracranial injuries were reduced during the entire pandemic. There was an alarming increase of hospitalizations for acute myocardial infarction, aortic aneurism/dissection and pulmonary embolism after the 1st wave.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "ANDREAS BOLLMANN", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Sven Hohenstein", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Vincent Pellissier", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Sebastian Koenig", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Laura Ueberham", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Gerhard Hindricks", + "author_inst": "Heart Center Leipzig at University of Leipzig and Leipzig Heart Institute" + }, + { + "author_name": "Andreas Meier-Hellmann", + "author_inst": "Helios Hospitals" + }, + { + "author_name": "Ralf Kuhlen", + "author_inst": "Helios Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2021.02.10.430668", "rel_title": "Data-driven analysis of COVID-19 reveals specific severity patterns distinct from the temporal immune response", @@ -936245,33 +937546,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.09.430451", - "rel_title": "A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: effects on proteolytic cleavage and ACE2 binding", - "rel_date": "2021-02-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.09.430451", - "rel_abs": "SARS-CoV-2 harbors a unique S1/S2 furin cleavage site within its spike protein, which can be cleaved by furin and other proprotein convertases. Proteolytic activation of SARS-CoV-2 spike protein at the S1/S2 boundary facilitates interaction with host ACE2 receptor for cell entry. To address this, high titer antibody was generated against the SARS-CoV-2-specific furin motif. Using a series of innovative ELISA-based assays, this furin site blocking antibody displayed high sensitivity and specificity for the S1/S2 furin cleavage site, and demonstrated effective blockage of both enzyme-mediated cleavage and spike-ACE2 interaction. The results suggest that immunological blocking of the furin cleavage site may afford a suitable approach to stem proteolytic activation of SARS-CoV-2 spike protein and curtail viral infectivity.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Michael G Spelios", - "author_inst": "EpigenTek" - }, - { - "author_name": "Jeanne M Capanelli", - "author_inst": "EpigenTek" - }, - { - "author_name": "Adam W Li", - "author_inst": "EpigenTek" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.09.430517", "rel_title": "Dual RNA-Seq analysis of SARS-CoV-2 correlates specific human transcriptional response pathways directly to viral expression", @@ -936551,6 +937825,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.07.21251311", + "rel_title": "Poor antigen-specific responses to the second BNT162b2 mRNA vaccine dose in SARS-CoV-2-experienced individuals", + "rel_date": "2021-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251311", + "rel_abs": "The use of COVID-19 vaccines will play the major role in helping to end the pandemic that has killed millions worldwide. COVID-19 vaccines have resulted in robust humoral responses and protective efficacy in human trials, but efficacy trials excluded individuals with a prior diagnosis of COVID-19. As a result, little is known about how immune responses induced by mRNA vaccines differ in individuals who recovered from COVID-19. Here, we evaluated longitudinal immune responses to two-dose BNT162b2 mRNA vaccination in 15 adults who recovered from COVID-19, compared to 21 adults who did not have prior COVID-19 diagnosis. Consistent with prior studies of mRNA vaccines, we observed robust cytotoxic CD8+ T cell responses in both cohorts following the second dose. Furthermore, SARS-CoV-2-naive individuals had progressive increases in humoral and antigen-specific antibody-secreting cell (ASC) responses following each dose of vaccine, whereas SARS-CoV-2-experienced individuals demonstrated strong humoral and antigen-specific ASC responses to the first dose but muted responses to the second dose of the vaccine at the time points studied. Together, these data highlight the relevance of immunological history for understanding vaccine immune responses and may have significant implications for personalizing mRNA vaccination regimens used to prevent COVID-19, including booster shots.\n\nOne Sentence SummaryPrior history of COVID-19 affects adaptive immune responses to mRNA vaccination.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Marie Ines Samanovic-Golden", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Amber R Cornelius", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Sophie L Gray-Gaillard", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Joseph Richard Allen", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Trishala Karmacharya", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Jimmy P Wilson", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Sara Wesley Hyman", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Michael Tuen", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Sergei B Koralov", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Mark J Mulligan", + "author_inst": "NYU School of Medicine" + }, + { + "author_name": "Ramin Sedaghat Herati", + "author_inst": "NYU School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.07.21251309", "rel_title": "The effect of respiratory activity, ventilatory therapy and facemasks on total aerosol emissions", @@ -937771,77 +939104,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.03.21251089", - "rel_title": "TOP-Plus is a Versatile Biosensor Platform for Monitoring SARS-CoV-2 Antibody Durability", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.03.21251089", - "rel_abs": "BackgroundThere is a concern that low initial SARS-CoV-2 antibody titers in individuals may drop to undetectable levels within months after infection. Although this may raise concerns over long term immunity, both the antibody levels and avidity of the antibody-antigen interaction should be examined to understand the quality of the antibody response.\n\nMethodsA testing-on-a-probe \"plus\" panel (TOP-Plus) was developed, which included a newly developed avidity assay built into the previously described SARS-CoV-2 TOP assays that measured total antibody (TAb), surrogate neutralizing antibody (SNAb), IgM and IgG on a versatile biosensor platform. TAb and SNAb levels were compared with avidity in previously infected individuals at 1.3 and 6.2 months post-infection in paired samples from 80 COVID-19 patients.\n\nResultsThe newly designed avidity assay in this TOP panel correlated well with a reference Bio-Layer Interferometry avidity assay (R=0.88). The imprecision of the TOP avidity assay was less than 9%. Although TAb and neutralization activity (by SNAb) decreased between 1.3 and 6.2 months post infection, the antibody avidity increased significantly (P < 0.0001).\n\nConclusionThis highly precise and versatile TOP-Plus panel with the ability to measure SARS-CoV-2 TAb, SNAb, IgG and IgM antibody levels and avidity of individual sera on one sensor can become a valuable asset in monitoring not only SARS-CoV-2-infected patients, but also the status of individuals COVID-19 vaccination response.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Sabrina E Racine-Brzostek", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Mohsen Karbaschi", - "author_inst": "ET HealthCare" - }, - { - "author_name": "Christian Gaebler", - "author_inst": "The Rockefeller Univeristy" - }, - { - "author_name": "PJ Klasse", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Jim Yee", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Marina Caskey", - "author_inst": "The Rockefeller Univeristy" - }, - { - "author_name": "He S Yang", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Ying Hao", - "author_inst": "Beijing University of Chinese Medicine" - }, - { - "author_name": "Amy Chadburn", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Yuanyuan Shi", - "author_inst": "Beijing University of Chinese Medicine" - }, - { - "author_name": "Robert Zuk", - "author_inst": "ET HealthCare" - }, - { - "author_name": "Michel C Nussenzweig", - "author_inst": "The Rockefeller Univeristy" - }, - { - "author_name": "Melissa M Cushing", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Zhen Zhao", - "author_inst": "Weill Cornell Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.02.04.21250670", "rel_title": "COVID-19 transmission in educational institutions August to December 2020, Rhineland-Palatinate, Germany: a study of index cases and close contact cohorts", @@ -938161,6 +939423,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.04.21251131", + "rel_title": "Using Machine Learning to Predict Mortality for COVID-19 Patients on Day Zero in the ICU", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251131", + "rel_abs": "RationaleGiven the expanding number of COVID-19 cases and the potential for upcoming waves of infection, there is an urgent need for early prediction of the severity of the disease in intensive care unit (ICU) patients to optimize treatment strategies.\n\nObjectivesEarly prediction of mortality using machine learning based on typical laboratory results and clinical data registered on the day of ICU admission.\n\nMethodsWe studied retrospectively 263 COVID-19 ICU patients. To find parameters with the highest predictive values, Kolmogorov-Smirnov and Pearson chi-squared tests were used. Logistic regression and random forest (RF) algorithms were utilized to build classification models. The impact of each marker on the RF model predictions was studied by implementing the local interpretable model-agnostic explanation technique (LIME-SP).\n\nResultsAmong 66 documented parameters, 15 factors with the highest predictive values were identified as follows: gender, age, blood urea nitrogen (BUN), creatinine, international normalized ratio (INR), albumin, mean corpuscular volume, white blood cell count, segmented neutrophil count, lymphocyte count, red cell distribution width (RDW), and mean cell hemoglobin along with a history of neurological, cardiovascular, and respiratory disorders. Our RF model can predict patients outcomes with a sensitivity of 70% and a specificity of 75%.\n\nConclusionsThe most decisive variables in our model were increased levels of BUN, lowered albumin levels, increased creatinine, INR, and RDW along with gender and age. Complete blood count parameters were also crucial for some patients. Considering the importance of early triage decisions, this model can be a useful tool in COVID-19 ICU decision-making.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Elham Jamshidi", + "author_inst": "Division of Pulmonary Medicine, Department of Medicine, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), Lausanne, Switzerland." + }, + { + "author_name": "Amirhossein Asgary", + "author_inst": "Department of Biotechnology, College of Sciences, University of Tehran, Tehran, Iran." + }, + { + "author_name": "Nader Tavakoli", + "author_inst": "Trauma and Injury Research Center, Iran University of Medical Sciences, Tehran, Iran." + }, + { + "author_name": "Alireza Zali", + "author_inst": "Functional Neurosurgery Research Center, Shohada Tajrish Comprehensive Neurosurgical Center of Excellence, Shahid Beheshti University of Medical Sciences, Tehra" + }, + { + "author_name": "Hadi Esmaily", + "author_inst": "Department of Clinical Pharmacy, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran." + }, + { + "author_name": "Seyed Hamid Jamaldini", + "author_inst": "Department of Genetic, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran" + }, + { + "author_name": "Amir Daaee", + "author_inst": "School of Mechanical Engineering, Sharif University of Technology, Tehran, Iran" + }, + { + "author_name": "Amirhesam Babajani", + "author_inst": "Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Mohammad Ali Sendani Kashi", + "author_inst": "Master of Business Administration (MBA)-University of Tehran, Tehran, Iran." + }, + { + "author_name": "Masoud Jamshidi", + "author_inst": "Department of Exercise Physiology, Tehran University, Iran." + }, + { + "author_name": "Sahand Rahi", + "author_inst": "Laboratory of the Physics of Biological Systems, Institute of Physics, Ecole polytechnique federale de Lausanne (EPFL), Lausanne, Switzerland" + }, + { + "author_name": "Nahal Mansouri", + "author_inst": "Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Ecole polytechnique federale de Lausanne (EPFL), Lausanne, Switzerland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.04.21251170", "rel_title": "Symptoms of COVID-19 infection and magnitude of antibody response in a large community-based study", @@ -939321,97 +940646,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.05.21251182", - "rel_title": "Antibodies elicited by SARS-CoV-2 infection and boosted by vaccination neutralize an emerging variant and SARS-CoV-1", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.05.21251182", - "rel_abs": "Emerging SARS-CoV-2 variants have raised concerns about resistance to neutralizing antibodies elicited by previous infection or vaccination. We examined whether sera from recovered and naive donors collected prior to, and following immunizations with existing mRNA vaccines, could neutralize the Wuhan-Hu-1 and B.1.351 variants. Pre-vaccination sera from recovered donors neutralized Wuhan-Hu-1 and sporadically neutralized B.1.351, but a single immunization boosted neutralizing titers against all variants and SARS-CoV-1 by up to 1000-fold. Neutralization was due to antibodies targeting the receptor binding domain and was not boosted by a second immunization. Immunization of naive donors also elicited cross-neutralizing responses, but at lower titers. Our study highlights the importance of vaccinating both uninfected and previously infected persons to elicit cross-variant neutralizing antibodies.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Leonidas Stamatatos", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Julie Czartoski", - "author_inst": "Fred Hutch." - }, - { - "author_name": "Yu-Hsin Wan", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Leah Homad", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Vanessa Rubin", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Hayley Glantz", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Moni Neradilek", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Emilie Seydoux", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Madeleine F. Jennewein", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Anna MacCamy", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Junli Feng", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Greogry Mize", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Stephen C De Rosa", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Andres Finzi", - "author_inst": "Universite de Montreal" - }, - { - "author_name": "Maria Lemos", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Kristen W. Cohen", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Zoe Moodie", - "author_inst": "Fred Hutch" - }, - { - "author_name": "M. Juliana McElrath", - "author_inst": "Fred Hutch" - }, - { - "author_name": "Andrew McGuire", - "author_inst": "Fred Hutch" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.05.21251067", "rel_title": "Immune cell residency in the nasal mucosa and COVID-19 severity across the age range", @@ -940139,6 +941373,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.06.21251099", + "rel_title": "COVID-19 increases age- and sex-controlled 21-day fatality rates for patients with melanoma, hematologic malignancies, uterine cancer, or kidney cancer", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.06.21251099", + "rel_abs": "IntroductionPrior research has reported an increased risk of fatality for cancer patients, but most studies investigated the risk by comparing cancer patients to non-cancer patients among COVID-19 infections. Only a few studies have compared the impact of a COVID-19 infection to non-infection with matched cancer patients and types.\n\nMethods & MaterialsWe conducted survival analyses of 4,606 cancer patients with COVID-19 test results from March 16 to October 11, 2020 in UK Biobank and estimated the overall hazard ratio of fatality with and without COVID-19 infection. We also examined the hazard ratios of thirteen specific cancer types with at least 100 patients.\n\nResultsCOVID-19 resulted in an overall hazard ratio of 7.76 (95% CI: [5.78, 10.40], p<10-10) by studying the survival rate of 4,606 cancer patients for 21-days after the tests. The hazard ratio was shown to vary among cancer type, with over a 10-fold increase in fatality rate (false discovery rate[≤]0.02) for melanoma, hematologic malignancies, uterine cancer, and kidney cancer using a stratified analysis on each of the cancer types. Although COVID-19 imposed a higher risk for localized cancers compared to distant metastasis ones, those of distant metastasis yielded higher fatality rates due to their multiplicative effects.\n\nConclusionThe results highlight the importance of timely care for localized and hematological cancer patients and the necessity to vaccinate uninfected patients as soon as possible, particularly for the cancer types influenced most by COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Haiquan Li", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Edwin Alexander Baldwin", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Xiang Zhang", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Colleen Kenost", + "author_inst": "Department of Biomedical Informatics, University of Utah" + }, + { + "author_name": "Wenting Luo", + "author_inst": "Statistics and Data Science GIDP, Biosystems Analytics & Technology Program, University of Arizona" + }, + { + "author_name": "Elizabeth A Calhoun", + "author_inst": "Department of Population Health, University of Kansas Medical Center" + }, + { + "author_name": "Lingling An", + "author_inst": "Department of Biosystems Engineering, University of Arizona" + }, + { + "author_name": "Charles L Bennett", + "author_inst": "Department of Clinical Pharmacy and Outcomes Sciences, University of South Carolina" + }, + { + "author_name": "Yves A Lussier", + "author_inst": "Department of Biomedical Informatics, University of Utah" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2021.02.05.21251085", "rel_title": "Molecular Mechanism of Parosmia", @@ -941607,29 +942892,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.02.06.430088", - "rel_title": "Insights on SARS-CoV-2's Mutations for Evading Human Antibodies: Sacrifice and Survival", - "rel_date": "2021-02-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.06.430088", - "rel_abs": "Recent mutations on the receptor binding domain (RBD) of the SARS-CoV-2s spike protein have been manifested as the major cause of the wide and rapid spread of the virus. Especially, the variant B.1.351 in South Africa with the hallmark of triple mutations (N501Y, K417N and E484K) is worrisome. Quickly after the outbreak of this new variant, several studies showed that both N501Y and E484K can enhance the binding between RBD and the human ACE2 receptor. However, the mutation K417N seems to be unfavorable because it removes one interfacial salt-bridge. So far, it is still not well understood why the K417N mutation is selected in the viral evolution. Here, we show that despite the loss in the binding affinity (1.48 kcal/mol) between RBD and ACE2 the K417N mutation abolishes a buried interfacial salt-bridge between RBD and the neutralizing antibody CB6 and thus substantially reduces their binding energy by 9.59 kcal/mol, facilitating the variants to efficiently elude CB6 (as well as many other antibodies). Thus, when proliferating from person to person the virus might have adapted to the human immune system through evasive mutations. Taking into account limited and relevant experimental works in the field, we show that our theoretical predictions are consistent with existing experimental findings. By harnessing the revealed molecular mechanism for variants, it becomes feasible to redesign therapeutic antibodies accordingly to make them more efficacious.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC=\"FIGDIR/small/430088v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (52K):\norg.highwire.dtl.DTLVardef@1ce030eorg.highwire.dtl.DTLVardef@2a9f85org.highwire.dtl.DTLVardef@4f1265org.highwire.dtl.DTLVardef@140c0be_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Binquan Luan", - "author_inst": "IBM T J Watson Research" - }, - { - "author_name": "Tien Huynh", - "author_inst": "IBM T J Watson Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.02.05.428685", "rel_title": "Self-assembling SARS-CoV-2 nanoparticle vaccines targeting the S protein induces protective immunity in mice", @@ -941933,6 +943195,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.04.21251111", + "rel_title": "SARS-CoV-2 Worldwide Replication Drives Rapid Rise and Selection of Mutations across the Viral Genome: A Time-Course StudyPotential Challenge for Vaccines and Therapies", + "rel_date": "2021-02-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251111", + "rel_abs": "Scientists and the public were alarmed at the first large viral variant of SARS-CoV2 reported in December 2020. We have followed the time course of emerging viral mutants and variants during the SARS-CoV-2 pandemic in ten countries on four continents. We examined complete SARS-CoV-2 nucleotide sequences in GISAID, (Global Initiative of Sharing All Influenza Data) with sampling dates extending until January 20, 2021. These sequences originated from ten different countries: United Kingdom, South Africa, Brazil, USA, India, Russia, France, Spain, Germany, and China. Among the novel mutations, some previously reported mutations waned and some of them increased in prevalence over time. VUI2012/01 (B.1.1.7) and 501Y.V2 (B.1.351), the so-called UK and South Africa variants, respectively, and two variants from Brazil, 484K.V2, now called P.1 and P.2, increased in prevalence. Despite lockdowns, worldwide active replication in genetically and socio-economically diverse populations facilitated selection of new mutations. The data on mutant and variant SARS-CoV-2 strains provided here comprise a global resource for easy access to the myriad mutations and variants detected to date globally. Rapidly evolving new variant and mutant strains might give rise to escape variants, capable of limiting the efficacy of vaccines, therapies, and diagnostic tests.\n\nSignificance and New Aspects of Study - SynopsisO_LIWe examine the time course of emerging mutations in the SARS-CoV-2 genome that have rapidly been selected in the worlds populations through the beginning of 2021. A study of the prevalence of viral mutations in the GISAID database in ten different countries - United Kingdom, South Africa, Brazil, US, India, Russia, France, Spain, Germany, and China - revealed widespread mutations along the genome.\nC_LIO_LIWe previously identified about 10 hotspot mutations in the SARS-CoV-2 genome that became prevalent in many of the countries studied1. Since the beginning of February, many new mutations arose in the ten countries (and worldwide). The preponderance of variants and mutations correlated with the increased spread of Covid-19.\nC_LIO_LIThere was a temporal progression from about 10 predominant mutants shared by several countries up to the end of May 2020, followed by a consistent and rapid increase in the number of new mutations between June and December along with the emergence of variants of concern, first reported in December 2020.\nC_LIO_LIWe examine the relative frequencies of mutations, along with variants of interest, in 10 countries up until January 20, 2021. Investigations on the pathogenic properties of individual SARS-CoV-2 mutations will be urgently needed to understand the kaleidoscopic patterns of worldwide Covid-19 outbreaks and symptoms. Monitoring the frequency and speed of mutant selection have direct relevance to diagnostic testing, vaccines and therapeutics.\nC_LIO_LIAs an explanation for efficient viral mutagenesis, we hypothesize that the viral spike protein - as documented - facilitates viral entry via the cells ACE receptor2. This in turn interacts with the APOBEC polypeptide, an m-RNA editing function. The actually observed frequent C to U (T) transitions and other base exchanges are thus effected. Hence, as one of the earliest steps upon viral entry, active mutagenesis commences, since SARS-CoV-2 exploits one of the cells defenses against viral infections.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Stefanie Weber", + "author_inst": "University of Cologne/Erlangen University" + }, + { + "author_name": "Christina C.M. Ramirez", + "author_inst": "UCLA School of Public Health, Los Angeles" + }, + { + "author_name": "Barbara Weiser", + "author_inst": "University of California, Davis," + }, + { + "author_name": "Harold Burger", + "author_inst": "University of California, Davis" + }, + { + "author_name": "Walter Doerfler", + "author_inst": "Friedrich-Alexander University Erlangen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.04.21250932", "rel_title": "The systemic inflammatory response and clinicopathological characteristics in patients admitted to hospital with COVID-19 infection: Comparison of 2 consecutive cohorts", @@ -943517,41 +944814,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.03.21251065", - "rel_title": "Impact of systemic corticosteroids on hospitalized patients with COVID-19: January 2021 Meta-analysis of randomized controlled trials", - "rel_date": "2021-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.03.21251065", - "rel_abs": "BackgroundThe COVID-19 pandemic has stimulated worldwide investigation into a myriad of potential therapeutic agents, including corticosteroids. The first RCT reporting results on the impact of systemic corticosteroids on COVID-19 in a peer reviewed journal was the RECOVERY trial published in July, 2020. The RECOVERY trial showed a reduced risk of 28-day mortality in patients who received oral or intravenous dexamethasone for 10 days.\n\nThis study is a meta-analysis of peer reviewed RCTs aims to estimate the association of systemic corticosteroid therapy compared to the usual care or placebo on all-cause mortality in hospitalized patients with COVID-19. Software based tools to accelerate the analysis process.\n\nMethodsMeta-analysis of peer reviewed RCTs comparing systemic corticosteroids to usual care or placebo.\n\nResultsFive English language RCTs were identified, including data from 7645 hospitalized patients worldwide using systemic dexamethasone, hydrocortisone and methylprednisolone in COVID-19 positive patients. Three RCTs were discontinued when preliminary results from the RECOVERY trial became available.\n\nMeta-analysis of all identified RCTs showed no difference in survival in patients who received systemic corticosteroid therapy compared to usual care or placebo (Odds ratio 0.82, 95% CI 0.64-1.05, p = 0.09). Subgroup analysis from the 1967 critically ill patients in the identified RCTs showed improved survival in patients who received systemic corticosteroid therapy (Odds ratio 0.67, 95% CI 0.51-0.87, p = 0.01).\n\nConclusionsThis meta-analysis of randomized controlled trials published in peer-reviewed literature by January 1, 2021 showed reduced mortality in critically ill patients but not all hospitalized patients with COVID-19 who received systemic corticosteroids. The early termination of three of the included RCTs because of the preliminary results of the RECOVERY trial is likely to have dramatically influenced the results of this meta-analysis. Further research is needed to clarify the role of systemic corticosteroid therapy in the management of COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Robert Robinson", - "author_inst": "Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL, USA" - }, - { - "author_name": "Vidhya Prakash", - "author_inst": "Division of Infectious Diseases, Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL, USA" - }, - { - "author_name": "Raad Al Tamimi", - "author_inst": "College of Medicine, Alfaisal University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Nour Albast", - "author_inst": "College of Medicine, Alfaisal University, Riyadh, Saudi Arabia" - }, - { - "author_name": "Basma Al-Bast", - "author_inst": "Division of Cardiology, Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL, USA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.03.21251059", "rel_title": "Arabic validation and cross-cultural adaptation of the 5C scale for assessment of COVID-19 vaccines psychological antecedents", @@ -943771,6 +945033,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.02.02.21251043", + "rel_title": "COVID-19 infection and subsequent thromboembolism: A self-controlled case series analysis of a population cohort", + "rel_date": "2021-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21251043", + "rel_abs": "ObjectiveAn unexpectedly large number of people infected with Covid-19 had experienced a thrombotic event. This study aims to assess the associations between Covid-19 infection and thromboembolism including myocardial infarction (MI), ischaemic stroke, deep-vein thrombosis (DVT), and pulmonary embolism (PE).\n\nPatients and MethodsA self-controlled case-series study was conducted covering the whole of Scotlands general population. The study population comprised individuals with confirmed (positive test) Covid-19 and at least one thromboembolic event between March 2018 and October 2020. Their incidence rates during the risk interval (5 days before to 56 days after the positive test) and the control interval (the remaining periods) were compared intra-personally.\n\nResultsAcross Scotland, 1,449 individuals tested positive for Covid-19 and experienced a thromboembolic event. The risk of thromboembolism was significantly elevated over the whole risk period but highest in the 7 days following the positive test (IRR 12.01, 95% CI 9.91-14.56) in all included individuals. The association was also present in individuals not originally hospitalised for Covid-19 (IRR 4.07, 95% CI 2.83-5.85). Risk of MI, stroke, PE and DVT were all significantly higher in the week following a positive test. The risk of PE and DVT was particularly high and remained significantly elevated even 56 days following the test.\n\nConclusionConfirmed Covid-19 infection was associated with early elevations in risk with MI, ischaemic stroke, and substantially stronger and prolonged elevations with DVT and PE both in hospital and community settings. Clinicians should consider thromboembolism, especially PE, among people with Covid-19 in the community.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Frederick Ho", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Kenneth Man", + "author_inst": "UCL" + }, + { + "author_name": "Mark Toshner", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Colin Church", + "author_inst": "NHS Greater Glasgow and Clyde" + }, + { + "author_name": "Carlos Celis-Morales", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Ian Wong", + "author_inst": "UCL" + }, + { + "author_name": "Colin Berry", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Naveed Sattar", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Jill Pell", + "author_inst": "University of Glasgow" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.02.03.21251011", "rel_title": "GPS-estimated foot traffic data and venue selection for COVID-19 serosurveillance studies", @@ -946275,73 +947588,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.02.04.429604", - "rel_title": "Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH", - "rel_date": "2021-02-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.04.429604", - "rel_abs": "The current COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The positive-sense single-stranded RNA virus contains a single linear RNA segment that serves as a template for transcription and replication, leading to the synthesis of positive and negative-stranded viral RNA (vRNA) in infected cells. Tools to visualize viral RNA directly in infected cells are critical to analyze its replication cycle, screen for therapeutic molecules or study infections in human tissue. Here, we report the design, validation and initial application of fluorescence in situ hybridization (FISH) probes to visualize positive or negative RNA of SARS-CoV-2 (CoronaFISH). We demonstrate sensitive visualization of vRNA in African green monkey and several human cell lines, in patient samples and human tissue. We further demonstrate the adaptation of CoronaFISH probes to electron microscopy (EM). We provide all required oligonucleotide sequences, source code to design the probes, and a detailed protocol. We hope that CoronaFISH will complement existing techniques for research on SARS-CoV-2 biology and COVID-19 pathophysiology, drug screening and diagnostics.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Elena I. Rensen", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Stefano Pietropaoli", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Florian Mueller", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Christian Weber", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sylvie Souquere", - "author_inst": "Gustave Roussy" - }, - { - "author_name": "Pierre Isnard", - "author_inst": "APHP" - }, - { - "author_name": "Marion Rabant", - "author_inst": "APHP" - }, - { - "author_name": "Jean-Baptiste Gibier", - "author_inst": "CHU Lille" - }, - { - "author_name": "Etienne Simon-Loriere", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Marie-Anne Rameix-Welti", - "author_inst": "INSERM" - }, - { - "author_name": "Gerard Pierron", - "author_inst": "Gustave Roussy" - }, - { - "author_name": "Giovanna Barba-Spaeth", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Christophe Zimmer", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.02.04.429751", "rel_title": "Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of Nsp1, Nsp2, and Nucleocapsid proteins from SARS-CoV-2", @@ -946621,6 +947867,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.02.03.429646", + "rel_title": "Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens", + "rel_date": "2021-02-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429646", + "rel_abs": "The ongoing SARS-CoV-2 pandemic is the third zoonotic coronavirus identified in the last twenty years. Enzootic and epizootic coronaviruses of diverse lineages also pose a significant threat to livestock, as most recently observed for virulent strains of porcine epidemic diarrhea virus (PEDV) and swine acute diarrhea-associated coronavirus (SADS-CoV). Unique to RNA viruses, coronaviruses encode a proofreading exonuclease (ExoN) that lowers point mutation rates to increase the viability of large RNA virus genomes, which comes with the cost of limiting virus adaptation via point mutation. This limitation can be overcome by high rates of recombination that facilitate rapid increases in genetic diversification. To compare dynamics of recombination between related sequences, we developed an open-source computational workflow (IDPlot) to measure nucleotide identity, locate recombination breakpoints, and infer phylogenetic relationships. We analyzed recombination dynamics among three groups of coronaviruses with noteworthy impacts on human health and agriculture: SARSr-CoV, Betacoronavirus-1, and SADSr-CoV. We found that all three groups undergo recombination with highly diverged viruses from sparsely sampled or undescribed lineages, which can disrupt the inference of phylogenetic relationships. In most cases, no parental origin of recombinant regions could be found in genetic databases, suggesting that much coronavirus diversity remains unknown. These patterns of recombination expand the genetic pool that may contribute to future zoonotic events. Our results also illustrate the limitations of current sampling approaches for anticipating zoonotic threats to human and animal health.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Stephen A. Goldstein", + "author_inst": "University of Utah" + }, + { + "author_name": "Joe Brown", + "author_inst": "University of Utah" + }, + { + "author_name": "Brent S Pedersen", + "author_inst": "University of Utah" + }, + { + "author_name": "Aaron R. Quinlan", + "author_inst": "University of Utah" + }, + { + "author_name": "Nels C. Elde", + "author_inst": "University of Utah" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.02.04.429819", "rel_title": "Codon arrangement modulates MHC-I peptides presentation: implications for a SARS-CoV-2 peptide-based vaccine", @@ -948201,69 +949482,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.01.21250944", - "rel_title": "Epidemiological and evolutionary considerations of SARS-CoV-2 vaccine dosing regimes", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250944", - "rel_abs": "As the threat of Covid-19 continues and in the face of vaccine dose shortages and logistical challenges, various deployment strategies are being proposed to increase population immunity levels. How timing of delivery of the second dose affects infection burden but also prospects for the evolution of viral immune escape are critical questions. Both hinge on the strength and duration (i.e. robustness) of the immune response elicited by a single dose, compared to natural and two-dose immunity. Building on an existing immuno-epidemiological model, we find that in the short-term, focusing on one dose generally decreases infections, but longer-term outcomes depend on this relative immune robustness. We then explore three scenarios of selection, evaluating how different second dose delays might drive immune escape via a build-up of partially immune individuals. Under certain scenarios, we find that a one-dose policy may increase the potential for antigenic evolution. We highlight the critical need to test viral loads and quantify immune responses after one vaccine dose, and to ramp up vaccination efforts throughout the world.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Chadi M. Saad-Roy", - "author_inst": "Princeton University" - }, - { - "author_name": "Sinead E. Morris", - "author_inst": "Columbia University" - }, - { - "author_name": "C. Jessica E. Metcalf", - "author_inst": "Princeton University" - }, - { - "author_name": "Michael J Mina", - "author_inst": "Harvard School of Public Health" - }, - { - "author_name": "Rachel E. Baker", - "author_inst": "Princeton University" - }, - { - "author_name": "Jeremy Farrar", - "author_inst": "The Wellcome Trust" - }, - { - "author_name": "Edward C Holmes", - "author_inst": "University of Sydney" - }, - { - "author_name": "Oliver Pybus", - "author_inst": "University of Oxford" - }, - { - "author_name": "Andrea L. Graham", - "author_inst": "Princeton University" - }, - { - "author_name": "Simon A. Levin", - "author_inst": "Princeton University" - }, - { - "author_name": "Bryan T. Grenfell", - "author_inst": "Princeton University" - }, - { - "author_name": "Caroline E Wagner", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.01.21250781", "rel_title": "Changes in Characteristics of Opioid Overdose Death Trends during the COVID-19 Pandemic", @@ -948499,6 +949717,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.02.21250825", + "rel_title": "Evaluation of Depression, Anxiety and Sleep Quality in the Brazilian Population During Social Isolation Due to the New Coronavirus (SARS-CoV-2) pandemic: the DEGAS-CoV Study", + "rel_date": "2021-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250825", + "rel_abs": "IntroductionThe new coronavirus infection (COVID-19) has caused distress and repercussions in mental and physical health of individuals. Depression, anxiety and worsening of sleep quality have been reported in several recent articles that surveyed populations all over the globe. Our work meant to access, through a cross-sectional study, these disorders in the Brazilian population, through the application of an online questionnaire conducted on the second trimester of 2020.\n\nMaterials and MethodsWe applied an online questionnaire, filled with questions regarding social, economic, financial, educational and health status, as well as questions from the Hospital Anxiety and Depression Scale (HAD), and from the Pittsburgh Sleep Quality Index (PSQI).\n\nResultsWe collected 2,695 valid answers, from April 24th to May 31st, 2020. Age ranged from 18 to 79 years, mean of 31.3. Women were 76.3%, men 23.7%. Symptoms of Anxiety were found in 56.5%, of depression in 46.1%, and of bad sleep in 49.2%. Some groups were more prone than others to one or more of those conditions, such as: younger people, women, mestizos, Northeasterners, people with lesser years of education, of lower income or whose income dropped significantly during the pandemic, caregivers, students, sedentary or people practicing less physical activity, people who followed more hours of news of COVID-19 and those less engaged in social and instrumental activities.\n\nConclusionanxiety, depression and bad sleep quality were significantly high in our survey. Mental and sleep health is heterogeneously affected among individuals, depending on social, economic, financial, educational and health status.\n\nO_TEXTBOXHIGHLIGHTS\n\n- An online survey (DEGAS-CoV) was conducted between April 30th and May 31st, 2020, with people living in Brazil, aged 18 or more. The study obtained 2,695 valid answers.\n- Rates of possible anxiety, possible depression and bad sleep quality were 56.5%, 46.1% and 49.2%, respectively. Rates are similar to another Brazilian survey, with 45,161 participants, conducted in a similar time window.\n- Were more prone to mental and/or sleep conditions: younger participants, women, mestizos, unemployed, students, people with less years of education, people with lower income or with considerable drops of income during the virus outbreak, caregivers, people who followed more news of COVID-19, people less engaged in social and instrumental activities, smokers, sedentary or those who practiced less physical activity, and people who had symptoms suspected (confirmed or not) of SARS-CoV-2 infection.\n- Alcohol drinkers were slightly less likely to be possibly depressed. That finding needs more clarification and may be due to confounders.\n\n\nC_TEXTBOX", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Paulo Afonso Mei", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Amanda Sasse", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Ana Lara Navarrete Fernandez", + "author_inst": "Pontificia Universidade Catolica de Goias" + }, + { + "author_name": "Barbara Neiva Perri", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Breno Alexander Bispo", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Giselly Brito Santana", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Gabriela Sakita Munhos", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Giovanni Giuliani Verghetti", + "author_inst": "Universidade Sao Leopoldo Mandic Araras" + }, + { + "author_name": "Guilherme Barbosa de Almeida Oliveira Martins", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Jennifer Pereira da Rocha", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Jessyca Rosa Lopes Mendonca", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Julia Patel Lebl", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Valdemiro Da Rolt Jr", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Lais Grabner Ruivo", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Laura Loeb", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Marielly Isepon", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Marina Joseane Pachecco", + "author_inst": "Universidade Sao Leopoldo Mandic Araras" + }, + { + "author_name": "Cintia Zonta Baptista", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Fabio Soares Nespoli", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Paloma Ricciardi de Castro", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Paola Ricciardi de Castro", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Rafaela Dotta Brustolin", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Taysa Maria Pimentel Goncalves Gomes Silva", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Victoria Gomes Andreata", + "author_inst": "Universidade Sao Leopoldo Mandic" + }, + { + "author_name": "Amilton Santos Jr", + "author_inst": "Universidade Estadual de Campinas" + }, + { + "author_name": "Tania Marchiori de Oliveira Cardoso", + "author_inst": "Universidade Estadual de Campinas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.02.01.21250943", "rel_title": "Seroprevalence of SARS-CoV-2 during pregnancy and associated outcomes: results from an ongoing prospective cohort study, New York City", @@ -949855,81 +951192,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.02.02.429311", - "rel_title": "Potent in vitro Neutralization of SARS-CoV-2 by Hetero-bivalent Alpaca Nanobodies Targeting the Spike Receptor-Binding Domain", - "rel_date": "2021-02-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.02.429311", - "rel_abs": "Cell entry by SARS-CoV-2 requires the binding between the receptor-binding domain (RBD) of the viral Spike protein and the cellular angiotensin-converting enzyme 2 (ACE2). As such, RBD has become the major target for vaccine development, while RBD-specific antibodies are pursued as therapeutics. Here, we report the development and characterization of SARS-CoV-2 RBD-specific VHH/nanobody (Nb) from immunized alpacas. Seven RBD-specific Nbs with high stability were identified using phage display. They bind to SARS-CoV-2 RBD with affinity KD ranging from 2.6 to 113 nM, and six of them can block RBD-ACE2 interaction. The fusion of the Nbs with IgG1 Fc resulted in homodimers with greatly improved RBD-binding affinities (KD ranging from 72.7 pM to 4.5 nM) and nanomolar RBD-ACE2 blocking abilities. Furthermore, fusion of two Nbs with non-overlapping epitopes resulted in hetero-bivalent Nbs, namely aRBD-2-5 and aRBD-2-7, with significantly higher RBD binding affinities (KD of 59.2 pM and 0.25 nM) and greatly enhanced SARS-CoV-2 neutralizing potency. The 50% neutralization dose (ND50) of aRBD-2-5 and aRBD-2-7 was 1.22 ng/mL ([~]0.043 nM) and 3.18 ng/mL ([~]0.111 nM), respectively. These high-affinity SARS-CoV-2 blocking Nbs could be further developed into therapeutics as well as diagnosis reagents for COVID-19.\n\nImportanceTo date, SARS-CoV-2 has caused tremendous loss of human life and economic output worldwide. Although a few COVID-19 vaccines have been approved in several countries, the development of effective therapeutics including SARS-CoV-2 targeting antibodies remains critical. Due to their small size (13-15 kDa), highly solubility and stability, Nbs are particularly well suited for pulmonary delivery and more amenable to engineer into multi-valent formats, compared to the conventional antibody. Here, we report a serial of new anti-SARS-CoV-2 Nbs isolated from immunized alpaca and two engineered hetero-bivalent Nbs. These potent neutralizing Nbs showed promise as potential therapeutics against COVID-19.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Huan Ma", - "author_inst": "Department of pulmonary and critical care medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Tec" - }, - { - "author_name": "Weihong Zeng", - "author_inst": "Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, D" - }, - { - "author_name": "Xiangzhi Meng", - "author_inst": "Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA" - }, - { - "author_name": "Xiaoxue Huang", - "author_inst": "Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, D" - }, - { - "author_name": "Yunru Yang", - "author_inst": "Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, D" - }, - { - "author_name": "Dan Zhao", - "author_inst": "Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, D" - }, - { - "author_name": "Peigen Zhou", - "author_inst": "Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA" - }, - { - "author_name": "Xiaofang Wang", - "author_inst": "The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China" - }, - { - "author_name": "Changcheng Zhao", - "author_inst": "Department of Infectious Diseases, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China," - }, - { - "author_name": "Yong Sun", - "author_inst": "Anhui Provincial Center for Disease Control and Prevention, Hefei, Anhui 230001, China" - }, - { - "author_name": "Peihui Wang", - "author_inst": "Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, 2" - }, - { - "author_name": "Huichao Ou", - "author_inst": "Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, D" - }, - { - "author_name": "Xiaowen Hu", - "author_inst": "Department of pulmonary and critical care medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Tec" - }, - { - "author_name": "Yan Xiang", - "author_inst": "Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA" - }, - { - "author_name": "Tengchuan Jin", - "author_inst": "Hefei National Laboratory for Physical Sciences at Microscale, Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, D" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.03.429351", "rel_title": "Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection", @@ -950397,6 +951659,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.02.429431", + "rel_title": "Potential global impact of the N501Y mutation on MHC-II presentation and immune escape", + "rel_date": "2021-02-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.02.429431", + "rel_abs": "The B.1.1.7 SARS-CoV-2 variant, characterized by the N501Y mutation, is rapidly emerging, raising concerns about its effectiveness on natural as well as vaccine-induced adaptive viral immunity at the population level. Since CD4 T cell responses are of critical importance to the antibody response, we examined the global effects of N501Y mutation on MHC-II presentation compared to the N501 wildtype and found poorer presentation across the majority of MHC-II alleles. This suggests that the N501Y mutation may not only diminish binding of antibodies to the RBD but also interfere with their production by weakening the cooperation between T and B cells, facilitating immune escape.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Andrea Castro", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Hannah Carter", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Maurizio Zanetti", + "author_inst": "University of California, San Diego" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.02.03.429355", "rel_title": "Impact of the B.1.1.7 variant on neutralizing monoclonal antibodies recognizing diverse epitopes on SARS-CoV-2 Spike", @@ -952061,45 +953350,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.28.428568", - "rel_title": "Evolution of ACE2 and SARS-CoV-2 Interplay Across 247 Vertebrates", - "rel_date": "2021-02-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.28.428568", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cause the most serious pandemics of Coronavirus Disease 2019 (COVID-19), which threatens human health and public safety. SARS-CoV-2 spike (S) protein uses angiotensin-converting enzyme 2 (ACE2) as recognized receptor for its entry into host cell that contributes to the infection of SARS-CoV-2 to hosts. Using computational modeling approach, this study resolved the evolutionary pattern of bonding affinity of ACE2 in 247 jawed vertebrates to the spike (S) protein of SARS-CoV-2. First, high-or-low binding affinity phenotype divergence of ACE2 to the S protein of SARS-CoV-2 has appeared in two ancient species of jawed vertebrates, Scyliorhinus torazame (low-affinity, Chondrichthyes) and Latimeria chalumnae (high-affinity, Coelacanthimorpha). Second, multiple independent affinity divergence events recur in fishes, amphibians-reptiles, birds, and mammals. Third, high affinity phenotypes go up in mammals, possibly implying the rapid expansion of mammals might accelerate the evolution of coronaviruses. Fourth, we found natural mutations at eight amino acid sites of ACE2 can determine most of phenotype divergences of bonding affinity in 247 vertebrates and resolved their related structural basis. Moreover, we also identified high-affinity or low-affinity-associated concomitant mutation group.The group linked to extremely high affinity may provide novel potentials for the development of human recombinant soluble ACE2 (hrsACE2) in treating patients with COVID-19 or for constructing genetically modified SARS-CoV-2 infection models promoting vaccines studies. These findings would offer potential benefits for the treatment and prevention of SARS-CoV-2.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Zhigang Zhang", - "author_inst": "Yunnan University" - }, - { - "author_name": "Tao Zhang", - "author_inst": "Yunnan University" - }, - { - "author_name": "Qunfu Wu", - "author_inst": "Yunnan University" - }, - { - "author_name": "Yicheng Ma", - "author_inst": "Yunnan University" - }, - { - "author_name": "Wenjing Liu", - "author_inst": "Yunnan University" - }, - { - "author_name": "Chenggang Zou", - "author_inst": "Yunnan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2021.02.02.429327", "rel_title": "Computational insights into differential interaction of mamalian ACE2 with the SARS-CoV-2 spike receptor binding domain", @@ -952311,6 +953561,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.31.429023", + "rel_title": "Mn2+ coordinates Cap-0-RNA to align substrates for efficient 2'-O-methyl transfer by SARS-CoV-2 nsp16", + "rel_date": "2021-02-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.31.429023", + "rel_abs": "Capping viral messenger RNAs is essential for efficient translation and prevents their detection by host innate immune responses. For SARS-CoV-2, RNA capping includes 2'-O-methylation of the first ribonucleotide by methyltransferase nsp16 in complex with activator nsp10. The reaction requires substrates, a short RNA and SAM, and is catalyzed by divalent cations, with preference for Mn2+. Crystal structures of nsp16-nsp10 with capped RNAs revealed a critical role of metal ions in stabilizing interactions between ribonucleotides and nsp16, resulting in precise alignment of the substrates for methyl transfer. An aspartate residue that is highly conserved among coronaviruses alters the backbone conformation of the capped RNA in the binding groove. This aspartate is absent in mammalian methyltransferases and is a promising site for designing coronavirus-specific inhibitors.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "George Minasov", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Monica Rosas-Lemus", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Ludmilla Shuvalova", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Nicole L. Inniss", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Joseph S. Brunzelle", + "author_inst": "Northwestern Synchrotron Research Center" + }, + { + "author_name": "Courtney M. Daczkowski", + "author_inst": "Purdue University" + }, + { + "author_name": "Paul Hoover", + "author_inst": "Northwestern University, Feinberg School of Medicine" + }, + { + "author_name": "Andrew D Mesecar", + "author_inst": "Purdue University" + }, + { + "author_name": "Karla J Satchell", + "author_inst": "Northwestern University Feinberg School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.31.429001", "rel_title": "Identification of anti-severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) oxysterol derivatives in vitro", @@ -953647,49 +954948,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.24.21250418", - "rel_title": "Targeting TGF-b pathway with COVID-19 Drug Candidate ARTIVeda/PulmoHeal Accelerates Recovery from Mild-Moderate COVID-19", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.24.21250418", - "rel_abs": "Our COVID-19 drug candidate ARTIVeda/PulmoHeal is a novel gelatin capsule formulation of the Artemisia extract Ayurveda for oral delivery of TGF-{beta} targeting anti-malaria phytomedicine Artemisinin with documented anti-inflammatory and anti-SARS-CoV-2 activity. Here we report the safety and efficacy of ARTIVeda in adult COVID-19 patients with symptomatic mild-moderate COVID-19, who were treated in a randomized, open-label Phase IV study in Bangalore, Karnataka, India (Clinical Trials Registry India identifier: CTRI/2020/09/028044). ARTIVeda showed a very favorable safety profile, and the only ARTIVeda-related adverse events were transient mild rash and mild hypertension. Notably, ARTIVeda, when added to the SOC, accelerated the recovery of patients with mild-moderate COVID-19. While all patients were symptomatic at baseline (WHO score = 2-4), 31 of 39 (79.5%) of patients treated with ARTIVeda plus SOC became asymptomatic (WHO score = 1) by the end of the 5-day therapy, including 10 of 10 patients with severe dry cough 7 of 7 patients with severe fever. By comparison, 12 of 21 control patients (57.1%) treated with SOC alone became asymptomatic on day 5 (P=0.028, Fishers exact test). This clinical benefit was particularly evident when the treatment outcomes of hospitalized COVID-19 patients (WHO score = 4) treated with SOC alone versus SOC plus ARTIVeda were compared. The median time to becoming asymptomatic was only 5 days for the SOC plus ARTIVeda group (N=18) but 14 days for the SOC alone group (N=10) (P=0.004, Log-rank test). These data provide clinical proof of concept that targeting the TGF-{beta} pathway with ARTIVeda may contribute to a faster recovery of patients with mild-moderate COVID-19 when administered early in the course of their disease.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Vuong Trieu", - "author_inst": "Oncotelic, Inc." - }, - { - "author_name": "Saran Saund", - "author_inst": "Oncotelic, Inc." - }, - { - "author_name": "Prashant Rahate", - "author_inst": "Seven Star Hospital" - }, - { - "author_name": "Viljay Barge", - "author_inst": "Government Medical College" - }, - { - "author_name": "Sunil Nalk", - "author_inst": "Government Medical College" - }, - { - "author_name": "Hitesh Windlass", - "author_inst": "Windlass Biotech" - }, - { - "author_name": "Fatih Uckun", - "author_inst": "Ares Pharmaceuticals" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.28.21250675", "rel_title": "Age significantly influences the sensitivity of SARS-CoV-2 rapid antibody assays", @@ -954049,6 +955307,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.29.21250407", + "rel_title": "12-lead Electrocardiogram in Hospitalized COVID 19 Patients", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250407", + "rel_abs": "COVID-19 pandemic resulted in considerable morbidity and mortality. We analyzed 345 Electrocardiograms of 100 COVID-19 patients admitted to our tertiary care center in Detroit, during the initial month of Covid-19. Findings were correlated with mortality, cardiac injury and inflammatory markers. Our cohort included 61% males and 77% African Americans. The median age and BMI were 66 years (57-74) and 31 kg/m2 (26.1-39), respectively. We observed atrial arrhythmias in 29% of the patients (17% new onset), First degree heart block in 12%, ST-T segment changes in 17%, S1Q3T3 pattern in 19%, premature ventricular complexes in 23%, premature atrial complexes in 13%, Q waves in 27%, T wave inversion in 42% of the cases. While presence of premature atrial complexes or left atrial abnormality correlated with mortality (P = 0.02 & 0.03, respectively), other findings did not show significant correlation in this small cohort of patients.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Mohamed Shokr", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Omar Chehab", + "author_inst": "Department of Internal Medicine, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Mustafa Ajam", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Oregon Health & Science University, Portland, OR, USA" + }, + { + "author_name": "Manmohan Singh", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Said Ashraf", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "John Dawdy", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Mohit Pahuja", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Vivek Reddy", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Ahmed Subahi", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "M. Chadi Alraies", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Luis Afonso", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + }, + { + "author_name": "Randy Lieberman", + "author_inst": "Department of Cardiology, Wayne State University, Detroit, MI, USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.01.28.21250129", "rel_title": "Application of a 27-protein candidate cardiovascular surrogate endpoint to track risk ascendancy and resolution in COVID-19.", @@ -955433,45 +956754,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.29.21250764", - "rel_title": "Testing out of quarantine", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250764", - "rel_abs": "Since SARS-CoV-2 emerged, a 14-day quarantine has been recommended based on COVID-19\"s incubation period. Using an RT-PCR or rapid antigen test to \"test out\" of quarantine is a frequently proposed strategy to shorten duration without increasing risk. We calculated the probability that infected individuals test negative for SARS-CoV-2 on a particular day post-infection and remain symptom free for some period of time. We estimate that an infected individual has a 20.1% chance (95% CI 9.8-32.6) of testing RT-PCR negative on day five post-infection and remaining asymptomatic until day seven. We also show that the added information a test provides decreases as we move further from the test date, hence a less sensitive test that returns rapid results is often preferable to a more sensitive test with a delay.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Lucy D'Agostino McGowan", - "author_inst": "Wake Forest University" - }, - { - "author_name": "Elizabeth C. Lee", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Kyra H. Grantz", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Lauren Kucirka", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Emily S. Gurley", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Justin Lessler", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.29.21250762", "rel_title": "Predicting Prognosis in COVID-19 Patients using Machine Learning and Readily Available Clinical Data", @@ -955723,6 +957005,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.29.21250793", + "rel_title": "COVID-19 spread and Weather in U.S. states: a cross-correlative study on summer-autumn 2020.", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250793", + "rel_abs": "An effect of weather on sars-cov-2 transmission is regularly proposed as a putative cause of unexplained fluctuations of covid-19 new cases, but clear data supporting this hypothesis remains to be presented. Here I measured longitudinal time-series correlations between outdoor temperature, humidity and covid-19 reproduction number (Rt) in the 50 U.S. states (+DC). In order to mitigate the confounding influence of varying social restriction measures, the analysis spans a 5-month period during summer and autumn 2020 when restrictions were comparatively lower and more stable. I used a cross-covariance approach to account for a variable delay between infection and case report. For a delay near 11 days, most U.S. states exhibited a negative correlation between outdoor temperature and Rt, as well as between absolute humidity and Rt (mean r = -0.35). In 21 states, the correlation was strong (r < -0.5). Individual state data are presented, and associations between cold and/or dry weather episodes and short-term new case surges are proposed. After identifying potential confounding factors, I discuss 3 possible causal mechanisms that could explain a correlation between outdoor weather and indoor disease transmission: behavioral adaptations to cold weather, respiratory tract temperature, and the importing of outdoor absolute humidity to indoor spaces.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Emmanuel de Margerie", + "author_inst": "CNRS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.30.21250830", "rel_title": "Estimated SARS-CoV-2 Seroprevalence in Healthy Children and Those with Chronic Illnesses in The Washington Metropolitan Area as of October 2020", @@ -957171,49 +958472,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.27.21250502", - "rel_title": "Serosurveillance of SARS CoV 2 among the healthcare workers of a tertiary care teaching institution in Central Kerala during the post lockdown phase", - "rel_date": "2021-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250502", - "rel_abs": "BackgroundKerala was the first state to have the confirmed case of COVID-19 in the country and it was first confirmed in Thrissur district on 30 January2020.Our institute being in the heart of the city had to take adequate measures to mitigate the spread and treat the required patients by keeping its staff safe & Healthy. The hallmark of COVID 19 infection is high infectivity, pre-symptomatic transmission and asymptomatic prevalence which could result in high cumulative numbers of infections, hospitalizations, and deaths. Kerala was the first state to confirm community transmission in July 2020.Health care workers being in the forefront in the war against COVID19 are very prone in acquiring the infection and are possible to be asymptomatic sources for cluster formation. Knowing the development of immunity as shown by the presence of anti COV2 antibodies in the population contributes to the epidemiological understanding of the disease. The intent of the study is to do an antibody testing in our hospital to find the serosurveillance of SARS CoV 2 among the healthcare workers in our hospital.\n\nAimTo estimate the seropositivity of SARS CoV 2 among the healthcare workers at Jubilee Mission Medical College and Research Institute, Thrissur, Kerala, six months after revoking the lockdown\n\nMethodologyA cross sectional study among the health care workers of the medical college. Multistage Sampling was done with the hospital block as the first stage and departments as the second stage. In the final stage of sampling the test individuals were selected on a first come first served basis after the antibody test availability was declared open and free for all staff. A consent form and a Google form were given to all staff who volunteered for participating in the study. Each consented participant recruited into the investigation completed a questionnaire which covers details regarding demographics, exposure history, Residence & travel. Blood sample was collected and Anti-SARS COV2 IgG antibody testing which targets the Spike Protein 1(SP1) was done using the VITROS chemiluminescence platform (Orthoclinical diagnostics, USA). Sampling & testing ranged over a time frame from September 5th to December 15th, 2020\n\nResultsJubilee Mission Medical College has 2785 working staff at the time of study. A total of 420 staff consented and their samples were tested. 37 staff members tested positive for COVID-19 antibody, yielding an overall prevalence of 8.75% (95% CI, 6.23-11.86). 86.5 % (32/37) of them were having a history of COVID-19 Antigen / RT PCR Positivity. We identified a statistically significant linear trend (p value =0.00001), between seropositivity and the degree of severity of COVID 19. Among the various factors which increase the risk of seroconversion, history of undergoing quarantine (p value < 0.001), contact with a confirmed case (p value = 0.002), contact with a caregiver for COVID 19 (p value =0.001) and history of Upper respiratory symptoms (p value =0.001), were found to be significantly associated with positive serology.\n\nConclusionsThe overall seropositivity in the current study was found to be 8.75% which is comparable to seroprevalence studies conducted in the United States and Wuhan in China. The pattern of seropositivity across the different category of health workers observed in the present study showed a higher prevalence among nurses. This result is also in agreement with a recent published report from united states. Various measures advised by the national and state health authorities were adequately adhered to. Keeping track of the pattern of development of immunity in the community is part of understanding the illness and forecasting the spread. For the tested HCW, it will boost up morale by ending uncertainty. For the hospital administration it will help in decision making about relative focusing of interventions on patients in general and HCWs. By knowing the immunity status of HCWs, the Institution will be able to contribute authentically to the development of intervention strategies and guidelines from time to time, besides following the available guidelines. Being an educational institution, it is obligatory to train all the elements of care delivery to the future generation of health care workers. Getting experienced from a small but relevant sample was expected to facilitate larger community study envisaged in peripheral areas Jubilee served", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Aboobacker Mohamed Rafi", - "author_inst": "Jubilee Mission Medical College &Research Institute" - }, - { - "author_name": "Maglin Monica Lisa Joseph Tomy", - "author_inst": "Jubilee Mission Medical College & Research Institute" - }, - { - "author_name": "Ronnie Thomas", - "author_inst": "Government Medical College, Kottayam" - }, - { - "author_name": "Chithra Valsan", - "author_inst": "Jubilee Mission Medical College & Research Institute" - }, - { - "author_name": "U G Unnikrishnan", - "author_inst": "Jubilee Mission Medical College & Research Institute" - }, - { - "author_name": "Susheela J Innah", - "author_inst": "Jubilee Mission Medical College & Research Institute" - }, - { - "author_name": "Praveenlal Kuttichira", - "author_inst": "Jubilee Mission Medical College & Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.27.21250659", "rel_title": "SARS-CoV-2 antigen rapid diagnostic test enhanced with silver amplification technology", @@ -957541,6 +958799,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.28.21250700", + "rel_title": "Surveillance-to-Diagnostic Testing Program for Asymptomatic SARS-CoV-2 Infections on a Large, Urban Campus - Georgia Institute of Technology, Fall 2020", + "rel_date": "2021-01-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250700", + "rel_abs": "A SARS-CoV-2 testing program combining pooled saliva sample surveillance leading to diagnosis and intervention surveyed over 112,000 samples from 18,029 students, staff and faculty, as part of integrative efforts to mitigate transmission at the Georgia Institute of Technology in Fall 2020. Cumulatively, 1,508 individuals were confirmed diagnostically. The surveillance strategy, including focused intensification of testing given case clusters, was effective in disrupting transmission following rapid case increases upon entry in August 2020, and again in November 2020. Owing to broad adoption by the campus community, the program protected higher risk staff while allowing some normalization of research activities.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Greg C Gibson", + "author_inst": "Georgia Tech" + }, + { + "author_name": "Joshua S Weitz", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Michael P. Shannon", + "author_inst": "Georgia Tech Research Institute" + }, + { + "author_name": "Benjamin Holton", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Anton Bryksin", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Brian Liu", + "author_inst": "Georgia Tech Research Institute" + }, + { + "author_name": "Sandra Bramblett", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Julianne Williamson", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Michael Farrell", + "author_inst": "Georgia Tech Research Institute" + }, + { + "author_name": "Alexander Ortiz", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Chaouki T. Abdallah", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Andr\u00e9s Garc\u00eda", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.29.428890", "rel_title": "Recombinant production of a functional SARS-CoV-2 spike receptor binding domain in the green algae Chlamydomonas reinhardtii", @@ -959105,41 +960426,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.27.21250428", - "rel_title": "Diagnostic accuracy and utility of SARS-CoV-2 antigen lateral flow assays in medical admissions with possible COVID-19", - "rel_date": "2021-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250428", - "rel_abs": "We evaluated diagnostic accuracy of the Innova SARS-CoV-2 Antigen Rapid Qualitative Test compared to SARS-CoV-2 RT-PCR from nasopharyngeal swabs in adult admissions who met the COVID-19 case definition at a busy acute hospital in the UK. We found the Innova SARS-CoV-2 Antigen Rapid Qualitative Test had a good specificity in patients with symptoms of COVID-19 presenting to hospital. The Innova LFA can be used to rapidly identify COVID-19 cases amongst hospital admissions meeting the COVID-19 case definition, allowing patients to be allocated to COVID-19 cohort areas.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Hamish Houston", - "author_inst": "London North West University Healthcare NHS Trust" - }, - { - "author_name": "Ankur Gupta-Wright", - "author_inst": "Institute for Global Health, University College London, London, United Kingdom" - }, - { - "author_name": "Edward Toke-Bjolgerud", - "author_inst": "Northwick Park Hospital, London North West University Healthcare NHS Trust, Harrow, United Kingdom" - }, - { - "author_name": "James Biggin-Lamming", - "author_inst": "Northwick Park Hospital, London North West University Healthcare NHS Trust, Harrow, United Kingdom" - }, - { - "author_name": "Laurence John", - "author_inst": "Northwick Park Hospital, London North West University Healthcare NHS Trust, Harrow, United Kingdom" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.26.21250584", "rel_title": "First detection and report of SARS-CoV-2 Spike protein N501Y mutations in Oklahoma USA", @@ -959351,6 +960637,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.26.21250349", + "rel_title": "HLA-A*11:01:01:01, HLA*C*12:02:02:01-HLA-B*52:01:02:02, age and sex are associated with severity of Japanese COVID-19 with respiratory failure", + "rel_date": "2021-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250349", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing coronavirus disease 2019 (COVID-19) was announced as an outbreak by the World Health Organization (WHO) in January 2020 and as a pandemic in March 2020. The majority of infected individuals have experienced no or only mild symptoms, ranging from fully asymptomatic cases to mild pneumonic disease. However, a minority of infected individuals develop severe respiratory symptoms. The objective of this study was to identify susceptible HLA alleles and clinical markers for the early identification of severe COVID-19 among hospitalized COVID-19 patients. A total of 137 patients with mild COVID-19 (mCOVID-19) and 53 patients with severe COVID-19 (sCOVID-19) were recruited from the Center Hospital of the National Center for Global Health and Medicine (NCGM), Tokyo, Japan for the period of February-August 2020. High-resolution sequencing-based typing for eight HLA genes was performed using next-generation sequencing. In the HLA association studies, HLA-A*11:01:01:01 [Pc = 0.013, OR = 2.26 (1.27-3.91)] and HLA-C*12:02:02:01-HLA-B*52:01:01:02 [Pc = 0.020, OR = 2.25 (1.24-3.92)] were found to be significantly associated with the severity of COVID-19. After multivariate analysis controlling for other confounding factors and comorbidities, HLA-A*11:01:01:01 [P = 3.34E-03, OR = 3.41 (1.50-7.73)], age at diagnosis [P = 1.29E-02, OR = 1.04 (1.01-1.07)] and sex at birth [P = 8.88E-03, OR = 2.92 (1.31-6.54)] remained significant. Early identification of potential sCOVID-19 could help clinicians prioritize medical utility and significantly decrease mortality from COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Seik-Soon Khor", + "author_inst": "Genome Medical Science Project, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Yosuke Omae", + "author_inst": "Genome Medical Science Project, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Nao Nishida", + "author_inst": "Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan" + }, + { + "author_name": "Masaya Sugiyama", + "author_inst": "Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan" + }, + { + "author_name": "Noriko Kinoshita", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Tetsuya Suzuki", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Michiyo Suzuki", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Satoshi Suzuki", + "author_inst": "Biobank, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Shinyu Izumi", + "author_inst": "Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Masayuki Hojo", + "author_inst": "Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + }, + { + "author_name": "Masashi Mizokami", + "author_inst": "Genome Medical Sciences Project, National Center for Global Health and Medicine, 1-7-1 Kohnodai, Ichikawa, Chiba 272-8516, Japan" + }, + { + "author_name": "Katsushi Tokunaga", + "author_inst": "Genome Medical Science Project, National Center for Global Health and Medicine Hospital, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.27.21250048", "rel_title": "A Rapid and Low-Cost protocol for the detection of B.1.1.7 lineage of SARS-CoV-2 by using SYBR Green-Based RT-qPCR", @@ -960567,65 +961920,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2021.01.26.21250511", - "rel_title": "The angiotensin type 2 receptor agonist C21 restores respiratory function in COVID19 - a double-blind, randomized, placebo-controlled Phase 2 trial", - "rel_date": "2021-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250511", - "rel_abs": "BackgroundAlthough several therapies have been evaluated for treatment of COVID-19, the morbidity and mortality in COVID-19 are still significant, and the need for safe and effective drugs remains high even after launch of vaccine programs.\n\nMethodsWe conducted a double-blind, randomized, placebo-controlled trial with the novel oral angiotensin II type 2 receptor agonist C21 in hospitalized COVID-19 patients with C-reactive protein 50-150 mg/L but not needing mechanical ventilation. Patients were randomly assigned to oral C21 (100 mg twice daily) or placebo for 7 days in addition to standard of care, including glucocorticoids and remdesivir.\n\nResults106 patients underwent randomization (51 in the C21 group and 55 in the placebo group). At day 14 after start of treatment, the proportion of patients still requiring supplemental oxygen was significantly reduced by 90% in the C21 group compared to the placebo group (p=0.003). Moreover, fewer patients required mechanical ventilation (one C21 patient and four placebo patients), and C21 was associated with a numerical reduction in the mortality rate (one and three deaths in the C21 and placebo group, respectively). Treatment with C21 was safe and well tolerated.\n\nConclusionsAs studied in hospitalized COVID-19 patients, C21 on top of standard of care led to a clinically beneficial improvement in respiratory function compared to placebo, paving the way for a pivotal randomised controlled trial.\n\nThis study is registered at ClinicalTrials.gov with identifier NCT04452435.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Goran Tornling", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Rohit Batta", - "author_inst": "Vicore Pharma AB" - }, - { - "author_name": "Joanna Porter", - "author_inst": "University College London" - }, - { - "author_name": "Thomas Bengtsson", - "author_inst": "StatMind AB" - }, - { - "author_name": "Kartikeya Parmar", - "author_inst": "Civil Hospital and B J Medical College" - }, - { - "author_name": "Reema Kashiva", - "author_inst": "Noble Hospitals Pvt Ltd" - }, - { - "author_name": "Anne Kartine Cohrt", - "author_inst": "Vicore Pharma AB" - }, - { - "author_name": "Kate Westergaard", - "author_inst": "Vicore Pharma AB" - }, - { - "author_name": "Anders Hallberg", - "author_inst": "Uppsala University" - }, - { - "author_name": "Carl-Johan Dalsgaard", - "author_inst": "Vicore Pharma AB" - }, - { - "author_name": "Johan Raud", - "author_inst": "Karolinska Institutet" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.01.26.21250480", "rel_title": "Individual factors underlie temperature variation in sickness and in health: influence of age, BMI and genetic factors in a multi-cohort study", @@ -960985,6 +962279,153 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2021.01.27.428516", + "rel_title": "SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral Spike vaccines", + "rel_date": "2021-01-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.27.428516", + "rel_abs": "The SARS-CoV-2 Spike glycoprotein mediates virus entry and is a major target for neutralizing antibodies. All current vaccines are based on the ancestral Spike with the goal of generating a protective neutralizing antibody response. Several novel SARS-CoV-2 variants with multiple Spike mutations have emerged, and their rapid spread and potential for immune escape have raised concerns. One of these variants, first identified in the United Kingdom, B.1.1.7 (also called VUI202012/01), contains eight Spike mutations with potential to impact antibody therapy, vaccine efficacy and risk of reinfection. Here we employed a lentivirus-based pseudovirus assay to show that variant B.1.1.7 remains sensitive to neutralization, albeit at moderately reduced levels (~2-fold), by serum samples from convalescent individuals and recipients of two different vaccines based on ancestral Spike: mRNA-1273 (Moderna), and protein nanoparticle NVX-CoV2373 (Novavax). Some monoclonal antibodies to the receptor binding domain (RBD) of Spike were less effective against the variant while others were largely unaffected. These findings indicate that B.1.1.7 is not a neutralization escape variant that would be a major concern for current vaccines, or for an increased risk of reinfection.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Haili Tang", + "author_inst": "Duke University" + }, + { + "author_name": "Charlene McDana", + "author_inst": "Duke University" + }, + { + "author_name": "Xiaoying Shen", + "author_inst": "Duke University" + }, + { + "author_name": "Kshitij Wagh", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Haili Tang", + "author_inst": "Duke University" + }, + { + "author_name": "Will Fischer", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Charlene McDana", + "author_inst": "Duke University" + }, + { + "author_name": "James Theiler", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Kshitij Wagh", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Hyejin Yoon", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Will Fischer", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Dapeng Li", + "author_inst": "Duke University" + }, + { + "author_name": "James Theiler", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Barton F Haynes", + "author_inst": "Duke University" + }, + { + "author_name": "Hyejin Yoon", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "S. Gnanakaran", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Dapeng Li", + "author_inst": "Duke University" + }, + { + "author_name": "Nicholas W Hengartner", + "author_inst": "Los Alamos Nationa Lab" + }, + { + "author_name": "Barton F Haynes", + "author_inst": "Duke University" + }, + { + "author_name": "Rolando Pajon", + "author_inst": "Moderna Inc" + }, + { + "author_name": "S. Gnanakaran", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Nicholas W Hengartner", + "author_inst": "Los Alamos Nationa Lab" + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Rolando Pajon", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Gregory M Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Bette Korber", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Filip Dubovsky", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "David Montefiori", + "author_inst": "Duke University" + }, + { + "author_name": "Gregory M Glenn", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Bette Korber", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "David Montefiori", + "author_inst": "Duke University" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.27.428534", "rel_title": "Unbiased interrogation of memory B cells from convalescent COVID-19 patients reveals a broad antiviral humoral response targeting SARS-CoV-2 antigens beyond the spike protein", @@ -962561,37 +964002,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.01.27.428372", - "rel_title": "Zinc supplement augments the suppressive effects of repurposed drugs of NF-kappa B inhibitor on ACE2 expression in human lung cell lines in vitro.", - "rel_date": "2021-01-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.27.428372", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a vast number of infections and fatalities worldwide. As the development and safety validation of effective vaccines are ongoing, drug repurposing is most efficient approach to search FDA approved agents against coronavirus disease 2019 (COVID-19). In the present study, we found that endogenous ACE2 expressions could be detected in H322M and Calu-3 cell lines, as well as their ACE2 mRNA and protein expressions were suppressed by pyrrolidine dithiocarbamate (PDTC), a NF-kappa B inhibitor, in dose- and time-dependent manners. Moreover, N-acetyl-cysteine (NAC) pretreatment reversed PDTC-induced ACE2 suppression, as well as the combined treatment of hydrogen peroxide and knockdown of p50 subunit of NF-kappa B by siRNA reduced ACE2 expression in H322M cells. In addition, anthelmintic drug triclabendazole and antiprotozoal drug emetine, repurposed drugs of NF-kappa B inhibitor, also inhibited ACE2 mRNA and protein expressions in H322M cells. Moreover, zinc supplement augmented the suppressive effects of triclabendazole and emetine on ACE2 suppression in H322M and Calu-3 cells. Taken together, these results indicate that ACE2 expression is modulated by reactive oxygen species (ROS) and NF-kappa B signal in human lung cell lines, and zinc combination with triclabendazole or emetine has the clinical potential for the prevention and treatment of COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ming Cheng Lee", - "author_inst": "National Taiwan University Hospital" - }, - { - "author_name": "Yin-Kai Chen", - "author_inst": "National Taiwan University Cancer Center" - }, - { - "author_name": "Yih-Jen Hsu", - "author_inst": "National Taiwan University Hospital" - }, - { - "author_name": "Bor-Ru Lin", - "author_inst": "National Taiwan University Hospital and National Taiwan University College of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.01.27.426895", "rel_title": "E484K as an innovative phylogenetic event for viral evolution: Genomic analysis of the E484K spike mutation in SARS-CoV-2 lineages from Brazil", @@ -962763,6 +964173,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.01.26.428208", + "rel_title": "Do examinations prepare students for higher education? A lesson from the Covid-19 lockdown.", + "rel_date": "2021-01-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.26.428208", + "rel_abs": "The COVID-19 pandemic caused severe disruption to education in the UK in 2020, with most of the school teaching moving online and national school examinations being cancelled. This was particularly disruptive for those taking end of school examinations in preparation for higher education. Biological science courses require students to absorb a lot of new vocabulary and concepts, with examinations traditionally focusing on content recall rather than reasoning. Students who had entered university in September 2019 were compared with those arriving in September 2020 with respect to their knowledge of bioscience vocabulary and understanding of key concepts. Results showed no significant difference between those who had gone through the examination process in 2019 relative to those who had not, in 2020. This suggests the cramming of information for examinations has no detectable effect on the knowledge and understanding of biology that students take with them to university.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Harriet L Jones", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Valentina Zini", + "author_inst": "University of East Anglia" + }, + { + "author_name": "Jon R Green", + "author_inst": "University of Birmingham" + }, + { + "author_name": "John R Prendergast", + "author_inst": "JRP Information Services" + }, + { + "author_name": "Jon Scott", + "author_inst": "University of Leicester" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.01.21.21250249", "rel_title": "Evaluation of six commercial SARS-CoV-2 Enzyme-Linked Immunosorbent assays for clinical testing and serosurveillance.", @@ -964075,57 +965520,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2021.01.23.21250164", - "rel_title": "Assessment of the knowledge, preferences and concern regarding the prospective COVID- 19 vaccine among adults residing in New Delhi, India-A cross-sectional study.", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.23.21250164", - "rel_abs": "BackgroundUnderstanding the perception and concerns of people about COVID-19 vaccine in developing and populous country like India will help in understanding demand for the vaccine and further tailoring out public health information and education activities before the launch of the vaccine. The study was carried out to assess the present state of knowledge people have about the probable vaccine for COVID-19, to know the preferences of respondents about this vaccine and to learn the expectations and apprehensions of people about features of this prospective COVID-19 vaccine residing in the capital city of India.\n\nMethodsThis cross-sectional study was conducted amongst the residents of Delhi, India from July-October 2020. Both offline and online interview method was used to collect date from 513 participants representing various occupational strata. Data was collected on socio demographic variable, vaccine acceptance and concerns regarding COVID-19 vaccine.\n\nResultsAmong the study population 79.5% said they will take the vaccine while 8.8% said they were not going to take the vaccine and remaining 11.7% had not yet decided about it. Most of them(78.8%),believed that vaccine would be available to public next year but at the same time half(50.1%) of them believe that it may not be in sufficient amount for everyone to get. More than 50% were willing to pay for the vaccine and 72% felt vaccine should first be given to health workers and high risk group.\n\nConclusionThe following study has helped to understand the percentage of people who are hesitant to take the vaccine and also the concerns regarding the vaccine. Also since half of the population is willing to pay for the vaccine, a strategical approach considering the various economical classes of people could be applied in a developing country like India.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Farzana Islam", - "author_inst": "Professor, Department of Community Medicine, Hamdard Institute of Medical Sciences and Research ,New Delhi, India" - }, - { - "author_name": "Rashmi Agarwalla", - "author_inst": "Assistant Professor, Department of Community and Family Medicine, All Indian Institute of Medical Sciences, Guwahati, Assam, India." - }, - { - "author_name": "Meely Panda", - "author_inst": "Assistant Professor, Department of Community and Family Medicine, All Indian Institute of Medical Sciences, Bibinagar, Telangana, India." - }, - { - "author_name": "Yasir Alvi", - "author_inst": "Assistant Professor, Department of Community Medicine, Hamdard Institute of Medical Sciences and Research ,New Delhi, India" - }, - { - "author_name": "Vishal Singh", - "author_inst": "Post Graduate, Department of Community Medicine, Hamdard Institute of Medical Sciences and Research, New Delhi, India" - }, - { - "author_name": "Arup Debroy", - "author_inst": "Public Health Expert" - }, - { - "author_name": "Arindam Ray", - "author_inst": "Public Health Expert" - }, - { - "author_name": "Amruta Vadnerkar", - "author_inst": "Project Manager, International Paediatric Association" - }, - { - "author_name": "Shraddha Uttekar", - "author_inst": "Project Manager, International Paediatric Association" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.01.22.21250339", "rel_title": "Pooled Sample Testing for SARS-CoV-2", @@ -964505,6 +965899,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.25.21250082", + "rel_title": "SARS-CoV-2 RNA screening in routine pathology specimens", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.25.21250082", + "rel_abs": "Virus detection methods are important to cope with the SARS-CoV-2 pandemics. Apart from the lung, SARS-CoV-2 was detected in multiple organs in severe cases. Less is known on organ tropism in patients developing mild or no symptoms, and some of such patients might be missed in symptom-indicated swab testing.\n\nHere we tested and validated several approaches and selected the most reliable RT-PCR protocol for the detection of SARS-CoV-2 RNA in patients routine diagnostic formalin-fixed and paraffin-embedded (FFPE) specimens available in pathology, to assess a) organ tropism in samples from COVID-19-positive patients, b) unrecognized cases in selected tissues from negative or not-tested patients during a pandemic peak, and c) retrospectively, pre-pandemic lung samples.\n\nWe identified SARS-CoV-2 RNA in four samples from confirmed COVID-19 patients, in two gastric biopsies, one colon resection, and one pleural effusion specimen, while all other specimens, particularly from patients with mild COVID-19 disease course, were negative. In the pandemic peak cohort, we identified one previously unrecognized COVID-19 case in tonsillectomy samples. All pre-pandemic lung samples were negative.\n\nIn conclusion, SARS-CoV-2 RNA detection in FFPE pathology specimens can potentially improve surveillance of COVID-19, allow retrospective studies, and advance our understanding of SARS-CoV-2 organ tropism and effects.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Saskia E von Stillfried", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Sophia Villwock", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Roman D Buelow", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Sonja Djudjaj", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Eva M Buhl", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Angela Maurer", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Nadina Ortiz-Bruechle", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Peter Celec", + "author_inst": "Institute of Virology, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia; Institute of Pathophysiology, Faculty of Medicine, Comenius" + }, + { + "author_name": "Barbara M Klinkhammer", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Dickson WL Wong", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Claudio Cacchi", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Till Braunschweig", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Ruth Knuechel", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Edgar Dahl", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" + }, + { + "author_name": "Peter Boor", + "author_inst": "Institute of Pathology, RWTH Aachen University Hospital, Aachen, Germany and Departments of Nephrology and Immunology, RWTH Aachen University Hospital, Aachen, " + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.21.21249906", "rel_title": "Genomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil", @@ -966117,45 +967586,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.25.21250404", - "rel_title": "ARE GEOGRAPHIC FACTORS ASSOCIATED WITH POORER OUTCOMES IN PATIENTS DIAGNOSED WITH COVID-19?", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.25.21250404", - "rel_abs": "BackgroundThe prognosis of patients with COVID-19, with older age and comorbidities, is associated with a more severe course and higher fatality rates but no analysis has yet included factors related to the geographical area/municipality in which the affected patients live. So the objective of this study is to analyse the prognosis of patients with COVID-19 in terms of sex, age, comorbidities, and geographic variables.\n\nMethodsA retrospective cohort of 6286 patients diagnosed with COVID-19 was analysed, considering demographic data, previous comorbidities and geographic variables. The main study variables were hospital admission, Intensive Care Unit (ICU) admission and death due to worsening symptoms; and the secondary variables were sex, age, comorbidities and geographic variables (size of the area of residence, distance to the hospital and the driving time to the hospital). A comparison analysis and a multivariate Cox model were performed.\n\nResultsThe multivariate Cox model showed that women had a better prognosis in any type of analysed prognosis. Most of the comorbidities studied were related to a poorer prognosis except for dementia, which is related to lower admissions and higher mortality. Suburban areas were associated with greater mortality and with less hospital or ICU admission. Distance to the hospital was also associated with hospital admission.\n\nConclusionsFactors such as type of municipality and distance to hospital act as social health determinants. This fact must be taken account in order to stablish specifics prevention measures and treatment protocols.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Rosa Magallon-Botaya Sr.", - "author_inst": "UNIVERSIDAD DE ZARAGOZA" - }, - { - "author_name": "Barbara Olivan-Blazquez", - "author_inst": "University of Zaragoza" - }, - { - "author_name": "Karen Ramirez-Cervantes", - "author_inst": "Intituto de Investigacion Hospital La Paz" - }, - { - "author_name": "Fatima Lopez-Mendez", - "author_inst": "Institute od Research Aragon-IIS-Aragon" - }, - { - "author_name": "Marc Casajuana-Closas", - "author_inst": "Institute of Research Idiap Gol y Gorina Barcelona" - }, - { - "author_name": "Eva Andres-Esteban", - "author_inst": "Institute of Research Hospital La Paz. Madrid" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2021.01.25.21250315", "rel_title": "A cross-sectional survey of the workplace factors contributing to symptoms of anxiety and depression among nurses and physicians during the first wave of COVID-19 pandemic in two US healthcare systems", @@ -966431,6 +967861,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.26.21250507", + "rel_title": "Estimation of the SARS-CoV-2 infection fatality rate in Germany", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21250507", + "rel_abs": "Assessing the infection fatality rate (IFR) of SARS-CoV-2 is one of the most controversial issues during the pandemic. Due to asymptomatic or mild courses of COVID-19, many infections remain undetected. Reported case fatality rates - COVID-19-associated deaths divided by number of detected infections - are therefore poor estimates of the IFR. Endogenous changes of the population at risk of a SARS-CoV-2 infection, changing test practices and an improved understanding of the pathogenesis of COVID-19 further exacerbate the estimation of the IFR. Here, we propose a strategy to estimate the IFR of SARS-CoV-2 in Germany that combines official data on reported cases and fatalities supplied by the Robert Koch Institute (RKI) with data from seroepidemiological studies in two infection hotspots, the Austrian town Ischgl and the German municipality Gangelt, respectively. For this purpose, we use the law of total probability to derive an approximate formula for the IFR that is based on a set of assumptions regarding data quality and test specificity and sensitivity. The resulting estimate of the IFR in Germany of 0.83% (95% CI: [0.69%; 0.98%]) that is based on a combination of the RKI and Ischgl data is notably higher than the IFR estimate reported in the Gangelt study (0.36% [0.29%; 0.45%]). It is closer to the consolidated estimate based on a meta-analysis (0.68% [0.53%; 0.82%]), where the difference can be explained by Germanys disadvantageous age structure. As a result of virus mutations, vaccination strategies, and improved therapy, a re-estimation of the IFR will eventually be mandated; the proposed method is able to account for such developments.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Thomas Dimpfl", + "author_inst": "University of T\u00fcbingen, Department of Statistics and Econometrics" + }, + { + "author_name": "Jantje S\u00f6nksen", + "author_inst": "University of T\u00fcbingen, Department of Statistics and Econometrics" + }, + { + "author_name": "Ingo Bechmann", + "author_inst": "University of Leipzig, Institute of Anatomy" + }, + { + "author_name": "Joachim Grammig", + "author_inst": "University of T\u00fcbingen, Department of Statistics and Econometrics" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.25.21250505", "rel_title": "Community structured model for vaccine strategies to control COVID19 spread: a mathematical study", @@ -967879,77 +969340,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.01.25.427948", - "rel_title": "mRNA-1273 vaccine induces neutralizing antibodies against spike mutants from global SARS-CoV-2 variants", - "rel_date": "2021-01-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.25.427948", - "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative infection of a global pandemic that has led to more than 2 million deaths worldwide. The Moderna mRNA-1273 vaccine has demonstrated ~94% efficacy in a Phase 3 study and has been approved under Emergency Use Authorization. The emergence of SARS-CoV-2 variants with mutations in the spike protein, most recently circulating isolates from the United Kingdom (B.1.1.7) and Republic of South Africa (B.1.351), has led to lower neutralization from convalescent serum by pseudovirus neutralization (PsVN) assays and resistance to certain monoclonal antibodies. Here, using two orthogonal VSV and lentivirus PsVN assays expressing spike variants of 20E (EU1), 20A.EU2, D614G-N439, mink cluster 5, B.1.1.7, and B.1.351 variants, we assessed the neutralizing capacity of sera from human subjects or non-human primates (NHPs) that received mRNA-1273. No significant impact on neutralization against the B.1.1.7 variant was detected in either case, however reduced neutralization was measured against the mutations present in B.1.351. Geometric mean titer (GMT) of human sera from clinical trial participants in VSV PsVN assay using D614G spike was 1/1852. VSV pseudoviruses with spike containing K417N-E484K-N501Y-D614G and full B.1.351 mutations resulted in 2.7 and 6.4-fold GMT reduction, respectively, when compared to the D614G VSV pseudovirus. Importantly, the VSV PsVN GMT of these human sera to the full B.1.351 spike variant was still 1/290, with all evaluated sera able to fully neutralize. Similarly, sera from NHPs immunized with 30 or 100g of mRNA-1273 had VSV PsVN GMTs of ~ 1/323 or 1/404, respectively, against the full B.1.351 spike variant with a ~ 5 to 10-fold reduction compared to D614G. Individual mutations that are characteristic of the B.1.1.7 and B.1.351 variants had a similar impact on neutralization when tested in VSV or in lentivirus PsVN assays. Despite the observed decreases, the GMT of VSV PsVN titers in human vaccinee sera against the B.1.351 variant remained at ~1/300. Taken together these data demonstrate reduced but still significant neutralization against the full B.1.351 variant following mRNA-1273 vaccination.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kai Wu", - "author_inst": "Moderna" - }, - { - "author_name": "Anne P. Werner", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Juan I. Moliva", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Matthew Koch", - "author_inst": "Moderna" - }, - { - "author_name": "Angela Choi", - "author_inst": "Moderna" - }, - { - "author_name": "Guillaume B.E. Stewart-Jones", - "author_inst": "Moderna" - }, - { - "author_name": "Hamilton Bennett", - "author_inst": "Moderna" - }, - { - "author_name": "Seyhan Boyoglu-Barnum", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Wei Shi", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Barney S Graham", - "author_inst": "Vaccine Research Center, NIAID, NIH" - }, - { - "author_name": "Andrea Carfi", - "author_inst": "Moderna" - }, - { - "author_name": "Kizzmekia S. Corbett", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Robert A. Seder", - "author_inst": "Vaccine Research Center; National Institute of Allergy and Infectious Diseases; National Institutes of Health" - }, - { - "author_name": "Darin K. Edwards", - "author_inst": "Moderna" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.23.21250358", "rel_title": "An effect of the COVID-19 pandemic: significantly more complicated appendicitis due to delayed presentation of patients!", @@ -968149,6 +969539,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.21.21249176", + "rel_title": "Distinct Autoimmune Antibody Signatures Between Hospitalized Acute COVID-19 Patients, SARS-CoV-2 Convalescent Individuals, and Unexposed Pre-Pandemic Controls", + "rel_date": "2021-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21249176", + "rel_abs": "Increasing evidence suggests that autoimmunity may play a role in the pathophysiology of SARS-CoV-2 infection during both the acute and long COVID phases of disease. However, an assessment of autoimmune antibodies in convalescent SARS-CoV-2 patients has not yet been reported.\n\nMethodologyWe compared the levels of 18 different IgG autoantibodies (AABs) between four groups: (1) unexposed pre-pandemic subjects from the general population (n = 29); (2) individuals hospitalized with acute moderate-severe COVID-19 (n = 20); (3) convalescent SARS-COV-2-infected subjects with asymptomatic to mild viral symptoms during the acute phase with samples obtained between 1.8 and 7.3 months after infection (n = 9); and (4) unexposed pre-pandemic subjects with systemic lupus erythematous (SLE) (n = 6). Total IgG and IgA levels were also measured from subjects in groups 1-3 to assess non-specific pan-B cell activation.\n\nResultsAs expected, in multivariate analysis, AABs were detected at much higher odds in SLE subjects (5 of 6, 83%) compared to non-SLE pre-pandemic controls (11 of 29, 38%) [odds ratio (OR) 19.4,95% CI, 2.0 - 557.0, p = 0.03]. AAB detection (percentage of subjects with one or more autoantibodies) was higher in SARS-CoV-2 infected convalescent subjects (7 of 9, 78%) [OR 17.4, 95% CI, 2.0 - 287.4, p = 0.02] and subjects with acute COVID-19 (12 of 20, 60%) compared with non-SLE pre-pandemic controls, but was not statistically significant among the latter [OR 1.8,95% CI, 0.6 - 8.1, p = 0.23]. Within the convalescent subject group, AABs were detected in 5/5 with reported persistent symptoms and 2/4 without continued symptoms (p = 0.17). The multivariate computational algorithm Partial Least Squares Determinant Analysis (PLSDA) was used to determine if distinct AAB signatures distinguish subject groups 1-3. Of the 18 autoantibodies measured, anti-Beta 2-Glycoprotein, anti-Proteinase 3-ANCA, anti-Mi-2 and anti-PM/Scl-100 defined the convalescent group; anti-Proteinase 3-ANCA, anti-Mi-2, anti-Jo-1 and anti-RNP/SM defined acute COVID-19 subjects; and anti-Proteinase 3-ANCA, anti-Mi-2, anti-Jo-1, anti-Beta 2-Glycoprotein distinguished unexposed controls. The AABs defining SARS-COV-2 infected from pre-pandemic subjects are widely associated with myopathies, vasculitis, and antiphospholipid syndromes, conditions with some similarities to COVID-19. Compared to pre-pandemic non-SLE controls, subjects with acute COVID-19 had higher total IgG concentration (p-value=0.006) but convalescent subjects did not (p-value=0.08); no differences in total IgA levels were found between groups.\n\nConclusionsOur findings support existing studies suggesting induction of immune responses to self-epitopes during acute, severe COVID-19 with evidence of general B cell hyperactivation. Also, the preponderance of AAB positivity among convalescent individuals up to seven months after infection indicates potential initiation or proliferation, and then persistence of self-reactive immunity without severe initial disease. These results underscore the importance of further investigation of autoimmunity during SARS-CoV-2 infection and its role in the onset and persistence of post-acute sequelae of COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Nahid Bhadelia", + "author_inst": "Department of Medicine, Boston University School of Medicine and National Emerging Infectious Diseases Laboratories (NEIDL), Boston University" + }, + { + "author_name": "Anna Belkina", + "author_inst": "Flow Cytometry Core Facility and Department of Pathology and Laboratory Medicine, Boston University School of Medicine" + }, + { + "author_name": "Alex Olson", + "author_inst": "Department of Medicine, Boston University School of Medicine" + }, + { + "author_name": "Thomas Winter", + "author_inst": "Research Occupational Health Program, Boston University" + }, + { + "author_name": "Patricia Urick", + "author_inst": "Research Occupational Health Program, Boston University" + }, + { + "author_name": "Nina Lin", + "author_inst": "Department of Medicine, Boston University School of Medicine" + }, + { + "author_name": "Ian Rifkin", + "author_inst": "Renal Section, Department of Medicine, Boston University School of Medicine and Renal Section, Department of Medicine, VA Boston Healthcare System" + }, + { + "author_name": "Yachana Kataria", + "author_inst": "Department of Pathology and Laboratory Medicine, Boston University School of Medicine" + }, + { + "author_name": "Rachel Yuen", + "author_inst": "Department of Microbiology; Boston University School of Medicine" + }, + { + "author_name": "Manish Sagar", + "author_inst": "Department of Medicine, Boston University School of Medicine" + }, + { + "author_name": "Jennifer Cappione", + "author_inst": "Department of Microbiology; Boston University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.22.21249716", "rel_title": "An interactive COVID-19 virus Mutation Tracker (CovMT) with a particular focus on critical mutations in the Receptor Binding Domain (RBD) region of the Spike protein", @@ -969877,41 +971326,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.25.428042", - "rel_title": "Ubiquitin ligase RIPLET mediates polyubiquitination of RIG-I and LGP2 and regulates the innate immune responses to SARS-CoV-2 infection", - "rel_date": "2021-01-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.25.428042", - "rel_abs": "RIG-I, a cytoplasmic viral RNA sensor, is crucial for innate antiviral immune responses; however, there are controversies about RIG-Is regulatory mechanism by several ubiquitin ligases and LGP2. Our genetic study revealed that the RIPLET ubiquitin ligase was a general activating factor for RIG-I signaling, whereas another ubiquitin ligase, TRIM25, activated RIG-I in a cell-type-specific manner. These RIPLET and TRIM25 functions were modulated by accessory factors, such as ZCCH3C and NLRP12. Interestingly, we found an additional role of RIPLET in innate immune responses. RIPLET induced delayed polyubiquitination of LGP, resulting in the attenuation of excessive cytokine expression at the late phase. Moreover, RIPLET was involved in the innate immune responses against SARS-CoV-2 infection, a cause of the recent COVID-19 pandemic. Our data indicate that RIPLET fine-tunes innate immune responses via polyubiquitination of RIG-I and LGP2 against virus infection, including SARS-CoV-2.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Takahisa Kouwaki", - "author_inst": "Kumamoto University" - }, - { - "author_name": "Tasuku Nishimura", - "author_inst": "Kumamoto University" - }, - { - "author_name": "Guanming Wang", - "author_inst": "Kumamoto University" - }, - { - "author_name": "Reiko Nakagawa", - "author_inst": "RIKEN Center for Biosystems Dynamics Research in Kobe" - }, - { - "author_name": "Hiroyuki Oshiumi", - "author_inst": "Kumamoto University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.25.427896", "rel_title": "A multiscale model suggests that a moderately weak inhibition of SARS-CoV-2 replication by type I IFN could accelerate the clearance of the virus", @@ -970123,6 +971537,133 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.01.25.428136", + "rel_title": "mRNA-1273 efficacy in a severe COVID-19 model: attenuated activation of pulmonary immune cells after challenge", + "rel_date": "2021-01-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.25.428136", + "rel_abs": "The mRNA-1273 vaccine was recently determined to be effective against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from interim Phase 3 results. Human studies, however, cannot provide the controlled response to infection and complex immunological insight that are only possible with preclinical studies. Hamsters are the only model that reliably exhibit more severe SARS-CoV-2 disease similar to hospitalized patients, making them pertinent for vaccine evaluation. We demonstrate that prime or prime-boost administration of mRNA-1273 in hamsters elicited robust neutralizing antibodies, ameliorated weight loss, suppressed SARS-CoV-2 replication in the airways, and better protected against disease at the highest prime-boost dose. Unlike in mice and non-human primates, mRNA-1273- mediated immunity was non-sterilizing and coincided with an anamnestic response. Single-cell RNA sequencing of lung tissue permitted high resolution analysis which is not possible in vaccinated humans. mRNA-1273 prevented inflammatory cell infiltration and the reduction of lymphocyte proportions, but enabled antiviral responses conducive to lung homeostasis. Surprisingly, infection triggered transcriptome programs in some types of immune cells from vaccinated hamsters that were shared, albeit attenuated, with mock-vaccinated hamsters. Our results support the use of mRNA-1273 in a two-dose schedule and provides insight into the potential responses within the lungs of vaccinated humans who are exposed to SARS-CoV-2.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Michelle Meyer", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Yuan Wang", + "author_inst": "Princeton University" + }, + { + "author_name": "Darin Edwards", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Gregory R Smith", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Aliza B Rubenstein", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Palaniappan Ramanathan", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Chad E Mire", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Colette Pietzsch", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Xi Chen", + "author_inst": "Flatiron Institute, Simons Foundation" + }, + { + "author_name": "Yongchao Ge", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Wan Sze Cheng", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Carole Henry", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Angela Woods", + "author_inst": "Moderna Inc" + }, + { + "author_name": "LingZhi Ma", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Guillaume B. E. Stewart-Jones", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Kevin W Bock", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Minai Mahnaz", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Bianca M Nagata", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Sivakumar Periasamy", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Barney S Graham", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Ian N Moore", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Irene Ramos", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Olga G. Troyanskaya", + "author_inst": "Princeton University" + }, + { + "author_name": "Elena Zaslavsky", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Andrea Carfi", + "author_inst": "Moderna Inc" + }, + { + "author_name": "Stuart C Sealfon", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alexander Bukreyev", + "author_inst": "University of Texas Medical Branch at Galveston" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.25.428122", "rel_title": "Profiling transcription factor sub-networks in type I interferon signaling and in response to SARS-CoV-2 infection", @@ -971315,53 +972856,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.21.21250266", - "rel_title": "Excess mortality associated with the COVID-19 pandemic among Californians 18-65 years of age, by occupational sector and occupation: March through October 2020", - "rel_date": "2021-01-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21250266", - "rel_abs": "BackgroundThough SARS-CoV-2 outbreaks have been documented in occupational settings and though there is speculation that essential workers face heightened risks for COVID-19, occupational differences in excess mortality have, to date, not been examined. Such information could point to opportunities for intervention, such as workplace modifications and prioritization of vaccine distribution.\n\nMethods and findingsUsing death records from the California Department of Public Health, we estimated excess mortality among Californians 18-65 years of age by occupational sector and occupation, with additional stratification of the sector analysis by race/ethnicity. During the COVID-19 pandemic, working age adults experienced a 22% increase in mortality compared to historical periods. Relative excess mortality was highest in food/agriculture workers (39% increase), transportation/logistics workers (28% increase), facilities (27%) and manufacturing workers (23% increase). Latino Californians experienced a 36% increase in mortality, with a 59% increase among Latino food/agriculture workers. Black Californians experienced a 28% increase in mortality, with a 36% increase for Black retail workers. Asian Californians experienced an 18% increase, with a 40% increase among Asian healthcare workers. Excess mortality among White working-age Californians increased by 6%, with a 16% increase among White food/agriculture workers.\n\nConclusionsCertain occupational sectors have been associated with high excess mortality during the pandemic, particularly among racial and ethnic groups also disproportionately affected by COVID-19. In-person essential work is a likely venue of transmission of coronavirus infection and must be addressed through strict enforcement of health orders in workplace settings and protection of in-person workers. Vaccine distribution prioritizing in-person essential workers will be important for reducing excess COVID mortality.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yea-Hung Chen", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Maria Glymour", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Alicia Riley", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "John Balmes", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kate Duchowny", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Robert Harrison", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Ellicott Matthay", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kirsten Bibbins-Domingo", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.01.21.21250231", "rel_title": "Potential contribution of climate conditions on COVID-19 pandemic transmission over West and North African countries", @@ -971625,6 +973119,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.22.21250289", + "rel_title": "Development and validation of a predictive model for critical illness in adult patients requiring hospitalization for COVID-19", + "rel_date": "2021-01-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.22.21250289", + "rel_abs": "BackgroundIdentifying factors that can predict severe disease in patients needing hospitalization for COVID-19 is crucial for early recognition of patients at greatest risk.\n\nObjective1) Identify factors predicting intensive care unit (ICU) transfer and (2) develop a simple calculator for clinicians managing patients hospitalized with COVID-19.\n\nMethodsA total of 2,685 patients with laboratory-confirmed COVID-19 admitted to a large metropolitan health system in Georgia, USA between March and July 2020 were included in the study. Seventy-five percent of patients were included in the training dataset (admitted March 1 to July 10). Through multivariable logistic regression, we developed a prediction model (probability score) for ICU transfer. Then, we validated the model by estimating its performance accuracy (area under the curve [AUC]) using data from the remaining 25% of patients (admitted July 11 to July 31).\n\nResultsWe included 2,014 and 671 patients in the training and validation datasets, respectively. Diabetes mellitus, coronary artery disease, chronic kidney disease, serum C-reactive protein, and serum lactate dehydrogenase were identified as significant risk factors for ICU transfer, and a prediction model was developed. The AUC was 0.752 for the training dataset and 0.769 for the validation dataset. We developed a free, web-based calculator to facilitate use of the prediction model (https://icucovid19.shinyapps.io/ICUCOVID19/).\n\nConclusionOur validated, simple, and accessible prediction model and web-based calculator for ICU transfer may be useful in assisting healthcare providers in identifying hospitalized patients with COVID-19, who are at high risk for clinical deterioration.\n\nTriage of such patients for early aggressive treatment can impact clinical outcomes for this potentially deadly disease.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Neha Paranjape", + "author_inst": "Wellstar Medical Group" + }, + { + "author_name": "Lauren Staples", + "author_inst": "Kennesaw State University" + }, + { + "author_name": "Christina Stradwick", + "author_inst": "Kennesaw State University" + }, + { + "author_name": "Herman Ray", + "author_inst": "Kennesaw State University" + }, + { + "author_name": "Ian Saldanha", + "author_inst": "Brown University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.01.21.21250261", "rel_title": "Using body temperature and variables commonly available in the EHR to predict acute infection: A proof-of-concept study showing improved pretest probability estimates for acute COVID-19 infection among discharged emergency department patients", @@ -973041,33 +974570,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.01.21.427676", - "rel_title": "Personalized Virus Load Curves of SARS-CoV-2 Infection", - "rel_date": "2021-01-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.21.427676", - "rel_abs": "This manuscript has been withdrawn due to submission errors. Therefore, the authors do not wish this work to be cited as a reference. Please see and cite for reference the manuscript posted on medRxiv https://doi.org/10.1101/2021.01.21.21250268 If you have any questions, please contact the corresponding author.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Thomas Hillen", - "author_inst": "University of Alberta" - }, - { - "author_name": "Carlos Contreras", - "author_inst": "University of Alberta" - }, - { - "author_name": "Jay Newby", - "author_inst": "University of Alberta" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "physiology" - }, { "rel_doi": "10.1101/2021.01.21.427629", "rel_title": "Survey of peridomestic mammal susceptibility to SARS-CoV-2 infection", @@ -973303,6 +974805,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.01.15.21249893", + "rel_title": "COVID-19 propagation by diffusion - a two-dimensional approach for Germany", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.15.21249893", + "rel_abs": "Diffusion comes anytime and everywhere. If there is a gradient or a potential difference of a quantity a diffusion process happens and this ends if an equilibrium is reached only. The concentration of a species maybe such quantity, or the voltage. An electric currant will be driven by a voltage difference for example.\n\nIn this COVID-19 pandemic one observes both regions with low incidence and other ones with high incidence. The local different people density could be a reason for that. In populous areas like big cities or congested urban areas higher COVID-19 incidences could be observed than in rural regions.\n\nThe aim of this paper consists in the application of a diffusion concept to describe one possible issue of the the COVID-19 propagation.\n\nThis will be discussed for the German situation based on the quite different incidence data for the different federal states of Germany.\n\nWith this ansatz some phenomenoms of the actual development of the pandemic could be confirmed. The model gives a possibility to investigate certain scenarios like border-crossings or local spreading events and their influence on the COVID-19 propagation as well.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Guenter K.F. Baerwolff", + "author_inst": "Technical University Berlin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.15.20249089", "rel_title": "Physician Perceptions of Catching COVID-19", @@ -974507,45 +976028,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.18.21249463", - "rel_title": "Viral dispersion in open air", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21249463", - "rel_abs": "The SARS-CoV-2 pandemic has revived the debate about the routes of virus transmission and their likelihoods. It is of utmost importance to assess the risks of contamination of susceptible people by infectious individuals and to evaluate the level of viral transmission in the community. Most countries have imposed non-pharmaceutical measures to contain SARS-CoV-2 transmission, including social distancing and mask wearing. Here we evaluated the spreading of viruses in open air using harmless Escherichia coli bacteriophages as a surrogate. Phages were sprayed towards Petri dishes seeded with bacteria at different lengths and angles. Median droplets size was 127 {micro}m, similar to those produced by sneeze. Our results showed that the transmission rate decreased exponentially with distance. The highest recorded transmission rate was 9 x 10-6 PFU/plate when phages were sprayed from a 1 m distance, suggesting that the probability of transmission of a single virus at a 1 m distance is 1:100,000. These results agree with the WHO recommendation that face mask protection in an uncrowded well-ventilated space is not required.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Gabriella Trombini Machado", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Claudia Ramos de Carvalho Pinto", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Luisa Andrea Villanueva da Fonseca", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Taissa Cristina dos Santos Ramos", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Tuanny Fernanda Pereira Paggi", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Beny Spira", - "author_inst": "Universidade de Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.16.21249937", "rel_title": "Meta-Analysis of Robustness of COVID-19 Diagnostic Kits During Early Pandemic", @@ -974709,6 +976191,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.18.21250012", + "rel_title": "Studying the course of Covid-19 by a recursive delay approach", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21250012", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWIn an earlier paper we proposed a recursive model for epidemics; in the present paper we generalize this model to include the asymptomatic or unrecorded symptomatic people, which we call dark people (dark sector). We call this the SEPARd-model. A delay differential equation version of the model is added; it allows a better comparison to other models. We carry this out by a comparison with the classical SIR model and indicate why we believe that the SEPARd model may work better for Covid-19 than other approaches.\n\nIn the second part of the paper we explain how to deal with the data provided by the JHU, in particular we explain how to derive central model parameters from the data. Other parameters, like the size of the dark sector, are less accessible and have to be estimated more roughly, at best by results of representative serological studies which are accessible, however, only for a few countries. We start our country studies with Switzerland where such data are available. Then we apply the model to a collection of other countries, three European ones (Germany, France, Sweden), the three most stricken countries from three other continents (USA, Brazil, India). Finally we show that even the aggregated world data can be well represented by our approach.\n\nAt the end of the paper we discuss the use of the model. Perhaps the most striking application is that it allows a quantitative analysis of the influence of the time until people are sent to quarantine or hospital. This suggests that imposing means to shorten this time is a powerful tool to flatten the curves.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Erhard Scholz", + "author_inst": "University of Wuppertal" + }, + { + "author_name": "Matthias Kreck", + "author_inst": "University of Bonn" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.18.21249998", "rel_title": "The Association between Early Country-level Testing Capacity and Later COVID-19 Mortality Outcomes", @@ -976333,65 +977838,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2021.01.19.20248560", - "rel_title": "Modelling pooling strategies for SARS-CoV-2 testing in a university setting", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.19.20248560", - "rel_abs": "Pre-symptomatic and asymptomatic transmission of SARS-CoV-2 are important elements in the Covid-19 pandemic, and until vaccines are made widely available there remains a reliance on testing to manage the spread of the disease, alongside non-pharmaceutical interventions such as measures to reduce close social interactions. In the UK, many universities opened for blended learning for the 2020-2021 academic year, with a mixture of face to face and online teaching. In this study we present a simulation framework to evaluate the effectiveness of different asymptomatic testing strategies within a university setting, across a range of transmission scenarios. We show that when positive cases are clustered by known social structures, such as student households, the pooling of samples by these social structures can substantially reduce the total cost of conducting RT-qPCR tests. We also note that routine recording of quantitative RT-qPCR results would facilitate future modelling studies.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Gibran Hemani", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol; Population Health Sciences, Bristol Medical School, University of Bristol" - }, - { - "author_name": "Amy C Thomas", - "author_inst": "Bristol Veterinary School, University of Bristol" - }, - { - "author_name": "Josephine G Walker", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol" - }, - { - "author_name": "Adam Trickey", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol" - }, - { - "author_name": "Emily Nixon", - "author_inst": "Bristol Veterinary School, University of Bristol; School of Biological Sciences, University of Bristol" - }, - { - "author_name": "David Ellis", - "author_inst": "School of Mathematics, University of Bristol, Fry Building, Woodland Road, Bristol BS8 1UG, UK" - }, - { - "author_name": "Rachel Kwiatkowska", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol" - }, - { - "author_name": "Caroline Relton", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol; Population Health Sciences, Bristol Medical School, University of Bristol" - }, - { - "author_name": "Leon Danon", - "author_inst": "Computer Science, University of Exeter, Exeter, UK; Alan Turing Institute, British Library, London, UK" - }, - { - "author_name": "Hannah Christensen", - "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol; NIHR Health Protection Research Unit in Behavioural Science and Evaluation" - }, - { - "author_name": "Ellen Brooks-Pollock", - "author_inst": "NIHR Health Protection Research Unit in Behavioural Science and Evaluation; Bristol Veterinary School, University of Bristol" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.19.427320", "rel_title": "Coevolutionary Analysis and Perturbation-Based Network Modeling of the SARS-CoV-2 Spike Protein Complexes with Antibodies: Binding-Induced Control of Dynamics, Allosteric Interactions and Signaling", @@ -976635,6 +978081,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.01.19.426622", + "rel_title": "Evaluation of the effects of SARS-CoV-2 genetic mutations on diagnostic RT-PCR assays", + "rel_date": "2021-01-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.19.426622", + "rel_abs": "Several mutant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging. Mismatch(es) in primer/probe binding regions would decrease the detection sensitivity of the PCR test, thereby affecting the results of clinical testing. In this study, we conducted an in silico survey on SARS-CoV-2 sequence variability within the binding regions of primer/probe published by the Japan National Institute of Infectious Diseases (NIID) and Centers for Disease Control and Prevention (CDC). In silico analysis revealed the presence of mutations in the primer/probe binding regions. We performed RT-PCR assays using synthetic RNAs containing the mutations and showed that some mutations significantly decreased the detection sensitivity of the RT-PCR assays.\n\nOur results highlight the importance of genomic monitoring of SARS-CoV-2 and evaluating the effects of mismatches on PCR testing sensitivity.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Takeru Nakabayashi", + "author_inst": "H.U. Group Research Institute G.K." + }, + { + "author_name": "Yuki Kawasaki", + "author_inst": "H.U. Group Research Institute G.K." + }, + { + "author_name": "Koichiro Murashima", + "author_inst": "H.U. Group Research Institute G.K." + }, + { + "author_name": "Kazuya Omi", + "author_inst": "H.U. Group Research Institute G.K." + }, + { + "author_name": "Satoshi Yuhara", + "author_inst": "H.U. Group Research Institute G.K." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2021.01.20.427105", "rel_title": "Use Of Canine Olfactory Detection For COVID-19 Testing Study On U.A.E. Trained Detection Dog Sensitivity", @@ -977991,105 +979472,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2021.01.15.426849", - "rel_title": "The impact of Spike mutations on SARS-CoV-2 neutralization", - "rel_date": "2021-01-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.15.426849", - "rel_abs": "Multiple SARS-CoV-2 vaccines have shown protective efficacy, which is most likely mediated by neutralizing antibodies recognizing the viral entry protein, Spike. Antibodies from SARS-CoV-2 infection neutralize the virus by focused targeting of Spike and there is limited serum cross-neutralization of the closely-related SARS-CoV. As new SARS-CoV-2 variants are rapidly emerging, exemplified by the B.1.1.7, 501Y.V2 and P.1 lineages, it is critical to understand if antibody responses induced by infection with the original SARS-CoV-2 virus or the current vaccines will remain effective against virus variants. In this study we evaluate neutralization of a series of mutated Spike pseudotypes including a B.1.1.7 Spike pseudotype. The analyses of a panel of Spike-specific monoclonal antibodies revealed that the neutralizing activity of some antibodies was dramatically reduced by Spike mutations. In contrast, polyclonal antibodies in the serum of patients infected in early 2020 remained active against most mutated Spike pseudotypes. The majority of serum samples were equally able to neutralize the B.1.1.7 Spike pseudotype, however potency was reduced in a small number of samples (3 of 36) by 5-10-fold. This work highlights that changes in the SARS-CoV-2 Spike can alter neutralization sensitivity and underlines the need for effective real-time monitoring of emerging mutations and their impact on vaccine efficacy.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Chloe Rees-Spear", - "author_inst": "University College London" - }, - { - "author_name": "Luke Muir", - "author_inst": "University College London" - }, - { - "author_name": "Sarah A Griffith", - "author_inst": "University College London" - }, - { - "author_name": "Judith Heaney", - "author_inst": "University College London Hospitals" - }, - { - "author_name": "Yoann Aldon", - "author_inst": "Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Netherlands" - }, - { - "author_name": "Jonne Snitselaar", - "author_inst": "Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Netherlands" - }, - { - "author_name": "Peter Thomas", - "author_inst": "University College London" - }, - { - "author_name": "Carl Graham", - "author_inst": "Kings College London" - }, - { - "author_name": "Jeffrey Seow", - "author_inst": "Kings College London" - }, - { - "author_name": "Nayung Lee", - "author_inst": "University College London" - }, - { - "author_name": "Annachiara Rosa", - "author_inst": "The Francis Crick Institute, UK" - }, - { - "author_name": "Chloe Roustan", - "author_inst": "The Francis Crick Institute, UK" - }, - { - "author_name": "Catherine F Houlihan", - "author_inst": "University College London" - }, - { - "author_name": "Rogier W Sanders", - "author_inst": "Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Netherlands" - }, - { - "author_name": "Ravindra K Gupta", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Peter Cherepanov", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Hans Stauss", - "author_inst": "University College London" - }, - { - "author_name": "Eleni Nastouli", - "author_inst": "University College London" - }, - { - "author_name": "Katie J Doores", - "author_inst": "Kings College London" - }, - { - "author_name": "Marit J van Gils", - "author_inst": "Academic Medical Center Amsterdam" - }, - { - "author_name": "Laura E McCoy", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.18.427182", "rel_title": "Experimental re-infected cats do not transmit SARS-CoV-2", @@ -978457,6 +979839,65 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.01.19.427282", + "rel_title": "SARS-CoV-2 infection of circulating immune cells is not responsible for virus dissemination in severe COVID-19 patients", + "rel_date": "2021-01-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.19.427282", + "rel_abs": "In late 2019 a novel coronavirus (SARS-CoV-2) emerged, and has since caused a global pandemic. Understanding the pathogenesis of COVID-19 disease is necessary to inform development of therapeutics, and management of infected patients. Using scRNAseq of blood drawn from SARS-CoV-2 patients, we asked whether SARS-CoV-2 may exploit immune cells as a Trojan Horse to disseminate and access multiple organ systems. Our data suggests that circulating cells are not actively infected with SARS-CoV-2, and do not appear to be a source of viral dissemination.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Nicole L Rosin", + "author_inst": "University of Calgary" + }, + { + "author_name": "Arzina Jaffer", + "author_inst": "University of Calgary" + }, + { + "author_name": "Sarthak Sinha", + "author_inst": "University of Calgary" + }, + { + "author_name": "Rory P Mulloy", + "author_inst": "University of Calgary" + }, + { + "author_name": "Carolyn Robinson", + "author_inst": "University of Calgary" + }, + { + "author_name": "Elodie Labit", + "author_inst": "University of Calgary" + }, + { + "author_name": "Luiz G Almeida", + "author_inst": "University of Calgary" + }, + { + "author_name": "Antoine Dufour", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jennifer A Corcoran", + "author_inst": "University of Calgary" + }, + { + "author_name": "Bryan Yipp", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jeff Biernaskie", + "author_inst": "University of Calgary" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.01.19.427250", "rel_title": "COVID-19 Knowledge, Attitudes, and Practices of United Arab Emirates Medical and Health Sciences Students: A Cross Sectional Study", @@ -980697,77 +982138,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.12.21249694", - "rel_title": "Optimal SARS-CoV-2 vaccine allocation using real-time seroprevalence estimates in Rhode Island and Massachusetts", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.21249694", - "rel_abs": "As three SARS-CoV-2 vaccines come to market in Europe and North America in the winter of 2020-2021, distribution networks will be in a race against a major epidemiological wave of SARS-CoV-2 that began in autumn 2020. Rapid and optimized vaccine allocation is critical during this time. With 95% efficacy reported for two of the vaccines, near-term public health needs require that distribution is prioritized to the elderly, health-care workers, teachers, essential workers, and individuals with co-morbidities putting them at risk of severe clinical progression. Here, we evaluate various age-based vaccine distributions using a validated mathematical model based on current epidemic trends in Rhode Island and Massachusetts. We allow for varying waning efficacy of vaccine-induced immunity, as this has not yet been measured. We account for the fact that known COVID-positive cases may not be included in the first round of vaccination. And, we account for current age-specific immune patterns in both states. We find that allocating a substantial proportion (> 75%) of vaccine supply to individuals over the age of 70 is optimal in terms of reducing total cumulative deaths through mid-2021. As we do not explicitly model other high mortality groups, this result on vaccine allocation applies to all groups at high risk of mortality if infected. Our analysis confirms that for an easily transmissible respiratory virus, allocating a large majority of vaccinations to groups with the highest mortality risk is optimal. Our analysis assumes that health systems during winter 2020-2021 have equal staffing and capacity to previous phases of the SARS-CoV-2 epidemic; we do not consider the effects of understaffed hospitals or unvaccinated medical staff. Vaccinating only seronegative individuals avoids redundancy in vaccine use on individuals that may already be immune, and will result in 1% to 2% reductions in cumulative hospitalizations and deaths by mid-2021. Assuming high vaccination coverage (> 28%) and no major relaxations in distancing, masking, gathering size, or hygiene guidelines between now and spring 2021, our model predicts that a combination of vaccination and population immunity will lead to low or near-zero transmission levels by the second quarter of 2021.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Thu Nguyen-Anh Tran", - "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA" - }, - { - "author_name": "Nathan Wikle", - "author_inst": "Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University, University Park, PA" - }, - { - "author_name": "Joseph Albert", - "author_inst": "Department of Physics, Pennsylvania State University, University Park, PA" - }, - { - "author_name": "Haider Inam", - "author_inst": "Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University, University Park, PA" - }, - { - "author_name": "Emily R Strong", - "author_inst": "Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University, University Park, PA" - }, - { - "author_name": "Karel Brinda", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA" - }, - { - "author_name": "Scott M Leighow", - "author_inst": "Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University, University Park, PA" - }, - { - "author_name": "Fuhan Yang", - "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA" - }, - { - "author_name": "Sajid Hossain", - "author_inst": "Yale School of Medicine, Yale University, New Haven, CT" - }, - { - "author_name": "Justin R Pritchard", - "author_inst": "Center for Infectious Disease Dynamics, Department of Bioengineering, Pennsylvania State University, University Park, PA" - }, - { - "author_name": "Philip Chan", - "author_inst": "Department of Medicine, Brown University, Providence, RI" - }, - { - "author_name": "William P Hanage", - "author_inst": "Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA" - }, - { - "author_name": "Ephraim M Hanks", - "author_inst": "Center for Infectious Disease Dynamics, Department of Statistics, Pennsylvania State University, University Park, PA" - }, - { - "author_name": "Maciej F Boni", - "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.12.21249682", "rel_title": "Socioeconomic status determines COVID-19 incidence and related mortality in Santiago, Chile", @@ -980950,6 +982320,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.14.21249637", + "rel_title": "SARS-CoV-2 infection control implementation based on sources of infection showing directions for three age groups in Japan", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249637", + "rel_abs": "BackgroundSome aspects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in children and adults remain unclear. This report describes different SARS-CoV-2 transmission patterns by age group in Japan.\n\nMethods and findingsThis retrospective observational case series study analyzed transmission patterns of real-time polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 infections found by local health authorities and commercial laboratories during January 14 through July 31, 2020 in Japan. After ascertaining the infection source for every symptomatic case as clusters at households, daycare facilities, schools, hospitals and workplaces etc., their associated transmission patterns were analyzed. Identified cases were divided into three groups: underage, < 20; adults, 20-59; and elderly people 60 years old and older. The reproductive number (R)s of respective transmission directions found for the respective age groups were compared.\n\nOf 26,986 total cases, 23,746 unknown cases were found, leaving 3,240 ascertained sources of infection (12.0%) comprising 125 (3.9%) underage, 2350 (72.5%) adult, and 765 (23.6%) elderly people. The respective Rs of underage infection sources directed to underage, adult, and elderly people were estimated respectively as 0.0415 (95% CI, 0.0138-0.0691), 1.11 (95% CI, 0.9171-1.3226), and 0.2811 (95% CI, 0.2074-0.3687). The respective Rs of adult infection source directed to underage, adult, and elderly people were estimated respectively as 0.0140 (95% CI, 0.0120-0.0162), 0.5392 (95% CI, 0.5236-0.5550), and 0.1135 (95% CI, 0.1074-0.1197). The respective Rs of elderly infection source directed to underage, adult, and elderly people were estimated as 0.065 (95% CI, 0.0039-0.0091), 0.3264 (95% CI, 0.3059-0.3474), and 0.3991 (95% CI, 0.3757-0.4229).\n\nConclusionsThe main sources of SARS-CoV-2 infection were adults and elderly people. The R of underage people directed to adults was greater than 1 because of close familial contact but they were unlikely to become carriers transmitting SARS-CoV-2 because they accounted for a minority for transmissions. Apparently, SARS-CoV-2 was transmitted among adults and elderly people, suggesting that infection control of SARS-CoV-2 should be managed specifically by generation.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Atsuko Hata", + "author_inst": "Kitano hospital, The Tazuke Kofukai Medical Research Institute" + }, + { + "author_name": "Junko Kurita", + "author_inst": "Tokiwa University, Ibaraki, Japan" + }, + { + "author_name": "Eri Muso", + "author_inst": "Kyoto Kacho University" + }, + { + "author_name": "Toshiro Katayama", + "author_inst": "Morinomiya University of Medical Sciences" + }, + { + "author_name": "Takahide Hata", + "author_inst": "Kitano hospital, The Tazuke Kofukai Medical Research Institute" + }, + { + "author_name": "Yasushi Ohkusa", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.01.15.21249863", "rel_title": "How to best test suspected cases of COVID-19: an analysis of the diagnostic performance of RT-PCR and alternative molecular methods for the detection of SARS-CoV-2", @@ -982514,41 +983923,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.01.10.21249370", - "rel_title": "Dynamic Prediction of SARS-CoV-2 RT-PCR status on Chest Radiographs using Deep Learning Enabled Radiogenomics", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.10.21249370", - "rel_abs": "Reverse Transcription-Polymerase Chain Reaction (RT-PCR) is the gold standard for diagnosis of SARS-CoV-2 infection, but requires specialized equipment and reagents and suffers from long turnaround times. While valuable, chest imaging currently only detects COVID-19 pneumonia, but if it can predict actual RT-PCR SARS-CoV-2 status is unknown. Radiogenomics may provide an effective and accurate RT-PCR-based surrogate. We describe a deep learning radiogenomics (DLR) model (RadGen) that predicts a patient's RT-PCR SARS-CoV-2 status solely from their frontal chest radiograph (CXR).", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Wan Hang Keith Chiu", - "author_inst": "Department of Diagnostic Radiology, The University of Hong Kong; Medical Artificial Intelligence Laboratory Program, Department of Diagnostic Radiology, The Uni" - }, - { - "author_name": "Dmytro Poplavskiy", - "author_inst": "Ensemblehealth.ai, Scottsdale, AZ, USA" - }, - { - "author_name": "Sailong Zhang", - "author_inst": "Department of Diagnostic Radiology, The University of Hong Kong" - }, - { - "author_name": "Philip Leong Ho Yu", - "author_inst": "Department of Mathematics and Information Technology, The Education University of Hong Kong SAR" - }, - { - "author_name": "Michael D Kuo", - "author_inst": "Ensemblehealth.ai, Scottsdale, AZ, USA; Medical Artificial Intelligence Laboratory Program, Department of Diagnostic Radiology, The University of Hong Kong, Hon" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2021.01.11.21249265", "rel_title": "A Viral Fragmentation Signature for SARS-CoV-2 in Clinical Samples Correlating with Contagiousness", @@ -982880,6 +984254,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.12.21249603", + "rel_title": "Isolation of SARS-CoV-2 from the air in a car driven by a COVID patient with mild illness", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.21249603", + "rel_abs": "We used a Sioutas personal cascade impactor sampler (PCIS) to screen for SARS-CoV-2 in a car driven by a COVID-19 patient. SARS-CoV-2 was detectable at all PCIS stages by PCR and was cultured from the section of the sampler collecting particles in the 0.25 to 0.50 {square}m size range.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "John A Lednicky", + "author_inst": "University of Florida" + }, + { + "author_name": "Michael Lauzardo", + "author_inst": "University of Florida" + }, + { + "author_name": "Md. Mabubul Alam", + "author_inst": "Univesrity of Florida" + }, + { + "author_name": "Maha Elbadry", + "author_inst": "Univesrity of Florida" + }, + { + "author_name": "Caroline Stephenson", + "author_inst": "Univesrity of Florida" + }, + { + "author_name": "Julia C. Gibson", + "author_inst": "University of Florida" + }, + { + "author_name": "John Glenn Morris Jr.", + "author_inst": "University of Florida" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.10.20248871", "rel_title": "Emergence of multiple SARS-CoV-2 mutations in an immunocompromised host", @@ -984508,77 +985925,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.13.21249629", - "rel_title": "A Novel Multiplex PCR Based Detection Assay Using Saliva or Nasopharyngeal Samples for SARS-Cov-2, Influenza A and B: Clinical Validation and Utility for Mass Surveillance.", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.13.21249629", - "rel_abs": "BackgroundThe COVID-19 pandemic has resulted in a significant diversion of human and material resources to COVID-19 diagnostics, to the extent that testing of viral pathogens normally contributing to seasonal respiratory tract infections have been markedly neglected. The global health burden due to influenza viruses and co-infection in COVID-19 patients remains undocumented but clearly pose serious public health consequences. To address these clinical and technical challenges, we have optimized and validated a highly sensitive RT-PCR based multiplex assay for the detection of SARS-CoV-2, Influenza A and B viruses in a single test.\n\nMethodsThis study evaluated clinical specimens (n=1411) that included 1019 saliva and 392 nasopharyngeal swab (NPS) samples collected in either healthcare or community setting. Samples were tested using two assays: FDA-EUA approved SARS-CoV-2 assay that targets N and ORF1ab gene, and the PKamp RT-PCR based assay that targets SARS-CoV-2, Influenza viruses A and B. The limit of detection (LoD) studies was conducted as per the FDA guidelines using SARS-CoV-2 and Influenza A and B reference control materials.\n\nResultsOf the 1019 saliva samples, 17.0% (174/1019) tested positive for SARS-CoV-2 using either assay. The detection rate for SARS-CoV-2 was higher with our multiplex assay compared to SARS-specific assay [91.9% (160/174) vs. 87.9% (153/174)], respectively. Of the 392 NPS samples, 10.4% (41/392) tested positive for SARS-CoV-2 using either assay. The detection rate for SARS-CoV-2 was higher with our multiplex assay compared to SARS-specific assay [97.5% (40/41) vs. 92.1% (39/41)], respectively. The Ct values for SARS-CoV-2 were comparable between the two assays, whereas the Ct values of the housekeeping gene was significantly lower with multiplex assay compared to SARS-specific assay. The LoD was established as 60 copies/ml for SARS-CoV-2 and 180 copies/ml for Influenza A and B viruses for both saliva and NPS samples.\n\nConclusionThis study presents clinical validation of a multiplex PCR assay for testing SARS-CoV-2, Influenza A and B viruses, using NPS and saliva samples, and demonstrates the feasibility of implementing the assay without disrupting the existing laboratory workflow. This novel assay uses the same instruments, sample types, supplies, and laboratory personnel as needed for the testing of SARS-CoV-2 virus.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Nikhil Shri Sahajpal", - "author_inst": "Augusta University" - }, - { - "author_name": "Ashis K Mondal", - "author_inst": "Augusta University" - }, - { - "author_name": "Sudha Ananth", - "author_inst": "Augusta University" - }, - { - "author_name": "Allan Njau", - "author_inst": "Aga Khan University Hospital" - }, - { - "author_name": "Pankaj Ahluwalia", - "author_inst": "Augusta University" - }, - { - "author_name": "Eesha Oza", - "author_inst": "Augusta university" - }, - { - "author_name": "Ted Ross", - "author_inst": "University System of Georgia" - }, - { - "author_name": "Vamsi Kota", - "author_inst": "Augusta University" - }, - { - "author_name": "Arvind Kothandaraman", - "author_inst": "Perkin Elmer Inc." - }, - { - "author_name": "Sadanand Fulzele", - "author_inst": "Augusta University" - }, - { - "author_name": "Madhuri Hegde", - "author_inst": "Perkin Elmer Inc." - }, - { - "author_name": "Alka Chaubey", - "author_inst": "Augusta University" - }, - { - "author_name": "Amyn M Rojiani", - "author_inst": "Augusta University" - }, - { - "author_name": "Ravindra Kolhe", - "author_inst": "Augusta University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.13.21249749", "rel_title": "Mass Testing with Contact Tracing Compared to Test and Trace for Effective Suppression of COVID-19 in the UK: A rapid review", @@ -984862,6 +986208,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.12.20248588", + "rel_title": "Bacterial superinfection pneumonia in SARS-CoV-2 respiratory failure", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.20248588", + "rel_abs": "BackgroundSevere community-acquired pneumonia secondary to SARS-CoV-2 is a leading cause of death. Current guidelines recommend patients with SARS-CoV-2 pneumonia receive empirical antibiotic therapy for suspected bacterial superinfection, but little evidence supports these recommendations.\n\nMethodsWe obtained bronchoscopic bronchoalveolar lavage (BAL) samples from patients with SARS-CoV-2 pneumonia requiring mechanical ventilation. We analyzed BAL samples with multiplex PCR and quantitative culture to determine the prevalence of superinfecting pathogens at the time of intubation and identify episodes of ventilator-associated pneumonia (VAP) over the course of mechanical ventilation. We compared antibiotic use with guideline-recommended care.\n\nResultsThe 179 ventilated patients with severe SARS-CoV-2 pneumonia discharged from our hospital by June 30, 2020 were analyzed. 162 (90.5%) patients had at least one BAL procedure; 133 (74.3%) within 48 hours after intubation and 112 (62.6%) had at least one subsequent BAL during their hospitalization. A superinfecting pathogen was identified within 48 hours of intubation in 28/133 (21%) patients, most commonly methicillin-sensitive Staphylococcus aureus or Streptococcus species (21/28, 75%). BAL-based treatment reduced antibiotic use compared with guideline-recommended care. 72 patients (44.4%) developed at least one VAP episode. Only 15/72 (20.8%) of initial VAPs were attributable to multidrug-resistant pathogens. The incidence rate of VAP was 45.2/1000 ventilator days.\n\nConclusionsWith use of sensitive diagnostic tools, bacterial superinfection at the time of intubation is infrequent in patients with severe SARS-CoV-2 pneumonia. Treatment based on current guidelines would result in substantial antibiotic overuse. The incidence rate of VAP in ventilated patients with SARS-CoV-2 pneumonia are higher than historically reported.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Chiagozie O. Pickens", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Catherine A. Gao", + "author_inst": "Northwestern" + }, + { + "author_name": "Michael J. Cuttica", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Sean B. Smith", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Lorenzo Pesce", + "author_inst": "Department of Pharmacology, Northwestern University Department of Pharmacology School of Medicine" + }, + { + "author_name": "Rogan Grant", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Mengjia Kang", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Luisa Morales-Nebreda", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Avni A. Bavishi", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Jason Arnold", + "author_inst": "Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Anna Pawlowski", + "author_inst": "Clinical Translational Sciences Institute, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Chao Qi", + "author_inst": "Department of Pathology, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "GR Scott Budinger", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Benjamin D. Singer", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "Richard G. Wunderink", + "author_inst": "Division of Pulmonary and Critical Care, Department of Medicine, Northwestern University Feinberg School of Medicine" + }, + { + "author_name": "- NU COVID Investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.01.14.21249831", "rel_title": "Increased peripheral blood neutrophil activation phenotypes and NETosis in critically ill COVID-19 patients", @@ -986458,73 +987883,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.11.21249562", - "rel_title": "Model-based cellular kinetic analysis of SARS-CoV-2 infection: different immune response modes and treatment strategies", - "rel_date": "2021-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.21249562", - "rel_abs": "Increasing number in global COVID-19 cases demands for mathematical model to analyze the interaction between the virus dynamics and the response of innate and adaptive immunity. Here, based on the assumption of a weak and delayed response of the innate and adaptive immunity in SARS-CoV-2 infection, we constructed a mathematical model to describe the dynamic processes of immune system. Integrating theoretical results with clinical COVID-19 patients data, we classified the COVID-19 development processes into three typical modes of immune responses, correlated with the clinical classification of mild & moderate, severe and critical patients. We found that the immune efficacy (the ability of host to clear virus and kill infected cells) and the lymphocyte supply (the abundance and pool of naive T and B cell) play important roles in the dynamic process and determine the clinical outcome, especially for the severe and critical patients. Furthermore, we put forward possible treatment strategies for the three typical modes of immune response. We hope our results can help to understand the dynamical mechanism of the immune response against SARS-CoV-2 infection, and to be useful for the treatment strategies and vaccine design.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Zhengqing Zhou", - "author_inst": "School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China" - }, - { - "author_name": "Ziheng Zhao", - "author_inst": "Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing 100191, China" - }, - { - "author_name": "Shuyu Shi", - "author_inst": "Peking University Third Hospital, Peking University, Beijing 100191, China." - }, - { - "author_name": "Jianghua Wu", - "author_inst": "Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China" - }, - { - "author_name": "Dianjie Li", - "author_inst": "School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China" - }, - { - "author_name": "Jianwei Li", - "author_inst": "School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China" - }, - { - "author_name": "Jingpeng Zhang", - "author_inst": "School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China" - }, - { - "author_name": "Ke Gui", - "author_inst": "Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing 100191, China" - }, - { - "author_name": "Yu Zhang", - "author_inst": "Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University, Beijing 100191, China" - }, - { - "author_name": "Heng Mei", - "author_inst": "Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China" - }, - { - "author_name": "Yu Hu", - "author_inst": "Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China" - }, - { - "author_name": "Qi Ouyang", - "author_inst": "School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China" - }, - { - "author_name": "Fangting Li", - "author_inst": "School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.08.20248771", "rel_title": "Detection of SARS-CoV-2 nucleocapsid antigen from serum can aid in timing of COVID-19 infection", @@ -986776,6 +988134,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.11.21249630", + "rel_title": "Determining the optimal COVID-19 policy response using agent-based modelling linked to health and cost modelling: Case study for Victoria, Australia", + "rel_date": "2021-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.21249630", + "rel_abs": "ImportanceDetermining the best policy on social restrictions and lockdowns for the COVID-19 pandemic is challenging.\n\nObjectiveTo determine the optimal policy response ranging from aggressive and moderate elimination, tight suppression (aiming for 1 to 5 cases per million per day) and loose suppression (5 to 25 cases per million per day).\n\nDesignTwo simulation models in series: an agent-based model to estimate daily SARS-CoV-2 infection rates and time in four stages of social restrictions; a proportional multistate lifetable model to estimate long-run health impacts (health adjusted life years (HALYs) arising from SARS-CoV-2) and costs (health systems, and health system plus GDP).\n\nThe net monetary benefit (NMB) of each policy option at varying willingness to pay (WTP) per HALY was calculated: NMB = HALYs x WTP - cost. The optimal policy response was that with the highest NMB.\n\nSetting and participantsThe State of Victoria, Australia, using simulation modeling of all residents.\n\nMain Outcome and MeasuresSARS-CoV-2 infection rates, time under various stages of restrictions, HALYs, health expenditure and GDP losses.\n\nResultsAggressive elimination resulted in the highest percentage of days with the lowest level of restrictions (median 31.7%, 90% simulation interval 6.6% to 64.4%). However, days in hard lockdown were similar across all four strategies (medians 27.5% to 36.1%).\n\nHALY losses (compared to a no-COVID-19 scenario) were similar for aggressive elimination (286, 219 to 389) and moderate elimination (314, 228 to 413), and nearly eight and 40-times higher for tight and loose suppression. The median GDP loss was least for moderate elimination ($US41.7 billion, $29.0 to $63.6 billion), but there was substantial overlap in simulation intervals between the four strategies.\n\nFrom a health system perspective aggressive elimination was optimal in 64% of simulations above a willingness to pay of $15,000 per HALY, followed by moderate elimination in 35% of simulations.\n\nModerate elimination was optimal from a partial societal perspective in half the simulations followed by aggressive elimination in a quarter.\n\nShortening the pandemic duration to 6 months saw loose suppression become preferable under a partial societal perspective.\n\nConclusions and RelevanceElimination strategies were preferable over a 1-year pandemic duration.\n\nFundingAnonymous philanthropic donation to the University of Melbourne.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSTo determine the optimal of four policy responses to COVID-19 in the State of Victoria, Australia (aggressive and moderate elimination, tight suppression (aiming for 1 to 5 cases per million per day) and loose suppression (5 to 25 cases per million per day), based on estimated future health loss and costs from both a health system and partial societal perspective.\n\nFindingsFrom a health system perspective aggressive elimination was optimal in 64% of simulations above a willingness to pay of $15,000 per HALY, followed by moderate elimination in 35% of simulations. Moderate elimination was optimal from a partial societal perspective (i.e., including GDP losses) in half the simulations followed by aggressive elimination in a quarter.\n\nMeaningWhilst there is considerable uncertainty in outcomes for all the four policy options, the two elimination options are usually optimal from both a health system and a partial societal (health expenditure plus GDP cost) perspective.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Professor Tony Blakely", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Dr Jason Thompson", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Dr Laxman Bablani", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Patrick Andersen", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Dr Driss Ait Ouakrim", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Dr Natalie Carvalho", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Patrick Abraham", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Marie-Anne Boujaoude", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Ameera Katar", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Edifofon Akpan", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Nick Wilson", + "author_inst": "University of Otago, Wellington" + }, + { + "author_name": "Professor Mark Stevenson", + "author_inst": "University of Melbourne" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.11.21249564", "rel_title": "The 2020 SARS-CoV-2 epidemic in England: key epidemiological drivers and impact of interventions", @@ -988160,81 +989581,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.11.426287", - "rel_title": "Emergence and Evolution of a Prevalent New SARS-CoV-2 Variant in the United States", - "rel_date": "2021-01-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.11.426287", - "rel_abs": "Genomic surveillance can lead to early identification of novel viral variants and inform pandemic response. Using this approach, we identified a new variant of the SARS-CoV-2 virus that emerged in the United States (U.S.). The earliest sequenced genomes of this variant, referred to as 20C-US, can be traced to Texas in late May of 2020. This variant circulated in the U.S. uncharacterized for months and rose to recent prevalence during the third pandemic wave. It initially acquired five novel, relatively unique non-synonymous mutations. 20C-US is continuing to acquire multiple new mutations, including three independently occurring spike protein mutations. Monitoring the ongoing evolution of 20C-US, as well as other novel emerging variants, will be essential for understanding SARS-CoV-2 host adaptation and predicting pandemic outcomes.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Adrian A Pater", - "author_inst": "Southern Illinois University" - }, - { - "author_name": "Michael S Bosmeny", - "author_inst": "Southern Illinois University School of Medicine" - }, - { - "author_name": "Christopher L Barkau", - "author_inst": "Southern Illinois University School of Medicine" - }, - { - "author_name": "Katy N Ovington", - "author_inst": "Southern Illinois University School of Medicine" - }, - { - "author_name": "Ramdevi Chilamkurthy", - "author_inst": "Southern Illinois University School of Medicine" - }, - { - "author_name": "Mansi Parasrampuria", - "author_inst": "Southern Illinois University School of Medicine" - }, - { - "author_name": "Seth B Eddington", - "author_inst": "Southern Illinois University School of Medicine" - }, - { - "author_name": "Abadat O Yinusa", - "author_inst": "Southern Illinois University" - }, - { - "author_name": "Adam A White", - "author_inst": "Southern Illinois University School of Medicine" - }, - { - "author_name": "Paige E Metz", - "author_inst": "Southern Illinois University School of Medicine" - }, - { - "author_name": "Rourke J Sylvain", - "author_inst": "Southern Illinois University School of Medicine" - }, - { - "author_name": "Madison M Hebert", - "author_inst": "Southern Illinois University" - }, - { - "author_name": "Scott W Benzinger", - "author_inst": "Southern Illinois University" - }, - { - "author_name": "Koushik T Sinha", - "author_inst": "Southern Illinois University" - }, - { - "author_name": "Keith T Gagnon", - "author_inst": "Southern Illinois University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.01.13.425144", "rel_title": "Fatal neuroinvasion of SARS-CoV-2 in K18-hACE2 mice is partially dependent on hACE2 expression", @@ -988474,6 +989820,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.09.21249489", + "rel_title": "Impact of COVID-19 pandemic on use of Pediatric Emergency Health Services in a Tertiary Care Pediatric Hospital in North India", + "rel_date": "2021-01-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.09.21249489", + "rel_abs": "ObjectiveTo compare Pediatric Emergency attendance pre-COVID 19 to that during COVID 19 pandemic and to study changes in patient profiles attending Pediatric Emergency Department during COVID 19 pandemic.\n\nMethodsWe conducted a retrospective cross-sectional observational study and collected data from Medical Record Section during the COVID-19 pandemic from January to June 2020 and compared it with data from 2019 in similar months. Data collected was analyzed to find out the impact of COVID - 19 on use of pediatric emergency health services with respect to patient attendance, age and clinical profile before and during COVID-19 in a tertiary care hospital in New Delhi.\n\nResultsWe observed a 43% decline in PED visits which increased to 75% during the period of lock-down (p value = 0.005). There was a significant decrease in children of age group 1-5 years attending PED. Mortality rate during lockdown had gone up by nearly 3times than the average monthly mortality.\n\nConclusionsWhile children might not have been directly affected by the COVID-19 pandemic, but the fear of COVID 19 and measures taken to control the pandemic has affected the health seeking behavior of patients to an extent that indirectly caused more damage than anticipated.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ravitanaya Sodani", + "author_inst": "Lady Hardinge Medical College, New Delhi, India" + }, + { + "author_name": "Shalu Gupta", + "author_inst": "Lady Hardinge Medical College & Kalawati Saran Children's Hospital, New Delhi, India" + }, + { + "author_name": "Virendra Kumar", + "author_inst": "Lady Hardinge Medical College & Kalawati Saran Children's Hospital, New Delhi, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.01.06.20249030", "rel_title": "Convergence of Comorbidity and COVID-19 Infection to Fatality: An Investigation Based on Concurrent Health Status Evaluation among the Elderly Population in Kerala", @@ -989814,37 +991187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.10.21249520", - "rel_title": "Viral mutation, contact rates and testing: a DCM study of fluctuations", - "rel_date": "2021-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.10.21249520", - "rel_abs": "This report considers three mechanisms that might underlie the course of the secondary peak of coronavirus infections in the United Kingdom. It considers: (i) fluctuations in transmission strength; (ii) seasonal fluctuations in contact rates and (iii) fluctuations in testing. Using dynamic causal modelling, we evaluated the contribution of all combinations of these three mechanisms using Bayesian model comparison. We found overwhelming evidence for the combination of all mechanisms, when explaining 16 types of data. Quantitatively, there was clear evidence for an increase in transmission strength of 57% over the past months (e.g., due to viral mutation), in the context of increased contact rates (e.g., rebound from national lockdowns) and increased test rates (e.g., due to the inclusion of lateral flow tests). Models with fluctuating transmission strength outperformed models with fluctuating contact rates. However, the best model included all three mechanisms suggesting that the resurgence during the second peak can be explained by an increase in effective contact rate that is the product of a rebound of contact rates following a national lockdown and increased transmission risk due to viral mutation.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Karl Friston", - "author_inst": "UCL" - }, - { - "author_name": "Anthony Costello", - "author_inst": "UCL" - }, - { - "author_name": "Guillaume Flandin", - "author_inst": "UCL" - }, - { - "author_name": "Adeel Razi", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.10.21249550", "rel_title": "Acute Metabolic Emergencies in Diabetes and COVID-19: a systematic review and meta-analysis of case reports", @@ -990180,6 +991522,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.01.10.21249548", + "rel_title": "Atmospheric PM2.5 before and after Lockdown in relation to COVID-19 Evolution and daily Viral Counts: Could Viral Natural Selection have occurred due to changes in the Airborne Pollutant PM2.5 acting as a Vector for SARS-CoV-2?", + "rel_date": "2021-01-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.10.21249548", + "rel_abs": "BackgroundGenes coding for SARS-CoV-2 have been detected on the microscopic airborne pollutant particulate matter, which has been suggested as a vector for COVID-19 transmission. Lockdown in China has been shown to be associated with significant reduction in pollution including the particulate matter component which coincided with the appearance of a viral mutant (Clade G) which steadily displaced the original Clade D after lockdown. The reason why Clade G developed a fitness advantage is as yet unknown. This paper examines the possible role of airborne particulate matter PM2.5 as selective pressure determining viral Clade predominance and further shedding light on the mode of SARS-CoV-2 transmission.\n\nMethodsThe average levels of PM2.5 of a number of cities were obtained from the Air Quality Index (AQI), a real-time assessment of atmospheric pollution. The daily average PM2.5 levels were assessed between January 23rd and April 29th 2020 determined by the timeline when viral counts in Beijing and other cities were available. Daily viral counts of Clades D and G were available starting from the 12th February as determined by the scientific literature published in August 2020. The cities chosen were Beijing, Sheffield, Nottingham, Sydney and Cambridge because of their substantially elevated viral counts compared to other cities. Cities as opposed to vaster areas/nations were chosen as PM2.5 levels vary across regions and countries.\n\nResultsFor the time period assessed, the Beijing PM2.5 pattern initiated with highly elevated mean PM2.5 levels of 155.8{micro}g/m3 (SD+/-73.6) during high viral counts, followed by 82.1{micro}g/m3 (SD+/-44.9) (p<0.04) when the viral counts decreased. In all the other cities assessed, the pattern differed whereby the PM2.5 levels increased significantly over the preceding baseline contemporaneously with the viral count rise. The changes in these cities PM2.5 levels were on average 31.5{micro}g/m3 before viral counts rose and 56.35{micro}g/m3 contemporaneous with viral count rise. The average levels of PM2.5 in these cities started to decrease one week after lockdown to 46{micro}g/m3 when measured over 2 weeks post-lockdown.\n\nAs regards the viral counts from data retrieved from Beijing, the latter part of the bell-shaped curve and a subsequent smaller curve of the viral count was available for evaluation. The average viral count for Clade D in Beijing was 11.1(SD+/-13.5) followed by a mean viral count for Clade G was 13.8(SD+/-9.2). Conversely in all the other cities besides Beijing, the viral counts averaged 45.8 for Clade D and 161 for Clade G. The variation in viral counts between cities suggests the strong possibility of variation in the availability of sampling between cities.\n\nThe newer variant, Clade G demonstrated viral counts initially appearing in mid-February in Beijing to later displace Clade D as the dominant viral Clade. The appearance of Clade G coincided with the decreasing gradient of PM2.5 levels. A number of significant correlations were obtained between PM2.5 levels and the viral count in all the cities reviewed.\n\nConclusionCOVID-19 viral counts appear to increase concomitant with increasing PM2.5 levels. Viral counts of both Clades correlated differentially with PM2.5 levels in all the cities assessed. The significantly highly elevated PM2.5 levels in Beijing resulted in correlating mainly with Clade D, however Clade G began to appear with decreasing PM2.5 levels, suggesting the beginnings for the initial SARS-CoV-2 Clade evolution. Clade G, the newer variant was able to flourish at lower levels of PM2.5 than Clade D. Clade G may possibly have utilized other sources of particulate matter as a viral vector, such as that derived from tobacco smoking, whereby 66% of Chinese males are smokers and 70% of the Chinese non-smoking population are exposed to 2nd hand smoking.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Yves Muscat Baron", + "author_inst": "Medical School, University of Malta." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.10.21249151", "rel_title": "Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples", @@ -992160,25 +993521,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.08.21249467", - "rel_title": "An Augmented SEIR Model with Protective and Hospital Quarantine Dynamics for the Control of COVID-19 Spread", - "rel_date": "2021-01-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.08.21249467", - "rel_abs": "In this work, an attempt is made to analyse the dynamics of COVID-19 outbreak mathematically using a modified SEIR model with additional compartments and a nonlinear incidence rate with the help of bifurcation theory. Existence of a forward bifurcation point is presented by deriving conditions in terms of parameters for the existence of disease free and endemic equilibrium points. The significance of having two additional compartments, viz., protective and hospital quarantine compartments, is then illustrated via numerical simulations. From the analysis and results, it is observed that, by properly selecting transfer functions to place exposed and infected individuals in protective and hospital quarantine compartments, respectively, and with apt governmental action, it is possible to contain the COVID-19 spread effectively. Finally, the capability of the proposed model in predicting/representing the COVID-19 dynamics is presented by comparing with real-time data.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Rohith G.", - "author_inst": "Indian Institute of Technology Gandhinagar" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.08.21249379", "rel_title": "Detection of SARS-CoV-2 variants in Switzerland by genomic analysis of wastewater samples", @@ -992486,6 +993828,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.08.20249041", + "rel_title": "The incremental value of computed tomography of COVID-19 pneumonia in predicting ICU admission", + "rel_date": "2021-01-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.08.20249041", + "rel_abs": "RationaleTriage is crucial for patients management and estimation of the required Intensive Care Unit (ICU) beds is fundamental for Health Systems during the COVID-19 pandemic.\n\nObjectiveTo assess whether chest Computed Tomography (CT) of COVID-19 pneumonia has an incremental role in predicting patients admission to ICU.\n\nMethodsWe performed volumetric and texture analysis of the areas of the affected lung in CT of 115 outpatients with COVID-19 infection presenting to the Emergency Room with dyspnea and unresponsive hypoxyemia. Admission blood laboratory including lymphocyte count, serum lactate dehydrogenase, D-dimer and C-Reactive Protein and the ratio between the arterial partial pressure of oxygen and inspired oxygen were collected. By calculating the areas under the receiver-operating characteristic curves (AUC), we compared the performance of blood laboratory-arterial gas analyses features alone and combined with the CT features in two hybrid models (Hybrid radiological and Hybrid radiomics)for predicting ICU admission. Following a machine learning approach, 63 patients were allocated to the training and 52 to the validation set.\n\nMeasurements and Main ResultsTwenty-nine (25%) of patients were admitted to ICU. The Hybrid radiological model comprising the lung %consolidation performed significantly (p=0.04) better in predicting ICU admission in the validation (AUC=0.82; 95%Confidence Interval 0.68-0.95) set than the blood laboratory-arterial gas analyses features alone (AUC=0.71; 95%Confidence Interval 0.56-0.86). A risk calculator for ICU admission was derived and is available at:https://github.com/cgplab/covidapp\n\nConclusionsThe volume of the consolidated lung in CT of patients with COVID-19 pneumonia has a mild but significant incremental value in predicting ICU admission.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Maurizio Bartolucci", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Matteo Benelli", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Margherita Betti", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Sara Bicchi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Luca Fedeli", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Federico Giannelli", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Donatella Aquilini", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Alessio Baldini", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Guglielmo Consales", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Massimo Edoardo Di Natale", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Pamela Lotti", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Letizia Vannucchi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Michele Trezzi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Lorenzo Nicola Mazzoni", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Sandro Santini", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Roberto Carpi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Daniela Matarrese", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Luca Bernardi", + "author_inst": "Azienda USL Toscana Centro" + }, + { + "author_name": "Mario Mascalchi", + "author_inst": "University of Florence" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2021.01.06.21249325", "rel_title": "Pregnancy and neonatal outcomes of COVID-19, co-reporting of common outcomes from the PAN-COVID and AAP SONPM registry", @@ -993954,73 +995387,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.07.21249418", - "rel_title": "Center-Based Experiences Implementing Strategies to Reduce Risk of Horizontal Transmission of SARS-Cov-2: Potential for Compromise of Neonatal Microbiome Assemblage", - "rel_date": "2021-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.07.21249418", - "rel_abs": "Perinatal transmission of COVID-19 is poorly understood and many neonatal intensive care units (NICU) policies minimize mother-infant contact to prevent transmission. We present our units approach and ways it may impact neonatal microbiome acquisition. We attended COVID-19 positive mothers deliveries from March-August 2020. Delayed cord clamping and skin-to-skin were avoided and infants were admitted to the NICU. No parents visits were allowed and discharge was arranged with COVID-19 negative family members. Maternal breast milk was restricted in the NICU. All twenty-one infants tested negative at 24 and 48 hours and had average hospital stays of nine days. 40% of mothers expressed breastmilk and 60% of infants were discharged with COVID-19 negative caregivers. Extended hospital stays, no skin-to-skin contact, limited maternal milk use, and discharge to caregivers outside primary residences, potentially affect the neonatal microbiome. Future studies are warranted to explore how ours and other centers similar policies influence this outcome.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Joann Romano-Keeler", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Dana Fiszbein", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Jilei Zhang", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Joseph Horowitz", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Karen Hayani", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Irina Buhimschi", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Christina Lopez", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Zaynab Kadhem", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "James Berman", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Phornphat Rasamimari", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Aarti Raghavan", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "De-Ann M Pillers", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Jun Sun", - "author_inst": "University of Illinois at Chicago" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.01.07.21249323", "rel_title": "A Novel Abnormality Annotation Database for COVID-19 Affected Frontal Lung X-rays", @@ -994324,6 +995690,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.07.21249381", + "rel_title": "Comparing the age and sex trajectories of SARS-CoV-2 morbidity with other respiratory pathogens points to potential immune mechanisms.", + "rel_date": "2021-01-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.07.21249381", + "rel_abs": "Comparing age and sex differences in SARS-CoV-2 hospitalization and mortality with influenza and other health outcomes opens the way to generating hypotheses as to the underlying mechanisms, building on the extraordinary advances in immunology and physiology that have occurred over the last year. Notable departures in health outcomes starting around puberty suggest that burdens associated with influenza and other causes are reduced relative to the two emergent coronaviruses over much of adult life. Two possible hypotheses could explain this: protective adaptive immunity for influenza and other infections, or greater sensitivity to immunosenescence in the coronaviruses. Comparison of sex differences suggest an important role for adaptive immunity; but immunosenescence might also be relevant, if males experience faster immunosenescence. Involvement of the renin-angiotensin-system in SARS-CoV-2 infection might drive high sensitivity to disruptions of homeostasis. Overall, these results highlight the long tail of vulnerability in the age profile relevant to the emergent coronaviruses, which more transmissible variants have the potential to uncover at the younger end of the scale, and aging populations will expose at the other end of the scale.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "C. Jessica E. Metcalf", + "author_inst": "Princeton University" + }, + { + "author_name": "Juliette Paireau", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Megan ODriscoll", + "author_inst": "Department of Genetics, Cambridge University" + }, + { + "author_name": "Mathilde Pivette", + "author_inst": "Sante publique France, French national public health agency, Saint Maurice, France" + }, + { + "author_name": "Bruno Hubert", + "author_inst": "Sante publique France, French national public health agency, Saint Maurice, France" + }, + { + "author_name": "Isabelle Pontais", + "author_inst": "Sante publique France, French national public health agency, Saint Maurice, France" + }, + { + "author_name": "Derek Cummings", + "author_inst": "Department of Biology, University of Florida, Gainesville, USA" + }, + { + "author_name": "Simon Cauchemez", + "author_inst": "Institut Pasteur, Paris" + }, + { + "author_name": "Henrik Salje", + "author_inst": "Department of Biology, University of Florida, Gainesville, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.07.21249392", "rel_title": "Predicting severity of Covid-19 using standard laboratory parameters", @@ -995455,49 +996872,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.01.04.21249233", - "rel_title": "A novel computational approach to reconstruct SARS-CoV-2 infection dynamics through the inference of unsampled sources of infection", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.04.21249233", - "rel_abs": "Infectious diseases such as the COVID19 pandemic cemented the importance of disease tracking. The role of asymptomatic, undiagnosed individuals in driving infection has become evident. Their unaccountability results in ineffective prevention. We developed a pipeline using genomic data to accurately predict a populations transmission network complete with the inference of unsampled sources. The system utilises Bayesian phylogenetics to capture evolutionary and infection dynamics of SARS-CoV-2. It identified the effectiveness of preventive measures in Canadas Atlantic bubble and mobile populations such as New York State. Its robustness extends to the prediction of cross-species disease transmission as we inferred SARS-CoV-2 transmission from humans to lions and tigers in New York Citys Bronx Zoo. The proposed methods ability to generate such complete transmission networks, provides a more detailed insight into the transmission dynamics within a population. This potential frontline tool will be of direct help in \"the battle to bend the curve\".", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Deshan Perera", - "author_inst": "University of Calgary" - }, - { - "author_name": "Ben Perks", - "author_inst": "University of Calgary" - }, - { - "author_name": "Michael Potemkin", - "author_inst": "University of Calgary" - }, - { - "author_name": "Paul Gordon", - "author_inst": "University of Calgary" - }, - { - "author_name": "John Gill", - "author_inst": "University of Calgary" - }, - { - "author_name": "Guido van Marle", - "author_inst": "University of Calgary" - }, - { - "author_name": "Quan Long", - "author_inst": "University of Calgary" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.06.21249318", "rel_title": "Stochastic model for COVID-19 in slums: interaction between biology and public policies", @@ -995713,6 +997087,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.05.21249247", + "rel_title": "SARS-CoV-2 seroprevalence in the urban population of Qatar: An analysis of antibody testing on a sample of 112,941 individuals", + "rel_date": "2021-01-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.05.21249247", + "rel_abs": "BackgroundQatar has experienced a large SARS-CoV-2 epidemic. Our first objective was to assess the proportion of the urban population that has been infected with SARS-CoV-2, by measuring the prevalence of detectable antibodies. Our second objective was to identify predictors for infection and for having higher antibody titers.\n\nMethodsResidual blood specimens from individuals receiving routine and other clinical care between May 12-September 9, 2020 were tested for anti-SARS-CoV-2 antibodies. Associations with seropositivity and higher antibody titers were identified through regression analyses. Probability weights were applied in deriving the epidemiological measures.\n\nResultsWe tested 112,941 individuals ([~]10% of Qatars urban population), of whom 51.6% were men and 66.0% were 20-49 years of age. Seropositivity was 13.3% (95% CI: 13.1-13.6%) and was significantly associated with sex, age, nationality, clinical-care type, and testing date. The proportion with higher antibody titers varied by age, nationality, clinical-care type, and testing date. There was a strong correlation between higher antibody titers and seroprevalence in each nationality, with a Pearson correlation coefficient of 0.85 (95% CI: 0.47-0.96), suggesting that higher antibody titers may indicate repeated exposure to the virus. The percentage of antibody-positive persons with prior PCR-confirmed diagnosis was 47.1% (95% CI: 46.1-48.2%), severity rate was 3.9% (95% CI: 3.7-4.2%), criticality rate was 1.3% (95% CI: 1.1-1.4%), and fatality rate was 0.3% (95% CI: 0.2-0.3%).\n\nConclusionsFewer than two in every 10 individuals in Qatars urban population had detectable antibodies against SARS-CoV-2 between May 12-September 9, 2020, suggesting that this population is still far from the herd immunity threshold and at risk from a subsequent epidemic wave.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Peter V. Coyle", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Hiam Chemaitelly", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + }, + { + "author_name": "Mohamed Ali Ben Hadj Kacem", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Naema Hassan Abdulla Al Molawi", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Reham Awni El Kahlout", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Imtiaz Gilliani", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Nourah Younes", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Zaina Al Kanaani", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Abdullatif Al Khal", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Einas Al Kuwari", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Adeel A Butt", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Andrew Jeremijenko", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Anvar Hassan Kaleeckal", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Ali Nizar Latif", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Riyazuddin Mohammad Shaik", + "author_inst": "Hamad Medical Corporation, Doha, Qatar" + }, + { + "author_name": "Hanan F. Abdul Rahim", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Gheyath K. Nasrallah", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Hadi M. Yassine", + "author_inst": "Qatar University, Doha, Qatar" + }, + { + "author_name": "Mohamed G. Al Kuwari", + "author_inst": "Primary Health Care Corporation, Doha, Qatar" + }, + { + "author_name": "Hamad Eid Al Romaihi", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Mohamed H. Al-Thani", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Roberto Bertollini", + "author_inst": "Ministry of Public Health, Doha, Qatar" + }, + { + "author_name": "Laith J Abu-Raddad", + "author_inst": "Weill Cornell Medicine-Qatar, Doha, Qatar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.04.21249235", "rel_title": "Machine Learning Forecast of Growth in COVID-19 Confirmed Infection Cases with Non-Pharmaceutical Interventions and Cultural Dimensions: Algorithm Development and Validation", @@ -997153,105 +998634,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.01.06.20249035", - "rel_title": "Dynamics of antibodies to SARS-CoV-2 in convalescent plasma donors", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.20249035", - "rel_abs": "The novel SARS-CoV-2 virus emerged in late 2019 and has caused a global health and economic crisis. The characterization of the human antibody response to SARS-CoV-2 infection is vital for serosurveillance purposes as well for treatment options such as transfusion with convalescent plasma or immunoglobin products derived from convalescent plasma. In this study, we measured antibody responses in 844 longitudinal samples from 151 RT-PCR positive SARS-CoV-2 convalescent adults during the first 34 weeks after onset of symptoms. All donors were seropositive at the first sampling moment and only one donor seroreverted during follow-up analysis. Anti-RBD IgG and anti-nucleocapsid IgG levels slowly declined with median half-lifes of 62 and 59 days during 2-5 months after symptom onset, respectively. The rate of decline of antibody levels diminished during extended follow-up. In addition, the magnitude of the IgG response correlated with neutralization capacity measured in a classic plaque reduction assay as well in our in-house developed competition assay. The result of this study gives valuable insight into the longitudinal response of antibodies to SARS-CoV-2.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Maurice Steenhuis", - "author_inst": "Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands, and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amste" - }, - { - "author_name": "Gerard van Mierlo", - "author_inst": "Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands, and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amste" - }, - { - "author_name": "Ninotska I.L Derksen", - "author_inst": "Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands, and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amste" - }, - { - "author_name": "Pleuni Ooijevaar-de Heer", - "author_inst": "Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands, and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amste" - }, - { - "author_name": "Simone Kruithof", - "author_inst": "Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands, and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amste" - }, - { - "author_name": "Floris L Loeff", - "author_inst": "Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands, and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amste" - }, - { - "author_name": "Lea C Berkhout", - "author_inst": "Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands, and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amste" - }, - { - "author_name": "Federica Linty", - "author_inst": "Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands" - }, - { - "author_name": "Chantal Reusken", - "author_inst": "Department of Infectious Diseases, Public Health Service region Utrecht, Utrecht, the Netherlands" - }, - { - "author_name": "Johan Reimerink", - "author_inst": "Department of Infectious Diseases, Public Health Service region Utrecht, Utrecht, the Netherlands" - }, - { - "author_name": "Boris Hogema", - "author_inst": "Department of Virology, Sanquin Diagnostic Services, Amsterdam, The Netherlands." - }, - { - "author_name": "Hans Zaaijer", - "author_inst": "Sanquin Blood Supply Foundation and Amsterdam University Medical Centre, Amsterdam, the Netherlands" - }, - { - "author_name": "Leo van de Watering", - "author_inst": "Sanquin Blood Bank, Unit Transfusion Medicine, Leiden, the Netherlands." - }, - { - "author_name": "Francis Swaneveld", - "author_inst": "Department of Transfusion Medicine, Sanquin Blood Bank, 1066 CX Amsterdam, the Netherlands" - }, - { - "author_name": "Marit J van Gils", - "author_inst": "Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands." - }, - { - "author_name": "Berend Jan Bosch", - "author_inst": "Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, the Netherlands." - }, - { - "author_name": "Marieke van Ham", - "author_inst": "Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands, and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amste" - }, - { - "author_name": "Anja ten Brinke", - "author_inst": "Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands, and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amste" - }, - { - "author_name": "Gestur Vidarsson", - "author_inst": "Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands" - }, - { - "author_name": "Ellen C van der Schoot", - "author_inst": "Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory Academic Medical Centre, 1066 CX Amsterdam, the Netherlands" - }, - { - "author_name": "Theo Rispens", - "author_inst": "Department of Immunopathology, Sanquin Research, Amsterdam, The Netherlands, and Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amste" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.06.21249332", "rel_title": "No association between the SARS-CoV-2 variants and mortality rates in the Eastern Mediterranean Region", @@ -997483,6 +998865,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.06.425543", + "rel_title": "Heterogeneity versus the COVID-19 Pandemic", + "rel_date": "2021-01-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.06.425543", + "rel_abs": "In this paper, heterogeneity is formally defined, and its properties are explored. We define and distinguish observable versus non-observable heterogeneity. It is proposed that heterogeneity among the vulnerable is a significant factor in the contagion impact of COVID-19, as demonstrated with incidence rates on a Diamond Princess Cruise ship in February 2020. Given the nature of the disease, its heterogeneity and human social norms, pre-voyage and post-voyage quick testing procedures may become the new standard for cruise ship passengers and crew. The technological advances in testing available today would facilitate more humanistic treatment as compared to more archaic quarantine and isolation practices for all onboard ship. With quick testing, identification of those infected and thus not allowed to embark on a cruise or quarantining those disembarking and other mitigation strategies, the popular cruise adventure could be available safely again. Whatever the procedures implemented, the methodological purpose of this study should add valuable insight in the modeling of disease and specifically, the COVID-19 virus.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ramalingam Shanmugam", + "author_inst": "Texas State University" + }, + { + "author_name": "Gerald Ledlow", + "author_inst": "University of Texas Health Science Center at Tyler: The University of Texas Health Science Center at Tyler" + }, + { + "author_name": "Karan P. Singh", + "author_inst": "University of Texas Health Science Center Tyler" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "scientific communication and education" + }, { "rel_doi": "10.1101/2021.01.06.425544", "rel_title": "Complex Systems Analysis Informs on the Spread of COVID-19", @@ -998483,57 +999892,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.03.21249182", - "rel_title": "COVID-HEART: Development and Validation of a Multi-Variable Model for Real-Time Prediction of Cardiovascular Complications in Hospitalized Patients with COVID-19", - "rel_date": "2021-01-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.03.21249182", - "rel_abs": "Cardiovascular (CV) manifestations of COVID-19 infection carry significant morbidity and mortality. Current risk prediction for CV complications in COVID-19 is limited and existing approaches fail to account for the dynamic course of the disease. Here, we develop and validate the COVID-HEART predictor, a novel continuously-updating risk prediction technology to forecast CV complications in hospitalized patients with COVID-19. The risk predictor is trained and tested with retrospective registry data from 2178 patients to predict two outcomes: cardiac arrest and imaging-confirmed thromboembolic events. In repeating model validation many times, we show that it predicts cardiac arrest with an average median early warning time of 18 hours (IQR: 13-20 hours) and an AUROC of 0.92 (95% CI: 0.91-0.92), and thromboembolic events with a median early warning time of 72 hours (IQR: 12-204 hours) and an AUROC of 0.70 (95% CI: 0.67-0.73). The COVID-HEART predictor is anticipated to provide tangible clinical decision support in triaging patients and optimizing resource utilization, with its clinical utility potentially extending well beyond COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Julie K Shade", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Ashish N Doshi", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Eric Sung", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Dan M Popescu", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Anum S Minhas", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Nisha A Gilotra", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Konstantinos N Aronis", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Allison G Hays", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Natalia A Trayanova", - "author_inst": "Johns Hopkins University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.12.31.20249099", "rel_title": "Optimizing vaccine allocation for COVID-19 vaccines: critical role of single-dose vaccination.", @@ -998721,6 +1000079,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2021.01.04.21249195", + "rel_title": "The incidence, characteristics and outcomes of pregnant women hospitalized with symptomatic and asymptomatic SARS-CoV-2 infection in the UK from March to September 2020: a national cohort study using the UK Obstetric Surveillance System (UKOSS)", + "rel_date": "2021-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.04.21249195", + "rel_abs": "BackgroundEvidence on risk factors, incidence and impact of SARS-CoV-2 infection in pregnant mothers and their babies has rapidly expanded but there is a lack of population level data to inform accurate incidence rates and unbiased descriptions of characteristics and outcomes. The primary aim of this study was to describe the incidence, characteristics and outcomes of hospitalized pregnant women with symptomatic and asymptomatic SARS-CoV-2 in the UK compared to pregnant women without SARS-CoV-2 in order to inform future clinical guidance and management.\n\nMethods and FindingsWe conducted a national, prospective cohort study of all hospitalized pregnant women with confirmed SARS-CoV-2 from 1st March 2020 to 31st August 2020 using the UK Obstetric Surveillance System (UKOSS) across all 194 hospitals in the UK with a consultant-led maternity unit. Incidence was estimated using the latest national maternity data. Overall, 1148 hospitalized women had confirmed SARS-CoV-2 in pregnancy, 63% of which were symptomatic. Therefore, the estimated incidence of hospitalization with symptomatic SARS-CoV-2 was 2.0 per 1000 maternities (95% CI 1.9-2.2) and for asymptomatic SARS-CoV-2 was 1.2 per 1000 maternities (95% CI 1.1-1.4). Compared to pregnant women without SARS-CoV-2, women hospitalized with symptomatic SARS-CoV-2 were more likely to be overweight or obese (adjusted OR 1.86, 95% CI 1.39-2.48 and aOR 2.07, 95% CI 1.53-2.29 respectively), to be of Black, Asian or Other minority ethnic group (aOR 6.24, 95% CI 3.93-9.90, aOR 4.36, 95% CI 3.19-5.95 and aOR 12.95, 95% CI 4.93-34.01 respectively), and to have a relevant medical comorbidity (aOR 1.83, 95% CI 1.32-2.54). Compared to pregnant women without SARS-CoV-2, hospitalized pregnant women with symptomatic SARS-CoV-2 were more likely to be admitted to intensive care (aOR 57.67, 95% CI 7.80-426.70) but the absolute risk of poor outcomes was low. Cesarean births and neonatal unit admission were increased regardless of symptom status (symptomatic aOR 2.60, 95% CI 1.97-3.42 and aOR 3.08, 95% CI 1.99-4.77 respectively; asymptomatic aOR 2.02, 95% CI 1.52-2.70 and aOR 1.84, 95% 1.12-3.03 respectively). Iatrogenic preterm births were more common in women with symptomatic SARS-CoV-2 (aOR 11.43, 95% CI 5.07-25.75). The risks of stillbirth or neonatal death were not significantly increased, regardless of symptom status but numbers were small. The limitations of this study include the restriction to women hospitalized with SARS-CoV-2, who may by nature of their admission have been at greater risk of adverse outcome.\n\nConclusionsWe have identified factors that increase the risk of symptomatic and asymptomatic SARS-CoV-2 in pregnancy. The increased risks of cesarean and iatrogenic preterm birth provide clear evidence of the indirect impact of SARS-CoV-2 on mothers and maternity care in high income settings. Clinicians can be reassured that the majority of women do not experience severe complications of SARS-CoV-2 in pregnancy and women with mild disease can be discharged to continue their pregnancy safely.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Nicola Vousden", + "author_inst": "University of Oxford" + }, + { + "author_name": "Kathryn Bunch", + "author_inst": "University of Oxford" + }, + { + "author_name": "Edward Morris", + "author_inst": "Royal College of Obstetricians and Gynaecologists" + }, + { + "author_name": "Nigel Simpson", + "author_inst": "University of Leeds" + }, + { + "author_name": "Christopher Gale", + "author_inst": "Imperial College London" + }, + { + "author_name": "Patrick O'Brien", + "author_inst": "University College London" + }, + { + "author_name": "Maria Quigley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peter Brocklehurst", + "author_inst": "University College London" + }, + { + "author_name": "Jennifer J Kurinczuk", + "author_inst": "University of Oxford" + }, + { + "author_name": "Marian Knight", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2021.01.04.425336", "rel_title": "SARS-CoV-2 susceptibility of cell lines and substrates commonly used in diagnosis and isolation of influenza and other viruses", @@ -999993,45 +1001406,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.12.29.20248900", - "rel_title": "Efficiency of Artificial Intelligence in Detecting COVID-19 Pneumonia and Other Pneumonia Causes by Quantum Fourier Transform Method", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.29.20248900", - "rel_abs": "The new coronavirus (COVID-19) appeared in Wuhan in December 2019 and has been announced as a pandemic by the World Health Organization (WHO). Currently, this deadly pandemic has caused more than 1 million deaths worldwide. Therefore, it is essential to detect positive cases as early as possible to prevent the further spread of this outbreak. Currently, the most widely used COVID-19 detection technique is a real-time reverse transcription-polymerase chain reaction (RT-PCR). However, RT-PCR is time-consuming to confirm infection in the patient. Because RT-PCR is less sensitive, it provides high false-negative results. Computed tomography (CT) is recommended as a solution to this problem by healthcare professionals because of its higher sensitivity for early and rapid diagnosis. In addition, radiation used in CT poses a serious threat to patients. In this study, we propose a CNN-based method to distinguish COVID-19 pneumonia from other types of viral and bacterial pneumonia using low-dose CT images to reduce the radiation dose used in CT. In our study, we used a data set consisting of 7717 CT images of 350 patients that we collected from Canakkale Onsekiz Mart University Research Hospital. We used a CNN-based network that suppresses noise to remove interference from low-dose CT images. In the image preprocessing phase, we provided lung segmentation from CT images and applied quantum Fourier transform. By evaluating all possible variations of local knowledge at the same time with quantum Fourier transformation, the most informative spatial information was extracted. In CNN-based architecture, we used pre-trained ResNet50v2 as a feature extractor and fine-tune by training with our dataset. We visualized the efficiency of the ResNet50v2 network using the t-SNE method. We performed the classification process with a fully connected layer. We created a heat map using the GradCam technique to see where the model focuses on the images while classifying. In this experimental study, the results of 99.5%, 99.2%, 99.0%, 99.7%, and 99.1%, were obtained in the context of performance criteria such as accuracy, precision, sensitivity, specificity, and f1 score, respectively. This study revealed the artificial intelligence-based computer-aided diagnosis (CAD)system as an effective and fast method to accurately diagnose COVID-19 pneumonia.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Erdi ACAR", - "author_inst": "Institute of Science of Canakkale Onsekiz Mart University" - }, - { - "author_name": "Bilge Oztoprak", - "author_inst": "Dept. of Radiology, Faculty of Medicine, Canakkale Onsekiz Mart University" - }, - { - "author_name": "Mustafa Resorlu", - "author_inst": "Dept. of Radiology, Faculty of Medicine, Canakkale Onsekiz Mart University" - }, - { - "author_name": "Murat Das", - "author_inst": "Dept. of Radiology, Faculty of Medicine, Canakkale Onsekiz Mart University" - }, - { - "author_name": "Ihsan Yilmaz", - "author_inst": "Dept. of Computer Engineering, Institute of Science, Canakkale Onsekiz Mart University" - }, - { - "author_name": "Ibrahim Oztoprak", - "author_inst": "Dept. of Radiology, Faculty of Medicine, Canakkale Onsekiz Mart University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.12.30.20249057", "rel_title": "Evaluation of three rapid lateral flow antigen detection tests for the diagnosis of SARS-CoV-2 infection", @@ -1000383,6 +1001757,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.30.20248890", + "rel_title": "Detection of SARS-CoV-2 in the air from hospitals and closed rooms occupied by COVID-19 patients", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20248890", + "rel_abs": "To understand air transmission characteristics of SARS-CoV-2 and risks for health care personnel and visitors to hospitals, we analyzed air samples collected from various enclosures in hospitals at Hyderabad and Mohali and performed closed room experiments with COVID-19 positive individuals. We collected 64 air samples from COVID and non-COVID areas of various hospitals and 17 samples from closed rooms occupied by COVID patients. 4 samples from COVID care areas were positive for SARS-CoV-2 with no obvious predilection towards ICU/non-ICU areas in the hospital samples. In the closed room experiments, where one or more COVID-19 patients spent a short duration of time, one sample - collected immediately after the departure of three symptomatic patients from the room - was positive. Our results indicate that the chance of picking up SARS-CoV-2 in the air is directly related to a number of COVID positive cases in the room, their symptomatic status, and the duration of exposure and that the demarcation of hospital areas into COVID and non-COVID areas is a successful strategy to prevent cross infections. In neutral environmental conditions, the virus does not seem to spread farther away from the patients, especially if they are asymptomatic, giving an objective evidence for the effectiveness of physical distancing in curbing the spread of the epidemic.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Shivranjani Moharir", + "author_inst": "CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India" + }, + { + "author_name": "Sharat Sharath Chandra", + "author_inst": "CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India" + }, + { + "author_name": "Arushi Goel", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Bhuwaneshwar Thakur", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Gurpreet Singh Bhalla", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Dinesh Kumar", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Digvijay Singh Naruka", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Ashwani Kumar", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Amit Tuli", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Swathi Suravaram", + "author_inst": "ESI Hospital and Medical College, Hyderabad, India" + }, + { + "author_name": "Thrilok Chander Bingi", + "author_inst": "COVID-19 nodal centre, Hyderabad, India" + }, + { + "author_name": "M Srinivas", + "author_inst": "ESI Hospital and Medical College, Hyderabad, India" + }, + { + "author_name": "Rajarao Mesipogu", + "author_inst": "COVID-19 nodal centre, Hyderabad, India" + }, + { + "author_name": "Krishna Reddy", + "author_inst": "Durgabai Deshmukh Hospital, Hyderabad, India" + }, + { + "author_name": "Sanjeev Khosla", + "author_inst": "CSIR- Institute of Microbial Technology (CSIR-IMTech), Chandigarh, India" + }, + { + "author_name": "Karthik Bharadwaj Tallapaka", + "author_inst": "CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India" + }, + { + "author_name": "Rakesh K Mishra", + "author_inst": "CSIR- Centre for Cellular and Molecular Biology (CSIR-CCMB), Hyderabad, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.23.20248803", "rel_title": "Clinical diagnosis of COVID-19: a prompt, feasible, and sensitive diagnostic tool for COVID-19 based on a 1,757-patient cohort (The AndroCoV Clinical Scoring for COVID-19 diagnosis).", @@ -1001423,33 +1002880,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.03.21249117", - "rel_title": "Analysis of the intensity of the COVID-19 epidemic in Berlin towards an universal prognostic relationship", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.03.21249117", - "rel_abs": "The present work is a continuation and development of research on prediction and analysis of the spread of the COVID-19 epidemic.\n\nThe proposed model adequately describes the development of the coronavirus epidemic with insufficient adherence to quarantine and social distancing. The transition from the absolute number of infected persons to their relative number per inhabitant of a settlement makes it possible to obtain universal calculation ratios.\n\nIn performing the calculations, the choice of the date of the beginning of the epidemic is of great importance. Recommendations are given on how to determine the date of the beginning of the epidemic based on the analysis of statistical data on the spread of the epidemic. The coefficient of virus transmission rate k included in the calculated prognostic relation depends on the population size and the type of virus strain in the settlement in question. A simple ratio for calculating this coefficient as a function of population size is proposed.\n\nControl calculations performed using only a single empirical coefficient showed high accuracy. The calculated curves for Germany, Berlin, and its districts agree well with the corresponding statistical data. The correlation coefficients between the corresponding curves reach values of 0.93 to 0.97. The further development of the model should thus go in the direction of identifying causal links between the intensity of the epidemic and the main factors affecting this process. Some of these factors are related to the characteristics of the populations behaviour and the infrastructure of cities. The increase in the incidence in areas with a large percentage of the population rooted in Islamic countries is one of the main factors determining the development of the epidemic in Berlin. In order to explain and clarify this conclusion, it is necessary to make further assumptions about the possible emergence of a new strain of coronavirus in Berlin and in Germany and, accordingly, about the possibility of new epidemic waves. A preliminary ratio for predicting the spread of the epidemic under conditions of simultaneous existence of both strains of coronavirus is given.\n\nSimplicity of the proposed prognostic method and high accuracy of the results allow to recommend it as an effective tool for operative analysis of various measures aimed to control the spread of COVID-19 epidemic including mass vaccination of population.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Denis Below", - "author_inst": "University of Potsdam" - }, - { - "author_name": "Jana Mairanowski", - "author_inst": "Sibsoft Group" - }, - { - "author_name": "Felix Mairanowski", - "author_inst": "Sibsoft Group" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.02.21249140", "rel_title": "Changes in COVID-19-related outcomes and the impacts of the potential risk factors over time: a follow-up analysis", @@ -1001685,6 +1003115,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.31.20249088", + "rel_title": "Stages of COVID-19 pandemic and paths to herd immunity by vaccination: dynamical model comparing Austria, Luxembourg and Sweden", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.31.20249088", + "rel_abs": "BackgroundWorldwide more than 72 million people have been infected and 1.6 million died with SARS-CoV-2 by 15th December 2020. Non-pharmaceutical interventions which decrease social interaction have been implemented to reduce the spread of SARS-CoV-2 and to mitigate stress on healthcare systems and prevent deaths. The pandemic has been tackled with disparate strategies by distinct countries resulting in different epidemic dynamics. However, with vaccines now becoming available, the current urgent open question is how the interplay between vaccination strategies and social interaction will shape the pandemic in the next months.\n\nMethodsTo address this question, we developed an extended Susceptible-Exposed-Infectious-Removed (SEIR) model including social interaction, undetected cases and the progression of patients trough hospitals, intensive care units (ICUs) and death. We calibrated our model to data of Luxem-bourg, Austria and Sweden, until 15th December 2020. We incorporated the effect of vaccination to investigate under which conditions herd immunity would be achievable in 2021.\n\nResultsThe model reveals that Sweden has the highest fraction of undetected cases, Luxembourg displays the highest fraction of infected population, and all three countries are far from herd immunity as of December 2020. The model quantifies the level of social interactions, and allows to assess the level which would keep Reff (t) below 1. In December 2020, this level is around 1/3 of what it was before the pandemic for all the three countries. The model allows to estimate the vaccination rate needed for herd immunity and shows that 2700 vaccinations/day are needed in Luxembourg to reach it by mid of April and 45,000 for Austria and Sweden. The model estimates that vaccinating the whole countrys population within 1 year could lead to herd immunity by July in Luxembourg and by August in Austria and Sweden.\n\nConclusionThe model allows to shed light on the dynamics of the epidemics in different waves and countries. Our results emphasize that vaccination will help considerably but not immediately and therefore social measures will remain important for several months before they can be fully alleviated.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Francoise Kemp", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Daniele Proverbio", + "author_inst": "University of Luxembourg" + }, + { + "author_name": "Atte Aalto", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Laurent Mombaerts", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Aymeric Fouquier d Herouel", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Andreas Husch", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Christophe Ley", + "author_inst": "University of Ghent" + }, + { + "author_name": "Jorge Goncalves", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Alexander Skupin", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + }, + { + "author_name": "Stefano Magni", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.30.20249066", "rel_title": "Need of care in interpreting Google Trends-based COVID-19 infodemiological study results: potential risk of false-positivity", @@ -1002933,33 +1004418,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.01.03.425141", - "rel_title": "Glycan reactive anti-HIV-1 antibodies bind the SARS-CoV-2 spike protein but do not block viral entry", - "rel_date": "2021-01-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.03.425141", - "rel_abs": "The SARS-CoV-2 spike glycoprotein is a focal point for vaccine immunogen and therapeutic antibody design, and also serves as a critical antigen in the evaluation of immune responses to COVID-19. A common feature amongst enveloped viruses such as SARS-CoV-2 and HIV-1 is the propensity for displaying host-derived glycans on entry spike proteins. Similarly displayed glycosylation motifs can serve as the basis for glyco-epitope mediated cross-reactivity by antibodies, which can have important implications on virus neutralization, antibody-dependent enhancement (ADE) of infection, and the interpretation of antibody titers in serological assays. From a panel of nine anti-HIV-1 gp120 reactive antibodies, we selected two (PGT126 and PGT128) that displayed high levels of cross-reactivity with the SARS-CoV-2 spike. We report that these antibodies are incapable of neutralizing pseudoviruses expressing SARS-CoV-2 spike proteins and are unlikely to mediate ADE via Fc{gamma}RII receptor engagement. Nevertheless, ELISA and other immunoreactivity experiments demonstrate these antibodies are capable of binding the SARS-CoV-2 spike in a glycan-dependent manner. These results contribute to the growing literature surrounding SARS-CoV-2 S cross-reactivity, as we demonstrate the ability for cross-reactive antibodies to interfere in immunoassays.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Dhiraj Mannar", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Karoline Leopold", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Sriram Subramaniam", - "author_inst": "University of British Columbia" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.31.425021", "rel_title": "Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies", @@ -1003223,6 +1004681,81 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.26.20248878", + "rel_title": "Direct detection of SARS-CoV-2 RNA using high-contrast pH-sensitive dyes", + "rel_date": "2021-01-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.26.20248878", + "rel_abs": "The worldwide COVID-19 pandemic has had devastating effects on health, healthcare infrastructure, social structure, and economics. One of the limiting factors in containing the spread of this virus has been the lack of widespread availability of fast, inexpensive, and reliable methods for testing of individuals. Frequent screening for infected and often asymptomatic people is a cornerstone of pandemic management plans. Here, we introduce two pH sensitive LAMPshade dyes as novel readouts in an isothermal RT-LAMP amplification assay for SARS-CoV-2 RNA. The resulting JaneliaLAMP (jLAMP) assay is robust, simple, inexpensive, has low technical requirements and we describe its use and performance in direct testing of contrived and clinical samples without RNA extraction.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Timothy A Brown", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Katherine S. Schaefer", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Arthur Tsang", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Hyun Ah Yi", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Jonathan B. Grimm", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Andrew L. Lemire", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Fadi M. Jradi", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Charles Kim", + "author_inst": "Sensei Biotherapeutics" + }, + { + "author_name": "Kevin McGowan", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Kimberly Ritola", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Derek T Armstrong", + "author_inst": "Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Heba H. Mostafa", + "author_inst": "Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine" + }, + { + "author_name": "Wyatt Korff", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Ronald D. Vale", + "author_inst": "HHMI Janelia Research Campus" + }, + { + "author_name": "Luke D Lavis", + "author_inst": "HHMI Janelia Research Campus" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.31.424987", "rel_title": "Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses", @@ -1004619,77 +1006152,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.26.20248865", - "rel_title": "Non-medical COVID-19-related personal impact in medical ecological perspective: A global multileveled, mixed method study", - "rel_date": "2021-01-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.26.20248865", - "rel_abs": "BackgroundThe COVID-19 pandemic has led to widespread public health measures to reduce transmission, morbidity, and mortality attributed to the SARS-CoV-2 virus. While much research and focus surrounds COVID-19 vaccine development, testing, and supportive management, little is known about the determinants of non-medical, personal impact of COVID-19 prevention policies. We aimed to understand determinants of non-medical COVID-19 impact and to account for its multileveled, intersectional nature of associations.\n\nMethodsThis cross-sectional, multi-level, convergent mixed-methods study assessed a range of beliefs, practices, and experiences relating to COVID-19. We recruited a global sample (n=7,411) using both Facebook and Amazon mTURK platforms. We constructed a novel data-driven non-medical COVID-19 Impact Score and four subcomponents (\"Personal Action,\" \"Supply-related,\" \"Cancellations,\" and \"Livelihood\" impacts). We used generalized estimating equation models with identity link functions to determine concomitant association of individual, household, and country-level variables on the impact scores. We also classified 20,015 qualitative excerpts from 6859 respondents using an 80-code codebook.\n\nResultsTotal and component impact scores varied significantly by region with Asia, Africa, and Latin America and the Caribbean observing the highest impact scores. Multilevel modeling indicated that individual-level sociocultural variables accounted for much of this variation with COVID-related worry, knowledge, struggles in accessing food and supplies, and worsening mental health most strongly associated with non-medical impact. Family responsibilities, personal COVID medical experience, and health locus of control - in addition to country-level variables reflecting social and health challenge - were also significantly and independently associated with non-medical impact.\n\nDiscussionNon-medical personal impact of COVID-19 affects most people internationally, largely in response to shutdowns, implementing prevention requirements, and through economic consequences. In the context where most of the worlds population does not have direct medical experience with COVID-19, this phenomena of non-medical impact is profound, and likely impacts sustainability of public health interventions aimed at containing COVID-19.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Timothy De Ver Dye", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Brooke Levandowski", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Shazia Siddiqi", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Jose G. Perez Ramos", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Dongmei Li", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Saloni Sharma", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Erin Muir", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Sophia Wiltse", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Rebecca Royzer", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Tiffany Panko", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Wyatte Hall", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Monica Barbosu", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Carrie Irvine", - "author_inst": "University of Rochester School of Medicine and Dentistry" - }, - { - "author_name": "Eva Pressman", - "author_inst": "University of Rochester School of Medicine and Dentistry" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.30.424878", "rel_title": "MVA Vector Vaccines Inhibit SARS CoV-2 Replication in Upper and Lower Respiratory Tracts of Transgenic Mice and Prevent Lethal Disease", @@ -1004893,6 +1006355,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.12.29.424728", + "rel_title": "In vitro Targeting of Transcription Factors to Control the Cytokine Release Syndrome in COVID-19", + "rel_date": "2020-12-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.29.424728", + "rel_abs": "Treatment of the cytokine release syndrome (CRS) has become an important part of rescuing hospitalized COVID-19 patients. Here, we systematically explored the transcriptional regulators of inflammatory cytokines involved in the COVID-19 CRS to identify candidate transcription factors (TFs) for therapeutic targeting using approved drugs. We integrated a resource of TF-cytokine gene interactions with single-cell RNA-seq expression data from bronchoalveolar lavage fluid cells of COVID-19 patients. We found 581 significantly correlated interactions, between 95 TFs and 16 cytokines upregulated in the COVID-19 patients, that may contribute to pathogenesis of the disease. Among these, we identified 19 TFs that are targets of FDA approved drugs. We investigated the potential therapeutic effect of 10 drugs and 25 drug combinations on inflammatory cytokine production in peripheral blood mononuclear cells, which revealed two drugs that inhibited cytokine production and numerous combinations that show synergistic efficacy in downregulating cytokine production. Further studies of these candidate repurposable drugs could lead to a therapeutic regimen to treat the CRS in COVID-19 patients.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Clarissa S Santoso", + "author_inst": "Boston University" + }, + { + "author_name": "Zhaorong Li", + "author_inst": "Boston University" + }, + { + "author_name": "Jaice T Rottenberg", + "author_inst": "Boston University" + }, + { + "author_name": "Xing Liu", + "author_inst": "Boston University" + }, + { + "author_name": "Vivian X Shen", + "author_inst": "Boston University" + }, + { + "author_name": "Juan I Fuxman Bass", + "author_inst": "Boston University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.30.424801", "rel_title": "Pharmacophore-based peptide biologics neutralize SARS-CoV-2 S1 and deter S1-ACE2 interaction in vitro", @@ -1006300,49 +1007801,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.12.29.424715", - "rel_title": "Design of Specific Primer Set for Detection of B.1.1.7 SARS-CoV-2 Variant using Deep Learning", - "rel_date": "2020-12-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.29.424715", - "rel_abs": "The SARS-CoV-2 variant B.1.1.7 lineage, also known as clade GR from Global Initiative on Sharing All Influenza Data (GISAID), Nextstrain clade 20B, or Variant Under Investigation in December 2020 (VUI - 202012/01), appears to have an increased transmissability in comparison to other variants. Thus, to contain and study this variant of the SARS-CoV-2 virus, it is necessary to develop a specific molecular test to uniquely identify it. Using a completely automated pipeline involving deep learning techniques, we designed a primer set which is specific to SARS-CoV-2 variant B.1.1.7 with >99% accuracy, starting from 8,923 sequences from GISAID. The resulting primer set is in the region of the synonymous mutation C16176T in the ORF1ab gene, using the canonical sequence of the variant B.1.1.7 as a reference. Further in-silico testing shows that the primer sets sequences do not appear in different viruses, using 20,571 virus samples from the National Center for Biotechnology Information (NCBI), nor in other coronaviruses, using 487 samples from National Genomics Data Center (NGDC). In conclusion, the presented primer set can be exploited as part of a multiplexed approach in the initial diagnosis of Covid-19 patients, or used as a second step of diagnosis in cases already positive to Covid-19, to identify individuals carrying the B.1.1.7 variant.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alejandro Lopez-Rincon", - "author_inst": "Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University" - }, - { - "author_name": "Carmina Perez-Romero", - "author_inst": "Departamento de Investigacion, Universidad Central de Queretaro" - }, - { - "author_name": "Alberto Tonda", - "author_inst": "UMR 518 MIA-Paris, INRAE" - }, - { - "author_name": "Lucero Mendoza-Maldonado", - "author_inst": "Hospital Civil de Guadalajara \"Dr. Juan I. Menchaca\"" - }, - { - "author_name": "Eric Claassen", - "author_inst": "Department of Viroscience, Erasmus Medical Center" - }, - { - "author_name": "Johan Garssen", - "author_inst": "Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University" - }, - { - "author_name": "Aletta D. Kraneveld", - "author_inst": "Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.12.28.424413", "rel_title": "Non-covalent TMPRSS2 inhibitors identified from virtual screening", @@ -1006566,6 +1008024,169 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2020.12.28.424622", + "rel_title": "Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients", + "rel_date": "2020-12-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.28.424622", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the pandemic of coronavirus disease 2019 (COVID-19). Great international efforts have been put into the development of prophylactic vaccines and neutralizing antibodies. However, the knowledge about the B cell immune response induced by the SARS-CoV-2 virus is still limited. Here, we report a comprehensive characterization of the dynamics of immunoglobin heavy chain (IGH) repertoire in COVID-19 patients. By using next-generation sequencing technology, we examined the temporal changes in the landscape of the patients immunological status, and found dramatic changes in the IGH within the patients immune system after the onset of COVID-19 symptoms. Although different patients have distinct immune responses to SARS-CoV-2 infection, by employing clonotype overlap, lineage expansion and clonotype network analyses, we observed a higher clonotype overlap and substantial lineage expansion of B cell clones during 2-3 weeks of illness, which is of great importance to B-cell immune responses. Meanwhile, for preferences of V gene usage during SARS-CoV-2 infection, IGHV3-74 and IGHV4-34 and IGHV4-39 in COVID-19 patients were more abundant than that of healthy controls. Overall, we present an immunological resource for SARS-CoV-2 that could promote both therapeutic development as well as mechanistic research.", + "rel_num_authors": 37, + "rel_authors": [ + { + "author_name": "Haitao Xiang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Yingze Zhao", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Xinyang Li", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Peipei Liu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Longlong Wang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Meiniang Wang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Lei Tian", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Haixi Sun", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Wei Zhang", + "author_inst": "Department of Computer Science, City University of Hong Kong" + }, + { + "author_name": "Ziqian Xu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Beiwei Ye", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Xiaoju Yuan", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Pengyan Wang", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Ning Zhang", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Yuhuan Gong", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Chengrong Bian", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Zhaohai Wang", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Linxiang Yu", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Jin Yan", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Fanping Meng", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Changqing Bai", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Xiaoshan Wang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Xiaopan Liu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Kai Gao", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Liang Wu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Longqi F. Liu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Ying Gu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Yuhai J. Bi", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Yi Shi", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences" + }, + { + "author_name": "Shaogeng Zhang", + "author_inst": "The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Chen Zhu", + "author_inst": "The Fifth Medical Center of PLA General Hospital, National Clinical Research Center for Infectious Diseases" + }, + { + "author_name": "Xun Xu", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Guizhen Wu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "George Gao", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Naibo Yang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "William Liu", + "author_inst": "National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention" + }, + { + "author_name": "Penghui Yang", + "author_inst": "5th Medical Center of Chinese PLA General Hospital, National Clinical Research Center for Infectious Diseases" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.29.424682", "rel_title": "ACE2 peptide fragment interacts with several sites on the SARS-CoV-2 spike protein S1", @@ -1007881,101 +1009502,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.23.20248425", - "rel_title": "Mechanical ventilation affects respiratory microbiome of COVID-19 patients and its interactions with the host", - "rel_date": "2020-12-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248425", - "rel_abs": "Understanding the pathology of COVID-19 is a global research priority. Early evidence suggests that the respiratory microbiome may be playing a role in disease progression, yet current studies report contradictory results. Here, we examine potential confounders in COVID-19 respiratory microbiome studies by analyzing the upper (n=58) and lower (n=35) respiratory tract microbiome in well-phenotyped COVID-19 patients and controls combining microbiome sequencing, viral load determination, and immunoprofiling. We found that time in the intensive care unit and the type of oxygen support, both of which are associated to additional treatments such as antibiotic usage, explained the most variation within the upper respiratory tract microbiome, while SARS-CoV-2 viral load had a reduced impact. Specifically, mechanical ventilation was linked to altered community structure, lower species- and higher strain-level diversity, and significant shifts in oral taxa previously associated with COVID-19. Single-cell transcriptomic analysis of the lower respiratory tract of mechanically ventilated COVID-19 patients identified specific oral bacteria, different to those observed in controls. These oral taxa were found physically associated with proinflammatory immune cells, which showed higher levels of inflammatory markers. Overall, our findings suggest confounders are driving contradictory results in current COVID-19 microbiome studies and careful attention needs to be paid to ICU stay and type of oxygen support, as bacteria favored in these conditions may contribute to the inflammatory phenotypes observed in severe COVID-19 patients.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Ver\u00f3nica Llor\u00e9ns-Rico", - "author_inst": "VIB - KU Leuven Center for Microbiology" - }, - { - "author_name": "Ann C. Gregory", - "author_inst": "VIB - KU Leuven Center for Microbiology" - }, - { - "author_name": "Johan Van Weyenbergh", - "author_inst": "KU Leuven" - }, - { - "author_name": "Sander Jansen", - "author_inst": "KU Leuven" - }, - { - "author_name": "Tina Van Buyten", - "author_inst": "KU Leuven" - }, - { - "author_name": "Junbin Qian", - "author_inst": "VIB - KU Leuven Center for Cancer Biology" - }, - { - "author_name": "Marcos Braz", - "author_inst": "KU Leuven" - }, - { - "author_name": "Soraya Maria Menezes", - "author_inst": "KU Leuven" - }, - { - "author_name": "Pierre Van Mol", - "author_inst": "VIB - KU Leuven Center for Cancer Biology" - }, - { - "author_name": "Lore Vanderbeke", - "author_inst": "KU Leuven" - }, - { - "author_name": "Christophe Dooms", - "author_inst": "KU Leuven" - }, - { - "author_name": "Jan Gunst", - "author_inst": "KU Leuven" - }, - { - "author_name": "Greet Hermans", - "author_inst": "KU Leuven" - }, - { - "author_name": "Philippe Meersseman", - "author_inst": "KU Leuven" - }, - { - "author_name": "- CONTAGIOUS collaborators", - "author_inst": "-" - }, - { - "author_name": "Els Wauters", - "author_inst": "UZ Leuven" - }, - { - "author_name": "Johan Neyts", - "author_inst": "KU Leuven" - }, - { - "author_name": "Diether Lambrechts", - "author_inst": "VIB - KU Leuven Center for Cancer Biology" - }, - { - "author_name": "Joost Wauters", - "author_inst": "UZ Leuven" - }, - { - "author_name": "Jeroen Raes", - "author_inst": "VIB - KU Leuven Center for Microbiology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.23.20248547", "rel_title": "Changes in inflammatory and immune drivers in response to immunomodulatory therapies in COVID-19", @@ -1008303,6 +1009829,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.23.20248444", + "rel_title": "Association between Use of Qingfei Paidu Tang and Mortality in Hospitalized Patients with COVID-19: A national retrospective registry study", + "rel_date": "2020-12-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248444", + "rel_abs": "BackgroundQingfei Paidu Tang (QPT), a formula of traditional Chinese medicine, which was suggested to be able to ease symptoms in patients with Coronavirus Disease 2019 (COVID-19), has been recommended by clinical guidelines and widely used to treat COVID-19 in China. However, whether it decreases mortality remains unknown.\n\nPurposeWe aimed to explore the association between QPT use and in-hospital mortality among patients hospitalized for COVID-19.\n\nStudy designA retrospective study based on a real-world database was conducted.\n\nMethodsWe identified patients consecutively hospitalized with COVID-19 in 15 hospitals from a national retrospective registry in China, from January through May 2020. Data on patients characteristics, treatments, and outcomes were extracted from the electronic medical records. The association of QPT use with mortality was evaluated using Cox proportional hazards models based on propensity score analysis.\n\nResultsOf the 8939 patients included, 28.7% received QPT. The crude mortality was 1.2% (95% confidence interval [CI] 0.8% to 1.7%) among the patients receiving QPT and 4.8% (95% CI 4.3% to 5.3%) among those not receiving QPT. After adjustment for patient characteristics and concomitant treatments, QPT use was associated with a relative reduction of 50% in in-hospital mortality (hazard ratio, 0.50; 95% CI, 0.37 to 0.66 P <0.001). This association was consistent across subgroups by sex and age. Meanwhile, the incidence of acute liver injury (8.9% [95% CI, 7.8% to 10.1%]vs. 9.9% [95% CI, 9.2% to 10.7%]; odds ratio, 0.96 [95% CI, 0.81% to 1.14%], P =0.658) and acute kidney injury (1.6% [95% CI, 1.2% to 2.2%] vs. 3.0% [95% CI, 2.6% to 3.5%]; odds ratio, 0.85 [95% CI, 0.62 to 1.17], P =0.318) was comparable between patients receiving QPT and those not receiving QPT. The major study limitations included that the study was an observational study based on real-world data rather than a randomized control trial, and the quality of data could be affected by the accuracy and completeness of medical records.\n\nConclusionsQPT was associated with a substantially lower risk of in-hospital mortality, without extra risk of acute liver injury or acute kidney injury among patients hospitalized with COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Lihua Zhang", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Xin Zheng", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Xueke Bai", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Qing Wang", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Bowang Chen", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Haibo Wang", + "author_inst": "Clinical Trial Unit, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou Province,PRC" + }, + { + "author_name": "Jiapeng Lu", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Shuang Hu", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Xiaoyan Zhang", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Haibo Zhang", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Jiamin Liu", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Ying Shi", + "author_inst": "China Standard Medical Information Research Center, Shenzhen,PRC" + }, + { + "author_name": "Zhiye Zhou", + "author_inst": "China Standard Medical Information Research Center, Shenzhen,PRC" + }, + { + "author_name": "Lanxia Gan", + "author_inst": "China Standard Medical Information Research Center, Shenzhen,PRC" + }, + { + "author_name": "Xi Li", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + }, + { + "author_name": "Jing Li", + "author_inst": "National Clinical Research Center for Cardiovascular Diseases, State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascula" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.23.20248784", "rel_title": "The importance of continued non-pharmaceutical interventions during the upcoming SARS-COV-2 vaccination campaign", @@ -1009547,185 +1011152,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.12.23.424229", - "rel_title": "Patterns of within-host genetic diversity in SARS-CoV-2", - "rel_date": "2020-12-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.23.424229", - "rel_abs": "Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1,181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within and between host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "Gerry Tonkin-Hill", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Inigo Martincorena", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Roberto Amato", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Andrew R J Lawson", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Moritz Gerstung", - "author_inst": "European Bioinformatics Institute" - }, - { - "author_name": "Ian Johnston", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "David K Jackson", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Naomi R Park", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Stefanie V Lensing", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Michael A Quail", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "S\u00f3nia Gon\u00e7alves", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Cristina Ariani", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Michael Spencer Chapman", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "William L Hamilton", - "author_inst": "Department of Medicine, University of Cambridge" - }, - { - "author_name": "Luke W Meredith", - "author_inst": "Department of Pathology, University of Cambridge" - }, - { - "author_name": "Grant Hall", - "author_inst": "Department of Pathology, University of Cambridge" - }, - { - "author_name": "Aminu S Jahun", - "author_inst": "Department of Pathology, University of Cambridge" - }, - { - "author_name": "Yasmin Chaudhry", - "author_inst": "Department of Pathology, University of Cambridge" - }, - { - "author_name": "Myra Hosmillo", - "author_inst": "Department of Pathology, University of Cambridge" - }, - { - "author_name": "Malte L Pinckert", - "author_inst": "Department of Pathology, University of Cambridge" - }, - { - "author_name": "Iliana Georgana", - "author_inst": "Department of Pathology, University of Cambridge" - }, - { - "author_name": "Anna Yakovleva", - "author_inst": "Department of Pathology, University of Cambridge" - }, - { - "author_name": "Laura G Caller", - "author_inst": "Department of Pathology, University of Cambridge and The Francis Crick Institute" - }, - { - "author_name": "Sarah L Caddy", - "author_inst": "Department of Medicine, University of Cambridge" - }, - { - "author_name": "Theresa Feltwell", - "author_inst": "Department of Pathology, University of Cambridge" - }, - { - "author_name": "Fahad A Khokhar", - "author_inst": "Department of Medicine, University of Cambridge and Cambridge Institute of Therapeutic Immunology and Infectious Disease" - }, - { - "author_name": "Charlotte J Houldcroft", - "author_inst": "Department of Medicine, University of Cambridge" - }, - { - "author_name": "Martin D Curran", - "author_inst": "Public Health England" - }, - { - "author_name": "Surendra Parmar", - "author_inst": "Public Health England" - }, - { - "author_name": "- The COVID-19 Genomics UK (COG-UK) Consortium", - "author_inst": "COG-UK" - }, - { - "author_name": "Alex Alderton", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Rachel Nelson", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Ewan Harrison", - "author_inst": "Wellcome Sanger Institute and European Bioinformatics Institute" - }, - { - "author_name": "John Sillitoe", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Stephen D Bentley", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Jeffrey C Barrett", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "M. Estee Torok", - "author_inst": "Department of Medicine, University of Cambridge" - }, - { - "author_name": "Ian G Goodfellow", - "author_inst": "Department of Pathology, University of Cambridge" - }, - { - "author_name": "Cordelia Langford", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Dominic Kwiatkowski", - "author_inst": "Wellcome Sanger Institute and Oxford University" - }, - { - "author_name": "- Wellcome Sanger Institute COVID-19 Surveillance Team", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.12.23.424171", "rel_title": "A SARS-CoV-2 spike binding DNA aptamer that inhibits pseudovirus infection in vitro by an RBD independent mechanism", @@ -1010001,6 +1011427,77 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.12.23.424254", + "rel_title": "Cell-type apoptosis in lung during SARS-CoV-2 infection", + "rel_date": "2020-12-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.23.424254", + "rel_abs": "The SARS-CoV-2 pandemic has inspired renewed interest in understanding the fundamental pathology of acute respiratory distress syndrome (ARDS) following infection because fatal COVID-19 cases are commonly linked to respiratory failure due to ARDS. The pathologic alteration known as diffuse alveolar damage in endothelial and epithelial cells is a critical feature of acute lung injury in ARDS. However, the pathogenesis of ARDS following SRAS-CoV-2 infection remains largely unknown.\n\nIn the present study, we examined apoptosis in post-mortem lung sections from COVID-19 patients and lung tissues from a non-human primate model of SARS-CoV-2 infection, in a cell-type manner, including type 1 and 2 alveolar cells and vascular endothelial cells (ECs), macrophages, and T cells. Multiple-target immunofluorescence (IF) assays and western blotting suggest both intrinsic and extrinsic apoptotic pathways are activated during SARS-CoV-2 infection. Furthermore, we observed that SARS-CoV-2 fails to induce apoptosis in human bronchial epithelial cells (i.e., BEAS2B cells) and primary human umbilical vein endothelial cells (HUVECs), which are refractory to SARS-CoV-2 infection. However, infection of co-cultured Vero cells and HUVECs or Vero cells and BEAS2B cells with SARS-CoV-2 induced apoptosis in both Vero cells and HUVECs/BEAS2B cells, but did not alter the permissiveness of HUVECs or BEAS2B cells to the virus. Post-exposure treatment of the co-culture of Vero cells and HUVECs with an EPAC1-specific activator ameliorated apoptosis in HUVECs. These findings may help to delineate a novel insight into the pathogenesis of ARDS following SARS-CoV-2 infection.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Yakun Liu", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Tania M. Garron", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Qing Chang", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Zhengchen Su", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Changcheng Zhou", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Eric C. Gong", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Junying Zheng", + "author_inst": "The University of Texas Medical Branch" + }, + { + "author_name": "Whitney Yin", + "author_inst": "University of Texas Medical Branch, Galveston" + }, + { + "author_name": "Thomas Ksiazek", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Trevor Brasel", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Yang Jin", + "author_inst": "Boston University Medical Campus" + }, + { + "author_name": "Paul Boor", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Jason Edward Comer", + "author_inst": "UTMB" + }, + { + "author_name": "Bin Gong", + "author_inst": "University of Texas Medical Branch" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.12.23.424189", "rel_title": "Berberine and obatoclax inhibit SARS-CoV-2 replication in primary human nasal epithelial cells in vitro", @@ -1011473,45 +1012970,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.22.20245993", - "rel_title": "Evaluation of the Effect of Zinc, Quercetin, Bromelain and Vitamin C on COVID-19 Patients", - "rel_date": "2020-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20245993", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is an infectious disease caused by a new strain of coronavirus. There are three phases of COVID-19: early infection stage, pulmonary stage and hyper-inflammation stage respectively. It is important to prevent lung or other organs injuries by preventing phase-II and phase-III via pharmacological or non-pharmacological treatments. This was a case series study done on twenty-two patients confirmed to be infected with SARS-CoV-2 and diagnosed with COVID-19. Patients in this study have been used quercetin 800 mg, bromelain 165 mg, zinc acetate 50 mg and ascorbic acid 1 g once daily as supplements for 3 to 5 days during SARS-CoV-2 infection. The aim of this study is to evaluate the safety and efficacy of quercetin, bromelain, zinc and ascorbic acid combination supplements on patients with COVID-19. The mean levels of WBC, ANC, ALC, AMC and AST were normal among all included patients before and after taking quercetin, bromelain, zinc and ascorbic acid supplements (P-value > 0.05). Quercetin 800 mg, bromelain 165 mg, zinc acetate 50 mg and ascorbic acid 1 g once daily supplements were safe for patients infected with SARS-CoV-2 and may prevent poor prognosis. Randomized clinical trials needed in the future to ensure the efficacy of quercetin, bromelain, zinc and vitamin c combination.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Amr Ahmed", - "author_inst": "Ministry ofHealth" - }, - { - "author_name": "Hiba Abdelseed", - "author_inst": "Ministry of Health" - }, - { - "author_name": "Yousef Albalawi", - "author_inst": "Ministry of Health" - }, - { - "author_name": "Yousef Almutairi", - "author_inst": "Ministry of Health" - }, - { - "author_name": "Eman Alsalameen", - "author_inst": "King Saud University" - }, - { - "author_name": "Abdullah Alkattan", - "author_inst": "Ministry of Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.23.20248671", "rel_title": "Hydrating the Respiratory Tract: An Alternative Explanation Why Masks Lower Severity of COVID-19 Disease", @@ -1011727,6 +1013185,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.23.20248790", + "rel_title": "A Systematic Review of the Incubation Period of SARS-CoV-2: The Effects of Age, Biological Sex, and Location on Incubation Period", + "rel_date": "2020-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248790", + "rel_abs": "A systematic review of the incubation period of COVID-19 was compiled and analyzed from 21 quantitative studies. We investigated the incubation period of COVID-19 with regard to age, biological sex, location, and severity of the disease. Based on the data extracted, we report an overall mean and median incubation period for SARS-CoV-2 of 5.894 days and 5.598 days, respectively. The incubation period did not statistically vary for biological sex or age, but some studies suggest a longer incubation period in the young and elderly. Cases of COVID-19 in Wuhan and Hubei Province of China may have a shorter incubation period for COVID-19 but the shorter incubation period may be due to an increase in viral load. In studying coronavirus strains such as SARS and MERS, researchers have discovered an inverse relationship between incubation period length and virus severity. Taking into consideration that SARS-CoV-2 is part of the beta-coronavirus family, as well as the study mentioned above, we suggest that people who experience more severe disease due to SARS-CoV-2 may have a shorter incubation period.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Caitlin Daley", + "author_inst": "Wheaton College" + }, + { + "author_name": "Megan Fydenkevez", + "author_inst": "Wheaton College" + }, + { + "author_name": "Shari Ackerman-Morris", + "author_inst": "Wheaton College" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.22.20248736", "rel_title": "REAL-TIME MECHANISTIC BAYESIAN FORECASTS OF COVID-19 MORTALITY", @@ -1013098,53 +1014583,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.22.424071", - "rel_title": "In Vivo Pharmacokinetic Study of Remdesivir Dry Powder for Inhalation in Hamsters", - "rel_date": "2020-12-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.22.424071", - "rel_abs": "Remdesivir dry powder for inhalation was previously developed using thin film freezing (TFF). A single-dose 24-hour pharmacokinetic study in hamsters, a small animal model for SARS-CoV-2, demonstrated that pulmonary delivery of TFF remdesivir can achieve plasma remdesivir and GS-441524 levels higher than the reported EC50s of both remdesivir and GS-441524 (in human epithelial cells) over 20 hours. The half-life of GS-4412524 following dry powder insufflation was about 7 hours, suggesting the dosing regimen would be twice daily administration. Although the remdesivir-Captisol(R) (80/20 w/w) formulation showed faster and greater absorption of remdesivir and GS-4412524 in the lung, remdesivir-leucine (80/20 w/w) exhibited a greater Cmax with shorter Tmax and lower AUC of GS-441524, indicating lower total drug exposure is required to achieve a high effective concentration against SAR-CoV-2. In conclusion, remdesivir dry powder for inhalation would be a promising alternative dosage form for the treatment of COVID-19 disease.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "sawittree sahakijpijarn", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Chaeho Moon", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Zachary N Warnken", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Esther Maier", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Jennie E DeVore", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Dale J Christensen", - "author_inst": "TFF Pharmaceuticals, Inc." - }, - { - "author_name": "John J Koleng", - "author_inst": "TFF Pharmaceuticals, Inc." - }, - { - "author_name": "Robert O Williams III", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.12.21.20248613", "rel_title": "Low vitamin K status predicts mortality in a cohort of 138 hospitalized patients with COVID-19", @@ -1013372,6 +1014810,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.17.20248234", + "rel_title": "Airflow and air velocity measurements while playing wind instruments, with respect to risk assessment of a SARS-CoV-2 infection", + "rel_date": "2020-12-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.17.20248234", + "rel_abs": "Due to airborne transmission of infection with the coronavirus, the question arose as to how high the risk of spreading infectious particles can be while playing a wind instrument.\n\nTo contribute to this question and to help clarify the possible risks, we analyzed 14 wind instruments, first qualitative by making airflows visible while playing and second quantitative by measuring air velocities at three distances (1m, 1.5m and 2m) in direction of the instruments bell.\n\nMeasurements took place with wind instrumentalists of the Bamberg Symphony in their concert hall.\n\nOur findings highlight that while playing all wind instruments no airflow escaping from the instruments - from the bell with brass instruments, from the mouthpiece, keyholes and bell with woodwinds - was measured beyond a distance of 1.5m from the instruments bell, regardless of volume, pitch or what was played. With that, air velocity while playing corresponded to the usual value of hall-like rooms, of 0.1 m/s. For air-jet woodwinds, alto flute and piccolo, significant air movements were seen close to their mouthpieces, which escaped directly into the room without passing through the instrument and therefore generating directed air movements.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Claudia Spahn", + "author_inst": "Freiburg Institute for Musicians' Medicine" + }, + { + "author_name": "Anna Maria Hipp", + "author_inst": "Freiburg Institute for Musicians' Medicine" + }, + { + "author_name": "Bernd Schubert", + "author_inst": "Tintschl BioEnergie und Stroemungstechnik AG" + }, + { + "author_name": "Marcus Rudolf Axt", + "author_inst": "Bamberg Symphony" + }, + { + "author_name": "Markus Stratmann", + "author_inst": "Bamberg Symphony" + }, + { + "author_name": "Christian Schmoelder", + "author_inst": "Bamberg Symphony" + }, + { + "author_name": "Bernhard Richter", + "author_inst": "Freiburg Institute for Musicians' Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.12.21.20248608", "rel_title": "Adaptive immunity to SARS-CoV-2 in cancer patients: The CAPTURE study", @@ -1014972,209 +1016453,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.21.20248640", - "rel_title": "Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248640", - "rel_abs": "Continued uncontrolled transmission of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for significant virus evolution. Here, we describe a new SARS-CoV-2 lineage (501Y.V2) characterised by eight lineage-defining mutations in the spike protein, including three at important residues in the receptor-binding domain (K417N, E484K and N501Y) that may have functional significance. This lineage emerged in South Africa after the first epidemic wave in a severely affected metropolitan area, Nelson Mandela Bay, located on the coast of the Eastern Cape Province. This lineage spread rapidly, becoming within weeks the dominant lineage in the Eastern Cape and Western Cape Provinces. Whilst the full significance of the mutations is yet to be determined, the genomic data, showing the rapid displacement of other lineages, suggest that this lineage may be associated with increased transmissibility.", - "rel_num_authors": 47, - "rel_authors": [ - { - "author_name": "Houriiyah Tegally", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal," - }, - { - "author_name": "Eduan Wilkinson", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal," - }, - { - "author_name": "Marta Giovanetti", - "author_inst": "Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil" - }, - { - "author_name": "Arash Iranzadeh", - "author_inst": "Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa" - }, - { - "author_name": "Vagner Fonseca", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal," - }, - { - "author_name": "Jennifer Giandhari", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal," - }, - { - "author_name": "Deelan Doolabh", - "author_inst": "Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Sureshnee Pillay", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal," - }, - { - "author_name": "Emmanuel James San", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal," - }, - { - "author_name": "Nokukhanya Msomi", - "author_inst": "Discipline of Virology, University of KwaZulu-Natal, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service, Durban, South Af" - }, - { - "author_name": "Koleka Mlisana", - "author_inst": "National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Anne von Gottberg", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Sibongile Walaza", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Mushal Allam", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Arshad Ismail", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Thabo Mohale", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Allison J Glass", - "author_inst": "School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa" - }, - { - "author_name": "Susan Engelbrecht", - "author_inst": "Division of Medical Virology at NHLS Tygerberg Hospital and Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa" - }, - { - "author_name": "Gert Van Zyl", - "author_inst": "Division of Medical Virology at NHLS Tygerberg Hospital and Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa" - }, - { - "author_name": "Wolfgang Preiser", - "author_inst": "Division of Medical Virology at NHLS Tygerberg Hospital and Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa" - }, - { - "author_name": "Francesco Petruccione", - "author_inst": "Centre for Quantum Technology, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Alex Sigal", - "author_inst": "Africa Health Research Institute, Durban, South Africa" - }, - { - "author_name": "Diana Hardie", - "author_inst": "Division of Medical Virology at NHLS Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Gert Marais", - "author_inst": "Division of Medical Virology at NHLS Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Marvin Hsiao", - "author_inst": "Division of Medical Virology at NHLS Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Stephen Korsman", - "author_inst": "Division of Medical Virology at NHLS Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Mary-Ann Davies", - "author_inst": "Division of Medical Virology at NHLS Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Lynn Tyers", - "author_inst": "Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Innocent Mudau", - "author_inst": "Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Denis York", - "author_inst": "Molecular Diagnostics Services, Durban, South Africa" - }, - { - "author_name": "Caroline Maslo", - "author_inst": "Department of Quality Leadership, Netcare Hospitals, Johannesburg, South Africa" - }, - { - "author_name": "Dominique Goedhals", - "author_inst": "Division of Virology at NHLS Universitas Academic Laboratories, University of The Free State, Bloemfontein, South Africa" - }, - { - "author_name": "Shareef Abrahams", - "author_inst": "National Health Laboratory Service, Port Elizabeth, South Africa" - }, - { - "author_name": "Oluwakemi Laguda-Akingba", - "author_inst": "National Health Laboratory Service, Port Elizabeth, South Africa" - }, - { - "author_name": "Arghavan Alisoltani-Dehkordi", - "author_inst": "National Health Laboratory Service, Port Elizabeth, South Africa" - }, - { - "author_name": "Adam Godzik", - "author_inst": "Division of Biomedical Sciences, University of California Riverside School of Medicine, Riverside, California, USA" - }, - { - "author_name": "Constantinos Kurt Wibmer", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Bryan Trevor Sewell", - "author_inst": "Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Rondebosch, South Africa" - }, - { - "author_name": "Jose Lourenco", - "author_inst": "Department of Zoology, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Luiz Carlos Junior Alcantara", - "author_inst": "Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil" - }, - { - "author_name": "Sergei L Kosakovsky Pond", - "author_inst": "Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Steven Weaver", - "author_inst": "Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, USA" - }, - { - "author_name": "Darren Martin", - "author_inst": "Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, 7925, South Africa" - }, - { - "author_name": "Richard J Lessells", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal," - }, - { - "author_name": "Jinal N Bhiman", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa" - }, - { - "author_name": "Carolyn Williamson", - "author_inst": "Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Tulio de de Oliveira", - "author_inst": "University of KwaZulu-Natal" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.21.20248673", "rel_title": "CovidSIMVL -- Transmission Trees, Superspreaders and Contact Tracing in Agent Based Models of Covid-19", @@ -1015358,6 +1016636,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.21.20248627", + "rel_title": "COVID-19 pandemic dynamics in Ukraine after September 1, 2020", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248627", + "rel_abs": "BackgroundThe threats of the COVID-19 pandemic require the mobilization of scientists, including mathematicians. To understand how the number of cases increases versus time, various models based on direct observations of a random number of new cases and differential equations can be used. Complex mathematical models contain many unknown parameters, the values of which must be determined using a limited number of observations of the disease over time. Even long-term monitoring of the epidemic may not provide reliable estimates of its parameters due to the constant change of testing conditions, isolation of infected and quarantine. Therefore, simpler approaches should also be used, for example, some smoothing of the dependence of the number of cases on time and the known SIR (susceptible-infected-removed) model. These approaches allowed to detect the waves of pandemic in different countries and regions and to make adequate predictions of the duration, hidden periods, reproduction numbers, and final sizes of its waves. In particular, seven waves of the COVID-19 pandemic in Ukraine were investigated.\n\nObjectiveWe will detect new epidemic waves in Ukraine that occurred after September 1, 2020 and estimate the epidemic characteristics with the use of generalized SIR model. Some predictions of the epidemic dynamics will be presented.\n\nMethodsIn this study we use the smoothing method for the dependence of the number of cases on time; the generalized SIR model for the dynamics of any epidemic wave, the exact solution of the linear differential equations and statistical approach developed before.\n\nResultsSeventh and eights epidemic waves in Ukraine were detected and the reasons of their appearance were discussed. The optimal values of the SIR model parameters were calculated. The prediction for the COVID-19 epidemic dynamics in Ukraine is not very optimistic: new cases will not stop appearing until June 2021. Only mass vaccination and social distancing can change this trend.\n\nConclusionsNew waves of COVID-19 pandemic can be detected, calculated and predicted with the use of rather simple mathematical simulations. The expected long duration of the pandemic forces us to be careful and in solidarity.The government and all Ukrainians must strictly adhere to quarantine measures in order to avoid fatal consequences.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Igor Nesteruk", + "author_inst": "Institute of Hydromechanics National Academy of sciences of Ukraine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.22.20248622", "rel_title": "Optimal strategies for combining vaccine prioritization and social distancing to reduce hospitalizations and mitigate COVID19 progression", @@ -1016298,29 +1017595,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.12.19.20248493", - "rel_title": "Minimizing cumulative risk to control airborne transmission of SARS-Cov-2 in schools", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.19.20248493", - "rel_abs": "Open schools in winter in highly epidemic areas pose a controversial issue: ventilation of classrooms (an essential mitigation factor for airborne transmission) is expected to sensibly decrease due to outdoor temperatures getting colder and regulators going to allow less restrictive policies on windows closure. Fundamental questions to be addressed are therefore: to which extent can we contain airborne transmission risk in schools? what would be the optimal ventilation strategy during the cold season considering the fact that most schools are not provided with mechanical ventilation systems? To try answering these questions a risk model for airborne transmission of covid-19 in classrooms has been develped based on previous models for tubercolosis and influenza. The separate cases of infective student and infective teacher, as well as infective teacher with microphone are investigated. We explored 3500 different air ventilation cycles for different lesson+break times and carried out a numerical optimization of the risk function. Safety risk-zones for breaks and lessons durations were estimated combining the effect of surgical masks and optimal windows opening cycles.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Alessandro Zivelonghi", - "author_inst": "ITCS \"Lorgna-Pindemonte\", Verona, Italy" - }, - { - "author_name": "Massimo Lai", - "author_inst": "Certara, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.12.18.20248439", "rel_title": "Spatial Allocation of Scarce Vaccine and Antivirals for COVID-19", @@ -1016692,6 +1017966,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.20.20248587", + "rel_title": "Predicting intention to receive COVID-19 vaccine among the general population using the Health Belief Model and the Theory of Planned Behavior Model", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.20.20248587", + "rel_abs": "BackgroundA novel coronavirus (COVID-19) was declared a global pandemic by the World Health Organization (WHO) in March, 2020. Until such time as a vaccine becomes available, it is important to identify the determining factors that influence the intention of the general public to accept a future COVID-19 vaccine. Consequently, we aim to explore behavioral-related factors predicting intention to receive COVID-19 vaccine among the general population using the Health Belief Model (HBM) and the Theory of Planned Behavior (TPB) model.\n\nMethodsAn online survey was conducted among adults aged 18 years and older from May 24 to June 24, 2020. The survey included socio-demographic and health-related questions, questions related to the HBM and TPB dimensions, and intention to receive COVID-19 vaccine. Associations between questionnaire variables and COVID-19 vaccination intention were assessed by univariate and multivariate analyses.\n\nResultsEighty percent of 398 eligible respondents stated their willingness to receive COVID-19 vaccine. A unified model including HBM and TPB covariates as well as demographic and health-related factors, proved to be a powerful predictor of intention to receive COVID-19 vaccine, explaining 78% of the variance (adjusted R2 = 0.78). Men (OR=4.35, 95% CI 1.58-11.93), educated respondents (OR=3.54, 95% CI 1.44-8.67) and respondents who had received the seasonal influenza vaccine in the previous year (OR=3.31, 95% CI 1.22-9.00) stated higher intention to receive COVID-19 vaccine. Participants were more likely to be willing to get vaccinated if they reported higher levels of perceived benefits of COVID-19 vaccine (OR=4.49, 95% CI 2.79-7.22), of perceived severity of COVID-19 infection (OR=2.36, 95% CI 1.58-3.51) and of cues to action (OR=1.99, 95% CI 1.38-2.87), according to HBM, and if they reported higher levels of subjective norms (OR=3.04, 95% CI 2.15-4.30) and self-efficacy (OR=2.05, 95% CI 1.54-2.72) according to TPB. Although half of the respondents reported they had not received influenza vaccine last year, 40% of them intended to receive influenza vaccine in the coming winter and 66% of them intended to receive COVID-19 vaccine.\n\nConclusionsProviding data on the public perspective and predicting intention for COVID-19 vaccination using HBM and TPB is important for health policy makers and healthcare providers and can help better guide compliance as the COVID-19 vaccine becomes available to the public.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Liora Shmueli", + "author_inst": "Bar-Ilan university" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.19.20248559", "rel_title": "Changes in UK hospital mortality in the first wave of COVID-19: the ISARIC WHO Clinical Characterisation Protocol prospective multicentre observational cohort study", @@ -1018652,69 +1019945,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.18.20248479", - "rel_title": "Population Changes in Seroprevalence among a Statewide Sample in the United States", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248479", - "rel_abs": "Antibody surveillance provides essential information for public health officials to work with communities to discuss the spread and impact of COVID-19. At the start of the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in the United States, diagnostic testing was limited with many asymptomatic and thus undetected cases. Irrespective of symptom severity, antibodies develop within two to three weeks after exposure and may persist 6 months or more.; Thus, antibody surveillance is an important tool for tracking trends in past infections across diverse populations. This study includes adults and children ([≥]12 years old) recruited from a statewide sample of past 2014-2020 Survey of the Health of Wisconsin (SHOW) participants. SHOW, an ongoing population-based health examination study including a randomly selected sample of households, partnered with the Wisconsin Department of Health Services and the Wisconsin State Laboratory of Hygiene to conduct longitudinal antibody surveillance using the Abbott Architect SARS-CoV-2 IgG antibody test, which detects antibodies against the nucleocapsid protein. Three WAVES of sample collection were completed in 2020-2021, tracking mid-summer, late fall, and early spring COVID-19 trends prior to vaccine availability. Crude estimates of seroprevalence in the total study population increased ten-fold from 1.4% during WAVE I to 11.5% in WAVE III. Within the statewide probability sample, weighted estimates increased from 1.6% (95% CI:0.6-2.5%), to 6.8% (95% CI:4.3-9.4%) in WAVE II and to 11.4% (95% CI:8.2, 14.6%) in WAVE III. Longitudinal trends in seroprevalence match statewide case counts. Local seroprevalence showed variation by state health region with increasing prevalence among higher income (>200% poverty income ratio), and rural health regions of the state seeing the highest increase in COVID-19 prevalence over time. Significant disparities in prevalence by racial and ethnic groups also exist, with greater than two times seroprevalence among Latino and black participants compared to non-Hispanic whites. This public health and academic partnership provides critical data for the ongoing pandemic response and lays the foundation for future research into longer-term immunity, health impacts and population-level disparities.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Kristen Malecki", - "author_inst": "Department of Population Health Sciences, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA." - }, - { - "author_name": "Maria Nikodemova", - "author_inst": "Department of Population Health Sciences, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA." - }, - { - "author_name": "Amy A. Schultz", - "author_inst": "Department of Population Health Sciences, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA." - }, - { - "author_name": "Andrew Bersch", - "author_inst": "Department of Population Health Sciences, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA." - }, - { - "author_name": "Matthew C Walsh", - "author_inst": "Department of Population Health Sciences, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA." - }, - { - "author_name": "Ajay K Sethi", - "author_inst": "Department of Population Health Sciences, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA." - }, - { - "author_name": "Paul Peppard", - "author_inst": "Department of Population Health Sciences, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA." - }, - { - "author_name": "Corinne Engelman", - "author_inst": "Department of Population Health Sciences, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA." - }, - { - "author_name": "Lisa Cadmus-Bertram", - "author_inst": "Department of Kinesiology, University of Wisconsin Madison, Madison, WI, USA." - }, - { - "author_name": "Nasia Safdar", - "author_inst": "Department of Medicine, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA." - }, - { - "author_name": "Allen Bateman", - "author_inst": "Wisconsin State Laboratory of Hygiene, University of Wisconsin Madison School of Medicine and Public Health, Madison, WI, USA." - }, - { - "author_name": "Ryan Westergaard", - "author_inst": "Wisconsin Department of Health Services, Madison, WI, USA. Department of Medicine, University of Wisconsin Madison School of Medicine and Public Health, Madison" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.18.20248509", "rel_title": "Assessment of effective mitigation and prediction of the spread of SARS-CoV-2 in Germany using demographic information and spatial resolution", @@ -1019062,6 +1020292,85 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.12.22.423893", + "rel_title": "Transcriptional and epi-transcriptional dynamics of SARS-CoV-2 during cellular infection", + "rel_date": "2020-12-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.22.423893", + "rel_abs": "SARS-CoV-2 uses subgenomic (sg)RNA to produce viral proteins for replication and immune evasion. We applied long-read RNA and cDNA sequencing to in vitro human and primate infection models to study transcriptional dynamics. Transcription-regulating sequence (TRS)-dependent sgRNA was upregulated earlier in infection than TRS-independent sgRNA. An abundant class of TRS-independent sgRNA consisting of a portion of ORF1ab containing nsp1 joined to ORF10 and 3UTR was upregulated at 48 hours post infection in human cell lines. We identified double-junction sgRNA containing both TRS-dependent and independent junctions. We found multiple sites at which the SARS-CoV-2 genome is consistently more modified than sgRNA, and that sgRNA modifications are stable across transcript clusters, host cells and time since infection. Our work highlights the dynamic nature of the SARS-CoV-2 transcriptome during its replication cycle. Our results are available via an interactive web-app at http://coinlab.mdhs.unimelb.edu.au/.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Jessie J.-Y. Chang", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Daniel Rawlinson", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Miranda E. Pitt", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "George Taiaroa", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Josie Gleeson", + "author_inst": "Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne" + }, + { + "author_name": "Chenxi Zhou", + "author_inst": "Department of Clinical Pathology, University of Melbourne," + }, + { + "author_name": "Francesca L. Mordant", + "author_inst": "Department of Clinical Pathology, University of Melbourne," + }, + { + "author_name": "Ricardo De Paoli-Iseppi", + "author_inst": "Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne" + }, + { + "author_name": "Leon Caly", + "author_inst": "Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Damian F. J. Purcell", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Tim P. Stinear", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Sarah L. Londrigan", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Michael B. Clark", + "author_inst": "Centre for Stem Cell Systems, Department of Anatomy and Neuroscience, The University of Melbourne" + }, + { + "author_name": "Deborah A. Williamson", + "author_inst": "Department of Microbiology and Immunology, University of Melbourne" + }, + { + "author_name": "Kanta Subbarao", + "author_inst": "WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Lachlan J M Coin", + "author_inst": "Department of Microbiology and Immunology, The University of Melbourne" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.22.423920", "rel_title": "Evolutionary tracking of SARS-CoV-2 genetic variants highlights intricate balance of stabilizing and destabilizing mutations", @@ -1020518,41 +1021827,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.18.20248405", - "rel_title": "Public adherence to governmental recommendations regarding quarantine and testing for COVID-19 in two Norwegian cohorts", - "rel_date": "2020-12-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248405", - "rel_abs": "BackgroundCombatting the COVID-19 pandemic relies at present on non-pharmacological interventions. Governments are using various approaches from general advice to full lockdown. There is a need to describe and understand adherence to public health actions.\n\nMethodsParticipants from two ongoing cohorts, the Norwegian Mother, Father and Child Cohort Study (MoBa) and The Norwegian Influenza Pregnancy Cohort (NorFlu), answered questionnaires every 14 days since March 2020. From the summer of 2020, testing for presence of SARS-CoV-2 became easily available. Recommendations were that respiratory symptoms should lead to testing, and that confirmed or suspected COVID-19 should be followed by quarantine. We estimated the adherence to these guidelines in responses from cohort participants in the period August to October 2020.\n\nResultsLess than 40% of men who were ill and less than 45% of women who were ill, tested themselves for SARS-CoV-2 during the same 14-day periods. Among subjects tested for COVID-19, about 53% of men and 59% of women reported quarantine. For subjects with a confirmed or suspected COVID-19 diagnosis, the proportions quarantined were 65% for men and 72% for women.\n\nConclusionsPublic adherence to governmental recommendations regarding testing and quarantine were lower than expected in a country with high trust in government. This leaves considerable room for improvement in adherence, possibly reducing the need for more restrictive interventions.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ellen \u00d8en Carlsen", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Ida Henriette Caspersen", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Lill Trogstad", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "H\u00e5kon Gjessing", - "author_inst": "University of Bergen; Norwegian Institute of Public Health" - }, - { - "author_name": "Per Magnus", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.19.423537", "rel_title": "An expedited approach towards the rationale design of non-covalent SARS-CoV-2 main protease inhibitors with in vitro antiviral activity", @@ -1020939,6 +1022213,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.19.423597", + "rel_title": "A comprehensive transcriptome analysis reveals broader but weaker host response of SARS-CoV-2 than SARS-CoV", + "rel_date": "2020-12-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.19.423597", + "rel_abs": "COVID-19, which has resulted a worldwide health crisis with more than 74.9 million confirmed cases worldwide by December 2020, is caused by a newly emerging coronavirus identified and named SARS-CoV-2 in February in Wuhan, China. Experiences in defeating SARS, which infested during 2002-2003, can be used in treating the new disease. However, comparative genomics and epidemiology studies have shown much difference between SARS-CoV and SARS-CoV-2, which underlies the different clinical features and therapies in between those two diseases. Further studies comparing transcriptomes infected by these two viruses to uncover the differences in host responses would be necessary. Here we conducted a comprehensive transcriptome analysis of SARS-CoV and SARS-CoV-2-infected human cell lines, including Caco-2, Calu-3, H1299. Clustering analysis and expression of ACE2 show that SARS-CoV-2 has broader but weaker infection, where the largest discrepancy occurs in the epithelial lung cancer cell, Calu-3. SARS-CoV-2 genes also show less tissue specificity than SARS-CoV genes. Furthermore, we detected more general but moderate immune responses in SARS-CoV-2 infected transcriptomes by comparing weighted gene co-expression networks and modules. Our results suggest a different immune therapy and treatment scheme for COVID-19 patients than the ones used on SARS patients. The wider but weaker permissiveness and host responses of virus infection may also imply a long-term existence of SARS-CoV-2 among human populations.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Chi Sum Leung", + "author_inst": "AmazingX Academy" + }, + { + "author_name": "Songhong Xie", + "author_inst": "AmazingX Academy" + }, + { + "author_name": "Jiali Feng", + "author_inst": "AmazingX Academy" + }, + { + "author_name": "Dongjing Chen", + "author_inst": "AmazingX Academy" + }, + { + "author_name": "Aimei Dai", + "author_inst": "School of Life Science, Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.18.20248455", "rel_title": "The impact of the first UK Covid-19 lockdown on carers and people living with low prevalence dementia: results from the Rare Dementia Support survey", @@ -1022547,109 +1023856,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.19.20248172", - "rel_title": "Blood group A Secretors are associated with a higher risk of COVID-19 cardiovascular disease complications", - "rel_date": "2020-12-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.19.20248172", - "rel_abs": "The SARS-CoV-2 virus causes COVID-19, an infection capable of causing severe disease and death but which may also be asymptomatic or oligosymptomatic in many individuals. While several risk factors, including age, have been described, the mechanisms of this variation are poorly understood. Several studies have described associations between blood group and COVID-19 severity, while others do not. Expression of ABO glycans on secreted proteins and non-erythroid cells is controlled by a fucosyltransferase (FUT2). Inactivating mutations result in a non-secretor phenotype which is known to protect against some viral infections. We investigated whether ABO or secretor status was associated with COVID-19 severity. Data combined from healthcare records and laboratory tests (n=275) of SARS-CoV-2 PCR positive patients hospitalised with COVID-19, confirmed higher than expected numbers of blood group A individuals compared to O (RR=1.24, CI 95% [1.05,1.47], P=0.0111). There was also a significant association between group A and COVID-19-related cardiovascular complications (RR=2.56, CI 95% [1.43,4.55], P=0.0011) which is independent of gender. Molecular analysis of phenotype revealed that group A patients who are non-secretors are significantly less likely to be hospitalised than secretors. In a larger cohort of 1000 convalescent plasma donors, among whom the majority displayed COVID-19 symptoms and only a small minority required hospitalisation, group A non-secretors were slightly over-represented. Our findings indicate that group A non-secretors are not resistant to infection by SARS-CoV-2, but they are likely to experience a less severe form of its associated disease.\n\nKey PointsO_LIBlood group type A is associated with an increased risk of cardiovascular complications in COVID-19 patients.\nC_LIO_LIFUT2 \"non-secretor\" status reduces the risk of severe COVID-19 outcomes in patients with blood group A.\nC_LI", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Tosti J Mankelow", - "author_inst": "Bristol Institute for Transfusion Sciences, NHSBT, North Bristol Park, Filton, Bristol BS34 7QH, United Kingdom" - }, - { - "author_name": "Belinda K Singleton", - "author_inst": "Bristol Institute for Transfusion Sciences, NHSBT, North Bristol Park, Filton, Bristol BS34 7QH, United Kingdom" - }, - { - "author_name": "Pedro L Moura", - "author_inst": "Center for Hematology and Regenerative Medicine, Department of Medicine (MedH), Karolinska Institutet, Stockholm, Sweden" - }, - { - "author_name": "Christian J Stevens-Hernandez", - "author_inst": "Bristol Institute for Transfusion Sciences, NHSBT, North Bristol Park, Filton, Bristol BS34 7QH, United Kingdom" - }, - { - "author_name": "Nicola M Cogan", - "author_inst": "Bristol Institute for Transfusion Sciences, NHSBT, North Bristol Park, Filton, Bristol BS34 7QH, United Kingdom" - }, - { - "author_name": "Gyongyver Gyorffy", - "author_inst": "Bristol Institute for Transfusion Sciences, NHSBT, North Bristol Park, Filton, Bristol BS34 7QH, United Kingdom" - }, - { - "author_name": "Sabine Kupzig", - "author_inst": "Bristol Institute for Transfusion Sciences, NHSBT, North Bristol Park, Filton, Bristol BS34 7QH, United Kingdom" - }, - { - "author_name": "Luned Nicholas", - "author_inst": "5Acute Medical Unit, Southmead Hospital, North Bristol NHS Trust, Bristol, BS10 5NB" - }, - { - "author_name": "Claire Asby", - "author_inst": "Acute Medical Unit, Southmead Hospital, North Bristol NHS Trust, Bristol, BS10 5NB" - }, - { - "author_name": "Jennifer Pooley", - "author_inst": "Acute Medical Unit, Southmead Hospital, North Bristol NHS Trust, Bristol, BS10 5NB" - }, - { - "author_name": "Gabriella Ruffino", - "author_inst": "Acute Medical Unit, Southmead Hospital, North Bristol NHS Trust, Bristol, BS10 5NB" - }, - { - "author_name": "Faroakh Hossseini", - "author_inst": "Acute Medical Unit, Southmead Hospital, North Bristol NHS Trust, Bristol, BS10 5NB" - }, - { - "author_name": "Fiona Moghaddas", - "author_inst": "Acute Medical Unit, Southmead Hospital, North Bristol NHS Trust, Bristol, BS10 5NB" - }, - { - "author_name": "Marie Attwood", - "author_inst": "Infection Sciences, Southmead Hospital, North Bristol NHS Trust, BS10 5NB" - }, - { - "author_name": "Alan Noel", - "author_inst": "Infection Sciences, Southmead Hospital, North Bristol NHS Trust, BS10 5NB" - }, - { - "author_name": "Alex Cooper", - "author_inst": "Infection Sciences, Southmead Hospital, North Bristol NHS Trust, BS10 5NB" - }, - { - "author_name": "David Arnold", - "author_inst": "Academic Respiratory Unit, Southmead Hospital, North Bristol NHS Trust, Bristol, BS10 5NB" - }, - { - "author_name": "Fergus Hamilton", - "author_inst": "Infection Sciences, Southmead Hospital, North Bristol NHS Trust, BS10 5NB" - }, - { - "author_name": "Catherine Hyams", - "author_inst": "Population Health Sciences, University of Bristol, Bristol, UK" - }, - { - "author_name": "Adam Finn", - "author_inst": "Bristol Children's Vaccine Centre, University of Bristol, Upper Maudlin Street, Bristol BS2 8AE, UK" - }, - { - "author_name": "Ashley Mark Toye", - "author_inst": "University of Bristol, School of Biochemistry, Biomedical Sciences Building, University Walk, Bristol. BS8 1TD" - }, - { - "author_name": "David J Anstee", - "author_inst": "Bristol Institute for Transfusion Sciences, NHSBT, North Bristol Park, Filton, Bristol BS34 7QH, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2020.12.18.20248398", "rel_title": "SARS-CoV-2 infection, risk perception, behaviour, and preventive measures at schools in Berlin, Germany, during the early post-lockdown phase: A cross-sectional study", @@ -1022929,6 +1024135,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.18.20248434", + "rel_title": "Excess deaths among Latino people in California during the COVID-19 pandemic", + "rel_date": "2020-12-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248434", + "rel_abs": "BackgroundLatino people in the US are experiencing higher excess deaths during the COVID-19 pandemic than any other racial/ethnic group, but it is unclear which subgroups within this diverse population are most affected. Such information is necessary to target policies that prevent further excess mortality and reduce inequities.\n\nMethodsUsing death certificate data for January 1, 2016 through February 29, 2020 and time-series models, we estimated the expected weekly deaths among Latino people in California from March 1 through October 3, 2020. We quantified excess mortality as observed minus expected deaths and risk ratios (RR) as the ratio of observed to expected deaths. We considered subgroups defined by age, sex, place of birth, education, occupation, and combinations of these factors.\n\nFindingsDuring the first seven months of the pandemic, Latino deaths in California exceeded expected deaths by 10,316, a 31% increase. Excess death rates were greatest for individuals born in Mexico (RR 1.44; 95% PI, 1.41, 1.48) or Central America (RR 1.49; 95% PI, 1.37, 1.64), with less than a high school degree (RR 1.41; 95% PI, 1.35, 1.46), or in food-and-agriculture (RR 1.60; 95% PI, 1.48, 1.74) or manufacturing occupations (RR 1.59; 95% PI, 1.50, 1.69). Immigrant disadvantages in excess death were magnified among working-age Latinos in essential occupations.\n\nInterpretationThe pandemic has disproportionately impacted mortality among Latino immigrants and Latinos in unprotected essential jobs; Interventions to reduce these disparities should include early vaccination, workplace safety enforcement, and expanded access to medical care.\n\nFundingNational Institute on Aging; UCSF\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSSeveral articles have suggested all-cause excess mortality estimates are superior to official COVID-19 counts for assessing the impact of the pandemic on marginalized populations that lack access to testing and healthcare. We searched PubMed, Google scholar, and the medRxiv preprint database through December 22, 2020 for studies of (\"excess mortality\" or \"excess death\") AND (\"COVID-19\" or \"coronavirus\") set in the United States and we identified two empirical studies with estimates of excess mortality among Latinos during the pandemic. The study set in California (from our research team) found per capita excess mortality was highest among Black and Latino people. The national study found percent excess mortality was significantly higher among Latino people than any other racial/ethnic group. Neither study further disaggregated the diverse Latino population or provided subgroup estimates to clarify why excess pandemic mortality is so high in this population. In the U.S., official COVID-19 statistics are rarely disaggregated by place of birth, education, or occupation which has resulted in a lack of evidence of how these factors have impacted mortality during the pandemic. No study to date of excess mortality in the U.S. has provided estimates for immigrant or occupational subgroups.\n\nAdded value of this studyOur population-based observational study of all-cause mortality during the COVID-19 pandemic provides the first estimates of within-group heterogeneity among the Latino population in California - one of the populations hardest hit by COVID-19 in the U.S. We provide the first subgroup estimates by place of birth and occupational sector, in addition to combined estimates by foreign-birth and participation in an essential job and education. In doing so, we reveal that Latino immigrants in essential occupations have the highest risk of excess death during the pandemic among working-age Latinos. We highlight the heightened risk of excess mortality associated with food/agriculture and manufacturing occupational sectors, essential sectors in which workers may lack COVID-19 protections.\n\nImplications of all the available evidenceOur study revealed stark disparities in excess mortality during the COVID-19 pandemic among Latinos, pointing to the particularly high vulnerability of Latino immigrants and Latinos in essential jobs. These findings may offer insight into the disproportionate COVID-19 mortality experienced by immigrants or similarly marginalized groups in other contexts. Interventions to reduce these disparities should include policies enforcing occupational safety, especially for immigrant workers, early vaccination, and expanded access to medical care.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Alicia R. Riley", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + }, + { + "author_name": "Yea-Hung Chen", + "author_inst": "Institute for Global Health Sciences, University of California, San Francisco" + }, + { + "author_name": "Ellicott C. Matthay", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + }, + { + "author_name": "M. Maria Glymour", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + }, + { + "author_name": "Jacqueline M. Torres", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + }, + { + "author_name": "Alicia Fernandez", + "author_inst": "Department of Medicine, University of California, San Francisco" + }, + { + "author_name": "Kirsten Bibbins-Domingo", + "author_inst": "Department of Epidemiology and Biostatistics, University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.18.20248449", "rel_title": "Coinfection with Respiratory Pathogens in COVID-19 in Korea", @@ -1024441,33 +1025690,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.15.20248278", - "rel_title": "Modelling of COVID-19 vaccination strategies and herd immunity, in scenarios of limited and full vaccine supply in NSW, Australia.", - "rel_date": "2020-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.15.20248278", - "rel_abs": "Several vaccines for SARS-CoV-2 are expected to be available in Australia in 2021. Initial supply is likely to be limited, and will require a judicious vaccination strategy until supply is unrestricted. If vaccines have efficacy as post-exposure prophylaxis (PEP) in contacts, this provides more policy options. We used a deterministic mathematical model of epidemic response with limited supply (age-targeted or ring vaccination) and mass vaccination for the State of New South Wales (NSW) in Australia. For targeted vaccination, the effectiveness of vaccinating health workers, young people and older adults was compared. For mass vaccination, we tested varying vaccine efficacy (VE) and distribution capacities. With a limited vaccine stockpile of 1 million doses in NSW, if there is efficacy as PEP, the most efficient way to control COVID-19 will be ring vaccination, however at least 90% of contacts per case needs to be traced and vaccinated. Health worker vaccination is required for health system resilience. Age based strategies with restricted doses make minimal impact on the epidemic, but vaccinating older people prevents more deaths. Herd immunity can only be achieved with mass vaccination. With 90% VE, herd immunity can be achieved by vaccinating 66% of the population. A vaccine with less than 70% VE cannot achieve herd immunity and will result in ongoing risk of outbreaks. For mass vaccination, distributing at least 60,000 doses per day is required to achieve control. Slower rates of vaccination will result in the population living with COVID-19 longer, and higher cases and deaths.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Chandini Raina MacIntyre", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Valentina Costantino", - "author_inst": "The Biosecurity Program, The Kirby Institute, University of New South Wales" - }, - { - "author_name": "Mallory J Trent", - "author_inst": "The Biosecurity Program, The Kirby Institute, The University of New South Wales" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.16.20248157", "rel_title": "The Wood equation allows consistent fitting of individual antibody responses profiles in Zika virus or SARS-CoV-2 infected patients", @@ -1024867,6 +1026089,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.12.17.20248382", + "rel_title": "Sub-national forecasts of COVID-19 vaccine acceptance across the UK: a large-scale cross-sectional spatial modelling study", + "rel_date": "2020-12-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.17.20248382", + "rel_abs": "The rollout of COVID-19 vaccines has begun to at-risk populations around the world. It is currently unclear whether rejection of the vaccine will pose challenges for achieving herd/community immunity either through large-scale rejection or localised pockets. Here we predict uptake of the vaccine at unprecedented spatial resolution across the UK using a large-scale survey of over 17,000 individuals. Although the majority of the UK population would likely take the vaccine, there is substantial heterogeneity in uptake intent across the UK. Large urban areas, including London and North West England, females, Black or Black British ethnicities, and Polish-speakers are among the least accepting. This study helps identify areas and socio-demographic groups where vaccination levels may not reach those levels required for herd immunity. Identifying clusters of non-vaccinators is extremely important in the context of achieving herd immunity as vaccination \"cold-spots\" can amplify epidemic spread and disproportionately increase vaccination levels required for herd protection.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Alex de Figueiredo", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.15.20247981", "rel_title": "SIREN protocol: Impact of detectable anti-SARS-CoV-2 on the subsequent incidence of COVID-19 in 100,000 healthcare workers: do antibody positive healthcare workers have less reinfection than antibody negative healthcare workers?", @@ -1026127,49 +1027368,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.12.15.20248256", - "rel_title": "Covid Fast Fax: A system for real-time triage of Covid-19 case report faxes", - "rel_date": "2020-12-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.15.20248256", - "rel_abs": "The scale and speed of the COVID-19 pandemic has strained many parts of the national healthcare infrastructure, including communicable disease monitoring and prevention. Many local health departments now receive hundreds or thousands of COVID-19 case reports a day. Many arrive via faxed handwritten forms, often intermingled with other faxes sent to a general fax line, making it difficult to rapidly identify the highest priority cases for outreach and monitoring. We present an AI-based system capable of real-time identification and triage of handwritten faxed COVID-19 forms. The system relies on two models: one model to identify which received pages correspond to case report forms, and a second model to extract information from the set of identified case reports. We evaluated the system on a set of 1,224 faxes received by a local health department over a two-week period. For the 88% of faxes of sufficient quality, the system detects COVID-19 reports with high precision, 0.98, and high recall, 0.91. Among all received COVID-19 faxes, the system identifies high priority cases with a specificity of 0.87, a precision of 0.46 and recall of 0.83. Our system can be adapted to new forms, after a brief training period. Covid Fast Fax can support local health departments in their efforts to control the spread of COVID-19 and limit its impact on the community. The tool is freely available.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Adam Lavertu", - "author_inst": "Stanford University" - }, - { - "author_name": "Alison Stribling", - "author_inst": "Contra Costa Health Services" - }, - { - "author_name": "Matt White", - "author_inst": "Contra Costa Health Services" - }, - { - "author_name": "Greg McInnes", - "author_inst": "Stanford University" - }, - { - "author_name": "Russ B Altman", - "author_inst": "Stanford University" - }, - { - "author_name": "Rajiv Pramanik", - "author_inst": "Contra Costa Health Services" - }, - { - "author_name": "Amit Kaushal", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2020.12.15.20247999", "rel_title": "Exposure to Renin-Angiotensin System Inhibitors Is Associated with Reduced Mortality of Older Hypertensive Covid-19 Patients", @@ -1026465,6 +1027663,45 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.12.17.423130", + "rel_title": "Suppression of miR-155 attenuates lung cytokine storm induced by SARS-CoV-2 infection in human ACE2-transgenic mice", + "rel_date": "2020-12-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.17.423130", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is a recent global pandemic. It is a deadly human viral disease, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with a high rate of infection, morbidity and mortality. Therefore, there is a great urgency to develop new therapies to control, treat and prevent this disease. Endogenous microRNAs (miRNAs, miRs) of the viral host are key molecules in preventing viral entry and replication, and building an antiviral cellular defense. Here, we have analyzed the role of miR-155, one of the most powerful drivers of host antiviral responses including immune and inflammatory responses, in the pathogenicity of SARS-CoV-2 infection. Subsequently, we have analyzed the potency of anti-miR-155 therapy in a COVID-19 mouse model (mice transgenic for human angiotensin I-converting enzyme 2 receptor (tg-mice hACE2)). We report for the first time that miR-155 expression is elevated in COVID-19 patients. Further, our data indicate that the viral load as well as miR-155 levels are higher in male relative to female patients. Moreover, we find that the delivery of anti-miR-155 to SARS-CoV-2-infected tg-mice hACE2 effectively suppresses miR-155 expression, and leads to improved survival and clinical scores. Importantly, anti-miR-155-treated tg-mice hACE2 infected with SARS-CoV-2 not only exhibit reduced levels of pro-inflammatory cytokines, but also have increased anti-viral and anti-inflammatory cytokine responses in the lungs. Thus, our study suggests anti-miR-155 as a novel therapy for mitigating the lung cytokine storm induced by SARS-CoV-2 infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Dharmendra Kumar Soni", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Juan Cabrera-Luque", + "author_inst": "GeneDx" + }, + { + "author_name": "Swagata Kar", + "author_inst": "Bioqual Inc." + }, + { + "author_name": "Chaitali Sen", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Joseph Devaney", + "author_inst": "GeneDx" + }, + { + "author_name": "Roopa Biswas", + "author_inst": "Uniformed Services University of the Health Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.16.423166", "rel_title": "Molecular diversity analysis of the spike glycoprotein (S) gene from Hong Kong - China", @@ -1027597,33 +1028834,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.12.15.20248238", - "rel_title": "It makes you realise your own mortality: A qualitative study on mental health of older adults in the UK during COVID-19", - "rel_date": "2020-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.15.20248238", - "rel_abs": "BackgroundOlder adults have been disproportionately affected by COVID-19, with high fatalities and health complications reported. Adults over the age of 70 in the UK were advised to self-isolate for 3 months early during the pandemic and it is unclear which factors influenced their experiences during this time.\n\nObjectiveThe aim of this qualitative study was to explore factors that threatened and protected the wellbeing of older adults living in the UK during the COVID-19 pandemic.\n\nMethodsWe undertook semi-structured interviews with 20 adults aged over 70. Purposive sampling methods were used to increase diversity within the group. Transcripts were analysed using thematic analysis.\n\nResultsParticipants were aged 72-93, 9 women and 11 men, 80% were White British, 40% lived alone. We identified 2 superordinate themes, including (1) Threats to wellbeing: mortality concerns, grief and loss of normal life, restricted health service access, COVID-19 concerns, and restricted access to activities that protect wellbeing. (2) Factors protective of wellbeing: slower pace of life, maintaining routine, socialising, and use of past coping skills. Many participants drew on their resilience and life experience to self-manage fear and uncertainty associated with the pandemic, using their time during lockdown to reflect or organise end-of-life affairs.\n\nConclusionsThis study provides evidence that while older adults experienced challenges, many were resilient against COVID-19 restrictions despite early concerns of mental health consequences. Our findings highlight the importance of maintaining access to essentials to promote feelings of normality and social support to help reduce uncertainty in times of pandemics.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Alison Ruth McKinlay", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - }, - { - "author_name": "Alexandra Burton", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.15.20248251", "rel_title": "Risk of Stress/Depression and Functional Impairment in Denmark Immediately Following a COVID-19 Shutdown", @@ -1028187,6 +1029397,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.14.20248181", + "rel_title": "Predicting the need for escalation of care or death from repeated daily clinical observations and laboratory results in patients with SARS-CoV-2 during 2020: a retrospective population-based cohort study from the United Kingdom", + "rel_date": "2020-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248181", + "rel_abs": "ObjectivesCurrently used prognostic tools for patients with SARS-CoV-2 infection are based on clinical and laboratory parameters measured at a single point in time, usually on admission. We aimed to determine how dynamic changes in clinical and laboratory parameters relate to SARS-CoV-2 prognosis.\n\nDesignretrospective, observational cohort study using routinely collected clinical data to model the dynamic change in prognosis of SARS-CoV-2.\n\nSettinga single, large hospital in England.\n\nParticipantsall patients with confirmed SARS-CoV-2 admitted to Nottingham University Hospitals (NUH) NHS Trust, UK from 1st February 2020 until 30th November 2020.\n\nMain outcome measuresIntensive Care Unit (ICU) admission, death and discharge from hospital.\n\nStatistical MethodsWe split patients into 1st (admissions until 30th June) and 2nd (admissions thereafter) waves. We incorporated all clinical observations, blood tests and other covariates from electronic patient records and follow up until death or 30 days from the point of hospital discharge. We modelled daily risk of admission to ICU or death with a time varying Cox proportional hazards model.\n\nResults2,964 patients with confirmed SARS-CoV-2 were included. Of 1,374 admitted during the 1st wave, 593 were eligible for ICU escalation, and 466 had near complete ascertainment of all covariates at admission. Our validation sample included 1,590 confirmed cases, of whom 958 were eligible for ICU admission. Our model had good discrimination of daily need for ICU admission or death (C statistic = 0.87 (IQR 0.85-0.90)) and predicted this daily prognosis better than previously published scores (NEWS2, ISCARIC 4C). In validation in the 2nd wave the score overestimated escalation (calibration slope 0.55), whilst retaining a linear relationship and good discrimination (C statistic = 0.88 (95% CI 0.81 -0.95)).\n\nConclusionsA bespoke SARS-CoV-2 escalation risk prediction score can predict need for clinical escalation better than a generic early warning score or a single estimation of risk at admission.\n\nWhat is already known on this topicSARS-CoV-2 is a recently emerged viral infection, which presents typically with flu like symptoms, can have severe sequelae and has caused a pandemic during 2020.\n\nA number of risk factors for poor outcomes including obesity, age and comorbidity have been recognized.\n\nRisk scores have been developed to stratify risk of poor outcome for patients with SARS-CoV-2 at admission, but these do not take account of dynamic changes in severity of disease on a daily basis.\n\nWhat this study addsWe have developed a dynamic risk score to predict escalation to ICU or death within the next 24 hours.\n\nOur score has good discrimination between those who will and not require ICU admission (or die) in both our derivation and validation cohorts.\n\nOur bespoke SARS-CoV-2 escalation risk prediction score can predict need for clinical escalation better than a generic early warning score or a single estimation of risk at admission.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Colin J Crooks", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Joe West", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Andrew Fogarty", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Joanne R Morling", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Matthew J Grainge", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Sherif Gonem", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Mark Simmonds", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Andrea Race", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Irene Juurlink", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Stephen Briggs", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Simon Cruikshank", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Susan Hammond-Pears", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Timothy R Card", + "author_inst": "University of Nottingham" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.15.20248279", "rel_title": "Shared genetic etiology between idiopathic pulmonary fibrosis and COVID-19 severity", @@ -1029459,81 +1030736,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.13.20248129", - "rel_title": "Using Mobility Data to Understand and Forecast COVID19 Dynamics", - "rel_date": "2020-12-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.13.20248129", - "rel_abs": "Disease dynamics, human mobility, and public policies co-evolve during a pandemic such as COVID-19. Understanding dynamic human mobility changes and spatial interaction patterns are crucial for understanding and forecasting COVID-19 dynamics. We introduce a novel graph-based neural network(GNN) to incorporate global aggregated mobility flows for a better understanding of the impact of human mobility on COVID-19 dynamics as well as better forecasting of disease dynamics. We propose a recurrent message passing graph neural network that embeds spatio-temporal disease dynamics and human mobility dynamics for daily state-level new confirmed cases forecasting. This work represents one of the early papers on the use of GNNs to forecast COVID-19 incidence dynamics and our methods are competitive to existing methods. We show that the spatial and temporal dynamic mobility graph leveraged by the graph neural network enables better long-term forecasting performance compared to baselines.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Lijing Wang", - "author_inst": "University of Virginia" - }, - { - "author_name": "Xue Ben", - "author_inst": "Google" - }, - { - "author_name": "Aniruddha Adiga", - "author_inst": "University of Virginia" - }, - { - "author_name": "Adam Sadilek", - "author_inst": "Google" - }, - { - "author_name": "Ashish Tendulkar", - "author_inst": "Google" - }, - { - "author_name": "Srinivasan Venkatramanan", - "author_inst": "University of Virginia" - }, - { - "author_name": "Anil Vullikanti", - "author_inst": "University of Virginia" - }, - { - "author_name": "Gaurav Aggarwal", - "author_inst": "Google" - }, - { - "author_name": "Alok Talekar", - "author_inst": "Google" - }, - { - "author_name": "Jiangzhuo Chen", - "author_inst": "University of Virginia" - }, - { - "author_name": "Bryan Leroy Lewis", - "author_inst": "University of Virginia" - }, - { - "author_name": "Samarth Swarup", - "author_inst": "University of Virginia" - }, - { - "author_name": "Amol Kapoor", - "author_inst": "Google" - }, - { - "author_name": "Milind Tambe", - "author_inst": "Harvard University" - }, - { - "author_name": "Madhav Marathe", - "author_inst": "University of Virginia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.14.422601", "rel_title": "Rapid SARS-CoV-2 Detection and Classification Using Phase Imaging with Computational Specificity", @@ -1029853,6 +1031055,33 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.12.14.422793", + "rel_title": "Genomic diversity analysis of SARS-CoV-2 genomes in Rwanda", + "rel_date": "2020-12-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.14.422793", + "rel_abs": "COVID-19 (Coronavirus disease 2019) is an emerging pneumonia-like respiratory disease of humans and is recently spreading across the globe.\n\nObjectiveTo analyze the genome sequence of SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) isolated from Rwanda with other viral strains from African countries.\n\nMethodsWe downloaded 75 genomes sequences of clinical SARS-CoV-2 from the GISAID (global initiative on sharing all influenza data) database and we comprehensively analyzed these SARS-CoV-2 genomes sequences alongside with Wuhan SARS-CoV-2 sequences as the reference strains.\n\nResultsWe analyzed 75 genomes sequences of SARS-CoV-2 isolated in different African countries including 10 samples of SARS-CoV-2 isolated in Rwanda between July and August 2020. The phylogenetic analysis of the genome sequence of SARS-CoV-2 revealed a strong identity with reference strains between 90-95%. We identified a missense mutation in four proteins including orf1ab polyprotein, NSP2, 2-O-ribose methyltransferase and orf1a polyprotein. The most common changes in the base are C > T. We also found that all clinically SARS-CoV-2 isolated from Rwanda had genomes belonging to clade G and lineage B.1.\n\nConclusionsTracking the genetic evolution of SARS-CoV-2 over time is important to understand viral evolution pathogenesis. These findings may help to implement public health measures in curbing COVID-19 in Rwanda.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Nzungize Lambert", + "author_inst": "Synthetic Biology Rwanda" + }, + { + "author_name": "Ndishimye Pacifique", + "author_inst": "Rwanda Joint Task Force COVID-19, Rwanda Biomedical Center, Ministry of Health, Kigali, Rwanda." + }, + { + "author_name": "Fathiah Zakham", + "author_inst": "Laboratory of Virology, University of Helsinki, Helsinki 00014, Finland." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.12.10.20245944", "rel_title": "Azithromycin in Hospitalised Patients with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", @@ -1031277,49 +1032506,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.12.12.20248102", - "rel_title": "How the COVID-19 pandemic has adversely affected the economics of U.S. emergency care", - "rel_date": "2020-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.12.20248102", - "rel_abs": "ObjectiveWe describe how the coronavirus (COVID-19) pandemic impacted emergency department (ED) economics, acuity, and staffing.\n\nMethodsWe conducted an observational study of visits during January to September 2020 compared to 2019 in 136 EDs staffed by a national emergency medicine group. We created ratios of three-week moving averages for 2020 visits, acuity, costs divided by 2019 moving averages, by age and ED size. We tabulated reductions in clinician hours and FTEs compared to early 2020 staffing.\n\nResults2020-2019 ED visit ratios declined in March nadiring mid-April for both adults (to 0.60) and children (to 0.30) and rose thereafter but remained below 2019 levels through September 2020. The ratio of adult RVUs/visit rose to 1.1 for adults and 1.2 for children in the early pandemic, falling to 1.04 and 1.1 through September. The ratio of direct salary expenses in freestanding (FSED) and small EDs declined less dramatically than in medium and large EDs. Clinical revenues in medium and large EDs declined more sharply and recovered slowly but plateaued well below 2019 levels. By September 2020, expenses were still higher than revenues for small EDs, similar for FSEDs, and somewhat higher for medium and large EDs. During the pandemic, physician hours fell 15% and APP hours 27% during COVID-19 translating to 174 lost physician and 193 lost APP FTEs.\n\nConclusionThe COVID-19 pandemic reduced ED visits and increased acuity in the first 7 months of the pandemic, leading to a contraction of the ED workforce, and threatening ED economics, more so in small and FSEDs.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jesse M Pines", - "author_inst": "US Acute Care Solutions" - }, - { - "author_name": "Mark S Zocchi", - "author_inst": "Brandeis University" - }, - { - "author_name": "Bernard S Black", - "author_inst": "Northwestern University" - }, - { - "author_name": "Rebecca Kornas", - "author_inst": "US Acute Care Solutions" - }, - { - "author_name": "Pablo Celedon", - "author_inst": "US Acute Care Solutions" - }, - { - "author_name": "Ali Moghtaderi", - "author_inst": "George Washington University" - }, - { - "author_name": "Arvind Venkat", - "author_inst": "Allegheny Health Network" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.12.14.20248117", "rel_title": "Predicting the Peak and COVID-19 trend in six high incidence countries: A study based on Modified SEIRD model", @@ -1031607,6 +1032793,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.14.20248160", + "rel_title": "Acceptability and feasibility of strategies to shield the vulnerable during the COVID-19 outbreak: a qualitative study in six Sudanese communities", + "rel_date": "2020-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20248160", + "rel_abs": "BackgroundShielding of high-risk groups from coronavirus disease (COVID-19), either within their households or safe communal structures, has been suggested as a realistic alternative to severe movement restrictions in response to the COVID-19 epidemic in low-income countries. To our knowledge, this concept has not been tested or evaluated in resource-poor settings. This study aimed to explore the acceptability and feasibility of strategies to shield persons at higher risk of severe COVID-19 outcomes, during the COVID-19 epidemic in six communities in Sudan.\n\nMethodsWe purposively sampled participants from six communities, illustrative of urban, rural and forcibly-displaced settings. In-depth telephone interviews were held with 59 members of households with one or more members at higher risk of severe COVID-19 outcomes. Follow-up interviews were held with 30 community members after movement restrictions were eased across the country. All interviews were audio-recorded, transcribed verbatim, and analysed using a two-stage deductive and inductive thematic analysis.\n\nResultsMost participants were aware that some people are at higher risk of severe COVID-19 outcomes but were unaware of the concept of shielding. Most participants found shielding acceptable and consistent with cultural inclinations to respect elders and protect the vulnerable. However, extra-household shielding arrangements were mostly seen as socially unacceptable. Participants reported feasibility concerns related to the social isolation of shielded persons and loss of income for shielding families. The acceptability and feasibility of shielding strategies were reduced after movement restrictions were eased, as participants reported lower perception of risk in their communities and increased pressure to comply with social commitments outside the house.\n\nConclusionShielding is generally acceptable in the study communities. Acceptability is influenced by feasibility, and by contextual changes in the epidemic and associated policy response. The promotion of shielding should capitalise on the cultural and moral sense of duty towards elders and vulnerable groups. Communities and households should be provided with practical guidance to implement feasible shielding options. Households must be socially, psychologically and financially supported to adopt and sustain shielding effectively.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nada Abdelmagid", + "author_inst": "London School of Hygiene and Tropical Medicine, (Department of Infectious Disease Epidemiology), London, (London), United Kingdom / Sudan COVID-19 Research Grou" + }, + { + "author_name": "Salma A.E. Ahmed", + "author_inst": "Independent public health researcher, Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Nazik Nurelhuda", + "author_inst": "University of Khartoum, Faculty of Dentistry, Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Israa Zainalabdeen", + "author_inst": "Y-PEER Sudan, Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Aljaile Ahmed", + "author_inst": "Y-PEER Sudan, Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Mahmoud Ali Fadlallah", + "author_inst": "Asian Institute of Technology, Bangkok, (Bangkok), Thailand / Public Health Institute (PHI), Khartoum, (Khartoum), Sudan / Sudan COVID-19 Research Group" + }, + { + "author_name": "Maysoon Dahab", + "author_inst": "London School of Hygiene and Tropical Medicine, (Department of Infectious Disease Epidemiology), London, (London), United Kingdom / Sudan COVID-19 Research Grou" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.11.20247262", "rel_title": "COVID-19 in persons affected by Hansen's disease in Brazil", @@ -1033067,20 +1034296,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.08.20246009", - "rel_title": "Impact of mass testing during an epidemic rebound of SARS-CoV-2: A modelling study", - "rel_date": "2020-12-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20246009", - "rel_abs": "We used a mathematical model to evaluate the impact of mass testing in the control of SARS-CoV-2. Under optimistic assumptions, we find that one round of mass testing may reduce daily infections by up to 20-30%. As a consequence, very frequent testing would be required to control a quickly growing epidemic if other control measures were to be relaxed. Mass testing is most relevant when epidemic growth remains limited, thanks to a combination of interventions.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.11.422139", "rel_title": "The MERS-CoV receptor gene is among COVID-19 risk factors inherited from Neandertals", @@ -1033348,6 +1034563,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2020.11.22.20235184", + "rel_title": "Neurological Disorders associated with COVID-19 Hospital Admissions : Experience of a Single Tertiary Healthcare Centre", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.22.20235184", + "rel_abs": "BackgroundEarly reports have detailed a range of neurological symptoms in patients with the SARS-CoV-2 infection. However, there is a lack of detailed description and incidence of the neurological disorders amongst hospitalized COVID-19 patients. We describe a range of neurological disorders (other than non-specific neurological symptoms), including their clinical, radiological and laboratory findings, encountered in our cohort of COVID-19 patients admitted to a large tertiary institution.\n\nMethodsWe reviewed our prospectively collated database of all adult Neurology referrals, Neurology and Stroke admissions and Neurological multi-disciplinary team meetings for all hospitalized patients with suspected or proven COVID-19 from 17 March 2020 to 31 August 2020.\n\nResultsTwenty-nine of 1243 COVID-19 inpatients (2.3%) presented with COVID-19-related neurological disorders. The mean age was 68.9 +/- 13.5(SD) years, age range of 34-97 years, and there were 16 males. 22 patients had confirmed, 5 were probable and 2 had suspected COVID-19 infection according to the WHO case classification. Eight patients (27%) required critical care admission. Neurological symptoms at presentation included acute confusion and delirium, seizures, and new focal neurological deficits. Based on the pre-defined neurological phenotype, COVID-19 patients were grouped into four main categories. 16 patients had cerebrovascular events (13 with acute ischaemic stroke and 3 had haemorrhagic features), 7 patients were found to have inflammatory, non-inflammatory and autoimmune encephalopathy (including 2 with known Multiple Sclerosis), whilst disorders of movement and peripheral nervous system were diagnosed in 3 patients each.\n\nConclusionAlthough the exact prevalence and aetiology remain unclear, new onset of neurological disorders, in addition to anosmia, is non-sporadic during the acute COVID-19-infection. Longitudinal follow-up of these patients is required to determine the clinical and functional outcome, treatment response and long-term effects of the SARS-CoV-2 infection.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Permesh Singh Dhillon", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Robert Dineen", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Haley Morris", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Radu Tanasescu", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Esmaeil Nikfekr", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Jonathan Evans", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Cris S Constantinescu", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Akram A Hosseini", + "author_inst": "Nottingham University Hospitals NHS Trust" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.12.08.20246140", "rel_title": "How detection ranges and usage stops impact digital contact tracing effectiveness for COVID-19", @@ -1034856,53 +1036118,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, - { - "rel_doi": "10.1101/2020.12.09.20246462", - "rel_title": "Into the SARS-CoV-2 playgrounds: investigating the origins of the Belgian second wave, from an Antwerp perspective", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.09.20246462", - "rel_abs": "The goal of this study was to estimate rates of SARS-CoV-2 carriership and viral loads in the general Antwerp population and to compare the estimated prevalences and incidences with governmental data (numbers of detected positive cases, stringency measure index) in order to evaluate the dynamics leading to the second wave. We used (pre)admission screening results from the major Antwerp hospitals for estimating community prevalences and incidences. 43.545 samples were included (April - November 2020). High SARS-CoV-2 carriership rates (mean week prevalence of 1.3%) were found in the general Antwerp population. 35.4% of positive cases carried high viral loads. Only a small proportion (15.3%) of the viral circulation was detected by the nationally implemented testing policy. In the weeks before the second Belgian wave, increasing prevalences and incidences were found, together with country-wide easing of restriction measures. In our opinion these findings have led to origin of the second viral wave.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Reinout Naesens", - "author_inst": "ZiekenhuisNetwerk Antwerp" - }, - { - "author_name": "Laura Heireman", - "author_inst": "ZiekenhuisNetwerk Antwerpen" - }, - { - "author_name": "Sarah Vandamme", - "author_inst": "University Hospital Antwerp" - }, - { - "author_name": "Philippe Willems", - "author_inst": "GasthuisZusters Antwerpen" - }, - { - "author_name": "Bruno Van Herendael", - "author_inst": "GasthuisZusters Antwerpen" - }, - { - "author_name": "Walter Verstrepen", - "author_inst": "ZiekenhuisNetwerk Antwerpen" - }, - { - "author_name": "Pieter De Schouwer", - "author_inst": "ZiekenhuisNetwerk Antwerpen" - }, - { - "author_name": "Peggy Bruynseels", - "author_inst": "ZiekenhuisNetwerk Antwerpen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.09.20239673", "rel_title": "SARS-CoV-2-specific humoral and cellular immunity in renal transplant and haemodialysis patients treated with convalescent plasma", @@ -1035186,6 +1036401,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.10.20246884", + "rel_title": "SARS-CoV-2/COVID-19 hospitalised patients in Switzerland: a prospective cohort profile", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20246884", + "rel_abs": "BackgroundSARS-CoV-2/COVID-19, which emerged in China in late 2019, rapidly spread across the world causing several million victims in 213 countries. Switzerland was severely hit by the virus, with 43000 confirmed cases as of September 1st, 2020.\n\nAimIn cooperation with the Federal Office of Public Health, we set up a surveillance database in February 2020 to monitor hospitalised patients with COVID-19 in addition to their mandatory reporting system.\n\nMethodsPatients hospitalised for more than 24 hours with a positive PCR test, from 20 Swiss hospitals, are included. Data collection follows a custom Case Report Form based on WHO recommendations and adapted to local needs. Nosocomial infections were defined as infections for which the onset of symptoms started more than 5 days after the patients admission date.\n\nResultsAs of September 1st, 2020, 3645 patients were included. Most patients were male (2168 - 59.5%),and aged between 50 and 89 years (2778 - 76.2%), with a median age of 68 (IQR 54-79). Community infections dominated with 3249 (89.0%) reports. Comorbidities were frequently reported: hypertension (1481 - 61.7%), cardiovascular diseases (948 - 39.5%), and diabetes (660 - 27.5%) being the most frequent in adults; respiratory diseases and asthma (4 -21.1%), haematological and oncological diseases (3 - 15.8%) being the most frequent in children. Complications occurred in 2679 (73.4%) episodes, mostly for respiratory diseases (2470 - 93.2% in adults, 16 - 55.2% in children), renal (681 - 25.7%) and cardiac (631 - 23.8%) complication for adults. The second and third most frequent complications in children affected the digestive system and the liver (7 - 24.1%). A targeted treatment was given in 1299 (35.6%) episodes, mostly with hydroxychloroquine (989 - 76.1%). Intensive care units stays were reported in 578 (15.8%) episodes. 527 (14.5%) deaths were registered, all among adults.\n\nConclusionThe surveillance system has been successfully initiated and provides a very representative set of data for Switzerland. We therefore consider it to be a valuable addition to the existing mandatory reporting, providing more precise information on the epidemiology, risk factors, and clinical course of these cases.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Amaury Thiabaud", + "author_inst": "Institut de Sant\u00e9 Globale, Facult\u00e9 de M\u00e9decine de l'Universit\u00e9 de Gen\u00e8ve, Geneva, Switzerland" + }, + { + "author_name": "Anne Iten", + "author_inst": "Service de pr\u00e9vention et contr\u00f4le de l'infection, Direction m\u00e9dicale et qualit\u00e9, HUG, Geneva, Switzerland" + }, + { + "author_name": "Carlo Balmelli", + "author_inst": "Infection Control Programme, EOC Hospitals, Ticino, Switzerland" + }, + { + "author_name": "Laurence Senn", + "author_inst": "Service de m\u00e9decine pr\u00e9ventive hospitali\u00e8re, CHUV, Lausanne, Switzerland" + }, + { + "author_name": "Nicolas Troillet", + "author_inst": "Service of Infectious Diseases, Central Institute, Valais Hospitals, Sion, Switzerland" + }, + { + "author_name": "Andreas Widmer", + "author_inst": "Department of Infectious Diseases, University Hospital Basel, Basel, Switzerland" + }, + { + "author_name": "Domenica Flury", + "author_inst": "Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St. Gallen, St. Gallen, Switzerland" + }, + { + "author_name": "Peter W. Schreiber", + "author_inst": "Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Miriam V\u00e1zquez", + "author_inst": "Department of Infectious Diseases, Bern University Hospital (Inselspital), Bern, Switzerland" + }, + { + "author_name": "Lauro Damonti", + "author_inst": "Department of Infectious Diseases, Bern University Hospital (Inselspital), Bern, Switzerland" + }, + { + "author_name": "Michael Buettcher", + "author_inst": "Paediatric Infectious Diseases, Department of Paediatrics, Children's Hospital, Cantonal Hospital Lucerne, Switzerland" + }, + { + "author_name": "Danielle Vuichard-Gysin", + "author_inst": "Department of Infectious Diseases, Thurgau Cantonal Hospital, Thurgau, Switzerland" + }, + { + "author_name": "Christoph Kuhm", + "author_inst": "Department of Infectious Diseases, Thurgau Cantonal Hospital, Thurgau, Switzerland" + }, + { + "author_name": "Alexia Cusini", + "author_inst": "Department of Infectious Diseases, Cantonal Hospital Graubuenden, Chur, Switzerland" + }, + { + "author_name": "Thomas Riedel", + "author_inst": "Department of Pediatrics, Cantonal Hospital Graubuenden, Chur, Switzerland" + }, + { + "author_name": "Yvonne Nussbaumer", + "author_inst": "Klinik f\u00fcr Innere Medizin, Kantonsspital Spit\u00e4ler Schaffhausen, Schaffhausen, Switzerland" + }, + { + "author_name": "Roman Gaudenz", + "author_inst": "Innere Medizin und Infektiologie, Kantonsspital Nidwalden, Stans, Switzerland" + }, + { + "author_name": "Ulrich Heininger", + "author_inst": "Infectious Diseases and Vaccinology, University of Basel Children's Hospital, Basel, Switzerland" + }, + { + "author_name": "Christoph Berger", + "author_inst": "Division of Infectious Diseases, and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland" + }, + { + "author_name": "Franziska Zucol", + "author_inst": "Paediatric Infectious Diseases, Department of Paediatrics, Cantonal Hospital Winterthur, Winterthur, Switzerland" + }, + { + "author_name": "Sara Bernhard-Stirnemann", + "author_inst": "Children's Hospital Aarau, Aarau, Switzerland" + }, + { + "author_name": "Natascia Corti", + "author_inst": "Unit of General Internal Medicine, Hirslanden Clinic, Zurich, Switzerland" + }, + { + "author_name": "Petra Zimmermann", + "author_inst": "Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; and Department of Paediatrics, Fribourg Hospital HFR, Fribourg, Switzerland" + }, + { + "author_name": "Anita Uka", + "author_inst": "Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland; and Department of Paediatrics, Fribourg Hospital HFR, Fribourg, Switzerland" + }, + { + "author_name": "Anita Niederer-Loher", + "author_inst": "Children's Hospital of Eastern Switzerland, St. Gallen, Switzerland" + }, + { + "author_name": "C\u00e9line Gardiol", + "author_inst": "Swiss Federal Office of Public Health, Bern, Switzerland" + }, + { + "author_name": "Maroussia Roelens", + "author_inst": "Institut de Sant\u00e9 Globale, Facult\u00e9 de M\u00e9decine de l'Universit\u00e9 de Gen\u00e8ve, Geneva, Switzerland" + }, + { + "author_name": "Olivia Keiser", + "author_inst": "Institut de Sant\u00e9 Globale, Facult\u00e9 de M\u00e9decine de l'Universit\u00e9 de Gen\u00e8ve, Geneva, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.09.20246363", "rel_title": "Risk of adverse outcomes with COVID-19 in the Republic of Ireland", @@ -1036326,61 +1037668,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.12.11.20247676", - "rel_title": "The COVID University Challenge: a Hazard Analysis of Critical Control Points Assessment of the Return of Students to Higher Education Establishments", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20247676", - "rel_abs": "The COVID-19 pandemic disrupted economies and societies throughout the world in 2020. Education was especially affected, with schools and universities widely closed for long periods. People under 25 years have the lowest risk of severe disease but their activities can be key to persistent ongoing community transmission. A challenge arose for how to provide education, including university level, without the activities of students increasing wider community SARS- CoV-2 infections.\n\nWe used a Hazard Analysis of Critical Control Points (HACCP) framework to assess the risks associated with university student activity and recommend how to mitigate these risks. This tool appealed because it relies on multi-agency collaboration and interdisciplinary expertise and yet is low cost, allowing rapid generation of evidence-based recommendations.\n\nWe identified key critical control points associated with university student activities, lifestyle and interaction patterns both on-and-off campus. Unacceptable contact thresholds and the most up-to-date guidance were used to identify levels of risk for potential SARS-CoV-2 transmission, as well as recommendations based on existing research and emerging evidence for strategies that can reduce the risks of transmission. Employing the preventative measures we suggest can reduce the risks of SARS-CoV-2 transmission among and from university students. Reduction of infectious disease transmission in this demographic will reduce overall community transmission, lower demands on health services and reduce risk of harm to clinically vulnerable individuals while allowing vital education activity to continue. HACCP assessment proved a flexible tool for risk analysis in a specific setting in response to an emerging infectious disease threat.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Kelly L Edmunds", - "author_inst": "School of Biological Sciences, University of East Anglia" - }, - { - "author_name": "Laura Bowater", - "author_inst": "Norwich Medical School, University of East Anglia" - }, - { - "author_name": "Julii S Brainard", - "author_inst": "Norwich Medical School, University of East Anglia" - }, - { - "author_name": "Jean-Charles de Coriolis", - "author_inst": "School of Biological Sciences, University of East Anglia" - }, - { - "author_name": "Iain R Lake", - "author_inst": "School of Environmental Sciences, University of East Anglia" - }, - { - "author_name": "Rimsha R Malik", - "author_inst": "Norwich Medical School, University of East Anglia" - }, - { - "author_name": "Lorraine Newark", - "author_inst": "Learning and Teaching Service, University of East Anglia" - }, - { - "author_name": "Neil Ward", - "author_inst": "Vice Chancellor's Office, University of East Anglia" - }, - { - "author_name": "Kay Yeoman", - "author_inst": "School of Biological Sciences, University of East Anglia" - }, - { - "author_name": "Paul R Hunter", - "author_inst": "Norwich Medical School, University of East Anglia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.10.20247205", "rel_title": "Diverse Functional Autoantibodies in Patients with COVID-19", @@ -1036884,6 +1038171,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.10.20247361", + "rel_title": "COVID-19 prediction in South Africa: Understanding the unascertained cases -- the hidden part of the epidemiological iceberg", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20247361", + "rel_abs": "Understanding the impact of non-pharmaceutical interventions as well as acscounting for the unascertained cases remain critical challenges for epidemiological models for understanding the transmission dynamics of COVID-19 spread. In this paper, we propose a new epidemiological model (eSEIRD) that extends the widely used epidemiological models such as extended Susceptible-Infected-Removed model (eSIR) and SAPHIRE (initially developed and used for analyzing data from Wuhan). We fit these models to the daily ascertained infected (and removed) cases from March 15, 2020 to Dec 31, 2020 in South Africa that reported the largest number of confirmed COVID-19 cases and deaths from the WHO African region. Using the eSEIRD model, the COVID-19 transmission dynamics in South Africa was characterized by the estimated basic reproduction number (R0) starting at 3.22 (95%CrI: [3.19, 3.23]) then dropping below 2 following a mandatory lockdown implementation and subsequently increasing to 3.27 (95%CrI: [3.27, 3.27]) by the end of 2020. The initial decrease of effective reproduction number followed by an increase suggest the effectiveness of early interventions and the combined effect of relaxing strict interventions and emergence of a new coronavirus variant in South Africa. The low estimated ascertainment rate was found to vary from 1.65% to 9.17% across models and time periods. The overall infection fatality ratio (IFR) was estimated as 0.06% (95%CrI: [0.04%, 0.22%]) accounting for unascertained cases and deaths while the reported case fatality ratio was 2.88% (95% CrI: [2.45%, 6.01%]). The models predict that from December 31, 2020, to April 1, 2021, the predicted cumulative number of infected would reach roughly 70% of total population in South Africa. Besides providing insights on the COVID-19 dynamics in South Africa, we develop powerful forecasting tools that enable estimation of ascertainment rates and IFR while quantifying the effect of intervention measures on COVID-19 spread.\n\nAMS ClassificationPlace Classification here. Leave as is, if there is no classification", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xuelin Gu", + "author_inst": "Department of Biostatistics, University of Michigan" + }, + { + "author_name": "Bhramar Mukherjee", + "author_inst": "Department of Biostatistics, University of Michigan; Department of Epidemiology, University of Michigan" + }, + { + "author_name": "Sonali Das", + "author_inst": "Department of Business Management, University of Pretoria" + }, + { + "author_name": "Jyotishka Datta", + "author_inst": "Department of Statistics, Virginia Polytechnic Institute and State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.10.20247247", "rel_title": "Mathematical modelling projections versus the actual course of the COVID-19 epidemic following the nationwide lockdown in Kyrgyzstan", @@ -1038780,49 +1040098,6 @@ "type": "new results", "category": "synthetic biology" }, - { - "rel_doi": "10.1101/2020.12.10.420109", - "rel_title": "SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential", - "rel_date": "2020-12-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.10.420109", - "rel_abs": "Coronaviruses have caused multiple epidemics in the past two decades, in addition to the current COVID-19 pandemic that is severely damaging global health and the economy. Coronaviruses employ between twenty and thirty proteins to carry out their viral replication cycle including infection, immune evasion, and replication. Among these, nonstructural protein 16 (Nsp16), a 2-O-methyltransferase, plays an essential role in immune evasion. Nsp16 achieves this by mimicking its human homolog, CMTr1, which methylates mRNA to enhance translation efficiency and distinguish self from other. Unlike human CMTr1, Nsp16 requires a binding partner, Nsp10, to activate its enzymatic activity. The requirement of this binding partner presents two questions that we investigate in this manuscript. First, how does Nsp10 activate Nsp16? While experimentally-derived structures of the active Nsp16/Nsp10 complex exist, structures of inactive, monomeric Nsp16 have yet to be solved. Therefore, it is unclear how Nsp10 activates Nsp16. Using over one millisecond of molecular dynamics simulations of both Nsp16 and its complex with Nsp10, we investigate how the presence of Nsp10 shifts Nsp16s conformational ensemble in order to activate it. Second, guided by this activation mechanism and Markov state models (MSMs), we investigate if Nsp16 adopts inactive structures with cryptic pockets that, if targeted with a small molecule, could inhibit Nsp16 by stabilizing its inactive state. After identifying such a pocket in SARS-CoV-2 Nsp16, we show that this cryptic pocket also opens in SARS-CoV-1 and MERS, but not in human CMTr1. Therefore, it may be possible to develop pan-coronavirus antivirals that target this cryptic pocket.\n\nStatement of SignificanceCoronaviruses are a major threat to human health. These viruses employ molecular machines, called proteins, to infect host cells and replicate. Characterizing the structure and dynamics of these proteins could provide a basis for designing small molecule antivirals. In this work, we use computer simulations to understand the moving parts of an essential SARS-CoV-2 protein, understand how a binding partner turns it on and off, and identify a novel pocket that antivirals could target to shut this protein off. The pocket is also present in other coronaviruses but not in the related human protein, so it could be a valuable target for pan-coronavirus antivirals.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Neha Vithani", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Michael D Ward", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Maxwell I Zimmerman", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Borna Novak", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Jonathan H. Borowsky", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Sukrit Singh", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Gregory R. Bowman", - "author_inst": "Washington University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.12.09.418806", "rel_title": "Cross-neutralization of SARS-CoV-2 by HIV-1 specific broadly neutralizing antibodies and polyclonal plasma", @@ -1039043,6 +1040318,20 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.12.08.416677", + "rel_title": "Intranasal administration of SARS-CoV-2 neutralizing human antibody prevents infection in mice", + "rel_date": "2020-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.08.416677", + "rel_abs": "Prevention of SARS-CoV-2 infection at the point of nasal entry is a novel strategy that has the potential to help contain the ongoing pandemic. Using our proprietary technologies, we have engineered a human antibody that recognizes SARS-CoV-2 S1 spike protein with an enhanced affinity for mucin to improve the antibodys retention in respiratory mucosa. The modified antibody, when administered into mouse nostrils, was shown to block infection in mice that were exposed to high titer SARS-CoV-2 pseudovirus 10 hours after the initial antibody treatment. Our data show that the protection against SARS-CoV-2 infection is effective in both nasal and lung areas 7 days after viral exposure. The modified antibody is stable in a nasal spray formulation and maintains its SARS-CoV-2 neutralizing activity. Nasal spray of the modified antibody can be developed as an affordable and effective prophylactic product to protect people from infection by exposure to SARS-CoV-2 virus in the air.\n\nOne-sentence summaryA Fc-modified human antibody prevents SARS-CoV-2 viral infection via nasal administration", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.12.09.417741", "rel_title": "Characterization of protease activity of Nsp3 from SARS-CoV-2 and its in vitro inhibition by nanobodies", @@ -1040559,117 +1041848,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.12.07.20245431", - "rel_title": "Evaluation of SARS-CoV-2 neutralization assays for antibody monitoring in natural infection and vaccine trials", - "rel_date": "2020-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.07.20245431", - "rel_abs": "Determinants of protective immunity against SARS-CoV-2 infection require the development of well-standardized, reproducible antibody assays to be utilized in concert with clinical trials to establish correlates of risk and protection. This need has led to the appearance of a variety of neutralization assays used by different laboratories and companies. Using plasma samples from COVID-19 convalescent individuals with mild-to-moderate disease from a localized outbreak in a single region of the western US, we compared three platforms for SARS-CoV-2 neutralization: assay with live SARS-CoV-2, pseudovirus assay utilizing lentiviral (LV) and vesicular stomatitis virus (VSV) packaging, and a surrogate ELISA test. Vero, Vero E6, HEK293T cells expressing human angiotensin converting enzyme 2 (hACE2), and TZM-bl cells expressing hACE2 and transmembrane serine protease 2 (TMPRSS2) were evaluated. Live-virus and LV-pseudovirus assay with HEK293T cells showed similar geometric mean titers (GMTs) ranging 141-178, but VSV-pseudovirus assay yielded significantly higher GMT (310 95%CI 211-454; p < 0.001). Fifty percent neutralizing dilution (ND50) titers from live-virus and all pseudovirus assay readouts were highly correlated (Pearson r = 0.81-0.89). ND50 titers positively correlated with plasma concentration of IgG against SARS-CoV-2 spike and receptor binding domain (RBD) (r = 0.63-0.89), but moderately correlated with nucleoprotein IgG (r = 0.46-0.73). There was a moderate positive correlation between age and spike (Spearmans rho=0.37, p=0.02), RBD (rho=0.39, p=0.013) and nucleoprotein IgG (rho=0.45, p=0.003). ND80 showed stronger correlation with age than ND50 (ND80 rho=0.51 (p=0.001), ND50 rho=0.28 (p=0.075)). Our data demonstrate high concordance between cell-based assays with live and pseudotyped virions.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Anton M Sholukh", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Andrew Fiore-Gartland", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Emily S Ford", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Yixuan Hou", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Longping Victor Tse", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Florian A Lempp", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Hanna Kaiser", - "author_inst": "Vir Biotechnology" - }, - { - "author_name": "Russell Saint Germain", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Emily Bossard", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Jia Jin Kee", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Kurt Diem", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Andrew B Stuart", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Peter B Rupert", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Chance Brock", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Matthew Buerger", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Margaret K Doll", - "author_inst": "Albany College of Pharmacy and Health Sciences" - }, - { - "author_name": "April Kaur Randhawa", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Leonidas Stamatatos", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Roland K Strong", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Colleen McLaughlin", - "author_inst": "Albany College of Pharmacy and Health Sciences" - }, - { - "author_name": "Keith R. Jerome", - "author_inst": "University of WA/Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Ralph S. Baric", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "David Montefiori", - "author_inst": "Duke University" - }, - { - "author_name": "Lawrence Corey", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.07.20245621", "rel_title": "Excess deaths associated with the Iranian COVID-19 epidemic: a province-level analysis", @@ -1040816,6 +1041994,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.06.20243691", + "rel_title": "What is the probability that this patient, who presents to a UK hospital, will be diagnosed with Covid-19? Prospective validation of the open-source CovidCalculatorUK resource.", + "rel_date": "2020-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.06.20243691", + "rel_abs": "IntroductionThe novel coronavirus SARS-CoV2 and the associated disease, Covid-19, continue to pose a global health threat. The CovidCalculatorUK is an open-source online tool (covidcalculatoruk.org) that estimates the probability that an individual patient, who presents to a UK hospital, will later test positive for SARS-CoV2. The objective is to aid cohorting decisions and minimise nosocomial transmission of SARS-CoV2.\n\nMethodsThis n = 500 prospective, observational, multicentre, validation study compared the CovidCalculatorUKs estimated probability of Covid-19 with the first SARS-CoV2 oropharyngeal/nasopharyngeal swab result for individual patients admitted to hospital during the study period (01.04.20 - 18.05.20). A comparison with senior clinicians estimates of the probability of Covid-19 was also made.\n\nResultsPatients who were prospectively grouped, by the CovidCalculatorUK, into 0-30% estimated probability, 30-60% and 60-100% estimated probability went on to have first swab SARS-CoV2 positive results in: 15.7%, 30.5% and 61.9% of cases, respectively. CovidCalculatorUK performance demonstrated an area under the curve of 0.76 (95% CI 0.71 - 0.81) (p < 0.001). Senior clinician stratification of the estimated probability of Covid-19 performed similarly to the CovidCalculatorUK.\n\nConclusionThe CovidCalculatorUK provides a reasonably accurate estimate of the probability of an individual testing positive on their first SARS-CoV2 nasopharyngeal/oropharyngeal swab. The CovidCalculatorUK output performs similarly to a senior clinicians estimate. Further evolution of the calculator may improve performance.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "George A Chapman", + "author_inst": "Oxford University Hospitals NHS Trust" + }, + { + "author_name": "Lewis Mundell", + "author_inst": "Lanarkshire NHS Trust" + }, + { + "author_name": "Charlotte H Harrison", + "author_inst": "Oxford University Hospitals NHS Trust" + }, + { + "author_name": "Tamsin Cargill", + "author_inst": "Oxford University Hospitals NHS Trust" + }, + { + "author_name": "Odhran Keating", + "author_inst": "Buckinghamshire Healthcare NHS Trust" + }, + { + "author_name": "Mark Johnson", + "author_inst": "Buckinghamshire Healthcare NHS Trust" + }, + { + "author_name": "Andrew Smith", + "author_inst": "Lanarkshire NHS Trust" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.06.20244756", "rel_title": "Comparing Decision Tree-Based Ensemble Machine Learning Models for COVID-19 Death Probability Profiling", @@ -1042079,25 +1043300,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.12.04.20244244", - "rel_title": "On the Effects of Misclassification in Estimating Efficacy With Application to Recent COVID-19 Vaccine Trials", - "rel_date": "2020-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20244244", - "rel_abs": "The recent trials for proposed COVID-19 vaccines have garnered a considerable amount of attention and as of this writing extensive vaccination efforts are underway. The first two vaccines approved in the United States are the Moderna and Pfizer vaccines both with estimated efficacy near 95%. One question which has received limited attention, and which we address here, is what affect false positives or false negatives have on the estimated efficacy. Expressions for potential bias due to misclassification of COVID status are developed as are general formulas to adjust for misclassification, allowing for either differential or non-differential misclassification. These results are illustrated with numerical investigations pertinent to the Moderna and Pfizer trials. The general conclusion, fortunately, is that the potential misclassification of COVID status almost always would lead to underestimation of the efficacy and that correcting for false positives or negatives will typically lead to even higher estimated efficacy.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "John P Buonaccorsi", - "author_inst": "University of Massachusetts-Amherst" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.04.20244087", "rel_title": "N95 Filtering Facepiece Respirators Remain Effective After Extensive Reuse During the COVID-19 Pandemic.", @@ -1042333,6 +1043535,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.12.05.20244426", + "rel_title": "Exploring drugs and vaccines associated with altered risks and severity of COVID-19: a UK Biobank cohort study of all ATC level-4 drug categories", + "rel_date": "2020-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.05.20244426", + "rel_abs": "BackgroundCOVID-19 is a major public health concern, yet its risk factors are not well-understood and effective therapies are lacking. It remains unclear how different drugs may increase or decrease the risks of infection and severity of disease.\n\nMethodsWe studied associations of prior use of all level-4 ATC drug categories (including vaccines) with COVID-19 diagnosis and outcome, based on a prospective cohort of UK Biobank(UKBB). Drug history was based on general practitioner(GP) records. Effects of prescribed medications/vaccinations on the risk of infection, severity of disease and mortality were investigated separately. Hospitalized and fatal cases were categorized as severe infection. We also considered different study designs and conducted analyses within infected patients, tested subjects and the whole population respectively, and for 5 different time-windows of prescriptions. Missing data were accounted for by multiple imputation and inverse probability weighting was employed to reduce testing bias. Multivariable logistic regression was conducted which controls for main confounders.\n\nResultsWe placed a greater focus on protective associations here, as (residual) confounding by indication and comorbidities tends to bias towards harmful effects. Across all categories, statins showed the strongest and most consistent protective associations. Significant protective effects against severe infection were seen among infected subjects (OR for prescriptions within a 12-month window, same below: 0.50, 95% CI:0.42-0.60), tested subjects (OR=0.63, 0.54-0.73) or in the general population (OR=0.49, 0.42-0.57). A number of top-listed drugs with protective effects were also cardiovascular medications, such as angiotensin converting enzyme inhibitors, angiotensin receptor blockers, calcium channel blocker and beta-blockers. Some other drugs showing protective associations included biguanides (metformin), estrogens, thyroid hormones and proton pump inhibitors, among others.\n\nInterestingly, we also observed protective associations by numerous vaccines. The most consistent association was observed for influenza vaccines, which showed reduced odds of infection (OR= 0.73 for vaccination in past year, CI 0.65-0.83) when compared cases to general population controls or test-negative controls (OR=0.60, 0.53-0.68). Protective associations were also observed when severe or fatal infection was considered as the outcome. Pneumococcal, tetanus, typhoid and combined bacterial and viral vaccines (ATC code J07CA) were also associated with lower odds of infection/severity.\n\nFurther subgroup and interaction analyses revealed difference in protective effects in different clinical subgroups. For example, protective effects of flu and pneumococcal vaccines were weaker in obese individuals, while we observed stronger protective effects of statins in those with cardiometabolic disorders, such as diabetes, coronary artery disease, hypertension and obesity.\n\nConclusionsA number of drugs, including many for cardiometabolic disorders, may be associated with lower odds of infection/severity of infection. Several existing vaccines, especially flu vaccines, may be beneficial against COVID-19 as well. However, causal relationship cannot be established due to risk of confounding. While further studies are required to validate the findings, this work provides a useful reference for future meta-analyses, clinical trials or experimental studies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Yong XIANG", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Kenneth Chi-Yin WONG", + "author_inst": "The Chinese University of Hong Kong" + }, + { + "author_name": "Hon-Cheong SO", + "author_inst": "Chinese University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2020.12.04.20244327", "rel_title": "COVID-19 RELATED IMMUNIZATION DISRUPTIONS IN RAJASTHAN, INDIA: A RETROSPECTIVE OBSERVATIONAL STUDY", @@ -1043505,41 +1044734,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.12.05.20244566", - "rel_title": "Does higher BMI increase COVID-19 severity?: a systematic review and meta-analysis", - "rel_date": "2020-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.05.20244566", - "rel_abs": "IntroductionCOVID-19 pandemic has caused havoc worldwide, and different comorbidities have been seen to exacerbate the condition. Obesity is one of the leading comorbidities, which is associated with many other diseases. In this paper, we present a systematic review and meta-analysis estimating the effects of overweight and obesity on COVID-19 disease severity.\n\nMethodologyTwo electronic databases (Medline and Cochrane library) and one grey literature database (Grey Literature Report) were searched using the following keywords: overweight, obesity, body mass index, respiratory disease, coronavirus, COVID-19. The risks of bias of the selected studies were assessed by using the Navigation Guide method for human data. Both random and fixed effect meta-analysis were determined using Review Manager (RevMan) software version 5.4.\n\nResultsAfter initial screening, 12 studies (7 cohort studies, four case-control studies, and one cross-sectional study) were fulfilled the eligibility criteria, comprising a total of 405359 patients and included in the systematic review. The pooled risk of disease severity was 1.31 times higher based on both fixed and random effect model among those overweight patients, I2 0% and 2.09 and 2.41 times higher based on fixed and random effect respectively among obese patients, I2 42% compared to healthy individuals.\n\nConclusionOverweight and obesity are common risk factors for disease severity of COVID-19 patients. However, further assessment of metabolic parameters included BMI, waist-hip ratio, and insulin levels, are required to estimate the risk factors of COVID-19 patients and understanding the mechanism between COVID-19 and body mass index.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Akibul Islam Chowdhury", - "author_inst": "Department of Food Technology and Nutrition Science, Noakhali Science and Technology University, Bangladesh" - }, - { - "author_name": "Md. Fazley Rabbi", - "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Bangladesh" - }, - { - "author_name": "Tanjina Rahman", - "author_inst": "Department of Food Technology and Nutrition Science, Noakhali Science and Technology University, Bangladesh" - }, - { - "author_name": "Sompa Reza", - "author_inst": "Institute of Nutrition and Food Science, University of Dhaka, Bangladesh" - }, - { - "author_name": "Mohammad Rahanur Alam", - "author_inst": "Department of Food Technology and Nutrition Science, Noakhali Science and Technology University, Bangladesh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.04.20234450", "rel_title": "A two-pronged approach for rapid and high-throughput SARS-CoV-2 nucleic acid testing", @@ -1043791,6 +1044985,73 @@ "type": "contradictory results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.06.413443", + "rel_title": "Efficient inhibition of SARS-CoV-2 strains by a novel ACE2-IgG4-Fc fusion protein with a stabilized hinge region", + "rel_date": "2020-12-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.06.413443", + "rel_abs": "The novel severe acute respiratory syndrome (SARS)-like coronavirus (SARS-CoV-2) enters its host cells after binding to the angiotensin-converting enzyme 2 (ACE2) via its spike glycoprotein. This interaction is critical for virus entry and virus-host membrane fusion. Soluble ACE2 ectodomains bind and neutralize the virus but the short in vivo half-lives of soluble ACE2 limits its therapeutic use. Fusion of the fragment crystallizable (Fc) part of human immunoglobulin G (IgG) to the ACE2 ectodomain can prolong the in vivo half-life but bears the risk of unwanted Fc-receptor activation and antibody-dependent disease enhancement. Here, we describe optimized ACE2-Fc fusion constructs that avoid Fc-receptor binding by using IgG4-Fc as a fusion partner. The engineered ACE2-IgG4-Fc fusion proteins described herein exhibit promising pharmaceutical properties and a broad antiviral activity at single-digit nanomolar concentration. In addition, they allow to maintain the beneficial enzymatic activity of ACE2 and thus are very promising candidate antivirals broadly acting against coronaviruses.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Hristo L Svilenov", + "author_inst": "Department of Chemistry, Technical University of Munich, Garching, Germany" + }, + { + "author_name": "Julia Sacherl", + "author_inst": "Institute of Virology, Technical University of Munich / Helmholtz Zentrum Munich, Munich, Germany" + }, + { + "author_name": "Alwin Reiter", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Lisa Wolff", + "author_inst": "Institute of Virology, Technical University of Munich / Helmholtz Zentrum Munich, Munich, Germany" + }, + { + "author_name": "Cho-Chin Chen", + "author_inst": "Institute of Virology, Technical University of Munich / Helmholtz Zentrum Munich, Munich, Germany / German Center for Infection Research, Munich partner site, M" + }, + { + "author_name": "Marcel Stern", + "author_inst": "Max von Pettenkofer Institute & Gene Center, Virology, LMU Muenchen, Munich, Germany / German Center for Infection Research, Munich partner site, Munich, German" + }, + { + "author_name": "Frank-Peter Wachs", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Nicole Simonavicius", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Susanne Pippig", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Florian Wolschin", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Johannes Buchner", + "author_inst": "Department of Chemistry, Technical University of Munich, Garching, Germany" + }, + { + "author_name": "Carsten Brockmeyer", + "author_inst": "Formycon AG, Martinsried/Planegg, Germany" + }, + { + "author_name": "Ulrike Protzer", + "author_inst": "Institute of Virology, Technical University of Munich / Helmholtz Zentrum Munich, Munich, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.06.412759", "rel_title": "The new generation hDHODH inhibitor MEDS433 hinders the in vitro replication of SARS-CoV-2", @@ -1045379,49 +1046640,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.02.20242743", - "rel_title": "Modelling the Test, Trace and Quarantine Strategy to Control the COVID-19 Epidemic in the State of Sao Paulo, Brazil", - "rel_date": "2020-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.02.20242743", - "rel_abs": "Testing for detecting the infection by SARS-CoV-2 is the bridge between the lockdown and the opening of society. In this paper we modelled and simulated a test-trace-and-quarantine strategy to control the COVID-19 outbreak in the State of Sao Paulo, Brasil. The State of Sao Paulo failed to adopt an effective social distancing strategy, reaching at most 59% in late March and started to relax the measures in late June, dropping to 41% in 08 August. Therefore, Sao Paulo relies heavily on a massive testing strategy in the attempt to control the epidemic.\n\nTwo alternative strategies combined with economic evaluations were simulated. One strategy included indiscriminately testing the entire population of the State, reaching more than 40 million people at a maximum cost of 2.25 billion USD, that would reduce the total number of cases by the end of 2020 by 90%. The second strategy investigated testing only symptomatic cases and their immediate contacts - this strategy reached a maximum cost of 150 million USD but also reduced the number of cases by 90%.\n\nThe conclusion is that if the State of Sao Paulo had decided to adopt the simulated strategy on April the 1st, it would have been possible to reduce the total number of cases by 90% at a cost of 2.25 billion US dollars for the indiscriminate strategy but at a much smaller cost of 125 million US dollars for the selective testing of symptomatic cases and their contacts.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Marcos Amaku", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Dimas Tadeu Covas", - "author_inst": "Instituto Butantan" - }, - { - "author_name": "Francisco Antonio Bezerra Coutinho", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Raymundo Soares Azevedo", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Claudio Struchiner", - "author_inst": "Fundacao Getulio Vargas" - }, - { - "author_name": "Annelies Wilder-Smith", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Eduardo Massad", - "author_inst": "Fundacao Getulio Vargas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.01.407486", "rel_title": "Nasopharyngeal microbial communities of patients infected with SARS-COV-2 that developed COVID-19.", @@ -1045661,6 +1046879,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.02.20242925", + "rel_title": "Mapping each pre-existing conditions association to short-term and long-term COVID-19 complications", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.02.20242925", + "rel_abs": "Understanding the relationships between pre-existing conditions and complications of COVID-19 infection is critical to identifying which patients will develop severe disease. Here, we leverage 1.1 million clinical notes from 1,903 hospitalized COVID-19 patients and deep neural network models to characterize associations between 21 pre-existing conditions and the development of 20 complications (e.g. respiratory, cardiovascular, renal, and hematologic) of COVID-19 infection throughout the course of infection (i.e. 0-30 days, 31-60 days, and 61-90 days). Pleural effusion was the most frequent complication of early COVID-19 infection (23% of 383 complications) followed by cardiac arrhythmia (12% of 383 complications). Notably, hypertension was the most significant risk factor associated with 10 different complications including acute respiratory distress syndrome, cardiac arrhythmia and anemia. Furthermore, novel associations between cancer (risk ratio: 3, p=0.02) or immunosuppression (risk ratio: 4.3, p=0.04) with early-onset heart failure have also been identified. Onset of new complications after 30 days is rare and most commonly involves pleural effusion (31-60 days: 24% of 45 patients, 61-90 days: 25% of 36 patients). Overall, the associations between pre-COVID conditions and COVID-associated complications presented here may form the basis for the development of risk assessment scores to guide clinical care pathways.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "AJ Venkatakrishnan", + "author_inst": "nference" + }, + { + "author_name": "Colin Pawlowski", + "author_inst": "nference" + }, + { + "author_name": "David Zemmour", + "author_inst": "nference" + }, + { + "author_name": "Travis Hughes", + "author_inst": "nference" + }, + { + "author_name": "Akash Anand", + "author_inst": "nference Labs" + }, + { + "author_name": "Gabriela Berner", + "author_inst": "nference" + }, + { + "author_name": "Nikhil Kayal", + "author_inst": "nference" + }, + { + "author_name": "Arjun Puranik", + "author_inst": "nference" + }, + { + "author_name": "Ian Conrad", + "author_inst": "nference" + }, + { + "author_name": "Sairam Bade", + "author_inst": "nference Labs" + }, + { + "author_name": "Rakesh Barve", + "author_inst": "nference Labs" + }, + { + "author_name": "Purushottam Sinha", + "author_inst": "nference Labs" + }, + { + "author_name": "Jack O'Horo", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew D Badley", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Venky Soundararajan", + "author_inst": "nference" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.02.20242958", "rel_title": "Longitudinal lab test analysis confirms pre-existing anemia as a severe risk factor for post-viral clearance hospitalization in COVID-19 patients", @@ -1047077,29 +1048370,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.04.20243832", - "rel_title": "The Full Database of Countries with Potential COVID-19 Data Misreport based on Benford's Law", - "rel_date": "2020-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20243832", - "rel_abs": "The aim of this database is to provide researchers and scholars a unified database for potential data misreport by 171 countries regarding their COVID-19 daily reported cases. The analysis employs three different tests (chi-square, Kuiper, and Mean Absolute Deviation) to determine if the data given by each country in the world fit Benfords Law.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ahmad Kilani", - "author_inst": "RUDN University" - }, - { - "author_name": "Georgios P. Georgiou", - "author_inst": "University of Nicosia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.03.20243246", "rel_title": "The impact of the COVID-19 pandemic on mental health and well-being of people living with a long-term physical health condition: a qualitative study", @@ -1047315,6 +1048585,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2020.12.03.20239681", + "rel_title": "Spatial risk factors for Pillar 1 COVID-19 case counts and mortality in rural eastern England, UK", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20239681", + "rel_abs": "Understanding is still developing about risk factors for COVID-19 infection or mortality. This is especially true with respect to identifying spatial risk factors and therefore identifying which geographic areas have populations who are at greatest risk of acquiring severe disease. This is a secondary analysis of patient records in a confined area of eastern England, covering persons who tested positive for SARS-CoV-2 through end May 2020, including dates of death and residence area. For each residence area (local super output area), we obtained data on air quality, deprivation levels, care home bed capacity, age distribution, rurality, access to employment centres and population density. We considered these covariates as risk factors for excess cases and excess deaths in the 28 days after confirmation of positive covid status relative to the overall case load and death recorded for the study area as a whole. We used the conditional autoregressive Besag-York-Mollie model to investigate the spatial dependency of cases and deaths allowing for a Poisson error structure. Structural equation models were also applied to clarify relationships between predictors and outcomes. Excess case counts or excess deaths were both predicted by the percentage of population age 65 years, care home bed capacity and less rurality: older population and more urban areas saw excess cases. Greater deprivation did not correlate with excess case counts but was significantly linked to higher mortality rates after infection. Neither excess cases nor excess deaths were predicted by population density, travel time to local employment centres or air quality indicators. Only 66% of mortality could be explained by locally high case counts. The results show a clear link between greater deprivation and higher COVID-19 mortality that is separate from wider community prevalence and other spatial risk factors.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Julii S Brainard", + "author_inst": "university of east anglia" + }, + { + "author_name": "Steve Rushton", + "author_inst": "Newcastle University" + }, + { + "author_name": "Tim Winters", + "author_inst": "Norfolk County Council" + }, + { + "author_name": "Paul R Hunter", + "author_inst": "University of East Anglia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.03.20243535", "rel_title": "OpenSAFELY: impact of national guidance on switching from warfarin to direct oral anticoagulants (DOACs) in early phase of COVID-19 pandemic in England", @@ -1048551,69 +1049852,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.01.20242131", - "rel_title": "Sewage, Salt, Silica and SARS-CoV-2 (4S): An economical kit-free method for direct capture of SARS-CoV-2 RNA from wastewater.", - "rel_date": "2020-12-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20242131", - "rel_abs": "Wastewater-based epidemiology is an emerging tool to monitor COVID-19 infection levels by measuring the concentration of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in wastewater. There remains a need to improve wastewater RNA extraction methods sensitivity, speed, and reduce reliance on often expensive commercial reagents to make wastewater-based epidemiology more accessible. We present a kit-free wastewater RNA extraction method, titled \"Sewage, Salt, Silica and SARS-CoV-2\" (4S), that employs the abundant and affordable reagents sodium chloride (NaCl), ethanol and silica RNA capture matrices to recover 6-fold more SARS-CoV-2 RNA from wastewater than an existing ultrafiltration-based method. The 4S method concurrently recovered pepper mild mottle virus (PMMoV) and human 18S ribosomal subunit rRNA, both suitable as fecal concentration controls. The SARS-CoV-2 RNA concentrations measured in three sewersheds corresponded to the relative prevalence of COVID-19 infection determined via clinical testing. Lastly, controlled experiments indicate that the 4S method prevented RNA degradation during storage of wastewater samples, was compatible with heat pasteurization, and could be performed in approximately 3 hours. Overall, the 4S method is promising for effective, economical, and accessible wastewater-based epidemiology for SARS-CoV-2, providing another tool to fight the global pandemic.\n\nSYNOPSISThe 4S method for measuring SARS-CoV-2 in wastewater is promising for effective, economical, and accessible wastewater-based epidemiology.\n\nABSTRACT ART\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=70 SRC=\"FIGDIR/small/20242131v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@192784eorg.highwire.dtl.DTLVardef@11879e7org.highwire.dtl.DTLVardef@1eb315borg.highwire.dtl.DTLVardef@1f560cf_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Oscar N. Whitney", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Lauren C. Kennedy", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Vinson Fan", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Adrian Hinkle", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Rose Kantor", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Hannah Greenwald", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Alexander Crits-Christoph", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Basem Al-Shayeb", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Mira Chaplin", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Anna C. Maurer", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Robert Tjian", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Kara L. Nelson", - "author_inst": "University of California, Berkeley" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.01.20238006", "rel_title": "A Novel COVID-19 Early Warning Tool: Moore Swab Method for Wastewater Surveillance at an Institutional Level", @@ -1048861,6 +1050099,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.01.20241885", + "rel_title": "Prediction of Covid-19 spreading and optimal coordination of counter-measures: From microscopic to macroscopic models to Pareto fronts", + "rel_date": "2020-12-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241885", + "rel_abs": "The Covid-19 disease has caused a world-wide pandemic with more than 60 million positive cases and more than 1.4 million deaths by the end of November 2020. As long as effective medical treatment and vaccination are not available, non-pharmaceutical interventions such as social distancing, self-isolation and quarantine as well as far-reaching shutdowns of economic activity and public life are the only available strategies to prevent the virus from spreading. These interventions must meet conflicting requirements where some objectives, like the minimization of disease-related deaths or the impact on health systems, demand for stronger counter-measures, while others, such as social and economic costs, call for weaker counter-measures. Therefore, finding the optimal compromise of counter-measures requires the solution of a multi-objective optimization problem that is based on accurate prediction of future infection spreading for all combinations of counter-measures under consideration. We present a strategy for construction and solution of such a multi-objective optimization problem with real-world applicability. The strategy is based on a micro-model allowing for accurate prediction via a realistic combination of person-centric data-driven human mobility and behavior, stochastic infection models and disease progression models including micro-level inclusion of governmental intervention strategies. For this micro-model, a surrogate macro-model is constructed and validated that is much less computationally expensive and can therefore be used in the core of a numerical solver for the multi-objective optimization problem. The resulting set of optimal compromises between counter-measures (Pareto front) is discussed and its meaning for policy decisions is outlined.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hanna Wulkow", + "author_inst": "Zuse Institute Berlin" + }, + { + "author_name": "Tim Conrad", + "author_inst": "Zuse Institute Berlin and Freie Universitaet Berlin" + }, + { + "author_name": "Natasa Djurdjevac Conrad", + "author_inst": "Zuse Institute Berlin" + }, + { + "author_name": "Sebastian Alexander Mueller", + "author_inst": "TU Berlin" + }, + { + "author_name": "Kai Nagel", + "author_inst": "TU Berlin" + }, + { + "author_name": "Christof Schuette", + "author_inst": "FU Berlin" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.01.20242289", "rel_title": "The COVID-19 herd immunity threshold is not low: A re-analysis of European data from spring of 2020", @@ -1050141,33 +1051418,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.30.20241083", - "rel_title": "Risk assessment for airborne disease transmission bypoly-pathogen aerosols", - "rel_date": "2020-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20241083", - "rel_abs": "In the case of airborne diseases, pathogen copies are transmitted by droplets of respiratory tract fluid that are exhaled by the infectious that stay suspended in the air for some time and, after partial or full drying, inhaled as aerosols by the susceptible. The risk of infection in indoor environments is typically modelled using the Wells-Riley model or a Wells-Riley-like formulation, usually assuming the pathogen dose follows a Poisson distribution (mono-pathogen assumption). Aerosols that hold more than one pathogen copy, i.e. poly-pathogen aerosols, break this assumption even if the aerosol dose itself follows a Poisson distribution. For the largest aerosols where the number of pathogen in each aerosol can sometimes be several hundred or several thousand, the effect is non-negligible, especially in diseases where the risk of infection per pathogen is high. Here we report on a generalization of the Wells-Riley model and dose-response models for poly-pathogen aerosols by separately modeling each number of pathogen copies per aerosol, while the aerosol dose itself follows a Poisson distribution. This results in a model for computational risk assessment suitable for mono-/poly-pathogen aerosols. We show that the mono-pathogen assumption significantly overestimates the risk of infection for high pathogen concentrations in the respiratory tract fluid. The model also includes the aerosol removal due to filtering by the individuals which becomes significant for poorly ventilated environments with a high density of individuals, and systematically includes the effects of facemasks in the infectious aerosol source and sink terms and dose calculations.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Freja Nordsiek", - "author_inst": "Max Planck Institute for Dynamics and Self-Organization" - }, - { - "author_name": "Eberhard Bodenschatz", - "author_inst": "Max Planck Institute for Dynamics and Self-Organization" - }, - { - "author_name": "Gholamhossein Bagheri", - "author_inst": "Max Planck Institute for Dynamics and Self-Organization" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.30.20240911", "rel_title": "Missed childhood immunizations during the COVID-19 pandemic in Brazil: analyses of routine statistics and of a national household survey", @@ -1050347,6 +1051597,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.12.01.20241570", + "rel_title": "The Acceleration Index as a Test-Controlled Reproduction Number: Application to COVID-19 in France", + "rel_date": "2020-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241570", + "rel_abs": "We provide a novel way to correct the effective reproduction number for the time-varying amount of tests, using the acceleration index (Baunez et al., 2021) as a simple measure of viral spread dynamics. Not correcting results in the reproduction number being a biased estimate of viral acceleration and we provide a formal decomposition of the resulting bias, involving the useful notions of test and infectivity intensities. When applied to French data for the COVID-19 pandemic (May 13, 2020 - October 26, 2022), our decomposition shows that the reproduction number, when considered alone, characteristically underestimates the resurgence of the pandemic, compared to the acceleration index which accounts for the time-varying volume of tests. Because the acceleration index aggregates all relevant information and captures in real time the sizable time variation featured by viral circulation, it is a more parsimonious indicator to track the dynamics of an infectious disease outbreak in real time, compared to the equivalent alternative which would combine the reproduction number with the test and infectivity intensities.\n\nJEL Classification NumbersI18; H12", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Christelle Baunez", + "author_inst": "Institut Neurosciences Timone" + }, + { + "author_name": "Mickael Degoulet", + "author_inst": "Institut Neurosciences Timone" + }, + { + "author_name": "Stephane Luchini", + "author_inst": "Aix-Marseille School of Economics" + }, + { + "author_name": "Matteo Louis Pintus", + "author_inst": "AgroParisTech" + }, + { + "author_name": "Patrick Pintus", + "author_inst": "Aix-Marseille University and CNRS" + }, + { + "author_name": "Miriam Teschl", + "author_inst": "Aix-Marseille School of Economics" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.11.30.20240986", "rel_title": "A Net Benefit Approach for the Optimal Allocation of a COVID-19 Vaccine", @@ -1051595,61 +1052884,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.02.408112", - "rel_title": "Hepatitis C Virus Protease Inhibitors Show Differential Efficacy and Interactions with Remdesivir for Treatment of SARS-CoV-2 in Vitro", - "rel_date": "2020-12-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.02.408112", - "rel_abs": "Antivirals targeting SARS-CoV-2 could improve treatment of COVID-19. We evaluated the efficacy of clinically relevant hepatitis C virus (HCV) NS3 protease inhibitors (PI) against SARS-CoV-2 and their interactions with remdesivir, the only antiviral approved for treatment of COVID-19. HCV PI showed differential potency in VeroE6 cell-based antiviral assays based on detection of the SARS-CoV-2 Spike protein. Linear PI boceprevir, telaprevir and narlaprevir had 50% effective concentrations (EC50) of ~40 M. Among macrocyclic PI simeprevir, paritaprevir, grazoprevir, glecaprevir, voxilaprevir, vaniprevir, danoprevir and deldeprevir, simeprevir had the highest (EC50 15 M) and glecaprevir the lowest (EC50 >178 M) potency. Acyclic PI asunaprevir and faldaprevir had EC50 of 72 and 23 M, respectively. ACH-806, an HCV NS3 protease co-factor NS4A inhibitor, had EC50 of 46 M. For selected PI, potency was similar in human hepatoma Huh7.5 cells. Selectivity indexes, based on antiviral and cell viability assays, were highest for linear PI. In combination with remdesivir, linear PI boceprevir and narlaprevir showed antagonism, while macrocyclic PI simeprevir, paritaprevir and grazoprevir showed synergism with drug reduction indexes of up to 27 for simeprevir. Treatment of infected cultures with equipotent concentrations (1-fold EC50) of HCV PI revealed minor differences in barrier to SARS-CoV-2 escape. Complete viral suppression was achieved treating with [≥]3-fold EC50 boceprevir or combination of 1-fold EC50 simeprevir with 0.4-fold EC50 remdesivir, not leading to significant viral suppression in single treatments. Considering potency, human plasma concentrations and synergism with remdesivir, simeprevir seemed the most promising compound for optimization of future antiviral treatments of COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Karen A. Gammeltoft", - "author_inst": "Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health a" - }, - { - "author_name": "Yuyong Zhou", - "author_inst": "Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health a" - }, - { - "author_name": "Andrea Galli", - "author_inst": "Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health a" - }, - { - "author_name": "Anna Offersgaard", - "author_inst": "Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health a" - }, - { - "author_name": "Long V. Pham", - "author_inst": "Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health a" - }, - { - "author_name": "Ulrik Fahn\u00f8e", - "author_inst": "Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health a" - }, - { - "author_name": "Shan Feng", - "author_inst": "Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health a" - }, - { - "author_name": "Santseharay Ramirez", - "author_inst": "Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health a" - }, - { - "author_name": "Jens Bukh", - "author_inst": "Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health a" - }, - { - "author_name": "Judith M. Gottwein", - "author_inst": "Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital and Department of Immunology and Microbiology, Faculty of Health a" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.02.408047", "rel_title": "Effective in-vitro inactivation of SARS-CoV-2 by commercially available mouthwashes", @@ -1051973,6 +1053207,137 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.12.01.405738", + "rel_title": "Guidelines for accurate genotyping of SARS-CoV-2 using amplicon-based sequencing of clinical samples", + "rel_date": "2020-12-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.01.405738", + "rel_abs": "BackgroundSARS-CoV-2 genotyping has been instrumental to monitor virus evolution and transmission during the pandemic. The reliability of the information extracted from the genotyping efforts depends on a number of aspects, including the quality of the input material, applied technology and potential laboratory-specific biases. These variables must be monitored to ensure genotype reliability. The current lack of guidelines for SARS-CoV-2 genotyping leads to inclusion of error-containing genome sequences in studies of viral spread and evolution.\n\nResultsWe used clinical samples and synthetic viral genomes to evaluate the impact of experimental factors, including viral load and sequencing depth, on correct sequence determination using an amplicon-based approach. We found that at least 1000 viral genomes are necessary to confidently detect variants in the genome at frequencies of 10% or higher. The broad applicability of our recommendations was validated in >200 clinical samples from six independent laboratories. The genotypes of clinical isolates with viral load above the recommended threshold cluster by sampling location and period. Our analysis also supports the rise in frequency of 20A.EU1 and 20A.EU2, two recently reported European strains whose dissemination was favoured by travelling during the summer 2020.\n\nConclusionsWe present much-needed recommendations for reliable determination of SARS-CoV-2 genome sequence and demonstrate their broad applicability in a large cohort of clinical samples.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Slawomir Kubik", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Ana Claudia Marques", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Xiaobin Xing", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Janine Silvery", + "author_inst": "LABCON-OWL GmbH, Siemensstrasse 40, D-32105 Bad Salzuflen, USt-IdNr. DE814960283, Germany" + }, + { + "author_name": "Claire Bertelli", + "author_inst": "Genomics and Metagenomics Laboratory, Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland" + }, + { + "author_name": "Flavio De Maio", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Universita Cattolica del Sacro Cuore, L.go Agostino Gemelli 8, 00168 Roma, Italy" + }, + { + "author_name": "Spyros Pournaras", + "author_inst": "Laboratory of Clinical Microbiology, Attikon University Hospital Medical School, National and Kapodistrian University of Athens, Athens, Rimini 1, Chaidari 124 " + }, + { + "author_name": "Tom Burr", + "author_inst": "Source BioScience, Units 24/25, William James House, Cowley Road, Cambridge, CB4 0WU, United Kingdom" + }, + { + "author_name": "Yannis Duffourd", + "author_inst": "Equipe GAD - Inserm U1231, CHU Francois Mitterrand; 21000 Dijon, France" + }, + { + "author_name": "Helena Siemens", + "author_inst": "LABCON-OWL GmbH, Siemensstrasse 40, D-32105 Bad Salzuflen, USt-IdNr. DE814960283, Germany" + }, + { + "author_name": "Chakib Alloui", + "author_inst": "Laboratoire de Virologie, CHU Avicenne, AP-HP, 93000 Bobigny, France" + }, + { + "author_name": "Lin Song", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Yvan Wenger", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Alexandra Saitta", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Morgane Macheret", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Ewan W Smith", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Philippe Menu", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Marion Brayer", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + }, + { + "author_name": "Lars M Steinmetz", + "author_inst": "Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA" + }, + { + "author_name": "Ali Si-Mohammed", + "author_inst": "Laboratoire de Virologie, CHU Francois Mitterrand; 2, rue Angelique Ducoudray, 2100 Dijon, France" + }, + { + "author_name": "Josiane Chuisseu", + "author_inst": "Source BioScience, Units 24/25, William James House, Cowley Road, Cambridge, CB4 0WU, United Kingdom" + }, + { + "author_name": "Richard Stevens", + "author_inst": "Source BioScience, Units 24/25, William James House, Cowley Road, Cambridge, CB4 0WU, United Kingdom" + }, + { + "author_name": "Pantelis Constantoulakis", + "author_inst": "BioAnalytica Genotypos SA, 3-5 Ilision str, 115 28 Athens, Greece" + }, + { + "author_name": "Michela Sali", + "author_inst": "Dipartimento di Scienze biotecnologiche di base, cliniche intensivologiche e perioperatorie - Sezione di Microbiologia, Universita Cattolica del Sacro Cuore, Ro" + }, + { + "author_name": "Gilbert Greub", + "author_inst": "Genomics and Metagenomics Laboratory, Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Bugnon 48, 1011 Lausanne, Switzerland" + }, + { + "author_name": "Carsten Tiemann", + "author_inst": "LABCON-OWL GmbH, Siemensstrasse 40, D-32105 Bad Salzuflen, USt-IdNr. DE814960283, Germany" + }, + { + "author_name": "Vicent Pelechano", + "author_inst": "SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17165 Solna, Sweden" + }, + { + "author_name": "Adrian Willig", + "author_inst": "SOPHiA Genetics, Chemin des Mines 9, CH-1202 Geneva, Switzerland" + }, + { + "author_name": "Zhenyu Xu", + "author_inst": "SOPHiA Genetics, Rue du Centre 172, CH-1025 Saint Sulpice, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.11.30.405340", "rel_title": "Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2", @@ -1053777,33 +1055142,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.25.20239004", - "rel_title": "Optimal shutdown strategies for COVID-19 with economic and mortality costs: BC as a case study", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20239004", - "rel_abs": "Decision makers with the responsibility of managing policy for the COVID-19 epidemic have faced difficult choices in balancing the competing claims of saving lives and the high economic cost of shutdowns. In this paper we formulate a model with both epidemiological and economic content to assist this decision making process. We consider two ways to handle the balance between economic costs and deaths. First, we use the statistical value of life, which in Canada is about C$7 million, to optimise over a single variable, which is the sum of the economic cost and the value of lives lost. Our second method is to calculate the Pareto optimal front when we look at the two variables - deaths and economic costs.\n\nIn both cases we find that, for most parameter values, the optimal policy is to adopt an initial shutdown level which reduces the reproduction number of the epidemic to close to 1. This level is then reduced once a vaccination program is underway. Our model also indicates that an oscillating policy of strict and mild shutdowns is less effective than a policy which maintains a moderate shutdown level.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Martin T Barlow", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Noah D Marshall", - "author_inst": "McGill University" - }, - { - "author_name": "Rebecca Claire Tyson", - "author_inst": "University of British Columbia Okanagan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.29.20240416", "rel_title": "SARS-CoV-2 infection hospitalization, severity, criticality, and fatality rates", @@ -1054015,6 +1055353,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.11.26.20239103", + "rel_title": "I'm alone but not lonely. U-shaped pattern of perceived loneliness during the COVID-19 pandemic in the UK and Greece", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.26.20239103", + "rel_abs": "Many countries have adopted lengthy lockdown measures to mitigate the spreading of the COVID-19 virus. In this study, we train a RandomForest model using 10 variables quantifying individuals living environment, physical and mental health statuses to predict how long each of the UK participants (N=382) had been in lockdown. Self-perceived loneliness was found to be the most important variable predicting time in lockdown and, therefore, the aspect most influenced by the time the participant spent in lockdown. Subsequent statistical analysis showed a significant U-shaped curve for the levels of perceived loneliness (p<0.012), specifically decreasing during the 4th and 5th lockdown weeks. The same pattern was found on data from Greek citizens (N=129, p<0.041). These results suggest that lockdown measures may have affected how people evaluated their social support while in lockdown, leading to a decreased sense of loneliness. Implications of this study should be reflected on policies and countermeasures to current and future pandemics.\n\nState of relevanceThis study aims to inform policies for the current and/or future pandemics, particularly those involving lockdown restrictions. It highlights that self-perceived loneliness was the trait most affected by the time spent in lockdown: data show that the very first period of lockdown was characterised by a decrease in levels of perceived loneliness. The machine learning approach adopted and the statistical validation on two different Western European countries ensure that the uncovered pattern is substantial. This result highlights the dissociation between objective social support and perceived loneliness: initially, restrictions may have triggered better social behaviours among communities or increased the level of gratitude for the social support people have always received. The short duration of these desirable effects suggests that measures and campaigns promoting better social support strategies could be potentially effective, even in social isolation, to keep the levels of perceived loneliness low.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Alessandro Carollo", + "author_inst": "University of Trento" + }, + { + "author_name": "Andrea Bizzego", + "author_inst": "University of Trento" + }, + { + "author_name": "Giulio Gabrieli", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Keri Ka-Yee Wong", + "author_inst": "Department of Psychology and Human Development, University College London, London, UK" + }, + { + "author_name": "Adrian Raine", + "author_inst": "Departments of Criminology, Psychiatry, and Psychology, University of Pennsylvania" + }, + { + "author_name": "Gianluca Esposito", + "author_inst": "Nanyang Technological University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.11.25.20238741", "rel_title": "I dont feel safe sitting in my own yard: Chicago resident experiences with urban rats during a COVID-19 stay-at-home order", @@ -1055279,97 +1056656,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.27.20239699", - "rel_title": "Evaluation of the accuracy and ease-of-use of Abbott PanBio - A WHO emergency use listed, rapid, antigen-detecting point-of-care diagnostic test for SARS-CoV-2", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.27.20239699", - "rel_abs": "BackgroundDiagnostics are essential for controlling the pandemic. Identifying a reliable and fast diagnostic is needed to support testing. We assessed performance and ease-of-use of the Abbott PanBio antigen-detecting rapid diagnostic test (Ag-RDT).\n\nMethodsThis prospective, multi-centre diagnostic accuracy study enrolled at two sites in Germany. Following routine testing with RT-PCR, a second study-exclusive swab was performed for Ag-RDT testing. Routine swabs were nasopharyngeal (NP) or combined NP/oropharyngeal (OP) whereas the study-exclusive swabs were NP. To evaluate performance, sensitivity and specificity were assessed overall and in predefined sub analyses accordingly to cycle-threshold values, days of symptoms, disease severity and study site. Additionally, an ease-of-use assessment and System Usability Scale (SUS) were performed.\n\nFindings1108 participants were enrolled between Sept 28 and Oct 30, 2020. Of these, 106 (9{middle dot}6%) were PCR-positive. The Abbott PanBio detected 92/106 PCR-positive participants with a sensitivity of 86{middle dot}8% (95% CI: 79{middle dot}0% - 92{middle dot}0%) and a specificity of 99{middle dot}9% (95% CI: 99{middle dot}4%-100%). The sub analyses indicated that sensitivity was 95{middle dot}8% in CT-values <25 and within the first seven days from symptom onset. The test was characterized as easy to use (SUS: 86/100) and considered suitable for point-of- care settings.\n\nInterpretationThe Abbott PanBio Ag-RDT performs well for SARS-CoV-2 testing in this large manufacturer independent study, confirming its WHO recommendation for Emergency Use in settings with limited resources.\n\nFundingThe Foundation of Innovative New Diagnostics supplied the test kits for the study. The internal funds from the Heidelberg University as well as the Charite Berlin supported this study.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Lisa Johanna Kr\u00fcger", - "author_inst": "Division of Clinical Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Mary Gaeddert", - "author_inst": "Division of Clinical Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Frank Tobian", - "author_inst": "Division of Clinical Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Federica Lainati", - "author_inst": "Division of Clinical Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Julian A.F. Klein", - "author_inst": "Division of Clinical Tropical Medicine, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Paul Schnitzler", - "author_inst": "Virology, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Hans-Georg Kr\u00e4usslich", - "author_inst": "Virology, Heidelberg University Hospital, Heidelberg, Germany" - }, - { - "author_name": "Olga Nikolai", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Andreas K. Lindner", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Frank P. Mockenhaupt", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Joachim Seybold", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Medical Dire" - }, - { - "author_name": "Victor M. Corman", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin, and Berlin Institute of Health; Institute of" - }, - { - "author_name": "Nira R. Pollock", - "author_inst": "Department of Laboratory Medicine, Boston Childrens Hospital, Boston, MA, USA" - }, - { - "author_name": "Britta Knorr", - "author_inst": "Department of Public Health Rhein Neckar Region, Germany" - }, - { - "author_name": "Andreas Welker", - "author_inst": "Department of Public Health Rhein Neckar Region, Germany" - }, - { - "author_name": "Margaretha de Vos", - "author_inst": "Foundation for Innovative New Diagnostics, Geneva, Switzerland" - }, - { - "author_name": "Jilian Sacks", - "author_inst": "Foundation for Innovative New Diagnostics, Geneva, Switzerland" - }, - { - "author_name": "Claudia M. Denkinger", - "author_inst": "Division of Clinical Tropical Medicine, Heidelberg University Hospital, German Centre for Infection Research (DZIF), partner site Heidelberg University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.27.20239608", "rel_title": "Saliva, a relevant alternative sample for SARS-CoV2 detection", @@ -1055681,6 +1056967,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.28.20240259", + "rel_title": "Threatening second wave of COVID-19 is imminent: A deep learning perspective", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.28.20240259", + "rel_abs": "When the entire world is waiting restlessly for a safe and effective COVID-19 vaccine that could soon become a reality, numerous countries around the globe are grappling with unprecedented surges of new COVID-19 cases. As the number of new cases is skyrocketing, pandemic fatigue and public apathy towards different intervention strategies are posing new challenges to the government officials to combat the pandemic. Henceforth, it is indispensable for the government officials to understand the future dynamics of COVID-19 flawlessly in order to develop strategic preparedness and resilient response planning. In light of the above circumstances, probable future outbreak scenarios in Brazil, Russia and the United kingdom have been sketched in this study with the help of four deep learning models: long short term memory (LSTM), gated recurrent unit (GRU), convolutional neural network (CNN) and multivariate convolutional neural network (MCNN). In our analysis, CNN algorithm has outperformed other deep learning models in terms of validation accuracy and forecasting consistency. It has been unearthed in our study that CNN can provide robust long term forecasting results in time series analysis due to its capability of essential features learning, distortion invariance and temporal dependence learning. However, the prediction accuracy of LSTM algorithm has been found to be poor as it tries to discover seasonality and periodic intervals from any time series dataset, which were absent in our studied countries. Our study has highlighted the promising validation of using convolutional neural networks instead of recurrent neural networks when it comes to forecasting with very few features and less amount of historical data.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Khondoker Nazmoon Nabi", + "author_inst": "Bangladesh University of Engineering and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.27.20240036", "rel_title": "Rapid disappearance of influenza following the implementation of COVID-19 mitigation measures in Hamilton, Ontario", @@ -1056769,49 +1058074,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.11.30.403873", - "rel_title": "Multi-parameter formulation development for an HIV-vaccine protein with direct validation of epitope binding integrity and stoichiometry", - "rel_date": "2020-11-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.30.403873", - "rel_abs": "Vaccines are on the front line-of-defense against infectious diseases, ranging from threats we are familiar with, including polio, tuberculosis, or HIV, to novel and emerging threats such as SARS-CoV-2. Successful development of new protein-based vaccines requires sophisticated and efficient development of storage and formulation conditions. Here we demonstrate the combined power of 2binds sophisticated buffer matrix FORMOscreen(R) and NanoTemper Technologies novel Prometheus Panta high-throughput Dynamic Light Scattering/Nano Differential Scanning Fluorimetry instrument. We show that this combination can comprehensively improve critical biophysical parameters for the HIV-1 vaccine BG505-SOSIP and find the optimal formulation condition with unmatched efficiency.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Corinna Popp", - "author_inst": "2bind GmbH, Am Biopark 11, 93053 Regensburg, Germany" - }, - { - "author_name": "Philipp Schramm", - "author_inst": "NanoTemper Technologies GmbH, Floessergasse 4, 81369 Munich, Germany" - }, - { - "author_name": "Ralf Wagner", - "author_inst": "Institute of Medical Microbiology and Hygiene, University Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany" - }, - { - "author_name": "David Peterhoff", - "author_inst": "Institute of Medical Microbiology and Hygiene, University Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany" - }, - { - "author_name": "Christopher Battle", - "author_inst": "NanoTemper Technologies GmbH, Floessergasse 4, 81369 Munich, Germany" - }, - { - "author_name": "Christian Kleusch", - "author_inst": "NanoTemper Technologies GmbH, Floessergasse 4, 81369 Munich, Germany" - }, - { - "author_name": "Maximilian G Plach", - "author_inst": "2bind GmbH, Am Biopark 11, 93053 Regensburg, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.11.30.399154", "rel_title": "A Novel SARS-CoV-2 Multitope Protein/Peptide Vaccine Candidate is Highly Immunogenic and Prevents Lung Infection in an Adeno Associated Virus Human Angiotensin-Converting Enzyme 2 (AAV hACE2) Mouse Model", @@ -1057167,6 +1058429,61 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2020.11.30.20240721", + "rel_title": "Remote working in mental health services: a rapid umbrella review of pre-COVID-19 literature", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20240721", + "rel_abs": "BackgroundTele-mental health care has been rapidly adopted to maintain services during the pandemic, and there is now substantial interest in its future role. Service planning and policy making for recovery from the pandemic and beyond should draw not only on COVID-19 experiences, but also on the substantial research evidence accumulated prior to this.\n\nAimsto conduct an umbrella review of systematic reviews of research literature and evidence-based guidance on remote working in mental health, including both qualitative and quantitative literature.\n\nMethodThree databases were searched between January 2010 and August 2020 for systematic reviews meeting pre-defined criteria. Reviews retrieved were independently screened and those meeting inclusion criteria were synthesised and assessed for risk of bias. Narrative synthesis was used to report findings\n\nResultsNineteen systematic reviews met inclusion criteria. Fifteen examined clinical effectiveness, eight reported on aspects of tele-mental health implementation, ten reported on acceptability to service users and clinicians, two on cost-effectiveness and one on guidance. Most reviews were assessed as low quality. Findings suggested that video-based communication could be as effective and acceptable as face-face formats, at least in the short-term. Evidence was lacking on extent of digital exclusion and how it can be overcome, or on significant context such as children and young people and inpatient settings.\n\nConclusionsThis umbrella review suggests that tele-mental health has potential to be an effective and acceptable form of service delivery. However, we found limited evidence on impacts of large-scale implementation across catchment areas. Combining previous evidence and COVID-19 experiences may allow realistic planning for future tele-mental health implementation.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Phoebe Barnett", + "author_inst": "University College London" + }, + { + "author_name": "Lucy Goulding", + "author_inst": "King's College London" + }, + { + "author_name": "Cecilia Casetta", + "author_inst": "King's College London" + }, + { + "author_name": "Harriet Jordan", + "author_inst": "King's College London" + }, + { + "author_name": "Luke Sheridan Rains", + "author_inst": "University College London" + }, + { + "author_name": "Thomas Steare", + "author_inst": "University College London" + }, + { + "author_name": "Julie Williams", + "author_inst": "King's College London" + }, + { + "author_name": "Lisa Wood", + "author_inst": "University College London" + }, + { + "author_name": "Fiona Gaughran", + "author_inst": "King's College London" + }, + { + "author_name": "Sonia Johnson", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.11.25.20234914", "rel_title": "The efficacy and safety of hydroxychloroquine in COVID19 patients : a multicenter national retrospective cohort", @@ -1058243,45 +1059560,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.24.20237529", - "rel_title": "Preterm birth rates in a large tertiary Australian maternity centre during COVID-19 mitigation measures", - "rel_date": "2020-11-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237529", - "rel_abs": "ObjectivesTo compare the prevalence of live preterm birth rates during COVID-19 restriction measures with infants born during the same weeks in 2013-2019 in Queensland, Australia.\n\nDesign, setting, participantsDeidentified obstetric and neonatal data were extracted from the Mater Mothers electronic healthcare records database. This is a supra-regional tertiary perinatal centre.\n\nMain outcome measuresLogistic regressions were used to examine preterm birth rates during the beginning of COVID-19 restrictions (16 March-17 April; \"early\"; 6,955 births) and during the strictest part of COVID-19 restrictions (30 March-1 May; \"late\"; 6,953 births), according to gestational age subgroups and birth onset (planned or spontaneous). We adjusted for multiple covariates, including maternal age, body mass index, ethnicity, parity, socioeconomic status, maternal asthma, diabetes mellitus and/or hypertensive disorder. Stillbirth rates were also examined (16 March-1 May).\n\nResultsA reduction in planned moderate/late preterm births was observed primarily during the early restriction period compared with the same calendar weeks in the previous seven years (29 versus an average of 64 per 1,000 births; adjusted odds ratio [aOR] 0.39, 95% CI 0.22-0.71). There was no effect on extremely or very preterm infants, spontaneous preterm births, or stillbirth rates. Rolling averages from January to June revealed a two-week non-significant spike in spontaneous preterm births from late-April to early-May, 2020.\n\nConclusionsPlanned births for moderate/late preterm infants more than halved during early COVID-19 mitigation measures. Together with evidence from other nations, the COVID-19 pandemic provides a unique opportunity to identify causal and preventative factors for preterm birth.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Linda A Gallo", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Tania F Gallo", - "author_inst": "Melbourne, Victoria" - }, - { - "author_name": "Danielle J Borg", - "author_inst": "Mater Research Institute-University of Queensland" - }, - { - "author_name": "Karen M Moritz", - "author_inst": "Child Health Research Centre, The University of Queensland" - }, - { - "author_name": "Vicki L Clifton", - "author_inst": "Mater Research Institute-University of Queensland" - }, - { - "author_name": "Sailesh Kumar", - "author_inst": "Mater Research Institute-University of Queensland, Mater Mothers Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2020.11.24.20238204", "rel_title": "Marginal Value of Quarantine", @@ -1058457,6 +1059735,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.24.20238139", + "rel_title": "Prediction of evolution of the second wave of Covid-19 pandemic in Italy", + "rel_date": "2020-11-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20238139", + "rel_abs": "A relevant problem in the study of the Covid-19 pandemic is the study of its temporal evolution. Such evolution depends on a number of factors, among which the average rate of contacts between susceptible and infected individuals, the duration of infectiousness and the transmissibility, that is the probability of infection after a contact between susceptible and infected individuals. In a previous study, we analyzed the potentiality of a number of distributions to describe the evolution of the pandemic and the potentiality of each distribution to mathematically predict the evolution of the pandemic in Italy. Since the number of daily tests was changing and increasing with time, we used the ratio of the new daily cases per swab. We considered distributions of the type of Gauss (normal), Gamma, Beta, Weibull, Lognormal and in addition of the type of the Planck blackbody radiation law. The Planck law, describing the amount of energy of the electromagnetic radiation emitted by a black body at each wavelength or at each frequency, marked in 1900 the beginning of Quantum Mechanics. The result of our analysis was that, among the considered distributions, the Planck law has the best potentiality to mathematically predict the evolution of the pandemic and the best fitting capability. In this paper, we analyze the time evolution of the second wave of the Covid-19 pandemic in Italy and in particular we predict the ratio of the new daily cases per swab at Christmas 2020 using the data in the interval from 17 Oct to 21 Nov. According to Figure 4 and Figure 8, the prediction for such a ratio around Christmas is approximately within 6% and 7%. In this study there is also an attempt to account for the effects of the governmental containment measures.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ignazio Ciufolini", + "author_inst": "University of Salento" + }, + { + "author_name": "Antonio Paolozzi", + "author_inst": "School of Aerospace Engineering, Sapienza University of Rome" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.25.20237776", "rel_title": "Body mass index and risk of COVID-19 diagnosis, hospitalisation, and death: a population-based multi-state cohort analysis including 2,524,926 people in Catalonia, Spain", @@ -1060113,41 +1061414,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.11.25.20236646", - "rel_title": "Systematic evaluation of transcriptomic disease risk and diagnostic biomarker overlap between COVID-19 and tuberculosis: a patient-level meta-analysis", - "rel_date": "2020-11-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20236646", - "rel_abs": "BackgroundThe novel coronavirus, SARS-CoV-2, has increased the burden on healthcare systems already strained by a high incidence of tuberculosis (TB) as co-infection and dual presentation are occurring in syndemic settings. We aimed to understand the interaction between these diseases by profiling COVID-19 gene expression signatures on RNA-sequencing data from TB-infected individuals.\n\nMethodsWe performed a systematic review and patient-level meta-analysis by querying PubMed and pre-print servers to derive eligible COVID-19 gene expression signatures from human whole blood (WB), PBMCs or BALF studies. A WB influenza dataset served as a control respiratory disease signature. Three large TB RNA-seq datasets, comprising multiple cohorts from the UK and Africa and consisting of TB patients across the disease spectrum, were chosen to profile these signatures. Putative \"COVID-19 risk scores\" were generated for each sample in the TB datasets using the TBSignatureProfiler package. Risk was stratified by time to TB diagnosis in progressors and contacts of pulmonary and extra-pulmonary TB. An integrative analysis between TB and COVID-19 single-cell RNA-seq data was performed and a population-level meta-analysis was conducted to identify shared gene ontologies between the diseases and their relative enrichment in COVID-19 disease severity states.\n\nResults35 COVID-19 gene signatures from nine eligible studies comprising 98 samples were profiled on TB RNA-seq data from 1181 samples from 853 individuals. 25 signatures had significantly higher COVID-19 risk in active TB (ATB) compared with latent TB infection (p <0{middle dot}005), 13 of which were validated in two independent datasets. FCN1- and SPP1-expressing macrophages enriched in BALF during severe COVID-19 were identified in circulation during ATB. Shared perturbed ontologies included antigen presentation, epigenetic regulation, platelet activation, and ROS/RNS production were enriched with increasing COVID-19 severity. Finally, we demonstrate that the overlapping transcriptional responses may complicate development of blood-based diagnostic signatures of co-infection.\n\nInterpretationOur results identify shared dysregulation of immune responses in COVID-19 and TB as a dual risk posed by co-infection to COVID-19 severity and TB disease progression. These individuals should be followed up for TB in the months subsequent to SARS-CoV-2 diagnosis.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Dylan Sheerin", - "author_inst": "Infectious Diseases and Immune Defence Division, WEHI (formerly The Walter & Eliza Hall Institute of Medical Research), Parkville 3279, VIC, Australia." - }, - { - "author_name": "Abhimanyu Abhimanyu", - "author_inst": "Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Rd, Observatory, 7925," - }, - { - "author_name": "Xutao Wang", - "author_inst": "Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA; Department of Biostatistics, Boston University, Boston, MA" - }, - { - "author_name": "William Evan Johnson", - "author_inst": "Division of Computational Biomedicine and Bioinformatics Program, Boston University, Boston, MA, USA; Department of Biostatistics, Boston University, Boston, MA" - }, - { - "author_name": "Anna Coussens", - "author_inst": "Infectious Diseases and Immune Defence Division, WEHI (formerly The Walter & Eliza Hall Institute of Medical Research), Parkville 3279, VIC, Australia." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.25.20238345", "rel_title": "Diabetes and Mortality Among 1.6 Million Adult Patients Screened for SARS-CoV-2 in Mexico", @@ -1060411,6 +1061677,49 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.11.25.399055", + "rel_title": "Triple Combination Nitazoxanide, Ribavirin, and Hydroxychloroquine results in the multiplicative reduction of in vitro SARS-CoV-2 viral replication", + "rel_date": "2020-11-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.25.399055", + "rel_abs": "BackgroundAn immediate unmet medical need exists to test and develop existing approved drugs against SARS-COV-2. Despite many efforts, very little progress has been made regarding finding low-cost oral medicines that can be made widely available worldwide to address the global pandemic.\n\nMethodsWe sought to examine if a triple combination of nitazoxanide (using its active metabolite tizoxanide), ribavirin, and hydroxychloroquine would lead to a multiplicative effects on viral replication of SARS-COV-2 resulting in a significant reduction of virus yield using VERO E6 cells as a model of viral replication.\n\nResultsVirus yield measured in PFU/ml was ~ 2 logs lower with triple combination versus either drug alone, resulting in the prolongation of time to peak cytopathic effects (CPE). The time to produce 50% CPE increased from 2.8 days for viral controls versus 5.3 days for triple combination therapy. Finally, for each 1-log reduction in virus yield 24 hours post-infection, there was an additional 0.7-day delay in onset of CPE.\n\nConclusionsA triple combination of tizoxanide, ribavirin, and hydroxychloroquine produced a reduction in SARS-COV-2 viral replication in Vero E6 cells, warranting exploration in additional cell lines as well as human clinical trials.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Elena Lian", + "author_inst": "Colorado State University" + }, + { + "author_name": "Carley McAlister", + "author_inst": "Colorado State University" + }, + { + "author_name": "Gabriela Ramirez", + "author_inst": "Colorado State University" + }, + { + "author_name": "David N Chernoff", + "author_inst": "Synavir Corporation" + }, + { + "author_name": "Gregory Went", + "author_inst": "Synavir Corporation" + }, + { + "author_name": "Justin Hoopes", + "author_inst": "Synavir Corporation" + }, + { + "author_name": "Rushika Perera", + "author_inst": "Colorado State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.26.399436", "rel_title": "Host-directed FDA-approved drugs with antiviral activity against SARS-CoV-2 identified by hierarchical in silico/in vitro screening methods", @@ -1061763,65 +1063072,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.23.20237362", - "rel_title": "Association of antihypertensive agents with the risk of in-hospital death in patients with Covid-19", - "rel_date": "2020-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20237362", - "rel_abs": "In this retrospective multicenter cohort study, we aimed to investigate the association between antihypertensive agent exposure and in-hospital mortality in patients with Covid-19. Of 8,078 hospitalized patients for Covid-19, 3,686 (45.6%) had hypertension including 2043 (55.4%) patients exposed to a renin-angiotensin-aldosterone inhibitors (RAASi), 1624 (44.1%) to calcium channel blockers (CCB) and 1154 (37.7%) to beta-blockers. Overall in-hospital 30-day mortality was 23.1%. Compared to non-users, the risk of mortality was lower in CCB (aOR, 0.83 [0.70-0.99]) and beta-blockers users (aOR, 0.80 [0.67-0.95]), and not different in RAASi users. These findings support the continuation of antihypertensive agents in patients with Covid-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Laurent Chouchana", - "author_inst": "AP-HP" - }, - { - "author_name": "Nathanael Beeker", - "author_inst": "AP-HP" - }, - { - "author_name": "Nicolas Garcelon", - "author_inst": "Institut Imagine" - }, - { - "author_name": "Bastien Rance", - "author_inst": "AP-HP" - }, - { - "author_name": "Nicolas Paris", - "author_inst": "AP-HP" - }, - { - "author_name": "Elisa Salamanca", - "author_inst": "AP-HP" - }, - { - "author_name": "Elisabeth Polard", - "author_inst": "CHU Rennes" - }, - { - "author_name": "Anita Burgun", - "author_inst": "AP-HP" - }, - { - "author_name": "Jean-Marc Treluyer", - "author_inst": "AP-HP" - }, - { - "author_name": "Antoine Neuraz", - "author_inst": "Necker-Enfants Malades Hospital" - }, - { - "author_name": "- AP-HP / Universities / Inserm COVID-19 research collaboration", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2020.11.23.20237149", "rel_title": "Experimental efficacy of the face shield and the mask against emitted and potentially received particles", @@ -1062125,6 +1063375,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.11.23.20237198", + "rel_title": "The sensitivity of SARS-CoV-2 antigen tests in the view of large-scale testing", + "rel_date": "2020-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20237198", + "rel_abs": "ObjectivesAntigen tests have recently emerged as an interesting alternative to SARS-CoV-2 diagnostic PCR, thought to be valuable especially for the screening of bigger communities. To check appropriateness of the antigen based testing, we determined sensitivity of two point-of-care antigen tests when applied to a cohort of COVID-19 symptomatic, COVID-19 asymptomatic and healthy persons.\n\nMethodsWe examined nasopharyngeal swabs with antigen test 1 (Panbio Covid-19 Ag Rapid Test, Abbott) and antigen test 2 (Standard F Covid-19 Ag FIA, SD Biosensor). An additional nasopharyngeal and oropharyngeal swab of the same individual was checked with PCR (Allplex SARS-nCoV-2, Seegene). Within a 4-day period in October 2020, we collected specimens from 591 subjects. Of them, 290 had COVID-19 associated symptoms.\n\nResultsWhile PCR positivity was detected in 223 cases, antigen test 1 and antigen test 2 were found positive in 148 (sensitivity 0.664, 95% CI 0.599 - 0.722) and 141 (sensitivity 0.623, 95% CI 0.558 - 0.684) patients, respectively. When only symptomatic patients were analysed, sensitivity increased to 0.738 (95% CI 0.667 - 0.799) for the antigen test 1 and to 0.685 (95% CI 0.611 - 0.750) for the antigen test 2. The substantial drop in sensitivity to 12.9% (95% CI 0.067 - 0.234) was observed for samples with the PCR threshold cycle above > 30.\n\nConclusionsLow sensitivity of antigen tests leads to the considerable risk of false negativity. It is advisable to implement repeated testing with high enough frequency if the antigen test is used as a frontline screening tool.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Pavel Drevinek", + "author_inst": "2nd Faculty of Medicine, Charles University and Motol University Hospital" + }, + { + "author_name": "Jakub Hurych", + "author_inst": "2nd Faculty of Medicine, Charles University and Motol University Hospital" + }, + { + "author_name": "Zdenek Kepka", + "author_inst": "Motol University Hospital" + }, + { + "author_name": "Ales Briksi", + "author_inst": "Motol University Hospital" + }, + { + "author_name": "Michal Kulich", + "author_inst": "Faculty of Mathematics and Physics, Charles University" + }, + { + "author_name": "Miroslav Zajac", + "author_inst": "Motol University Hospital" + }, + { + "author_name": "Petr Hubacek", + "author_inst": "2nd Faculty of Medicine, Charles University and Motol University Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.24.20237560", "rel_title": "Demography, social contact patterns and the COVID-19 burden in different settings of Ethiopia: a modeling study", @@ -1063413,121 +1064706,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.11.23.20236810", - "rel_title": "Healthcare workers hospitalized due to COVID-19 have no higher risk of death than general population. Data from the Spanish SEMI-COVID-19 Registry.", - "rel_date": "2020-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20236810", - "rel_abs": "AimTo determine whether healthcare workers (HCW) hospitalized in Spain due to COVID-19 have a worse prognosis than non-healthcare workers (NHCW).\n\nMethodsObservational cohort study based on the SEMI-COVID-19 Registry, a nationwide registry that collects sociodemographic, clinical, laboratory, and treatment data on patients hospitalised with COVID-19 in Spain. Patients aged 20-65 years were selected. A multivariate logistic regression model was performed to identify factors associated with mortality.\n\nResultsAs of 22 May 2020, 4393 patients were included, of whom 419 (9.5%) were HCW. Median (interquartile range) age of HCW was 52 (15) years and 62.4% were women. Prevalence of comorbidities and severe radiological findings upon admission were less frequent in HCW. There were no difference in need of respiratory support and admission to intensive care unit, but occurrence of sepsis and in-hospital mortality was lower in HCW (1.7% vs. 3.9%; p=0.024 and 0.7% vs. 4.8%; p<0.001 respectively). Age, male sex and comorbidity, were independently associated with higher in-hospital mortality and healthcare working with lower mortality (OR 0.219, 95%CI 0.069-0.693, p=0.01). 30-days survival was higher in HCW (0.968 vs. 0.851 p<0.001).\n\nConclusionsHospitalized COVID-19 HCW had fewer comorbidities and a better prognosis than NHCW. Our results suggest that professional exposure to COVID-19 in HCW does not carry more clinical severity nor mortality.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Jesus Diez-Manglano", - "author_inst": "Royo Villanova Hospital" - }, - { - "author_name": "Nataya Solis Marquinez", - "author_inst": "San Agustin University Hospital" - }, - { - "author_name": "Andrea Alvarez Garcia", - "author_inst": "San Agustin University Hospital" - }, - { - "author_name": "Nicolas Alcala Rivera", - "author_inst": "Royo Villanova Hospital" - }, - { - "author_name": "Irene Maderuelo Riesco", - "author_inst": "San Agustin University Hospital" - }, - { - "author_name": "Martin Gerico Aseguinolaza", - "author_inst": "Royo Villanova Hospital" - }, - { - "author_name": "Jose Luis Beato Perez", - "author_inst": "Albacete University Hospital" - }, - { - "author_name": "Manuel Mendez Bailon", - "author_inst": "San Carlos Clinical Hospital" - }, - { - "author_name": "Ane Elbire Laburua-Iturburu Ruiz", - "author_inst": "Santa Marina Hospital" - }, - { - "author_name": "Miriam Garcia Gomez", - "author_inst": "Urduliz Alfredo Espinosa Hospital" - }, - { - "author_name": "Carmen Martinez Cilleros", - "author_inst": "HLA Moncloa Hospital" - }, - { - "author_name": "Paula Maria Pesqueira Fontan", - "author_inst": "Santiago Clinical Hospital" - }, - { - "author_name": "Lucy Abella Vazquez", - "author_inst": "Ntra Sra Candelaria University Hospital" - }, - { - "author_name": "Julio Cesar Blazquez Encinar", - "author_inst": "Torrevieja University Hospital" - }, - { - "author_name": "Ramon Boixeda", - "author_inst": "Mataro Hospital" - }, - { - "author_name": "Ricardo Gil Sanchez", - "author_inst": "La Fe University Hospital" - }, - { - "author_name": "Andres de la Pena Fernandez", - "author_inst": "Son Llatzer Hospital" - }, - { - "author_name": "Jose Loureiro Amigo", - "author_inst": "Moises Broggi Hospital" - }, - { - "author_name": "Joaquin Escobar Sevilla", - "author_inst": "Virgen de las Nieves University Hospital" - }, - { - "author_name": "Marcos Guzman Garcia", - "author_inst": "San Juan de la Cruz Hospital" - }, - { - "author_name": "Maria Dolores Martin Escalante", - "author_inst": "Costa del Sol Hospital" - }, - { - "author_name": "Jeffrey Oskar Magallanes Gamboa", - "author_inst": "Nuestra Senora del Prado Hospital" - }, - { - "author_name": "Angel Luis Martinez Gonzalez", - "author_inst": "Leon University Hospital" - }, - { - "author_name": "Carlos Lumbreras Bermejo", - "author_inst": "12 de Octubre University Hospital" - }, - { - "author_name": "Juan Miguel Anton Santos", - "author_inst": "Infanta Cristina University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.24.393405", "rel_title": "Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking", @@ -1063899,6 +1065077,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.20.20233890", + "rel_title": "A Data Driven Change-point Epidemic Model for Assessing the Impact of Large Gathering and Subsequent Movement Control Order on COVID-19 Spread in Malaysia", + "rel_date": "2020-11-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20233890", + "rel_abs": "The second wave of COVID-19 in Malaysia is largely attributed to a mass gathering held in Sri Petaling between February 27, 2020 and March 1, 2020, which contributed to an exponential rise of COVID-19 cases in the country. Starting March 18, 2020, the Malaysian government introduced four consecutive phases of a Movement Control Order (MCO) to stem the spread of COVID-19. The MCO was implemented through various non-pharmaceutical interventions (NPIs). The reported number of cases reached its peak by the first week of April and then started to reduce, hence proving the effectiveness of the MCO. To gain a quantitative understanding of the effect of MCO on the dynamics of COVID-19, this paper develops a class of mathematical models to capture the disease spread before and after MCO implementation in Malaysia. A heterogeneous variant of the Susceptible-Exposed-Infected-Recovered (SEIR) model is developed with additional compartments for asymptomatic transmission. Further, a change-point is incorporated to model the before and after disease dynamics, and is inferred based on data. Related statistical analyses for inference are developed in a Bayesian framework and are able to provide quantitative assessments of (1) the impact of the Sri Petaling gathering, and (2) the extent of decreasing transmission during the MCO period. The analysis here also quantitatively demonstrates how quickly transmission rates fall under effective NPI implemention within a short time period.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sarat Chandra Dass", + "author_inst": "Heriot-Watt University Malaysia Campus" + }, + { + "author_name": "Wai Meng Kwok", + "author_inst": "Heriot-Watt University Malaysia Campus" + }, + { + "author_name": "Gavin J Gibson", + "author_inst": "Heriot-Watt University Edinburgh Campus" + }, + { + "author_name": "Balvinder S Gill", + "author_inst": "Institute for Medical Research Malaysia" + }, + { + "author_name": "Bala M Sundram", + "author_inst": "Institute for Medical Research Malaysia" + }, + { + "author_name": "Sarbhan Singh", + "author_inst": "Institute for Medical Research Malaysia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.20.20220749", "rel_title": "Community Transmission of SARS-CoV-2 by Fomites: Risks and Risk Reduction Strategies", @@ -1065027,37 +1066244,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.22.20236059", - "rel_title": "What have we learned so far about COVID-19 volunteering in the UK? A rapid review of the literature", - "rel_date": "2020-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.22.20236059", - "rel_abs": "BackgroundCommunity engagement and volunteering are essential for the public response to COVID-19. Since March 2020 a large number of people in the UK have been regularly doing unpaid activities to benefit others besides their close relatives. Although most mutual aid groups emerged from local neighbourhoods and communities, official public institutions also fostered community volunteering, namely through the community champions scheme. By considering a broad definition of COVID-19 volunteering, this article describes a systematic review of the literature focused on two broad questions: What have we learned so far from COVID-19 volunteering both at the UK national level and the more local community level? What have we learned from engagement with local communities and community champions during the COVID-19 period?\n\nMethodsA rapid review of the literature in peer-reviewed databases and grey literature was applied in our search, following the PRISMA principles. The search was conducted from 10 to 16 of October 2020, and sources were included on the basis of having been published between January and October 2020, focusing on COVID-19 and addressing community groups, volunteering groups, volunteers, or community champions in the UK.\n\nResultsAfter initial screening, a total of 40 relevant sources were identified. From these, 28 were considered eligible. Findings suggest that food shopping and emotional support were the most common activities, but there were diverse models of organisation and coordination in COVID-19 volunteering. Additionally, community support groups seem to be adjusting their activities and scope of action to current needs and challenges. Volunteers were mostly women, middle-class, highly educated, and working-age people. Social networks and connections, local knowledge, and social trust were key dimensions associated with community organising and volunteering. Furthermore, despite the efforts of a few official public institutions and councils, there has been limited community engagement and collaboration with volunteering groups and other community-based organisations.\n\nConclusionsWe identified important factors for fostering community engagement and COVID volunteering as well as gaps in the current literature. We suggest that future research should be directed towards deepening knowledge on sustaining community engagement, collaboration and community participation over time, during and beyond this pandemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Guanlan Mao", - "author_inst": "University of Sussex" - }, - { - "author_name": "Maria Fernandes-Jesus", - "author_inst": "University of Sussex" - }, - { - "author_name": "Evangelos Ntontis", - "author_inst": "Canterbury Christ Church University" - }, - { - "author_name": "John Drury", - "author_inst": "University of Sussex" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.20.20235978", "rel_title": "Pay-as-you-go LPG supports sustainable clean cooking in Kenyan informal urban settlement, including during a period of COVID-19 lockdown", @@ -1065305,6 +1066491,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.21.392555", + "rel_title": "Interactions of anti-COVID-19 drug candidates with multispecific ABC and OATP drug transporters", + "rel_date": "2020-11-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.21.392555", + "rel_abs": "In the COVID-19 epidemic, several repurposed drugs have been proposed to alleviate the major health effects of the disease. These drugs are often applied together with analgesics or non-steroid anti-inflammatory compounds, and co-morbid patients may also be treated with anticancer, cholesterol-lowering or antidiabetic agents. Since drug ADME-tox properties may be significantly affected by multispecific transporters, here we examined the interactions of the repurposed drugs with the key human multidrug transporters, present in the major tissue barriers and strongly affecting pharmacokinetics. Our in vitro studies, using a variety of model systems, explored the interactions of the antimalarial agents chloroquine and hydroxychloroquine, the antihelmintic ivermectin, and the proposed antiviral compounds, ritonavir, lopinavir, favipiravir and remdesivir with the ABCB1/Pgp, ABCG2/BCRP and ABCC1/MRP1 exporters, as well as the OATP2B1 and OATP1A2 uptake transporters. The results presented here show numerous pharmacologically relevant transporter interactions and may provide a warning for the potential toxicities of these repurposed drugs, especially in drug combinations at the clinic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Agnes Telbisz", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Csilla Ambrus", + "author_inst": "Solvo Biotechnology Ltd" + }, + { + "author_name": "Orsolya Mozner", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Edit Szabo", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Gyorgy Varady", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Eva Bakos", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Balazs Sarkadi", + "author_inst": "Research Centre for Natural Sciences" + }, + { + "author_name": "Csilla Ozvegy-Laczka", + "author_inst": "Research Centre for Natural Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.11.21.392670", "rel_title": "A repurposed, blood gene signature is associated with poor outcomes in SARS-CoV-2", @@ -1066625,49 +1067858,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.11.19.20234567", - "rel_title": "Association of HLA class I genotypes with age at death of COVID-19 patients", - "rel_date": "2020-11-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234567", - "rel_abs": "BackgroundHLA class I molecules play a crucial role in the development of a specific immune response to viral infections by presenting viral peptides to cell surface where they will be further recognized by T cells. In the present manuscript we explored whether HLA class I genotype can be associated with critical course of COVID-19 by searching possible connections between genotypes of deceased patients and their age at death.\n\nMethods and FindingsHLA-A, HLA-B and HLA-C genotypes of n = 111 deceased patients with COVID-19 (Moscow, Russia) and n = 428 volunteers were identified with targeted next-generation sequencing. Deceased patients were splitted into two groups according to age at death: n = 26 adult patients with age at death below 60 completed years (inclusively) and n = 85 elderly patients over 60. With the use of HLA class I genotypes we developed a risk score which is associated with the ability to present SARS-CoV-2 peptides by an individuals HLA class I molecule set. The resulting risk score was significantly higher in the group of deceased adults compared to elderly adults (p = 0.00348, AUC ROC = 0.68). In particular, presence of HLA-A*01:01 allele was associated with high risk, while HLA-A*02:01 and HLA-A*03:01 mainly contributed to the low risk group. The analysis of homozygous patients highlighted the results even stronger: homozygosity by HLA-A*01:01 mainly accompanied early deaths, while only one HLA-A*02:01 homozygote died before 60.\n\nConclusionsThe obtained results suggest the important role of HLA class I peptide presentation in the development of a specific immune response to COVID-19. While prediction of age at death by HLA class I genotype had a reliable performance, involvement of HLA class II genotype can make it even higher in the future studies.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Maxim Shkurnikov", - "author_inst": "HSE University" - }, - { - "author_name": "Stepan Nersisyan", - "author_inst": "HSE University" - }, - { - "author_name": "Tatjana Jankevic", - "author_inst": "Pirogov Russian National Research Medical University" - }, - { - "author_name": "Alexei Galatenko", - "author_inst": "Lomonosov Moscow State University" - }, - { - "author_name": "Ivan Gordeev", - "author_inst": "O.M. Filatov City Clinical Hospital" - }, - { - "author_name": "Valery Vechorko", - "author_inst": "O.M. Filatov City Clinical Hospital" - }, - { - "author_name": "Alexander Tonevitsky", - "author_inst": "HSE University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.11.19.20235036", "rel_title": "Statistical techniques to estimate the SARS-CoV-2 infection fatality rate", @@ -1067063,6 +1068253,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.19.20234849", + "rel_title": "Community factors and excess mortality in first wave of the COVID-19 pandemic.", + "rel_date": "2020-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234849", + "rel_abs": "Risk factors for increased risk of death from Coronavirus Disease 19 (COVID-19) have been identified1,2 but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality at the community level during the first wave of the pandemic in England. We used geocoded data on all deaths in people aged 40 years and older during March-May 2020 compared with 2015-2019 in 6,791 local communities. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or high percent of people with a non-White ethnicity (including Black, Asian and other minority ethnic groups). Conversely, after accounting for other community characteristics, we found no association between population density or air pollution and excess mortality. Overall, the social and environmental variables accounted for around 15% of the variation in mortality at community level. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed if England and other industrialised countries are to avoid further widening of inequalities in mortality patterns during the second wave.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Bethan Davies", + "author_inst": "Imperial College London" + }, + { + "author_name": "Brandon L Parkes", + "author_inst": "Imperial College London" + }, + { + "author_name": "James Bennett", + "author_inst": "Imperial College London" + }, + { + "author_name": "Daniela Fecht", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marta Blangiardo", + "author_inst": "Imperial College London" + }, + { + "author_name": "Majid Ezzati", + "author_inst": "Imperial College London" + }, + { + "author_name": "Paul Elliott", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.21.392639", "rel_title": "Anti-COVID-19 efficacy of ivermectin in the golden hamster", @@ -1069039,73 +1070272,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.19.20234583", - "rel_title": "Impact of the home confinement related to COVID-19 on the device-assessed physical activity and sedentary patterns of Spanish older adults", - "rel_date": "2020-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.19.20234583", - "rel_abs": "ObjectivesThe main objective of this study was to device-assess the levels of physical activity and sedentary behaviour patterns of older adults during the situation prior to COVID-19 pandemic, home-quarantine and the ending of isolation. We also aimed analysing the effectiveness of an unsupervised home-based exercise routine to counteract the potential increase in sedentary behaviour during the periods within the pandemic.\n\nMethods18 non-institutionalized elderly (78.4{+/-}6.0 y.), members of the Spanish cohort of EXERNET-Elder 3.0 project participated in the study. They were recommended to perform an exercise prescription based on resistance, balance and aerobic exercises during the pandemic. Wrist triaxial accelerometers (ActiGraph GT9X) were used to assess the percentage of sedentary time, physical activity and sedentary bouts and breaks of sedentary time. An ANOVA for repeated measures was performed to analyse the differences between the three different periods.\n\nResultsDuring home-quarantine, older adults spent more time in sedentary behaviours (71.6{+/-}5.3%) in comparison with either the situation prior to the pandemic (65.5{+/-}6.7%) or the ending of isolation (67.7{+/-}7.1%) (all p<0.05). Moreover, participants performed less bouts of physical activity and with a shorter duration during home quarantine (both p<0.05). Additionally, no differences in the physical activity behaviours were found between the situation prior to the pandemic and the ending of isolation.\n\nConclusionsAccording with our results, the home-quarantine could negatively affect health due to increased sedentary lifestyle and the reduction of physical activity. Therefore, our unsupervised exercise program does not seem to be a completely effective strategy at least in this period.\n\nWhat is already known on this topicO_LIAlthough the available information is scarce and includes subjective methodology (questionnaires), it seems that the COVID-19 pandemic has negatively affected physical activity patterns.\nC_LIO_LIIt is known that physical activity interventions are effective in improving health and reducing sedentary lifestyle in older adults. Nevertheless, little is known about whether an unsupervised home-based exercise routine is an effective alternative to counteract the potential increase in sedentary behaviour in this specific population during the pandemic lockdown.\nC_LI\n\nWhat are the findings? / What this study addsO_LIDespite unsupervised training, during home-quarantine, older adults spent more sedentary time than in the situation prior to COVID-19 and the ending of isolation (phase 0).\nC_LIO_LIThere were no differences in break of sedentary time patterns between the situation prior to COVID-19 and the periods within the pandemic.\nC_LIO_LIDuring home-quarantine older adults performed fewer and shorter physical activity bouts than in the situation prior to COVID-19 despite unsupervised training.\nC_LIO_LIOur unsupervised home-exercise routine was not a completely effective alternative to avoid the increase of sedentary behaviour during home-quarantine.\nC_LI\n\nHow might it impact on clinical practice in the future?O_LIOur findings can be used as a starting point to manage isolation restrictions more effectively and to develop strategies to promote physical activity and reduce sedentary behaviour among older adults during situations of forced lockdowns, as in the present COVID-19 pandemic.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Angel Ivan Fernandez-Garcia Jr.", - "author_inst": "University of Zaragoza" - }, - { - "author_name": "Jorge Marin-Puyalto", - "author_inst": "Universidad de Zaragoza" - }, - { - "author_name": "Alba Maria Gomez-Cabello", - "author_inst": "Centro Universitario de la Defensa, Zaragoza" - }, - { - "author_name": "Angel Matute-Llorente", - "author_inst": "Universidad de Zaragoza" - }, - { - "author_name": "Jorge Subias-Perie", - "author_inst": "Universidad de Zaragoza" - }, - { - "author_name": "Jorge Perez-Gomez", - "author_inst": "HEME (Health, Economy, Motricity and Education) research group. University of Extremadura, Caceres" - }, - { - "author_name": "Gabriel Lozano-Berges", - "author_inst": "Universidad de Zaragoza" - }, - { - "author_name": "Asier Manas", - "author_inst": "GENUD Toledo Research Group, Universidad de Castilla-La Mancha, Toledo" - }, - { - "author_name": "Amelia Guadalupe-Grau", - "author_inst": "ImFine Research Group. Facultad de Ciencias de la Actividad Fisica y del Deporte-INEF, Universidad Politecnica de Madrid, Madrid" - }, - { - "author_name": "Marcela Gonzalez-Gross", - "author_inst": "ImFine Research Group. Facultad de Ciencias de la Actividad Fisica y del Deporte-INEF, Universidad Politecnica de Madrid, Madrid" - }, - { - "author_name": "Ignacio Ara", - "author_inst": "GENUD Toledo Research Group, Universidad de Castilla-La Mancha, Toledo" - }, - { - "author_name": "Jose Antonio Casajus", - "author_inst": "Universidad de Zaragoza" - }, - { - "author_name": "German Vicente-Rodriguez", - "author_inst": "Universidad de Zaragoza" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "sports medicine" - }, { "rel_doi": "10.1101/2020.11.18.20233882", "rel_title": "IMPACT OF THE CORONAVIRUS DISEASE 2019 PANDEMIC ON SURGICAL VOLUME IN JAPAN: A COHORT STUDY USING ADMINISTRATIVE DATA", @@ -1069561,6 +1070727,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.18.20225029", + "rel_title": "The Invasive Respiratory Infection Surveillance (IRIS) Initiative reveals significant reductions in invasive bacterial infections during the COVID-19 pandemic", + "rel_date": "2020-11-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20225029", + "rel_abs": "BackgroundStreptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis are leading causes of invasive diseases including bacteraemic pneumonia and meningitis, and of secondary infections post-viral respiratory disease. They are typically transmitted via respiratory droplets. We investigated rates of invasive disease due to these pathogens during the early phase of the COVID-19 pandemic.\n\nMethodsLaboratories in 26 countries across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae and N meningitidis from 1 January 2018 to 31 May 2020. Weekly cases in 2020 vs 2018-2019 were compared. Streptococcus agalactiae data were collected from nine laboratories for comparison to a non-respiratory pathogen. The stringency of COVID-19 containment measures was quantified by the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed by Google COVID-19 Community Mobility Reports. Interrupted time series modelling quantified changes in rates of invasive disease in 2020 relative to when containment measures were imposed.\n\nFindingsAll countries experienced a significant, sustained reduction in invasive diseases due to S pneumoniae, H influenzae and N meningitidis, but not S agalactiae, in early 2020, which coincided with the introduction of COVID-19 containment measures in each country. Similar impacts were observed across most countries despite differing stringency in COVID-19 control policies. There was no evidence of a specific effect due to enforced school closures.\n\nInterpretationThe introduction of COVID-19 containment policies and public information campaigns likely reduced transmission of these bacterial respiratory pathogens, leading to a significant reduction in life-threatening invasive diseases in many countries worldwide.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Angela B Brueggemann", + "author_inst": "University of Oxford" + }, + { + "author_name": "Melissa J Jansen van Rensburg", + "author_inst": "University of Oxford" + }, + { + "author_name": "David Shaw", + "author_inst": "University of Oxford" + }, + { + "author_name": "Noel D McCarthy", + "author_inst": "University of Warwick" + }, + { + "author_name": "Keith A Jolley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Martin CJ Maiden", + "author_inst": "University of Oxford" + }, + { + "author_name": "Mark PG van der Linden", + "author_inst": "University Hospital RWTH Aachen" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.18.388140", "rel_title": "Detecting SARS-CoV-2 variants with SNP genotyping", @@ -1070913,53 +1072122,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.16.20231597", - "rel_title": "Declining Trend in the Initial SARS-CoV-2 Viral Load During the Pandemic: Preliminary Observations from Detroit, Michigan", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20231597", - "rel_abs": "We report a downward trend in the initial SARS-CoV-2 viral load in nasopharyngeal swab samples of hospitalized patients with COVID-19 in Detroit, Michigan, coinciding with a decrease in the number of deaths during April-June 2020. A gradual decrease in the initial viral load reflected the downward progression of the pandemic.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Said El Zein", - "author_inst": "Wayne State University / Detroit Medical Center" - }, - { - "author_name": "Omar Chehab", - "author_inst": "Wayne State University / Detroit Medical Center" - }, - { - "author_name": "Nivine El-Hor", - "author_inst": "Wayne State University / Detroit Medical Center" - }, - { - "author_name": "Samer Alkassis", - "author_inst": "Wayne State University / Detroit Medical Center" - }, - { - "author_name": "Tushar Mishra", - "author_inst": "Wayne State University / Detroit Medical Center" - }, - { - "author_name": "Vichar Trivedi", - "author_inst": "Wayne State University / Detroit Medical Center" - }, - { - "author_name": "Hossein Salimnia", - "author_inst": "Wayne State University / Detroit Medical Center" - }, - { - "author_name": "Pranatharthi Chandrasekar", - "author_inst": "Wayne State University / Detroit Medical Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.16.20232389", "rel_title": "HOW IS THE IMPACT ON PUBLIC HEALTH OF SECOND WAVE OF COVID-19 PANDEMIC COMPARED TO THE FIRST WAVE? CASE STUDY OF ITALY", @@ -1071195,6 +1072357,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.16.20232850", + "rel_title": "The impact of COVID-19 employment shocks on suicide and poverty alleviation programs: An early-stage investigation", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232850", + "rel_abs": "This paper examines whether the COVID-19-induced employment shocks are associated with increases in suicides and safety net use in the second and third quarters of 2020. We exploit plausibly exogenous regional variation in the magnitude of the employment shocks in Japan and adopt a difference-in-differences research design to examine and control for possible confounders. Our preferred point estimates suggest that a one-percentage-point increase in the unemployment rate in the second quarter of 2020 is associated with, approximately, an additional 0.52 suicides, 28 unemployment benefit recipients, 88 recipients of a temporary loan program, and 10 recipients of public assistance per 100,000 population per month. A simple calculation based on these estimates suggests that if a region experienced a one-percentage-point increase in the unemployment rate caused by the COVID-19 crisis in the second quarter of 2020, which is roughly equivalent to the third-highest regional employment shock, this would be associated with 37.4%, 60.5%, and 26.5% increases in the total, female, and male suicide rates respectively in July 2020 compared with July 2019. Our baseline findings are robust to several different model specifications, although we do not assert that our research design perfectly solves the problem of estimation bias.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Michihito Ando", + "author_inst": "Rikkyo University" + }, + { + "author_name": "Masato Furuichi", + "author_inst": "Teikyo University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.11.16.20227389", "rel_title": "Designing Efficient Contact Tracing Through Risk-Based Quarantining", @@ -1072367,41 +1073552,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.11.18.20233973", - "rel_title": "COVID-19 Twitter-based analysis reveals differential concerns across areas with socioeconomic disparities", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20233973", - "rel_abs": "ObjectiveWe sought to understand how U.S. residents responded to COVID-19 as it emerged, and the extent to which spatial-temporal factors impacted response.\n\nMaterials and MethodsWe mined and reverse-geocoded 269,556 coronavirus-related social media postings on Twitter from January 23rd to March 25th, 2020. We then ranked tweets based on the socioeconomic status of the county they originated from using the Area Deprivation Index (ADI); that we also used to identify areas with high initial disease counts (\"hotspots\"). We applied topic modeling on the tweets to identify chief concerns and determine their evolution over time. We also investigated how topic proportions varied based on ADI and between hotspots and non-hotspots.\n\nResultsWe identified 45 topics, which shifted from early-outbreak-related content in January, to the presidential election and governmental response in February, to lifestyle changes in March. Highly resourced areas (low ADI) were concerned with stocks, social distancing, and national-level policies, while high ADI areas shared content with negative expression, prayers, and discussion of the CARES Act economic relief package. Within hotspots, these differences stand, with the addition of increased discussion regarding employment in high ADI versus low ADI hotspots.\n\nDiscussionTopic modeling captures the major concerns in COVID-19-related discussion on a social media platform in the early months of the pandemic. Our study extends previous studies that utilized topic modeling on COVID-19 related tweets and linked the identified topics to socioeconomic status using ADI. Comparisons between low and high ADI areas indicate differential Twitter discussions, corresponding to greater concern with economic hardship and impacts of the pandemic in less resourced communities, and less focus on general public health messaging.\n\nConclusionThis work demonstrates a novel framework for assessing differential topics of conversation correlating to income, education, and housing disparities. This, with integration of COVID-19 hotspots, offers improved analysis of crisis response on Twitter. Such insight is critical for informed public health messaging campaigns in future waves of the pandemic, which should focus in part specifically on the interests of those who are most vulnerable in the lowest resourced health settings.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yihua Su", - "author_inst": "Health Informatics Program, Yale School of Public Health, New Haven, CT, USA" - }, - { - "author_name": "Aarthi Venkat", - "author_inst": "Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA" - }, - { - "author_name": "Yadush Yadav", - "author_inst": "Health Informatics Program, Yale School of Public Health, New Haven, CT, USA" - }, - { - "author_name": "Lisa B. Puglisi", - "author_inst": "Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA; Pain Research, Informatics, Multimorbidities and Education Center, VA Connecticut " - }, - { - "author_name": "Samah Fodeh", - "author_inst": "Health Informatics Program, Yale School of Public Health, New Haven, CT, USA; Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, " - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.11.18.20233825", "rel_title": "COVIDStrategyCalculator: A standalone software to assess testing- and quarantine strategies for incoming travelers, contact person management and de-isolation", @@ -1072613,6 +1073763,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.16.20232884", + "rel_title": "Comparative Efficacy and Safety of Current Drugs against COVID-19: a Systematic Review and Net-work Meta Analysis", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232884", + "rel_abs": "The rapid spread of coronavirus disease (COVID-19) has greatly disrupted the livelihood of many people around the world. To date, more than 35.16 million COVID-19 cases with 1.037million total deaths have been reported worldwide. Compared with China, where the disease was first reported, cases of COVID-19, the number of confirmed cases for the disease in the rest of the world have been incredibly high. Even though several dugs have been suggested to be used against the disease, the said interventions should be backed by empirical clinical evidence. Therefore, this paper provides a systematic review and a meta-analysis of efficacy and safety of different COVID-19 drugs.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSCurrently, Covid-19 is one of the most urgent and significant health challenge, globally. However, so far there is no specific and effective treatment strategy against the disease. Nonetheless, there are numerous debates over the effectiveness and potential adverse effects of different COVID-19 antivirals. In general, there is invaluable need to continually report on new advances and successes against COVID-19, apparently to aid in managing the pandemic.\n\nAdded value of this studyThis study provides a comprehensive, evidence-based guide on the management of multiple COVID-19 symptoms. In particular, we provide a review of 14 drugs, placebos and standard treatments against COVID 19. Meanwhile, we also performed a meta-analysis based on four clinical outcome indicators, to measure and compare the efficacy and safety of current interventions.\n\nImplications of all the available evidenceFindings of this research will guide clinical decision in COVID-19 patients. It will also provide a basis for predicting clinical outcomes such as efficacy, mortality and safety of interventions against the disease.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Yi Li", + "author_inst": "China Pharmaceutical University" + }, + { + "author_name": "Wei He", + "author_inst": "China Pharmaceutical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.17.20233080", "rel_title": "COVID-19: more than a little flu? Insights from the Swiss hospital-based surveillance of Influenza and COVID-19", @@ -1073885,25 +1075058,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.11.18.388983", - "rel_title": "HLA class I genotypes customize vaccination strategies in immune simulation to combat COVID-19", - "rel_date": "2020-11-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.18.388983", - "rel_abs": "Memory CD8+ T cells are associated with a better outcome in Coronavirus Disease 2019 (COVID-19) and recognized as promising vaccine targets against viral infections. This study determined the efficacy of population-dominant and infection-relevant human leukocyte antigens (HLA) class I proteins to present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peptides through calculating binding affinities and simulating CD8+ T cell responses. As a result, HLA class I proteins distinguished or shared various viral peptides derived from viruses. HLA class I supertypes clustered viral peptides through recognizing anchor and preferred residues. SARS-CoV-2 peptides overlapped significantly with SARS but minimally with common human coronaviruses. Immune simulation of CD8+ T cell activation using predicted SARS-CoV-2 peptide antigens depended on high-affinity peptide binding, anchor residue interaction, and synergistic presentation of HLA class I proteins in individuals. Results demonstrated that multi-epitope vaccination, employing a strong binding affinity, viral adjuvants, and heterozygous HLA class I genes, induced potent immune responses. Therefore, optimal CD8+ T cell responses can be achieved and customized contingent on HLA class I genotypes in human populations, supporting a precise vaccination strategy to combat COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Shouxiong Huang", - "author_inst": "University of Cincinnati College of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.11.18.388991", "rel_title": "Production of anti-SARS-CoV-2 hyperimmune globulin from convalescent plasma", @@ -1074251,6 +1075405,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.16.20231100", + "rel_title": "Deconditioning in people living with dementia during the COVID-19 pandemic: findings from the Promoting Activity, Independence and Stability in Early Dementia (PrAISED) process evaluation", + "rel_date": "2020-11-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20231100", + "rel_abs": "BackgroundRestrictions introduced in response to the COVID-19 pandemic led to increased risk of deconditioning in the general population. No empirical evidence of this effect however has been empirically gathered in people living with dementia.\n\nObjectiveThis study aims to identify the causes and effects of COVID-19-related deconditioning in people living with dementia.\n\nDesignLongitudinal phenomenological qualitative study.\n\nSubjectsParticipants living with dementia, their carers and therapists involved in the Promoting Activity, Independence and Stability in Early Dementia (PrAISED) process evaluation during the COVID-19 pandemic.\n\nMethodsQualitative interviews with participants were conducted remotely at two time points. The data were analysed through deductive thematic analysis.\n\nResultsTwenty-four participants living with dementia, 19 carers and 15 therapists took part in the study. A self-reinforcing pattern was common, whereby lockdown made the person apathetic, demotivated, socially-disengaged, and frailer. This reduced activity levels, which in turn reinforced the effects of deconditioning over time. Without external supporters, most participants lacked the motivation / cognitive abilities to keep active. Provided the proper infrastructure and support, some participants could use tele-rehabilitation to combat deconditioning.\n\nConclusionThe added risks and effects of deconditioning on people with dementia require considerable efforts from policy makers and clinicians to ensure that they initiate and maintain physical activity in prolonged periods of social distancing. Delivering rehabilitation in the same way as before the pandemic might not be feasible or sustainable and innovative approaches must be found. Digital support for this population has shown promising results, but still remains a challenge.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Claudio Di Lorito", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Tahir Masud", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "John Gladman", + "author_inst": "University of Notitngham" + }, + { + "author_name": "Maureen Godfrey", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Marianne Dunlop", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Rowan H Harwood", + "author_inst": "University of Nottingham" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2020.11.16.20232009", "rel_title": "The total number and mass of SARS-CoV-2 virions in an infected person", @@ -1076003,41 +1077196,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.12.20230458", - "rel_title": "Seroprevalence of SARS-CoV-2 IgG in healthcare workers and other staff at North Bristol NHS Trust: a sociodemographic analysis", - "rel_date": "2020-11-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20230458", - "rel_abs": "Structured summaryO_ST_ABSBackgroundC_ST_ABSHealthcare workers (HCWs) are at increased risk of infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). There are limited data exploring the relative impact of geographical and socioeconomic factors on risk of SARS-CoV-2 infection among HCWs.\n\nAimTo estimate and explore SARS-CoV-2 IgG antibody seroprevalence in HCWs and support staff at a hospital in South West England.\n\nMethodsWe conducted a nested cross-sectional study from May-July 2020. Inverse probability weighted regression was used to estimate seroprevalence of SARS-CoV-2 and associations with demographic and socioeconomic risk factors that were robust to selection into testing.\n\nFindingsAttendance for testing varied by demographic and socioeconomic factors. The overall rate of SARS-CoV-2 IgG seroprevalence among tested staff was 9.3% (638/6858). The highest seroprevalence was found in wards associated with SARS-CoV-2 outbreaks and among junior staff with patient-facing roles. Black, Asian and Minority Ethnic (BAME) staff had increased odds of SARS-CoV-2 seroprevalence (adjusted OR: 1.99, 95%CI: 1.69, 2.34; p<0.001) relative to White staff, except for those categorised as Medical/Dental. We found a significant association between neighbourhood deprivation and seroprevalence (p<0.01). Seroprevalence ranged from 12% in staff residing in areas with the greatest relative deprivation to 8.4% in the least deprived.\n\nConclusionTransmission between staff groups is evident within the healthcare setting. BAME individuals were at increased risk of infection with SARS-CoV-2. Work role, area of residence, and neighbourhood deprivation all contribute to SARS-CoV-2 infection risk. As hospitals introduce routine staff SARS-CoV-2 testing they should consider differential uptake of testing among staff groups.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Christopher R Jones", - "author_inst": "Department of Infection Science, Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom" - }, - { - "author_name": "Fergus W Hamilton", - "author_inst": "Department of Infection Science, Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom" - }, - { - "author_name": "Ameeka Thompson", - "author_inst": "Department of Infection Science, Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom" - }, - { - "author_name": "Tim T Morris", - "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom" - }, - { - "author_name": "Ed Moran", - "author_inst": "Department of Infection Science, Southmead Hospital, North Bristol NHS Trust, Bristol, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.13.20229781", "rel_title": "Epigenetic clocks are not accelerated in COVID-19 patients", @@ -1076353,6 +1077511,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.12.20230912", + "rel_title": "Prevalence of IgG antibodies against the severe acute respiratory syndrome coronavirus-2 among healthcare workers in Tennessee during May and June, 2020", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20230912", + "rel_abs": "SARS-CoV-2 seroprevalence was low (<1%) in this large population of healthcare workers (HCWs) across the state of Tennessee (n=11,787) in May-June 2020. Among those with PCR results, 81.5% of PCR and antibody test results were concordant. SARS-CoV-2 seroprevalence was higher among HCWs working in high-community-transmission regions and among younger workers.\n\nImportanceThese results may be seen as a baseline assessment of SARS-CoV-2 seroprevalence among HCWs in the American South during a period of growth, but not yet saturation, of infections among susceptible populations. In fact, this period of May-June 2020 was marked by the extension of renewed and sustained community-wide transmission after mandatory quarantine periods expired in several more populous regions of Tennessee. Where community transmission remains low, HCWs may still be able to effectively mitigate SARS-CoV-2 transmission, preserving resources for populations at high risk of severe disease, and these sorts of data help highlight such strategies.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Peter F Rebeiro", + "author_inst": "Vanderbilt University School of Medicine, Department of Medicine, Divisions of Infectious Diseases & Epidemiology; Department of Biostatistics" + }, + { + "author_name": "Kara J Levinson", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "Lindsay Jolly", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "Elizabeth Kassens", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "George J Dizikes", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "Richard S Steece", + "author_inst": "Tennessee Department of Health, Division of Laboratory Services" + }, + { + "author_name": "David C Metzger", + "author_inst": "Ballad Health" + }, + { + "author_name": "Matthew Loos", + "author_inst": "Ballad Health" + }, + { + "author_name": "Ron Buchheit", + "author_inst": "Department Of Emergency Medicine, University Of Tennessee College of Medicine Chattanooga, Erlanger Health System" + }, + { + "author_name": "Lisa D Duncan", + "author_inst": "University of Tennessee Medical Center, Department of Pathology" + }, + { + "author_name": "Lori A Rolando", + "author_inst": "Vanderbilt University School of Medicine, Department of Medicine, Division of General Internal Medicine & Public Health and Vanderbilt Health and Wellness" + }, + { + "author_name": "Jonathan Schmitz", + "author_inst": "Vanderbilt University School of Medicine , Department of Pathology, Microbiology and Immunology" + }, + { + "author_name": "Heather A Hart", + "author_inst": "Vanderbilt University School of Medicine, Department of Surgery, Division of Trauma" + }, + { + "author_name": "David M Aronoff", + "author_inst": "Vanderbilt University School of Medicine, Department of Medicine, Division of Infectious Diseases; Department of Pathology, Microbiology and Immunology" + }, + { + "author_name": "- Tennessee COVID-19 Serology Study Team", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.12.20230656", "rel_title": "Development and validation of a highly sensitive and specific electrochemical assay to quantify anti-SARS-CoV-2 IgG antibodies to facilitate pandemic surveillance and monitoring of vaccine response", @@ -1077677,85 +1078910,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.15.20231985", - "rel_title": "Assessment of functional capacity with cardiopulmonary exercise testing in non-severe COVID-19 patients at three months follow-up", - "rel_date": "2020-11-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.15.20231985", - "rel_abs": "IntroductionLong-term effects of Coronavirus Disease of 2019 (COVID-19) and their sustainability in a large number of patients are of the utmost relevance. We aimed to determine: 1)functional capacity of non-severe COVID-19 survivors by cardiopulmonary exercise testing (CPET); 2)those characteristics associated with worse CPET performance.\n\nMethodsWe prospectively enrolled the first 150 consecutive subjects with laboratory-confirmed COVID-19 infection discharged alive from March to April 2020 at Azienda Sanitaria Locale (ASL)3, Genoa, Italy. At 3-month from hospital discharge, complete clinical evaluation, trans-thoracic echocardiography, cardiopulmonary exercise testing (CPET), pulmonary function test (PFT), and dominant leg extension (DLE) maximal strength evaluation were performed.\n\nResultsExcluding severe and incomplete/missing cases, 110 patients were analyzed. Median percent predicted peak oxygen uptake (%pVO2) was 90.9(79.2-109.0)%. Thirty-eight(34.5%) patients had %pVO2 below, whereas 72(65.5%) above the 85% predicted value (indicating normality). Median PFT parameters were within normal limits.\n\nEight(21.1%) patients had a mainly respiratory, 9(23.7%) a mainly cardiac, 3(7.9%) a mixed-cardiopulmonary, and 18(47.4%) a non-cardiopulmonary limitation of exercise. Eighty-one(73.6%) patients experimented at least one symptom, without relationship with %pVO2 (p>0.05).\n\nMultivariate linear regression analysis showed age ({beta}=0.46, p=0.020), percent weight loss ({beta}=-0.77, p=0.029), active smoke status ({beta}=-7.07, p=0.019), length of hospital stay ({beta}=-0.20, p=0.042), and DLE maximal strength ({beta}=1.65, p=0.039) independently associated with %pVO2.\n\nConclusionsHalf of non-severe COVID-19 survivors show functional capacity limitation mainly explained by muscular impairment, albeit cardiopulmonary causes are possible. These findings call for future research to identify patients at higher risk of long-term effects, that may benefit from careful surveillance and targeted rehabilitation.\n\nTake-home messagesat 3-month cardiopulmonary exercise testing 38/110(34.5%) non-severe COVID-19 survivors had percent predicted peak oxygen uptake (%pVO2) < 85% (indicating normality). Half of them had functional capacity limitation mainly explained by muscular impairment.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Piero Clavario", - "author_inst": "Cardiac Rehabilitation Center of Genoa, Azienda Sanitaria Locale, ASL 3 Genovese, Genoa, Italy" - }, - { - "author_name": "Vincenzo De Marzo", - "author_inst": "IRCCS Ospedale Policlinico San Martino" - }, - { - "author_name": "Roberta Lotti", - "author_inst": "Cardiology Unit, DICATOV - Cardiothoracic and Vascular Department, IRCCS San Martino Hospital, Genoa, Italy" - }, - { - "author_name": "Cristina Barbara", - "author_inst": "Cardiac Rehabilitation Center of Genoa, Azienda Sanitaria Locale, ASL 3 Genovese, Genoa, Italy" - }, - { - "author_name": "Annalisa Porcile", - "author_inst": "Cardiac Rehabilitation Center of Genoa, Azienda Sanitaria Locale, ASL 3 Genovese, Genoa, Italy" - }, - { - "author_name": "Carmelo Russo", - "author_inst": "Cardiac Rehabilitation Center of Genoa, Azienda Sanitaria Locale, ASL 3 Genovese, Genoa, Italy" - }, - { - "author_name": "Federica Beccaria", - "author_inst": "Cardiac Rehabilitation Center of Genoa, Azienda Sanitaria Locale, ASL 3 Genovese, Genoa, Italy" - }, - { - "author_name": "Marco Bonavia", - "author_inst": "Cardiac Rehabilitation Center of Genoa, Azienda Sanitaria Locale, ASL 3 Genovese, Genoa, Italy" - }, - { - "author_name": "Luigi Carlo Bottaro", - "author_inst": "Cardiac Rehabilitation Center of Genoa, Azienda Sanitaria Locale, ASL 3 Genovese, Genoa, Italy" - }, - { - "author_name": "Marta Caltabellotta", - "author_inst": "Cardiac Rehabilitation Center of Genoa, Azienda Sanitaria Locale, ASL 3 Genovese, Genoa, Italy" - }, - { - "author_name": "Flavia Chioni", - "author_inst": "Cardiac Rehabilitation Center of Genoa, Azienda Sanitaria Locale, ASL 3 Genovese, Genoa, Italy" - }, - { - "author_name": "Monica Santangelo", - "author_inst": "Cardiac Rehabilitation Center of Genoa, Azienda Sanitaria Locale, ASL 3 Genovese, Genoa, Italy" - }, - { - "author_name": "Arto Hautala", - "author_inst": "Cardiovascular Research Group, Division of Cardiology, Oulu University Hospital, University of Oulu, Finland" - }, - { - "author_name": "Pietro Ameri", - "author_inst": "Cardiology Unit, DICATOV - Cardiothoracic and Vascular Department, IRCCS San Martino Hospital, Genoa, Italy" - }, - { - "author_name": "Marco Canepa", - "author_inst": "Cardiology Unit, DICATOV - Cardiothoracic and Vascular Department, IRCCS San Martino Hospital, Genoa, Italy" - }, - { - "author_name": "Italo Porto", - "author_inst": "Cardiology Unit, DICATOV - Cardiothoracic and Vascular Department, IRCCS San Martino Hospital, Genoa, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.11.14.20231803", "rel_title": "The occurrence of cardiovascular complications associated with SARS-CoV-2 infection: a systematic review", @@ -1077999,6 +1079153,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.11.13.20231571", + "rel_title": "No evidence of increase in suicide in Greece during the first wave of Covid-19", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.13.20231571", + "rel_abs": "Background and ObjectiveMental health outcomes have reportedly worsened in several countries during the Covid-19 pandemic and associated lockdowns. In the present study we examined whether suicides increased in Greece during the first wave of the pandemic.\n\nMethodsWe used daily suicide estimates from a Suicide Observatory in Greece from 2015-2020 and followed three methodologies: A descriptive approach, an interrupted time series analysis, and a differences-in-differences econometric model.\n\nResultsWe did not find any empirical evidence of any increase in suicides during the first wave of Covid-19 and the lockdown in any of the three approaches used.\n\nConclusionsSuicides did not seem to increase during the first wave of covid-19 and lockdown in Greece. However, this does not mean that mental health did not deteriorate, or that we will not observe an increase in suicides during the second wave. Protective factors for Greece during the first wave may include working from home (for those able to tele-work), strong family ties, advertising of a suicide hotline and income support for the unemployed.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Sotiris Vandoros", + "author_inst": "King's College London and Harvard T.H. Chan School of Public Health, Harvard University" + }, + { + "author_name": "Olga Theodorikakou", + "author_inst": "Suicide Prevention Center, KLIMAKA NGO" + }, + { + "author_name": "Kyriakos Katsadoros", + "author_inst": "Suicide Prevention Center, KLIMAKA NGO" + }, + { + "author_name": "Dimitra Zafeiropoulou", + "author_inst": "Suicide Prevention Center, KLIMAKA NGO" + }, + { + "author_name": "Ichiro Kawachi", + "author_inst": "Harvard T.H. Chan School of Public Health, Harvard University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.14.20229096", "rel_title": "Chest CT features of COVID-19 in the region of Abu Dhabi, UAE- A single institute study", @@ -1079399,105 +1080588,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.12.20230136", - "rel_title": "Protective behaviours and secondary harms from non-pharmaceutical interventions during the COVID-19 epidemic in South Africa: a multisite prospective longitudinal study", - "rel_date": "2020-11-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20230136", - "rel_abs": "BackgroundIn March 2020 South Africa implemented strict non-pharmaceutical interventions (NPIs) to contain Covid-19. Over the subsequent five months NPIs were eased in stages according to national strategy. Covid-19 spread throughout the country heterogeneously, reaching rural areas by July and peaking in July-August. Data on the impact of NPI policies on social and economic wellbeing and access to healthcare is limited. We therefore analysed how rural residents of three South African provinces changed their behaviour during the first epidemic wave.\n\nMethodsThe South African Population Research Infrastructure Network (SAPRIN) nodes in Mpumalanga (Agincourt), KwaZulu-Natal (AHRI) and Limpopo (DIMAMO) provinces conducted longitudinal telephone surveys among randomly sampled households from rural and peri-urban surveillance populations every 2-3 weeks. Interviews included questions on: Covid-19 knowledge and behaviours; health and economic impact of NPIs; and mental health.\n\nResults2262 households completed 10,966 interviews between April and August 2020. By August, self-reported satisfaction with Covid-19 knowledge had risen from 48% to 85% and facemask use to over 95%. As selected NPIs were eased mobility increased, and economic losses and anxiety and depression symptoms fell. When Covid-19 cases spiked at one node in July, movement dropped rapidly, and missed daily medication rates doubled. Economic concerns and mental health symptoms were lower in households receiving a greater number of government-funded old-age pensions.\n\nConclusionsSouth Africans reported complying with stringent Covid-19 NPIs despite the threat of substantial social, economic and health repercussions. Government-supported social welfare programmes appeared to buffer interruptions in income and healthcare access during local outbreaks. Epidemic control policies must be balanced against impacts on wellbeing in resource-limited settings and designed with parallel support systems where they threaten income and basic service access.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Guy Harling", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Francesc Xavier G\u00f3mez-Oliv\u00e9", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Joseph Tlouyamma", - "author_inst": "University of Limpopo" - }, - { - "author_name": "Tinofa Mutevedzi", - "author_inst": "DSI-MRC South African Population Research Infrastructure Network" - }, - { - "author_name": "Chodziwadziwa Whiteson Kabudula", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Ruth Mahlako", - "author_inst": "University of Limpopo" - }, - { - "author_name": "Urisha Singh", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Daniel Ohene-Kwofie", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Rose Buckland", - "author_inst": "University College London" - }, - { - "author_name": "Pedzisa Ndagurwa", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Dickman Gareta", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Resign Gunda", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Thobeka Mngomezulu", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Siyabonga Nxumalo", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Emily B Wong", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Kathleen Kahn", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Mark J Siedner", - "author_inst": "Africa Heatlh Research Institute" - }, - { - "author_name": "Eric Maimela", - "author_inst": "University of Limpopo" - }, - { - "author_name": "Stephen Tollman", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Mark Collinson", - "author_inst": "DSI-MRC South African Population Research Infrastructure Network" - }, - { - "author_name": "Kobus Herbst", - "author_inst": "DSI-MRC South African Population Research Infrastructure Network" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.12.20230391", "rel_title": "Correlation of Body Mass Index (BMI), initial neutralizing antibodies (nAb), ABO group and kinetics of nAb and anti-nucleocapsid (NP) SARS-CoV-2 antibodies in convalescent plasma (CCP) donors: A longitudinal study with proposals for better quality of CCP collections.", @@ -1079941,6 +1081031,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.11.20229815", + "rel_title": "Excess mortality for care home residents during the first 23 weeks of the COVID-19 pandemic in England: a national cohort study", + "rel_date": "2020-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20229815", + "rel_abs": "BackgroundTo estimate excess mortality for care home residents during the COVID-19 pandemic in England, exploring associations with care home characteristics.\n\nMethodsDaily number of deaths in all residential and nursing homes in England notified to the Care Quality Commission (CQC) from 1st January 2017 to 7th August 2020. Care home level data linked with CQC care home register to identify homes characteristics: client type (over 65s/children and adults), ownership status (for-profit/not-for-profit; branded/independent), and size (small/medium/large).\n\nExcess deaths computed as the difference between observed and predicted deaths using local authority fixed-effect Poisson regressions on pre-pandemic data. Fixed-effect logistic regressions were used to model odds of experiencing COVID-19 suspected/confirmed deaths.\n\nFindingsUp to 7th August 2020 there were 29,542 (95%CI: 25,176 to 33,908) excess deaths in all care homes. Excess deaths represented 6.5% (95%CI: 5.5% to 7.4%) of all care home beds, higher in nursing (8.4%) than residential (4.6%) homes. 64.7% (95%CI: 56.4% to 76.0%) of the excess deaths were confirmed/suspected COVID-19. Almost all excess deaths were recorded in the quarter (27.4%) of homes with any COVID-19 fatalities.\n\nThe odds of experiencing COVID-19 attributable deaths were higher in homes providing nursing services (OR: 1.8, 95%CI: 1.6 to 2.0); to older people and/or with dementia (OR: 5.5, 95%CI: 4.4 to 6.8); among larger (vs. small) homes (OR: 13.3, 95%CI: 11.5 to 15.4); belonging to a large provider/brand (OR: 1.2, 95%CI: 1.1 to 1.3). There was no significant association with for-profit status of providers.\n\nInterpretationTo limit excess mortality, policy should be targeted at care homes to minimise the risk of ingress of disease and limit subsequent transmission. Our findings provide specific characteristic targets for further research on mechanisms and policy priority.\n\nFundingNIHR.\n\nSummary boxO_ST_ABSEvidence before this studyC_ST_ABSGlobally, residents in care homes have experienced disproportionately high morbidity and mortality from COVID-19. Excess mortality incorporates all direct and indirect mortality effects of the pandemic.\n\nWe searched MEDLINE for published literature, pre-publication databases (medRxiv and Lancet pre-print) and grey literature (ONS and Google) for care homes AND COVID-19 AND mortality, to 31st October 2020. We screened for evidence on excess deaths in care homes in England, and international evidence of the association of COVID-19 deaths and outbreaks with care home characteristics.\n\nOfficial estimates from England and Wales have reported aggregated excess deaths by place of occurrence, but we identified no peer-reviewed excess deaths study in this setting. These aggregates, however, do not account for care home residents dying in other settings (e.g. hospital), nor provide sufficient information to reflect on the impacts of enacted policies over the period, or to inform new policies for future virus waves.\n\nPrevious peer-reviewed and pre-publication studies have also shown the heterogeneous effects of COVID-19 by care home characteristics in other countries. Particularly important from the current literature appears to be care home size, with larger care homes tending to be associated with more negative outcomes in studies with smaller sample sizes. A study from the Lothian region of Scotland additionally found excess deaths concentrated in a minority of homes that experienced an outbreak. However, a national breakdown of excess deaths by care home characteristics is largely lacking from the current literature in England, with a specific market structure and policy context.\n\nAdded value of this studyWe use nationally representative administrative data from all care homes in England to estimate overall excess deaths and by care home characteristics: setting type (nursing or residential home), client types (offering services for people aged 65+ and/or people with dementia or offering services to children and adults), ownership status (whether not-for-profit - charity/NHS/LA-run homes - or for-profit), whether known to be affiliated to a large provider/brand or independent, and classification according to their registered maximum bed capacity (small, medium and large).\n\nWe then used multivariable logistic regression to estimate the adjusted odds of a care home experiencing a suspected or confirmed COVID-19 death across these characteristics.\n\nWe found that only 65% of excess deaths were flagged as officially confirmed/suspected COVID-19 attributed. However, almost all excess deaths occurred in the roughly quarter of care homes that reported at least one suspected/confirmed COVID-19 death. After adjusting for other care home characteristics, larger care homes (vs. small) had the highest odds of experiencing at least one suspected/confirmed COVID-19 death. These findings confirm those from the previous literature, in a unique policy context and with national data.\n\nImplications of all the available evidenceThe fact that nearly all excess deaths occurred in care homes with at least one COVID-19 attributed death suggests that directly-attributed deaths are very likely to be under-recorded. It also suggests that any indirect mortality effect, of COVID-19 and any enacted policies, were predominantly constrained to those homes experiencing an outbreak.\n\nLarger homes are likely to experience higher footfall in general, and so higher probability of contact with an infected individual, which is likely a contributing factor to the association. Furthermore, it might be easier to ensure person-centred protocols in small care homes due to the scale.\n\nThere is an urgent need for further research to explore the mechanisms in relation to care home characteristics. Also, to empirically test effective interventions, in consideration of additional impacts on quality of life and psychological wellbeing. However, until this is possible, prioritising existing resources, such as testing and PPE equipment, for care homes to prevent ingress of disease is key to preventing large excess mortality.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Marcello Morciano", + "author_inst": "University of Manchester" + }, + { + "author_name": "Jonathan M Stokes", + "author_inst": "University of Manchester" + }, + { + "author_name": "Evangelos Kontopantelis", + "author_inst": "University of Manchester" + }, + { + "author_name": "Ian Hall", + "author_inst": "University of Manchester" + }, + { + "author_name": "Alexander J Turner", + "author_inst": "University of Manchester" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.11.20229393", "rel_title": "Using Convergent Sequential Design for Rapid Complex Case Study Descriptions: Example of Public Health Briefings During the Onset of the COVID-19 Pandemic", @@ -1081313,37 +1082438,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.11.10.20228759", - "rel_title": "Parents' Likelihood to Vaccinate Their Children and Themselves Against COVID-19", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.10.20228759", - "rel_abs": "BackgroundVaccination against COVID-19 will likely involve children in order to mitigate transmission risks in community settings. Successful implementation of COVID-19 immunization in the United States may hinge on factors associated with parents likelihood of immunizing their children and themselves.\n\nMethodsWe fielded a national household survey in English and Spanish from June 5-10, 2020 (n=1,008). Parents were asked about their likelihood of immunizing their children and themselves against COVID-19. We fit separate regression models of parents likelihood to vaccinate themselves and their children against COVID-19, using bivariate and multivariable approaches in analyses weighted to be nationally representative.\n\nResultsOverall, 63% of parents (95% CI: 59%, 66%) were likely to vaccinate their children against COVID-19, and 60% (57%, 64%) were likely to get a vaccine themselves. These responses were highly correlated (Pearsons r=0.89). Parent age, sex, marital status, education level, and income were all associated with parents likelihood to vaccinate their children and themselves in bivariate analyses; race/ethnicity was significantly associated with parents likelihood to vaccinate their children. In multivariable analyses, younger parents were significantly less likely than older parents to vaccinate their children and themselves against COVID-19, as were parents with high school or less education compared with parents with bachelors degrees and non-Hispanic White parents compared with Hispanic parents (all p<.05).\n\nConclusionIn this national survey, only approximately 60% of U.S. parents stated that they are likely to vaccinate their children or themselves against COVID-19. Addressing parents hesitancy to vaccinate themselves and their children against COVID-19 will be instrumental to achieving herd immunity in the US.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Matthew M Davis", - "author_inst": "Stanley Manne Children's Research Institute, Department of Pediatrics, Ann & Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg" - }, - { - "author_name": "Joseph S Zickafoose", - "author_inst": "Vanderbilt Center for Child Health Policy, Vanderbilt University Medical Center, Nashville, TN" - }, - { - "author_name": "Alese E Halvorson", - "author_inst": "Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN" - }, - { - "author_name": "Stephen Patrick", - "author_inst": "Vanderbilt Center for Child Health Policy, Vanderbilt University Medical Center, Nashville, TN" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2020.11.10.20229039", "rel_title": "Subjective mental health and need for care among psychiatric outpatients during the COVID-19 pandemic: results from an outreach initiative in Sweden", @@ -1081643,6 +1082737,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.10.20229005", + "rel_title": "Non-occupational and occupational factors associated with specific SARS-CoV-2 antibodies among Hospital Workers - a multicentre cross-sectional study", + "rel_date": "2020-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.10.20229005", + "rel_abs": "ObjectivesProtecting healthcare workers (HCW) from Coronavirus Disease-19 (COVID-19) is critical to preserve the functioning of healthcare systems. We therefore assessed seroprevalence and identified risk factors for Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) seropositivity in this population.\n\nMethodsBetween June 22nd and August 15th 2020, HCW from institutions in Northern/Eastern Switzerland were screened for SARS-CoV-2 antibodies. We recorded baseline characteristics, non-occupational and occupational risk factors. We used pairwise tests of associations and multivariable logistic regression to identify factors associated with seropositivity.\n\nResultsAmong 4664 HCW from 23 healthcare facilities, 139 (3%) were seropositive. Non-occupational exposures independently associated with seropositivity were contact with a COVID-19-positive household (adjusted OR=54, 95%-CI: 31-97) and stay in a COVID-19 hotspot (aOR=2.2, 95%-CI: 1.1-3.9). Blood group 0 vs. non-0 (aOR=0.4, 95%-CI: 0.3-0.7), active smoking (aOR=0.5, 95%-CI: 0.3-0.9) and living with children <12 years (aOR=0.3, 95%-CI: 0.2-0.6) were associated with decreased risk. Occupational risk factors were close contact to COVID-19 patients (aOR=2.8, 95%-CI: 1.5-5.5), exposure to COVID-19-positive co-workers (aOR=2.0, 95%-CI: 1.2-3.1), poor knowledge of standard hygiene precautions (aOR=2.0, 95%-CI: 1.3-3.2), and frequent visits to the hospital canteen (aOR=1.9, 95%-CI: 1.2-3.1).\n\nConclusionsLiving with COVID-19-positive households showed by far the strongest association with SARS-CoV-2 seropositivity. We identified several potentially modifiable risk factors, which might allow mitigation of the COVID-19 risk among HCW. The lower risk among those living with children, even after correction for multiple confounders, is remarkable and merits further study.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Christian R. Kahlert", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland; Children's Hospital of Eastern Switzerland, Depa" + }, + { + "author_name": "Raphael Persi", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Sabine Guesewell", + "author_inst": "Clinical Trials Unit, Cantonal Hospital of St. Gallen, St. Gallen, Switzerland" + }, + { + "author_name": "Thomas Egger", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Onicio B. Leal-Neto", + "author_inst": "Epitrack, Recife, Brazil; Department of Economics, University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Johannes Sumer", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Domenica Flury", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Angela Brucher", + "author_inst": "Psychiatry Services of the Canton of St. Gallen (South), Switzerland" + }, + { + "author_name": "Eva Lemmenmeier", + "author_inst": "Clienia Littenheid AG, Private Clinic for Psychiatry and Psychotherapy, Littenheid, Switzerland" + }, + { + "author_name": "Carsten Moeller", + "author_inst": "Rehabilitation Clinic, Zihlschlacht, Switzerland" + }, + { + "author_name": "Philip Rieder", + "author_inst": "Hirslanden Clinic, Zurich, Switzerland" + }, + { + "author_name": "Reto Stocker", + "author_inst": "Hirslanden Clinic, Zurich, Switzerland" + }, + { + "author_name": "Danielle Vuichard-Gysin", + "author_inst": "Thurgau Hospital Group, Division of Infectious Diseases and Hospital Epidemiology, Muensterlingen, Switzerland; Swiss National Center for Infection Prevention (" + }, + { + "author_name": "Benedikt Wiggli", + "author_inst": "Kantonsspital Baden, Division of Infectious Diseases and Hospital Epidemiology, Baden, Switzerland" + }, + { + "author_name": "Werner C. Albrich", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Baharak Babouee Flury", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Ulrike Besold", + "author_inst": "Geriatric Clinic St. Gallen, St. Gallen, Switzerland" + }, + { + "author_name": "Jan Fehr", + "author_inst": "Department of Public and Global Health, University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Stefan P. Kuster", + "author_inst": "Federal Office of Public Health, Bern, Switzerland; University Hospital and University of Zurich, Division of Infectious Diseases and Hospital Epidemiology, Zur" + }, + { + "author_name": "Allison McGeer", + "author_inst": "Sinai Health System, Toronto, Canada" + }, + { + "author_name": "Lorenz Risch", + "author_inst": "Labormedizinisches Zentrum Dr Risch Ostschweiz AG, Buchs, Switzerland; Private Universitaet im Fuerstentum Liechtenstein, Triesen, Liechtenstein; Center of Labo" + }, + { + "author_name": "Matthias Schlegel", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Pietro Vernazza", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + }, + { + "author_name": "Andree Friedl", + "author_inst": "Kantonsspital Baden, Division of Infectious Diseases and Hospital Epidemiology, Baden, Switzerland" + }, + { + "author_name": "Philipp Kohler", + "author_inst": "Cantonal Hospital St Gallen, Division of Infectious Diseases and Hospital Epidemiology, St Gallen, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.10.20228973", "rel_title": "Comparison of SARS-COV-2 nasal antigen test to nasopharyngeal RT-PCR in mildly symptomatic patients", @@ -1083163,53 +1084372,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.11.20228130", - "rel_title": "A higher ratio of green spaces means a lower racial disparity in severe acute respiratory syndrome coronavirus 2 infection rates: A nationwide study of the United States", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20228130", - "rel_abs": "There is striking racial disparity in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection rates in the United States. We hypothesize that the disparity is significantly smaller in areas with a higher ratio of green spaces at the county level. This study used the 135 most urbanized counties across the United States as sample sites. County level data on the SARS-CoV-2 infection rates of black and white individuals in each county were collected. The ratio of green spaces by land-cover type at the county level was calculated from satellite imagery. An ecological hierarchical regression analysis measured cross-sectional associations between racial disparity in infection rates and green spaces, after controlling for socioeconomic, demographic, pre-existing chronic disease, and built-up area factors. We found significantly higher infection rate among black individuals compared to white individuals. More importantly, a higher ratio of green spaces at the county level is significantly associated with a lower racial disparity in the SARS-CoV-2 infection rate. Further, we identified four green space factors that have significant negative associations with the racial disparity in SARS-CoV-2 infection rates, including open space in developed areas, forest, shrub and scrub, and grassland and herbaceous. We suggest that green spaces are an equalizing salutogenic factor, modifying infection exposure.\n\nHighlightsO_LIThe first study to identify significant relationships between green spaces and the racial disparity of SARS-CoV-2 infection rates.\nC_LIO_LIA nationwide study of the 135 most urbanized counties of the United States.\nC_LIO_LIA within-subject study: The black-white racial disparity of SARS-CoV-2 infection rates was measured within each county.\nC_LIO_LIA higher ratio of green spaces in a county is associated with a lower racial disparity of SARS-CoV-2 infection rates after controlling for socio-economic, demographic, pre-existing chronic disease, and built-up area factors.\nC_LIO_LIFour green space factors are significantly associated with a lower racial disparity of SARS-CoV-2 infection rates.\nC_LI", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yi Lu", - "author_inst": "Department of Architecture and Civil Engineering, College of Engineering, City University of Hong Kong, Hong Kong SAR" - }, - { - "author_name": "Long Chen", - "author_inst": "Department of Architecture and Civil Engineering, College of Engineering, City University of Hong Kong, Hong Kong SAR" - }, - { - "author_name": "Xueming Liu", - "author_inst": "Virtual Reality Lab of Urban Environments and Human Health, HKUrbanLabs, The University of Hong Kong, Hong Kong SAR" - }, - { - "author_name": "Yuwen Yang", - "author_inst": "Virtual Reality Lab of Urban Environments and Human Health, HKUrbanLabs, Division of Landscape Architecture, Department of Architecture, The University of Hong " - }, - { - "author_name": "Wenyan Xu", - "author_inst": "Virtual Reality Lab of Urban Environments and Human Health, HKUrbanLabs, Division of Landscape Architecture, Department of Architecture, The University of Hong " - }, - { - "author_name": "Chris Webster", - "author_inst": "HKUrbanLabs, Faculty of Architecture, The University of Hong Kong, Hong Kong SAR" - }, - { - "author_name": "William C. Sullivan", - "author_inst": "Smart, Healthy Communities initiative, University of Illinois at Urbana-Champaign, U.S.A." - }, - { - "author_name": "Bin Jiang", - "author_inst": "Virtual Reality Lab of Urban Environments and Human Health, HKUrbanLabs, Division of Landscape Architecture, Department of Architecture, The University of Hong " - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.11.20229724", "rel_title": "Epidemiological and immunological features of obesity and SARS-CoV-2", @@ -1083481,6 +1084643,49 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.11.08.20227819", + "rel_title": "Detection of COVID-19 Disease from Chest X-Ray Images: A Deep Transfer Learning Framework", + "rel_date": "2020-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.08.20227819", + "rel_abs": "World economy as well as public health have been facing a devastating effect caused by the disease termed as Coronavirus (COVID-19). A significant step of COVID-19 affected patients treatment is the faster and accurate detection of the disease which is the motivation of this study. In this paper, implementation of a deep transfer learning-based framework using a pre-trained network (ResNet-50) for detecting COVID-19 from the chest X-rays was done. Our dataset consists of 2905 chest X-ray images of three categories: COVID-19 affected (219 cases), Viral Pneumonia affected (1345 cases), and Normal Chest X-rays (1341 cases). The implemented neural network demonstrates significant performance in classifying the cases with an overall accuracy of 96%. Most importantly, the model has shown a significantly good performance over the current research-based methods in detecting the COVID-19 cases in the test dataset (Precision = 1.00, Recall = 1.00, F1-score = 1.00 and Specificity = 1.00). Therefore, our proposed approach can be adapted as a reliable method for faster and accurate COVID-19 affected case detection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Shadman Sakib", + "author_inst": "Leading University" + }, + { + "author_name": "Md. Abu Bakr Siddique", + "author_inst": "International University of Business Agriculture and Technology" + }, + { + "author_name": "Mohammad Mahmudur Rahman Khan", + "author_inst": "Vanderbilt University" + }, + { + "author_name": "Nowrin Yasmin", + "author_inst": "Ahsanullah University of Science and Technology" + }, + { + "author_name": "Anas Aziz", + "author_inst": "Military Institute of Science and Technology" + }, + { + "author_name": "Madiha Chowdhury", + "author_inst": "Bangladesh University of Engineering and Technology" + }, + { + "author_name": "Ihtyaz Kader Tasawar", + "author_inst": "BRAC University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.08.20227884", "rel_title": "Host genetic liability for severe COVID-19 overlaps with alcohol drinking behavior and diabetic outcomes and in over 1 million participants", @@ -1085085,81 +1086290,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.09.20228411", - "rel_title": "Quantitative measurement of IgG to SARS-CoV-2 proteins using ImmunoCAP", - "rel_date": "2020-11-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20228411", - "rel_abs": "BackgroundDetailed understanding of the immune response to SARS-CoV-2, the cause of coronavirus disease 2019 (COVID-19), has been hampered by a lack of quantitative antibody assays.\n\nObjectiveTo develop a quantitative assay for IgG to SARS-CoV-2 proteins that could readily be implemented in clinical and research laboratories.\n\nMethodsThe biotin-streptavidin technique was used to conjugate SARS-CoV-2 spike receptor-binding-domain (RBD) or nucleocapsid protein to the solid-phase of the ImmunoCAP resin. Plasma and serum samples from patients with COVID-19 (n=51) and samples from donors banked prior to the emergence of COVID-19 (n=109) were used in the assay. SARS-CoV-2 IgG levels were followed longitudinally in a subset of samples and were related to total IgG and IgG to reference antigens using an ImmunoCAP 250 platform.\n\nResultsPerformance characteristics demonstrated 100% sensitivity and 99% specificity at a cut-off level of 2.5 {micro}g/mL for both SARS-CoV-2 proteins. Among 36 patients evaluated in a post-hospital follow-up clinic, median levels of IgG to spike-RBD and nucleocapsid were 34.7 {micro}g/mL (IQR 18-52) and 24.5 {micro}g/mL (IQR 9-59), respectively. Among 17 patients with longitudinal samples there was a wide variation in the magnitude of IgG responses, but generally the response to spike-RBD and to nucleocapsid occurred in parallel, with peak levels approaching 100 {micro}g/mL, or 1% of total IgG.\n\nConclusionsWe have described a quantitative assay to measure IgG to SARS-CoV-2 that could be used in clinical and research laboratories and implemented at scale. The assay can easily be adapted to measure IgG to novel antigens, has good performance characteristics and a read-out in standardized units.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Behnam Keshavarz", - "author_inst": "University of Virginia" - }, - { - "author_name": "Joesph R. Wiencek", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Lisa J. Workman", - "author_inst": "University of Virginia" - }, - { - "author_name": "Matthew D. Straesser", - "author_inst": "University of Virginia" - }, - { - "author_name": "Lyndsey M. Muehling", - "author_inst": "University of Virginia" - }, - { - "author_name": "Glenda Canderan", - "author_inst": "University of Virginia" - }, - { - "author_name": "Fabrizio Drago", - "author_inst": "University of Virginia" - }, - { - "author_name": "Catherine A. Bonham", - "author_inst": "University of Virginia" - }, - { - "author_name": "Jeffrey M. Sturek", - "author_inst": "University of Virginia" - }, - { - "author_name": "Chintan Ramani", - "author_inst": "University of Virginia" - }, - { - "author_name": "Coleen A. McNamara", - "author_inst": "University of Virginia" - }, - { - "author_name": "Judith A. Woodfolk", - "author_inst": "University of Virginia" - }, - { - "author_name": "Alexandra Kadl", - "author_inst": "University of Virginia" - }, - { - "author_name": "Thomas A.E. Platts-Mills", - "author_inst": "University of Virginia" - }, - { - "author_name": "Jeffrey M. Wilson", - "author_inst": "University of Virginia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.11.11.20229922", "rel_title": "COVID-PCD a participatory research study on the impact of COVID-19 in people with Primary Ciliary Dyskinesia", @@ -1085459,6 +1086589,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.11.09.20228684", + "rel_title": "Retrospective Analyses of Interventions to Epidemics using a Continuously Updated Model, with Application to the COVID-19 Crisis in New York City", + "rel_date": "2020-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20228684", + "rel_abs": "Retrospective analyses of interventions to epidemics, in which the effectiveness of strategies implemented are compared to hypothetical alternatives, are valuable for performing the cost-benefit calculations necessary to optimize infection countermeasures. SIR (susceptible-infected-removed) models are useful in this regard but are limited by the challenge of deciding how and when to update the numerous parameters as the epidemic changes in response to population behaviors. Behaviors of particular interest include facemasks adoption (at various levels) and social distancing. We present a method that uses a \"dynamic spread function\" to systematically capture the continuous variation in the population behavior, and the gradual change in infection evolution, resulting from interventions. No parameter updates are made by the user. We use the tool to quantify the reduction in infection rate realizable from the population of New York City adopting different facemask strategies during COVID-19. Assuming a baseline facemask of 67% filtration efficiency, calculations show that increasing the efficiency to 80% could have reduced the roughly 5000 new infections per day occurring at the peak of the epidemic to around 4000. Population behavior that may not be varied as part of the retrospective analysis, such as social distancing in a facemask analysis, are automatically captured as part of the calibration of the dynamic spread function.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jenna Osborn", + "author_inst": "U. S. FDA" + }, + { + "author_name": "Shayna Berman", + "author_inst": "U. S. FDA" + }, + { + "author_name": "Sara Bender_Bier", + "author_inst": "U. S. FDA" + }, + { + "author_name": "Gavin D'Souza", + "author_inst": "U. S. FDA" + }, + { + "author_name": "Matthew Myers", + "author_inst": "U. S. FDA" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.09.20228098", "rel_title": "Peginterferon-lambda for the treatment of COVID-19 in outpatients", @@ -1087315,37 +1088480,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.09.375394", - "rel_title": "Network-based Virus-Host Interaction Prediction with Application to SARS-CoV-2", - "rel_date": "2020-11-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.09.375394", - "rel_abs": "COVID-19, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has quickly become a global health crisis since the first report of infection in December of 2019. However, the infection spectrum of SARS-CoV-2 and its comprehensive protein-level interactions with hosts remain unclear. There is a massive amount of under-utilized data and knowledge about RNA viruses highly relevant to SARS-CoV-2 and their hosts proteins. More in-depth and more comprehensive analyses of that knowledge and data can shed new insight into the molecular mechanisms underlying the COVID-19 pandemic and reveal potential risks. In this work, we constructed a multi-layer virus-host interaction network to incorporate these data and knowledge. A machine learning-based method, termed Infection Mechanism and Spectrum Prediction (IMSP), was developed to predict virus-host interactions at both protein and organism levels. Our approach revealed five potential infection targets of SARS-CoV-2, which deserved public health attention, and eight highly possible interactions between SARS-CoV-2 proteins and human proteins. Given a new virus, IMSP can utilize existing knowledge and data about other highly relevant viruses to predict multi-scale interactions between the new virus and potential hosts.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Hangyu Du", - "author_inst": "Brandeis University" - }, - { - "author_name": "Feng Chen", - "author_inst": "Brandeis University" - }, - { - "author_name": "Hongfu Liu", - "author_inst": "Brandeis University" - }, - { - "author_name": "Pengyu Hong", - "author_inst": "Brandeis University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.11.11.377739", "rel_title": "Nsp1 of SARS-CoV-2 Stimulates Host Translation Termination", @@ -1087697,6 +1088831,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.07.20227462", + "rel_title": "Synthetic Reproduction and Augmentation of COVID-19 Case Reporting Data by Agent-Based Simulation", + "rel_date": "2020-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.07.20227462", + "rel_abs": "We generate synthetic data documenting COVID-19 cases in Austria by the means of an agent-based simulation model. The model simulates the transmission of the SARS-CoV-2 virus in a statistical replica of the population and reproduces typical patient pathways on an individual basis while simultaneously integrating historical data on the implementation and expiration of population-wide countermeasures. The resulting data semantically and statistically aligns with an official epidemiological case reporting data set and provides an easily accessible, consistent and augmented alternative. Our synthetic data set provides additional insight into the spread of the epidemic by synthesizing information that cannot be recorded in reality.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Nikolas Popper", + "author_inst": "Information and Software Engineering, Vienna University of Technology" + }, + { + "author_name": "Melanie Zechmeister", + "author_inst": "DEXHELPP - Decision Support for Health Policy and Planning" + }, + { + "author_name": "Dominik Brunmeir", + "author_inst": "dwh simulation services" + }, + { + "author_name": "Claire Rippinger", + "author_inst": "dwh simulation services" + }, + { + "author_name": "Nadine Weibrecht", + "author_inst": "DEXHELPP - Decision Support for Health Policy and Planning" + }, + { + "author_name": "Christoph Urach", + "author_inst": "dwh simulation services" + }, + { + "author_name": "Martin Bicher", + "author_inst": "Information and Software Engineering, Vienna University of Technology" + }, + { + "author_name": "G\u00fcnter Schneckenreither", + "author_inst": "Information and Software Engineering, Vienna University of Technology" + }, + { + "author_name": "Andreas Rauber", + "author_inst": "Information and Software Engineering, Vienna University of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.06.20227330", "rel_title": "The COVID-19 epidemic in the Czech Republic: retrospective analysis of measures (not) implemented during the spring first wave", @@ -1088901,69 +1090086,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.10.375022", - "rel_title": "A benchmarking study of SARS-CoV-2 whole-genome sequencing protocols using COVID-19 patient samples", - "rel_date": "2020-11-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.10.375022", - "rel_abs": "The COVID-19 pandemic is a once-in-a-lifetime event, exceeding mortality rates of the flu pandemics from the 1950s and 1960s. Whole-genome sequencing (WGS) of SARS-CoV-2 plays a critical role in understanding the disease. Performance variation exists across SARS-CoV-2 viral WGS technologies, but there is currently no benchmarking study comparing different WGS sequencing protocols. We compared seven different SARS-CoV-2 WGS library protocols using RNA from patient nasopharyngeal swab samples under two storage conditions. We constructed multiple WGS libraries encompassing three different viral inputs: 1,000,000, 250,000 and 1,000 copies. Libraries were sequenced using two distinct platforms with varying sequencing depths and read lengths. We found large differences in mappability and genome coverage, and variations in sensitivity, reproducibility and precision of single-nucleotide variant calling across different protocols. We ranked the performance of protocols based on six different metrics. Our results indicated that the most appropriate protocol depended on viral input amount and sequencing depth. Our findings offer guidance in choosing appropriate WGS protocols to characterize SARS-CoV-2 and its evolution.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Tiantian Liu", - "author_inst": "Center for Genomics, School of Medicine, Loma Linda University" - }, - { - "author_name": "Zhong Chen", - "author_inst": "Center for Genomics, School of Medicine, Loma Linda University" - }, - { - "author_name": "Wanqiu Chen", - "author_inst": "Center for Genomics, School of Medicine, Loma Linda University" - }, - { - "author_name": "Xin Chen", - "author_inst": "Center for Genomics, School of Medicine, Loma Linda University" - }, - { - "author_name": "Maryam Hosseini Asanjan", - "author_inst": "Center for Genomics, School of Medicine, Loma Linda University" - }, - { - "author_name": "Zhaowei Yang", - "author_inst": "Loma Linda University Center for Genomics and Guangzhou Medical University" - }, - { - "author_name": "Jing Li", - "author_inst": "Guangzhou Medical University and Loma Linda University Center for Genomics" - }, - { - "author_name": "Diana Ho", - "author_inst": "Center for Genomics, School of Medicine, Loma Linda University" - }, - { - "author_name": "David Turay", - "author_inst": "Department of Surgery, School of Medicine, Loma Linda University" - }, - { - "author_name": "Ciprian Gheorghe", - "author_inst": "Department of Gynecology & Obstetrics, School of Medicine, Loma Linda University" - }, - { - "author_name": "Wendell Jones", - "author_inst": "EA Genomics, Division of Q2 Solutions" - }, - { - "author_name": "Charles Wang", - "author_inst": "Loma Linda University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.11.10.376277", "rel_title": "CD127 imprints functional heterogeneity to diversify monocyte responses in human inflammatory diseases", @@ -1089259,6 +1090381,93 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.11.10.376673", + "rel_title": "SARS-CoV-2 infection causes transient olfactory dysfunction in mice", + "rel_date": "2020-11-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.10.376673", + "rel_abs": "Olfactory dysfunction caused by SARS-CoV-2 infection represents as one of the most predictive and common symptoms in COVID-19 patients. However, the causal link between SARS-CoV-2 infection and olfactory disorders remains lacking. Herein we demonstrate intranasal inoculation of SARS-CoV-2 induces robust viral replication in the olfactory epithelium (OE), resulting in transient olfactory dysfunction in humanized ACE2 mice. The sustentacular cells and Bowmans gland cells in OE were identified as the major targets of SARS-CoV-2 before the invasion into olfactory sensory neurons. Remarkably, SARS-CoV-2 infection triggers cell death and immune cell infiltration, and impairs the uniformity of OE structure. Combined transcriptomic and proteomic analyses reveal the induction of antiviral and inflammatory responses, as well as the downregulation of olfactory receptors in OE from the infected animals. Overall, our mouse model recapitulates the olfactory dysfunction in COVID-19 patients, and provides critical clues to understand the physiological basis for extrapulmonary manifestations of COVID-19.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Cheng-Feng Qin", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Qing Ye", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Jia Zhou", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Guan Yang", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Rui-Ting Li", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Qi He", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Yao Zhang", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Shu-Jia Wu", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Qi Chen", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Jia-Hui Shi", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Rong-Rong Zhang", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Hui-Min Zhu", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Hong-Ying Qiu", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Tao Zhang", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Yong-Qiang Deng", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Xiao-Feng Li", + "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" + }, + { + "author_name": "Ping Xu", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + }, + { + "author_name": "Xiao Yang", + "author_inst": "State Key Laboratory of Proteomics, National Center for Protein Science (Beijing), Beijing Institute of Lifeomics" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.05.20224436", "rel_title": "Anxiety and depression among people living in quarantine centers during COVID-19 pandemic: A mixed method study from western Nepal", @@ -1090362,105 +1091571,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.11.09.20228551", - "rel_title": "Phase 1 Assessment of the Safety and Immunogenicity of an mRNA- Lipid Nanoparticle Vaccine Candidate Against SARS-CoV-2 in Human Volunteers", - "rel_date": "2020-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20228551", - "rel_abs": "There is an urgent need for vaccines to counter the COVID-19 pandemic due to infections with severe acute respiratory syndrome coronavirus (SARS-CoV-2). Evidence from convalescent sera and preclinical studies has identified the viral Spike (S) protein as a key antigenic target for protective immune responses. We have applied an mRNA-based technology platform, RNActive(R), to develop CVnCoV which contains sequence optimized mRNA coding for a stabilized form of S protein encapsulated in lipid nanoparticles (LNP). Following demonstration of protective immune responses against SARS-CoV-2 in animal models we performed a dose-escalation phase 1 study in healthy 18-60 year-old volunteers.\n\nThis interim analysis shows that two doses of CVnCoV ranging from 2 g to 12 g per dose, administered 28 days apart were safe. No vaccine-related serious adverse events were reported. There were dose-dependent increases in frequency and severity of solicited systemic adverse events, and to a lesser extent of local reactions, but the majority were mild or moderate and transient in duration. Immune responses when measured as IgG antibodies against S protein or its receptor-binding domain (RBD) by ELISA, and SARS-CoV-2-virus neutralizing antibodies measured by micro-neutralization, displayed dose-dependent increases. Median titers measured in these assays two weeks after the second 12 g dose were comparable to the median titers observed in convalescent sera from COVID-19 patients. Seroconversion (defined as a 4-fold increase over baseline titer) of virus neutralizing antibodies two weeks after the second vaccination occurred in all participants who received 12 g doses.\n\nPreliminary results in the subset of subjects who were enrolled with known SARS-CoV-2 seropositivity at baseline show that CVnCoV is also safe and well tolerated in this population, and is able to boost the pre-existing immune response even at low dose levels.\n\nBased on these results, the 12 g dose is selected for further clinical investigation, including a phase 2b/3 study that will investigate the efficacy, safety, and immunogenicity of the candidate vaccine CVnCoV.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Lidia Oostvogels", - "author_inst": "CureVac" - }, - { - "author_name": "Peter Kremsner", - "author_inst": "Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Andrea Kreidenweiss", - "author_inst": "Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Isabel Leroux-Roels", - "author_inst": "Ghent University Hospital, Ghent, Belgium" - }, - { - "author_name": "Geert Leroux-Roels", - "author_inst": "Ghent University Hospital, Ghent, Belgium" - }, - { - "author_name": "Arne Kroidl", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Germany" - }, - { - "author_name": "Mirjam Schunk", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich, Germany" - }, - { - "author_name": "Christoph Schindler", - "author_inst": "Hannover Medical School (MHH), Hannover, Germany" - }, - { - "author_name": "Jacobus Bosch", - "author_inst": "Hannover Medical School (MHH), Hannover, Germany" - }, - { - "author_name": "Rolf Fendel", - "author_inst": "Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Julian J Gabor", - "author_inst": "Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Thirumalaisamy P Velavan", - "author_inst": "Institute of Tropical Medicine, University Hospital Tuebingen, Tuebingen, Germany" - }, - { - "author_name": "Philipp Mann", - "author_inst": "Curevac AG, Frankfurt, Germany" - }, - { - "author_name": "Lisa Walz", - "author_inst": "Curevac AG, Frankfurt, Germany" - }, - { - "author_name": "Stefan Mueller", - "author_inst": "Curevac AG, Frankfurt, Germany" - }, - { - "author_name": "Oliver Schoenborn-Kellenberger", - "author_inst": "Cogitars, Heidelberg, Germany" - }, - { - "author_name": "Thomas Verstraeten", - "author_inst": "P95 Epidemiology and Pharmacovigilance, Leuven, Belgium" - }, - { - "author_name": "Mariola Fotin-Mleczek", - "author_inst": "Curevac AG, Tuebingen, Germany" - }, - { - "author_name": "Dominik Vahrenhorst", - "author_inst": "Curevac AG, Tuebingen, Germany" - }, - { - "author_name": "Gianluca Quintini", - "author_inst": "Curevac AG, Tuebingen, Germany" - }, - { - "author_name": "Olaf-Oliver Wolz", - "author_inst": "Curevac AG, Tuebingen, Germany" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.06.372227", "rel_title": "Variability of Accessory Proteins Rules the SARS-CoV-2 Pathogenicity", @@ -1090940,6 +1092050,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.06.20226977", + "rel_title": "Team contact sports in times of the COVID-19 pandemic- a scientific concept for the Austrian football league", + "rel_date": "2020-11-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20226977", + "rel_abs": "BackgroundSince the beginning of the COVID -19 pandemic, many contact sport teams are facing major challenges to safely continue training and competition.\n\nObjectiveWe present the design and implementation of a structured monitoring concept for the Austrian national football league\n\nMethods146 professional players from five clubs of the professional Austrian football league were monitored for a period of 12 weeks. Subjective health parameters, PCR- test results and data obtained from a geo-tracking app were collected. Simulations modelling the consequences of a COVID-19 case with increasing reproduction number were computed.\n\nResultsNo COVID-19 infection occurred during the observation period in the players. Infections in the nearer surroundings lead to increased perceived risk of infection. Geo tracking was particularly hindered due to technical problems and reluctance of users. Simulation models suggested a hypothetical shut-down of all training and competition activities.\n\nConclusionsA structured monitoring concept can help to continue contact sports safely in times of a pandemic. Cooperation of all involved is essential.\n\nTrial registrationID: DRKS00022166 15/6/2020 https://www.who.int/ictrp/search/en/\n\nKey Points- The results of this study can inform the development of future prevention and monitoring strategies in professional football and beyond, potentially serving as a blueprint for the safe continuation of sports and physical activity, across a broad range of settings, during and following a pandemic such as COVID-19.\n- Health parameters should be digitally recorded and closely monitored to enable quick response in case of a COVID-19 infection.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Antje van der Zee-Neuen", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Dagmar Schaffler-Schaden", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Juergen Herfert", + "author_inst": "Red Bull Athlete Performance Centre" + }, + { + "author_name": "James O Brien", + "author_inst": "Red Bull Athlete Performance Centre" + }, + { + "author_name": "Tim Johansson", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Patrick Kutschar", + "author_inst": "patrick.kutschar@pmu.ac.at" + }, + { + "author_name": "Alexander Seymer", + "author_inst": "University of Salzburg" + }, + { + "author_name": "Stephan Ludwig", + "author_inst": "University of Muenster" + }, + { + "author_name": "Thomas Stoeggl", + "author_inst": "University of Salzburg" + }, + { + "author_name": "David Keeley", + "author_inst": "Electronic Caregiver" + }, + { + "author_name": "Herbert Resch", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Juergen Osterbrink", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Maria Flamm", + "author_inst": "Paracelsus Medical University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.05.20226654", "rel_title": "Multiplexed, quantitative serological profiling of COVID-19 from a drop of blood by a point-of-care test", @@ -1092512,41 +1093689,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.04.20224758", - "rel_title": "Frequent testing and immunity-based staffing will help mitigate outbreaks in nursing home settings", - "rel_date": "2020-11-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20224758", - "rel_abs": "BackgroundNursing homes and other long term care facilities have been disproportionately impacted by the COVID-19 pandemic. Strategies are urgently needed to reduce transmission in these vulnerable populations. We aim to evaluate the reduction in transmission in nursing homes achieved through contact-targeted interventions and testing.\n\nMethodsWe developed an agent-based Susceptible-Exposed- Infectious(Asymptomatic/Symptomatic)-Recovered (SEIR) model to examine SARS-CoV-2 transmission in nursing homes. Residents and staff are modelled individually; residents are split into two cohorts based on COVID-19 diagnosis. We evaluate the effectiveness of two contact-targeted interventions. In the resident cohorting intervention, recovered residents are moved back from the COVID (infected) cohort to the non-COVID (susceptible/uninfected) cohort. In the immunity-based staffing intervention, recovered staff, who we assume have protective immunity, are assigned to work in the non-COVID cohort, while susceptible staff work in the COVID cohort and are assumed to have high levels of protection from personal protective equipment. These interventions aim to reduce the fraction of peoples contacts that are presumed susceptible (and therefore potentially infected) and replace them with recovered (immune) contacts. We further evaluate two types of screening tests conducted with varying frequency: 1) rapid antigen testing and 2) PCR testing.\n\nResultsThe frequency and type of testing has a larger impact on the size of outbreaks than the cohorting and staffing interventions. The most effective testing strategy modeled is daily antigen testing. Under all screening testing strategies, the resident cohorting intervention and the immunity-based staffing intervention reduce the final size of the outbreak among residents, with the latter reducing it more. The efficacy of these interventions among staff varies by testing strategy and outbreak size.\n\nConclusionsIncreasing the frequency of screening testing of all residents and staff, or even staff alone, in nursing homes has the potential to greatly reduce outbreaks in this vulnerable setting. Immunity-based staffing can further reduce spread at little or no additional cost and becomes particularly important when daily testing is not feasible.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Inga Holmdahl", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Rebecca Kahn", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "James Hay", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Caroline O Buckee", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Michael Mina", - "author_inst": "Harvard T.H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.04.20225912", "rel_title": "SARS-CoV-2 infection dynamics in Denmark, February through October 2020: Nature of the past epidemic and how it may develop in the future", @@ -1092742,6 +1093884,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.11.05.20226472", + "rel_title": "How has Covid-19 affected mental health nurses and the delivery of mental health nursing care in the UK? Results of a mixed methods study", + "rel_date": "2020-11-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20226472", + "rel_abs": "IntroductionWhile evidence has emerged concerning the impact of Covid-19 on the general population and the challenges facing health services, much less is known regarding how the pandemic has directly affected the delivery of mental health nursing care.\n\nAimThis paper aims to explore how Covid-19 has affected the ability of mental health nurses to deliver care in community and inpatient mental health services in the UK.\n\nMethodWe investigated staff reports regarding the impact of the Covid-19 pandemic on mental healthcare and mental health service users in the UK, using a mixed methods online survey. A total of 897 nurses across a range of inpatient and community settings participated.\n\nDiscussionKey themes within the data explore: new ways of working; remote working; risks of infection/infection control challenges; and the impact on service users. Targeted guidelines are required to support mental health nurses providing care and support during a pandemic to people in severe mental distress, often in unsuitable environments.\n\nImplications for PracticeService developments need to occur alongside tailored guidance and support for staff welfare supported by clear leadership. These findings identify areas requiring attention and investment to prepare for future crises and the consequences of the pandemic.\n\nAccessible SummaryO_ST_ABSWhat is known on the subject?C_ST_ABSDuring the Covid-19 pandemic there has been research considering the impact on medical healthcare professionals and the mental health needs of the general population. However, limited focus has been placed on mental health services or mental health staff providing care in the community and in hospitals. Whilst nurses make up the largest section of the mental health workforce in the UK, the impact that this pandemic has had on their work has been largely ignored.\n\nWhat the paper adds to existing knowledge?This paper provides a unique insight into the experiences and impact that the Covid-19 pandemic has had on mental health nurses across a range of community and inpatient settings to understand what has changed in their work and the care they can and do provide during this crisis. This includes exploring how services have changed, the move to remote working, the impact of the protective equipment crisis on nurses, and the difficult working conditions facing those in inpatient settings where there is minimal guidance provided.\n\nWhat are the implications for practice?By understanding the impact the pandemic has had on mental health nursing care, we can understand the gaps in guidance that exist, the challenges being faced, and the impact the crisis has had on care for mental health service users. By doing so we can plan for the ongoing nature of this pandemic as well as the aftermath that the crisis may leave for our service users and workforce alike.\n\nRelevance StatementThis paper provides insight into the impact that the Covid-19 pandemic has had on the service and care that mental health nurses are expected to and can provide. As a workforce that often requires ongoing face to face contact with service users, many in serious distress, in inpatient and community settings, it is important that we understand their experiences and the challenges and risks that face this workforce. This will enable us to ensure that future planning, guidance, support and safeguarding can take place during the ongoing and future crises.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Una Foye", + "author_inst": "King's College London" + }, + { + "author_name": "Christian Dalton-Locke", + "author_inst": "University College London" + }, + { + "author_name": "Jasmine Harju-Seppanen", + "author_inst": "University College London" + }, + { + "author_name": "Rebecca Lane", + "author_inst": "Kings College London" + }, + { + "author_name": "Lewys Beams", + "author_inst": "South London and Maudsley Foundation Trust" + }, + { + "author_name": "Norha Vera San Juan", + "author_inst": "King's College London" + }, + { + "author_name": "Sonia Johnson", + "author_inst": "University College London" + }, + { + "author_name": "Alan Simpson", + "author_inst": "Kings College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2020.11.04.20226118", "rel_title": "Elevated COVID-19 outcomes among persons living with diagnosed HIV infection in New York State: Results from a population-level match of HIV, COVID-19, and hospitalization databases", @@ -1094330,37 +1095519,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.11.06.369439", - "rel_title": "Allosteric hotspots in the main protease of SARS-CoV-2", - "rel_date": "2020-11-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.06.369439", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWInhibiting the main protease of SARS-CoV-2 is of great interest in tackling the COVID-19 pandemic caused by the virus. Most efforts have been centred on inhibiting the binding site of the enzyme. However, considering allosteric sites, distant from the active or orthosteric site, broadens the search space for drug candidates and confers the advantages of allosteric drug targeting. Here, we report the allosteric communication pathways in the main protease dimer by using two novel fully atomistic graph theoretical methods: Bond-to-bond propensity analysis, which has been previously successful in identifying allosteric sites without a priori knowledge in benchmark data sets, and, Markov transient analysis, which has previously aided in finding novel drug targets in catalytic protein families. We further score the highest ranking sites against random sites in similar distances through statistical bootstrapping and identify four statistically significant putative allosteric sites as good candidates for alternative drug targeting.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "L\u00e9onie Str\u00f6mich", - "author_inst": "Imperial College London" - }, - { - "author_name": "Nan Wu", - "author_inst": "Imperial College London" - }, - { - "author_name": "Mauricio Barahona", - "author_inst": "Imperial College London" - }, - { - "author_name": "Sophia N Yaliraki", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.11.06.371419", "rel_title": "Exosome-Mediated mRNA Delivery For SARS-CoV-2 Vaccination", @@ -1094724,6 +1095882,125 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.11.06.370676", + "rel_title": "Potent SARS-CoV-2 neutralizing antibodies selected from a human antibody library constructed decades ago", + "rel_date": "2020-11-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.06.370676", + "rel_abs": "Combinatorial antibody libraries not only effectively reduce antibody discovery to a numbers game, but enable documentation of the history of antibody responses in an individual. The SARS-CoV-2 pandemic has prompted a wider application of this technology to meet the public health challenge of pandemic threats in the modern era. Herein, we used a combinatorial human antibody library constructed 20 years before the COVID-19 pandemic to discover three highly potent antibodies that selectively bind SARS-CoV-2 spike protein and neutralize authentic SARS-CoV-2 virus. Compared to neutralizing antibodies from COVID-19 patients with generally low somatic hypermutation (SHM), these antibodies contain over 13-22 SHMs, many of which are involved in specific interactions in crystal structures with SARS-CoV-2 spike RBD. The identification of these somatically mutated antibodies in a pre-pandemic library raises intriguing questions about the origin and evolution of human immune responses to SARS-CoV-2.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Min Qiang", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Peixiang Ma", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Yu Li", + "author_inst": "ShanghaiTech University; Chinese Academy of Sciences; University of Chinese Academy of Sciences" + }, + { + "author_name": "Hejun Liu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Adam Harding", + "author_inst": "University of Oxford" + }, + { + "author_name": "Chenyu Min", + "author_inst": "Velox Pharmaceuticals" + }, + { + "author_name": "Lili Liu", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Meng Yuan", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Qun Ji", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Pingdong Tao", + "author_inst": "ShanghaiTech University; Chinese Academy of Sciences; University of Chinese Academy of Sciences" + }, + { + "author_name": "Xiaojie Shi", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Zhean Li", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Fulian Wang", + "author_inst": "ShanghaiTech University; Chinese Academy of Sciences; University of Chinese Academy of Sciences" + }, + { + "author_name": "Yu Zhang", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Nicholas C. Wu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Chang-Chun D. Lee", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Xueyong Zhu", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Javier Gilbert-Jaramillo", + "author_inst": "University of Oxford" + }, + { + "author_name": "Abhishek Saxena", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Xingxu Huang", + "author_inst": "ShanghaiTech University" + }, + { + "author_name": "Hou Wang", + "author_inst": "ShOx Science Limited" + }, + { + "author_name": "William James", + "author_inst": "University of Oxford" + }, + { + "author_name": "Raymond A. Dwek", + "author_inst": "Oxford Glycobiology Institute" + }, + { + "author_name": "Ian A. Wilson", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Guang Yang", + "author_inst": "ShanghaiTech University;Velox Pharmaceuticals" + }, + { + "author_name": "Richard A. Lerner", + "author_inst": "The Scripps Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.03.367391", "rel_title": "Evolution of Antibody Immunity to SARS-CoV-2", @@ -1096555,97 +1097832,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.04.369041", - "rel_title": "A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research", - "rel_date": "2020-11-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.04.369041", - "rel_abs": "MotivationIn the event of an outbreak due to an emerging pathogen, time is of the essence to contain or to mitigate the spread of the disease. Drug repositioning is one of the strategies that has the potential to deliver therapeutics relatively quickly. The SARS-CoV-2 pandemic has shown that integrating critical data resources to drive drug-repositioning studies, involving host-host, hostpathogen and drug-target interactions, remains a time-consuming effort that translates to a delay in the development and delivery of a life-saving therapy.\n\nResultsHere, we describe a workflow we designed for a semi-automated integration of rapidly emerging datasets that can be generally adopted in a broad network pharmacology research setting. The workflow was used to construct a COVID-19 focused multimodal network that integrates 487 host-pathogen, 74,805 host-host protein and 1,265 drug-target interactions. The resultant Neo4j graph database named \"Neo4COVID19\" is accessible via a web interface and via API calls based on the Bolt protocol. We believe that our Neo4COVID19 database will be a valuable asset to the research community and will catalyze the discovery of therapeutics to fight COVID-19.\n\nAvailabilityhttps://neo4covid19.ncats.io", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Gergely Zahoranszky-Kohalmi", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Vishal B Siramshetty", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Praveen Kumar", - "author_inst": "Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA; Department of Computer Science, University of New Mexico, Al" - }, - { - "author_name": "Manideep Gurumurthy", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Busola Grillo", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Biju Mathew", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Dimitrios Metaxatos", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Mark Backus", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Tim Mierzwa", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Reid Simon", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Ivan Grishagin", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH); Rancho BioSciences LLC., San Diego, CA USA" - }, - { - "author_name": "Laura Brovold", - "author_inst": "Rancho BioSciences LLC., San Diego, CA USA" - }, - { - "author_name": "Ewy A Math\u00e9", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Matthew D Hall", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Samuel G Michael", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Alexander G Godfrey", - "author_inst": "National Center for Advancing Translational Sciences (NCATS/NIH)" - }, - { - "author_name": "Jordi Mestres", - "author_inst": "5Research Group on Systems Pharmacology, Research Program on Biomedical Informatics (GRIB), IMIM Hospital del Mar Medical Research Institute and University Pomp" - }, - { - "author_name": "Lars J Jensen", - "author_inst": "Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark" - }, - { - "author_name": "Tudor I Oprea", - "author_inst": "Department of Internal Medicine, University of New Mexico School of Medicine, Albuquerque, NM, USA; Novo Nordisk Foundation Center for Protein Research, Faculty" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.11.05.369264", "rel_title": "The N-terminal domain of spike glycoprotein mediates SARS-CoV-2 infection by associating with L-SIGN and DC-SIGN", @@ -1097245,6 +1098431,101 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.11.05.370239", + "rel_title": "SARS-CoV-2 Assembly and Egress Pathway Revealed by Correlative Multi-modal Multi-scale Cryo-imaging", + "rel_date": "2020-11-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.05.370239", + "rel_abs": "Since the outbreak of the SARS-CoV-2 pandemic, there have been intense structural studies on purified recombinant viral components and inactivated viruses. However, investigation of the SARS-CoV-2 infection in the native cellular context is scarce, and there is a lack of comprehensive knowledge on SARS-CoV-2 replicative cycle. Understanding the genome replication, assembly and egress of SARS-CoV-2, a multistage process that involves different cellular compartments and the activity of many viral and cellular proteins, is critically important as it bears the means of medical intervention to stop infection. Here, we investigated SARS-CoV-2 replication in Vero cells under the near-native frozen-hydrated condition using a unique correlative multi-modal, multi-scale cryo-imaging approach combining soft X-ray cryo-tomography and serial cryoFIB/SEM volume imaging of the entire SARS-CoV-2 infected cell with cryo-electron tomography (cryoET) of cellular lamellae and cell periphery, as well as structure determination of viral components by subtomogram averaging. Our results reveal at the whole cell level profound cytopathic effects of SARS-CoV-2 infection, exemplified by a large amount of heterogeneous vesicles in the cytoplasm for RNA synthesis and virus assembly, formation of membrane tunnels through which viruses exit, and drastic cytoplasm invasion into nucleus. Furthermore, cryoET of cell lamellae reveals how viral RNAs are transported from double-membrane vesicles where they are synthesized to viral assembly sites; how viral spikes and RNPs assist in virus assembly and budding; and how fully assembled virus particles exit the cell, thus stablishing a model of SARS-CoV-2 genome replication, virus assembly and egress pathways.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Luiza Mendonca", + "author_inst": "University of Oxford" + }, + { + "author_name": "Andrew Howe", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "James B Gilchrist", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Dapeng Sun", + "author_inst": "University of Oxford" + }, + { + "author_name": "Michael Knight", + "author_inst": "University of Oxford" + }, + { + "author_name": "Laura C Zanetti-Domingues", + "author_inst": "Science and Technology Facility Council" + }, + { + "author_name": "Benji Bateman", + "author_inst": "Science and Technology Facility Council" + }, + { + "author_name": "Anna-Sophia Krebs", + "author_inst": "University of Oxford" + }, + { + "author_name": "Long Chen", + "author_inst": "University of Oxford" + }, + { + "author_name": "Julika Radecke", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Yuewen Sheng", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Vivian D Li", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Tao Ni", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ilias Kounatidis", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Mohamed A Koronfel", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Marta Szynkiewicz", + "author_inst": "Science and Technology Facility Council" + }, + { + "author_name": "Maria Harkiolaki", + "author_inst": "Diamond Light Source" + }, + { + "author_name": "Marisa L Martin-Fernandez", + "author_inst": "Science and Technology Facility Council" + }, + { + "author_name": "William James", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peijun Zhang", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.05.368647", "rel_title": "SLAMF7 engagement super-activates macrophages in acute and chronic inflammation", @@ -1098449,45 +1099730,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.02.20224469", - "rel_title": "SARS-CoV-2 Testing Disparities in Massachusetts", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224469", - "rel_abs": "ObjectiveEarly deficiencies in testing capacity contributed to poor control of transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In the context of marked improvement in SARS-CoV-2 testing infrastructure, we sought to examine the alignment of testing with epidemic intensity to mitigate subsequent waves of COVID-19 in Massachusetts.\n\nMethodsWe compiled publicly available weekly SARS-CoV-2 molecular testing data for period (May 27 to October 14, 2020) following the initial COVID-19 wave. We defined testing intensity as weekly SARS-CoV-2 tests performed per 100,000 population and used weekly test positivity (percent of tests positive) as a measure of epidemic intensity. We considered optimal alignment of testing resources to be matching community ranks of testing and positivity. In communities with a lower rank of testing than positivity in a given week, the testing gap was calculated as the additional tests required to achieve matching ranks. Multivariable Poisson modeling was utilized to assess for trends and association with community characteristics.\n\nResultsDuring the observation period, 4,262,000 tests were reported in Massachusetts and the misalignment of testing with epidemic intensity increased. The weekly testing gap increased 9.0% per week (adjusted rate ratio [aRR]: 1.090, 95% confidence interval [CI]: 1.08-1.10). Increasing levels of community socioeconomic vulnerability (aRR: 1.35 per quartile increase, 95% CI: 1.23-1.50) and the highest quartile of minority and language vulnerability (aRR: 1.46, 95% CI 0.96-1.49) were associated with increased testing gaps, but the latter association was not statistically significant. Presence of large university student population (>10% of population) was associated with a marked decrease in testing gap (aRR 0.21, 95% CI: 0.12-0.38).\n\nConclusionThese analyses indicate that despite objectives to promote equity and enhance epidemic control in vulnerable communities, testing resources across Massachusetts have been disproportionally allocated to more affluent communities. Worsening structural inequities in access to SARS-CoV-2 testing increase the risk for another intense wave of COVID-19 in Massachusetts, particularly among vulnerable communities.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Scott Dryden-Peterson", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Gustavo E. Vel\u00e1squez", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Thomas J. Stopka", - "author_inst": "Department of Public Health and Community Medicine, Tufts University School of Medicine" - }, - { - "author_name": "Sonya Davey", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Shahin Lockman", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Bisola O. Ojikutu", - "author_inst": "Brigham and Women's Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.01.20224105", "rel_title": "Experience from a COVID-19 screening centre of a tertiary care institution: A retrospective hospital-based study", @@ -1098703,6 +1099945,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.11.02.20224519", + "rel_title": "Are Mobile Phones part of the chain of transmission of SARS-CoV-2 in the hospital?", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224519", + "rel_abs": "SARS-CoV-2 cross-transmission has become an concern in hospitals. We investigate healthcare workers(HCWs) knowledge about SARS-CoV-2 cross-transmission and conceptions whether the virus can remain on HCWs mobile phones(MPs) and be part of the chain of transmission.\n\nA cross-sectional study was conducted at a COVID-19 Intensive Care Unit of a teaching-hospital. Fifty-one MPs were swabbed and a questionnaire about hand hygiene and MP use and disinfection was applied after an educational campaign. Although most of HCWs believed on the importance of cross-transmission and increased hand hygiene adhesion and MP disinfection during the pandemic, SARS-CoV-2 RNA was detected in two MPs(culture of the samples was negative).\n\nImplementation of official hospital policies to guide HCWs regarding disinfection and care of personal MP are needed.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Evelyn Patricia Sanchez Espinoza", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Marina Farrel Cortes", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Saidy Vasconez Nogueira", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Anderson Vincente de Paula", + "author_inst": "LIM52 Virology Laboratory, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Thais Guimaraes", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Lucy Santos Vilas Boas", + "author_inst": "LIM52 Virology Laboratory, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Marcelo Park", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Cristina Carvalho da Silva", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Ingra Morales", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Lauro Vieira Perdigao Neto", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Tania Regina Tozetto-Mendoza", + "author_inst": "Instituto de Medicina Tropical de Sao Paulo. Universidade de Sao Paulo." + }, + { + "author_name": "Icaro Boszczowski", + "author_inst": "Hospital das Clinicas, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Ester Sabino", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Maria Cassia Mendes-Correa", + "author_inst": "LIM52 Virology Laboratory, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Anna Sara Shafferman Levin", + "author_inst": "Department of Infectious Diseases, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil." + }, + { + "author_name": "Silvia Figueiredo Costa", + "author_inst": "Department of Infectious diseases, Instituto de Medicina Tropical, Universidade de Sao Paulo, Sao Paulo, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.11.01.20214122", "rel_title": "Simulation model for productivity, risk and GDP impact forecasting of the COVID-19 portfolio vaccines", @@ -1099823,45 +1101144,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.03.20223602", - "rel_title": "A Digital CRISPR-based Method for the Rapid Detection and Absolute Quantification of Viral Nucleic Acids", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.03.20223602", - "rel_abs": "Quantitative real-time PCR and CRISPR-based methods detect SARS-CoV-2 in 1 hour but do not allow for the absolute quantification of virus particles, which could reduce inter-lab variability and accelerate research. The 4-hour reaction time of the existing digital PCR-based method for absolute virus quantification is too long for widespread application. We report a RApid DIgital Crispr Approach (RADICA) for the absolute quantification of SARS-CoV-2 DNA and Epstein-Barr virus DNA in human samples that yields results within 1 hour. For validation, we compared RADICA to digital PCR for quantifying synthetic SARS-CoV-2 DNA and Epstein-Barr viral DNA. RADICA allows absolute quantification of DNA with a dynamic range from 0.6 to 2027 copies/{micro}L (R2 value > 0.98), without cross-reactivity on similar virus or human background DNA. Thus, RADICA can accurately detect and quantify nucleic acid in 1h without thermal cycling, providing a 4-fold faster alternative to digital PCR-based virus detection.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Xiaolin Wu", - "author_inst": "Singapore-MIT Alliance for Research and Technology (SMART)" - }, - { - "author_name": "Cheryl Chan", - "author_inst": "Singapore-MIT Alliance for Research and Technology, Critical Analytics for Manufacturing of Personalized Medicine Interdisciplinary Research Group, Singapore 13" - }, - { - "author_name": "Yie Hou Lee", - "author_inst": "Singapore-MIT Alliance for Research and Technology, Critical Analytics for Manufacturing of Personalized Medicine Interdisciplinary Research Group, Singapore 13" - }, - { - "author_name": "Stacy L. Springs", - "author_inst": "Singapore-MIT Alliance for Research and Technology, Critical Analytics for Manufacturing of Personalized Medicine Interdisciplinary Research Group, Singapore 13" - }, - { - "author_name": "Timothy K. Lu", - "author_inst": "Singapore-MIT Alliance for Research and Technology, Critical Analytics for Manufacturing of Personalized Medicine Interdisciplinary Research Group, Singapore 38" - }, - { - "author_name": "Hanry Yu", - "author_inst": "Singapore-MIT Alliance for Research and Technology, Critical Analytics for Manufacturing of Personalized Medicine Interdisciplinary Research Group, Singapore 13" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.03.20220699", "rel_title": "A prospective study of risk factors associated with seroprevalence of SARS-CoV-2 antibodies in healthcare workers at a large UK teaching hospital", @@ -1100301,6 +1101583,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.11.02.20224642", + "rel_title": "Vascular Thrombosis in COVID-19: A Potential Association with Antiphospholipid Antibodies. A Rapid Systematic Review", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224642", + "rel_abs": "BackgroundVascular thrombosis is common in patients with coronavirus disease 2019 (COVID-19). Etiologies underlying this complication are unclear.\n\nPurposeTo determine the prevalence of antiphospholipid (aPL), including lupus anticoagulant, anti-cardiolipin and anti-{beta}2-glycoprotein-1 antibodies, and its possible association with thrombotic manifestations of COVID-19.\n\nData SourcesWe searched MEDLINE indexed journals on September 24, 2020 using the tool LitCovid and the pre-print server medRxIV.\n\nStudy SelectionOriginal investigations (cross-sectional studies, cohort studies, case series, and research letters) on COVID-19 and thrombosis were included.\n\nData ExtractionData were independently extracted, and compiled into spreadsheets based on the PRISMA principles.\n\nData SynthesisHospitalized patients with COVID-19 showed a higher prevalence of lupus anticoagulant compared to non-COVID-19 patients. Temporally, lupus anticoagulant was generally positive early in the course of illness, whereas anti-cardiolipin and anti-{beta}2-glycoprotein-1 antibodies appeared to emerge later in the disease. Some patients who were aPL-negative at an early time-point after disease onset became aPL-positive at a later time-point. Lupus anticoagulant was independently associated with thrombosis in 60 COVID-19 patients in New York had who had 32 thrombotic events (8 arterial and 24 venous). In 88 patients in Wuhan, who had more than 20 each of arterial and venous thrombotic events, medium/high positivity for multiple aPL was significantly associated with arterial thrombosis. However, the association of aPL with thrombosis was not evident in reports that had an overall lower number of or predominantly venous thrombotic events. Analysis of pooled patients revealed that aPL were significantly more frequent in COVID-19 patients with stroke than stroke patients in the general population. Furthermore, injection of IgG aPL fractions from COVID-19 patients into mice accelerated venous thrombosis.\n\nLimitationLimited data and paucity of prospective studies.\n\nConclusionThe aPL are prevalent in patients with COVID-19 and their presence is associated with thrombosis. Importantly, these antibodies may be a key mechanism of thrombosis in COVID-19. Follow-up studies are required to understand the relationship between aPL and the spectrum of vascular thrombosis during and after infection with SARS-CoV-2.\n\nPrimary Funding SourceNone.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Aneesh S Kallapur", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Eric Y Yen", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Ram Raj Singh", + "author_inst": "UCLA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.11.02.20224709", "rel_title": "Gender-affirming care, mental health, and economic stability in the time of COVID-19: a global cross-sectional study of transgender and non-binary people", @@ -1101585,29 +1102894,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.10.28.20221986", - "rel_title": "Causal Impacts of Teaching Modality on U.S. COVID-19 Spread in Fall 2020 Semester", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221986", - "rel_abs": "We study the impact of college reopening in Fall 2020 on county-level COVID-19 cases and deaths using the information of 1,076 randomly chosen four- and two-year undergraduate degree-granting colleges from the National Center for Education Statistics. These institutions include public, private nonprofit, and for profit schools from 50 US states and the District of Columbia. We match college and county characteristics using several methods and calculate the average treatment effects of three teaching modalities: in-person, online, and hybrid on COVID-19 outcomes up to two months after college reopening. In pairwise comparison, colleges reopened with in-person teaching mode were found to have about 35 percentage points more cases within 15 days of reopening, compared to those that reopened online, and the gap widens over time at a decreasing rate. Death rates follow the pattern with a time lag. However, colleges with hybrid mode reach up to the rates of in-person mode after some time. We also find that greater endowment and student population, bigger class size, and fewer Republican voters in the county are major predictors of choosing remote teaching modes over in-person.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Syed Badruddoza", - "author_inst": "Texas Tech University" - }, - { - "author_name": "Modhurima Dey Amin", - "author_inst": "Texas Tech University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.10.28.20221572", "rel_title": "The Role of Societal Aspects in the Formation of Official COVID-19 Reports: A Data-Driven Analysis", @@ -1101903,6 +1103189,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.28.20221077", + "rel_title": "Simple discrete-time self-exciting models can describe complex dynamic processes: a case study of COVID-19", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221077", + "rel_abs": "Hawkes processes are a form of self-exciting process that has been used in numerous applications, including neuroscience, seismology, and terrorism. While these self-exciting processes have a simple formulation, they are able to model incredibly complex phenomena. Traditionally Hawkes processes are a continuous-time process, however we enable these models to be applied to a wider range of problems by considering a discrete-time variant of Hawkes processes. We illustrate this through the novel coronavirus disease (COVID-19) as a substantive case study. While alternative models, such as compartmental and growth curve models, have been widely applied to the COVID-19 epidemic, the use of discrete-time Hawkes processes allows us to gain alternative insights. This paper evaluates the capability of discrete-time Hawkes processes by retrospectively modelling daily counts of deaths as two distinct phases in the progression of the COVID-19 outbreak: the initial stage of exponential growth and the subsequent decline as preventative measures become effective. We consider various countries that have been adversely affected by the epidemic, namely, Brazil, China, France, Germany, India, Italy, Spain, Sweden, the United Kingdom and the United States. These countries are all unique concerning the spread of the virus and their corresponding response measures, in particular, the types and timings of preventative actions. However, we find that this simple model is useful in accurately capturing the dynamics of the process, despite hidden interactions that are not directly modelled due to their complexity, and differences both within and between countries. The utility of this model is not confined to the current COVID-19 epidemic, rather this model could be used to explain many other complex phenomena. It is of interest to have simple models that adequately describe these complex processes with unknown dynamics. As models become more complex, a simpler representation of the process can be desirable for the sake of parsimony.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Raiha Browning", + "author_inst": "Queensland University of Technology" + }, + { + "author_name": "Deborah Sulem", + "author_inst": "University of Oxford" + }, + { + "author_name": "Kerrie Mengersen", + "author_inst": "Queensland University of Technology" + }, + { + "author_name": "Vincent Rivoirard", + "author_inst": "Universit\u00e9 Paris-Dauphine" + }, + { + "author_name": "Judith Rousseau", + "author_inst": "University of Oxford; Universit\u00e9 Paris-Dauphine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.28.20221408", "rel_title": "ROLE OF CYTOKINES AND OTHER PROPHETIC VARIABLES IN THE DEVELOPMENT AND PROGRESSION OF DISEASE IN PATIENTS SUFFERING FROM COVID-19", @@ -1103263,53 +1104584,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.29.20222612", - "rel_title": "Features of alpha-HBDH in COVID-19 patients with different ages,outcomes and clinical types: a cohort study", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20222612", - "rel_abs": "BackgroundCoronavirus disease-2019 (COVID-19) has spread all over the world and brought extremely huge losses. At present, there is no study to systematically analyse the features of hydroxybutyrate dehydrogenase (-HBDH) in COVID-19 patients with different ages, clinical types and outcomes.\n\nMethodsElectronic medical records including demographics, clinical manifestation, -HBDH test results and outcomes of 131 hospitalized COVID-19 patients, with confirmed result of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral infection, were extracted and analyzed.\n\nResultsThe -HBDH value in [≥]61 years old group, severe group and critical group, death group all increased at first and then decreased, while no obvious changes were observed in other groups. And there were significant differences of the -HBDH value among different age groups (P<0.001), clinical type groups (P<0.001) and outcome groups (P<0.001). The optimal scale regression model showed that -HBDH value (P<0.001) and age (P<0.001) were related to clinical type.\n\nConclusions-HBDH value increases in some COVID-19 patients, obviously in [≥]61 years old, death and critical group, indicating that patients in these three groups suffer from more serious tissues and organs damage, higher -HBDH value and risk of death. The obvious difference between death and survival group in early stage may provide a approach to judge the prognosis. The accuracy of the model to distinguish severe/critical type and other types is 85.84%, suggesting that -HBDH could judge the clinical type of COVID-19 patients accurately. In brief, -HBDH is an important indicator to judge the severity and prognosis of COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Haoming Zhu", - "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China" - }, - { - "author_name": "Gaojing Qu", - "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China" - }, - { - "author_name": "Hui Yu", - "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China" - }, - { - "author_name": "Guoxin Huang", - "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China" - }, - { - "author_name": "Lei Chen", - "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China" - }, - { - "author_name": "Meiling Zhang", - "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China" - }, - { - "author_name": "Shanshan Wan", - "author_inst": "Postgraduate Training Basement of Jinzhou Medical University, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China" - }, - { - "author_name": "Bin Pei", - "author_inst": "Center of Evidence-Based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.28.20216887", "rel_title": "Pharmacokinetics of remdesivir in a COVID-19 patient with end-stage renal disease on intermittent hemodialysis", @@ -1103841,6 +1105115,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.29.20222505", + "rel_title": "The use of compassionate Ivermectin in the management of symptomatic outpatients and hospitalized patients with clinical diagnosis of COVID-19 at the Medical Center Bournigal and the Medical Center Punta Cana, Rescue Group, Dominican Republic, from may 1 to august 10, 2020.", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20222505", + "rel_abs": "No antiviral has been shown to reduce mortality in SARS-COV-2 patients to date. In the present observational and retrospective report, 3,099 patients with a definitive or highly probable diagnosis of infection due to COVID-19 were evaluated between May 1st to August 10th, 2020, at Centro Medico Bournigal (CMBO) and Centro Medico Punta Cana (CMPC), and all received compassionate treatment with Ivermectin. A total of 2,706 (87.3%) were discharged for outpatient treatment, all with mild severity of the infection. In 2,688 (99.33%) with outpatient treatment, the disease did not progress to warrant further hospitalization and there were no deaths. In 16 (0.59%) with outpatient treatment, it was necessary their subsequent hospitalization to a room without any death. In 2 (0.08%) with outpatient treatment, it was necessary their admission to the Intensive Care Unit (ICU) and 1 (0.04%) patient died. There were 411 (13.3%) patients hospitalized, being admitted at a COVID-19 room with a moderate disease 300 (9.7%) patients of which 3 (1%) died; and with a severe to critical disease were hospitalized in the ICU 111 (3.6%), 34 (30.6%) of whom died. The mortality percentage of patients admitted to the ICU of 30.6%, is similar with the percentage found in the literature of 30.9%. Total mortality was 37 (1.2%) patients, which is much lower than that reported in world statistics, which are around 3%.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jose Morgenstern", + "author_inst": "Rescue Group" + }, + { + "author_name": "Jose N Redondo", + "author_inst": "Rescue Group" + }, + { + "author_name": "Albida De Leon", + "author_inst": "Rescue Group" + }, + { + "author_name": "Juan M Canela", + "author_inst": "Rescue Group" + }, + { + "author_name": "Nelson Torres", + "author_inst": "Rescue Group" + }, + { + "author_name": "Johnny Tavares", + "author_inst": "Rescue Group" + }, + { + "author_name": "Migulina Minaya", + "author_inst": "Rescue Group" + }, + { + "author_name": "Oscar Lopez", + "author_inst": "Rescue Group" + }, + { + "author_name": "Ana M Placido", + "author_inst": "Rescue Group" + }, + { + "author_name": "Ana Castillo", + "author_inst": "Rescue Group" + }, + { + "author_name": "Rafael Pena Cruz", + "author_inst": "Rescue Group" + }, + { + "author_name": "Yudelka Merrete", + "author_inst": "Rescue Group" + }, + { + "author_name": "Marlenin Toribio", + "author_inst": "Rescue Group" + }, + { + "author_name": "Juan A Francisco", + "author_inst": "Rescue Group" + }, + { + "author_name": "Santiago Roca", + "author_inst": "Rescue Group" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.29.20219931", "rel_title": "A longitudinal comparison of spike and nucleocapsid SARS-CoV-2 antibody responses in a tertiary hospitals laboratory workers with validation of DBS specimen analysis.", @@ -1105260,97 +1106609,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.11.03.366138", - "rel_title": "Rapid development of SARS-CoV-2 receptor binding domain-conjugated nanoparticle vaccine candidate", - "rel_date": "2020-11-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.03.366138", - "rel_abs": "The ongoing of coronavirus disease 2019 (COVID-19) pandemic caused by novel SARS-CoV-2 coronavirus, resulting in economic losses and seriously threating the human health in worldwide, highlighting the urgent need of a stabilized, easily produced and effective preventive vaccine. The SARS-COV-2 spike protein receptor binding region (RBD) plays an important role in the process of viral binding receptor angiotensin-converting enzyme 2 (ACE2) and membrane fusion, making it an ideal target for vaccine development. In this study, we designed three different RBD-conjugated nanoparticles vaccine candidates, RBD-Ferritin (24-mer), RBD-mi3 (60-mer) and RBD-I53-50 (120-mer), with the application of covalent bond linking by SpyTag-SpyCatcher system. It was demonstrated that the neutralizing capability of sera from mice immunized with three RBD-conjugated nanoparticles adjuvanted with AddaVax or Sigma Systerm Adjuvant (SAS) after each immunization was ~8-to 120-fold greater than monomeric RBD group in SARS-CoV-2 pseudovirus and authentic virus neutralization assay. Most importantly, sera from RBD-conjugated NPs groups more efficiently blocked the binding of RBD to ACE2 or neutralizing antibody in vitro, a further proof of promising immunization effect. Besides, high physical stability and flexibility in assembly consolidated the benefit for rapid scale-up production of vaccine. These results supported that our designed SARS-CoV-2 RBD-conjugated nanoparticle was competitive vaccine candidate and the carrier nanoparticles could be adopted as universal platform for future vaccine development.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Yin-Feng Kang", - "author_inst": "Sun Yat-sen University Cancer Center, Sun Yat-sen University" - }, - { - "author_name": "Cong Sun", - "author_inst": "Sun Yat-sen University Cancer Center, Sun Yat-sen University" - }, - { - "author_name": "Zhen Zhuang", - "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Run-Yu Yuan", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Qing-Bing Zheng", - "author_inst": "Xiamen University" - }, - { - "author_name": "Ping-Ping Zhou", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Jiang-Ping Li", - "author_inst": "Sun Yat-sen University Cancer Center, Sun Yat-sen University" - }, - { - "author_name": "Xin-Chun Chen", - "author_inst": "Sun Yat-sen University Cancer Center, Sun Yat-sen University" - }, - { - "author_name": "Xiao Zhang", - "author_inst": "Sun Yat-sen University Cancer Center, Sun Yat-sen University" - }, - { - "author_name": "Xiao-Hui Yu", - "author_inst": "Sun Yat-sen University Cancer Center, Sun Yat-sen University" - }, - { - "author_name": "Xiang-Wei Kong", - "author_inst": "Sun Yat-sen University Cancer Center, Sun Yat-sen University" - }, - { - "author_name": "Qian-Ying Zhu", - "author_inst": "Sun Yat-sen University Cancer Center, Sun Yat-sen University" - }, - { - "author_name": "Miao Xu", - "author_inst": "Sun Yat-sen University Cancer Center, Sun Yat-sen University" - }, - { - "author_name": "Nan-Shan Zhong", - "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Yi-Xin Zeng", - "author_inst": "Sun Yat-sen University Cancer Center, Sun Yat-sen University" - }, - { - "author_name": "Guo-Kai Feng", - "author_inst": "Sun Yat-sen University Cancer Center" - }, - { - "author_name": "Chang-Wen Ke", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Jin-Cun Zhao", - "author_inst": "the First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Mu-Sheng Zeng", - "author_inst": "Sun Yat-sen University Cancer Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.03.366757", "rel_title": "Structure of nonstructural protein 1 from SARS-CoV-2.", @@ -1105522,6 +1106780,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.27.20220707", + "rel_title": "Association of Mass Gatherings and COVID-19 Hospitalization", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220707", + "rel_abs": "We examined COVID-19 hospitalizations following mass gatherings in Wisconsin and Minnesota, United States (September 17-18, 2020). We found that the hospitalization rate increased 15-fold in the Minnesota gathering county, and 12.7-fold in the Wisconsin gathering county. On the state level, it increased 2-fold in Minnesota, and 2.3-fold in Wisconsin, while not increasing significantly in states without gatherings. Our findings suggest that mass gatherings are followed by increased COVID-19 hospitalizations, and that precautions should be taken.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Oren Miron", + "author_inst": "Ben Gurion University" + }, + { + "author_name": "Kun-Hsing Yu", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Rachel Wilf-Miron", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Nadav Davidovitch", + "author_inst": "Ben Gurion University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.03.366609", "rel_title": "Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design", @@ -1107066,69 +1108355,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.10.28.20221226", - "rel_title": "The characteristics of HIV-positive patients with mild/asymptomatic and moderate/severe course of COVID-19 disease. A report from Central and Eastern Europe", - "rel_date": "2020-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221226", - "rel_abs": "BackgroundThere is currently no evidence suggesting that COVID-19 takes a different course in HIV-positive patients on antiretroviral treatment compared to the general population. However, little is known about the relation between specific HIV-related factors and the severity of the COVID-19 disease.\n\nMethodsWe performed a retrospective analysis of cases collected through an on-line survey distributed by the Euroguidelines in Central and Eastern Europe Network Group. In statistical analyses characteristics of HIV-positive patients asymptomatic/moderate and moderate/severe course were compared.\n\nResultsIn total 34 HIV-positive patients diagnosed with COVID-19 were reported by 12 countries (Estonia, Czech Republic, Lithuania, Albania, Belarus, Romania, Serbia, Bosnia and Herzegovina, Poland, Russia, Hungary, Bulgaria). Asymptomatic courses of COVID-19 were reported in four (12%) cases, 11 (32%) patients presented with mild disease not requiring hospitalization, moderate disease with respiratory and/or systemic symptoms was observed in 14 (41%) cases, and severe disease with respiratory failure was found in five (15%) patients. The only HIV-related characteristics differentiating a moderate/severe course of the disease from asymptomatic/mild disease course was the use of or PI or NNRTI as part of the cART regimen (40.0% vs. 5.3%, p=0.0129 for PI and 31.6 % vs. 0.0%, p= 0.0239 for NNRTI).\n\nConclusionsIn our analyses HIV viral suppression and immunological status were not playing a role in the course of COVID-19 disease. On the contrary the cART regimen could contribute to severity of SARS-CoV-2 infection. Large and prospective studies are necessary to further investigate this relations.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Justyna Dominika Kowalska", - "author_inst": "Medical University of Warsaw" - }, - { - "author_name": "Kerstin Kase", - "author_inst": "West Tallinn Central Hospital, Estonia" - }, - { - "author_name": "Anna Vassilenko", - "author_inst": "Belarusian State Medical University, Minsk, Belarus" - }, - { - "author_name": "Arjan Harxhi", - "author_inst": "University Hospital Center of Tirana, Infectious Disease Service, Albania" - }, - { - "author_name": "Botond Lakatos", - "author_inst": "National Institute of Hematology and Infectious Diseases, South-Pest Central Hospital, National Center of HIV, Hungary" - }, - { - "author_name": "Gordana Dragovic Lukic", - "author_inst": "Department of pharmacology, clinical pharmacology and toxicology, School of Medicine, University of Belgrade, Serbia" - }, - { - "author_name": "Antonija Verhaz", - "author_inst": "Clinic for Infectious Diseases, University Clinical Centre of the Republic of Srpska, Banja Luka, the Republic of Srpska, Bosnia and Herzegovina; Department for" - }, - { - "author_name": "Nina Yancheva", - "author_inst": "Department for AIDS. Specialized Hospital for Active Treatment of Infectious and Parasitic Disease Sofia, Bulgaria" - }, - { - "author_name": "Florentina Dumitrescu", - "author_inst": "Department of Infectious Diseases, 1st Faculty of Medicine, Charles University in Prague and Na Bulovce Hospital" - }, - { - "author_name": "David Jilich", - "author_inst": "Department of Infectious Diseases, 1st Faculty of Medicine, Charles University in Prague and Na Bulovce Hospital" - }, - { - "author_name": "Ladislav Machala", - "author_inst": "Department of Infectious Diseases, 3rd Faculty of Medicine, Charles University in Prague and Na Bulovce Hospital" - }, - { - "author_name": "Raimonda Matulionyte", - "author_inst": "Department of Infectious Diseases and Dermatovenerology, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Lithuania." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "hiv aids" - }, { "rel_doi": "10.1101/2020.10.28.20221119", "rel_title": "Features of creatine-kinase in COVID-19 patients within various specific periods: A cohort study", @@ -1107368,6 +1108594,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.28.20221093", + "rel_title": "Features of creatine-kinase in COVID-19 patients with different ages, clinical types and outcomes: A cohort study", + "rel_date": "2020-11-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221093", + "rel_abs": "ObjectivesTo study the features of creatine-kinase (CK) in COVID-19 patients with different ages, clinical types and outcomes and quantify the relationship between CK value and clinical type.\n\nMethodsAll laboratory confirmed COVID-19 patients hospitalized in Xiangyang No.1 Peoples Hospital were included. Patients general information, clinical type, all CK values and outcome were collected.\n\nResultsThe peak median value of CK in cases aged [≥] 71 years old (appeared at T2) was higher than that in cases aged [≤] 70 years old. There was statistical difference between the two groups (P=0.001). Similarly, the peak in critical cases (appeared at T2) was higher than moderate and severe types, and significant difference were existed among moderate, severe, and critical types (P=0.000). Moreover, the peak value in death group (appeared at T2) was higher than those in survival group. Significant difference was also found between them (P=0.000). According to the optimal scale regression model, the CK value (P=0.000) and age (P=0.000) were associated with the clinical type.\n\nConclusionsDifference of the CK in different ages, clinical types, and outcomes were significant. The results of the optimal scale regression model are helpful to judge the clinical type of COVID-19 patients.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Shanshan Wan", + "author_inst": "Postgraduate Training Basement of Jinzhou Medical University, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Gaojing Qu", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Hui Yu", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Haoming Zhu", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Guoxin Huang", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Lei Chen", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Meiling Zhang", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Jiangtao Liu", + "author_inst": "Department of Orthopedics, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + }, + { + "author_name": "Bin Pei", + "author_inst": "Center of Evidence-based Medicine, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang 441000, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.28.20221069", "rel_title": "Psychological and social impact of COVID-19 in Pakistan: Need for Gender Responsive Policies", @@ -1108508,129 +1109785,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.28.20221143", - "rel_title": "Major new lineages of SARS-CoV-2 emerge and spread in South Africa during lockdown.", - "rel_date": "2020-10-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221143", - "rel_abs": "In March 2020, the first cases of COVID-19 were reported in South Africa. The epidemic spread very fast despite an early and extreme lockdown and infected over 600,000 people, by far the highest number of infections in an African country. To rapidly understand the spread of SARS-CoV-2 in South Africa, we formed the Network for Genomics Surveillance in South Africa (NGS-SA). Here, we analyze 1,365 high quality whole genomes and identify 16 new lineages of SARS-CoV-2. Most of these unique lineages have mutations that are found hardly anywhere else in the world. We also show that three lineages spread widely in South Africa and contributed to [~]42% of all of the infections in the country. This included the first identified C lineage of SARS-CoV-2, C.1, which has 16 mutations as compared with the original Wuhan sequence. C.1 was the most geographically widespread lineage in South Africa, causing infections in multiple provinces and in all of the eleven districts in KwaZulu-Natal (KZN), the most sampled province. Interestingly, the first South-African specific lineage, B.1.106, which was identified in April 2020, became extinct after nosocomial outbreaks were controlled. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify and control the spread of SARS-CoV-2.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Houriiyah Tegally", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal" - }, - { - "author_name": "Eduan Wilkinson", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal" - }, - { - "author_name": "Richard John Lessells", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal" - }, - { - "author_name": "Jennifer Giandhari", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal" - }, - { - "author_name": "Sureshnee Pillay", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal" - }, - { - "author_name": "Nokukhanya Msomi", - "author_inst": "Discipline of Virology, University of KwaZulu-Natal" - }, - { - "author_name": "Koleka Mlisana", - "author_inst": "National Health Laboratory Service (NHLS)" - }, - { - "author_name": "Jinal Bhiman", - "author_inst": "National Institute For Communicable Diseases (NICD)" - }, - { - "author_name": "Mushal Allam", - "author_inst": "National Institute For Communicable Diseases (NICD)" - }, - { - "author_name": "Arshad Ismail", - "author_inst": "National Institute For Communicable Diseases (NICD)" - }, - { - "author_name": "Susan Engelbrecht", - "author_inst": "Division of Medical Virology at NHLS Tygerberg Hospital, Stellenbosch University" - }, - { - "author_name": "Gert Van Zyl", - "author_inst": "Division of Medical Virology at NHLS Tygerberg Hospital, Stellenbosch University" - }, - { - "author_name": "Wolfgang Preiser", - "author_inst": "Division of Medical Virology at NHLS Tygerberg Hospital, Stellenbosch University" - }, - { - "author_name": "Carolyn Williamson", - "author_inst": "Division of Medical Virology at NHLS Groote Schuur Hospital, University of Cape Town," - }, - { - "author_name": "Francesco Pettruccione", - "author_inst": "University of KwaZulu-Natal" - }, - { - "author_name": "Alex Sigal", - "author_inst": "Africa Health Research Institute" - }, - { - "author_name": "Inbal Gazy", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal" - }, - { - "author_name": "Diana Hardie", - "author_inst": "Division of Medical Virology at NHLS Groote Schuur Hospital, University of Cape Town" - }, - { - "author_name": "Marvin Hsiao", - "author_inst": "Division of Medical Virology at NHLS Groote Schuur Hospital, University of Cape Town" - }, - { - "author_name": "Darren Martin", - "author_inst": "The Computational Biology Division at The University of Cape Town" - }, - { - "author_name": "Denis York", - "author_inst": "Molecular Diagnostics Services (MDS)" - }, - { - "author_name": "Dominique Goedhals", - "author_inst": "Division of Virology at NHLS Universitas Academic Laboratories, University of The Free State" - }, - { - "author_name": "Emmanuel James San", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal" - }, - { - "author_name": "Marta Giovanetti", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Jose Lourenco", - "author_inst": "University of Oxford" - }, - { - "author_name": "Luiz Carlos Junior Alcantara", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "University of KwaZulu-Natal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.28.20221275", "rel_title": "Symptom based and transmission-prevention based testing in long-term care facilities: Symptomatology, clinical course and mortality for residents with COVID-19", @@ -1108950,6 +1110104,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.27.20220731", + "rel_title": "Mental Health Impact of the First Wave of COVID-19 Pandemic on Spanish Healthcare Workers: a Large Cross-sectional Survey", + "rel_date": "2020-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220731", + "rel_abs": "IntroductionHealthcare workers are vulnerable to adverse mental health impacts of COVID-19. We assessed prevalence of mental disorders and associated factors during the first wave of the pandemic among healthcare professionals in Spain.\n\nMethodsAll workers in 18 healthcare institutions (6 AACC) in Spain were invited to a series of online surveys assessing a wide range of individual characteristics, COVID-19 infection status and exposure, and mental health status. Here we report: current mental disorders (Major Depressive Disorder-MDD- [PHQ-8[≥]10], Generalized Anxiety Disorder-GAD- [GAD-7[≥]10], Panic attacks, Posttraumatic Stress Disorder -PTSD- [PCL-5[≥]7]; and Substance Use Disorder -SUD-[CAGE-AID[≥]2]. Severe disability assessed by the Sheehan Disability Scale was used to identify \"disabling\" current mental disorders.\n\nResults9,138 healthcare workers participated. Prevalence of screen-positive disorder: 28.1% MDD; 22.5% GAD, 24.0% Panic; 22.2% PTSD; and 6.2% SUD. Overall 45.7% presented any current and 14.5% any disabling current mental disorder. Healthcare workers with prior lifetime mental disorders had almost twice the prevalence of current disorders than those without. Adjusting for all other variables, odds of any disabling mental disorder were: prior lifetime disorders (TUS: OR=5.74; 95%CI 2.53-13.03; Mood: OR=3.23; 95%CI:2.27-4.60; Anxiety: OR=3.03; 95%CI:2.53-3.62); age category 18-29 years (OR=1.36; 95%CI:1.02-1.82), caring \"all of the time\" for COVID-19 patients (OR=5.19; 95%CI: 3.61-7.46), female gender (OR=1.58; 95%CI: 1.27-1.96) and having being in quarantine or isolated (OR= 1.60; 95CI:1.31-1.95).\n\nConclusionsCurrent mental disorders were very frequent among Spanish healthcare workers during the first wave of COVID-19. As the pandemic enters its second wave, careful monitoring and support is needed for healthcare workers, especially those with previous mental disorders and those caring COVID-19 very often.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Jordi Alonso", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Gemma Vilagut", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Philippe Mortier", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Montse Ferrer", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Itxaso Alayo", + "author_inst": "Health Services Research Unit, IMIM-Institut Hospital del Mar d'Investigacions M\u00e8diques" + }, + { + "author_name": "Andr\u00e9s Arag\u00f3n-Pe\u00f1a", + "author_inst": "Epidemiology Unit, Regional Ministry of Health, Community of Madrid" + }, + { + "author_name": "Enric Aragon\u00e8s", + "author_inst": "Institut d'Investigaci\u00f3 en Atenci\u00f3 Prim\u00e0ria IDIAP Jordi Gol" + }, + { + "author_name": "Mireia Campos", + "author_inst": "Service of Prevention of Labor Risks, Medical Emergencies System, Generalitat de Catalunya" + }, + { + "author_name": "Isabel del Cura-Gonz\u00e1lez", + "author_inst": "Research Unit. Primary Care Management. Madrid Health Service" + }, + { + "author_name": "Jos\u00e9 I. Emparanza", + "author_inst": "Hospital Universitario Donostia" + }, + { + "author_name": "Meritxell Espuga", + "author_inst": "Occupational Health Service. Hospital Universitari Vall d'Hebron" + }, + { + "author_name": "Joao Forjaz", + "author_inst": "National Center of Epidemiology, Instituto de Salud Carlos III (ISCIII)" + }, + { + "author_name": "Ana Gonz\u00e1lez Pinto", + "author_inst": "Hospital Universitario Araba-Santiago" + }, + { + "author_name": "Josep M. Haro", + "author_inst": "Parc Sanitari Sant Joan de D\u00e9u" + }, + { + "author_name": "Nieves L\u00f3pez Fresne\u00f1a", + "author_inst": "Hospital General Universitario Gregorio Mara\u00f1\u00f3n" + }, + { + "author_name": "Alma Mart\u00ednez de Sal\u00e1zar", + "author_inst": "UGC Salud Mental, Hospital Universitario Torrec\u00e1rdenas" + }, + { + "author_name": "Juan D. Molina", + "author_inst": "Villaverde Mental Health Center. Clinical Management Area of Psychiatry and Mental Health, Psychiatric Service, Hospital Universitario 12 de Octubre" + }, + { + "author_name": "Rafael M. Ort\u00ed Lucas", + "author_inst": "Hospital Cl\u00ednic Universitari de Valencia" + }, + { + "author_name": "Mara Parellada", + "author_inst": "Hospital General Universitario Gregorio Mara\u00f1\u00f3n" + }, + { + "author_name": "Jos\u00e9 Maria Pelayo-Ter\u00e1n", + "author_inst": "Hospital El Bierzo" + }, + { + "author_name": "Aurora P\u00e9rez Zapata", + "author_inst": "Pr\u00edncipe de Asturias University Hospital" + }, + { + "author_name": "Jos\u00e9 I. Pijoan", + "author_inst": "Hospital Universitario Cruces/ OSI EEC" + }, + { + "author_name": "Nieves Plana", + "author_inst": "Pr\u00edncipe de Asturias University Hospital" + }, + { + "author_name": "Teresa Puig", + "author_inst": "Department of Epidemiology and Public Health, Hospital de la Santa Creu i Sant Pau" + }, + { + "author_name": "Cristina Rius", + "author_inst": "Ag\u00e8ncia de Salut P\u00fablica de Barcelona" + }, + { + "author_name": "Carmen Rodriguez-Blazquez", + "author_inst": "National Center of Epidemiology, Instituto de Salud Carlos III (ISCIII)" + }, + { + "author_name": "Ferran Sanz", + "author_inst": "Research Progamme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)" + }, + { + "author_name": "Consol Serra", + "author_inst": "Parc de Salut Mar PSMAR" + }, + { + "author_name": "Ronald C. Kessler", + "author_inst": "Department of Health Care Policy, Harvard Medical School" + }, + { + "author_name": "Ronny Bruffaerts", + "author_inst": "Center for Public Health Psychiatry, Universitair Psychiatrisch Centrum, KU Leuven" + }, + { + "author_name": "Eduard Vieta", + "author_inst": "Fundaci\u00f3 Cl\u00ednic per a la Recerca Biom\u00e8dica de Barcelona" + }, + { + "author_name": "V\u00edctor P\u00e9rez-Sol\u00e1", + "author_inst": "Parc de Salut Mar PSMAR" + }, + { + "author_name": "- MINDCOVID Working group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.29.20222372", "rel_title": "The COVID-19 Healthcare Personnel Study (CHPS): Overview, Methods and Preliminary Report", @@ -1111262,101 +1112563,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.10.28.359356", - "rel_title": "A genome-wide CRISPR/Cas9 knock-out screen identifies the DEAD box RNA helicase DDX42 as a broad antiviral inhibitor", - "rel_date": "2020-10-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.28.359356", - "rel_abs": "Genome-wide screens are powerful approaches to unravel new regulators of viral infections. Here, we used a CRISPR/Cas9 screen to reveal new HIV-1 inhibitors. This approach led us to identify the RNA helicase DDX42 as an intrinsic antiviral inhibitor. DDX42 was previously described as a non-processive helicase, able to bind RNA secondary structures such as G-quadruplexes, with no clearly defined function ascribed. Our data show that depletion of endogenous DDX42 significantly increased HIV-1 DNA accumulation and infection in cell lines and primary cells. DDX42 overexpression inhibited HIV-1, whereas a dominant-negative mutant increased infection. Importantly, DDX42 also restricted retrotransposition of LINE-1, infection with other retroviruses and positive-strand RNA viruses, including CHIKV and SARS-CoV-2. However, DDX42 did not inhibit infection with three negative-strand RNA viruses, arguing against a general, unspecific effect on target cells, which was confirmed by RNA-seq analysis. DDX42 was found in the vicinity of viral elements by proximity ligation assays, and cross-linking RNA immunoprecipitation confirmed a specific interaction of DDX42 with RNAs from sensitive viruses. This strongly suggested a direct mode of action of DDX42 on viral ribonucleoprotein complexes. Taken together, our results show for the first time a new and important role of DDX42 in intrinsic antiviral immunity.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Boris Bonaventure", - "author_inst": "IRIM, CNRS, Montpellier University" - }, - { - "author_name": "Antoine Rebendenne", - "author_inst": "IRIM, CNRS, Montpellier University" - }, - { - "author_name": "Francisco Garcia de Gracia", - "author_inst": "IRIM, CNRS, Montpellier University" - }, - { - "author_name": "Joe McKellar", - "author_inst": "IRIM, CNRS, Montpellier University" - }, - { - "author_name": "S\u00e9gol\u00e8ne Gracias", - "author_inst": "Institut Pasteur, Virus Sensing and Signaling Unit, Department of Virology, CNRS UMR 3569, Paris, France" - }, - { - "author_name": "Emmanuel Labaronne", - "author_inst": "LBMC, Universit\u00e9 de Lyon, ENS de Lyon, CNRS, INSERM, Lyon, France" - }, - { - "author_name": "Marine Tauziet", - "author_inst": "IRIM, CNRS, Montpellier University" - }, - { - "author_name": "Ana Luiza Chaves Valad\u00e3o", - "author_inst": "IRIM, CNRS, Montpellier University" - }, - { - "author_name": "Eric Bernard", - "author_inst": "IRIM, CNRS, Montpellier University" - }, - { - "author_name": "Laurence Briant", - "author_inst": "IRIM, CNRS, Montpellier University" - }, - { - "author_name": "Nathalie Gros", - "author_inst": "CEMIPAI, CNRS, Montpellier University" - }, - { - "author_name": "Wassila Djilli", - "author_inst": "IRIM, CNRS, Montpellier University" - }, - { - "author_name": "Mary Arnaud-Arnould", - "author_inst": "IRIM, CNRS, Montpellier University" - }, - { - "author_name": "Val\u00e9rie Courgnaud", - "author_inst": "IGMM, CNRS, Montpellier University" - }, - { - "author_name": "Hugues Parrinello", - "author_inst": "Montpellier GenomiX" - }, - { - "author_name": "St\u00e9phanie Rialle", - "author_inst": "Montpellier GenomiX" - }, - { - "author_name": "Emiliano P. Ricci", - "author_inst": "LBMC UMR5239, Universit\u00e9 de Lyon, ENS de Lyon, CNRS, INSERM, Lyon, France" - }, - { - "author_name": "Nolwenn Jouvenet", - "author_inst": "Institut Pasteur, Virus Sensing and Signaling Unit, Department of Virology, CNRS UMR 3569, Paris, France" - }, - { - "author_name": "Olivier Moncorg\u00e9", - "author_inst": "IRIM, CNRS, Montpellier University" - }, - { - "author_name": "Caroline Goujon", - "author_inst": "IRIM, CNRS, Montpellier University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.27.354563", "rel_title": "Aglycone polyether ionophores as broad-spectrum agents inhibit multiple enveloped viruses including SARS-CoV-2 in vitro and successfully cure JEV infected mice", @@ -1111760,6 +1112966,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.10.28.355305", + "rel_title": "5-amino levulinic acid inhibits SARS-CoV-2 infection in vitro", + "rel_date": "2020-10-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.28.355305", + "rel_abs": "The current COVID-19 pandemic requires urgent development of effective therapeutics. 5-amino levulinic acid (5-ALA) is a naturally synthesized amino acid and has been used for multiple purposes including as an anticancer therapy and as a dietary supplement due to its high bioavailability. In this study, we demonstrated that 5-ALA treatment potently inhibited infection of SARS-CoV-2, a causative agent of COVID-19. The antiviral effects could be detected in both human and non-human cells, without significant cytotoxicity. Therefore, 5-ALA is a candidate as an oral antiviral drug for COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yasuteru Sakurai", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Mya Myat Ngwe Tun", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Yohei Kurosaki", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Takaya Sakura", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Daniel Ken Inaoka", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Kiyotaka Fujine", + "author_inst": "neopharma Japan Co., Ltd." + }, + { + "author_name": "Kiyoshi Kita", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Kouichi Morita", + "author_inst": "Nagasaki University" + }, + { + "author_name": "Jiro Yasuda", + "author_inst": "Nagasaki University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.28.359257", "rel_title": "In vitro assessment of the virucidal activity of four mouthwashes containing Cetylpyridinium Chloride, ethanol, zinc and a mix of enzyme and proteins against a human coronavirus", @@ -1113092,41 +1114349,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.23.20218396", - "rel_title": "The impact of the COVID-19 pandemic on the mental health and wellbeing of UK healthcare workers", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20218396", - "rel_abs": "BackgroundThere is an urgent need to understand the psychological impact the COVID-19 pandemic has had on UK healthcare workers (HCW).\n\nAimsTo reveal risk and protective factors associated with poor mental wellbeing of HCW working during the COVID-19 pandemic in the UK.\n\nMethod2773 UK HCWs completed a survey between 22ndApril and 10th May 2020 containing scales measuring anxiety, depression, PTSD, and stress, and questions about roles and COVID-19-related factors including workplace preparation and risk management. Respondents were classified as high or low symptomatic on each mental health scale and logistic regression revealed risk and protective factors associated with each outcome. Change in wellbeing from pre to during COVID-19 was also quantified.\n\nResultsA large proportion of UK HCW had high mental health symptoms. Fixed risk factors of poor mental health included being female, being frontline, pre-existing mental health diagnoses, and experience of stressful/traumatic events. An additional set of controllable factors also significantly increased risk: PPE availability, workload, lack of COVID-19 preparation and training, and insufficient communication of clinical procedures. Resilience and sharing stress reduced risk, as did ethical support for those making treatment decisions. Allied HCW and managers were at elevated risk of high symptoms particularly PTSD. Wellbeing, especially of frontline workers, had significantly worsened compared to before COVID-19.\n\nConclusionsPoor mental wellbeing was prevalent in HCW during the UK COVID-19 response. A number of controllable factors should be targeted, and protective factors promoted, to reduce the detrimental effect of COVID-19 and other pandemics on HCW mental health.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "James Gilleen", - "author_inst": "University of Roehampton" - }, - { - "author_name": "Aida Santaolalla", - "author_inst": "School of Cancer & Pharmaceutical Sciences, Kings College London, London." - }, - { - "author_name": "Lorena Valdearenas", - "author_inst": "Barnet, Enfield and Haringey Mental Health NHS Trust. St Ann's Road. London" - }, - { - "author_name": "Clara Salice", - "author_inst": "Barts Health NHS Trust, The Royal London Hospital, Whitechapel Road, London" - }, - { - "author_name": "Monserrat Fuste", - "author_inst": "North East London Foundation Trust. Ilford, UK." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.10.22.20218032", "rel_title": "Prediction and control of COVID-19 infection based on a hybrid intelligent model", @@ -1113326,6 +1114548,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.23.20218255", + "rel_title": "Characteristics and outcomes of hospitalized adult COVID-19 patients in Georgia", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20218255", + "rel_abs": "ObjectiveDescribe presenting characteristics of hospitalized patients and explore factors associated with in-hospital mortality during the first wave of pandemic in Georgia.\n\nMethodsThis retrospective study included 582 adult patients admitted to 9 dedicated COVID-19 hospitals as of July 30, 2020 (72% of all hospitalizations). Data were abstracted from medical charts. Factors associated with mortality were evaluated in multivariable Poisson regression analysis.\n\nResultsAmong 582 adults included in this analysis 14.9% were 65+ years old, 49.1% were women, 59.3% had uni- or bi-lateral lung involvement on chest computed tomography, 27.1% had any co-morbidity, 13.2% patients had lymphopenia, 4.1% had neutophilosis, 4.8% had low platelet count, 37.6% had d-dimer levels of >0.5 mcg/l. Overall mortality was 2.1% (12/582). After excluding mild infections, mortality among patients with moderate-to-critical disease was 3.0% (12/399), while among patients with severe-to-critical disease mortality was 12.7% (8/63). Baseline characteristics associated with increased risk of mortality in multivariate regression analysis included: age [≥]65 years (RR: 10.38, 95% CI: 1.30-82.75), presence of any chronic co-morbidity (RR: 20.71, 95% CI: 1.58-270.99), lymphopenia (RR: 4.76, 95% CI: 1.52-14.93), neutrophilosis (RR: 7.22, 95% CI: 1.27-41.12), low platelet count (RR: 6.92, 95% CI: 1.18-40.54), elevated d-dimer (RR: 4.45, 95% CI: 1.48-13.35), elevated AST (RR: 6.33, 95% CI: 1.18-33.98).\n\nConclusionIn-hospital mortality during the first wave of pandemic in Georgia was low. We identified several risk factors (older age, co-morbidities and laboratory abnormalities) associated with poor outcome that should provide guidance for planning health sector response as pandemic continues to evolve.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Tengiz Tsertsvadze", + "author_inst": "1) Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia; 2) Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia" + }, + { + "author_name": "Marina Ezugbaia", + "author_inst": "Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia" + }, + { + "author_name": "Marina Endeladze", + "author_inst": "Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia" + }, + { + "author_name": "Levani Ratiani", + "author_inst": "First University Clinic, Tbilisi, Georgia" + }, + { + "author_name": "Neli Javakhishvili", + "author_inst": "Giorgi Abramishvili Military Hospital, Gori, Georgia" + }, + { + "author_name": "Lika Mumladze", + "author_inst": "St. King Mirian and Queen Nana Mtskheta Regional Medical Center, Georgia" + }, + { + "author_name": "Manana Khotcholava", + "author_inst": "Childrens Infectious Diseases Hospital, Tbilisi, Georgia" + }, + { + "author_name": "Maiko Janashia", + "author_inst": "University Clinic Rukhi, Georgia" + }, + { + "author_name": "Diana Zviadadze", + "author_inst": "LJ Clinic, Kutaisi, Georgia" + }, + { + "author_name": "Levan Gopodze", + "author_inst": "Central Republican Hospital, Tbilisi, Georgia" + }, + { + "author_name": "Alex Gokhelashvili", + "author_inst": "Medalpha Clinic, Batumi, Georgia" + }, + { + "author_name": "Revaz Metchurchtlishvili", + "author_inst": "Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia" + }, + { + "author_name": "Akaki Abutidze", + "author_inst": "1) Infectious Diseases, AIDS and Clinical Immunology Research Center, Tbilisi, Georgia; 2) Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia" + }, + { + "author_name": "Nikoloz Chkhartishvili", + "author_inst": "1) Infectious Diseases, AIDS and Clinical Immunology Research Center; 2) Caucasus International University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.23.20218164", "rel_title": "SARS-CoV-2 seroprevalence in healthcare workers of dedicated COVID hospitals and non COVID hospitals of District Srinagar, Kashmir", @@ -1114414,49 +1115707,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2020.10.25.20218982", - "rel_title": "Clinical Outcome of Asymptomatic COVID-19 Infection Among a Large Nationwide Cohort of 5,621 Hospitalized Patients in Korea", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.25.20218982", - "rel_abs": "We investigated clinical outcome of asymptomatic coronavirus disease 2019 (COVID-19) and identified risk factors associated with high patient mortality using Korean nationwide public database of 5,621 hospitalized patients. The mortality rate and admission rate to intensive care unit were compared between asymptomatic and symptomatic patients. The prediction model for patient mortality was developed through risk factor analysis among asymptomatic patients. The prevalence of asymptomatic COVID-19 infection was 25.8%. The mortality rates were not different between groups (3.3% vs. 4.5%, p=0.17). However, symptomatic patients were more likely to receive ICU care compared to asymptomatic patients (4.1% vs. 1.0%, p<0.0001). The age-adjusted Charlson comorbidity index score (CCIS) was the most potent predictor for patient mortality in asymptomatic patients. The clinicians should predict the risk of death by evaluating age and comorbidities but not the presence of symptoms.\n\nArticle Summary LineSince asymptomatic patients have similar mortality rate with symptomatic patients, the clinicians should not classify clinical severity according to initial presence of symptom.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Hayne Cho Park", - "author_inst": "Kangnam Sacred Heart Hospital" - }, - { - "author_name": "Do Hyoung Kim", - "author_inst": "Kangnam Sacred Heart Hospital" - }, - { - "author_name": "AJin Cho", - "author_inst": "Kangnam Sacred Heart Hospital" - }, - { - "author_name": "Juhee Kim", - "author_inst": "Kangnam Sacred Heart Hospital" - }, - { - "author_name": "Kyu-sang Yun", - "author_inst": "Kangnam Sacred Heart Hospital" - }, - { - "author_name": "Jinseog Kim", - "author_inst": "Dongguk University" - }, - { - "author_name": "Young-Ki Lee", - "author_inst": "Kangnam Sacred Heart Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.25.20215285", "rel_title": "Clinical evaluation of a fully automated, lab developed multiplex RT-PCR assay integrating dual-target SARS-CoV-2 and Influenza-A/B detection on a high-throughput platform", @@ -1114892,6 +1116142,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.24.20218685", + "rel_title": "Increasing SARS-CoV-2 RT-qPCR testing capacity by sample pooling", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.24.20218685", + "rel_abs": "ObjectivesLimited testing capacity has characterized the ongoing COVID-19 pandemic in Spain, hampering a timely control of outbreaks and the possibilities to reduce the escalation of community transmissions. Here we investigated the potential of using pooling of samples followed by one-step retrotranscription and quantitative PCR (RT-qPCR) to increase SARS-CoV-2 testing capacity.\n\nMethodsWe first evaluated different sample pooling (1:5, 1:10 and 1:15) prior to RNA extractions followed by standard RT-qPCR for SARS-CoV-2/COVID-19 diagnosis. The pool size achieving reproducible results in independent tests was then used for assessing nasopharyngeal samples in a tertiary hospital during August 2020.\n\nResultsWe found that pool size of five samples achieved the highest sensitivity compared to pool sizes of 10 and 15, showing a mean ({+/-} SD) Ct shift of 3.5 {+/-} 2.2 between the pooled test and positive samples in the pool. We then used a pool size of five to test a total of 895 pools (4,475 prospective samples) using two different RT-qPCR kits available at that time. The Real Accurate Quadruplex corona-plus PCR Kit (PathoFinder) reported the lowest mean Ct ({+/-} SD) shift (2.2 {+/-} 2.4) among the pool and the individual samples. The strategy allows detecting individual samples in the positive pools with Cts in the range of 16.7-39.4.\n\nConclusionsWe found that pools of five samples combined with RT-qPCR solutions helped to increase SARS-CoV-2 testing capacity with minimal loss of sensitivity compared to that resulting from testing the samples independently.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Julia Alcoba-Florez", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Helena Gil-Campesino", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Diego Garcia-Martinez de Artola", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Oscar Diez-Gil", + "author_inst": "Servicio de Microbiologia, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Agustin Valenzuela-Fernandez", + "author_inst": "Laboratorio de Inmunologia Celular y Viral, Unidad de Farmacologia, Universidad de La Laguna" + }, + { + "author_name": "Rafaela Gonzalez-Montelongo", + "author_inst": "Genomics Division, Instituto Tecnologico y de Energias Renovables" + }, + { + "author_name": "Laura Ciuffreda", + "author_inst": "Unidad de Investigacion, Hospital Universitario Nuestra Senora de Candelaria" + }, + { + "author_name": "Carlos Flores", + "author_inst": "Hospital Universitario Nuestra Senora de Candelaria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.24.20218974", "rel_title": "Low serum vitamin D level and COVID-19 infection and outcomes, a multivariate meta-analysis", @@ -1116064,89 +1117361,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.26.20219527", - "rel_title": "Effects of New York's Executive Order on Face Mask Use on COVID-19 Infections and Mortality: A Modeling Study", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219527", - "rel_abs": "BackgroundNew York City (NYC) was the epicenter of the COVID-19 pandemic in the United States. On April 17, 2020, the State of New York implemented an Executive Order that requires all people in New York to wear a face mask or covering in public settings where social distancing cannot be maintained. It is unclear how this Executive Order has affected the spread of COVID-19 in NYC.\n\nMethodsA dynamic compartmental model of COVID-19 transmission among NYC residents was developed to assess the effect of the Executive Order on face mask use on infections and deaths due to COVID-19 in NYC. Data on daily and cumulative COVID-19 infections and deaths were obtained from the NYC Department of Health and Mental Hygiene.\n\nResultsThe Executive Order on face mask use is estimated to avert 99,517 (95% CIs: 72,723-126,312) COVID-19 infections and 7,978 (5,692-10,265) deaths in NYC. If the Executive Order was implemented one week earlier (on April 10), the averted infections and deaths would be 111,475 (81,593-141,356) and 9,017 (6,446-11,589), respectively. If the Executive Order was implemented two weeks earlier (on April 3 when the Centers for Disease Control and Prevention recommended face mask use), the averted infections and deaths would be 128,598 (94,373-162,824) and 10,515 (7,540-13,489), respectively.\n\nConclusionsNew Yorks Executive Order on face mask use is projected to have significantly reduced the spread of COVID-19 in NYC. Implementing the Executive Order at an earlier date would avert even more COVID-19 infections and deaths.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Mingwang Shen", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Jian Zu", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Christopher K. Fairley", - "author_inst": "Monash University" - }, - { - "author_name": "Jose A. Pagan", - "author_inst": "New York University" - }, - { - "author_name": "Bart Ferket", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Bian Liu", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Stella S. Yi", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Earle Chambers", - "author_inst": "Montefiore Health System" - }, - { - "author_name": "Guoqiang Li", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Yuming Guo", - "author_inst": "Monash University" - }, - { - "author_name": "Libin Rong", - "author_inst": "University of Florida" - }, - { - "author_name": "Yanni Xiao", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Guihua Zhuang", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Alexis Zebrowski", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Brendan G. Carr", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Yan Li", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Lei Zhang", - "author_inst": "Xi'an Jiaotong University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.25.20218990", "rel_title": "Cathepsin L plays a key role in SARS-CoV-2 infection in humans and humanized mice and is a promising target for new drug development", @@ -1116366,6 +1117580,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.26.20219626", + "rel_title": "Hyper-Exponential Growth of COVID-19 during Resurgence of the Disease in Russia", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219626", + "rel_abs": "In Russia, COVID-19 has currently been growing hyper-exponentially. This type of a spread pattern was not seen during the first wave of the pandemic the world over. Indeed when the disease had first appeared, in the accelerating stage the spread pattern was observed to have followed a highly nonlinear pattern that could be said to be approximately exponential or sub-exponential. As to why in the resurgence the growth has become hyper-exponential is another matter. But this has been happening in Europe and how long this would continue cannot be predicted. It may so happen that in the countries in which retardation has already been taking place, there may be resurgence of the disease. It was observed that in the World as a whole, retardation was on the threshold during the second half of September. But if the resurgence happens to follow the hyper-exponential growth pattern in different countries, there may be resurgence in the World as a whole.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Hemanta Kumar Baruah", + "author_inst": "The Assam Royal Global University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.22.20184630", "rel_title": "COVID-19 infections following outdoor mass gatherings in low incidence areas: retrospective cohort study", @@ -1118082,85 +1119315,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.26.20219907", - "rel_title": "SARS-CoV-2 seroprevalence and detection fraction in Utah urban populations from a probability-based sample", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20219907", - "rel_abs": "This projects aim was to generate an unbiased estimate of the incidence of SARS-CoV-2 infection in four urban counties in Utah. A multi-stage sampling design was employed to randomly select community-representative participants 12 years and over. Between May 4 and June 30, 2020, surveys were completed and sera drawn from 8,108 individuals belonging to 5,125 households. A qualitative chemiluminescent microparticle immunoassay was used to detect the presence of IgG antibody to SARS-CoV-2. The overall prevalence of IgG antibody to SARS-CoV-2 was estimated at 0.8%. The estimated seroprevalence-to-case count ratio was 2.4, corresponding to a detection fraction of 42%. Only 0.2% of individuals who had a nasopharyngeal swab collected were reverse transcription polymerase chain reaction (RT-PCR) positive. The prevalence of antibodies to SARS-CoV-2 in Utah urban areas between May and June was low and the prevalence of positive RT-PCR even lower. The detection fraction for COVID-19 in Utah was comparatively high.\n\nArticle SummaryProbability-based sampling provides an effective method for robust estimates of community-based SARS-CoV-2 seroprevalence and detection fraction among urban populations in Utah.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Matthew Samore", - "author_inst": "University of Utah" - }, - { - "author_name": "Adam Looney", - "author_inst": "University of Utah" - }, - { - "author_name": "Brian Orleans", - "author_inst": "University of Utah" - }, - { - "author_name": "Tom Greene", - "author_inst": "University of Utah" - }, - { - "author_name": "Nathan Seegert", - "author_inst": "University of Utah" - }, - { - "author_name": "Julio C Delgado", - "author_inst": "University of Utah" - }, - { - "author_name": "Angela Presson", - "author_inst": "University of Utah" - }, - { - "author_name": "Chong Zhang", - "author_inst": "University of Utah" - }, - { - "author_name": "Jian Ying", - "author_inst": "University of Utah" - }, - { - "author_name": "Yue Zhang", - "author_inst": "University of Utah" - }, - { - "author_name": "Jincheng Shen", - "author_inst": "University of Utah" - }, - { - "author_name": "Patricia Slev", - "author_inst": "University of Utah" - }, - { - "author_name": "Maclean Gaulin", - "author_inst": "University of Utah" - }, - { - "author_name": "Mu-Jeung Yang", - "author_inst": "University of Utah" - }, - { - "author_name": "Andrew T. Pavia", - "author_inst": "University of Utah" - }, - { - "author_name": "Stephen C Alder", - "author_inst": "University of Utah" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.26.20219709", "rel_title": "Social inequalities in human mobility during the Spanish lockdown and post-lockdown in the Covid-19 pandemic of 2020", @@ -1118544,6 +1119698,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.27.357954", + "rel_title": "Tuning Intrinsic Disorder Predictors for Virus Proteins", + "rel_date": "2020-10-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.27.357954", + "rel_abs": "Many virus-encoded proteins have intrinsically disordered regions that lack a stable folded threedimensional structure. These disordered proteins often play important functional roles in virus replication, such as down-regulating host defense mechanisms. With the widespread availability of next-generation sequencing, the number of new virus genomes with predicted open reading frames is rapidly outpacing our capacity for directly characterizing protein structures through crystallography. Hence, computational methods for structural prediction play an important role. A large number of predictors focus on the problem of classifying residues into ordered and disordered regions, and these methods tend to be validated on a diverse training set of proteins from eukaryotes, prokaryotes and viruses. In this study, we investigate whether some predictors outperform others in the context of virus proteins. We evaluate the prediction accuracy of 21 methods, many of which are only available as web applications, on a curated set of 126 proteins encoded by viruses. Furthermore, we apply a random forest classifier to these predictor outputs. Based on cross-validation experiments, this ensemble approach confers a substantial improvement in accuracy, e.g., a mean 36% gain in Matthews correlation coefficient. Lastly, we apply the random forest predictor to SARS-CoV-2 ORF6, an accessory gene that encodes a short (61 AA) and moderately disordered protein that inhibits the host innate immune response.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gal Almog", + "author_inst": "Department of Pathology & Laboratory Medicine, Western University, London, Canada" + }, + { + "author_name": "Abayomi Samuel Olabode", + "author_inst": "Department of Pathology & Laboratory Medicine, Western University, London, Canada" + }, + { + "author_name": "Art FY Poon", + "author_inst": "Department of Pathology & Laboratory Medicine, Western University, London, Canada" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.27.357731", "rel_title": "SARS-CoV-2 viroporin triggers the NLRP3 inflammatory pathway", @@ -1119700,57 +1120881,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.10.26.355677", - "rel_title": "The genomic epidemiology of SARS-CoV-2 in Palestine", - "rel_date": "2020-10-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.26.355677", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the novel coronavirus responsible for the COVID-19 pandemic, continues to cause significant public health burden and disruption globally. Genomic epidemiology approaches point to most countries in the world having experienced many independent introductions of SARS-CoV-2 during the early stages of the pandemic. However, this situation may change with local lockdown policies and restrictions on travel leading to the emergence of more geographically structured viral populations and lineages transmitting locally. Here, we report the first SARS-CoV-2 genomes from Palestine sampled from early March, when the first cases were observed, through to August of 2020. SARS-CoV-2 genomes from Palestine fall across the diversity of the global phylogeny, consistent with at least nine independent introductions into the region. We identify one locally predominant lineage in circulation represented by 50 Palestinian SARS-CoV-2, grouping with isolated viral samples from patients in Israel and the UK. We estimate the age of introduction of this lineage to 05/02/2020 (16/01/2020 - 19/02/2020), suggesting SARS-CoV-2 was already in circulation in Palestine predating its first detection in Bethlehem in early March. Our work highlights the value of ongoing genomic surveillance and monitoring to reconstruct the epidemiology of COVID-19 at both local and global scales.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Nouar Qutob", - "author_inst": "Department of Health Sciences, Arab American University, Palestine" - }, - { - "author_name": "Zaidoun Salah", - "author_inst": "Department of Health Sciences, Arab American University, Palestine" - }, - { - "author_name": "Damien Richard", - "author_inst": "UCL Genetics Institue" - }, - { - "author_name": "Hisham Darwish", - "author_inst": "Department of Health Sciences, Arab American University, Palestine" - }, - { - "author_name": "Husam Sallam", - "author_inst": "Department of Health Sciences, Arab American University, Palestine" - }, - { - "author_name": "Issa Shtayeh", - "author_inst": "Palestinian Ministry of Health, Palestine" - }, - { - "author_name": "Osama Najjar", - "author_inst": "Palestinian Ministry of Health, Palestine" - }, - { - "author_name": "Francois Balloux", - "author_inst": "UCL Genetics Institute" - }, - { - "author_name": "Lucy van Dorp", - "author_inst": "UCL Genetics Institute" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.10.26.354787", "rel_title": "Tracking cytosine depletion in SARS-CoV-2", @@ -1120138,6 +1121268,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.25.354571", + "rel_title": "Comparison of the in vitro-efficacy of different mouthwash solutions targeting SARS-CoV-2 based on the European Standard EN 14476", + "rel_date": "2020-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.25.354571", + "rel_abs": "The SARS-Cov-2 pandemic is triggering a global health emergency alert, and recent research is indicating the relevance of aerosols in the spread of SARS-CoV-2. Thus, in this study antiseptic mouthwashes based on the actives chlorhexidine (CHX) and octenidine (OCT) were investigated regarding their efficacy against SARS-CoV-2 using EN 14476. Based on the requirement of EN 14476 (i.e. reduction of viral titer by [≥] 4 log 10), the OCT-based formulation was effective within only 15 sec against SARS-CoV-2, and thus constitutes an interesting candidate for future clinical studies to prove its effectiveness in a potential prevention of SARS-CoV-2 transmission by aerosols.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Katrin Steinhauer", + "author_inst": "Department Research & Scientific Services, Schuelke & Mayr GmbH, Norderstedt, Germany; Faculty of Mechanical Engineering, Kiel University of Applied Sciences, K" + }, + { + "author_name": "Toni Luise Meister", + "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany" + }, + { + "author_name": "Daniel Todt", + "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany; European Virus Bioinformatics Center (EVBC), 07743 Jena, Germany" + }, + { + "author_name": "Adalbert Krawczyk", + "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany; European Virus Bioinformatics Center (EVBC), 07743 Jena, Germany" + }, + { + "author_name": "Lars Passvogel", + "author_inst": "Department Research & Scientific Services, Schuelke & Mayr GmbH, Norderstedt, Germany" + }, + { + "author_name": "Britta Becker", + "author_inst": "Dr. Brill + Partner GmbH Institut for Hygiene and Microbiology, Hamburg, Germany" + }, + { + "author_name": "Dajana Paulmann", + "author_inst": "Dr. Brill + Partner GmbH Institut for Hygiene and Microbiology, Hamburg, Germany" + }, + { + "author_name": "Birte Bischoff", + "author_inst": "Dr. Brill + Partner GmbH Institut for Hygiene and Microbiology, Hamburg, Germany" + }, + { + "author_name": "Stephanie Pfaender", + "author_inst": "Department of Molecular and Medical Virology, Ruhr University Bochum, 44801 Bochum, Germany" + }, + { + "author_name": "Florian Brill", + "author_inst": "Dr. Brill + Partner GmbH Institut for Hygiene and Microbiology, Hamburg, Germany" + }, + { + "author_name": "Eike Steinmann", + "author_inst": "Ruhr University Bochum" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.23.353219", "rel_title": "The papain-like protease of coronaviruses cleaves ULK1 to disrupt host autophagy", @@ -1121238,53 +1122427,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.20.20216457", - "rel_title": "Early intervention is the key to success in COVID-19 control", - "rel_date": "2020-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20216457", - "rel_abs": "New Zealand responded to the COVID-19 pandemic with a combination of border restrictions and an Alert Level system that included strict stay-at-home orders. These interventions were successful in containing the outbreak and ultimately eliminating community transmission of COVID-19. The timing of interventions is crucial to their success. Delaying interventions may both reduce their effectiveness and mean that they need to be maintained for a longer period. Here, we use a stochastic branching process model of COVID-19 transmission and control to simulate the epidemic trajectory in New Zealand and the effect of its interventions during its COVID-19 outbreak in March-April 2020. We use the model to calculate key measures, including the peak load on the contact tracing system, the total number of reported COVID-19 cases and deaths, and the probability of elimination within a specified time frame. We investigate the sensitivity of these measures to variations in the timing of interventions and show that changing the timing of Alert Level 4 (the strictest level of restrictions) has a far greater impact than the timing of border measures. Delaying Alert Level 4 restrictions results in considerably worse outcomes and implementing border measures alone, without Alert Level 4 restrictions, is insufficient to control the outbreak. We conclude that the rapid response in introducing stay-at-home orders was crucial in reducing the number of cases and deaths and increasing the probability of elimination.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Rachelle N Binny", - "author_inst": "Manaaki Whenua - Landcare Research" - }, - { - "author_name": "Michael G Baker", - "author_inst": "University of Otago" - }, - { - "author_name": "Shaun C Hendy", - "author_inst": "University of Auckland" - }, - { - "author_name": "Alex James", - "author_inst": "University of Canterbury" - }, - { - "author_name": "Audrey Lustig", - "author_inst": "Manaaki Whenua - Landcare Research" - }, - { - "author_name": "Michael J Plank", - "author_inst": "University of Canterbury" - }, - { - "author_name": "Kannan M Ridings", - "author_inst": "University of Auckland" - }, - { - "author_name": "Nicholas Steyn", - "author_inst": "University of Auckland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.21.20214338", "rel_title": "Supervised self-collected SARS-CoV-2 testing in indoor summer camps to inform school reopening", @@ -1121480,6 +1122622,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.10.20.20215608", + "rel_title": "Evidence for secondary thrombotic microangiopathy in COVID-19", + "rel_date": "2020-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20215608", + "rel_abs": "The causes of coagulopathy associated with COVID-19 disease are poorly understood. We aimed to investigate the relationship between markers of endothelial activation, intravascular hemolysis, coagulation, and organ damage in COVID-19 patients and study their association with disease severity and mortality. We conducted a retrospective study of 181 hospitalized COVID-19 patients randomly selected with equal distribution of survivors and non-survivors. Patients who died had significantly lower ADAMTS13 activity, significantly higher LDH, schistocytes and von Willebrand Factor levels compared to patients discharged alive. Only 30% of patients with an initial ADAMTS13 activity <43% survived vs. 60% with ADAMTS13 [≥]43% who survived. In conclusion, COVID-19 may manifest as a TMA-like illness in a subset of hospitalized patients. Presence of schistocytes on admission may warrant a work-up for TMA. These findings indicate the need for future investigation to study the relationship between endothelial and coagulation activation and the efficacy of TMA treatments in COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Joseph Sweeney", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Mohammad Barouqa", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Gregory J J Krause", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Jesus Gonzalez Lugo", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Shafia Rahman", + "author_inst": "Montefiore Medical Center" + }, + { + "author_name": "Morayma Reyes Gil", + "author_inst": "Montefiore Medical Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "hematology" + }, { "rel_doi": "10.1101/2020.10.21.20216192", "rel_title": "Broadly-targeted autoreactivity is common in severe SARS-CoV-2 Infection", @@ -1122888,49 +1124069,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.23.351916", - "rel_title": "Direct visualization of native infectious SARS-CoV-2 ant its inactivation forms using high resolution Atomic Force Microscopy", - "rel_date": "2020-10-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.23.351916", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for COVID19, a new emerging pandemic affecting humans. Here, single viruses were analyze by atomic force microscopy (AFM) operating directly in a level 3 biosafety (BSL3) facility, which appeared as a fast and powerful method to assess infectious virus morphology in its native conformation, or upon inactivation treatments, at the nanoscale level and in 3D. High resolution AFM reveals structurally intact infectious and inactivated SARS-CoV-2 upon low concentration of formaldehyde treatment. This protocol allows the preparation of intact inactivated SARS-CoV-2 particles for safe use of samples out of level 3 laboratory, as revealed by combining AFM and plaque assays, to accelerate researches against the COVID-19 pandemic. Overall, we illustrate how adapted BSL3-atomic force microscopy is a remarkable toolbox for rapid and direct virus identification and characterization.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Sebastien Lyonnais", - "author_inst": "CNRS" - }, - { - "author_name": "Mathilde Henaut", - "author_inst": "CNRS" - }, - { - "author_name": "Aymeric Neyret", - "author_inst": "University of Montpellier" - }, - { - "author_name": "Peggy Merida", - "author_inst": "CNRS" - }, - { - "author_name": "Nathalie Gros", - "author_inst": "CNRS" - }, - { - "author_name": "Christine Chable-Bessia", - "author_inst": "CNRS" - }, - { - "author_name": "Delphine Muriaux", - "author_inst": "CNRS" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.23.350348", "rel_title": "Transferrin receptor is another receptor for SARS-CoV-2 entry", @@ -1123206,6 +1124344,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.21.20216960", + "rel_title": "Emergency Response for Evaluating SARS-CoV-2 Immune Status, Seroprevalence and Convalescent Plasma in Argentina", + "rel_date": "2020-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216960", + "rel_abs": "We report the emergency development and application of a robust serologic test to evaluate acute and convalescent antibody responses to SARS-CoV-2 in Argentina. The assays, COVIDAR IgG and IgM, which were produced and provided for free to health authorities, private and public health institutions and nursing homes, use a combination of a trimer stabilized spike protein and the receptor binding domain (RBD) in a single enzyme-linked immunosorbent assay (ELISA) plate. Over half million tests have already been distributed to detect and quantify antibodies for multiple purposes, including assessment of immune responses in hospitalized patients and large seroprevalence studies in neighborhoods, slums and health care workers, which resulted in a powerful tool for asymptomatic detection and policy making in the country. Analysis of antibody levels and longitudinal studies of symptomatic and asymptomatic SARS-CoV-2 infections in over one thousand patient samples provided insightful information about IgM and IgG seroconversion time and kinetics, and IgM waning profiles. At least 35% of patients showed seroconversion within 7 days, and 95% within 45 days of symptoms onset, with simultaneous or close sequential IgM and IgG detection. Longitudinal studies of asymptomatic cases showed a wide range of antibody responses with median levels below those observed in symptomatic patients. Regarding convalescent plasma applications, a protocol was standardized for the assessment of end point IgG antibody titers with COVIDAR with more than 500 plasma donors. The protocol showed a positive correlation with neutralizing antibody titers, and was used to assess antibody titers for clinical trials and therapies across the country. Here, we demonstrate the importance of providing a robust and specific serologic assay for generating new information about antibody kinetics in infected individuals and mitigation policies to cope with pandemic needs.\n\nAUTHOR SUMMARYThe development of robust and specific serologic assays to detect antibodies to SARS-CoV-2 is essential to understand the pandemic evolution and to stablish mitigation strategies. Here, we report the emergency development, production and application of a versatile ELISA test for detecting antibodies against the whole spike protein and its receptor binding domain. Over half million tests have been freely distributed in public and private health institutions of Argentina for evaluating immune responses, convalescent plasma programs and for large seroprevalence studies in neighborhoods and health care workers. We are still learning how and when to use serologic testing in different epidemiological settings. This program allowed us to produce large amount of high quality data on antibody levels in symptomatic and asymptomatic SARS-CoV-2 infections and generate relevant information about IgM and IgG seroconversion time and kinetics. We also present standardized protocols for antibody quantification as guidance for convalescent donor plasma selection in hospitals throughout the country for compassionate use and clinical trials. Here, we provide a framework for generating widely available tools, protocols and information of antibody responses for pandemic management.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Diego Ojeda", + "author_inst": "Fundacion Instituto Leloir-CONICET" + }, + { + "author_name": "Maria Mora Gonzalez Lopez Ledesma", + "author_inst": "Fundacion Instituto Leloir CONICET" + }, + { + "author_name": "Horacio Palleres", + "author_inst": "Fundacion Instituto Leloir-CONICET" + }, + { + "author_name": "Guadalupe Costa Navarro", + "author_inst": "Fundacion Instituto Leloir-CONICET" + }, + { + "author_name": "Lautaro Sanchez", + "author_inst": "Fundacion Instituto Leloir CONICET" + }, + { + "author_name": "Beatriz Perazzi", + "author_inst": "Facultad de Farmacia y Bioquimica UBA" + }, + { + "author_name": "Sergio Villordo", + "author_inst": "Fundacion Instituto Leloir" + }, + { + "author_name": "Diego Alvarez", + "author_inst": "Instituto de Investigaciones Biotecnologicas, Universidad Nacional de San Martin" + }, + { + "author_name": "- BioBanco Working Group", + "author_inst": "" + }, + { + "author_name": "Marcela Echavarria", + "author_inst": "Centro de Educacion Medica e Investigaciones Clinicas" + }, + { + "author_name": "Kasopefoluwa Y. Oguntuyo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Christian Stevens", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Benhur Lee", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jorge Carradori", + "author_inst": "Laboratorio Lemos" + }, + { + "author_name": "Julio Caramelo", + "author_inst": "Fundacion Instituto Leloir CONICET" + }, + { + "author_name": "Marcelo Yanovsky", + "author_inst": "Fundacion Instituto Leloir" + }, + { + "author_name": "Andrea Gamarnik", + "author_inst": "FUNDACION INSTITUTO LELOIR" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.21.20216945", "rel_title": "The effect of COVID-19 on critical care research: A prospective longitudinal multinational survey", @@ -1124418,153 +1125639,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.19.20214494", - "rel_title": "Attributes and predictors of Long-COVID: analysis of COVID cases and their symptoms collected by the Covid Symptoms Study App", - "rel_date": "2020-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20214494", - "rel_abs": "Reports of \"Long-COVID\", are rising but little is known about prevalence, risk factors, or whether it is possible to predict a protracted course early in the disease. We analysed data from 4182 incident cases of COVID-19 who logged their symptoms prospectively in the COVID Symptom Study app. 558 (13.3%) had symptoms lasting >=28 days, 189 (4.5%) for >=8 weeks and 95 (2.3%) for >=12 weeks. Long-COVID was characterised by symptoms of fatigue, headache, dyspnoea and anosmia and was more likely with increasing age, BMI and female sex. Experiencing more than five symptoms during the first week of illness was associated with Long-COVID, OR=3.53 [2.76;4.50]. A simple model to distinguish between short and long-COVID at 7 days, which gained a ROC-AUC of 76%, was replicated in an independent sample of 2472 antibody positive individuals. This model could be used to identify individuals for clinical trials to reduce long-term symptoms and target education and rehabilitation services.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Carole H Sudre", - "author_inst": "KCL" - }, - { - "author_name": "Benjamin Murray", - "author_inst": "King's College London" - }, - { - "author_name": "Thomas Varsavsky", - "author_inst": "King's College London" - }, - { - "author_name": "Mark S Graham", - "author_inst": "King's College London" - }, - { - "author_name": "Rose S Penfold", - "author_inst": "King's College London" - }, - { - "author_name": "Ruth C.E Bowyer", - "author_inst": "King's College London" - }, - { - "author_name": "Joan Capdevila Pujol", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Kerstin Klaser", - "author_inst": "King's College London" - }, - { - "author_name": "Michela Antonelli", - "author_inst": "King's College London" - }, - { - "author_name": "Liane S Canas", - "author_inst": "King's College London" - }, - { - "author_name": "Erika Molteni", - "author_inst": "King's College London" - }, - { - "author_name": "Marc Modat", - "author_inst": "King's College London" - }, - { - "author_name": "M. Jorge Cardoso", - "author_inst": "King's College London" - }, - { - "author_name": "Anna May", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Sajaysurya Ganesh", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Richard Davies", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Long H Nguyen", - "author_inst": "Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "David Alden Drew", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Christina M Astley", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Amit D. Joshi", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Jordi Merino", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Neli Tsereteli", - "author_inst": "Lund University" - }, - { - "author_name": "Tove Fall", - "author_inst": "Uppsala University" - }, - { - "author_name": "Maria F Gomez", - "author_inst": "Lund University" - }, - { - "author_name": "Emma Duncan", - "author_inst": "King's College London" - }, - { - "author_name": "Christina Menni", - "author_inst": "King's College London" - }, - { - "author_name": "Frances MK Williams", - "author_inst": "King's College London" - }, - { - "author_name": "Paul W Franks", - "author_inst": "Lund University" - }, - { - "author_name": "Andrew T Chan", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Jonathan Wolf", - "author_inst": "Zoe Global Limited" - }, - { - "author_name": "Sebastien Ourselin", - "author_inst": "King's College London" - }, - { - "author_name": "Timothy Spector", - "author_inst": "King's College London" - }, - { - "author_name": "Claire J Steves", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.19.20215384", "rel_title": "Basrah experience among 6404 patients with COVID-19", @@ -1124820,6 +1125894,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.19.20213421", + "rel_title": "PREVALENCE OF ANTIBODIES AGAINST SARS-CoV-2 IN PROFESSIONALS OF A PUBLIC HEALTH LABORATORY AT SAO PAULO, SP, BRAZIL", + "rel_date": "2020-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20213421", + "rel_abs": "BackgroundCovid-19 Serology may document exposure and perhaps protection to the virus and serological test may help understand epidemic dynamics. We tested health workers form a public laboratory to evaluate previous exposure to the virus and estimate the prevalence of antibodies against-SARS-CoV-2 in Adolfo Lutz Institute, State of Sao Paulo, Brazil.\n\nMethodsThis study was an open, prospective evaluation among professionals of Adolfo Lutz Institute some administrative personnel from the Secretary of Health that shares common areas with the institute. We used a lateral flow immunoassay (rapid test) to detect IgG and IgM for SARS-CoV-2; positive samples were further evaluated using Roche Electrochemiluminescence assay. SARS-CoV-2 RNA by real time reverse transcriptase polymerase chain reaction (RT-PCR) was also offered to participants.\n\nResultsA total of 406 HPs participated. Thirty five (8.6%) tested positive on rapid test and 32 these rapid test seropositive cases were confirmed by ECLIA. 43 HPs had SARS-CoV-2 RNA detected at a median of 33 days, and the three cases not reactive at Roche ECLIA had a previous positive RNA. Outsourced professionals (34% seropositive), males (15%) workers referring COVID-19 patients at home (22%) and those living farther form the institute tended to have higher prevalence of seropositivity, but in multivariable logistic analysis only outsourced workers and those with COVID patients at home remained independently associated to seropositivity. We observed no relation of seropositivity to COVID samples handling. Presence of at least one symptom was common but some clinical manifestations as anosmia/dysgeusia. Fatigue, cough and fever were associated to seropositivity.\n\nConclusionsWe documented a relatively high (8.6%) of anti-SARS-CoV-2 serological reactivity in this population, higher among outsourced workers and those residing with COVID-19 patients. COVID related work did not increased seropositivity. Some symptoms show strong association to COVID-19 serology and may be used in scoring tools for screening or diagnosis in resort limited settings.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Valeria Oliveira Silva", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Elaine Lopes de Oliveira", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Marcia Jorge Castejon", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Rosemeire Yamashiro", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Cintia Mayumi Ahagon", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Giselle Ibette Lopez-Lopes", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Edilene Peres Real da Silveira", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Marisa Ailin Hong", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Maria do Carmo Timenetsky", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Carmem aparecida de Freitas Oliveira", + "author_inst": "Instituto Adolfo Lutz" + }, + { + "author_name": "Luis Fernando de Macedo Brigido", + "author_inst": "Instituto Adolfo Lutz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.20.20212522", "rel_title": "Analytical solution of equivalent SEIR and agent-based model of COVID-19; showing the bounds of contact tracing", @@ -1126207,29 +1127340,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.19.20215046", - "rel_title": "Modelling the dispersion of SARS-CoV-2 on a dynamic network graph", - "rel_date": "2020-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20215046", - "rel_abs": "BackgroundWhen modelling the dispersion of an epidemic using R0, one only considers the average number of individuals each infected individual will infect. However, we know from extensive studies of social networks that there is significant variation in the number of connections and thus social contacts each individual has. Individuals with more social contacts are more likely to attract and spread infection. These individuals are likely the drivers of the epidemic, so-called superspreaders. When many superspreaders are immune, it becomes more difficult for the disease to spread, as the connectedness of the social network dramatically decreases. If one assumes all individuals being equally connected and thus as likely to spread disease as in a SIR model, this is not true.\n\nMethodsTo account for the impact of social network structure on epidemic development, we model the dispersion of SARS-CoV-2 on a dynamic preferential attachment graph which changes appearance proportional to observed mobility changes. We sample a serial interval distribution that determines the probability of dispersion for all infected nodes each day. We model the dispersion in different age groups using age-specific infection fatality rates. We vary the infection probabilities in different age groups and analyse the outcome.\n\nResultsThe impact of movement on network dynamics plays a crucial role in the spread of infections. We find that higher movement results in higher spread due to an increased probability of new connections being made within a social network. We show that saturation in the dispersion can be reached much earlier on a preferential attachment graph compared to spread on a random graph, which is more similar to estimations using R0.\n\nConclusionsWe provide a novel method for modelling epidemics by using a dynamic network structure related to observed mobility changes. The social network structure plays a crucial role in epidemic development, something that is often overlooked.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Patrick Bryant", - "author_inst": "Stockholm University/Science for Life Laboratory" - }, - { - "author_name": "Arne Elofsson", - "author_inst": "Stockholm University/Science for Life Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.20.20215731", "rel_title": "Effect of park use and landscape structure on COVID-19 transmission rates", @@ -1126405,6 +1127515,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.14.20212662", + "rel_title": "Antibody Immunological Imprinting on COVID-19 Patients", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212662", + "rel_abs": "While the current pandemic remains a thread to human health, the polyclonal nature of the antibody response against SARS-CoV-2 is not fully understood. Other than SARS-CoV-2, humans are susceptible to six different coronaviruses, and previous exposure to antigenically related and divergent seasonal coronaviruses is frequent. We longitudinally profiled the early humoral immune response against SARS-CoV-2 on hospitalized COVID-19 patients, and quantify levels of pre-existing immunity to OC43, HKU1 and 223E seasonal coronaviruses. A strong back-boosting effect to conserved, but not variable regions of OC43 and HKU1 betacoronaviruses spike protein was observed. All patients developed antibodies against SARS-CoV-2 spike and nucleoprotein, with peak induction at day 7 post hospitalization. However a negative correlation was found between antibody memory boost to human coronaviruses and induction of IgG and IgM against SARS-CoV-2 spike. Our findings provide evidence of immunological imprinting that determine the antibody profile to COVID-19 patients in an original antigenic sin fashion.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Teresa Aydillo", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York;" + }, + { + "author_name": "Alexander Rombauts", + "author_inst": "Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, LHospitalet de Llo" + }, + { + "author_name": "Daniel Stadlbauer", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Sadaf Aslam", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Gabriela Abelenda-Alonso", + "author_inst": "Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, LHospitalet de Llo" + }, + { + "author_name": "Alba Escalera", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Fatima Amanat", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Kaijun Jiang", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + }, + { + "author_name": "Jordi Carratala", + "author_inst": "Department of Infectious Diseases, Bellvitge University Hospital, Bellvitge Biomedical Research Institute (IDIBELL), University of Barcelona, LHospitalet de Llo" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.15.20213223", "rel_title": "Prediction of Covid-19 Infections Through December 2020 for 10 US States Incorporating Outdoor Temperature and School Re-Opening Effects-September Update", @@ -1127805,89 +1128974,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.10.16.20213405", - "rel_title": "Lessons from applied large-scale pooling of 133,816 SARS-CoV-2 RT-PCR tests", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.16.20213405", - "rel_abs": "Pooling multiple swab samples prior to RNA extraction and RT-PCR analysis was proposed as a strategy to reduce costs and increase throughput of SARS-CoV-2 tests. However, reports on practical large-scale group testing for SARS-CoV-2 have been scant. Key open questions concern reduced sensitivity due to sample dilution; the rate of false positives; the actual efficiency (number of tests saved by pooling) and the impact of infection rate in the population on assay performance. Here we report analysis of 133,816 samples collected at April-September 2020, tested by pooling for the presence of SARS-CoV-2. We spared 76% of RNA extraction and RT-PCR tests, despite the reality of frequently changing prevalence rate (0.5%-6%). Surprisingly, we observed pooling efficiency and sensitivity that exceed theoretical predictions, which resulted from non-random distribution of positive samples in pools. Overall, the findings strongly support the use of pooling for efficient large high throughput SARS-CoV-2 testing.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Netta Barak", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Roni Ben-Ami", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Tal Sido", - "author_inst": "Hadassah Hebrew University Medical Center" - }, - { - "author_name": "Amir Perri", - "author_inst": "Hadassah Hebrew University Medical Center" - }, - { - "author_name": "Aviad Shtoyer", - "author_inst": "Hadassah Hebrew University Medical Center" - }, - { - "author_name": "Mila Rivkin", - "author_inst": "Hadassah Hebrew University Medical Center" - }, - { - "author_name": "Tamar Licht", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Ayelet Peretz", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Judith Magenheim", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Irit Fogel", - "author_inst": "Hadassah Hebrew University Medical Center" - }, - { - "author_name": "Ayala Livneh", - "author_inst": "Hadassah Hebrew University Medical Center" - }, - { - "author_name": "Yutti Daitch", - "author_inst": "Hadassah Hebrew University Medical Center" - }, - { - "author_name": "Esther Oiknine-Djian", - "author_inst": "Hadassah Hebrew University Medical Center" - }, - { - "author_name": "Gil Benedek", - "author_inst": "Hadassah Hebrew University Medical Center" - }, - { - "author_name": "Yuval Dor", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Dana G Wolf", - "author_inst": "Hadassah Hebrew University Medical Center" - }, - { - "author_name": "Moran Yassour", - "author_inst": "The Hebrew University of Jerusalem" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.17.20214445", "rel_title": "Temporal course of SARS-CoV-2 antibody positivity in patients with COVID-19 following the first clinical presentation", @@ -1128155,6 +1129241,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.17.20214312", + "rel_title": "Echo chambers as early warning signals of widespread vaccine refusal in social-epidemiological networks", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.17.20214312", + "rel_abs": "Sudden shifts in population health and vaccination rates occur as the dynamics of some epidemiological models go through a critical point; literature shows that this is sometimes foreshadowed by early warning signals (EWS). We investigate different structural measures of a network as candidate EWS of infectious disease outbreaks and changes in popular vaccine sentiment. We construct a multiplex disease model coupling infectious disease spread and social contact dynamics. We find that the number and mean size of echo chambers predict transitions in the infection dynamics, as do opinion-based communities. Graph modularity also gives early warnings, though the clustering coefficient shows no significant pre-outbreak changes. Change point tests applied to the EWS show decreasing efficacy as social norms strengthen. Therefore, many measures of social network connectivity can predict approaching critical changes in vaccine uptake and aggregate health, thereby providing valuable tools for improving public health.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Brendon C Phillips", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Chris Bauch", + "author_inst": "University of Waterloo" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.16.20214049", "rel_title": "Quantifying Asymptomatic Infection and Transmission of COVID-19 in New York City using Observed Cases, Serology and Testing Capacity", @@ -1129359,93 +1130468,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.10.20.346916", - "rel_title": "Isolation of cross-reactive monoclonal antibodies against divergent human coronaviruses that delineate a conserved and vulnerable site on the spike protein", - "rel_date": "2020-10-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.20.346916", - "rel_abs": "The coronavirus spike glycoprotein, located on the virion surface, is the key mediator of cell entry. As such, it is an attractive target for the development of protective antibodies and vaccines. Here we describe two human monoclonal antibodies, 1.6C7 and 28D9, that display a remarkable cross-reactivity against distinct species from three Betacoronavirus subgenera, capable of binding the spike proteins of SARS-CoV and SARS-CoV-2, MERS-CoV and the endemic human coronavirus HCoV-OC43. Both antibodies, derived from immunized transgenic mice carrying a human immunoglobulin repertoire, blocked MERS-CoV infection in cells, whereas 28D9 also showed weak cross-neutralizing potential against HCoV-OC43, SARS-CoV and SARS-CoV-2 in a neutralization-sensitive virus pseudotyping system, but not against authentic virus. Both cross-reactive monoclonal antibodies were found to target the stem helix in the spike protein S2 fusion subunit which, in the prefusion conformation of trimeric spike, forms a surface exposed membrane-proximal helical bundle, that is antibody-accessible. We demonstrate that administration of these antibodies in mice protects from a lethal MERS-CoV challenge in both prophylactic and/or therapeutic models. Collectively, these antibodies delineate a conserved, immunogenic and vulnerabe site on the spike protein which spurs the development of broad-range diagnostic, preventive and therapeutic measures against coronaviruses.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Chunyan Wang", - "author_inst": "Utrecht University" - }, - { - "author_name": "Rien van Haperen", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Javier Gutierrez-Alvarez", - "author_inst": "National Center for Biotechnology-Spanish National Research Council" - }, - { - "author_name": "Wentao Li", - "author_inst": "Utrecht University" - }, - { - "author_name": "Nisreen Okba", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Irina Albulescu", - "author_inst": "Utrecht University" - }, - { - "author_name": "Ivy Widjaja", - "author_inst": "Utrecht University" - }, - { - "author_name": "Brenda van Dieren", - "author_inst": "Utrecht University" - }, - { - "author_name": "Raul Fernandez-Delgado", - "author_inst": "National Center for Biotechnology-Spanish National Research Council" - }, - { - "author_name": "Isabel Sola", - "author_inst": "National Center for Biotechnology-Spanish National Research Council" - }, - { - "author_name": "Daniel Hurdiss", - "author_inst": "Utrecht University" - }, - { - "author_name": "Olalekan Daramola", - "author_inst": "AstraZeneca" - }, - { - "author_name": "Frank Grosveld", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Frank van Kuppeveld", - "author_inst": "Utrecht University" - }, - { - "author_name": "Bart Haagmans", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Luis Enjuanes", - "author_inst": "National Center for Biotechnology-Spanish National Research Council" - }, - { - "author_name": "Dubravka Drabek", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Berend-Jan Bosch", - "author_inst": "Utrecht University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.20.346783", "rel_title": "High-throughput detection of antibodies targeting the SARS-CoV-2 Spike in longitudinal convalescent plasma samples", @@ -1129705,6 +1130727,113 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.15.20208041", + "rel_title": "Analysis of respiratory and systemic immune responses in COVID-19 reveals mechanisms of disease pathogenesis", + "rel_date": "2020-10-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20208041", + "rel_abs": "Immune responses to respiratory viruses like SARS-CoV-2 originate and function in the lung, yet assessments of human immunity are often limited to blood. Here, we conducted longitudinal, high-dimensional profiling of paired airway and blood samples from patients with severe COVID-19, revealing immune processes in the respiratory tract linked to disease pathogenesis. Survival from severe disease was associated with increased CD4+T cells and decreased monocyte/macrophage frequencies in the airway, but not in blood. Airway T cells and macrophages exhibited tissue-resident phenotypes and activation signatures, including high level expression and secretion of monocyte chemoattractants CCL2 and CCL3 by airway macrophages. By contrast, monocytes in blood expressed the CCL2-receptor CCR2 and aberrant CD163+ and immature phenotypes. Extensive accumulation of CD163+monocyte/macrophages within alveolar spaces in COVID-19 lung autopsies suggested recruitment from circulation. Our findings provide evidence that COVID-19 pathogenesis is driven by respiratory immunity, and rationale for site-specific treatment and prevention strategies.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Peter A. Szabo", + "author_inst": "Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Pranay Dogra", + "author_inst": "Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Joshua I. Gray", + "author_inst": "Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Steven B. Wells", + "author_inst": "Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Thomas J. Connors", + "author_inst": "Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Stuart P. Weisberg", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Izabela Krupska", + "author_inst": "Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Rei Matsumoto", + "author_inst": "Department of Surgery, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Maya M.L. Poon", + "author_inst": "Department of Microbiology and Immunology, Columbia University Irving Medical Center, New York, NY 10032 and Medical Scientist Training Program, Columbia Univer" + }, + { + "author_name": "Emma Idzikowski", + "author_inst": "Department of Pediatrics, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Sinead E. Morris", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Pasin Chloe", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Andrew J. Yates", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Amy Ku", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Michael Chait", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Julia M. Davis-Porada", + "author_inst": "Medical Scientist Training Program, Columbia University" + }, + { + "author_name": "Jing Zhou", + "author_inst": "IsoPlexis Corporation, Branford, CT 06405" + }, + { + "author_name": "Matthew Steinle", + "author_inst": "IsoPlexis Corporation, Branford, CT 06405" + }, + { + "author_name": "Sean Mackay", + "author_inst": "IsoPlexis Corporation, Branford, CT 06405" + }, + { + "author_name": "Anjali Saqi", + "author_inst": "Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Matthew R. Baldwin", + "author_inst": "Department of Medicine, Columbia University Irving Medical Center, New York, NY 10032" + }, + { + "author_name": "Peter A. Sims", + "author_inst": "Department of Systems Biology, Columbia University Irving Medical Center, New York, NY 10032 and Department of Biochemistry and Molecular Biophysics, Columbia U" + }, + { + "author_name": "Donna L Farber", + "author_inst": "Columbia University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.17.343863", "rel_title": "Development and pre-clinical characterization of two therapeutic equine formulations towards SARS-CoV-2 proteins for the potential treatment of COVID-19", @@ -1130944,61 +1132073,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.10.17.339051", - "rel_title": "3D reconstruction of SARS-CoV-2 infection in ferrets emphasizes focal infection pattern in the upper respiratory tract", - "rel_date": "2020-10-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.17.339051", - "rel_abs": "The visualization of viral pathogens in infected tissues is an invaluable tool to understand spatial virus distribution, localization, and cell tropism in vivo. Commonly, virus-infected tissues are analyzed using conventional immunohistochemistry in paraffin-embedded thin sections. Here, we demonstrate the utility of volumetric three-dimensional (3D) immunofluorescence imaging using tissue optical clearing and light sheet microscopy to investigate host-pathogen interactions of pandemic SARS-CoV-2 in ferrets at a mesoscopic scale. The superior spatial context of large, intact samples (> 150 mm3) allowed detailed quantification of interrelated parameters like focus-to-focus distance or SARS-CoV-2-infected area, facilitating an in-depth description of SARS-CoV-2 infection foci. Accordingly, we could confirm a preferential infection of the ferret upper respiratory tract by SARS-CoV-2 and emphasize a distinct focal infection pattern in nasal turbinates. Conclusively, we present a proof-of-concept study for investigating critically important respiratory pathogens in their spatial tissue morphology and demonstrate the first specific 3D visualization of SARS-CoV-2 infection.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Luca M. Zaeck", - "author_inst": "Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Isle of Riems, Ge" - }, - { - "author_name": "David Scheibner", - "author_inst": "Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Isle of Riems, Ge" - }, - { - "author_name": "Julia Sehl", - "author_inst": "Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald" - }, - { - "author_name": "Martin M\u00fcller", - "author_inst": "Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Isle of Riems, Ge" - }, - { - "author_name": "Donata Hoffmann", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Isle of Riems, Germany" - }, - { - "author_name": "Martin Beer", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Isle of Riems, Germany" - }, - { - "author_name": "Elsayed M. Abdelwhab", - "author_inst": "Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Isle of Riems, Ge" - }, - { - "author_name": "Thomas C. Mettenleiter", - "author_inst": "Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Isle of Riems, Germany" - }, - { - "author_name": "Angele Breithaupt", - "author_inst": "Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald" - }, - { - "author_name": "Stefan Finke", - "author_inst": "Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald, Isle of Riems, Ge" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.17.344002", "rel_title": "Adult Stem Cell-derived Complete Lung Organoid Models Emulate Lung Disease in COVID-19", @@ -1131266,6 +1132340,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.10.14.20212449", + "rel_title": "TREATMENT PROFILES AND CLINICAL OUTCOMES OF COVID-19 PATIENTS AT PRIVATE HOSPITAL IN JAKARTA", + "rel_date": "2020-10-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20212449", + "rel_abs": "BackgroundSevere Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is a virus that causes COVID-19, which has become a worldwide pandemic. However, until now, there is no vaccine or specific drug to prevent or treat COVID-19.\n\nObjectivesTo find out the effective treatment as an antiviral agent for COVID-19, to determine the correlation between sociodemography with clinical outcomes and duration of treatment, and to determine the relationship between comorbidities with clinical outcomes and duration of treatment for COVID-19 patients.\n\nMethodsA prospective cohort study was conducted in this study. This study included only confirmed COVID-19 patients who were admitted to the hospital during April-May 2020. Convenience sampling was used to select 103 patients, but only 72 patients were suitable for inclusion.\n\nResultsThe survival analysis for COVID-19 patients using the Kaplan Meier method showed that patients receiving Oseltamivir + Hydroxychloroquine had an average survival rate of about 83% after undergoing treatment for about ten days. Gender (p = 0.450) and age (p = 0.226) did not have a significant correlation with the duration of treatment for COVID-19 patients. Gender (p = 0.174) and age (p = 0.065) also did not have a significant correlation with clinical outcome of COVID-19 patients. Comorbidities showed a significant correlation with duration of treatment (p = 0.002) and clinical outcome (p = 0.014) of COVID-19 patients.\n\nConclusionThe most effective antiviral agent in this study based on treatment duration was the combination of Oseltamivir + Hydroxychloroquine. The higher the patients average treatment duration, the lower the average survival rate for COVID-19 patients.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Diana Laila Ramatillah", + "author_inst": "Universitas 17 Agustus 1945 Jakarta" + }, + { + "author_name": "Suri Isnaini", + "author_inst": "Pharmacy Faculty, Universitas 17 Agustus 1945 Jakarta" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.10.20207449", "rel_title": "Recovery of monocyte exhaustion is associated with resolution of lung injury in COVID-19 convalescence.", @@ -1132802,41 +1133899,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.16.342782", - "rel_title": "Targeting androgen regulation of TMPRSS2 and ACE2 as a therapeutic strategy to combat COVID-19", - "rel_date": "2020-10-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.16.342782", - "rel_abs": "Epidemiological data showing increased severity and mortality of COVID-19 in men suggests a potential role for androgen in SARS-CoV-2 infection. Here, we present evidence for the transcriptional regulation of SARS-CoV-2 host cell receptor ACE2 and TMPRSS2 by androgen in mouse and human cells. Additionally, we demonstrate the endogenous interaction between TMPRSS2 and ACE2 in human cells and validate ACE2 as a TMPRSS2 substrate. Further, Camostat - a TMPRSS2 inhibitor, blocked the cleavage of pseudotype SARS-CoV-2 surface Spike without disrupting TMPRSS2-ACE2 interaction. Thus providing evidence for the first time a direct role of TMPRSS2 in priming the SARS-CoV-2 Spike, required for viral fusion to the host cell. Importantly, androgen-deprivation, anti-androgens, or Camostat attenuated the SARS-CoV-2 S-mediated cellular entry. Together, our data provide a strong rationale for clinical evaluations of TMPRSS2 inhibitors, androgen-deprivation therapy/androgen receptor antagonists alone or in combination with antiviral drugs as early as clinically possible to prevent COVID-19 progression.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Qu Deng", - "author_inst": "Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania." - }, - { - "author_name": "Reyaz ur Rasool", - "author_inst": "Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Ronnie M Russell", - "author_inst": "Department of Microbiology, University of Pennsylvania." - }, - { - "author_name": "Ramakrishnan Natesan", - "author_inst": "Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Irfan A Asangani", - "author_inst": "Department of Cancer Biology, Abramson Family Cancer Research Institute, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, 421 Cur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.10.14.338053", "rel_title": "Shark conservation risks associated with the use of shark liver oil in SARS-CoV-2 vaccine development", @@ -1133124,6 +1134186,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.14.20090985", + "rel_title": "An attempt to optimize human resources allocation based on spatial diversity of COVID-19 cases in Poland", + "rel_date": "2020-10-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.14.20090985", + "rel_abs": "Our task is to examine the relationship between the SARS-CoV-2 arrival and the number of confirmed COVID-19 cases in the first wave (period from March 4 to May 22, 2020 (unofficial data)), and socio-economic variables at the powiat (county) level (NUTS-4) using simple statistical techniques such as data visualization, correlation analysis, spatial clustering and multiple linear regression. We showed that immigration and the logarithm of general mobility is the best predictor of SARS-CoV-2 arrival times, while emigration, industrialization and air quality explain the most of the size of the epidemic in poviats. On the other hand, infection dynamics is driven to a lesser extent by previously postulated variables such as population size and density, income or the size of the elderly population. Our analyses could support Polish authorities in preparation for the second wave of infections and optimal management of resources as we have provided a proposition of optimal distribution of human resources between poviats.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Andrzej Jarynowski", + "author_inst": "Institute for Interdisciplinary Research" + }, + { + "author_name": "Monika Wojta-Kempa", + "author_inst": "Wroclaw Medical Universtity" + }, + { + "author_name": "Lukasz Krzowski", + "author_inst": "Military University of Technology in Warsaw" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.13.20211284", "rel_title": "Stay-at-home policy: is it a case of exception fallacy? An internet-based ecological study", @@ -1134328,25 +1135417,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.10.11.20211052", - "rel_title": "COVID-CT-Mask-Net: Prediction of COVID-19 from CT Scans Using Regional Features", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.11.20211052", - "rel_abs": "We present COVID-CT-Mask-Net model that predicts COVID-19 from CT scans. The model works in two stages: first, it detects the instances of ground glass opacity and consolidation in CT scans, then predicts the condition from the ranked bounding box detections. To develop the solution for the three-class problem (COVID, common pneumonia and control), we used the COVIDx-CT dataset derived from the dataset of CT scans collected by China National Center for Bioinformation. We use about 5% of the training split of COVIDx-CT to train the model, and without any complicated data normalization, balancing and regularization, and training only a small fraction of the models parameters, we achieve a 90.80% COVID sensitivity, 91.62% common pneumonia sensitivity and 92.10% normal sensitivity, and an overall accuracy of 91.66% on the test data (21182 images), bringing the ratio of test/train data to 7.06, which implies a very high capacity of the model to generalize to new data. We also establish an important result, that ranked regional predictions (bounding boxes with scores) in Mask R-CNN can be used to make accurate predictions of the image class. The full source code, models and pretrained weights are available on https://github.com/AlexTS1980/COVID-CT-Mask-Net.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Aram Ter-Sarkisov", - "author_inst": "City, University of London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.10.12.20210997", "rel_title": "Scrutiny for Child Abuse and Neglect During the COVID-19 Pandemic", @@ -1134658,6 +1135728,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.10.11.20211045", + "rel_title": "Understanding the Los Angeles County Coronavirus Epidemic: The Critical Role of Intrahousehold Transmission", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.11.20211045", + "rel_abs": "We tracked the course of the COVID-19 epidemic among the approximately 300 communities comprising Los Angeles County. The epidemic, we found, had three distinct phases. During Phase I, from early March through about April 4, initial seeding of infection in relatively affluent areas was followed by radial geographic extension to adjoining communities. During Phase II, lasting until about July 11, COVID-19 cases continued to rise at a slower rate, and became increasingly concentrated in four geographic foci of infection across the county. Those communities with larger reductions in social mobility during April - as measured by the proportion of smartphones staying at home and number of smartphones visiting a gym - reported fewer COVID-19 cases in May. During Phase III, COVID-19 incidence only gradually declined, remaining as high as the incidence seen at the end of Phase I. Across communities, the prevalence of households at high risk for intergenerational transmission was strongly correlated with the persistence of continued COVID-19 propagation. This association was even stronger in those communities with a higher rate of gym attendance in Phase II. The map of the prevalence of at-risk households in Los Angeles County coincided strikingly with the map of cumulative COVID-19 incidence. These findings, taken together, support the critical role of household structure in the persistent propagation of COVID-19 infections in Los Angeles County. Public health policy needs to be reoriented from a focus on protecting the individual to a focus on protecting the household.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jeffrey E Harris", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.12.20211094", "rel_title": "Prioritisation of population groups with the most interactions for COVID-19 vaccination can substantially reduce total fatalities", @@ -1136038,53 +1137127,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.13.20212175", - "rel_title": "A comparative study of infection and mortality in COVID-19 across countries: A scaling analysis", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20212175", - "rel_abs": "Analysing infection and mortality data for COVID-19 as a function of days for 54 countries across all continents, we show that there is a simple scaling behaviour connecting these two quantities for any given nation when the data is segmented over few ranges of dates covering the most rapid spread of the pandemic and the recovery, wherever achieved. This scaling is described by two parameters, one representing a shift along the time axis and the other is a normalisation factor, providing a reliable definition of the mortality rate for each country in a given period. The number of segments for any country required in our analyses turns out to be surprisingly few with as many as 16 out of 54 countries being described by a single segment and no country requiring more than three segments. Estimates of the shift and mortality for these 54 countries in different periods show large spreads ranging over 0-16 days and 0.45-19.96%, respectively. Shift and mortality are found to be inversely correlated. Analyses of number of tests carried out for detecting COVID-19 and the number of infections detected due to such tests suggest that an effective way to increase the shift, and therefore, decrease mortality, is to increase number of tests per infection detected. This points to the need of a dynamic management of testing that should accelerate with the rise of the pandemic; it also suggests a basis for adjusting variations in the testing patterns in different geographical locations within a given country.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Ranjan Das", - "author_inst": "Indian Institute of Science (IISc)" - }, - { - "author_name": "Akmal Hossain", - "author_inst": "Indian Institute of Science (IISc)" - }, - { - "author_name": "Sayak Mandal", - "author_inst": "Indian Institute of Science (IISc)" - }, - { - "author_name": "Debasmita Pariari", - "author_inst": "Indian Institute of Science (IISc)" - }, - { - "author_name": "Rohit Kumar Rohj", - "author_inst": "Indian Institute of Science (IISc)" - }, - { - "author_name": "Swapnil Shukla", - "author_inst": "Indian Institute of Science (IISc)" - }, - { - "author_name": "Rahul Mahavir Varma", - "author_inst": "Indian Institute of Science (IISc)" - }, - { - "author_name": "Dipankar Das Sarma", - "author_inst": "Indian Institute of Science (IISc)" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.13.20211359", "rel_title": "School closures and SARS-CoV-2. Evidence from Sweden's partial school closure", @@ -1136272,6 +1137314,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.12.20211557", + "rel_title": "Nonspecific blood tests as proxies for COVID-19 hospitalization: are there plausible associations after excluding noisy predictors?", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.12.20211557", + "rel_abs": "This study applied causal criteria in directed acyclic graphs for handling covariates in associations for prognosis of severe COVID-19 (Corona virus disease 19) cases. To identify nonspecific blood tests and risk factors as predictors of hospitalization due to COVID-19, one has to exclude noisy predictors by comparing the concordance statistics (AUC) for positive and negative cases of SARS-CoV-2 (acute respiratory syndrome coronavirus 2). Predictors with significant AUC at negative stratum should be either controlled for their confounders or eliminated (when confounders are unavailable). Models were classified according to the difference of AUC between strata. The framework was applied to an open database with 5644 patients from Hospital Israelita Albert Einstein in Brazil with SARS-CoV-2 RT-PCR (Reverse Transcription - Polymerase Chain Reaction) exam. C-reactive Protein (CRP) was a noisy predictor: hospitalization could have happen due to causes other than COVID-19 even when SARS-CoV-2 RT-PCR is positive and CRP is reactive, as most cases are asymptomatic to mild. Candidates of characteristic response from moderate to severe inflammation of COVID-19 were: combinations of eosinophils, monocytes and neutrophils, with age as risk factor; and creatinine, as risk factor, sharpens the odds ratio of the model with monocytes, neutrophils, and age.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gerson Ishikawa", + "author_inst": "Universidade Tecnologica Federal do Parana" + }, + { + "author_name": "Graziela Argenti", + "author_inst": "Universidade Estadual de Ponta Grossa" + }, + { + "author_name": "Cristina Berger Fadel", + "author_inst": "Universidade Estadual de Ponta Grossa" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.13.20212118", "rel_title": "Does autism protect against COVID quarantine effects?", @@ -1137744,61 +1138813,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.10.14.340091", - "rel_title": "Use of convalescent serum reduces severity of COVID-19 in nonhuman primates", - "rel_date": "2020-10-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.14.340091", - "rel_abs": "Passive transfer of convalescent plasma or serum is a time-honored strategy for treating infectious diseases. Human convalescent plasma containing antibodies against SARS-CoV-2 is currently being used to treat COVID-19 patients. However, most patients have been treated outside of randomized clinical trials making it difficult to determine the efficacy of this approach. Here, we assessed the efficacy of convalescent sera in a newly developed African green monkey model of COVID-19. Groups of SARS-CoV-2-infected animals were treated with pooled convalescent sera containing either high or low to moderate anti-SARS-CoV-2 neutralizing antibody titers. Differences in viral load and disease pathology were minimal between monkeys that received the lower titer convalescent sera and untreated controls. However, and importantly, lower levels of SARS-CoV-2 in respiratory compartments, reduced gross and histopathological lesion severity in the lungs, and reductions in several parameters associated with coagulation and inflammatory processes were observed in monkeys that received convalescent sera versus untreated controls. Our data support human studies suggesting that convalescent plasma therapy is an effective strategy if donors with high level of antibodies against SARS-CoV-2 are employed and if recipients are at an early stage of disease.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "robert cross", - "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" - }, - { - "author_name": "Abhishek N Prasad", - "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" - }, - { - "author_name": "Viktoriya Borisevich", - "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" - }, - { - "author_name": "Courtney Woolsey", - "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" - }, - { - "author_name": "Krystle N Agans", - "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" - }, - { - "author_name": "Daniel J. Deer", - "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" - }, - { - "author_name": "Natalie S. Dobias", - "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" - }, - { - "author_name": "Joan B. Geisbert", - "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" - }, - { - "author_name": "Karla A. Fenton", - "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" - }, - { - "author_name": "Thomas W. Geisbert", - "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.08.20209619", "rel_title": "Associations between governor political affiliation and COVID-19 cases and deaths in the United States", @@ -1138002,6 +1139016,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.10.09.20210039", + "rel_title": "EVALUATION OF ELEVEN IMMUNOCHROMATOGRAPHIC ASSAYS FOR SARS-CoV-2 DETECTION: INVESTIGATING DENGUE CROSS-REACTION", + "rel_date": "2020-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20210039", + "rel_abs": "BackgroundCOVID-19 disease (Coronavirus disease 2019) caused by SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) is widespread worldwide, affecting more than 11 million people globally (July 6th, 2020). Diagnostic techniques have been studied in order to contain the pandemic. Immunochromatographic (IC) assays are feasible and low cost alternative for monitoring the spread of COVID-19 in the population.\n\nMethodsHere we evaluate the sensitivity and specificity of eleven different immunochromatographic tests in 98 serum samples from confirmed cases of COVID-19 through RT-PCR and 100 negative serum samples from blood donors collected in February 2019. Considering the endemic situation of Dengue in Brazil, we also evaluated the cross-reactivity with Dengue using 20 serum samples from patients with confirmed diagnosis for Dengue collected in early 2019 through four different tests.\n\nResultsOur results demonstrated agreement between immunochromatographic assays and RT-PCR, especially after 10 days since the onset of symptoms. The evaluation of IgG and IgM antibodies combined demonstrated a strong level of agreement (0.85) of IC assays and RT-PCR. It was observed cross-reactivity between Dengue and COVID-19 using four different IC assays for COVID-19 diagnosis. The specificity of IC assays to detected COVID-19 IgM antibodies using Dengue serum samples varied from 80% to 85%; the specificity of IgG detection was 100% and total antibody was 95%.\n\nConclusionsWe found high sensitivity, specificity and good agreement of IC assays, especially after 10 days onset of symptoms. However, we detected cross-reactivity between Dengue and COVID-19 mainly with IgM antibodies demonstrating the need for better studies about diagnostic techniques for these diseases.\n\nHighlightsO_LIImmunochromatographic assays demonstrated high sensitivity and specificity and good agreement with the gold-standard RT-PCR;\nC_LIO_LIIncrease in sensitivity and specificity of assays using samples collected after the 10th day of symptoms;\nC_LIO_LICross-reaction with Dengue serology in evaluation of IgM.\nC_LI", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Beatriz Araujo Oliveira", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Lea Campos de Oliveira", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Franciane Mendes de Oliveira", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Geovana Maria Pereira", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Regina Maia de Souza", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Erika Regina Manuli", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Fabricio Klerynton Marchini", + "author_inst": "Instituto Carlos Chagas, Fiocruz" + }, + { + "author_name": "Evelyn Patr\u00edcia Sanchez Espinoza", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Marcelo Park", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Leandro Taniguchi", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Pedro Vitale Mendes", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Lucas Augusto Moyses Franco", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Ana Catharina Nastri", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Maura Salaroli de Oliveira", + "author_inst": "Hospital das Cl\u00ednicas" + }, + { + "author_name": "Jos\u00e9 Mauro Vieira Junior", + "author_inst": "Hospital S\u00edrio Liban\u00eas" + }, + { + "author_name": "Esper Georges Kallas", + "author_inst": "Faculdade de Medicina da Universidade de S\u00e3o Paulo" + }, + { + "author_name": "Anna Sara Levin", + "author_inst": "Faculdade de Medicina da Universidade de S\u00e3o Paulo" + }, + { + "author_name": "Ester Cerdeira Sabino", + "author_inst": "Instituto de Medicina Tropical" + }, + { + "author_name": "Silvia Figueiredo Costa", + "author_inst": "Instituto de Medicina Tropical" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.08.20209544", "rel_title": "What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis", @@ -1139753,25 +1140858,6 @@ "type": "new results", "category": "synthetic biology" }, - { - "rel_doi": "10.1101/2020.10.11.20210799", - "rel_title": "FORECASTING COMBINATION OF HIERARCHICAL TIME SERIES: ANOVEL METHOD WITH AN APPLICATION TO COVID-19", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.11.20210799", - "rel_abs": "Multiple, hierarchically organized time series are routinely submitted to the forecaster upon request to provide estimates of their future values, regardless the level occupied in the hierarchy. In this paper, a novel method for the prediction of hierarchically structured time series will be presented. The idea is to enhance the quality of the predictions obtained using a technique of the type forecast reconciliation, by applying this procedure to a set of optimally combined predictions, generated by different statistical models. The goodness of the proposed method will be evaluated using the official time series related to the number of people tested positive to the SARS-CoV-2 in each of the Italian regions, between February 24th 2020 and August 31th 2020.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Livio Fenga", - "author_inst": "Istat" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.13.337287", "rel_title": "Sero-prevalence of anti-SARS-CoV-2 Antibodies in Addis Ababa, Ethiopia", @@ -1140127,6 +1141213,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.08.20204750", + "rel_title": "Estimating the effect of social inequalities in the mitigation of COVID-19 across communities in Santiago de Chile", + "rel_date": "2020-10-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20204750", + "rel_abs": "We study the spatio-temporal spread of SARS-CoV-2 in Santiago de Chile using anonymized mobile phone data from 1.4 million users, 22% of the whole population in the area, characterizing the effects of non-pharmaceutical interventions (NPIs) on the epidemic dynamics. We integrate these data into a mechanistic epidemic model calibrated on surveillance data. As of August 1st 2020, we estimate a detection rate of 102 cases per 1,000 infections (90% CI: [95 - 112 per 1,000]). We show that the introduction of a full lockdown on May 15th, 2020, while causing a modest additional decrease in mobility and contacts with respect to previous NPIs, was decisive in bringing the epidemic under control, highlighting the importance of a timely governmental response to COVID-19 outbreaks. We find that the impact of NPIs on individuals mobility correlates with the Human Development Index of comunas in the city. Indeed, more developed and wealthier areas became more isolated after government interventions and experienced a significantly lower burden of the pandemic. The hetero-geneity of COVID-19 impact raises important issues in the implementation of NPIs and highlights the challenges that communities affected by systemic health and social inequalities face adapting their behaviors during an epidemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nicol\u00f2 Gozzi", + "author_inst": "Networks and Urban Systems Centre, University of Greenwich, London, UK" + }, + { + "author_name": "Michele Tizzoni", + "author_inst": "ISI Foundation, Turin, Italy" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Leo Ferres", + "author_inst": "Data Science Institute, Universidad del Desarrollo, Santiago, Chile" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Nicola Perra", + "author_inst": "Networks and Urban Systems Centre, University of Greenwich, London, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.08.20209437", "rel_title": "Estimating the Burden of COVID-19 Symptoms Among Participants at the 2020 USA Curling Club Nationals Tournament", @@ -1141434,29 +1142559,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.07.20208504", - "rel_title": "Using test positivity and reported case rates to estimate state-level COVID-19 prevalence in the United States", - "rel_date": "2020-10-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208504", - "rel_abs": "Accurate estimates of infection prevalence and seroprevalence are essential for evaluating and informing public health responses needed to address the ongoing spread of COVID-19 in the United States. A data-driven Bayesian single parameter semi-empirical model was developed and used to evaluate state-level prevalence and seroprevalence of COVID-19 using daily reported cases and test positivity ratios. COVID-19 prevalence is well-approximated by the geometric mean of the positivity rate and the reported case rate. As of December 8, 2020, we estimate nation-wide a prevalence of 1.4% [Credible Interval (CrI): 0.8%-1.9%] and a seroprevalence of 11.1% [CrI: 10.1%-12.2%], with state-level prevalence ranging from 0.3% [CrI: 0.2%-0.4%] in Maine to 3.0% [CrI: 1.1%-5.7%] in Pennsylvania, and seroprevalence from 1.4% [CrI: 1.0%-2.0%] in Maine to 22% [CrI: 18%-27%] in New York. The use of this simple and easy-to-communicate model will improve the ability to make public health decisions that effectively respond to the ongoing pandemic.\n\nBiographical Sketch of AuthorsDr. Weihsueh A. Chiu, is a professor of environmental health sciences at Texas A&M University. He is an expert in data-driven Bayesian modeling of public health related dynamical systems. Dr. Martial L. Ndeffo-Mbah, is an Assistant Professor of Epidemiology at Texas A&M University. He is an expert in mathematical and computational modeling of infectious diseases.\n\nSummary LineRelying on reported cases and test positivity rates individually can result in incorrect inferences as to the spread of COVID-19, and public health decision-making can be improved by instead using their geometric mean as a measure of COVID-19 prevalence and transmission.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Weihsueh chiu", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Martial L Ndeffo-Mbah", - "author_inst": "Texas A&M University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.07.20208314", "rel_title": "Evaluating the impact of curfews and other measures on SARS-CoV-2 transmission in French Guiana", @@ -1141740,6 +1142842,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.10.20203034", + "rel_title": "Clarifying predictions for COVID-19 from testing data: the example of New-York State", + "rel_date": "2020-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.10.20203034", + "rel_abs": "In this article, we use testing data as an input of a new epidemic model. We get nice a concordance between the best fit the model to the reported cases data for New-York state. We also get a good concordance of the testing dynamic and the epidemics dynamic in the cumulative cases. Finally, we can investigate the effect of multiplying the number of tests by 2, 5, 10, and 100 to investigate the consequences on the reduction of the number of reported cases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Pierre Griette", + "author_inst": "University of Bordeaux" + }, + { + "author_name": "Pierre Magal", + "author_inst": "University of Bordeaux" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.07.20208744", "rel_title": "One size fits all?: Modeling face-mask fit on population-based faces", @@ -1143028,49 +1144153,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.08.20209650", - "rel_title": "Absence of SARS-CoV-2 neutralizing activity in pre-pandemic sera from individuals with recent seasonal coronavirus infection", - "rel_date": "2020-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209650", - "rel_abs": "Cross-reactive immune responses elicited by seasonal coronaviruses might impact SARS-CoV-2 susceptibility and disease outcomes. We measured neutralizing activity against SARS-CoV-2 in pre-pandemic sera from patients with prior PCR-confirmed seasonal coronavirus infection. While neutralizing activity against seasonal coronaviruses was detected in nearly all sera, cross-reactive neutralizing activity against SARS-CoV-2 was undetectable.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Daniel Poston", - "author_inst": "Rocekfeller University" - }, - { - "author_name": "Yiska Weisblum", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Helen Wise", - "author_inst": "3.\tRoyal Infirmary of Edinburgh" - }, - { - "author_name": "Kate Templeton", - "author_inst": "Royal Infirmary of Edinburgh" - }, - { - "author_name": "Sara Jenks", - "author_inst": "3.\tRoyal Infirmary of Edinburgh" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Paul D Bieniasz", - "author_inst": "Rockefeller University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.07.20205104", "rel_title": "Lockdown impact on age-specific contact patterns and behaviours in France", @@ -1143486,6 +1144568,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.10.20210328", + "rel_title": "SARS-CoV-2 infections in Italian schools: preliminary findings after one month of school opening during the second wave of the pandemic", + "rel_date": "2020-10-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.10.20210328", + "rel_abs": "IntroductionThe impact of school opening on the SARS-CoV-2 pandemic is still unknown. This study aims to provide preliminary information about the number of SARS-CoV-2 cases among students attending Italian schools.\n\nMethodsData are extracted and analysed from an open access, online dataset that monitor, on a daily basis, media news about SARS-CoV-2 infections of students attending Italian schools\n\nResultsAs of 5 October 2020, a total of 1350 cases of SARS-CoV-2 infections have been registered in the Italian territory schools (involving 1059 students, 145 teachers and 146 other school members), for a total of 1212 out of 65104 (1.8%) Italian schools involved. National schools reported only 1 case of SARS-CoV-2 infection in more than 90% of cases, and only in one high school a cluster of more than 10 cases have been described (P 0.015). The detection of one or more SARS-CoV-2 infections leaded to the closure of 192 (14.2%) entire schools, more frequently nursery/kindergartens (P<0.0005).\n\nDiscussionOur preliminary data support low transmission of SARS-CoV-2 within schools, at least among younger students. However, entire schools are frequently closed in the fear of larger outbreaks. Continuous monitoring of school settings, hopefully through daily updated open access datasets, are needed to better understand the impact of schools on the pandemic, and provide guidelines that better consider different risks within different age groups.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Danilo Buonsenso", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Cristina De Rose", + "author_inst": "Fondazione Universitaria Policlinico Gemelli, IRCSS, Rome, Italy" + }, + { + "author_name": "Rosanna Moroni", + "author_inst": "Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Piero Valentini", + "author_inst": "Fondazione Universitaria Policlinico A. Gemelli, IRCSS, Rome, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.10.07.20208389", "rel_title": "A Comparative COVID 19 Characterizations and Clinical Course Analysis between ICU and Non ICU Settings", @@ -1144934,97 +1146047,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.07.20208603", - "rel_title": "Serological Analysis Reveals an Imbalanced IgG Subclass Composition Associated with COVID-19 Disease Severity", - "rel_date": "2020-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208603", - "rel_abs": "COVID-19 is associated with a wide spectrum of disease severity, ranging from asymptomatic to acute respiratory distress syndrome (ARDS). Paradoxically, a direct relationship has been suggested between COVID-19 disease severity, and the levels of circulating SARS-CoV-2-specific antibodies, including virus neutralizing titers. Through a serological analysis of serum samples from 536 convalescent healthcare workers, we found that SARS-CoV-2-specific and virus-neutralizing antibody levels were indeed elevated in individuals that experienced severe disease. The severity-associated increase in SARS-CoV-2-specific antibody was dominated by IgG, with an IgG subclass ratio skewed towards elevated receptor binding domain (RBD)- and S1-specific IgG3. However, RBD- and S1-specific IgG1, rather than IgG3 were best correlated with virus-neutralizing titers. We propose that Spike-specific IgG3 subclass utilization contributes to COVID-19 disease severity through potent Fc-mediated effector functions. These results have significant implications for SARS-CoV-2 vaccine design, and convalescent plasma therapy.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Jennifer L. Yates", - "author_inst": "NYSDOH" - }, - { - "author_name": "Dylan J. Ehrbar", - "author_inst": "NYSDOH" - }, - { - "author_name": "Danielle T. Hunt", - "author_inst": "NYSDOH" - }, - { - "author_name": "Roxie Girardin", - "author_inst": "NYSDOH" - }, - { - "author_name": "Alan P. Dupuis II", - "author_inst": "NYSDOH" - }, - { - "author_name": "Anne F. Payne", - "author_inst": "NYSDOH" - }, - { - "author_name": "Mycroft Sowizral", - "author_inst": "NYSDOH" - }, - { - "author_name": "Scott Varney", - "author_inst": "Albany Medical College" - }, - { - "author_name": "Karen E. Kulas", - "author_inst": "NYSDOH" - }, - { - "author_name": "Valerie L. Demarest", - "author_inst": "NYSDOH" - }, - { - "author_name": "Kelly M. Howard", - "author_inst": "NYSDOH" - }, - { - "author_name": "Kyle Carson", - "author_inst": "NYSDOH" - }, - { - "author_name": "Margaux Hales", - "author_inst": "NYSDOH" - }, - { - "author_name": "Monir Ejemel", - "author_inst": "MassBiologics" - }, - { - "author_name": "Qi Li", - "author_inst": "MassBiologics" - }, - { - "author_name": "Yang Wang", - "author_inst": "MassBiologics" - }, - { - "author_name": "Nicholas J Mantis", - "author_inst": "NYSDOH" - }, - { - "author_name": "Kathleen A. McDonough", - "author_inst": "NYSDOH" - }, - { - "author_name": "William T. Lee", - "author_inst": "Wadsworth Center/New York State Department of Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.07.20205575", "rel_title": "Predictors of Death in Severe COVID-19 Patients at Millennium COVID-19 Care Center in Ethiopia: A Case-Control Study", @@ -1145304,6 +1146326,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.10.09.20209965", + "rel_title": "Pulmonary Embolism in Patients with COVID-19: A Systematic review and Meta-analysis", + "rel_date": "2020-10-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.09.20209965", + "rel_abs": "BackgroundThere is an increasing evidence that COVID-19 could be complicated by coagulopathy which may lead to death; especially in severe cases. Hence, this study aimed to build concrete evidence regarding the incidence and mortality of pulmonary embolism (PE) in patients with COVID-19.\n\nMethodsWe performed a systematic search for trusted databases/search engines including PubMed, Scopus, Cochrane library and Web of Science. After screening, the relevant data were extracted and the incidences and mortality rates from the different included studies were pooled for meta-analysis.\n\nResultsTwenty studies were finally included in our study consisting of 1896 patients. The results of the meta-analysis for the all included studies showed that the incidence of PE in patients with COVID-19 was 17.6% with the 95% confidence interval (CI) of 12.7 to 22.5%. There was significant heterogeneity (I2{square}={square}91.17%). Additionally, the results of meta-analysis including 8 studies showed that the mortality in patients with both PE and COVID-19 was 43.1% with the 95% confidence interval (CI) of 19 to 67.1%. There was significant heterogeneity (I2{square}={square}86.96%).\n\nConclusionPE was highly frequent in patients with COVID-19. The mortality in patients with both COVID-19 and PE was remarkable representing almost half of the patients. Appropriate prophylaxis and management are vital for better outcomes.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Omar Hamam", + "author_inst": "Alexandria Faculty of Medicine" + }, + { + "author_name": "Ahmed Goda", + "author_inst": "Faculty of Medicine, October 6th University, Cairo, 12585 Egypt" + }, + { + "author_name": "Radwa Awad", + "author_inst": "Faculty of Medicine, Benha University, Benha, 13518 Egypt" + }, + { + "author_name": "Amr Ussama", + "author_inst": "Faculty of Medicine, Al-azhar University, Cairo, 11651 Egypt" + }, + { + "author_name": "Moustafa Eldalal", + "author_inst": "Faculty of Medicine, Alexandria University, Alexandria21131, Egypt" + }, + { + "author_name": "Ahmed Fayez", + "author_inst": "Faculty of Medicine, October 6th University, Cairo, 12585 Egypt" + }, + { + "author_name": "Karim Elyamany", + "author_inst": "Faculty of Medicine, Alexandria University, Alexandria21131, Egypt" + }, + { + "author_name": "Renu Bhandari", + "author_inst": "Department of Internal Medicine, Manipal College of Medical Sciences, Kaski, 33700 Nepal." + }, + { + "author_name": "Waleed Ikram", + "author_inst": "Lahore Medical and Dental College, Lahore, 30022 Pakistan" + }, + { + "author_name": "Abdelrhman Elbaz", + "author_inst": "Bascom Palmer Eye Institute, Miami, FL 33136 United States of America" + }, + { + "author_name": "Smarika Baral", + "author_inst": "Department of Internal Medicine, Nepalgunj Medical College, Banke, 21900 Nepal." + }, + { + "author_name": "Yomna Elbandrawy", + "author_inst": "Faculty of Medicine, Tanta University, Tanta, 31951 Egypt" + }, + { + "author_name": "Alexander Egbe", + "author_inst": "Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, 55905 United States of America." + }, + { + "author_name": "Iraida Sharina", + "author_inst": "Division of Cardiology, Department of Internal Medicine, McGovern Medical School, The University of Texas Health Science Center Houston, Houston, TX 77225, Unit" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.10.07.20207845", "rel_title": "Isolation of infected people and their contacts is likely to be effective against many short-term epidemics", @@ -1146611,93 +1147704,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.06.20207092", - "rel_title": "Low-density lipoprotein cholesterol levels are associated with poor clinical outcomes in COVID-19", - "rel_date": "2020-10-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20207092", - "rel_abs": "STRUCTURED ABSTRACTO_ST_ABSBackgroundC_ST_ABSSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the sole causative agent of coronavirus infectious disease-19 (COVID-19).\n\nMethodsWe performed a retrospective single-center study of consecutively admitted patients between March 1st and May 15th, 2020, with a definitive diagnosis of SARS-CoV-2 infection. The primary end-point was to evaluate the association of lipid markers with 30-days all-cause mortality in COVID-19.\n\nResultsA total of 654 patients were enrolled, with an estimated 30-day mortality of 22.8% (149 patients). Non-survivors had lower total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-c) levels during the entire course of the disease with complete resolution among survivors. Both showed a significant inverse correlation with inflammatory markers and a positive correlation with lymphocyte count. In a multivariate analysis, LDL-c [≤] 69 mg/dl (hazard ratio [HR] 1.94; 95% confidence interval [CI] 1.14-3.31), C-reactive protein > 88 mg/dl (HR 2.44; 95% CI, 1.41-4.23) and lymphopenia < 1,000 (HR 2.68; 95% CI, 1.91-3.78) at admission were independently associated with 30-day mortality. This association was maintained 7 days after admission.\n\nConclusionHypolipidemia in SARS-CoV-2 infection may be secondary to an immune-inflammatory response, with complete recovery in survivors. Low LDL-c serum levels are independently associated with higher 30-day mortality in COVID-19 patients.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Alvaro Aparisi", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Carolina Iglesias-Echeverria", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Cristina Ybarra-Falcon", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Ivan Cusacovich", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Aitor Uribarri", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Mario Garcia-Gomez", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Raquel Ladron", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Raul Fuertes", - "author_inst": "Facultad de Medicina. Universidad de Valladolid, Spain" - }, - { - "author_name": "Jordi Candela", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Williams Hinojosa", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Carlos Duenas", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Roberto Gonzalez", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Leonor Nogales-Martin", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Dolores Calvo", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Manuel Carrasco-Moraleja", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "J. Alberto San Roman", - "author_inst": "Hospital Clinico Universitario de Valladolid" - }, - { - "author_name": "Ignacio J Amat-Santos", - "author_inst": "Hospital Clinico Universitario" - }, - { - "author_name": "David Andaluz Ojeda", - "author_inst": "Hospital Clinico Universitario de Valladolid" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.06.20171579", "rel_title": "Comparison of efficacy of Dexamethasone and Methylprednisolone in improving P/F ratio among COVID-19 patients", @@ -1146865,6 +1147871,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.06.20207993", + "rel_title": "Sars-Cov-2 in Argentina: Following Virus Spreading using Granger Causality", + "rel_date": "2020-10-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20207993", + "rel_abs": "There is a debate in Argentina on how COVID-19 outbreak in one district ends up infecting its neighbor districts. This contribution aims to use tools of time series analysis for understanding processes of contagious through regions. I use VAR and Granger causality for testing neighbor spreading via sequential rate of contagion. Results show that in the case of Argentina, contagion began in the capital city of Buenos Aires and then spread to its hinterland via specific districts. Once interior districts were infected a positive feedback dynamics emerge creating regions of high reproducibility of the virus where interventions may be focus in the very near future. This specific use of time series analysis may provide a tool for tracing infectiousness along regions that may help to anticipate infection and then for intervening for reducing the problems derived by the disease.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Juan M.C. Larrosa", + "author_inst": "Universidad Nacional del Sur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.06.20208009", "rel_title": "Misinterpretation of viral load in COVID-19.", @@ -1148241,45 +1149266,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.10.07.330068", - "rel_title": "NSP 11 of SARS-CoV-2 is an Intrinsically Disordered Protein", - "rel_date": "2020-10-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.07.330068", - "rel_abs": "The intrinsically disordered proteins/regions (IDPs/IDPRs) are known to be responsible for multiple cellular processes and are associated with many chronic diseases. In viruses, the existence of a disordered proteome is also proven and is related to its conformational dynamics inside the host. The SARS-CoV-2 has a large proteome, in which, structure and functions of many proteins are not known yet, along with nsp11. In this study, we have performed extensive experimentation on nsp11. Our results based on the CD spectroscopy gives characteristic disordered spectrum for IDPs. Further, we investigated the conformational behavior of nsp11 in the presence of membrane mimetic environment, -helix inducer, and natural osmolyte. In the presence of negatively charged and neutral liposomes, nsp11 remains disordered. However, with SDS micelle, it adopted an -helical conformation, suggesting the helical propensity of nsp11. Finally, we again confirmed the IDP behavior of nsp11 using MD simulations. In future, this conformational dynamic study could help to clarify its functional importance in SARS-CoV-2 infection.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kundlik Gadhave", - "author_inst": "Indian Institute of Technology Mandi" - }, - { - "author_name": "Prateek Kumar", - "author_inst": "Indian Institute of Technology Mandi" - }, - { - "author_name": "Ankur Kumar", - "author_inst": "Indian Institute of Technology Mandi" - }, - { - "author_name": "Taniya Bhardwaj", - "author_inst": "Indian Institute of Technology Mandi" - }, - { - "author_name": "Neha Garg", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Rajanish Giri", - "author_inst": "Indian Institute of Technology Mandi" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.10.07.329748", "rel_title": "Umbilical cord blood derived microglia-like cells to model COVID-19 exposure", @@ -1148687,6 +1149673,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.03.20205328", + "rel_title": "The Impact of COVID-19 on the Management of Heart Failure -A United Kingdom Patient Questionnaire Study", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20205328", + "rel_abs": "AimThe coronavirus disease 2019 (COVID-19) pandemic has created significant challenges to healthcare globally, necessitating rapid restructuring of service provision. This questionnaire survey was conducted amongst adult heart failure (HF) patients in the United Kingdom (UK), to understand the impact of COVID-19 upon HF services.\n\nMethods and ResultsThe survey was conducted by the Pumping Marvellous Foundation (PMF), a UK HF patient charity. \"Survey Monkey\" was used to disseminate the questionnaire in the PMFs online patient group and in 10 UK hospitals (out-patient hospital and community HF clinics). 1050 responses were collected (693/1050-66% women); 55% (579/1050) were aged over 60 years. Anxiety level was significantly higher regarding COVID19 (mean 7{+/-}2.5 on anxiety scale of 0 to 10) compared to anxiety regarding HF (6.1{+/-}2.4; p<0.001). Anxiety was higher amongst patients aged [≤]60 years about HF (6.3{+/-}2.2 versus 5.9{+/-}2.5 in those aged >60 years; p=0.005) and COVID-19 (7.3{+/-}2.3 versus 6.7{+/-}2.6 those aged >60 years; p<0.001). 65% respondents (686/1050) reported disruption to HF appointments (cancellation or postponement) during the lockdown period. 37% reported disruption to medication prescription services and 34% reported inability to access their HF teams promptly. 32% expressed reluctance to attend hospital (25% stated they would only attend hospital if there was no alternative and 7% stated that they would not attend hospital at all).\n\nConclusionsThe COVID-19 pandemic has caused significant anxiety amongst HF patients regarding COVID-19 and HF. Cancellation or postponement of scheduled clinic appointments, investigations, procedures, prescription and monitoring services were implicated as sources of anxiety.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Rajiv Sankaranarayanan", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Nick Hartshorne-Evans", + "author_inst": "The Pumping Marvellous Foundation" + }, + { + "author_name": "Sam Redmond-Lyon", + "author_inst": "The Pumping Marvellous Foundation" + }, + { + "author_name": "Jill Wilson", + "author_inst": "The Pumping Marvellous Foundation" + }, + { + "author_name": "Hani Essa", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Alastair Gray", + "author_inst": "Craigavon Area Hospital" + }, + { + "author_name": "Louise Clayton", + "author_inst": "University Hospitals of Leicester NHS Trust" + }, + { + "author_name": "Carys Barton", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Fozia Z Ahmed", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Colin Cunnington", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Duwarakan Satchithananda", + "author_inst": "University Hospital North Midlands" + }, + { + "author_name": "Clare Murphy", + "author_inst": "Royal Alexandra and Vale of Leven Hospitals" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.10.04.20206318", "rel_title": "The relationship between neighborhood poverty and COVID-19 mortality within racial/ethnic groups (Cook County, Illinois)", @@ -1149719,41 +1150768,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.10.05.20203687", - "rel_title": "Chest pain presentations to hospital during the COVID-19 lockdown: lessons for public health media campaigns", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20203687", - "rel_abs": "ObjectiveEmergency Department (ED) attendances with chest pain reduced during the COVID-19 lockdown. To understand factors influencing patients decisions to attend hospital, we performed a local service evaluation project in NHS Lothian.\n\nMethodsWe collated data on online searches and local clinical services on the number of ED presentations and chest pain clinic (CPC) referrals with suspected acute coronary syndrome between January and May 2020 and compared findings with the same period in 2019. We also carried out 28 semi-structured telephone interviews with patients who presented with chest pain during lockdown and in patients with known coronary heart disease under the outpatient care of a cardiologist in April and May 2020. Interviews were audio recorded and salient themes and issues documented as verbatim extracts.\n\nResultsOnline searches for the term \"chest pain\" doubled after 01/03/2020, peaking in week commencing 22/03/2020 and returning to 2019 levels during April 2020. In contrast, chest pain presentations to ED and CPC decreased, with the greatest reduction in the final week of March 2020 (128 v 287 (average weekly ED attendance 2019), and 6 v 23 (average weekly CPC referral 2019)). This aligned with key government messages to Protect the NHS and the NHS is open campaign. Patient interviews revealed three main themes; 1) pandemic help-seeking behaviour2) COVID-19 exposure concerns; 3) favourable Hospital experience if admitted.\n\nConclusionsDynamic monitoring of public health and media messaging should evaluate public response to healthcare campaigns to ensure the net impact on health, pandemic and non-pandemic related, is optimised.\n\nWhat is already known about the subject?Reports from around the world revealed a decrease in the numbers of patients attending hospital for serious health complaints such as chest pain during the lockdown restrictions imposed by governments to decrease the spread of SARS-CoV-2.\n\nWhat does this study add?This service evaluation project has provided insight into how patients experiencing chest pain made the decision to attend hospital for assessment during this period. It has revealed how the pandemic shaped help-seeking practices, how patients interpreted their personal vulnerability to the virus, and describes patient experience of attending hospital for assessment during this time.\n\nHow might this impact on clinical practice?Careful monitoring of the public response to health care messaging campaigns should be a key part of a pandemic strategy and careful adjustment of messaging, in a dynamically responsive way, should be considered in future.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Amy V Ferry", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Collette Keanie", - "author_inst": "Royal Infirmary of Edinburgh" - }, - { - "author_name": "Martin A Denvir", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Nicholas L Mills", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Fiona E Strachan", - "author_inst": "University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.10.05.20206706", "rel_title": "Vitamin D status and seroconversion for COVID-19 in UK healthcare workers who isolated for COVID-19 like symptoms during the 2020 pandemic.", @@ -1149997,6 +1151011,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.05.20207100", + "rel_title": "Updating Herd Immunity Models for the U.S. in 2020: Implications for the COVID-19 Response", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.05.20207100", + "rel_abs": "ObjectivesTo understand what levels of herd immunity are required in the COVID-19 pandemic, given spatial population heterogeneity, to best inform policy and action.\n\nMethodsUsing a network of counties in the United States connected by transit data we considered a set of coupled differential equations for susceptible-infectious-removed populations. We calculated the classical herd immunity level plus a version reflecting the heterogeneity of connections in the network by running the model forward in time until the epidemic completed.\n\nResultsNecessary levels of herd immunity vary greatly from county to county. A population weighted average for the United States is 47.5% compared to a classically estimated level of 77.1%.\n\nConclusionsCommon thinking argues that the nation needs to achieve at least 60% herd immunity to emerge from the COVID-19 pandemic. Heterogeneity in contact structure and individual variation in infectivity, susceptibility, and resistance are key factors that reduce the disease-induced herd immunity levels to 34.2-47.5% in our models. Looking forward toward vaccination strategies, these results suggest we should consider not just who is vaccinated but where those vaccinations will do the most good.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Natalie Elizabeth Sheils", + "author_inst": "UnitedHealth Group" + }, + { + "author_name": "Gregory D Lyng", + "author_inst": "UnitedHealth Group" + }, + { + "author_name": "Ethan M Berke", + "author_inst": "UnitedHealth Group" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.03.20206359", "rel_title": "PREDICTIONS FOR EUROPE FOR THE COVID-19 PANDEMICAFTER LOCKDOWN WAS LIFTED USING AN SIR MODEL", @@ -1151417,53 +1152458,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.05.327528", - "rel_title": "Sub-second heat inactivation of coronavirus", - "rel_date": "2020-10-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.05.327528", - "rel_abs": "Heat treatment denatures viral proteins that comprise the virion, making virus incapable of infecting a host. Coronavirus (CoV) virions contain single-stranded RNA genomes with a lipid envelope and 4 proteins, 3 of which are associated with the lipid envelope and thus are thought to be easily denatured by heat or surfactant-type chemicals. Prior studies have shown that a temperature of as low as 75 {degrees}C and treatment duration of 15 min can effectively inactivate CoV. The applicability of a CoV heat inactivation method greatly depends on the length of time of a heat treatment and the temperature needed to inactivate the virus. With the goal of finding conditions where sub-second heat exposure of CoV can sufficiently inactivate CoV, we designed and developed a simple system that can measure sub-second heat inactivation of CoV. The system is composed of capillary stainless-steel tubing immersed in a temperature-controlled oil bath followed by an ice bath, through which virus solution can be flowed at various speeds. Flowing virus solution at different speeds, along with a real-time temperature monitoring system, allows the virus to be accurately exposed to a desired temperature for various durations of time. Using mouse hepatitis virus (MHV), a beta-coronavirus, as a model system, we identified that 85.2 {degrees}C for 0.48 s exposure is sufficient to obtain > 5 Log10 reduction in viral titer (starting titer: 5 x 107 PFU/mL), and that when exposed to 83.4 {degrees}C for 0.95 s, the virus was completely inactivated (zero titer, > 6 Log10 reduction).\n\nIMPORTANCEThree coronaviruses (CoVs) have now caused global outbreaks within the past 20 years, with the COVID19 pandemic caused by SARS-CoV-2 still ongoing. Methods that can rapidly inactivate viruses, especially CoVs, can play critical roles in ensuring public safety and safeguarding personal health. Heat treatment of viruses to inactive them can be an efficient and inexpensive method, with the potential to be incorporated into various human-occupied spaces. In this work, a simple system that can heat-treat viruses for extremely short period was developed and utilized to show that sub-second exposure of CoV to heat is sufficient to inactivate CoV. This opens up the possibility of developing instruments and methods of disinfecting CoV in diverse settings, including rapid liquid disinfection and airborne virus disinfection. The developed method can also be broadly utilized to assess heat sensitivity of viruses other viral pathogens of interest and develop sub-second rapid heat inactivation approaches.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yuqian Jiang", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Han Zhang", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Jose A. Wippold", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Jyotsana Gupta", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Jing Dai", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Paul de Figueiredo", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Julian L. Leibowitz", - "author_inst": "Texas A & M Health Science Center" - }, - { - "author_name": "Arum Han", - "author_inst": "Texas A&M University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.10.05.327197", "rel_title": "A genetic variant protective for COVID-19 is inherited from Neanderthals", @@ -1151595,6 +1152589,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.02.20200931", + "rel_title": "Association of Pre-COVID-19 Lymphocytopenia with Fatality", + "rel_date": "2020-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20200931", + "rel_abs": "Lymphocytopenia during the COVID-19 has been associated with fatality. We tested whether pre-existing lymphocytopenia reported prior to any possible exposure to SARS-COV2 (from 2010 to 2019) was associated with fatality. Using all patients diagnosed on testing in a single regional laboratory, we identified 1137 subjects with PCR positive for SARS-COV2 and at least one available complete blood count from the decade prior to any possible exposure to the virus. Bivariate analysis indicated an association between pre-existing lymphocytopenia (defined as absolute lymphocyte count <0.9x109 /L) and fatality (18% versus 4%). Furthermore, a logistic regression model, accounting for both patient age and number of blood counts obtained, indicated the subjects with pre-existing lymphocytopenia were 1.4 times as likely to die. Because the absolute lymphocyte count is almost universally available and easily interpreted, this biomarker of the risk of fatality could be widely useful.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Richard Burack", + "author_inst": "University of Rochester" + }, + { + "author_name": "Philip Rock", + "author_inst": "University of Rochester" + }, + { + "author_name": "David Burtoon", + "author_inst": "University of Rochester" + }, + { + "author_name": "Xueya Cai", + "author_inst": "University of Rochester" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.02.20205880", "rel_title": "Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity irrespective of virus", @@ -1152919,49 +1153944,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.10.01.20204495", - "rel_title": "Religious affiliation and the risk of COVID 19 related mortality; a retrospective analysis of variation in pre and post lockdown risk by religious group in England and Wales.", - "rel_date": "2020-10-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.01.20204495", - "rel_abs": "BackgroundCOVID 19 mortality risk is associated with demographic and behavioural factors; furthermore religious gatherings have been linked with the spread of COVID. We sought to understand the variation in the risk of COVID 19 related death across religious groups in the UK both before and after lockdown.\n\nMethodsWe conducted a retrospective cohort study of usual residents in England and Wales enumerated at the 2011 Census (n = 48,422,583), for risk of death involving COVID-19 using linked death certificates. Cox regression models were estimated to compare risks between religious groups. Time dependent religion coefficients were added to the model allowing hazard ratios (HRs) pre and post lockdown period to be estimated separately.\n\nResultsCompared to Christians all religious groups had an elevated risk of death involving COVID-19; the largest age adjusted HRs were for Muslim and Jewish males at 2.5 (95% confidence interval 2.3-2.7) and 2.1 (1.9-2.5), respectively. The corresponding HRs for Muslim and Jewish females were 1.9 (1.7-2.1) and 1.5 (1.7-2.1). The difference in risk between groups contracted after lockdown. Those who affiliated with no religion had the lowest risk of COVID 19 related death before and after lockdown.\n\nConclusionThe majority of the variation in COVID 19 mortality risk was explained by controlling for socio demographic and geographic determinants; however, Jews remained at a higher risk of death compared to all other groups. Lockdown measures were associated with reduced differences in COVID 19 mortality rates between religious groups, further research is required to understand the causal mechanisms.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Charlotte Gaughan", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Daniel Ayoubkhani", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Vahe Nafilyan", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Peter Goldblatt", - "author_inst": "University College London" - }, - { - "author_name": "Chris White", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Karen Tingay", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Neil Bannister", - "author_inst": "Office for National Statistics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.01.20205492", "rel_title": "RT qLAMP--Direct Detection of SARS-CoV-2 in Raw Sewage", @@ -1153213,6 +1154195,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.09.30.20204537", + "rel_title": "SARS-CoV-2 seroprevalence and clinical features of COVID-19 in a German liver transplant recipient cohort: a prospective serosurvey study.", + "rel_date": "2020-10-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20204537", + "rel_abs": "In liver transplant (LT) recipients with severe COVID-19 fatal outcome has been reported in a substantial subset of patients. Whether LT recipients are at increased risk for severe COVID-19 compared to the general population is controversial. Here we report the first results of a SARS-CoV-2 serosurvey in a large LT recipient cohort.\n\nTaking into account known risk factors, LT recipients a priori represented a high-risk cohort for severe COVID-19 with 101/219 (46.1 %) presenting with more than 2 risk factors for severe COVID-19. Out of 219 LT recipients 8 (3.7%) were either tested positive for nasopharyngeal SARS-CoV-2 RNA or anti-SARS-CoV-2 serum IgG. 5/8 (62.5 %) did not show any clinical signs of infection, 3/8 (37.5%) had self-limited disease, none required hospitalization for COVID-19. 5/8 (67.5%) SARS-CoV-2 positive patients showed high utilization of the healthcare system. 2/8 (25 %) had known exposure to infected health care personal. A majority of 65.4 % often or always avoided outside family social contacts. Face masks were commonly worn by all patients.\n\nIn summary, LT recipients showed a SARS-CoV-2 seroconversion rate similar to the general population with a substantial percentage of unrecognized infections. The health care system can be the assumed source of infection in most of these cases.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Conrad Rauber", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Shilpa Tiwari-Heckler", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Jan Pfeiffenberger", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Arianeb Mehrabi", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Frederike Lund", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Philip Gath", + "author_inst": "Staedtisches Klinikum Ludwigshafen" + }, + { + "author_name": "Markus Mieth", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Uta Merle", + "author_inst": "Universitaetsklinikum Heidelberg" + }, + { + "author_name": "Christian Rupp", + "author_inst": "Universitaetsklinikum Heidelberg" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2020.10.01.20204255", "rel_title": "COVID-19 Pandemic in University Hospital: Impact on Medical Training of Medical Interns", @@ -1154609,37 +1155642,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.01.20205187", - "rel_title": "Vulnerability to rumors during the COVID-19 pandemic:Results of a national survey", - "rel_date": "2020-10-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.01.20205187", - "rel_abs": "Amidst the COVID-19 pandemic, many rumors have emerged. Given prior research linking rumor exposure to mental well-being, we conducted a nation-wide survey to document the base rate of rumor exposure and factors associated with rumor vulnerability. Between March to July 2020, 1237 participants were surveyed on 5 widely-disseminated COVID-19 rumors (that drinking water frequently could be preventive, that eating garlic could be preventive, that the outbreak arose because of bat soup consumption, that the virus was created in an American lab, and that the virus was created in a Chinese lab). For each rumor, participants reported whether they had heard, shared or believed each rumor. Although most participants had been exposed to COVID-19 rumors, few shared or believed these. Sharing behaviors sometimes occurred in the absence of belief; however, education emerged as a protective factor for both sharing and belief. Together, our results suggest that campaigns targeting skills associated with higher education (e.g. epistemology) may prove more effective than counter-rumor messages.\n\nHighlightsO_LIPrior studies linked exposure to COVID-19 rumors with poor mental health.\nC_LIO_LIIn a community sample, most participants reported having heard rumors.\nC_LIO_LIFew participants shared or believed rumors.\nC_LIO_LISharing sometimes occurred in the absence of belief.\nC_LIO_LIMore educated individuals believed and shared fewer rumors.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Victoria Jane En Long", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Wei Shien Koh", - "author_inst": "Duke-NUS Medical School" - }, - { - "author_name": "Young Ern Saw", - "author_inst": "Yale-NUS College" - }, - { - "author_name": "Jean CJ Liu", - "author_inst": "Yale-NUS College" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.01.20205021", "rel_title": "Theta autoregressive neural network model for COVID-19 outbreak predictions", @@ -1154907,6 +1155909,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.02.323915", + "rel_title": "A Multiscale Coarse-grained Model of the SARS-CoV-2 Virion", + "rel_date": "2020-10-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.02.323915", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations, however, are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and on-going development of a largely \"bottom-up\" coarse-grained (CG) model of the SARS-CoV-2 virion. Structural data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data becomes publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion.\n\nSignificance StatementThis study reports the construction of a molecular model for the SARS-CoV-2 virion and details our multiscale approach towards model refinement. The resulting model and methods can be applied to and enable the simulation of SARS-CoV-2 virions.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alvin Yu", + "author_inst": "University of Chicago" + }, + { + "author_name": "Alexander J Pak", + "author_inst": "University of Chicago" + }, + { + "author_name": "Peng He", + "author_inst": "University of Chicago" + }, + { + "author_name": "Viviana Monje-Galvan", + "author_inst": "University of Chicago" + }, + { + "author_name": "Lorenzo Casalino", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Zied Gaieb", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Abigail C Dommer", + "author_inst": "University of California San Diego" + }, + { + "author_name": "Rommie E Amaro", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Gregory A Voth", + "author_inst": "University of Chicago" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.10.02.324145", "rel_title": "SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs", @@ -1156471,37 +1157524,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.09.30.20204693", - "rel_title": "Randomized Controlled Trials of Early Ambulatory Hydroxychloroquine in the Prevention of COVID-19 Infection, Hospitalization, and Death: Meta-Analysis", - "rel_date": "2020-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20204693", - "rel_abs": "ObjectiveTo determine if hydroxychloroquine (HCQ) reduces the incidence of new illness, hospitalization or death among outpatients at risk for or infected with SARS-CoV-2 (COVID-19).\n\nDesignSystematic review and meta-analysis of randomized clinical trials.\n\nData sourcesSearch of MEDLINE, EMBASE, PubMed, medRxiv, PROSPERO, and the Cochrane Central Register of Controlled Trials. Also review of reference lists from recent meta-analyses.\n\nStudy selectionRandomized clinical trials in which participants were treated with HCQ or placebo/standard-of-care for pre-exposure prophylaxis, post-exposure prophylaxis, or outpatient therapy for COVID-19.\n\nMethodsTwo investigators independently extracted data on trial design and outcomes. Medication side effects and adverse reactions were also assessed. The primary outcome was COVID-19 hospitalization or death. When unavailable, new COVID-19 infection was used. We calculated random effects meta-analysis according to the method of DerSimonian and Laird. Heterogeneity between the studies was evaluated by calculation of Cochran Q and I2 parameters. An Egger funnel plot was drawn to investigate publication bias. We also calculated the fixed effects meta-analysis summary of the five studies. All calculations were done in Excel, and results were considered to be statistically significant at a two-sided threshold of P=.05.\n\nResultsFive randomized controlled clinical trials enrolling 5,577 patients were included. HCQ was associated with a 24% reduction in COVID-19 infection, hospitalization or death, P=.025 (RR, 0.76 [95% CI, 0.59 to 0.97]). No serious adverse cardiac events were reported. The most common side effects were gastrointestinal.\n\nConclusionHydroxychloroquine use in outpatients reduces the incidence of the composite outcome of COVID-19 infection, hospitalization, and death. Serious adverse events were not reported and cardiac arrhythmia was rare.\n\nSystematic review registrationThis review was not registered.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Joseph A. Ladapo", - "author_inst": "Division of General Internal Medicine and Health Services Research, David Geffen School of Medicine at University of California, Los Angeles, CA" - }, - { - "author_name": "John E. McKinnon", - "author_inst": "Division of Infectious Diseases, Henry Ford Hospital, Detroit, MI" - }, - { - "author_name": "Peter A. McCullough", - "author_inst": "Department of Internal Medicine, Baylor University Medical Center, Baylor Heart and Vascular Institute, Baylor Jack and Jane Hamilton Heart and Vascular Hospita" - }, - { - "author_name": "Harvey Risch", - "author_inst": "Yale School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.30.20204453", "rel_title": "An integrated clinical and genetic model for predicting risk of severe COVID-19", @@ -1156745,6 +1157767,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.29.20202416", + "rel_title": "Virus evolution affected early COVID-19 spread", + "rel_date": "2020-09-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.29.20202416", + "rel_abs": "As the SARS-Cov-2 virus spreads around the world afflicting millions of people, it has undergone divergent genetic mutations. Although most of these mutations are expected to be inconsequential, some mutations in the spike protein structure have been hypothesized to affect the critical stage at which the virus invades human cells, which could affect transmission probability and disease expression. If true, then we expect an increased growth rate of reported COVID-19 cases in regions dominated by viruses with these altered proteins. We modeled early global infection dynamics based on clade assignment along with other demographic and meteorological factors previously found to be important. Clade, but not variant D614G which has been associated with increased viral load, enhanced our ability to describe early COVID-19 growth dynamics. Including clade identity in models significantly improved predictions over earlier work based only on weather and demographic variables. In particular, higher proportions of clade 19A and 19B were negatively correlated with COVID-19 growth rate, whereas higher proportions of 20A and 20C were positively correlated with growth rate. A strong interaction between the prevalence of clade 20C and relative humidity suggests that the impact of clade identity might be more important when coupled with certain weather conditions. In particular, 20C an 20A generate the highest growth rates when coupled with low humidity. Projections based on data through April 2020 suggest that, without intervention, COVID-19 has the potential to grow more quickly in regions dominated by the 20A and 20C clades, including most of South and North America.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Derek Corcoran", + "author_inst": "University of Connecticut" + }, + { + "author_name": "Mark C Urban", + "author_inst": "University of Connecticut" + }, + { + "author_name": "Jill Wegrzyn", + "author_inst": "University of Connecticut" + }, + { + "author_name": "Cory Merow", + "author_inst": "University of Connecticut" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.30.20204644", "rel_title": "Estimation of novel coronavirus (covid-19) reproduction number and case fatality rate: a systematic review and meta-analysis", @@ -1158097,125 +1159150,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.09.29.319566", - "rel_title": "Functional Landscape of SARS-CoV-2 Cellular Restriction", - "rel_date": "2020-09-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.29.319566", - "rel_abs": "A deficient interferon response to SARS-CoV-2 infection has been implicated as a determinant of severe COVID-19. To identify the molecular effectors that govern interferon control of SARS-CoV-2 infection, we conducted a large-scale gain-of-function analysis that evaluated the impact of human interferon stimulated genes (ISGs) on viral replication. A limited subset of ISGs were found to control viral infection, including endosomal factors that inhibited viral entry, nucleic acid binding proteins that suppressed viral RNA synthesis, and a highly enriched cluster of ER and Golgi-resident ISGs that inhibited viral translation and egress. These included the type II integral membrane protein BST2/tetherin, which was found to impede viral release, and is targeted for immune evasion by SARS-CoV-2 Orf7a protein. Overall, these data define the molecular basis of early innate immune control of viral infection, which will facilitate the understanding of host determinants that impact disease severity and offer potential therapeutic strategies for COVID-19.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Laura Martin-Sancho", - "author_inst": "SBP Medical Discovery Institute" - }, - { - "author_name": "Mary K Lewinski", - "author_inst": "UCSD" - }, - { - "author_name": "Lars Pache", - "author_inst": "SBP Medical Discovery Institute" - }, - { - "author_name": "Charlotte Stoneham", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "XIN YIN", - "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" - }, - { - "author_name": "Dexter Pratt", - "author_inst": "UCSD" - }, - { - "author_name": "Christopher Churas", - "author_inst": "UCSD" - }, - { - "author_name": "Sara B Rosenthal", - "author_inst": "UCSD" - }, - { - "author_name": "Sophie Liu", - "author_inst": "UCSD" - }, - { - "author_name": "Paul D De Jesus", - "author_inst": "SBP Medical Discovery Institute" - }, - { - "author_name": "Anshu P Gounder", - "author_inst": "SBP Medical Discovery Institute" - }, - { - "author_name": "Courtney Nguyen", - "author_inst": "SBP Medical Discovery Institute" - }, - { - "author_name": "Yuan Pu", - "author_inst": "SBP Medical Discovery Institute" - }, - { - "author_name": "Aaron L Oom", - "author_inst": "UCSD" - }, - { - "author_name": "Lisa Miorin", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ariel Rodriguez-Frandsen", - "author_inst": "SBP Medical Discovery Institute" - }, - { - "author_name": "Matthew Urbanowski", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Megan L Shaw", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Max W Chang", - "author_inst": "UCSD" - }, - { - "author_name": "Christopher Benner", - "author_inst": "UCSD" - }, - { - "author_name": "Matthew Frieman", - "author_inst": "University of Maryland School of Medicine" - }, - { - "author_name": "Adolfo Garcia-Sastre", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Trey Ideker", - "author_inst": "UC San Diego" - }, - { - "author_name": "Judd F. Hultquist", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "John Guatelli", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Sumit Chanda", - "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.09.30.20204503", "rel_title": "Conservative Management of Acute Appendicitis In The Era Of COVID 19: A Multicenter prospective observational study at The United Arab Emirates", @@ -1158527,6 +1159461,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2020.09.28.20200915", + "rel_title": "COVID-19 seroprevalence surveys and antibody decline - A note of caution on antibody decline", + "rel_date": "2020-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20200915", + "rel_abs": "We analyzed 21,676 residual specimens from Ontario, Canada collected between March-August, 2020 to investigate the effect of antibody decline on SARS-CoV-2 seroprevalence estimates. Testing specimens orthogonally using the Abbott (anti-nucleocapsid) and then the Ortho (anti-spike) assays, seroprevalence estimates ranged from 0.4%-1.4%, despite ongoing disease activity. The geometric mean concentration (GMC) of antibody-positive specimens decreased over time (p=0.015), and the GMC of antibody-negative specimens increased over time (p=0.0018). The association between the two tests decreased each month (p<0.001), suggesting anti-N antibody decline. Lowering the Abbott index cut-off from 1.4 to 0.7 resulted in a 16% increase in positive specimens.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Shelly Bolotin", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Vanessa Tran", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Selma Osman", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Kevin A. Brown", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Sarah A. Buchan", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Eugene Joh", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Shelley L. Deeks", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Vanessa G. Allen", + "author_inst": "Public Health Ontario" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.27.20199737", "rel_title": "High-Quality Masks Can Reduce Infections and Deaths in the US", @@ -1160059,57 +1161040,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.29.317131", - "rel_title": "De Novo Discovery of High Affinity Peptide Binders for the SARS-CoV-2 Spike Protein", - "rel_date": "2020-09-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.29.317131", - "rel_abs": "The {beta}-coronavirus SARS-CoV-2 has caused a global pandemic. Affinity reagents targeting the SARS-CoV-2 spike protein, the most exposed surface structure of the virus, are of interest for the development of therapeutics and diagnostics. We used affinity selection-mass spectrometry for the rapid discovery of synthetic high affinity peptide binders for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. From library screening with 800 million synthetic peptides, we identified three sequences with nanomolar affinities (dissociation constants Kd = 80 to 970 nM) for RBD and selectivity over human serum proteins. Picomolar RBD concentrations in biological matrix could be detected using the biotinylated lead peptide in ELISA format. These peptides might associate with the SARS-CoV-2-spike-RBD at a site unrelated to ACE2 binding, making them potential orthogonal reagents for sandwich immunoassays. We envision our discovery as a robust starting point for the development of SARS-CoV-2 diagnostics or conjugates for virus directed delivery of therapeutics.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC=\"FIGDIR/small/317131v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (35K):\norg.highwire.dtl.DTLVardef@803e9borg.highwire.dtl.DTLVardef@18e5d74org.highwire.dtl.DTLVardef@1998310org.highwire.dtl.DTLVardef@16ba5cc_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sebastian Pomplun", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Muhammad Jbara", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Anthony J. Quartararo", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Genwei Zhang", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Joseph S. Brown", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Yen-Chun Lee", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Xiyun Ye", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Stephanie Hanna", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Bradley L. Pentelute", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.09.29.20203869", "rel_title": "Brief communication: A meta-analysis of randomized trials of hydroxychloroquine for the prevention of COVID-19", @@ -1160337,6 +1161267,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.29.317289", + "rel_title": "Susceptibility of midge and mosquito vectors to SARS-CoV-2 by natural route of infection", + "rel_date": "2020-09-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.29.317289", + "rel_abs": "SARS-CoV-2 is a recently emerged, highly contagious virus and the cause of the current pandemic. It is a zoonotic virus, although its animal origin is not clear yet. Person-to-person transmission occurs by inhalation of infected droplets and aerosols, or by direct contact with contaminated fomites. Arthropods transmit numerous viral, parasitic, and bacterial diseases; however, the potential role of arthropods in SARS-CoV-2 transmission is not fully understood. Thus far, a few studies have demonstrated that SARS-CoV-2 replication is not supported in cells from certain insect species nor in certain species of mosquitoes after intrathoracic inoculation. In this study, we expanded the work of SARS-CoV-2 susceptibility to biting insects after ingesting a SARS-CoV-2infected blood meal. Species tested included Culicoides sonorensis biting midges, as well as Culex tarsalis and Culex quinquefasciatus mosquitoes, all known biological vectors for numerous RNA viruses. Arthropods were allowed to feed on SARS-CoV-2 spiked blood and at various time points post infection analyzed for the presence of viral RNA and infectious virus. Additionally, cell lines derived from C. sonorensis (W8a), Ae. aegypti (C6/36), Cx. quinquefasciatus (HSU), and Cx. tarsalis (CxTrR2) were tested for SARS-CoV-2 susceptibility. Our results indicate that none of the biting insects, nor the insect cell lines support SARS-CoV-2 replication. We conclude, that biting insect do not pose a risk for transmission of SARS-CoV-2 to humans or animals following a SARS-CoV-2 infected blood meal.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Velmurugan Balaraman", + "author_inst": "Kansas State University" + }, + { + "author_name": "Barbara S. Drolet", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Natasha N Gaudreault", + "author_inst": "Kansas State University" + }, + { + "author_name": "William C. Wilson", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Jeana Owens", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Dashzeveg Bold", + "author_inst": "Kansas State University" + }, + { + "author_name": "Dustin A Swanson", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Dane C Jasperson", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Leela E Noronha", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + }, + { + "author_name": "Juergen A Richt", + "author_inst": "Kansas State University" + }, + { + "author_name": "Dana Mitzel", + "author_inst": "United States Department of Agriculture, Agricultural Research Service" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.28.317685", "rel_title": "SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo", @@ -1161697,113 +1162686,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.27.20202168", - "rel_title": "A novel haemocytometric COVID-19 prognostic score developed and validated in an observational multicentre European hospital-based study", - "rel_date": "2020-09-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.27.20202168", - "rel_abs": "COVID-19 induces haemocytometric changes. Complete blood count changes, including new cell activation parameters, from 982 confirmed COVID-19 adult patients from 11 European hospitals were retrospectively analysed for distinctive patterns based on age, gender, clinical severity, symptom duration and hospital days. The observed haemocytometric patterns formed the basis to develop a multi-haemocytometric-parameter prognostic score to predict, during the first three days after presentation, which patients will recover without ventilation or deteriorate within a two-week timeframe, needing intensive care or with fatal outcome. The prognostic score, with ROC curve AUC at baseline of 0.753 (95% CI 0.723-0.781) increasing to 0.875 (95% CI 0.806-0.926) on day 3, was superior to any individual parameter at distinguishing between clinical severity. Findings were confirmed in a validation cohort. Aim is that the score and haemocytometry results are simultaneously provided by analyser software, enabling wide applicability of the score as haemocytometry is commonly requested in COVID-19 patients.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Joachim Linssen", - "author_inst": "Sysmex Europe GMBH, Hamburg, Germany" - }, - { - "author_name": "Anthony Ermens", - "author_inst": "Amphia Hospital Breda, the Netherlands" - }, - { - "author_name": "Marvin Berrevoets", - "author_inst": "Elisabeth-Tweesteden Hospital Tilburg, the Netherlands" - }, - { - "author_name": "Michela Seghezzi", - "author_inst": "Hospital Papa Giovanni XXIII Bergamo, Italy" - }, - { - "author_name": "Giulia Previtali", - "author_inst": "Hospital Papa Giovanni XXIII Bergamo, Italy" - }, - { - "author_name": "Simone van der Sar-van der Brugge", - "author_inst": "Amphia Hospital Breda, the Netherlands" - }, - { - "author_name": "Henk Russcher", - "author_inst": "Erasmus MC, University Medical Center, Rotterdam, the Netherlands" - }, - { - "author_name": "Annelies Verbon", - "author_inst": "Erasmus MC, University Medical Center, Rotterdam, the Netherlands" - }, - { - "author_name": "Judith M.E.P. Gillis", - "author_inst": "Leiden University Medical Center, the Netherlands" - }, - { - "author_name": "Jurgen Riedl", - "author_inst": "Albert Schweitzer Hospital Dordrecht, the Netherlands" - }, - { - "author_name": "Eva de Jongh", - "author_inst": "Albert Schweitzer Hospital Dordrecht, the Netherlands" - }, - { - "author_name": "Jarob Saker", - "author_inst": "Sysmex Europe GMBH, Hamburg, Germany" - }, - { - "author_name": "Marion Munster", - "author_inst": "Sysmex Europe GMBH, Hamburg, Germany" - }, - { - "author_name": "Imke C.A. Munnix", - "author_inst": "Canisius Wilhelmina Hospital Nijmegen, the Netherlands" - }, - { - "author_name": "Anthonius Dofferhoff", - "author_inst": "Canisius Wilhelmina Hospital Nijmegen, the Netherlands" - }, - { - "author_name": "Volkher Scharnhorst", - "author_inst": "Catharina Hospital Eindhoven, the Netherlands" - }, - { - "author_name": "Heidi Ammerlaan", - "author_inst": "Catharina Hospital Eindhoven, the Netherlands" - }, - { - "author_name": "Kathleen Deiteren", - "author_inst": "University Hospital Antwerp, Antwerp, Belgium" - }, - { - "author_name": "Stephan J.L. Bakker", - "author_inst": "University Medical Center Groningen, University of Groningen, Groningen, the Netherlands" - }, - { - "author_name": "Lucas Joost van Pelt", - "author_inst": "University Medical Center Groningen, University of Groningen, Groningen, the Netherlands" - }, - { - "author_name": "Yvette Kluiters-de Hingh", - "author_inst": "Elisabeth-Tweesteden Hospital Tilburg, the Netherlands" - }, - { - "author_name": "Mathie P.G. Leers", - "author_inst": "Zuyderland Medical Center, Sittard-Geleen, the Netherlands" - }, - { - "author_name": "Andre van der Ven", - "author_inst": "Radboud University Medical Center, Nijmegen, Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.26.20202457", "rel_title": "Strong impact of closing schools, closing bars and wearing masks during the Covid-19 pandemic: results from a simple and revealing analysis", @@ -1162031,6 +1162913,49 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.09.27.315796", + "rel_title": "A Tethered Ligand Assay to Probe the SARS-CoV-2 ACE2 Interaction under Constant Force", + "rel_date": "2020-09-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.27.315796", + "rel_abs": "The current COVID-19 pandemic has a devastating global impact and is caused by the SARS-CoV-2 virus. SARS-CoV-2 attaches to human host cells through interaction of its receptor binding domain (RBD) located on the viral Spike (S) glycoprotein with angiotensin converting enzyme-2 (ACE2) on the surface of host cells. RBD binding to ACE2 is a critical first step in SARS-CoV-2 infection. Viral attachment occurs in dynamic environments where forces act on the binding partners and multivalent interactions play central roles, creating an urgent need for assays that can quantitate SARS-CoV-2 interactions with ACE2 under mechanical load and in defined geometries. Here, we introduce a tethered ligand assay that comprises the RBD and the ACE2 ectodomain joined by a flexible peptide linker. Using specific molecular handles, we tether the fusion proteins between a functionalized flow cell surface and magnetic beads in magnetic tweezers. We observe repeated interactions of RBD and ACE2 under constant loads and can fully quantify the force dependence and kinetics of the binding interaction. Our results suggest that the SARS-CoV-2 ACE2 interaction has higher mechanical stability, a larger free energy of binding, and a lower off-rate than that of SARS-CoV-1, the causative agents of the 2002-2004 SARS outbreak. In the absence of force, the SARS-CoV-2 RBD rapidly (within [≤]1 ms) engages the ACE2 receptor if held in close proximity and remains bound to ACE2 for 400-800 s, much longer than what has been reported for other viruses engaging their cellular receptors. We anticipate that our assay will be a powerful tool investigate the roles of mutations in the RBD that might alter the infectivity of the virus and to test the modes of action of neutralizing antibodies and other agents designed to block RBD binding to ACE2 that are currently developed as potential COVID-19 therapeutics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Magnus S. Bauer", + "author_inst": "LMU Munich" + }, + { + "author_name": "Sophia Gruber", + "author_inst": "LMU Munich" + }, + { + "author_name": "Lukas F. Milles", + "author_inst": "University of Washington, Seattle" + }, + { + "author_name": "Thomas Nicolaus", + "author_inst": "LMU Munich" + }, + { + "author_name": "Leonard C. Schendel", + "author_inst": "LMU Munich" + }, + { + "author_name": "Hermann E. Gaub", + "author_inst": "LMU Munich" + }, + { + "author_name": "Jan Lipfert", + "author_inst": "LMU Munich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.09.27.316174", "rel_title": "Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach", @@ -1163159,97 +1164084,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.25.20183459", - "rel_title": "Self-sampling of capillary blood for serological testing of SARS-CoV-2 by COVID-19 IgG ELISA", - "rel_date": "2020-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20183459", - "rel_abs": "Serological testing is emerging as a powerful tool to progress our understanding of COVID-19 exposure, transmission and immune response. Large-scale testing is limited by the need for in-person blood collection by staff trained in venepuncture. Capillary blood self-sampling and postage to laboratories for analysis could provide a reliable alternative. Two-hundred and nine matched venous and capillary blood samples were obtained from thirty nine participants and analysed using a COVID-19 IgG ELISA to detect antibodies against SARS-CoV-2. Thirty seven out of thirty eight participants were able to self-collect an adequate sample of capillary blood ([≥]50 l). Using plasma from venous blood collected in lithium heparin as the reference standard, matched capillary blood samples, collected in lithium heparin-treated tubes and on filter paper as dried blood spots, achieved a Cohen's kappa coefficient of >0.88 (near-perfect agreement). Storage of capillary blood at room temperature for up to 7 days post sampling did not affect concordance. Our results indicate that capillary blood self-sampling is a reliable and feasible alternative to venepuncture for serological assessment in COVID-19.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Lottie Brown", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Rachel Louise Byrne", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Alice Fraser", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Sophie I Owen", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Ana I Cubas Atienzar", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Chris Williams", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Grant A Kay", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Luis E Cuevas", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Joseph R A Fitchett", - "author_inst": "Mologic, UK" - }, - { - "author_name": "Tom Fletcher", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Gala Garrod", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Konstantina Kontogianni", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Sanjeev Krishna", - "author_inst": "St George's University of London" - }, - { - "author_name": "Stefanie Menzies", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Tim Planche", - "author_inst": "St George's University of London" - }, - { - "author_name": "Chris Sainter", - "author_inst": "Mologic, UK" - }, - { - "author_name": "Henry M Staines", - "author_inst": "St George's University of London" - }, - { - "author_name": "Lance Turtle", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Emily R Adams", - "author_inst": "Liverpool School of Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.25.20201558", "rel_title": "Modeling COVID-19 as a National Dynamics with a SARS-CoV-2 Prevalent Variant: Brazil - A Study Case", @@ -1163437,6 +1164271,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.09.22.20195628", + "rel_title": "Public health information on COVID-19 for international travellers: Lessons learned from a rapid mixed-method evaluation in the UK containment phase", + "rel_date": "2020-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20195628", + "rel_abs": "Introduction In the containment phase of the response to the COVID-19 outbreak, Public Health England (PHE) delivered advice to travellers arriving at major UK ports. We aimed to rapidly evaluate the impact and effectiveness of these communication materials for passengers in the early stages of the pandemic. Methods In stage I (Patient and Public Involvement, PPI) we interviewed seven travellers who had returned from China in January and February 2020. We used these results to develop a questionnaire and topic guides for stage II, a cross-sectional survey and follow-up interviews with passengers arriving at London Heathrow Airport on scheduled flights from China and Singapore. The survey assessed passengers' knowledge of symptoms, actions to take and attitudes towards PHE COVID-19 public health information; interviews explored their views of official public health information and self-isolation. Results In stage II, 121 passengers participated in the survey and 15 in follow-up interviews. 83% of surveyed passengers correctly identified all three COVID-19 associated symptoms listed in PHE information at that time. Most could identify the recommended actions and found the advice understandable and trustworthy. Interviews revealed that passengers shared concerns about the lack of wider official action, and that passengers' knowledge had been acquired elsewhere as much from PHE. Respondents also noted their own agency in choosing to self-isolate, partially as a self-protective measure. Conclusion PHE COVID-19 public health information was perceived as clear and acceptable, but we found that passengers acquired knowledge from various sources and they saw the provision of information alone on arrival as an insufficient official response. Our study provides fresh insights into the importance of taking greater account of diverse information sources and of the need for public assurance in creating public health information materials to address global health threats. Keywords COVID-19, public health advice, government, policy, airport, international travel", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tingting Zhang", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK" + }, + { + "author_name": "Charlotte Robin", + "author_inst": "Field Epidemiology, Field Service, National Infection Service, Public Health England, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science a" + }, + { + "author_name": "Shenghan Cai", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK" + }, + { + "author_name": "Clare Sawyer", + "author_inst": "UK Field Epidemiology Training Programme, Global Public Health Division, Public Health England, London, UK; Communicable Disease Surveillance Centre, Public Hea" + }, + { + "author_name": "Wendy Rice", + "author_inst": "Field Epidemiology, Field Service, National Infection Service, Public Health England, Bristol, UK" + }, + { + "author_name": "Louise E. Smith", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Health Protection Research Unit in Emergency Preparedness and Resp" + }, + { + "author_name": "Richard Aml\u00f4t", + "author_inst": "NIHR Health Protection Research Unit in Behavioural Science and Evaluation, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Health Protection R" + }, + { + "author_name": "G. James Rubin", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Health Protection Research Unit in Emergency Preparedness and Resp" + }, + { + "author_name": "Rosy Reynolds", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluati" + }, + { + "author_name": "Lucy Yardley", + "author_inst": "Health Protection Research Unit in Behavioural Science and Evaluation, Bristol Medical School, University of Bristol, Bristol, UK; School of Psychological Scien" + }, + { + "author_name": "Matthew Hickman", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluati" + }, + { + "author_name": "Isabel Oliver", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol; Field Epidemiology, Field Service, National Infection Service, Public Health England;" + }, + { + "author_name": "Helen Lambert", + "author_inst": "Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK; NIHR Health Protection Research Unit in Behavioural Science and Evaluati" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.23.20200212", "rel_title": "Impact of Personal Care Habits on Post-Lockdown COVID-19 Contagion: Insights from Agent-based Simulations", @@ -1164981,41 +1165882,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2020.09.24.20200436", - "rel_title": "When it is available, will we take it? Public perception of hypothetical COVID-19 vaccine in Nigeria", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20200436", - "rel_abs": "COVID-19 pandemic is a global public health threat facing mankind. There is no specific antiviral treatment for COVID-19, and no vaccine is currently available. This study aims to understand the perception of the public towards hypothetical COVID-19 vaccine in Nigeria. We conducted a cross-sectional survey in August 2020 across the 36 states of Nigeria using an online questionnaire. The questionnaire includes sections on the demographic characteristics of the respondents and their perception regarding hypothetical COVID-19 vaccine. A total of 517 respondents completed and returned the informed consent along with the questionnaire electronically. Data were coded and abstracted into the Microsoft Excel spreadsheet and loaded into the STATA 14 software for final analysis. The results showed that more than half of the respondents were male 294 (56.87%). Most of the respondents (385, 74.47%) intend to take the COVID-19 vaccine when it becomes available. Among the 132 respondents that would not take the COVID-19 vaccine, the major reason for non-acceptance is unreliability of the clinical trials 49 (37.12%), followed by the belief that their immune system is sufficient to combat the virus 36 (27.27%). There are significant association with the respondents age and having reservations toward vaccination [{chi}2= 19.0389 P-value=0.00] and COVID-19 vaccine acceptance [{chi}2=24.3316 P-value=0.00]. Furthermore, geographical location and acceptance of the COVID-19 vaccine [{chi}2=13.7786 P-value=0.02] are significantly associated. Even though the majority of our respondents are willing to take the COVID-19 vaccine, our findings reiterate the need to reassure the public that any vaccine which becomes available is safe and effective.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yusuff Adebayo Adebisi", - "author_inst": "University of Ibadan, Ibadan, Nigeria" - }, - { - "author_name": "Aishat Jumoke Alaran", - "author_inst": "Faculty of Pharmaceutical Sciences, University of Ilorin, Ilorin, Nigeria" - }, - { - "author_name": "Obasanjo Afolabi Bolarinwa", - "author_inst": "University of Kwazulu-Natal, Durban" - }, - { - "author_name": "Wuraola Akande-Sholabi", - "author_inst": "University of Ibadan, Ibadan, Nigeria" - }, - { - "author_name": "Don Eliseo Lucero-Prisno III", - "author_inst": "London School of Hygiene and Tropical Medicine, London, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.24.20201178", "rel_title": "Face Masks, Public Policies and Slowing the Spread of COVID-19: Evidence from Canada", @@ -1165179,6 +1166045,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.25.20201459", + "rel_title": "Performance of a point of care test for detecting IgM and IgG antibodies against SARS-CoV-2 and seroprevalence in blood donors and health care workers in Panama", + "rel_date": "2020-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20201459", + "rel_abs": "Novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic, which has reached 28 million cases worldwide in eight months. The serological detection of antibodies against the virus will play a pivotal role in complementing molecular tests to improve diagnostic accuracy, contact tracing, vaccine efficacy testing and seroprevalence surveillance. Here, we aimed first to evaluate a lateral flow assays ability to identify specific IgM and IgG antibodies against SARS-CoV-2 and second, to report the seroprevalence of these antibodies among health care workers and healthy volunteer blood donors in Panama. We recruited study participants between April 30th and July 7th, 2020. For the test validation and performance evaluation, we analyzed serum samples from participants with clinical symptoms and confirmed positive RT-PCR for SARS-CoV-2, participants with other confirmed infectious diseases, and a set of pre-pandemic serum samples. We used two by two table analysis to determine the test sensitivity and specificity as well as the kappa agreement value with a 95% confidence interval. Then, we used the lateral flow assay to determine seroprevalence among serum samples from COVID-19 patients, potentially exposed health care workers, and healthy volunteer donors. Our results show this assay reached a positive percent agreement of 97.2% (95% CI 84.2-100.0%) for detecting both IgM and IgG. The assay showed a kappa of 0.898 (95%CI 0.811-0.985) and 0.918 (95% CI 0.839-0.997) for IgM and IgG, respectively. The evaluation of serum samples from hospitalized COVID-19 patients indicates a correlation between test sensitivity and the number of days since symptom onset; the highest positive percent agreement (87% (95% CI 67.0-96.3%)) was observed at [≥]15 days post-symptom onset. We found an overall antibody seroprevalence of 11.6% (95% CI 8.5-15.8%) among both health care workers and healthy blood donors. Our findings suggest this lateral flow assay could contribute significantly to implementing seroprevalence testing in locations with active community transmission of SARS-CoV-2.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Alcibiades Villarreal", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Giselle Rangel", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Xu Zhang", + "author_inst": "CAS" + }, + { + "author_name": "Digna Wong", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Carolina De La Guardia", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Gabrielle Britton", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Patricia L. Fernandez", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Carlos M Restrepo", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Ambar Perez", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Diana Oviedo", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Maria B Carreira", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Gilberto A. Eskildsen", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Dilcia Sambrano", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Yamitzel Zaldivar", + "author_inst": "GORGAS" + }, + { + "author_name": "Danilo Franco", + "author_inst": "GORGAS" + }, + { + "author_name": "Sandra Lopez Verges", + "author_inst": "GORGAS" + }, + { + "author_name": "Dexi Zhang", + "author_inst": "CAS" + }, + { + "author_name": "Fangjing Fan", + "author_inst": "CAS" + }, + { + "author_name": "Baojun Wang", + "author_inst": "KEWEI" + }, + { + "author_name": "Xavier Saez-Llorens", + "author_inst": "CEVAXIN" + }, + { + "author_name": "Rodrigo DeAntonio", + "author_inst": "CEVAXIN" + }, + { + "author_name": "Ivonne Torres-Atencio", + "author_inst": "UP" + }, + { + "author_name": "Fernando Diaz Subia", + "author_inst": "Pacifica Salud" + }, + { + "author_name": "Eduardo Ortega-Barria", + "author_inst": "GSK" + }, + { + "author_name": "Rao Kosagisharaf", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Ricardo Lleonart", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "Chong Li", + "author_inst": "CAS" + }, + { + "author_name": "Amador Goodridge", + "author_inst": "INDICASAT-AIP" + }, + { + "author_name": "- COVID-19 SEROLOGY COLLABORATOR GROUP", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.24.20200394", "rel_title": "Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer", @@ -1166571,41 +1167568,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.23.20199463", - "rel_title": "Comparative Effectiveness of Famotidine in Hospitalized COVID-19 Patients", - "rel_date": "2020-09-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.23.20199463", - "rel_abs": "BackgroundFamotidine has been posited as a potential treatment for COVID-19. We compared the incidence of COVID-19 outcomes (i.e., death; and death or intensive services use) among hospitalized famotidine users vs. proton pump inhibitors (PPIs) users, hydroxychloroquine users or famotidine non-users separately.\n\nMethodsWe constructed a retrospective cohort study using data from COVID-19 Premier Hospital electronic health records. Study population were COVID-19 hospitalized patients aged 18 years or older. Famotidine, PPI and hydroxychloroquine exposure groups were defined as patients dispensed any medication containing one of the three drugs on the day of admission. The famotidine non-user group was derived from the same source population with no history of exposure to any drug with famotidine as an active ingredient prior to or on the day of admission. Time-at-risk was defined based on the intention-to-treat principle starting 1 day after admission to 30 days after admission. For each study comparison group, we fit a propensity score (PS) model through large-scale regularized B logistic regression. The outcome was modeled using a survival model.\n\nResultsWe identified 2193 users of PPI, 5950 users of the hydroxychloroquine, 1816 users of famotidine and 26,820 non-famotidine users. After PS stratification, the hazard ratios for death were as follows: famotidine vs no famotidine HR 1.03 (0.89-1.18); vs PPIs: HR 1.14 (0.94-1.39); vs hydroxychloroquine:1.03 (0.85-1.24). Similar results were observed for the risk of death or intensive services use.\n\nConclusionWe found no evidence of a reduced risk of COVID-19 outcomes among hospitalized COVID-19 patients who used famotidine compared to those who did not or compared to PPI or hydroxychloroquine users.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Azza Shoaibi", - "author_inst": "Janssen Research & Development, LLC, Titusville, NJ, USA" - }, - { - "author_name": "Stephen Fortin", - "author_inst": "Janssen Research & Development, LLC, Titusville, NJ, USA" - }, - { - "author_name": "Rachel Weinstein", - "author_inst": "Janssen Research & Development, LLC, Titusville, NJ, USA" - }, - { - "author_name": "Jesse Berlin", - "author_inst": "Johnson & Johnson" - }, - { - "author_name": "Patrick Ryan", - "author_inst": "Janssen Research & Development, LLC, Titusville, NJ, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2020.09.22.20197046", "rel_title": "Performance Assessment of First-Generation AntiSARS-CoV-2 Serological Assays", @@ -1166901,6 +1167863,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.09.23.310565", + "rel_title": "COVID-19 CG: Tracking SARS-CoV-2 mutations by locations and dates of interest", + "rel_date": "2020-09-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.23.310565", + "rel_abs": "COVID-19 CG is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs) and lineages while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides significant time, labor, and cost-saving utility to diverse projects on SARS-CoV-2 transmission, evolution, emergence, immune interactions, diagnostics, therapeutics, vaccines, and intervention tracking. Here, we describe case studies in which users can interrogate (1) SNVs in the SARS-CoV-2 Spike receptor binding domain (RBD) across different geographic regions to inform the design and testing of therapeutics, (2) SNVs that may impact the sensitivity of commonly used diagnostic primers, and (3) the recent emergence of a dominant lineage harboring an S477N RBD mutation in Australia. To accelerate COVID-19 research and public health efforts, COVID-19 CG will be continually upgraded with new features for users to quickly and reliably pinpoint mutations as the virus evolves throughout the pandemic and in response to therapeutic and public health interventions.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Albert Tian Chen", + "author_inst": "Broad Institute of MIT & Harvard" + }, + { + "author_name": "Kevin Altschuler", + "author_inst": "NA" + }, + { + "author_name": "Shing Hei Zhan", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Yujia Alina Chan", + "author_inst": "Broad Institute of MIT & Harvard" + }, + { + "author_name": "Benjamin E Deverman", + "author_inst": "Broad Institute of MIT and Harvard" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.09.24.310490", "rel_title": "Broad-spectrum, patient-adaptable inhaled niclosamide-lysozyme particles are efficacious against coronaviruses in lethal murine infection models", @@ -1168417,33 +1169414,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.20.20198366", - "rel_title": "The ground level ozone concentration is inversely correlated with the number of COVID-19 cases in Warsaw, Poland", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.20.20198366", - "rel_abs": "COVID-19, which is a consequence of infection with the novel viral agent SARS-CoV-2, first identified in China (Hubei Province), has been declared a pandemic by the WHO. As of September 10, 2020, over 70,000 cases and over 2,000 deaths have been recorded in Poland. Of the many factors contributing to the level of transmission of the virus, the weather appears to be significant. In this work we analyse the impact of weather factors such as temperature, relative humidity, wind speed and ground level ozone concentration on the number of COVID-19 cases in Warsaw, Poland. The obtained results show an inverse correlation between ground level ozone concentration and the daily number of COVID-19 cases.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Oskar Wisniewski", - "author_inst": "Department of Immunology, Nicolaus Copernicus University in Torun" - }, - { - "author_name": "Wieslaw Kozak", - "author_inst": "Department of Immunology, Nicolaus Copernicus University in Torun" - }, - { - "author_name": "Maciej Wisniewski", - "author_inst": "ImmQuest" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.22.20199174", "rel_title": "Optimal Dynamic Prioritization of Scarce COVID-19 Vaccines", @@ -1168647,6 +1169617,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2020.09.22.20198465", + "rel_title": "Seroprevalence of immunoglobulin M and G antibodies against SARS-CoV-2 in ophthalmic patients", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20198465", + "rel_abs": "Using serological test to estimate the prevalence and infection potential of coronavirus disease 2019 in ocular diseases patients help understand the relationship between ocular diseases and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We conducted a cross-sectional study assaying the IgG and IgM antibodies in 1331 individuals with ocular diseases by using a magnetic chemiluminescence enzyme immunoassay kit, during the period from February 2020 to May 2020. In our study, the seroposivity in total ocular disease patients was 0.83% (11/1331). The patients with different ocular diseases including xerophthalmia, keratitis, conjunctival cyst, cataract, glaucoma, refractive error, strabismus and others had seroposivity of 2.94%, 12.5%, 25%, 4.41%, 2.63%, 1.6%, 2.22% and 0%, respectively. Among that, two ocular surface disease groups (keratitis and conjunctival cyst) had higher seroprevalence compared with others. All the participants were reverse transcription polymerase chain reaction negative for SARS-CoV-2 from throat swabs. Our study evaluated the seroprevalence in patients with different ocular diseases, which will help us understand the relationship between ocular disease and SARS-CoV-2 infection. Furthermore, the serological test for the presence of IgM and/or IgG antibodies against SARS-CoV-2 might provide accurate estimate of the prevalence of SARS-CoV-2 infection in patients with ocular diseases.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "shengjie li Sr.", + "author_inst": "Fudan University" + }, + { + "author_name": "yichao qiu", + "author_inst": "fudan university" + }, + { + "author_name": "li tang", + "author_inst": "fudan university" + }, + { + "author_name": "zhujian wang", + "author_inst": "fudan university" + }, + { + "author_name": "wenjun cao", + "author_inst": "fudan university" + }, + { + "author_name": "xinghuai sun", + "author_inst": "fudan university" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.20.20198432", "rel_title": "COVID-19 dynamics across the US: A deep learning study of human mobility and social behavior", @@ -1170235,29 +1171244,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.21.20196725", - "rel_title": "An expert judgment model to predict early stages of the COVID-19 outbreak in the United States", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.21.20196725", - "rel_abs": "During early stages of the COVID-19 pandemic, forecasts provided actionable information about disease transmission to public health decision-makers. Between February and May 2020, experts in infectious disease modeling made weekly predictions about the impact of the pandemic in the U.S. We aggregated these predictions into consensus predictions. In March and April 2020, experts predicted that the number of COVID-19 related deaths in the U.S. by the end of 2020 would be in the range of 150,000 to 250,000, with scenarios of near 1m deaths considered plausible. The wide range of possible future outcomes underscored the uncertainty surrounding the outbreak's trajectory. Experts' predictions of measurable short-term outcomes had varying levels of accuracy over the surveys but showed appropriate levels of uncertainty when aggregated. An expert consensus model can provide important insight early on in an emerging global catastrophe.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Thomas Charles McAndrew", - "author_inst": "University of Massachusetts at Amherst" - }, - { - "author_name": "Nicholas G Reich", - "author_inst": "University of Massachusetts at Amherst" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.22.20128140", "rel_title": "Subclinical ocular inflammation in persons recovered from ambulatory COVID-19", @@ -1170481,6 +1171467,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.09.20.20197608", + "rel_title": "At home and online during the early months of the COVID-19 pandemic and the relationship to alcohol consumption in a national sample of U.S. adults", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.20.20197608", + "rel_abs": "ObjectiveThe current study seeks to understand the links between social media use and alcohol consumption during the early months of the COVID-19 pandemic.\n\nMethodData were from the national Understanding American Study, a probability-based Internet panel weighted to represent the U.S. population. Subjects (N=5874; 51% female) were adults, 18 years and older, who completed a March survey (wave 1) and a follow-up survey one month later (wave 3). Analyses assessed the relationship of social media use at wave 1 with wave 3 alcohol use, accounting for wave 1 alcohol use and the sociodemographic characteristics of the sample. We examined the effect of working or studying from home as a moderator.\n\nResultsTwitter and Instagram users, but not Facebook users, drank more frequently at wave 3 than non-users. For Instagram users, more frequent alcohol use at wave 3 was at least partially attributed to the frequency of drinking at wave 1. The interaction between Twitter use and working or studying from home was statistically significant. The combination of being on Twitter and working or studying from home was associated with drinking more days a week.\n\nConclusionsExposure to content about COVID-19 and increased alcohol consumption during the pandemic may contribute to more frequent alcohol use for some social media users, especially those sheltering at home. The study of public health messaging via social media to change alcohol use behaviors during traumatic events is warranted.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Karen G Chartier", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Jeanine P.D. Guidry", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Catherine A. Lee", + "author_inst": "George Mason University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "addiction medicine" + }, { "rel_doi": "10.1101/2020.09.20.20196907", "rel_title": "Microfluidic Affinity Profiling reveals a Broad Range of Target Affinities for Anti-SARS-CoV-2 Antibodies in Plasma of Covid Survivors", @@ -1172021,85 +1173034,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.21.299776", - "rel_title": "An automatic pipeline for the design of irreversible derivatives identifies a potent SARS-CoV-2 Mpro inhibitor.", - "rel_date": "2020-09-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.21.299776", - "rel_abs": "Designing covalent inhibitors is a task of increasing importance in drug discovery. Efficiently designing irreversible inhibitors, though, remains challenging. Here, we present covalentizer, a computational pipeline for creating irreversible inhibitors based on complex structures of targets with known reversible binders. For each ligand, we create a custom-made focused library of covalent analogs. We use covalent docking, to dock these tailored covalent libraries and to find those that can bind covalently to a nearby cysteine while keeping some of the main interactions of the original molecule. We found ~11,000 cysteines in close proximity to a ligand across 8,386 protein-ligand complexes in the PDB. Of these, the protocol identified 1,553 structures with covalent predictions. In prospective evaluation against a panel of kinases, five out of nine predicted covalent inhibitors showed IC50 between 155 nM - 4.2 M. Application of the protocol to an existing SARS-CoV-1 Mpro reversible inhibitor led to a new acrylamide inhibitor series with low micromolar IC50 against SARS-CoV-2 Mpro. The docking prediction was validated by 11 co-crystal structures. This is a promising lead series for COVID-19 antivirals. Together these examples hint at the vast number of covalent inhibitors accessible through our protocol.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Daniel Zaidman", - "author_inst": "The Weizmann Institute of Science" - }, - { - "author_name": "Paul Gehrtz", - "author_inst": "The Weizmann Institute of Science" - }, - { - "author_name": "Mihajlo Filep", - "author_inst": "The Weizmann Institute of Science" - }, - { - "author_name": "Daren Fearon", - "author_inst": "Diamond Light Source Ltd" - }, - { - "author_name": "Jaime Prilusky", - "author_inst": "The Weizmann Institute of Science" - }, - { - "author_name": "Shirly Duberstein", - "author_inst": "Diamond Light Source Ltd" - }, - { - "author_name": "Galit Cohen", - "author_inst": "The Weizmann Institute of Science" - }, - { - "author_name": "David Owen", - "author_inst": "Diamond Light Source Ltd" - }, - { - "author_name": "Efrat Resnick", - "author_inst": "The Weizmann Institute of Science" - }, - { - "author_name": "Claire Strain-Damerell", - "author_inst": "Diamond Light Source Ltd" - }, - { - "author_name": "Petra Lukacik", - "author_inst": "Diamond Light Source Ltd" - }, - { - "author_name": "- Covid-Moonshot Consortium", - "author_inst": "-" - }, - { - "author_name": "Haim Barr", - "author_inst": "The Weizmann Institute of Science" - }, - { - "author_name": "Martin A. Walsh", - "author_inst": "Diamond Light Source Ltd" - }, - { - "author_name": "Frank von Delft", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nir London", - "author_inst": "The Weizmann Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.09.22.20199331", "rel_title": "Experiences of receiving and providing maternity care during the COVID-19 Pandemic in Australia: a five-cohort cross-sectional comparison", @@ -1172271,6 +1173205,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.22.20199372", + "rel_title": "Limits and opportunities of SARS-CoV-2 antigen rapid Tests: an experience based perspective", + "rel_date": "2020-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.22.20199372", + "rel_abs": "Due to the currently increasing case numbers of SARS-CoV-2 infections worldwide there is an increasing need for rapid diagnostic devices in addition to existing PCR-capacities. Therefore, rapid antigen assays including lateral flow assays are discussed as an alternative method. In comparison to an established RT-PCR protocol, however the novel lateral flow assay unfortunately lowered the expectations set in these assays.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Verena Schildgen", + "author_inst": "Kliniken der Stadt Koeln gGmbH, Klinikum der Privaten Universitaet Witten/Herdecke" + }, + { + "author_name": "Sabrina Demuth", + "author_inst": "Kliniken der Stadt Koeln" + }, + { + "author_name": "Jessica Lusebrink", + "author_inst": "Kliniken der Stadt Koeln" + }, + { + "author_name": "Oliver Schildgen", + "author_inst": "Kliniken der Stadt Koeln gGmbH, Klinikum der Privaten Universtaet Witten/Herdecke" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.21.20199133", "rel_title": "Reorganization of Substance Use Treatment and Harm Reduction Services during the COVID-19 Pandemic: A Global Survey", @@ -1173730,49 +1174695,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.17.20196444", - "rel_title": "COMPARATIVE ANALYSIS OF COVID-19 MORTALITY IN BRAZIL, RIO DE JANEIRO, CAMPOS DOS GOYTACAZES, MACAE, CABO FRIO AND RIO DAS OSTRAS", - "rel_date": "2020-09-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20196444", - "rel_abs": "Objective: To analyze quantitatively and comparatively the deaths by COVID-19 of the four largest municipalities in the North of Rio de Janeiro and Baixada Litoranea of Rio de Janeiro, within the national context. Methods: We used data from the Civil Registry and demographic information to elaborate a general picture of the pandemic up to the 31st epidemiological week in several aspects: evolution, scope, age, sex, race and impact on other causes of death. Results: We characterized the evolution of the pandemic. We found an exponential dependence on the mortality rate by age and a higher lethality in the male population. We determined that COVID-19 represents an important fraction of the causes of death in 2020, being associated with a significant excess of deaths in relation to 2019 and also with the change in mortality patterns due to other causes. Conclusion: Mortality is an effective and powerful indicator for understanding the infection and its pandemic, and it must be taken into account during the construction of public policies to deal with it.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Antonio C. C. Guimar\u00e3es", - "author_inst": "Universidade Federal do Rio de Janeiro" - }, - { - "author_name": "Karla Santa Cruz Coelho", - "author_inst": "Universidade Federal do Rio de Janeiro" - }, - { - "author_name": "Kathleen Tereza da Cruz", - "author_inst": "Universidade Federal do Rio de Janeiro" - }, - { - "author_name": "B\u00e1rbara Soares de Oliveira Souza", - "author_inst": "Universidade Federal do Rio de Janeiro" - }, - { - "author_name": "Janimayri Forastieri de Almeida", - "author_inst": "Universidade Federal do Rio de Janeiro" - }, - { - "author_name": "Gustavo Fialho Coelho", - "author_inst": "Universidade Federal do Rio de Janeiro" - }, - { - "author_name": "Gabriella Ramos Lacerda Ferreira", - "author_inst": "Universidade Federal Fluminense" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.20.300574", "rel_title": "Common genetic variation in humans impacts in vitro susceptibility to SARS-CoV-2 infection", @@ -1174076,6 +1174998,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.20.297242", + "rel_title": "Comparative analysis reveals the species-specific genetic determinants of ACE2 required for SARS-CoV-2 entry", + "rel_date": "2020-09-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.20.297242", + "rel_abs": "Coronavirus interaction with its viral receptor is a primary genetic determinant of host range and tissue tropism. SARS-CoV-2 utilizes ACE2 as the receptor to enter host cell in a species-specific manner. We and others have previously shown that ACE2 orthologs from New World monkey, koala and mouse cannot interact with SARS-CoV-2 to mediate viral entry, and this defect can be restored by humanization of the restrictive residues in New World monkey ACE2. To better understand the genetic determinants behind the ability of ACE2 orthologs to support viral entry, we compared koala and mouse ACE2 sequences with that of human and identified the key residues in koala and mouse ACE2 that restrict viral receptor activity. Humanization of these critical residues rendered both koala and mouse ACE2 capable of binding the spike protein and facilitating viral entry. The single mutation that allowed for mouse ACE2 to serve as a viral receptor provides a potential avenue for the development of SARS-CoV-2 mouse model.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Wenlin Ren", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Gaowei Hu", + "author_inst": "Fudan University" + }, + { + "author_name": "Xiaomin Zhao", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Yuyan Wang", + "author_inst": "Fudan University" + }, + { + "author_name": "Hongyang Shi", + "author_inst": "Institut Pasteur of Shanghai, Chinese Academy of Sciences" + }, + { + "author_name": "Jun Lan", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Yunkai Zhu", + "author_inst": "Fudan University" + }, + { + "author_name": "Jianping Wu", + "author_inst": "Westlake University" + }, + { + "author_name": "Devin J. Kenney", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Douam Florian", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Yimin Tong", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Jin Zhong", + "author_inst": "Institut Pasteur of Shanghai" + }, + { + "author_name": "Youhua Xie", + "author_inst": "Fudan University" + }, + { + "author_name": "Xinquan Wang", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Zhenghong Yuan", + "author_inst": "Fudan University" + }, + { + "author_name": "Dongming Zhou", + "author_inst": "School of Basic Medical Sciences, Tianjin Medical University" + }, + { + "author_name": "Rong Zhang", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Qiang Ding", + "author_inst": "Tsinghua University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.21.306357", "rel_title": "Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19", @@ -1175184,41 +1176193,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "dentistry and oral medicine" }, - { - "rel_doi": "10.1101/2020.09.15.20194795", - "rel_title": "Acute, non-COVID related medical admissions during the first wave of COVID-19: A retrospective comparison of changing patterns of disease", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20194795", - "rel_abs": "BackgroundThe COVID-19 pandemic was associated with social restrictions in the UK from 16th March 2020. It was unclear if the lockdown period was associated with differences in the case-mix of non-COVID acute medical admissions compared with the previous year.\n\nMethodsRetrospective data were collected for 1st-30th April 2019 and 1st-30th April 2020 from University Hospitals Birmingham NHS Foundation Trust, one of the largest hospitals in the UK with over 2 million patient contacts per year. The latter time period was chosen to coincide with the peak of COVID-19 cases in the West Midlands. All patients admitted under acute medicine during these time periods were included. COVID-19 was confirmed by SARS-Cov-2 swab or a probable case of COVID-19 based on World Health Organization diagnostic parameters. Non-COVID patients were those with a negative SARS-Cov-2 swab and no suspicion of COVID-19. Data was sourced from UHBs in-house electronic health system (EHS).\n\nResultsThe total number of acute medical admissions fell comparing April 2019 (n = 2409) to April 2020 (n = 1682). As a proportion of total admissions, those aged under 45 years decreased, while those aged 46 and over did not change.\n\nThe number of admissions due to psychiatric conditions and overdoses was higher in April 2020 (p < 0.001). When viewed as a proportion of admissions, alcohol-related admissions (p = 0.004), psychiatric conditions and overdoses (p< 0.001) increased in April 2020 than in April 2019. The proportion of patients who were in hospital due to falls also increased in April 2020 (p< 0.001). In the same period, the absolute number and the proportion of admissions that were due to non-specific chest pain, to musculoskeletal complaints and patients who self-discharged prior to assessment decreased (p = 0.02, p = 0.01 and p = 0.002 respectively).\n\nThere were no significant differences in non-COVID-related intensive care admissions or mortality between the same months in the two years.\n\nConclusionIn this large, single-centre study, there was a change in hospitalised case-mix when comparing April 2019 with April 2020: an increase in conditions which potentially reflect social isolation (falls, drug and alcohol misuse and psychiatric illness) and a decrease in conditions which rarely require in-patient hospital treatment (musculoskeletal pain and non-cardiac chest pain) especially among younger adults. These results highlight two areas for further research; the impact of social isolation on health and whether younger adults could be offered alternative health services to avoid potentially unnecessary hospital assessment.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Bridget Riley", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Mary Packer", - "author_inst": "University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Suzy Gallier", - "author_inst": "PIONEER Hub, University Hospitals Birmingham NHS Foundation Trust" - }, - { - "author_name": "Elizabeth Sapey", - "author_inst": "PIONEER Hub, University of Birmingham" - }, - { - "author_name": "Catherine Atkin", - "author_inst": "PIONEER Hub, University of Birmingham" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.09.15.20194811", "rel_title": "Disease control as an optimization problem", @@ -1175410,6 +1176384,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.15.20194258", + "rel_title": "COVID-19 epidemic severity is associated with timing of non-pharmaceutical interventions", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20194258", + "rel_abs": "Background: Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. International comparisons are hampered by highly variable conditions under which epidemics spread and differences in the timing and scale of interventions. Cumulative COVID-19 morbidity and mortality are functions of both the rate of epidemic growth and the duration of uninhibited growth before interventions were implemented. Incomplete and sporadic testing during the early COVID-19 epidemic makes it difficult to identify how long SARS-CoV-2 was circulating in different places. SARS-CoV-2 genetic sequences can be analyzed to provide an estimate of both the time of epidemic origin and the rate of early epidemic growth in different settings. Methods: We carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates were cross-referenced with dates of the most stringent interventions in each location as well as the number of cumulative COVID-19 deaths following maximum intervention. Phylodynamic methods were used to estimate the rate of early epidemic growth and proxy estimates of epidemic size. Findings: The time elapsed between epidemic origin and maximum intervention is strongly associated with different measures of epidemic severity and explains 46% of variance in numbers infected at time of maximum intervention. The reproduction number is independently associated with epidemic severity. In multivariable regression models, epidemic severity was not associated with census population size. The time elapsed between detection of initial COVID-19 cases to interventions was not associated with epidemic severity, indicating that many locations experienced long periods of cryptic transmission. Interpretation: Locations where strong non-pharmaceutical interventions were implemented earlier experienced much less severe COVID-19 morbidity and mortality during the period of study.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Manon Ragonnet-Cronin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Olivia Boyd", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lily Geidelberg", + "author_inst": "Imperial College London" + }, + { + "author_name": "David Jorgensen", + "author_inst": "Imperial College London" + }, + { + "author_name": "Fabricia F Nascimento", + "author_inst": "Imperial College London" + }, + { + "author_name": "Igor Siveroni", + "author_inst": "Imperial College London" + }, + { + "author_name": "Robert Johnson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marc Baguelin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Zulma M Cucunuba", + "author_inst": "Imperial College London" + }, + { + "author_name": "Elita Jauneikaite", + "author_inst": "Imperial College London" + }, + { + "author_name": "Swapnil Mishra", + "author_inst": "Imperial College London" + }, + { + "author_name": "Hayley A Thompson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver J Watson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Neil Ferguson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christl A Donnelly", + "author_inst": "Imperial College London; University of Oxford" + }, + { + "author_name": "Erik Volz", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.14.20194589", "rel_title": "Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves", @@ -1176986,57 +1178039,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.17.20192088", - "rel_title": "The impact of the SARS-CoV-2 pandemic on healthcare provision in Italy to non-COVID patients: a systematic review", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20192088", - "rel_abs": "BackgroundItaly has been one of the countries most affected by the SARS-CoV-2 pandemic and the regional healthcare system has had to quickly adapt its organization to meet the needs of infected patients. This has led to a drastic change in the routine management of non-communicable diseases with a potential long-term impact on patient health care. We investigated the management of non-COVID-19 patients across all medical specialties during the pandemic in Italy.\n\nMethodsA PRISMA guideline-based systematic review of the available literature was performed using PubMed, Embase, and Scopus, restricting the search to the main outbreak period in Italy (from 20 February to 22 June, 2020). We selected articles in English or Italian that detailed changes in the Italian hospital care for non-COVID-19 patients due to the pandemic. Our keywords included all medical specialties in combination with our geographical focus (Italy) and COVID-19.\n\nFindingsOf the 4643 potentially eligible studies identified by the search, 247 studies were included in the systematic review. A decrease in the management of emergencies in non-COVID patients was found together with an increase in mortality. Similarly, non-deferrable conditions met a tendency toward decreased diagnosis. All specialties have been affected by the reorganization of healthcare provision in the hub-and-spoke system and have benefited from telemedicine during the pandemic.\n\nInterpretationOur work highlights the changes taking place in the Italian public healthcare system in order to tackle the developing health crisis due to the COVID-19 pandemic. The findings of our review may be useful to analyze future directions for the healthcare system in the case of new pandemic scenarios.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Gianmarco Lugli", - "author_inst": "Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy" - }, - { - "author_name": "Matteo Maria Ottaviani", - "author_inst": "Sant'Anna School of Avdanced Studies, Pisa, Italy" - }, - { - "author_name": "Annarita Botta", - "author_inst": "Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy" - }, - { - "author_name": "Guido Ascione", - "author_inst": "Department of Cardiac Surgery, IRCCS San Raffaele Hospital, Vita-Salute San Raffaele University, Milan, Italy" - }, - { - "author_name": "Alessandro Bruschi", - "author_inst": "Rizzoli Orthopaedic Insititute, University of Bologna, Bologna, Italy" - }, - { - "author_name": "Federico Cagnazzo", - "author_inst": "Department of Neuroradiology, Hopital Gui de Chauliac, Montpellier" - }, - { - "author_name": "Zammarchi Lorenzo", - "author_inst": "Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy." - }, - { - "author_name": "Paola Romagnani", - "author_inst": "Nephrology and Dialysis Unit, Department of Pediatrics, Meyer Children's University Hospital, Florence, Italy" - }, - { - "author_name": "Tommaso Portaluri", - "author_inst": "CEST Centre for Excellence and Transdisciplinary Studies, Turin, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.16.20195966", "rel_title": "Social distancing: barriers to its implementation and how they can be overcome - a rapid systematic review and synthesis of qualitative studies", @@ -1177344,6 +1178346,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.09.16.20195685", + "rel_title": "Integrative Genomics Analysis Reveals a Novel 21q22.11 Locus Contributing to Susceptibility of COVID-19", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20195685", + "rel_abs": "The systematic identification of host genetic risk factors is essential for the understanding and treatment of COVID-19. By performing a meta-analysis of two independent genome-wide association (GWAS) summary datasets (N = 680,128), a novel locus at 21q22.11 was identified to be associated with COVID-19 infection (rs9976829 in IFNAR2 and upstream of IL10RB, OR = 1.16, 95% CI = 1.09 - 1.23, P = 2.57x10-6). The rs9976829 represents a strong splicing quantitative trait locus (sQTL) for both IFNAR2 and IL10RB genes, especially in lung tissue (P 1.8x10-24). Gene-based association analysis also found IFNAR2 was significantly associated with COVID-19 infection (P = 2.58x10-7). Integrative genomics analysis of combining GWAS with eQTL data showed the expression variations of IFNAR2 and IL10RB have prominent effects on COVID-19 in various types of tissues, especially in lung tissue. The majority of IFNAR2-expressing cells were dendritic cells (40%) and plasmacytoid dendritic cells (38.5%), and IL10RB-expressing cells were mainly nonclassical monocytes (29.6%). IFNAR2 and IL10RB are targeted by several interferons-related drugs. Together, our results uncover 21q22.11 as a novel susceptibility locus for COVID-19, in which individuals with G alleles of rs9976829 have a higher probability of COVID-19 susceptibility than those with non-G alleles.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Yunlong Ma", + "author_inst": "Wenzhou Medical University" + }, + { + "author_name": "Yukuan Huang", + "author_inst": "Institute of Biomedical Big Data, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China" + }, + { + "author_name": "Sen Zhao", + "author_inst": "Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China" + }, + { + "author_name": "Yinghao Yao", + "author_inst": "Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325011, China" + }, + { + "author_name": "Yaru Zhang", + "author_inst": "Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 32" + }, + { + "author_name": "Jia Qu", + "author_inst": "Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 32" + }, + { + "author_name": "Nan Wu", + "author_inst": "Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China" + }, + { + "author_name": "Jianzhong Su", + "author_inst": "Institute of Biomedical Big Data, School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 32" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.09.17.20190595", "rel_title": "The \"Great Lockdown\": Inactive Workers and Mortality by Covid-19", @@ -1178544,73 +1179593,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.17.20196360", - "rel_title": "Factors associated with the spatial heterogeneity of COVID-19 in France: a nationwide ecological study", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20196360", - "rel_abs": "Like in many countries and regions, spread of the COVID 19 pandemic has exhibited important spatial heterogeneity across France, one of the most affected countries so far. To better understand factors associated with incidence, mortality and lethality heterogeneity across the 96 administrative departments of metropolitan France, we thus conducted a geoepidemiological analysis based on publicly available data, using hierarchical ascendant classification (HAC) on principal component analysis (PCA) of multidimensional variables, and multivariate analyses with generalized additive models (GAM). Our results confirm a marked spatial heterogeneity of in-hospital COVID 19 incidence and mortality, following the North East / South West diffusion of the epidemic. The delay elapsed between the first COVID-19 associated death and the onset of the national lockdown on March 17th, 2020, appeared positively associated with in-hospital incidence, mortality and lethality. Mortality was also strongly associated with incidence. Mortality and lethality rates were significantly higher in departments with older population, but they were not significantly associated with the number of intensive-care beds available in 2018. We did not find any significant association between incidence, mortality or lethality rates and incidence of new chloroquine and hydroxychloroquine dispensations in pharmacies either, nor between COVID 19 incidence and climate, nor between economic indicators and in-hospital COVID 19 incidence or mortality. This ecological study highlights the impact of population age structure, epidemic spread and transmission mitigation policies in COVID-19 morbidity or mortality heterogeneity.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jean Gaudart", - "author_inst": "Aix Marseille Univ" - }, - { - "author_name": "Jordi Landier", - "author_inst": "IRD" - }, - { - "author_name": "laetitia huiart", - "author_inst": "Luxembourg Institute of Health" - }, - { - "author_name": "Eva Legendre", - "author_inst": "Aix Marseille Univ" - }, - { - "author_name": "Laurent Lehot", - "author_inst": "Aix Marseille Univ" - }, - { - "author_name": "Marc-Karim Bendiane", - "author_inst": "Aix Marseille Univ" - }, - { - "author_name": "Laurent Chiche", - "author_inst": "Hopital Europeen Marseille" - }, - { - "author_name": "Aliette Petitjean", - "author_inst": "Aix Marseille Univ" - }, - { - "author_name": "Emilie Mosnier", - "author_inst": "Aix Marseille Univ" - }, - { - "author_name": "Fati Kirakoya-samadoulougou", - "author_inst": "Universite Libre de Bruxelles" - }, - { - "author_name": "Jacques Demongeot", - "author_inst": "Universite Grenoble Alpes" - }, - { - "author_name": "Renaud Piarroux", - "author_inst": "Sorbonne Univ" - }, - { - "author_name": "Stanislas Rebaudet", - "author_inst": "Aix Marseille Univ" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.16.20187484", "rel_title": "Model-based and model-free characterization of epidemic outbreaks", @@ -1179178,6 +1180160,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.17.20195131", + "rel_title": "Seroprevalence of Antibodies to SARS-CoV-2 in US Blood Donors", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20195131", + "rel_abs": "BackgroundTo identify blood donors eligible to donate Coronavirus Disease-2019 (COVID-19) Convalescent Plasma (CCP), a large blood center began testing for antibodies to SARS-CoV-2, the etiologic agent of COVID-19. We report the seroprevalence of total immunoglobulin directed against the S1 spike protein of SARS-CoV-2 in US blood donors.\n\nMethodsUnique non-CCP donor sera from June 1-July 31, 2020 were tested with the Ortho VITROS Anti-SARS-CoV-2 total immunoglobulin assay (positive: signal-to-cutoff (S/C) [≥]1). Donor age, sex, race/ethnicity, ABO/RhD, education, and experience were compared to June and July 2019. Multivariate regressions were conducted to identify demographics associated with the presence of antibodies and with S/C values.\n\nResultsUnique donors (n=252,882) showed an overall seroprevalence of 1.83% in June (1.37%) and July (2.26%), with the highest prevalence in northern New Jersey (7.3%). In a subset of donors with demographic information (n=189,565), higher odds of antibody reactivity were associated with non-Hispanic Native American/Alaskan (NH-NAA/A) and Black (NH-B), and Hispanic (H) race/ethnicity, age 18-64, middle school or lesser education, blood Group A, and never or non-recent donor status. In positive donors (n=2,831), antibody signal was associated with male sex, race/ethnicity (NH-NAA/A, NH-B and H) and geographic location.\n\nConclusionsSeroprevalence remains low in US blood donors but varies significantly by region. Temporal trends in reactivity may be used to gauge the effectiveness of public health measures. Before generalizing these data from healthy donors to the general population however, rates must be corrected for false positive test results among low prevalence test subjects and adjusted to match the wider demography.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ralph R Vassallo", + "author_inst": "Vitalant" + }, + { + "author_name": "Marjorie D Bravo", + "author_inst": "Vitalant" + }, + { + "author_name": "Larry J Dumont", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Kelsey Hazegh", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Hany Kamel", + "author_inst": "Vitalant" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.17.20196832", "rel_title": "COVID-19 pediatric mortality rates are heterogenous between countries", @@ -1180630,37 +1181647,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.18.20197467", - "rel_title": "IMPACT OF UNIVERSITY RE-OPENING ON TOTAL COMMUNITY COVID-19 BURDEN", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.18.20197467", - "rel_abs": "Purpose: Post-secondary students have higher than average contacts than the general population due to congregate living, use of public transit, high-density academic and social activities, and employment in the services sector. We evaluated the impact of a large student population returning to a mid-sized city currently experiencing a low rate of COVID-19 on community health outcomes. We consider whether targeted routine or one-time screening in this population can mitigate community COVID-19 impacts. Methods: We developed a dynamic transmission model of COVID-19 subdivided into three interacting populations: general population, university students, and long-term care residents. We parameterized the model using the medical literature and expert opinion. We calibrated the model to the observed outcomes in a mid-sized Canadian city between March 1 and August 15, 2020 prior to the arrival of a relatively large post-secondary student population. We evaluated the impact of the student population (20,000 people arriving on September 1) on cumulative COVID-19 infections over the fall semester, the timing of peak infections, the timing and peak level of critical care occupancy, and the timing of re-engaged social and economic restrictions. We consider multiple scenarios with different student and general population COVID-19 prevention behaviours as well as different COVID-19 screening strategies in students. Results: In a city with low levels of COVID-19 activity, the return of a relatively large student population substantially increases the total number of COVID-19 infections in the community. In a scenario in which students immediately engage in a 24% contact reduction compared to pre-COVID levels, the total number of infections in the community increases by 87% (from 3,900 without the students to 7,299 infections with the students), with 71% of the incremental infections occurring in the general population, causing social and economic restrictions to be re-engaged 3 weeks earlier and an incremental 17 COVID-19 deaths. Scenarios in which students have an initial, short-term increase in contacts with other students before engaging in contact reduction behaviours can increase infections in the community by 150% or more. In such scenarios, screening asymptomatic students every 5 days reduces the number of infections attributable to the introduction of the university student population by 42% and delays the re-engagement of social and economic restrictions by 1 week. Compared to screening every 5 days, one-time mass screening of students prevents fewer infections, but is highly efficient in terms of infections prevented per screening test performed. Discussion: University students are highly inter-connected with the city communities in which they live and go to school, and they have a higher number of contacts than the general population. High density living environments, enthusiasm for the new school year, and relatively high rates of asymptomatic presentation may decrease their self-protective behaviours and contribute to increased community transmission of COVID-19 affecting at-risk members of the city community. Screening targeted at this population provides significant public health benefits to the community through averted infections, critical care admissions, and COVID-19 deaths.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Lauren E Cipriano", - "author_inst": "University of Western Ontario" - }, - { - "author_name": "Wael M R Haddara", - "author_inst": "Division of Critical Care, London Health Sciences Centre" - }, - { - "author_name": "Gregory S Zaric", - "author_inst": "Ivey Business School, University of Western Ontario" - }, - { - "author_name": "Eva A Enns", - "author_inst": "Division of Health Policy and Management, University of Minnesota" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.18.20195024", "rel_title": "SARS-CoV-2 antibody seroprevalence in Tbilisi, the capital city of country of Georgia", @@ -1180960,6 +1181946,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.16.300871", + "rel_title": "Distinct SARS-CoV-2 Antibody Reactivity Patterns in Coronavirus Convalescent Plasma Revealed by a Coronavirus Antigen Microarray", + "rel_date": "2020-09-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.16.300871", + "rel_abs": "A coronavirus antigen microarray (COVAM) was constructed containing 11 SARS-CoV-2, 5 SARS-1, 5 MERS, and 12 seasonal coronavirus recombinant proteins. The array is designed to measure immunoglobulin isotype and subtype levels in serum or plasma samples against each of the individual antigens printed on the array. We probed the COVAM with COVID-19 convalescent plasma (CCP) collected from 99 donors who recovered from a PCR+ confirmed SARS-CoV-2 infection. The results were analyzed using two computational approaches, a generalized linear model (glm) and Random Forest (RF) prediction model, to classify individual specimens as either Reactive or Non-Reactive against the SARS-CoV-2 antigens. A training set of 88 pre-COVID-19 specimens (PreCoV) collected in August 2019 and102 positive specimens from SARS-CoV-2 PCR+ confirmed COVID-19 cases was used for these analyses. Results compared with an FDA emergency use authorized (EUA) SARS-CoV2 S1-based total Ig chemiluminescence immunoassay (Ortho Clinical Diagnostics VITROS(R) Anti-SARS-CoV-2 Total, CoV2T) and with a SARS-CoV-2 S1-S2 spike-based pseudovirus micro neutralization assay (SARS-CoV-2 reporter viral particle neutralization titration (RVPNT) showed high concordance between the 3 assays. Three CCP specimens that were negative by the VITROS CoV2T immunoassay were also negative by both COVAM and the RVPNT assay. Concordance between VITROS CoV2T and COVAM was 96%, VITROS CoV2T and RVPNT 93%, and RVPNT and COVAM 95%. The discordances were all weakly reactive samples near the cutoff threshold of the VITROS CoV2T immunoassay. The multiplex COVAM allows CCP to be grouped according to antibody reactivity patterns against 11 SARS-CoV-2 antigens. Unsupervised K-means analysis, via the gap statistics, as well as hierarchical clustering analysis revealed 3 main clusters with distinct reactivity intensities and patterns. These patterns were not recapitulated by adjusting the VITROS CoV2T or RVPNT assay thresholds. Plasma classified according to these reactivity patterns may be better associated with CCP treatment efficacy than antibody levels alone. The use of a SARS-CoV-2 antigen array may be useful to qualify CCP for administration as a treatment for acute COVID-19 and to interrogate vaccine immunogenicity and performance in preclinical and clinical studies to understand and recapitulate antibody responses associated with protection from infection and disease.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Rafael Ramiro de Assis", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Aarti Jain", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Rie Nakajima", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Algis Jasinskas", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Saahir Khan", + "author_inst": "University of Southern California" + }, + { + "author_name": "Larry J Dumont", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Kathleen Kelly", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Graham Simmons", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Mars Stone", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Clara Di Germanio", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Michael P Busch", + "author_inst": "Vitalant Research Institute" + }, + { + "author_name": "Philip L Felgner", + "author_inst": "University of California, Irvine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.16.300319", "rel_title": "A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture", @@ -1182536,33 +1183585,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.09.10.20191619", - "rel_title": "Safety and Efficacy of the combined use of ivermectin, dexamethasone, enoxaparin and aspirin against COVID-19", - "rel_date": "2020-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20191619", - "rel_abs": "From the first outbreak in Wuhan (China) in December 2019, until today the number of deaths worldwide due to the coronavirus pandemic exceeds eight hundred thousand people and the number of infected people arises to more than 25 million. No treatment tested worldwide has shown unquestionable efficacy in the fight against COVID 19, according to NICE reports. We have designed an experimental treatment called IDEA based on four affordable drugs already available on the market in Argentina, based on the following rationale: -Ivermectin solution at a relatively high dose to lower the viral load in all stages of COVID 19 -Dexamethasone 4-mg injection, as anti-inflammatory drug to treat hyperinflammatory reaction to COVID-infection -Enoxaparin injection as anticoagulant to treat hypercoagulation in severe cases. -Aspirin 250-mg tablets to prevent hypercoagulation in mild and moderate cases Except for Ivermection oral solution, which was used in a higher dose than approved for parasitosis, all other drugs were used in the already approved dose and indication. Regarding Ivermectin safety, several oral studies have shown it to be safe even when used at daily doses much higher than those approved already. A clinical study has been conducted on COVID-19 patients at Eurnekian Hospital in the Province of Buenos Aires, Argentina. The study protocol and its final outcomes are described in this article. Results were compared with published data and data from patients admitted to the hospital receiving other treatments. None of the patient presenting mild symptoms needed to be hospitalized. Only one patient died (0.59 % of all included patients vs. 2.1 % overall mortality for the disease in Argentina today; 3.1 % of hospitalized patients vs. 26.8 % mortality in published data). IDEA protocol appears to be a useful alternative to prevent disease progression of COVID-19 when applied to mild cases and to decrease mortality in patients at all stages of the disease with a favorable risk-benefit ratio.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Hector Eduardo Carvallo", - "author_inst": "Universidad Abierta Interamericana, Eurnekian Public Hospital, Argentina" - }, - { - "author_name": "Roberto Raul Hirsch", - "author_inst": "Universidad de Buenos Aires, Hospital of Infectious Diseases F.J. Muniz, Argentina" - }, - { - "author_name": "Maria Eugenia Farinella", - "author_inst": "Eurnekian Public Hospital, Argentina" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.14.20194092", "rel_title": "COVID-19 Mortality in Cancer Patients: A Report from a Tertiary Cancer Centre in India", @@ -1182778,6 +1183800,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.13.20193896", + "rel_title": "Are we there yet? An adaptive SIR model for continuous estimation of COVID-19 infection rate and reproduction number in the United States", + "rel_date": "2020-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.13.20193896", + "rel_abs": "BackgroundThe dynamics of the COVID-19 epidemic vary due to local population density and policy measures. When making decisions, policy makers consider an estimate of the effective reproduction number [R]t which is the expected number of secondary infections by a single infected individual.\n\nObjectiveWe propose a simple method for estimating the time-varying infection rate and reproduction number [R]t.\n\nMethodsWe use a sliding window approach applied to a Susceptible-Infectious-Removed model. The infection rate is estimated using the reported cases for a seven-day window to obtain continuous estimation of [R]t. The proposed adaptive SIR (aSIR) model was applied to data at the state and county levels.\n\nResultsThe aSIR model showed an excellent fit for the number of reported COVID-19 positive cases, a one-day forecast MAPE was less than 2.6% across all states. However, a seven-day forecast MAPE reached 16.2% and strongly overestimated the number of cases when the reproduction number was high and changing fast. The maximal [R]t showed a wide range of 2.0 to 4.5 across all states, with the highest values for New York (4.4) and Michigan (4.5). We demonstrate that the aSIR model can quickly adapt to an increase in the number of tests and associated increase in the reported cases of infections. Our results also suggest that intensive testing may be one of the effective methods of reducing [R]t.\n\nConclusionThe aSIR model provides a simple and accurate computational tool to obtain continuous estimation of the reproduction number and evaluate the efficacy of mitigation measures.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Mark B Shapiro", + "author_inst": "Anthem, Inc." + }, + { + "author_name": "Fazle Karim", + "author_inst": "Anthem, Inc." + }, + { + "author_name": "Guido Muscioni", + "author_inst": "Anthem, Inc." + }, + { + "author_name": "Abel Saju Augustine", + "author_inst": "Anthem, Inc." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.03.20187112", "rel_title": "Treatment with an Anti-CK2 Synthetic Peptide Improves Clinical Response in Covid-19 Patients with Pneumonia. A Randomized and Controlled Clinical Trial", @@ -1184382,37 +1185435,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.12.20192914", - "rel_title": "A snap shot of space and time dynamics of COVID-19 risk in Malawi. An application of spatial temporal model", - "rel_date": "2020-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.12.20192914", - "rel_abs": "Background: COVID-19 has been the greatest challenge the world has faced since the second world war. The aim of this study was to investigate the distribution of COVID-19 in both space and time in Malawi. Methods: The study used publicly available data of COVID-19 cases for the period from 24th June to 20th August, 2020. Semiparametric spatial temporal models were fitted to the number of weekly confirmed cases as an outcome data, with time and location as independent variables. Results: The study found significant main effect of location and time with the two interacting. The spatial distribution of COVID-19 showed major cities being at greater risk than rural areas. Over time the COVID-19 risk was increasing then decreasing in most districts with the rural districts being consistently at lower risk. Conclusion. Future or present strategies to avert the spread of COVID-19 should target major cities by limiting international exposure. In addition, the focus should be on time points that had shown high risk.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Alfred Ngwira Sr.", - "author_inst": "Lilongwe University of Agriculture and Natural Resources" - }, - { - "author_name": "Felix Kumwenda Sr.", - "author_inst": "Lilongwe University of Agriculture and Natural Resources" - }, - { - "author_name": "Eddons Munthali Sr.", - "author_inst": "Lilongwe University of Agriculture and Natural Resources" - }, - { - "author_name": "Duncan Nkolokosa Sr.", - "author_inst": "Lilongwe University of Agriculture and Natural Resources" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.12.20193250", "rel_title": "Environment influences SARS-CoV-2 transmission in the absence of non-pharmaceutical interventions", @@ -1184676,6 +1185698,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.12.20193334", + "rel_title": "Analysis of the interventions adopted due to the COVID-19 on ARI morbility for Colombia", + "rel_date": "2020-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.12.20193334", + "rel_abs": "Acute Respiratory Infections are among the leading causes of death globally, particularly in developing countries, and are highly correlated with the quality of health and surveillance systems and effective early interventions in high-risk age groups. According to the World Health Organization, about four million people die each year from mostly preventable respiratory tract infections, making it a public health concern. The official declaration of a pandemic in March 2020 due to the Sars-CoV-2 virus coincided with the influenza season in Colombia and with environmental alerts about low air quality that increase its incidence. The objective of this document is the application of a flexible model for the identification of the pattern and monitoring of ARI morbility for Colombia by age group that shows atypical patterns in the reported series for 5 departments and that coincide with the decisions implemented to contain the COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alvaro Quijano-Angarita", + "author_inst": "Instituto de Evaluacion Tecnologica en Salud - IETS" + }, + { + "author_name": "Oscar Espinosa", + "author_inst": "Instituto de Evaluacion Tecnologica en Salud - IETS" + }, + { + "author_name": "Marcela M Mercado-Reyes", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Diana Walteros", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Diana Carolina Malo", + "author_inst": "Instituto Nacional de Salud" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.12.20193409", "rel_title": "Clinical characteristics and outcomes of patients with COVID-19 and ARDS admitted to a third level health institution in Mexico City", @@ -1185896,25 +1186953,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.09.11.20192831", - "rel_title": "Taste alteration in COVID-19: a rapid review with data synthesis reveals significant geographical differences", - "rel_date": "2020-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192831", - "rel_abs": "To facilitate a timely understanding of the differences in the prevalence of gustatory disturbances (GD) in individuals infected with SARS-CoV-2, we undertook a rapid systematic review of articles published in the repository of the National Library of Medicine (MEDLINE/PubMed) and medRxiv from their inception until September 3, 2020. The minimum requirements for completing a restricted systematic review were met. Of the 431 articles retrieved, 61 eligible studies (28,374 confirmed COVID-19 cases) from 20 countries were included in the analysis. The results show strong significant differences in the overall reported prevalence of GD between East Asia [13%, 95% CI 0.14-26.06%], Middle East [38.83%, 95% CI 27.47-50.19%], Europe [57.18%, 95% CI 52.35-62.01%], and The Americas [66.78%, 95% CI 54.77-78.79%]. There were no trends showing differences of prevalence of GD in the available literature between February and August,, 2020. These data show that there is a distinct geographical distribution of GD in COVID-19 patients and this may explain the differences of diagnostic criteria for COVID-19 case definition.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "NIcola Cirillo", - "author_inst": "University of Melbourne" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.11.20192963", "rel_title": "The major predictors of testing positive for COVID-19 among symptomatic hospitalized patients", @@ -1186190,6 +1187228,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.09.20184143", + "rel_title": "The Effect of Early Hydroxychloroquine-based Therapy in COVID-19 Patients in Ambulatory Care Settings: A Nationwide Prospective Cohort Study", + "rel_date": "2020-09-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20184143", + "rel_abs": "ABSTRACT BACKGROUND: Currently, there is no proven effective therapy nor vaccine for the treatment of SARS-CoV-2. Evidence regarding the potential benefit of early administration of hydroxychloroquine (HCQ) therapy in symptomatic patients with Coronavirus Disease (COVID-19) is not clear. METHODS: This observational prospective cohort study took place in 238 ambulatory fever clinics in Saudi Arabia, which followed the Ministry of Health (MOH) COVID-19 treatment guideline. This guideline included multiple treatment options for COVID-19 based on the best available evidence at the time, among which was Hydroxychloroquine (HCQ). Patients with confirmed COVD-19 (by reverse transcriptase polymerase chain reaction (PCR) test) who presented to these clinics with mild to moderate symptoms during the period from 5-26 June 2020 were included in this study. Our study looked at those who received HCQ-based therapy along with supportive care (SC) and compared them to patients who received SC alone. The primary outcome was hospital admission within 28-days of presentation. The secondary outcome was a composite of intensive care admission (ICU) and/or mortality during the follow-up period. Outcome data were assessed through a follow-up telephonic questionnaire at day 28 and were further verified with national hospitalisation and mortality registries. Multiple logistic regression model was used to control for prespecified confounders. RESULTS: Of the 7,892 symptomatic PCR-confirmed COVID-19 patients who visited the ambulatory fever clinics during the study period, 5,541 had verified clinical outcomes at day 28 (1,817 patients in the HCQ group vs 3,724 in the SC group). At baseline, patients who received HCQ therapy were more likely to be males who did not have hypertension or chronic lung disease compared to the SC group. No major differences were noted regarding other comorbid conditions. All patients were presenting with active complaints; however, the HCQ groups had higher rates of symptoms compared to the SC group (fever: 84% vs 66.3, headache: 49.8 vs 37.4, cough: 44.5 vs 35.6, respectively). Early HCQ-based therapy was associated with a lower hospital admission within 28-days compared to SC alone (9.4% compared to 16.6%, RRR 43%, p-value <0.001). The composite outcome of ICU admission and/or mortality at 28-days was also lower in the HCQ group compared to the SC (1.2% compared to 2.6%, RRR 54%, p-value 0.001). Adjusting for age, gender, and major comorbid conditions, a multivariate logistic regression model showed a decrease in the odds of hospitalisation in patients who received HCQ compared to SC alone (adjusted OR 0.57 [95% CI 0.47-0.69], p-value <0.001). The composite outcome of ICU admission and/or mortality was also lower for the HCQ group compared to the SC group controlling for potential confounders (adjusted OR 0.55 [95% CI 0.34-0.91], p-value 0.019). CONCLUSION: Early intervention with HCQ-based therapy in patients with mild to moderate symptoms at presentation is associated with lower adverse clinical outcomes among COVID-19 patients, including hospital admissions, ICU admission, and/or death.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Tarek Sulaiman", + "author_inst": "King Fahad Medical City, Riyadh, Saudi Arabia" + }, + { + "author_name": "Abdulrhman Mohana", + "author_inst": "Saudi Center for Disease Prevention and Control" + }, + { + "author_name": "Laila Alawdah", + "author_inst": "King Fahad Medical City, Riyadh, Saudi Arabia" + }, + { + "author_name": "Nagla Mahmoud", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Mustafa Hassanein", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Tariq Wani", + "author_inst": "King Fahad Medical City, Riyadh, Saudi Arabia" + }, + { + "author_name": "Amel Alfaifi", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Eissa Alenazi", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Nashwa Radwan", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Nasser AlKhalifah", + "author_inst": "King Fahad Medical City, Riyadh. Saudi Arabia" + }, + { + "author_name": "Ehab Elkady", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Manwer AlAnazi", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Mohammed Alqahtani", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Khalid Abdalla", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Yousif Yousif", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Fouad AboGazalah", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Fuad Awwad", + "author_inst": "Quantitative analysis department, College of Business Administration, King Saud University, Riyadh, Saudi Arabia" + }, + { + "author_name": "Khaled AlabdulKareem", + "author_inst": "Assisting Deputyship for Primary Health Care, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Fahad AlGhofaili", + "author_inst": "King Fahad Medical City, Riyadh. Saudi Arabia" + }, + { + "author_name": "Ahmed AlJedai", + "author_inst": "Assistant Deputy Minister for Therapeutic Affairs, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Hani Jokhdar", + "author_inst": "Deputyship of Public Health, Ministry of Health, Riyadh, Saudi Arabia" + }, + { + "author_name": "Fahad Alrabiah", + "author_inst": "King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.11.20180521", "rel_title": "On Machine Learning-Based Short-Term Adjustment of Epidemiological Projections of COVID-19 in US", @@ -1187506,181 +1188647,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.09.11.293464", - "rel_title": "Immunologically distinct responses occur in the CNS of COVID-19 patients", - "rel_date": "2020-09-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.11.293464", - "rel_abs": "One third of COVID-19 patients develop significant neurological symptoms, yet SARS-CoV-2 is rarely detected in central nervous system (CNS) tissue, suggesting a potential role for parainfectious processes, including neuroimmune responses. We therefore examined immune parameters in cerebrospinal fluid (CSF) and blood samples from a cohort of patients with COVID-19 and significant neurological complications. We found divergent immunological responses in the CNS compartment, including increased levels of IL-12 and IL-12-associated innate and adaptive immune cell activation. Moreover, we found increased proportions of B cells in the CSF relative to the periphery and evidence of clonal expansion of CSF B cells, suggesting a divergent intrathecal humoral response to SARS-CoV-2. Indeed, all COVID-19 cases examined had anti-SARS-CoV-2 IgG antibodies in the CSF whose target epitopes diverged from serum antibodies. We directly examined whether CSF resident antibodies target self-antigens and found a significant burden of CNS autoimmunity, with the CSF from most patients recognizing neural self-antigens. Finally, we produced a panel of monoclonal antibodies from patients CSF and show that these target both anti-viral and anti-neural antigens--including one mAb specific for the spike protein that also recognizes neural tissue. This exploratory immune survey reveals evidence of a compartmentalized and self-reactive immune response in the CNS meriting a more systematic evaluation of neurologically impaired COVID-19 patients.\n\nOne Sentence SummaryA subset of COVID-19 patients with neurologic impairment show cerebrospinal fluid-specific immune alterations that point to both neuroinvasion and anti-neural autoimmunity as potential causes of impairment.", - "rel_num_authors": 40, - "rel_authors": [ - { - "author_name": "Eric Song", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Christopher M Bartley", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Ryan D Chow", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Thomas Ngo", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Roy Jiang", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Colin R Zamecnik", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Ravi Dandekar", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Rita Loudermilk", - "author_inst": "University of California, San Francicsco" - }, - { - "author_name": "Yile Dai", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Feimei Liu", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Isobel Hawes", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Bonny D Alvarenga", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Trung Huynh", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Lindsay McAlpine", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Nur-Taz Rahman", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Bertie Geng", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Jennifer Chiarella", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Benjamin Israelow", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Chantal BF Vogels", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Nathan D Grubaugh", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Arnau Casanovas-Massana", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Brett S Phinney", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Michelle Salemi", - "author_inst": "University of California, Davis" - }, - { - "author_name": "Jessa Alexander", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Juan A Gallego", - "author_inst": "Zucker School of Medicine at Hofstra/Northwell" - }, - { - "author_name": "Todd Lencz", - "author_inst": "Zucker School of Medicine at Hofstra/Northwell" - }, - { - "author_name": "Hannah Walsh", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Carolina Lucas", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Jon Klein", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Tianyang Mao", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Jieun Oh", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Aaron Ring", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Serena Spudich", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Albert Ko", - "author_inst": "Yale University School of Public Health" - }, - { - "author_name": "Steven Kleinstein", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Joseph L DeRisi", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Akiko Iwasaki", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Samuel J Pleasure", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Michael Wilson", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Shelli F Farhadian", - "author_inst": "Yale School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.09.11.293035", "rel_title": "Distinct mechanisms for TMPRSS2 expression explain organ-specific inhibition of SARS-CoV-2 infection by enzalutamide", @@ -1187924,6 +1188890,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.10.20192195", + "rel_title": "Mathematical Modeling and a Month Ahead Forecast of the Coronavirus Disease 2019 (COVID-19) Pandemic: An Indian Scenario", + "rel_date": "2020-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20192195", + "rel_abs": "India, the second-most populous country in the world, has been lately witnessing a daily surge in the COVID-19 infected cases. India is currently among the worst-hit nations worldwide, due to the COVID-19 pandemic, and ranks just behind Brazil and USA. In order to prevent the further worsening of the situation, predicting the future course of the pandemic is of utmost importance. In this paper, we model the past trajectory (March 01, 2020 - July 25, 2020) and make a month-long (July 26, 2020 - August 24, 2020) forecast of the future evolution of the COVID-19 pandemic in India using an autoregressive integrated moving average (ARIMA) model. According to our forecasting results, India is likely to have 3,800,989 cumulative infected cases, 1,634,142 cumulative active cases, 2,110,697 cumulative recoveries and 56,150 cumulative deaths by August 24, 2020, if the current trend of the pandemic continues to prevail. The implications of these forecasts are that in the upcoming month the infection rate of COVID-19 in India is going to escalate, while as the rate of recovery and the case-fatality rate is likely to reduce. In order to avert these possible scenarios, the administration and health-care personnel need to formulate and implement robust control measures, while the general public needs to be more responsible and strictly adhere to the established and newly formulated guidelines to slow down the spread of the pandemic and prevent it from transforming into a catastrophe.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Suhail Ganiny", + "author_inst": "National Institute of Technology, Srinagar" + }, + { + "author_name": "Owais Nisar", + "author_inst": "SKUAST-K" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.11.20192450", "rel_title": "Impacts of the COVID-19 epidemic on the department of stomatology in a tertiary hospital: a case study in the General Hospital of the Central Theater Command, Wuhan, China", @@ -1189092,49 +1190081,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.10.20192104", - "rel_title": "SARS-CoV-2 Antibody Formation Among Healthcare Workers", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20192104", - "rel_abs": "Many frontline healthcare workers throughout the world have been exposed to COVID-19 infection in the workplace and the community. We describe the nature of infection and the durability of antibodies among various types of healthcare workers at an acute care community hospital in northern New Jersey adjacent to New York City, part of the epicenter of the first wave of the US epidemic. Exposure was concentrated among frontline workers and in clusters among support staff. The antibody response correlated with symptoms and job type.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Thomas Birch", - "author_inst": "Holy Name Medical Center" - }, - { - "author_name": "Ravit Barkama", - "author_inst": "Holy Name Medical Center" - }, - { - "author_name": "Joanna Tyszkiewicz Georgescu", - "author_inst": "H" - }, - { - "author_name": "Emma Yamada", - "author_inst": "Holy Name Medical Center" - }, - { - "author_name": "Drew Olsen", - "author_inst": "Holy Name Medical Center" - }, - { - "author_name": "Ed Torres", - "author_inst": "H" - }, - { - "author_name": "Alison Sinclair", - "author_inst": "Holy" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.10.20190348", "rel_title": "Distinct regimes of particle and virus abundance explain face mask efficacy for COVID-19", @@ -1189518,6 +1190464,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.11.20192526", + "rel_title": "Increased extravascular lung water index (EVLWI) reflects rapid inflammatory oedema and mortality in COVID-19 associated ARDS", + "rel_date": "2020-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192526", + "rel_abs": "OBJECTIVENearly 5 % of the patients with COVID-19 develop an acute respiratory distress syndrome (ARDS). Extravascular lung water index (EVLWI) is a marker of pulmonary oedema which is associated with mortality in ARDS. In this study we evaluate whether EVLWI is higher in patients with COVID-19 associated ARDS as compared to controls and whether EVLWI has the potential to monitor disease progression.\n\nMETHODSFrom the day of intubation, EVLWI, cardiac function were monitored by transpulmonary thermodilution in n=25 patients with COVID-19 and compared to a control group of 49 non-COVID-19 ARDS-patients.\n\nRESULTSEVLWI in COVID-19-patients was noticeably elevated and significantly higher than in the control group (17 (11-38) vs. 11 (6-26) mL/kg; p<0.001). High pulmonary vascular permeability index values (2.9 (1.0-5.2) versus 1.9 (1.0-5.2); p=0.003) suggest inflammatory oedema. By contrast, the cardiac parameters SVI, GEF and GEDVI were comparable. High EVLWI values were associated with viral persistence, prolonged intensive care treatment and mortality (23.2{+/-}6.7% vs. 30.3{+/-}6.0%, p=0.025).\n\nCONCLUSIONSCompared to the control group, COVID-19 results in markedly elevated EVLWI-values in patients with ARDS. EVLWI reflects a non-cardiogenic pulmonary oedema in COVID-19 associated ARDS and could serve as parameter to monitor ARDS progression.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Sebastian Rasch", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Paul Schmidle", + "author_inst": "Technical University of Munich, School of Medicine, Department of Dermatology and Allergology, Biedersteiner Str. 29, 80802 Munich" + }, + { + "author_name": "Senguel Sancak", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Alexander Herner", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Christina Huberle", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Dominik Schulz", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Ulrich Mayr", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Jochen Schneider", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Christoph Spinner", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Fabian Geisler", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Roland M. Schmid", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Tobias Lahmer", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + }, + { + "author_name": "Wolfgang Huber", + "author_inst": "Technical University of Munich, School of Medicine, University hospital rechts der Isar, Department of Internal Medicine II, Ismaninger Str. 22, 81675 Munich, G" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.09.10.20191932", "rel_title": "Evaluating the effects of cardiometabolic exposures on circulating proteins which may contribute to SARS-CoV-2 severity", @@ -1190762,85 +1191775,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.08.20190975", - "rel_title": "Vitamin D and Covid-19 Susceptibility and Severity: a Mendelian Randomization Study", - "rel_date": "2020-09-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190975", - "rel_abs": "BackgroundIncreased vitamin D levels, as reflected by 25OHD measurements, have been proposed to protect against COVID-19 disease based on in-vitro, observational, and ecological studies. However, vitamin D levels are associated with many confounding variables and thus associations described to date may not be causal. Vitamin D Mendelian randomization (MR) studies have provided results that are concordant with large-scale vitamin D randomized trials. Here, we used two-sample MR to assess evidence supporting a causal effect of circulating 25OHD levels on COVID-19 susceptibility and severity.\n\nMethods and findingsGenetic variants strongly associated with 25OHD levels in a genome-wide association study (GWAS) of 443,734 participants of European ancestry (including 401,460 from the UK Biobank) were used as instrumental variables. GWASs of COVID-19 susceptibility, hospitalization, and severe disease from the COVID-19 Host Genetics Initiative were used as outcome GWASs. These included up to 14,134 individuals with COVID-19, and 1,284,876 without COVID-19, from 11 countries. SARS-CoV-2 positivity was determined by laboratory testing or medical chart review. Population controls without COVID-19 were also included in the control groups for all outcomes, including hospitalization and severe disease. Analyses were restricted to individuals of European descent when possible. Using inverse-weighted MR, genetically increased 25OHD levels by one standard deviation on the logarithmic scale had no clear association with COVID-19 susceptibility (OR = 0.97; 95% CI: 0.95, 1.10; P=0.61), hospitalization (OR = 1.11; 95% CI: 0.91, 1.35; P=0.30), and severe disease (OR = 0.93; 95% CI: 0.73, 1.17; P=0.53). We used an additional 6 meta-analytic methods, as well as sensitivity analyses after removal of variants at risk of horizontal pleiotropy and obtained similar results. These results may be limited by weak instrument bias in some analyses. Further, our results do not apply to individuals with vitamin D deficiency.\n\nConclusionIn this two-sample MR study, we did not observe evidence to support an association between 25OHD levels and COVID-19 susceptibility, severity, or hospitalization. Hence, vitamin D supplementation as a mean of protecting against worsened COVID-19 outcomes is not supported by genetic evidence. Other therapeutic or preventative avenues should be given higher priority for COVID-19 randomized controlled trials.\n\nAuthor SummaryO_LIWhy was this study done?\n- Vitamin D levels have been associated with COVID-19 outcomes in multiple observational studies, though confounders are likely to bias these associations.\n- By using genetic instruments which limit such confounding, Mendelian randomization studies have consistently obtained results concordant with vitamin D supplementation randomized trials. This provides rationale to undertake vitamin D Mendelian randomization studies for COVID-19 outcomes.\n\nC_LIO_LIWhat did the researchers do and find?\n- We used the genetic variants obtained from the largest consortium of COVID-19 cases and controls, and the largest study on genetic determinants of vitamin D levels.\nWe used Mendelian randomization to estimate the effect of increased vitamin D on COVID-19 outcomes, while limiting confounding.\n- In multiple analyses, our results consistently showed no evidence for an association between genetically predicted vitamin D levels and COVID-19 susceptibility, hospitalization, or severe disease.\n\nC_LIO_LIWhat do these findings mean?\n- Vitamin D is a highly confounded variable, and traditional observational studies are at high risk of biased estimates.\n- We did not find evidence that vitamin D supplementation would improve COVID-19 outcomes.\n- Given Mendelian randomizations past track-record of anticipating the results of vitamin D randomized controlled trials, other therapeutic and preventative avenues should be prioritized for COVID-19 trials.\n\nC_LI", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Guillaume Butler-Laporte", - "author_inst": "McGill University" - }, - { - "author_name": "Tomoko Nakanishi", - "author_inst": "McGill University" - }, - { - "author_name": "Vincent Mooser", - "author_inst": "McGill University" - }, - { - "author_name": "David R Morrison", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Tala Abdullah", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Olumide Adeleye", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Noor Mamlook", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Nofar Kimchi", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Zaman Afrasiabi", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Nardin Rezk", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Annarita Giliberti", - "author_inst": "University of Siena" - }, - { - "author_name": "Alessandra Renieri", - "author_inst": "University of Siena" - }, - { - "author_name": "Yiheng Chen", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Sirui Zhou", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "Vincenzo Forgetta", - "author_inst": "Lady Davis Institute" - }, - { - "author_name": "J Brent Richards", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.08.20190918", "rel_title": "Assessing the influence of climate on future wintertime SARS-CoV-2 outbreaks", @@ -1191064,6 +1191998,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.09.20191700", + "rel_title": "Altered blood cell traits underlie a major genetic locus of severe COVID-19", + "rel_date": "2020-09-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.09.20191700", + "rel_abs": "PurposeThe genetic locus 3p21.31 has been associated with severe coronavirus disease 2019 (COVID-19), but the underlying pathophysiological mechanism is unknown.\n\nMethodsTo identify intermediate traits of the COVID-19 risk variant, we performed a phenome-wide association study (PheWAS) with 923 phenotypes in 310,999 European individuals from UK Biobank. For candidate target genes, we examined associations between their expression and the polygenic score (PGS) of 1,263 complex traits in a meta-analysis of 31,684 blood samples.\n\nResultsOur PheWAS identified and replicated multiple blood cell traits to be associated with the COVID-19 risk variant, including monocyte count and percentage (p = 1.07x10-8, 4.09x10-13), eosinophil count and percentage (p = 5.73x10-3, 2.20x10-3), and neutrophil percentage (p = 3.23x10-3). The PGS analysis revealed positive associations between the expression of candidate genes and genetically predicted counts of specific blood cells: CCR3 with eosinophil and basophil (p = 5.73x10-21, 5.08x10-19); CCR2 with monocytes (p = 2.40x10-10); and CCRl with monocytes and neutrophil (p = 1.78x10-6, 7.17x10-5).\n\nConclusionsMultiple blood cell traits, especially monocyte, eosinophil, and neutrophil numbers, are associated with the COVID-19 risk variant and the expression of its candidate target genes, representing probable mechanistic links between the genetic locus 3p21.31 and severe COVID-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jingqi Zhou", + "author_inst": "University of Georgia" + }, + { + "author_name": "Yitang Sun", + "author_inst": "University of Georgia" + }, + { + "author_name": "Weishan Huang", + "author_inst": "Louisiana State University" + }, + { + "author_name": "Kaixiong Ye", + "author_inst": "University of Georgia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.09.08.20190884", "rel_title": "Prison population reductions and COVID-19: A latent profile analysis synthesizing recent evidence from the Texas state prison system", @@ -1192256,61 +1193221,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.09.07.20189688", - "rel_title": "COVID-19 transmission in a university setting: a rapid review of modelling studies", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20189688", - "rel_abs": "Managing COVID-19 within a university setting presents unique challenges. At the start of term, students arrive from geographically diverse locations and potentially have higher numbers of social contacts than the general population, particularly if living in university halls of residence accommodation. Mathematical models are useful tools for understanding the potential spread of infection and are being actively used to inform policy about the management of COVID-19. Our aim was to provide a rapid review and appraisal of the literature on mathematical models investigating COVID-19 infection in a university setting. We searched PubMed, Web of Science, bioRxiv/ medRxiv and sought expert input via social media to identify relevant papers. BioRxiv/ medRxiv and PubMed/Web of Science searches took place on 3 and 6 July 2020, respectively. Papers were restricted to English language. Screening of peer-reviewed and pre-print papers and contact with experts yielded five relevant papers - all of which were pre-prints. All models suggest a significant potential for transmission of COVID-19 in universities. Testing of symptomatic persons and screening of the university community regardless of symptoms, combined with isolation of infected individuals and effective contact tracing were critical for infection control in the absence of other mitigation interventions. When other mitigation interventions were considered (such as moving teaching online, social/physical distancing, and the use of face coverings) the additional value of screening for infection control was limited. Multiple interventions will be needed to control infection spread within the university setting and the interaction with the wider community is an important consideration. Isolation of identified cases and quarantine of contacts is likely to lead to large numbers of students requiring educational, psychological and behavioural support and will likely have a large impact on the attendance of students (and staff), necessitating online options for teaching, even where in-person classes are taking place. Models were highly sensitive to assumptions in the parameters, including the number and type of individuals contacts, number of contacts traced, frequency of screening and delays in testing. Future models could aid policy decisions by considering the incremental benefit of multiple interventions and using empirical data on mixing within the university community and with the wider community where available. Universities will need to be able to adapt quickly to the evolving situation locally to support the health and wellbeing of the university and wider communities.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Hannah Christensen", - "author_inst": "University of Bristol" - }, - { - "author_name": "Katy Turner", - "author_inst": "University of Bristol" - }, - { - "author_name": "Adam Trickey", - "author_inst": "University of Bristol" - }, - { - "author_name": "Ross D Booton", - "author_inst": "University of Bristol" - }, - { - "author_name": "Gibran Hemani", - "author_inst": "University of Bristol" - }, - { - "author_name": "Emily Nixon", - "author_inst": "University of Bristol" - }, - { - "author_name": "Caroline Relton", - "author_inst": "University of Bristol" - }, - { - "author_name": "Leon Danon", - "author_inst": "University of Exeter" - }, - { - "author_name": "Matthew Hickman", - "author_inst": "University of Bristol" - }, - { - "author_name": "Ellen Brooks Pollock", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.09.03.20158121", "rel_title": "Lack of protective effect of chloroquine derivatives on COVID-19 disease in a Spanish sample of chronically treated patients", @@ -1192578,6 +1193488,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.07.20188003", + "rel_title": "The Geography of Excess Deaths in England during the Covid-19 pandemic: Longer term impacts and monthly dynamics", + "rel_date": "2020-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20188003", + "rel_abs": "Physical social interaction relevant to the spread of infectious diseases occurs, by its nature, at a local level. If infection and related mortality are associated with social background, it is therefore natural to study variation in them in relation to the social composition of local areas. The first part of the paper studies the geographical impact of Covid-19 infection on age-standardised sex-specific excess death rates during the peak months of the pandemic so far, March through May 2020. The second part examines monthly mortality dynamics in relation to predictions from a spatial SIR (Susceptible, Infected, Recovered) model of infection introduced by Bisin and Moro (2020). The analysis indicates that during the peak months of the Covid-19 pandemic, a larger non-white population and higher social deprivation in an area were associated with higher excess mortality, particularly among men. Regarding dynamics, higher population density accelerated the growth in mortality during the upsurge in infection and increased its rate of decline after the peak of the epidemic, thereby producing a more peaked mortality profile. There is also evidence of a slower post-peak decline in mortality in more socially deprived areas but a more rapid decline in areas with a larger non-white population.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Richard Breen", + "author_inst": "University of Oxford" + }, + { + "author_name": "John Ermisch", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.04.20188235", "rel_title": "Trend prediction of COVID-19 based on ARIMA model in mainland of China", @@ -1194010,69 +1194943,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.07.20189050", - "rel_title": "Seroprevalence of the SARS-CoV-2 infection in health workers of the Sanitary Region VIII, at province of Buenos Aires", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20189050", - "rel_abs": "IntroductionThe aim of this study was to estimate the seroprevalence of the SARS-CoV-2 infection in health workers of the Sanitary Region VIII, at province of Buenos Aires during June 2020.\n\nMethodsA cross-sectional design was used. A probabilistic sampling by two-stage conglomerates was carried out. Data were collected from a self-administered questionnaire and a blood sample for antibody identification. The COVIDAR IgG and IgM test were used. RESULTS: 738 health workers were included; the overall response rate was 73.80%. 71.83% of that were women; age showed a normal distribution. Nurses and doctors accounted for more than half of the staff. 75.86% of people claimed to always use Personal Protective Equipment. 5.61% of people had close contact with a confirmed case of COVID-19. 4.60% of people had previously had a nasopharyngeal swab with a negative result. Five workers had positive IgG for SARS-CoV-2 (four women and one man) with negative IgM. The mean age of the cases was 35 years old; two of them were asymptomatic; neither of them had a swab sample taken. The overall seroprevalence was 0.75%, with no significant differences between strata.\n\nDiscussionThe seroprevalence found was low; indicating a large proportion of workers was susceptible to infection. We stress the need to complement passive epidemiological surveillance strategies with serological monitoring in health workers.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Andrea Silva", - "author_inst": "Instituto Nacional de Epidemiologia \"Dr. Juan H Jara\" (Administracion Nacional de Laboratorios e Institutos de Salud -ANLIS-), Mar del Plata, Argentina" - }, - { - "author_name": "Maria Fernanda Aguirre", - "author_inst": "Instituto Nacional de Epidemiologia \"Dr. Juan H Jara\" (Administracion Nacional de Laboratorios e Institutos de Salud -ANLIS-), Mar del Plata, Argentina" - }, - { - "author_name": "Christian Ballejo", - "author_inst": "Instituto Nacional de Epidemiologia \"Dr. Juan H Jara\" (Administracion Nacional de Laboratorios e Institutos de Salud -ANLIS-), Mar del Plata, Argentina" - }, - { - "author_name": "Maria Jimena Marro", - "author_inst": "Instituto Nacional de Epidemiologia \"Dr. Juan H Jara\" (Administracion Nacional de Laboratorios e Institutos de Salud -ANLIS-), Mar del Plata, Argentina" - }, - { - "author_name": "ANDREA GAMARNIK", - "author_inst": "FUNDACION INSTITUTO LELOIR" - }, - { - "author_name": "Gaston Vargas", - "author_inst": "Sanitary Region VIII, Mar del Plata, Argentina" - }, - { - "author_name": "Marina Pifano", - "author_inst": "Ministry of Health of Buenos Aires, Argentina" - }, - { - "author_name": "Teresa Varela", - "author_inst": "Ministry of Health of Buenos Aires, Argentina" - }, - { - "author_name": "Enio Garcia", - "author_inst": "Ministry of Health of Buenos Aires, Argentina" - }, - { - "author_name": "Alicia Lawrynowicz", - "author_inst": "Instituto Nacional de Epidemiologia \"Dr. Juan H Jara\" (Administracion Nacional de Laboratorios e Institutos de Salud -ANLIS-), Mar del Plata, Argentina" - }, - { - "author_name": "Osvaldo Uez", - "author_inst": "Instituto Nacional de Epidemiologia \"Dr. Juan H Jara\" (Administracion Nacional de Laboratorios e Institutos de Salud -ANLIS-), Mar del Plata, Argentina" - }, - { - "author_name": "Irene Pagano", - "author_inst": "Instituto Nacional de Epidemiologia \"Dr. Juan H Jara\" (Administracion Nacional de Laboratorios e Institutos de Salud -ANLIS-), Mar del Plata, Argentina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.07.20189621", "rel_title": "COVID-19 in patients with hepatobiliary and pancreatic diseases in East London: A single-centre cohort study", @@ -1194228,6 +1195098,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.08.20190397", + "rel_title": "The impact of COVID-19 restriction measures on loneliness among older adults in Austria", + "rel_date": "2020-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190397", + "rel_abs": "BackgroundTo halt the spread of COVID-19, Austria implemented a 7-week shut-down of public life in March/April 2020 which was followed by a gradual withdrawal of these restriction measures in May/June 2020. We expect that the ensuing reduction in social contacts led to increased loneliness among older adults (60+).\n\nMethodsWe conducted three analyses to assess the association between COVID-19 public health restriction measures and loneliness: (1) A comparison between pre-pandemic (SHARE: 2013-2017) and pandemic (May 2020) levels of loneliness (UCLA-3 scale), (2) an analysis of the correlation between being affected by COVID-19 restriction measures and loneliness based on cross-sectional survey data from early May 2020, and (3) a longitudinal analysis of weekly changes in loneliness (Corona panel data) from late March to early June 2020.\n\nResultsWe found (1) loneliness levels to have increased in 2020 in comparison with previous years, (2) an association between the number of restriction measures older adults reported to be affected from and loneliness, and (3) that loneliness was higher during shut-down compared to the subsequent re-opening phase, particularly among those who live alone.\n\nDiscussionOur results provide evidence that COVID-19 restriction measures in Austria have indeed resulted in increased levels of loneliness among older adults. However, these effects seem to be short-lived, and thus we do not expect strong negative consequences for older adults mental health downstream. Nonetheless, effects of longer and/or repeated future restriction measures aiming at social distancing should be closely monitored.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Erwin Stolz", + "author_inst": "Medical University of Graz" + }, + { + "author_name": "Hannes Mayerl", + "author_inst": "Medical University of Graz" + }, + { + "author_name": "Wolfgang Freidl", + "author_inst": "Medical University of Graz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.09.08.20190470", "rel_title": "Modelling the epidemic growth of preprints on COVID-19 and SARS-CoV-2", @@ -1195976,81 +1196873,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.09.08.285007", - "rel_title": "Brain volumetric changes in the general population following the COVID-19 outbreak and lockdown", - "rel_date": "2020-09-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.08.285007", - "rel_abs": "The COVID-19 outbreak introduced unprecedented health-risks, as well as pressure on the financial, social, and psychological well-being due to the response to the outbreak. Here, we examined the manifestations of the COVID-19 outbreak on the brain structure in the healthy population, following the initial phase of the pandemic in Israel. We pre-registered our hypothesis that the intense experience of the outbreak potentially induced stress-related brain modifications. Volumetric changes in n = 50 participants who were scanned before and after the COVID-19 outbreak and lockdown, were compared with n = 50 control participants who were scanned twice prior to the pandemic. The pandemic provided a rare opportunity to examine brain plasticity in a natural experiment. We found volumetric increases in bilateral amygdalae, putamen, and the anterior temporal cortices. Changes in the amygdalae diminished as time elapsed from lockdown relief, suggesting that the intense experience associated with the pandemic outbreak induced transient volumetric changes in brain regions commonly associated with stress and anxiety.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Tom Salomon", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Adi Cohen", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Daniel Barazany", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Gal Ben-Zvi", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Rotem Botvinik-Nezer", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Rani Gera", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Shiran Oren", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Dana Roll", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Gal Rozic", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Anastasia Saliy", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Niv Tik", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Galia Tsarfati", - "author_inst": "Sheba Medical Center, Tel-Hashomer, affiliated to the Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Ido Tavor", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Tom Schonberg", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Yaniv Assaf", - "author_inst": "Tel Aviv University, Tel Aviv, Israel" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2020.09.08.284737", "rel_title": "Many bat species are not potential hosts of SARS-CoV and SARS-CoV-2: Evidence from ACE2 receptor usage", @@ -1196198,6 +1197020,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.06.20189480", + "rel_title": "Antibody Responses to SARS-CoV-2 in Coronavirus Diseases 2019 Patients with Different Severity", + "rel_date": "2020-09-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.06.20189480", + "rel_abs": "BackgroundMore understanding of antibody responses in the SARS-CoV-2 infected population is useful for vaccine development.\n\nAimTo investigate SARS-CoV-2 IgA and IgG among COVID-19 Thai patients with different severity.\n\nMethodsWe used plasma from 118 adult patients who have confirmed SARS-CoV-2 infection and 49 patients under investigation without infection, 20 patients with other respiratory infections, and 102 healthy controls. Anti-SARS-CoV-2 IgA and IgG were performed by enzyme-linked immunosorbent assay from Euroimmun. The optical density ratio cut off for positive test was 1.1 for IgA and 0.8 for IgG. The association of antibody response with the severity of diseases and the day of symptoms was performed.\n\nResultsFrom Mar 10 to May 31, 2020, 289 participants were enrolled, and 384 samples were analyzed. Patients were categorized by clinical manifestations to mild (n = 59), moderate (n = 27) and severe (n = 32). The overall sensitivity of IgA and IgG from samples collected after day 7 is 87.9% (95% CI 79.8-93.6) and 84.8% (95% CI 76.2-91.3), respectively. The severe group had a significantly higher level of specific IgA and IgG to S1 antigen compared to the mild group. All moderate to severe patients have specific IgG while 20% of the mild group did not have any IgG detected after two weeks. Interestingly, SARS-CoV-2 IgG level was significantly higher in males compared to females among the severe group (p = 0.003).\n\nConclusionThe serologic test for SARS-CoV-2 has high sensitivity after the second week after onset of illness. Serological response differs among patients with different severity and different sex.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ekasit Kowitdamrong", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Thanyawee Puthanakit", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Watsamon Jantarabenjakul", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Eakachai Prompetchara", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Pintip Suchartlikitwong", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Opass Putcharoen", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + }, + { + "author_name": "Nattiya Hirankarn", + "author_inst": "Faculty of Medicine, Chulalongkorn University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.05.20188821", "rel_title": "Ethnicity and clinical outcomes in COVID-19A Systematic Review and Meta-analysis", @@ -1198682,85 +1199547,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.01.20184390", - "rel_title": "Convalescent plasma as potential therapy for severe COVID-19 pneumonia.", - "rel_date": "2020-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20184390", - "rel_abs": "At the beginning of the COVID-19 pandemic, there was high mortality and a lack of effective treatment for critically ill patients. Build on the experience in argentine hemorrhagic fever with convalescent plasma, we incorporated 90 patients into a multicenter study, and 87 were evaluable. We collected 397 donations from 278 convalescent donors. Patients received plasma with an IgG concentration of 0.7-0.8 (measured by Abbott chemiluminescence) for every 10 kg of body weight. Survival during the first 28 days was the primary objective. 77% were male, age 54 {+/-} 15.6 y/o (range 27-85); body mass index 29.7 {+/-} 4,4; hypertension 39% and diabetes 20%; 19.5% had an immunosuppression condition; 23% were healthcare workers. Plasma was administered to 55 patients (63%) on spontaneous breathing with oxygen supplementation (mainly oxygen mask with reservoir bag in 80%), and 32 patients (37%) were infused on mechanical ventilation. The 28-day survival rate was 80%, with 91% in patients infused on spontaneous breathing and 63% in those infused on mechanical ventilation (p = 0.0002). There was a significant improvement in the WHO pneumonia clinical scale at 7 and 14 days, and in PaO2 / FiO2, ferritin and LDH, in the week post-infusion. We observed an episode of circulatory volume overload and a febrile reaction, both mild. Convalescent plasma infusions are feasible, safe, and potentially effective, especially before requiring mechanical ventilation, and are an attractive clinical option for treating severe forms of COVID-19 until other effective therapies become available.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ricardo Valentini", - "author_inst": "Centro de Educacion Medica e Investigaciones Clinicas" - }, - { - "author_name": "Juan Dupont", - "author_inst": "Centro de Educacion Medica e Investigaciones Clinicas (CEMIC)" - }, - { - "author_name": "Jose Fernandez", - "author_inst": "Centro de Educacion Medica e Investigaciones Clinicas (CEMIC)" - }, - { - "author_name": "Jorge Solimano", - "author_inst": "Centro de Educacion Medica e Investigaciones Clinicas (CEMIC)" - }, - { - "author_name": "Fernando Palizas", - "author_inst": "Sanatorio Guemes" - }, - { - "author_name": "Dardo Riveros", - "author_inst": "Centro de Educacion Medica e Investigaciones Clinicas (CEMIC)" - }, - { - "author_name": "Pablo Saul", - "author_inst": "Policlinico Union Obrera Metalurgica" - }, - { - "author_name": "Laura Dupont", - "author_inst": "Instituto Universitario CEMIC" - }, - { - "author_name": "Juan Medina", - "author_inst": "Sanatorio Itoitz" - }, - { - "author_name": "Viviana Falasco", - "author_inst": "Hospital Pedro Fiorito" - }, - { - "author_name": "Florencia Fornillo", - "author_inst": "Instituto Universitario CEMIC" - }, - { - "author_name": "Julia Laviano", - "author_inst": "Instituto Universitario CEMIC" - }, - { - "author_name": "Daniela Maymo", - "author_inst": "Instituto Universitario CEMIC" - }, - { - "author_name": "Daniel Gotta", - "author_inst": "Centro de Educacion Medica e Investigaciones Clinicas (CEMIC)" - }, - { - "author_name": "Alfredo Martinez", - "author_inst": "Centro de Educacion Medica e Investigaciones Clinicas (CEMIC)" - }, - { - "author_name": "Pablo Bonvehi", - "author_inst": "Centro de Educacion Medica e Investigaciones Clinicas (CEMIC)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.04.20187849", "rel_title": "Association between population density and infection rate suggests the importance of social distancing and travel restriction in reducing the COVID-19 pandemic", @@ -1199056,6 +1199842,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.09.04.20185645", + "rel_title": "Predicting illness trajectory and hospital resource utilization of COVID-19 hospitalized patients - a nationwide study", + "rel_date": "2020-09-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20185645", + "rel_abs": "BackgroundThe spread of COVID-19 has led to a severe strain on hospital capacity in many countries. There is a need for a model to help planners assess expected COVID-19 hospital resource utilization.\n\nMethodsRetrospective nationwide cohort study following the day-by-day clinical status of all hospitalized COVID-19 patients in Israel from March 1st to May 2nd, 2020. Patient clinical course was modelled with a machine learning approach based on a set of multistate Cox regression-based models with adjustments for right censoring, recurrent events, competing events, left truncation, and time-dependent covariates. The model predicts the patients entire disease course in terms of clinical states, from which we derive the patients hospital length-of-stay, length-of-stay in critical state, the risk of in-hospital mortality, and total and critical care hospital-bed utilization. Accuracy assessed over eight cross-validation cohorts of size 330, using per-day Mean Absolute Error (MAE) of predicted hospital utilization averaged over 64 days; and area under the receiver operating characteristics (AUROC) for individual risk of critical illness and in-hospital mortality, assessed on the first day of hospitalization. We present predicted hospital utilization under hypothetical incoming patient scenarios.\n\nFindingsDuring the study period, 2,703 confirmed COVID-19 patients were hospitalized in Israel. The per-day MAEs for total and critical-care hospital-bed utilization, were 4{middle dot}72 {+/-} 1{middle dot}07 and 1{middle dot}68 {+/-} 0{middle dot}40 respectively; the AUROCs for prediction of the probabilities of critical illness and in-hospital mortality were 0{middle dot}88 {+/-} 0{middle dot}04 and 0{middle dot}96 {+/-} 0{middle dot}04, respectively. We further present the impact of several scenarios of patient influx on healthcare system utilization, and provide an R software package for predicting hospital-bed utilization.\n\nInterpretationWe developed a model that, given basic easily obtained data as input, accurately predicts total and critical care hospital utilization. The model enables evaluating the impact of various patient influx scenarios on hospital utilization and planning ahead of hospital resource allocation.\n\nFundingThe work was funded by the Israeli Ministry of Health. M.G. received support from the U.S.-Israel Binational Science Foundation (BSF, 2016126).\n\nO_TEXTBOXResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSCOVID19 outbreaks are known to lead to severe case load in hospital systems, stretching resources, partially due to the long hospitalizations needed for some of the patients. There is a crucial need for tools helping planners assess future hospitalization load, taking into account the specific characteristics and heterogeneity of currently hospitalized COVID19 patients, as well as the characteristics of incoming patients. We searched PubMed for articles published up to September 9, 2020, containing the words \"COVID19\" and combinations of \"hospital\", \"utilization\", \"resource\", \"capacity\" and \"predict\". We found 145 studies; out of them, several included models that predict the future trend of hospitalizations using compartment models (e.g. SIR models), or by using exponential or logistic models. We discuss two of the more prominent ones, which model explicitly the passage of patients through the ICU. These models (i) do not take into account individual patient characteristics; (ii) do not consider length-of-stay heterogeneity, despite the fact that bed utilization is in part determined by a long tail of patients requiring significantly longer stays than others; (iii) do not correct for competing risks bias. We further searched for studies containing the words \"COVID19\" and \"multistate\", and \"COVID19\" and \"length\" and \"stay\". Out of 317 papers, we found two using multistate models focusing only on patients undergoing ECMO treatment.\n\nAdded value of this studyWe present the first model predicting hospital load based on the individual characteristics of hospitalized patients: age, sex, clinical state, and time already spent in-hospital. We combine this with scenarios for incoming patients, allowing for variations by age, sex and clinical state. The models precise predictions are based on a large sample of complete, day-by-day disease trajectories of patients, with a full coverage of the entire COVID-19 hospitalized population in Israel up to early May, 2020 (n =2, 703). We provide the model, as well as software for fitting such a model to local data, and an anonymized version of the dataset used to create the model.\n\nImplications of all the available evidenceAccurate predictions for hospital utilization can be made based on easy to obtain patient data: age, sex, and patient clinical state (moderate, severe or critical). The model allows hospital-and regional-level planners to allocate resources in a timely manner, preparing for different patient influx scenarios.\n\nC_TEXTBOX", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Michael Roimi", + "author_inst": "Rambam Health Care Campus" + }, + { + "author_name": "Rom Gutman", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Jonathan Somer", + "author_inst": "Technion - Israel Institute of Technology" + }, + { + "author_name": "Asaf Ben Arie", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Ido Calman", + "author_inst": "Independent" + }, + { + "author_name": "Yaron Bar-Lavie", + "author_inst": "Rambam Health Care Campus" + }, + { + "author_name": "Udi Gelbshtein", + "author_inst": "Israel Ministry of Health" + }, + { + "author_name": "Sigal Liverant-Taub", + "author_inst": "Israel Ministry of Health" + }, + { + "author_name": "Arnona Ziv", + "author_inst": "Gertner Institute for Epidemiology and Health Policy Research" + }, + { + "author_name": "Danny Eytan", + "author_inst": "Technion - Israel Institute of Technology and Rambam Health Care Campus" + }, + { + "author_name": "Malka Gorfine", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Uri Shalit", + "author_inst": "Technion - Israeli Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.09.04.20184523", "rel_title": "MOLECULAR EPIDEMIOLOGY TO UNDERSTAND THE SARS-CoV-2 EMERGENCE IN THE BRAZILIAN AMAZON REGION", @@ -1200420,105 +1201269,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.09.06.284976", - "rel_title": "Notable sequence homology of the ORF10 protein introspects the architecture of SARS-COV-2", - "rel_date": "2020-09-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.06.284976", - "rel_abs": "The global public health is endangered due to COVID-19 pandemic, which is caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Despite having similar pathology to MERS and SARS-CoV, the infection fatality rate of SARS-CoV-2 is likely lower than 1%. SARS-CoV-2 has been reported to be uniquely characterized by the accessory protein ORF10, which contains eleven cytotoxic T lymphocyte (CTL) epitopes of nine amino acids length each, across various human leukocyte antigen (HLA) subtypes. In this study, all missense mutations found in sequence databases were examined across twnety-two unique SARS-CoV-2 ORF10 variants that could possibly alter viral pathogenicity. Some of these mutations decrease the stability of ORF10, e.g. I4L and V6I were found in the MoRF region of ORF10 which may also possibly contribute to Intrinsic protein disorder. Furthermore, a physicochemical and structural comparative analysis was carried out on SARS-CoV-2 and Pangolin-CoV ORF10 proteins, which share 97.37% amino acid homology. The high degree of physicochemical and structural similarity of ORF10 proteins of SARS-CoV-2 and Pangolin-CoV open questions about the architecture of SARS-CoV-2 due to the disagreement of these two ORF10 proteins over their sub-structure (loop/coil region), solubility, antigenicity and change from the strand to coil at amino acid position 26, where tyrosine is present. Altogether, SARS-CoV-2 ORF10 is a promising pharmaceutical target and a protein which should be monitored for changes which correlate to change pathogenesis and clinical course of COVID-19 infection.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Sk. Sarif Hassan", - "author_inst": "Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140,West Bengal, India" - }, - { - "author_name": "Diksha Attrish", - "author_inst": "Dr. B. R. Ambedkar Centre For Biomedical Research (ACBR), University of Delhi (North Campus), Delhi 110007, India" - }, - { - "author_name": "Shinjini Ghosh", - "author_inst": "Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700009, West Bengal, India" - }, - { - "author_name": "Pabitra Pal Choudhury", - "author_inst": "Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India" - }, - { - "author_name": "Vladimir N Uversky", - "author_inst": "University of South Florida" - }, - { - "author_name": "Bruce Uhal", - "author_inst": "Michigan State University" - }, - { - "author_name": "Kenneth Lundstrom", - "author_inst": "PanTherapeutics, Rte de Lavaux 49, CH1095 Lutry, Switzerland" - }, - { - "author_name": "Alaa A. A. Aljabali", - "author_inst": "Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid 566, Jordan" - }, - { - "author_name": "Murat Seyran", - "author_inst": "Doctoral studies in natural and technical sciences (SPL 44), University of Vienna, Austria" - }, - { - "author_name": "Damiano Pizzol", - "author_inst": "Italian Agency for Development Cooperation - Khartoum, Sudan Street 33, Al Amarat, Sudan" - }, - { - "author_name": "Parise Adadi", - "author_inst": "Department of Food Science, University of Otago, Dunedin 9054, New Zealand" - }, - { - "author_name": "Tarek Mohamed Abd El-Aziz", - "author_inst": "Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA" - }, - { - "author_name": "Antonio Soares", - "author_inst": "Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA" - }, - { - "author_name": "Ramesh Kandimalla", - "author_inst": "CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad-500007, Telangana State, India" - }, - { - "author_name": "Murtaza Tambuwala", - "author_inst": "School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK" - }, - { - "author_name": "Amos Lal", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota, USA" - }, - { - "author_name": "Gajendra Kumar Azad", - "author_inst": "Department of Zoology, Patna University, Patna-800005, Bihar, India" - }, - { - "author_name": "Samendra P. Sherchan", - "author_inst": "Department of Environmental Health Sciences, Tulane University, New Orleans, LA, 70112, USA" - }, - { - "author_name": "Wagner Baetas-da-Cruz", - "author_inst": "Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Jane" - }, - { - "author_name": "Giorgio Palu", - "author_inst": "University of Padova" - }, - { - "author_name": "Adam Brufsky", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.09.06.282145", "rel_title": "Cooperative efforts on developing vaccines and therapies for COVID-19", @@ -1200794,6 +1201544,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2020.09.03.20187757", + "rel_title": "The role of school reopening in the spread of COVID-19", + "rel_date": "2020-09-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187757", + "rel_abs": "Many countries chose to close schools as part of their response to the SARS-CoV2 coronavirus (COVID-19) pandemic. Whilst nations are gradually reopening schools, and many politicians advise that schools remain safe and the risks of increases in the spread of COVID-19 are low, little evidence has been presented to confirm those statements.\n\nA review of the numbers of new confirmed COVID-19 cases by country suggests that the reopening of schools is likely to be a driver in the increase of the number of new cases. This is likely exacerbated by accompanying changes and easing of restrictions. However, with the exception of China, notable for its robust test, track, trace, and isolate processes, no other countries that had significant numbers of COVID-19 cases have successfully reopened schools without an increase in cases as a consequence.\n\nWhilst reopening of schools following an initial peak and decrease in COVID-19 infections is desirable for a range of reasons, doing so without adequate controls and protections may lead to an exacerbation of spread within the school environment, which could then lead to increased community spread of disease.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Richard Beesley", + "author_inst": "Juvenile Arthritis Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.03.20187062", "rel_title": "College campuses and COVID-19 mitigation: clinical and economic value", @@ -1201926,125 +1202695,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.09.04.277426", - "rel_title": "Preliminary report of preclinical efficacy and safety analysis of gamma-irradiated inactivated SARS-CoV-2 vaccine candidates, SK-01 version 1 and OZG-3861 version 1", - "rel_date": "2020-09-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.04.277426", - "rel_abs": "COVID-19 outbreak caused by SARS-CoV-2 created an unprecedented health crisis since there is no vaccine for this novel virus. Therefore, SARS-CoV-2 vaccines have become crucial for reducing morbidity and mortality. In this study, in vitro and in vivo safety and efficacy analyzes of lyophilized vaccine candidates inactivated by gamma-irradiation were performed. The candidate vaccines in this study were OZG-3861 version 1 (V1), an inactivated SARS-CoV-2 virus vaccine, and SK-01 version 1 (V1), a GM-CSF adjuvant added vaccine. The candidate vaccines were applied intradermally to BALB/c mice to assess toxicity and immunogenicity. Preliminary results in vaccinated mice are reported in this study. Especially, the vaccine models containing GM-CSF caused significant antibody production with neutralization capacity in absence of the antibody-dependent enhancement feature, when considered in terms of T and B cell responses. Another important finding was that the presence of adjuvant was more important in T cell in comparison with B cell response. Vaccinated mice showed T cell response upon restimulation with whole inactivated SARS-CoV-2 or peptide pool. This study shows that the vaccines are effective and leads us to start the challenge test to investigate the gamma-irradiated inactivated vaccine candidates for infective SARS-CoV-2 virus in humanized ACE2+ mice.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Gozde SIR KARAKUS", - "author_inst": "Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey" - }, - { - "author_name": "Cihan Tastan", - "author_inst": "Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey" - }, - { - "author_name": "Derya Dilek Kancagi", - "author_inst": "Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey" - }, - { - "author_name": "Bulut Yurtsever", - "author_inst": "Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey" - }, - { - "author_name": "Gamze Tumentemur", - "author_inst": "Vocational School of Health Services, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey" - }, - { - "author_name": "Sevda Demir", - "author_inst": "Genetic and Bioengineering Department, Yeditepe University, Istanbul, Turkey" - }, - { - "author_name": "Raife Dilek Turan", - "author_inst": "Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey" - }, - { - "author_name": "Selen Abanuz", - "author_inst": "Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey" - }, - { - "author_name": "Didem Cakirsoy", - "author_inst": "Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey" - }, - { - "author_name": "Utku Seyis", - "author_inst": "Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey" - }, - { - "author_name": "Samed Ozer", - "author_inst": "Animal Application and Research Center, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey" - }, - { - "author_name": "Omer Elibol", - "author_inst": "Acibadem Altunizade Hospital, Istanbul, Turkey" - }, - { - "author_name": "Muhammer Elek", - "author_inst": "Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey" - }, - { - "author_name": "Gurcan Ertop", - "author_inst": "Vocational School of Health Services, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey" - }, - { - "author_name": "Serap Arbak", - "author_inst": "Histology and Embryology Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey" - }, - { - "author_name": "Merve Acikel Elmas", - "author_inst": "Histology and Embryology Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey" - }, - { - "author_name": "Cansu Hemsinlioglu", - "author_inst": "Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey" - }, - { - "author_name": "Ayse Sesin Kocagoz", - "author_inst": "Acibadem Altunizade Hospital, Infectious Disease Unit, Istanbul, Turkey" - }, - { - "author_name": "Ozden Hatirnaz Ng", - "author_inst": "Medical Biology Department, Acibadem Mehmet Ali Aydinlar University Istanbul, Turkey" - }, - { - "author_name": "Sezer Akyoney", - "author_inst": "Medical Biology Department, Acibadem Mehmet Ali Aydinlar University Istanbul, Turkey" - }, - { - "author_name": "Ilayda Sahin", - "author_inst": "Medical Biotechnology Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey" - }, - { - "author_name": "Ugur Ozbek", - "author_inst": "Medical Genetics Department, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey" - }, - { - "author_name": "Dilek Telci", - "author_inst": "Genetic and Bioengineering Department, Yeditepe University, Istanbul, Turkey" - }, - { - "author_name": "Fikrettin Sahin", - "author_inst": "Genetic and Bioengineering Department, Yeditepe University, Istanbul, Turkey" - }, - { - "author_name": "Koray Yalcin", - "author_inst": "Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey" - }, - { - "author_name": "Ercument Ovali", - "author_inst": "Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.09.04.280081", "rel_title": "Monoclonal Antibodies Capable of Binding SARS-CoV-2 Spike Protein Receptor Binding Motif Specifically Prevent GM-CSF Induction.", @@ -1202344,6 +1202994,113 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.01.20185793", + "rel_title": "Prognostic accuracy of emergency department triage tools for children with suspected COVID-19: The PRIEST observational cohort study", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185793", + "rel_abs": "ObjectivesEmergency department clinicians can use triage tools to predict adverse outcome and support management decisions for children presenting with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in children presenting to the emergency department (ED) with suspected COVID-19 infection.\n\nMethodsWe undertook a mixed prospective and retrospective observational cohort study in 44 EDs across the United Kingdom (UK). We collected data from children attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment using the WHO algorithm, swine flu hospital pathway for children (SFHPC), Paediatric Observation Priority Score (POPS) and Childrens Observation and Severity Tool (COAST). We recorded 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome.\n\nResultsWe collected data from 1530 children, including 26 (1.7%) with an adverse outcome. C-statistics were 0.80 (95% confidence interval 0.73-0.87) for the WHO algorithm, 0.80 (0.71-0.90) for POPS, 0.76 (0.67-0.85) for COAST, and 0.71 (0.59-0.82) for SFHPC. Using pre-specified thresholds, the WHO algorithm had the highest sensitivity (0.85) and lowest specificity (0.75), but POPS and COAST could optimise sensitivity (0.96 and 0.92 respectively) at the expense of specificity (0.25 and 0.38 respectively) by using a threshold of any score above zero instead of the pre-specified threshold.\n\nConclusionExisting triage tools have good but not excellent prediction for adverse outcome in children with suspected COVID-19. POPS and COAST could achieve an appropriate balance of sensitivity and specificity for supporting decisions to discharge home by considering any score above zero to be positive.\n\nRegistrationISRCTN registry, ISRCTN28342533, http://www.isrctn.com/ISRCTN28342533", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Katie Biggs", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Ben Thomas", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Steve Goodacre", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Ellen Lee", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Laura Sutton", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Matthew Bursnall", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Amanda Loban", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Simon Waterhouse", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Richard Simmonds", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Carl Marincowitz", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Jose Schutter", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Sarah Connelly", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Elena Sheldon", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Jamie Hall", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Emma Young", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Andrew Bentley", + "author_inst": "Manchester University NHS Foundation Trust" + }, + { + "author_name": "Kirsty Challen", + "author_inst": "Lancashire Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Chris Fitzsimmons", + "author_inst": "Sheffield Children's NHS Foundation Trust" + }, + { + "author_name": "Tim Harris", + "author_inst": "Barts Health NHS Trust" + }, + { + "author_name": "Fiona Lecky", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Andrew Lee", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Ian Maconochie", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Darren Walter", + "author_inst": "Manchester University NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.08.29.20184325", "rel_title": "Face-masking, an acceptable protective measure against COVID-19: Findings of Ugandan high-risk groups", @@ -1203492,61 +1204249,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.02.20185983", - "rel_title": "Racial/Ethnic Disparities in Hospital Admissions from COVID-19 and Determining the Impact of Neighborhood Deprivation and Primary Language.", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20185983", - "rel_abs": "BackgroundDespite past and ongoing efforts to achieve health equity in the United States, persistent disparities in socioeconomic status along with multilevel racism maintain disparate outcomes and appear to be amplified by COVID-19.\n\nObjectiveMeasure socioeconomic factors and primary language effects on the risk of COVID-19 severity across and within racial/ethnic groups.\n\nDesignRetrospective cohort study.\n\nSettingHealth records of 12 Midwest hospitals and 60 clinics in the U.S. between March 4, 2020 to August 19, 2020.\n\nPatientsPCR+ COVID-19 patients.\n\nExposuresMain exposures included race/ethnicity, area deprivation index (ADI), and primary language.\n\nMain Outcomes and MeasuresThe primary outcome was COVID-19 severity using hospitalization within 45 days of diagnosis. Logistic and competing-risk regression models (censored at 45 days and accounting for the competing risk of death prior to hospitalization) assessed the effects of neighborhood-level deprivation (using the ADI) and primary language. Within race effects of ADI and primary language were measured using logistic regression.\n\nResults5,577 COVID-19 patients were included, 866 (n=15.5%) were hospitalized within 45 days of diagnosis. Hospitalized patients were older (60.9 vs. 40.4 years, p<0.001) and more likely to be male (n=425 [49.1%] vs. 2,049 [43.5%], p=0.002). Of those requiring hospitalization, 43.9% (n=381), 19.9% (n=172), 18.6% (n=161), and 11.8% (n=102) were White, Black, Asian, and Hispanic, respectively.\n\nIndependent of ADI, minority race/ethnicity was associated with COVID-19 severity; Hispanic patients (OR 3.8, 95% CI 2.72-5.30), Asians (OR 2.39, 95% CI 1.74-3.29), and Blacks (OR 1.50, 95% CI 1.15-1.94). ADI was not associated with hospitalization. Non-English speaking (OR 1.91, 95% CI 1.51-2.43) significantly increased odds of hospital admission across and within minority groups.\n\nConclusionsMinority populations have increased odds of severe COVID-19 independent of neighborhood deprivation, a commonly suspected driver of disparate outcomes. Non-English-speaking accounts for differences across and within minority populations. These results support the continued concern that racism contributes to disparities during COVID-19 while also highlighting the underappreciated role primary language plays in COVID-19 severity across and within minority groups.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDoes socioeconomic factors or primary language account for racial disparities in COVID-19 disease severity?\n\nFindingsIn this observational study of 5,577 adults, race/ethnicity minorities and non-English as a primary language, independent of neighborhood-level deprivation, are associated with increased risk of severe COVID-19 disease.\n\nMeaningSocioeconomic factors do not account for racial/ethnic disparities related to COVID-19 severity which supports further investigation into the racism and highlights the need to focus on our non-English speaking populations.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Nicholas E Ingraham", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Laura N. Purcell", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Basil S. Karam", - "author_inst": "Medical College of Wisconsin" - }, - { - "author_name": "R. Adams Dudley", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Michael G. Usher", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Christopher A. Warlick", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Michelle L. Allen", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Genevieve B. Melton", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Anthony Charles", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Christopher J. Tignanelli", - "author_inst": "University of Minnesota" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.09.02.20186833", "rel_title": "Correction in Active Cases Data of COVID-19 for the US States by Analytical study", @@ -1203758,6 +1204460,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.02.20186916", + "rel_title": "Maximizing and evaluating the impact of test-trace-isolate programs", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186916", + "rel_abs": "September 2, 2020\n\nBackgroundTest-trace-isolate programs are an essential part of COVID-19 control that offer a more targeted approach than many other non-pharmaceutical interventions. Effective use of such programs requires methods to estimate their current and anticipated impact.\n\nMethods and FindingsWe present a mathematical modeling framework to evaluate the expected reductions in the reproductive number, R, from test-trace-isolate programs. This framework is implemented in a publicly available R package and an online application. We evaluated the effects of case detection, speed of isolation, contact tracing completeness and speed of quarantine using parameters consistent with COVID-19 transmission (R0 = 2.5, generation time 6.5 days). We show that R is most sensitive to changes to the proportion of infections detected in almost all scenarios, and other metrics have a reduced impact when case detection levels are low (< 30%). Although test-trace-isolate programs can contribute substantially to reducing R, exceptional performance across all metrics is needed to bring R below one through test-trace-isolate alone, highlighting the need for comprehensive control strategies. Formally framing the dynamical process also indicates that metrics used to evaluate performance of test-trace-isolate, such as the proportion of identified infections among traced contacts, may be misleading. While estimates of program performance are sensitive to assumptions about COVID-19 natural history, our qualitative findings are robust across numerous sensitivity analyses.\n\nConclusionsEffective test-trace-isolate programs first need to be strong in the \"test\" component, as case detection underlies all other program activities. Even moderately effective test-trace-isolate programs are an important tool for controlling the COVID-19 pandemic, and can alleviate the need for more restrictive social distancing measures.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kyra H Grantz", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Elizabeth C Lee", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Lucy D'Agostino McGowan", + "author_inst": "Department of Mathematics and Statistics, Wake Forest University" + }, + { + "author_name": "Kyu Han Lee", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "C. Jessica E. Metcalf", + "author_inst": "Department of Ecology and Evolutionary Biology, Princeton University; Princeton School of Public and International Affairs, Princeton University" + }, + { + "author_name": "Emily S Gurley", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Justin Lessler", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.02.20186734", "rel_title": "Could seasonal influenza vaccination influence COVID-19 risk?", @@ -1205038,57 +1205783,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2020.09.02.20185199", - "rel_title": "Development and validation of a multiplex bead based assay for the detection of antibodies directed against SARS-CoV-2 proteins", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20185199", - "rel_abs": "Transplant recipients who develop COVID-19 may be at increased risk for morbidity and mortality. Determining antibody status against SARS-CoV-2 in candidates and recipients will be important to understand the epidemiology and clinical course of COVID-19 infection in this population. There are multiple antibody tests to detect antibodies to SARS-CoV-2, but their performance varies according to their platforms and the antigenic targets, making interpretation of the results challenging. Additionally, currently available serological tests do not exclude the possibility that positive responses are due to cross reactive antibodies to community coronaviruses. This study describes the development and validation of a high throughput multiplex bead based antibody detection assay with the capacity to identify, simultaneously, patient responses to five distinct SARS-CoV-2 proteins. The antibody response to these proteins are SARS-CoV-2 specific as antibodies against four community coronaviruses do not cross-react. Assay configuration is essentially identical to the single antigen bead assays used in the majority of histocompatibility laboratories around the world and could easily be implemented into routine screening of transplant candidates and recipients. This new assay provides a novel tool to interrogate the spectrum of immune responses to SAR-CoV-2 and is uniquely suitable for use in the transplant setting.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Robert A Bray", - "author_inst": "Emory University Hospital" - }, - { - "author_name": "Jar-How Lee", - "author_inst": "terasaki Innovation Center" - }, - { - "author_name": "Peter Brescia", - "author_inst": "Th-ermo-Fisher Scientific" - }, - { - "author_name": "Deepali Kumar", - "author_inst": "University Health Network, Toronto, Ontario, Canada" - }, - { - "author_name": "Thoa Nong", - "author_inst": "Thermo-Fisher Scientific" - }, - { - "author_name": "Remi Shih", - "author_inst": "Thermo-Fisher Scientific" - }, - { - "author_name": "E Steve Woodle", - "author_inst": "University of Cincinnati School of Medicine" - }, - { - "author_name": "Jonathan S Maltzman", - "author_inst": "Stanford University School of Medicine and VA Palo Alto Health Care System, Palo Alto, CA" - }, - { - "author_name": "Howard M Gebel", - "author_inst": "Emory University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.01.20185777", "rel_title": "Clinical evaluation of BD Veritor SARS-CoV-2 point-of-care test performance compared to PCR-based testing and versus the Sofia SARS Antigen point-of-care test.", @@ -1205384,6 +1206078,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.01.20184101", + "rel_title": "Rapid 'mix and read' assay for scalable detection of SARS-CoV-2 antibodies in patient plasma", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20184101", + "rel_abs": "The human beta coronavirus SARS-CoV-2, causative virus of COVID-19, has infected more than 15 million people globally and continues to spread. Widespread, population level testing to detect active and past infections is critical to curb the COVID-19 pandemic. Antibody (serological) testing is the only option for detecting past infections outside the narrow window accessible to nucleic acid-based tests. However, currently available serological assays commonly lack scalability. Here, we describe the development of a rapid homogenous serological assay for the detection of antibodies to SARS-CoV-2 in patient plasma. We show that the fluorescence-based assay accurately detects seroconversion in COVID-19 patients from less than 1 L of plasma. Using a cohort of samples from COVID-19 infected or healthy individuals, we demonstrate detection with 100% sensitivity and specificity. This assay addresses an important need for a robust, low barrier to implementation, and scalable serological assay with complementary strengths to currently available serological platforms.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Hong Yue", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Rados\u0142aw P Nowak", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "Daan Overwijn", + "author_inst": "Dana-Farber Cancer Institute" + }, + { + "author_name": "N Connor Payne", + "author_inst": "Harvard University" + }, + { + "author_name": "Stephanie Fischinger", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Caroline Atyeo", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Lindsey R Baden", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Eric James Nilles", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Elizabeth W Karlson", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Xu G Yu", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Jonathan Z Li", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Ralph Mazitschek", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Eric S Fischer", + "author_inst": "Dana-Farber Cancer Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.02.20186742", "rel_title": "The role of masks in reducing the risk of new waves of COVID-19 in low transmission settings: a modeling study", @@ -1206464,61 +1207229,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.29.20184317", - "rel_title": "Excess cardiovascular deaths in the beginning of COVID-19 outbreak", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20184317", - "rel_abs": "ImportanceThe healthcare demand created by the COVID-19 pandemic was far beyond the hospital surge capacity in many countries, resulting in possible negative influence on prognosis of other severe diseases, such as cardiovascular disease (CVD).\n\nObjectiveTo assess the impact of the COVID-19 outbreak on CVD-related hospitalizations and mortality.\n\nDesignCommunity-based prospective cohort study.\n\nSetting the UK Biobank population.\n\nParticipants421,717 UK Biobank participants who were registered in England and alive on December 1st 2019.\n\nMain outcomes and measuresThe primary outcome of interest was CVD death, as deaths with CVD as a cause of death according to the death registers. We retrieved information on hospitalizations with CVD as the primary diagnosis based on the UK Biobank hospital inpatient data. The study period was between December 1st 2019 and May 30th 2020, and we used the same calendar period of the three preceding years as the reference period. Standardized mortality/incidence ratios (SMRs/SIRs) with 95% confidence intervals were used to estimate the relative risk of CVD outcomes during the study period, compared with the reference period, to control for seasonal variations and aging of the study population.\n\nResultsWe observed a distinct increase in CVD-related deaths in March and April 2020 as compared to the corresponding months of the three preceding years. The observed number of CVD death (n=217) was almost doubled in April, compared with the expected number (n=120), corresponding to an SMR of 1.81 (95% CI 1.58-2.06). We observed a sharp decline of CVD hospitalization in March (n=841) and April (n=454), compared with the expected number (n=1208 for March and 1026 for April), leading to an SIR of 0.70 (95% CI 0.65-0.74) for March and 0.44 (95% CI 0.40-0.48) for April. There was also a clear increase of death, but a clear decrease of hospitalization, in March and April for all the five major subtypes of CVD.\n\nConclusionsWe observed a distinct excess in CVD deaths in the beginning of the COVID-19 outbreak in the UK Biobank population. In addition to CVD complications of SARS-CoV-2 infections, the reduced hospital capacity might have contributed to the observed excess CVD deaths.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow did the COVID-19 outbreak affect rates of CVD-related death and hospitalization?\n\nFindingIn this prospective study involving 421,717 UK Biobank participants, we observed excess CVD-related mortality in parallel with decreased CVD-related hospitalization in the beginning of the COVID-19 pandemic, March and April 2020.\n\nMeaningIn addition to severe SARS-CoV-2 infection progressing to CVD-related death, reduced hospital resources might have partially contributed to the excess CVD mortality.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Junren Wang", - "author_inst": "Sichuan University" - }, - { - "author_name": "Jianwei Zhu", - "author_inst": "Sichuan University" - }, - { - "author_name": "Huazhen Yang", - "author_inst": "Sichuan University" - }, - { - "author_name": "Yao Hu", - "author_inst": "Sichuan University" - }, - { - "author_name": "Yajing Sun", - "author_inst": "Sichuan University" - }, - { - "author_name": "Zhiye Ying", - "author_inst": "Sichuan University" - }, - { - "author_name": "Yuanyuan Qu", - "author_inst": "Sichuan University" - }, - { - "author_name": "Unnur A Valdimarsdottir", - "author_inst": "University of Iceland" - }, - { - "author_name": "Fang Fang", - "author_inst": "Karolinska Institutet" - }, - { - "author_name": "Huan Song", - "author_inst": "Sichuan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.29.20182899", "rel_title": "Cytotoxic lymphocytes are dysregulated in multisystem inflammatory syndrome in children", @@ -1207090,6 +1207800,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.29.20184176", + "rel_title": "Estimating Unreported Deaths Associated with COVID-19", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20184176", + "rel_abs": "Efforts to mitigate the spread of coronavirus disease 2019 (COVID-19) in the United States require an accurate understanding of how the epidemic is progressing. The National Center for Health Statistics (NCHS) releases weekly numbers of deaths attributed to a set of select causes, including deaths from COVID-19 in the entire United States (US), by state, and cumulatively for individual counties. Comparing US and state level deaths from select causes recorded in 2020 with values from 2014-2019 identifies a number of differences that exceeded 95% confidence limits on historical mean values, including three states with deaths possibly from COVID-19 in December 2019. Comparing county-level NCHS datasets with county-level data on deaths from COVID-19 compiled by four public pandemic tracking sites suggests that a large number of COVID-19 deaths have not yet been reported to the NCHS. Dividing the numbers of COVID-19 deaths counted by the public tracking sites by the percentage of COVID-19 deaths reported to the NCHS suggests that approximately 20% of all US deaths from Natural Causes, as many as 200,000, may not yet have been reported to the NCHS. Evaluating changes in the fractions of deaths attributed to COVID-19 and other specific causes or nonspecific outcomes during the epidemic, relative to 2020 totals or historical mean values, can provide a valuable perspective on the public health consequences of COVID-19.\n\nSignificance StatementEstimating total deaths from natural causes using the percentage of natural cause deaths from COVID-19 reported to the CDC and the number of COVID-19 deaths counted by public tracking sites suggests that up to 200,000 deaths from natural causes between 22 April and 15 August, 2020, around 20% of the total recorded as of 26 August, have not yet been reported to the CDC.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Benjamin Stear", + "author_inst": "The Children's Hospital of Philadelphia" + }, + { + "author_name": "Kyle Hernandez", + "author_inst": "University of Chicago," + }, + { + "author_name": "Vidya Manian", + "author_inst": "University of Puerto Rico" + }, + { + "author_name": "Som Dutta", + "author_inst": "Utah State University" + }, + { + "author_name": "Deanne Taylor", + "author_inst": "University of Pennsylvania Perelman Medical School" + }, + { + "author_name": "Catharine Conley", + "author_inst": "NASA Ames Research Center" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.30.20184804", "rel_title": "To isolate or not to isolate: The impact of changing behavior on COVID-19 transmission", @@ -1208470,57 +1209219,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.01.20185850", - "rel_title": "Non-alcoholic fatty liver disease (NAFLD) and risk of hospitalization for Covid-19.", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20185850", - "rel_abs": "BackgroundCovid-19 disease causes significant morbidity and mortality through increase inflammation and thrombosis. Non-alcoholic fatty liver disease and non-alcoholic steatohepatitis are states of chronic inflammation and indicate advanced metabolic disease. We sought to understand the risk of hospitalization for Covid-19 associated with NAFLD/NASH.\n\nMethodsRetrospective analysis of electronic medical record data of 6,700 adults with a positive SARS-CoV-2 PCR from March 1, 2020 to Aug 25, 2020. Logistic regression and competing risk were used to assess odds of being hospitalized. Additional adjustment was added to assess risk of hospitalization among patients with a prescription for metformin use within the 3 months prior to the SARS-CoV-2 PCR result, history of home glucagon-like-peptide 1 receptor agonist (GLP-1 RA) use, and history of metabolic and bariatric surgery (MBS). Interactions were assessed by gender and race.\n\nResultsA history of NAFLD/NASH was associated with increased odds of admission for Covid-19: logistic regression OR 2.04 (1.55, 2.96, p<0.01), competing risks OR 1.43 (1.09-1.88, p<0.01); and each additional year of having NAFLD/NASH was associated with a significant increased risk of being hospitalized for Covid-19, OR 1.86 (1.43-2.42, p<0.01). After controlling for NAFLD/NASH, persons with obesity had decreased odds of hospitalization for Covid-19, OR 0.41 (0.34-0.49, p<0.01). NAFLD/NASH increased risk of hospitalization in men and women, and in all racial/ethnic subgroups. Mediation treatments for metabolic syndrome were associated with non-significant reduced risk of admission: OR 0.42 (0.18-1.01, p=0.05) for home metformin use and OR 0.40 (0.14-1.17, p=0.10) for home GLP-1RA use. MBS was associated with a significant decreased risk of admission: OR 0.22 (0.05-0.98, p<0.05).\n\nConclusionsNAFLD/NASH is a significant risk factor for hospitalization for Covid-19, and appears to account for risk attributed to obesity. Treatments for metabolic disease mitigated risks from NAFLD/NASH. More research is needed to confirm risk associated with visceral adiposity, and patients should be screened for and informed of treatments for metabolic syndrome.\n\nKey QuestionsO_ST_ABSQuestionC_ST_ABSDoes NAFLD/NASH independently increase risk for poor outcomes from Covid-19?\n\nFindingsIn this observational study, a history of NAFLD/NASH was associated with a significantly increased odds of hospitalization. Metabolic surgery was protective against admission in persons with NAFLD/NASH and Covid-19. Metformin and glucagon like peptide 1 receptor agonists were associated with non-significant protecting against admission.\n\nMeaningTreatment for metabolic syndrome greatly reduce the elevated risk of hospitalization for Covid-19 among persons with NAFLD/NASH.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Carolyn Bramante", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Christopher J. Tignanelli", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Nirjhar Dutta", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Emma Jones", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Leonardo Tamariz", - "author_inst": "University of Miami" - }, - { - "author_name": "Jeanne M Clark", - "author_inst": "Johns Hopkins" - }, - { - "author_name": "Michael Usher", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Genevieve Metlon-Meaux", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Sayeed Ikramuddin", - "author_inst": "University of Minnesota" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2020.09.01.20178848", "rel_title": "Mental healthcare and service user impact of the COVID-19 pandemic: results of a UK survey of staff working with people with intellectual disability and developmental disorders", @@ -1208864,6 +1209562,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.08.31.20185314", + "rel_title": "HYDROXICLOROQUINE FOR PRE-EXPOSURE PROPHYLAXIS FOR SARS-CoV-2", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20185314", + "rel_abs": "SARS-CoV-2 infection has a high transmission level. At the present time there is not a specific treatment approved but it is known that, in vitro, chloroquine and hydroxychloroquine can inhibit the coronavirus.\n\nObjectiveverifying if patients with autoimmune diseases that are on treatment with HCQ have less incidence and severity on COVID-19.\n\nMaterial and methodsthis is a retrospective cohort study. The exposed cohort was formed by individuals with autoimmune diseases with HCQ treatment. The control cohort was randomly selected using the Health Card database. To deal with confounding variables and evaluate the effect of HCQ on the incidence and severity of SARS-CoV-2 infection, propensity score matching was used. Risk difference and paired percentage difference between exposed and non-exposed groups was estimated.\n\nResults919 individuals formed the exposed cohort and 1351 the control cohort. After matching, there were 690 patients on each group. During the time of the study, in the exposed group there were 42 (6.1%) individuals with suspected COVID-19, 12(1.7%) with confirmed COVID-19 and 3(0.4%) were hospitalized. In the control group there were 30(4.3%) individuals with suspected COVID-19, 13(1.9%) with confirmed COVID-19 and 2(0.3%) were hospitalized. The risk difference between each cohort was: 0.017(-0.05-0.04) for suspected COVID-19; -0.014(-0.015-0.012) for confirmed COVID-19 and 0.001(-0.007-0.007) for hospitalized patients. There were not significant differences.\n\nConclusionthere is no difference neither on the incidence nor on the severity of COVID-19 between patients with autoimmune diseases with HCQ treatment and patients that do not take HCQ.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jaime Lopez de la Iglesia", + "author_inst": "GAP Leon" + }, + { + "author_name": "Naiara Cubelos", + "author_inst": "Licenciada en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Roi Naveiro", + "author_inst": "Instituto de Ciencias Matematicas. Estadistica e investigacion operativa. Consejo Superior de Investigacion Cientifica (ICMAT-CSIC)." + }, + { + "author_name": "Marina Montoro Gomez", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)" + }, + { + "author_name": "Francisco Javier Gonzalez de Haro", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Maria Ajenjo Gonzalez", + "author_inst": "Doctora en Medicina.GAP Leon (Spain)" + }, + { + "author_name": "Estefania Tobal Vicente", + "author_inst": "Doctora en Medicina. GAP Leon (Spain)" + }, + { + "author_name": "Maria Lamuedra Gil de Gomez", + "author_inst": "Graduada en Medicina. GAP Leon (Spain)" + }, + { + "author_name": "Maria Teresa Nuevo Guisado", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Isabel Torio Gomez", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Ana Penalver Andrada", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Nuria Martinez Cao", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Paula Gonzalez Figaredo", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Carlos Robles Garcia", + "author_inst": "Graduado en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Lidia Anastasia Alvarado Machon", + "author_inst": "Doctora en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Angeles Lafont Alcalde", + "author_inst": "Doctora en Medicina. GAP Leon (Spain)." + }, + { + "author_name": "Jose Cesareo Naveiro Rilo", + "author_inst": "Doctor en Salud Publica y Medicina Preventiva. Unidad Docente de Medicina Familiar y Comunitaria de Leon (Spain)." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2020.09.01.20183145", "rel_title": "Impact of COVID-19 pandemic on cancer care delivery : A Real World Experience", @@ -1210296,125 +1211077,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.26.20182246", - "rel_title": "Prevalence and risk factors of disability and anxiety in a retrospective cohort of 432 survivors of Coronavirus Disease-2019 (Covid-19) from China", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20182246", - "rel_abs": "ObjectiveTo estimate the prevalence of disability and anxiety in Covid-19 survivors at discharge from hospital and analyze relative risk by exposures.\n\nDesignMulti-center retrospective cohort study.\n\nSettingTwenty-eight hospitals located in eight provinces of China.\n\nMethodsA total of 432 survivors with laboratory-confirmed SARS CoV-2 infection participated in this study. At discharge, we assessed instrumental activities of daily living (IADL) with Lawtons IADL scale, dependence in activities of daily living (ADL) with the Barthel Index, and anxiety with Zungs self-reported anxiety scale. Exposures included comorbidity, smoking, setting (Hubei vs. others), disease severity, symptoms, and length of hospital stay. Other risk factors considered were age, gender, and ethnicity (Han vs. Tibetan).\n\nResultsPrevalence of at least one IADL problem was 36.81% (95% CI: 32.39-41.46). ADL dependence was present in 16.44% (95% CI: 13.23-20.23) and 28.70% (95% CI: 24.63-33.15) were screened positive for clinical anxiety. Adjusted risk ratio (RR) of IADL limitations (RR 2.48, 95% CI: 1.80-3.40), ADL dependence (RR 2.07, 95% CI 1.15-3.76), and probable clinical anxiety (RR 2.53, 95% CI 1.69-3.79) were consistently elevated in survivors with severe Covid-19. Age was an additional independent risk factor for IADL limitations and ADL dependence; and setting (Hubei) for IADL limitations and anxiety. Tibetan ethnicity was a protective factor for anxiety but a risk factor for IADL limitations.\n\nConclusionA significant proportion of Covid-19 survivors had disability and anxiety at discharge from hospital. Health systems need to be prepared for an additional burden resulting from rehabilitation needs of Covid-19 survivors.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Siyi Zhu", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Qiang Gao", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Lin Yang", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Yonghong Yang", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Wenguang Xia", - "author_inst": "Hubei Hospital of Integrated Traditional Chinese and Western Medicine" - }, - { - "author_name": "Xiguo Cai", - "author_inst": "Henan Provincial People's Hospital" - }, - { - "author_name": "Yanping Hui", - "author_inst": "The Second Affiliated Hospital, Medical College of Xi'an Jiaotong University" - }, - { - "author_name": "Di Zhu", - "author_inst": "Zhejiang provincial People's Hospital" - }, - { - "author_name": "Yanyan Zhang", - "author_inst": "Qilu Hospital of Shandong University" - }, - { - "author_name": "Guiqing Zhang", - "author_inst": "The First Affiliated Hospital, School of Medicine, Shihezi University" - }, - { - "author_name": "Shuang Wu", - "author_inst": "The Affiliated Hospital of Guizhou Medical University" - }, - { - "author_name": "Yiliang Wang", - "author_inst": "Chongqing Three Gorges Central Hospital" - }, - { - "author_name": "Zhiqiang Zhou", - "author_inst": "Inner Mongolia Autonomous Region Baotou Central Hospital" - }, - { - "author_name": "Hongfei Liu", - "author_inst": "General Hospital of General Bureau of Agricultural Reclamation of Heilongjiang Province" - }, - { - "author_name": "Changjie Zhang", - "author_inst": "The Second Xiangya Hospital of Central South University" - }, - { - "author_name": "Bo Zhang", - "author_inst": "Nanchong central hospital" - }, - { - "author_name": "Jianrong Yang", - "author_inst": "Garze People's Hospital" - }, - { - "author_name": "Mei Feng", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Zhong Ni", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Baoyu Chen", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Chunping Du", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Hongchen He", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Yun Qu", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Quan Wei", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Chengqi He", - "author_inst": "West China Hospital, Sichuan University" - }, - { - "author_name": "Jan D. Reinhardt", - "author_inst": "Institute for Disaster Management and Reconstruction of Sichuan University and Hong Kong Polytechnic University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.26.20182204", "rel_title": "Identifying COVID-19 cases in primary care settings", @@ -1210770,6 +1211432,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.08.27.20182923", + "rel_title": "Evaluation of production lots of a rapid point-of-care lateral flow serological test intended for identification of IgM and IgG against the N-terminal part of the spike protein (S1) of SARS-CoV-2", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20182923", + "rel_abs": "Background and objectivesSeveral antibody tests are available to detect SARS-CoV-2 specific antibodies, many of which address different antigens. Rapid point-of-care (POC) tests have been doubted due to an eventual risk of production errors, although it is unstudied whether such error would affect test sensitivity and/or specificity. We aimed to evaluate two separate production lots of a commercially available test intended for rapid detection of IgM and IgG against the N-terminal part of the SARS-CoV-2 spike protein (S1).\n\nMaterials and methodsSerum samples from individuals with confirmed SARS-CoV-2 infection, by RT-PCR and/or serology, and pre-COVID-19 negative control sera gathered from a biobank during 2018 were collected. The presence of anti-S1 IgM/IgG was verified by an in-house Luminex-based serological assay, serving as reference method. The index test was a commercially available rapid POC-test (the COVID-19 IgG/IgM Rapid Test Cassette [Zhejiang Orient Gene Biotech Co Ltd, Huzhou, Zhejiang, China/Healgen Scientific, LLC, U.S.A.]).\n\nResultsOne hundred samples were verified positive for anti-S1 IgG (median fluorescence intensity (MFI) [≥]900) and 74 for anti-S1 IgM (MFI [≥]700), confirmed by RT-PCR (n=90) and/or serology (n=89). None of the negative controls (n=200; MFI <300) had SARS-CoV-2 anti-S1 IgM, while one tested positive for SARS-CoV-2 anti-S1 IgG. For the two lots, the sensitivities of the rapid test were 93.2% (69/74; 95% CI: 85.1% - 97.1%) and 87.8% (65/74; 95% CI: 78.5% - 93.5%) for IgM, respectively 93.0% (93/100; 95% CI: 86.3% - 96.6%) and 100.0% for IgG (100/100; 95% CI: 96.3% - 100.0%). The specificity for both lots was 100% for IgM (200/200; 95% CI: 98.1% - 100%) and 99.5% for IgG (199/200; 95% CI: 97.2% - 99.9%). The positive predictive value was 100% for IgM and 98.9% and 99.0% for IgG. The negative predictive value was 95.7% and 97.6% for IgM, and 96.6% and 100.0% for IgG.\n\nConclusionThe rapid POC-test used in this study is suitable to assess SARS-CoV-2 anti-S1 specific IgM/IgG, as a measure of previous virus exposure on an individual level. While the specificity was not affected by production lot, external validation of separate lots of rapid POC-tests is encouraged to ensure high sensitivity before market introduction.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tove Hoffman", + "author_inst": "Uppsala University" + }, + { + "author_name": "Linda Kolstad", + "author_inst": "Uppsala University" + }, + { + "author_name": "Bengt Ronnberg", + "author_inst": "Uppsala University Hospital" + }, + { + "author_name": "Ake Lundkvist", + "author_inst": "Uppsala University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.26.20182675", "rel_title": "Epidemiological and socio-economic characteristics of the COVID-19 spring outbreak in Quebec, Canada: A population-based study", @@ -1212106,57 +1212799,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.27.20170589", - "rel_title": "Practical challenges to the clinical implementation of saliva for SARS-CoV-2 detection", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20170589", - "rel_abs": "Due to global shortages of flocked nasopharyngeal swabs and appropriate viral transport media during the COVID-19 pandemic, alternate diagnostic specimens for SARS-CoV-2 detection are sought. The accuracy and feasibility of saliva samples collected and transported without specialized collection devices or media were evaluated. Saliva demonstrated good concordance with paired nasopharyngeal swabs for SARS-CoV-2 detection in 67/74 cases (90.5%), though barriers to saliva collection were observed in long-term care residents and outbreak settings. SARS-CoV-2 RNA was stable in human saliva at room temperature for up to 48 hours after initial specimen collection, informing appropriate transport time and conditions.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Nancy Matic", - "author_inst": "Providence Health Care" - }, - { - "author_name": "Aleksandra Stefanovic", - "author_inst": "Providence Health Care" - }, - { - "author_name": "Victor Leung", - "author_inst": "Providence Health Care" - }, - { - "author_name": "Tanya Lawson", - "author_inst": "Providence Health Care" - }, - { - "author_name": "Gordon Ritchie", - "author_inst": "Providence Health Care" - }, - { - "author_name": "Lynne Li", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Sylvie Champagne", - "author_inst": "Providence Health Care" - }, - { - "author_name": "Marc G. Romney", - "author_inst": "Providence Health Care" - }, - { - "author_name": "Christopher F. Lowe", - "author_inst": "Providence Health Care" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.28.20183475", "rel_title": "A Systematic Review of Droplet and Aerosol Generation in Dentistry", @@ -1212372,6 +1213014,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.26.20182477", + "rel_title": "Modelling COVID-19 contagion:Risk assessment and targeted mitigation policies", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20182477", + "rel_abs": "We use a spatial epidemic model with demographic and geographic heterogeneity to study the regional dynamics of COVID-19 across 133 regions in England.\n\nOur model emphasises the role of variability of regional outcomes and heterogeneity across age groups and geographic locations, and provides a framework for assessing the impact of policies targeted towards sub-populations or regions. We define a concept of efficiency for comparative analysis of epidemic control policies and show targeted mitigation policies based on local monitoring to be more efficient than country-level or non-targeted measures. In particular, our results emphasise the importance of shielding vulnerable sub-populations and show that targeted policies based on local monitoring can considerably lower fatality forecasts and, in many cases, prevent the emergence of second waves which may occur under centralised policies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rama Cont", + "author_inst": "University of Oxford" + }, + { + "author_name": "RenYuan Xu", + "author_inst": "University of Oxford" + }, + { + "author_name": "Artur Kotlicki", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.26.20181990", "rel_title": "Empowering the crowd: Feasible strategies to minimize the spread of COVID-19 in high-density informal settlements", @@ -1213716,61 +1214385,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.28.20182295", - "rel_title": "healthcareCOVID: A national cross-sectional observational study identifying risk factors for developing suspected or confirmed COVID-19 in UK healthcare workers", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.28.20182295", - "rel_abs": "ObjectiveTo establish the prevalence and risk factors for the development of suspected or confirmed coronavirus disease 2019 (COVID-19) infection among healthcare workers (HCWs) in the United Kingdom (UK).\n\nDesignCross-sectional observational study.\n\nSettingUK-based primary and secondary care.\n\nParticipantsHCWs aged [≥]18 years working between 1 February and 25 May 2020.\n\nMain outcome measuresA composite endpoint of laboratory-confirmed diagnosis of SARS-CoV-2, or self-isolation or hospitalisation due to suspected or confirmed COVID-19.\n\nResultsOf 6152 eligible responses, the composite endpoint was present in 1806 (29.4%) HCWs, of whom 49 (0.8%) were hospitalised, 459 (7.5%) tested positive for SARS-CoV-2, and 1776 (28.9%) reported self-isolation. The strongest risk factor associated with the presence of the primary composite endpoint was increasing frequency of contact with suspected or confirmed COVID-19 cases without adequate personal protective equipment (PPE): \"Never\" (reference), \"Rarely\" (adjusted odds ratio 1.06, (95% confidence interval: 0.87 to 1.29)), \"Sometimes\" (1.7 (1.37 to 2.10)), \"Often\" (1.84 (1.28 to 2.63)), \"Always\" (2.93, (1.75 to 5.06)). Additionally, several comorbidities (cancer, respiratory disease, and obesity); working in a doctors role; using public transportation for work; regular contact with suspected or confirmed COVID-19 patients; and lack of PPE were also associated with the presence of the primary endpoint. 1382 (22.5%) HCWs reported lacking access to PPE items while having clinical contact with suspected or confirmed COVID-19 cases. Overall, between 11,870 and 21,158 days of self-isolation were required by the cohort, equalling approximately 71 to 127 working days lost per 1000 working days.\n\nConclusionsSuspected or confirmed COVID-19 was more common in HCWs than in the general population. Risk factors included inadequate PPE, which was reported by nearly a quarter of HCWs. Governments and policymakers must ensure adequate PPE is available as well as developing strategies to mitigate risk for high-risk HCWs during future COVID-19 waves.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Justin Kua", - "author_inst": "National Institute of Academic Anaesthesia, Royal College of Anaesthetists" - }, - { - "author_name": "Reshma Patel", - "author_inst": "National Institute of Academic Anaesthesia, Royal College of Anaesthetists" - }, - { - "author_name": "Eveliina Nurmi", - "author_inst": "Department of Anaesthesia, University College London Hospitals NHS Foundation Trust" - }, - { - "author_name": "Sarah Tian", - "author_inst": "Department of Anaesthesia, Guys and St Thomas NHS Foundation Trust" - }, - { - "author_name": "Harpreet Gill", - "author_inst": "Department of Anaesthesia, Guys and St Thomas NHS Foundation Trust" - }, - { - "author_name": "Calvin Moorley", - "author_inst": "London South Bank University" - }, - { - "author_name": "Danny JN Wong", - "author_inst": "Department of Anaesthesia, Guys and St Thomas NHS Foundation Trust" - }, - { - "author_name": "Dmitri Nepogodiev", - "author_inst": "National Institute for Health Research Global Health Research Unit on Global Surgery, University of Birmingham" - }, - { - "author_name": "Imran Ahmad", - "author_inst": "Department of Anaesthesia, Guys and St Thomas NHS Foundation Trust" - }, - { - "author_name": "Kariem El-Boghdadly", - "author_inst": "Department of Anaesthesia, Guys and St Thomas NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.28.20184010", "rel_title": "COVID-19 Seroprevalence in Baixada Santista Metropolitan Area, Sao Paulo, Brazil.", @@ -1214050,6 +1214664,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.08.29.20126201", + "rel_title": "Sex-based clinical and immunological differences in COVID-19", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20126201", + "rel_abs": "BackgroundMales and females differ in their immunological responses to foreign pathogens. However, most of the current COVID-19 clinical practices and trials do not take sex as consideration.\n\nMethodsWe performed an unbiased sex-based comparative analysis for the clinical outcomes, peripheral immune cells, and SARS-CoV-2 specific antibody levels of 1,558 males and 1,499 females COVID-19 patients from a single center. The lymphocyte subgroups were measured by Flow cytometry. Total antibody, Spike protein (S)-, receptor binding domain (RBD)-, and nucleoprotein (N)-specific IgM and IgG levels were measured by chemiluminescence.\n\nResultsWe found that the mortality and ICU admission rates were approximately 2-fold higher in males than that in females (P<0.005). Survival analysis revealed that sex is an independent prognostic factor for COVID-19 (Hazard ratio=2.2, P=0.003). The concentration of inflammatory factors in peripheral blood was significantly higher in males. Besides, the renal and hepatic abnormality induced by COVID-19 was more common in males during the hospitalization. The analysis of lymphocyte subsets revealed that the percentage of CD19+ B cell and CD4+ T cell was significantly higher in females (P<0.001) during hospitalization, indicating the stronger humoral immunity in females than males. Notably, the protective IgG sharply increased and reached a peak in the fourth week after symptom onset in females, while gradually increased and reached a peak in the seventh week in males.\n\nConclusionsThe unfavorable prognosis of male COVID-19 patients may result from the weak humoral immunity and indolent antibody responses during SARS-CoV-2 infection and recovery. Early medical intervention and close monitoring are important, especially for male COVID-19 patients. Hormonal or convalescent plasma therapy may help improve the immunity of males to fight against SARS-CoV-2 infection.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Kening Li", + "author_inst": "COVID-19 Research Center, Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine" + }, + { + "author_name": "Bin Huang", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Yun Cai", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Zhihua Wang", + "author_inst": "Department of Laboratory Medicine & Blood Transfusion, the 907th Hospital" + }, + { + "author_name": "Lu Li", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Lingxiang Wu", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Mengyan Zhu", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Jie Li", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Ziyu Wang", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Min Wu", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Wanlin Li", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Wei Wu", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Lishen Zhang", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + }, + { + "author_name": "Xinyi Xia", + "author_inst": "COVID-19 Research Center, Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine" + }, + { + "author_name": "Shukui Wang", + "author_inst": "Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University" + }, + { + "author_name": "Qianghu Wang", + "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.27.20183616", "rel_title": "A Comparison of Covid-19 Patient Characteristics Before versus After Partial Lockdown in Vietnam", @@ -1215454,121 +1216147,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.08.24.20177576", - "rel_title": "Clinical Features Associated with COVID-19 Outcome in MM: First Results from International Myeloma Society COVID-19 Dataset", - "rel_date": "2020-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20177576", - "rel_abs": "The primary cause of morbidity and mortality in patients with multiple myeloma (MM) is an infection. Therefore there is great concern about the susceptibility to the outcome of COVID-19 infected patients with multiple myeloma.\n\nThis retrospective study describes the baseline characteristics and outcome data of COVID-19 infection in 650 patients with plasma cell disorders (98 outpatinets and 538 hospitilized patinets), collected from 10 countries by the International Myeloma Society to understand the initial challenges faced by Myeloma patients during COVID-19 pandemic. Descriptive statistics, univariate logistic regression, and multivariate analysis were performed for hospitalized MM patinets.\n\nThe median age was 69 years, and nearly all patients (96%) had MM. Approximately 36% were recently diagnosed (2019-2020), and 54% of patients were receiving first-line therapy. Thirty-three percent of patients have died, with significant geographic variability, ranging from 27% to 57% of hospitalized patients. Univariate analysis identified age, ISS3, high-risk disease, renal disease, suboptimal myeloma control (active or progressive disease), and one or more comorbidities as risk factors for higher rates of death. Neither history of transplant, including within a year of COVID-19 diagnosis nor other anti-MM treatments were associated with outcomes. Multivariate analysis found that only age, high-risk MM, renal disease, and suboptimal MM control remained independent predictors of adverse outcome with COVID-19 infection.\n\nThe management of MM in the era of COVID-19 requires careful consideration of patient and disease-related factors to decrease the risk of acquiring COVID-19 infection, while not compromising the disease control through appropriate MM treatment. This study provides the data to develop recommendations for the management of MM patients at risk of COVID-19 infection.\n\nKey PointsO_LIHigh but variable mortality for hospitalized MM patients (27% to 57%)\nC_LIO_LIOptimal MM control was associated with COVID-19 associated death for MM patinets\nC_LI\n\nExplanation of noveltyThis study investigated the risk and outcome of COVID-19 infection in MM patients globally (10 countries)", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Ajai Chari", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Mehmet K Samur", - "author_inst": "Dana Farber Cancer Institute and Harvard TH Chan School of Public Health, Boston, MA, USA" - }, - { - "author_name": "Joaquin Martinez-Lopez", - "author_inst": "Hospital Universitario 12 de Octubre, Octubre, i+12, CNIO, Complutense University, Madrid, Comunidad de Madrid, Spain" - }, - { - "author_name": "Gordon Cook", - "author_inst": "Leeds Institute of Clinical Trial Research & Leeds Cancer Centre, University of Leeds, Leeds, UK" - }, - { - "author_name": "Noa Biran", - "author_inst": "John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ, USA" - }, - { - "author_name": "Kwee Yong", - "author_inst": "Department of Haematology, University College London Hospitals NHS Foundation Trust, London, UK" - }, - { - "author_name": "Vania Hungria", - "author_inst": "Clinica Sao Germano, Sao Paulo, Brazil" - }, - { - "author_name": "Monika Engelhardt", - "author_inst": "Medical Department, Hematology, Oncology & Stem Cell Transplantation, Clinical Cancer Research Group, Freiburg, Faculty of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Francesca Gay", - "author_inst": "Myeloma Unit, Division of Hematology, University of Torino, Azienda Ospedaliero-Universitaria Citta della Salute e della Scienza di Torino, Italy" - }, - { - "author_name": "Ana Garcia-Feria", - "author_inst": "Department of Hematology, Hospital de Manises, Valencia, Spain" - }, - { - "author_name": "Stefania Oliva", - "author_inst": "Myeloma Unit, Division of Hematology, University of Torino, Azienda Ospedaliero-Universitaria Citta della Salute e della Scienza di Torino, Italy" - }, - { - "author_name": "Rimke Oostvogels", - "author_inst": "Department of Haematology, University Medical Centre, Utrecht, The Netherlands" - }, - { - "author_name": "Alessandro Gozzetti", - "author_inst": "University of Siena, Department of Hematology, Siena, Italy" - }, - { - "author_name": "Cara Rosenbaum", - "author_inst": "Center for Myeloma, New York Presbyterian Hospital-Weill Cornell Medical Center, New York, NY, USA" - }, - { - "author_name": "Shaji Kumar", - "author_inst": "The Division of Hematology, Mayo Clinic, Rochester, MN, USA" - }, - { - "author_name": "Edward A Stadtmauer", - "author_inst": "Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA" - }, - { - "author_name": "Hermann Einsele", - "author_inst": "Department of Internal Medicine II, University Hospital of Wurzburg, Wurzburg, Germany" - }, - { - "author_name": "Meral Beksac", - "author_inst": "Department of Hematology, Ankara University, Ankara, Turkey" - }, - { - "author_name": "Katja Weisel", - "author_inst": "II. Medizinische Klinik, Universitatsklinikum Hamburg-Eppendorf, Hamburg, Germany" - }, - { - "author_name": "Kenneth C Anderson", - "author_inst": "Dana Farber Cancer Institute and Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Maria-Victoria Mateos", - "author_inst": "University Hospital of Salamanca-Instituto de Investigacion Biomedica de Salamanca (IBSAL), Salamanca, Spain" - }, - { - "author_name": "Philippe Moreau", - "author_inst": "Department of Hematology, University Hospital Hotel-Dieu, Nantes, France and Intergroupe Francophone du Myelome (IFM)" - }, - { - "author_name": "Jesus San-Miguel", - "author_inst": "Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), Instituto de Investigacion Sanitaria de Navarra (IDISNA), Centro de Investigacio" - }, - { - "author_name": "Nikhil C Munshi", - "author_inst": "Dana Farber Cancer Institute and Harvard Medical School and VA Boston Healthcare System, Boston, MA" - }, - { - "author_name": "Herve Avet-Loiseau", - "author_inst": "25.\tCentre de Recherche en Cancerologie de Toulouse INSERM U1037, Toulouse, France, and Intergroupe Francophone du Myelome (IFM)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.08.25.20181651", "rel_title": "Face mask use in the Community for Reducing the Spread of COVID-19: a systematic review", @@ -1215924,6 +1216502,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.25.20181487", + "rel_title": "Risk of COVID-19 hospitalisation rises exponentially with age, inversely proportional to T-cell production", + "rel_date": "2020-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20181487", + "rel_abs": "Here we report that COVID-19 hospitalisation rates follow an exponential relationship with age, doubling for every 16 years of age or equivalently increasing by 4.5% per year of life (R2=0.98). This mirrors the well studied exponential decline of both thymus volume and T-cell production, which halve every 16 years. COVID-19 can therefore be added to the list of other diseases with this property, including those caused by MRSA, MERS-CoV, West Nile virus, Streptococcus Pneumonia and certain cancers, such as chronic myeloid leukemia and brain cancers. In addition, incidence of severe disease and mortality due to COVID-19 are both higher in men, consistent with the degree to which thymic involution (and the decrease in T-cell production with age) is more severe in men compared to women. Since these properties are shared with some non-contagious diseases, we hypothesised that the age-dependence does not come from social-mixing patterns, i.e. that the probability of hospitalisation given infection rises exponentially, doubling every 16 years. A Bayesian analysis of daily hospitalisations, incorporating contact matrices, found that this relationship holds for every age group except for the under 20s. While older adults have less contacts than young adults, our analysis suggests that there is an approximate cancellation between the effects of less contacts for the elderly and higher infectiousness due to a higher probability of developing severe disease. Our model fitting suggests under 20s have 49-75% additional immune protection beyond that predicted by strong thymus function alone, consistent with increased juvenile cross-immunity from other viruses. We found no evidence for differences between age groups in susceptibility to infection or infectiousness to others (given disease state), i.e. the only important factor in the age-dependence of hospitalisation rates is the probability of hospitalisation given infection. These findings suggest the existence of a T-cell exhaustion threshold, proportional to thymic output, and that clonal expansion of peripheral T-cells does not affect disease risk. The strikingly simple inverse relationship between risk and thymic T-cell output adds to the evidence that thymic involution is an important factor in the decline of the immune system with age and may also be an important clue in understanding disease progression, not just for COVID-19 but other diseases as well.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sam Palmer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nik Cunniffe", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ruairi Donnelly", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.25.20154252", "rel_title": "SARS-CoV-2-RNA viremia is associated to hypercytokinemia and critical illness in COVID-19", @@ -1217760,61 +1218365,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.24.20181206", - "rel_title": "Seroprevalence and correlates of SARS-CoV-2 neutralizing antibodies: Results from a population-based study in Bonn, Germany", - "rel_date": "2020-08-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20181206", - "rel_abs": "BackgroundAccurate estimates of SARS-CoV-2 seroprevalence are crucial for the implementation of effective public health measures, but are currently largely lacking in regions with low infection rates. This is further complicated by inadequate test performance of many widely used serological assays. We therefore aimed to assess SARS-CoV-2 seroprevalence in a region with low COVID-19 burden, especially focusing on neutralizing antibodies that presumably constitute a major component of acquired immunity.\n\nMethodsWe invited all individuals who were enrolled in the Rhineland Study, an ongoing community-based prospective cohort study in people aged 30 years and above in the city of Bonn, Germany (N=5427). Between April 24th and June 30th, 2020, 4771 (88%) of these individuals participated in the serosurvey. Anti-SARS-CoV-2 IgG levels were measured using an ELISA assay, and all positive or borderline results were subsequently examined through both a recombinant immunofluorescent assay and a plaque reduction neutralisation test (PRNT).\n\nFindingsSeroprevalence was 0{middle dot}97% (95% CI: 0{middle dot}72-1{middle dot}30) by ELISA and 0{middle dot}36% (95% CI: 0{middle dot}21-0{middle dot}61) by PRNT, and did not vary with either age or sex. All PRNT+ individuals reported having experienced at least one symptom (odds ratio (OR) of PRNT+ for each additional symptom: 1{middle dot}12 (95% CI: 1{middle dot}04-1{middle dot}21)). Apart from living in a household with a SARS-CoV-2 confirmed or suspected person, a recent history of reduced taste or smell, fever, chills/hot flashes, pain while breathing, pain in arms/legs, as well as muscle pain and weakness were significantly associated with the presence of neutralizing antibodies in those with mild to moderate infection (ORs 3{middle dot}44 to 9{middle dot}97, all p<0{middle dot}018).\n\nInterpretationOur findings indicate a relatively low SARS-CoV-2 seroprevalence in Bonn, Germany (until June 30th, 2020), with neutralizing antibodies detectable in only one third of those with a positive immunoassay result, implying that almost the entire population in this region remains susceptible to SARS-CoV-2 infection.\n\nFundingThe Rhineland Study is predominantly funded through the German Center for Neurodegenerative Diseases (DZNE) by the Federal Ministry of Education and Research (BMBF) and the Ministry of Culture and Science of the German State of North Rhine-Westphalia. The National Consultant Laboratory for Coronaviruses is funded by the Federal Ministry of Health (BMG). No additional funding was received for this seroprevalence study.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "N. Ahmad Aziz", - "author_inst": "Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE) & Department of Neurology, Faculty of Medicine, University of Bonn" - }, - { - "author_name": "Victor M Corman", - "author_inst": "National Consultant Laboratory for Coronaviruses, Institute of Virology, Charite - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Antje K.C. Echterhoff", - "author_inst": "Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE)" - }, - { - "author_name": "Anja Richter", - "author_inst": "National Consultant Laboratory for Coronaviruses, Institute of Virology, Charite - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Antonio Schmandke", - "author_inst": "Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE)" - }, - { - "author_name": "Marie Luisa Schmidt", - "author_inst": "National Consultant Laboratory for Coronaviruses, Institute of Virology, Charite - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Thomas H. Schmidt", - "author_inst": "Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE)" - }, - { - "author_name": "Folgerdiena M De Vries", - "author_inst": "Population Health Sciences, German Center for Neurodegenerative Diseases (DZNE)" - }, - { - "author_name": "Christian Drosten", - "author_inst": "National Consultant Laboratory for Coronaviruses, Institute of Virology, Charite - Universit\u00e4tsmedizin Berlin" - }, - { - "author_name": "Monique M.B. Breteler", - "author_inst": "Population Health Sciences, German Center for Neurodegenerative diseases (DZNE) & Institute for Medical Biometry, Informatics and Epidemiology (IMBIE), Faculty " - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.24.20180679", "rel_title": "Cellular immune response to SARS-CoV-2 infection in humans: a systematic review", @@ -1218058,6 +1218608,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.29.272864", + "rel_title": "A simplified cell-based assay to identify coronavirus 3CL protease inhibitors", + "rel_date": "2020-08-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.29.272864", + "rel_abs": "We describe a mammalian cell-based assay capable of identifying coronavirus 3CL protease (3CLpro) inhibitors without requiring the use of live virus. By enabling the facile testing of compounds across a range of coronavirus 3CLpro enzymes, including the one from SARS-CoV-2, we are able to quickly identify compounds with broad or narrow spectra of activity. We further demonstrate the utility of our approach by performing a curated compound screen along with structure-activity profiling of a series of small molecules to identify compounds with antiviral activity. Throughout these studies, we observed concordance between data emerging from this assay and from live virus assays. By democratizing the testing of 3CL inhibitors to enable screening in the majority of laboratories rather than the few with extensive biosafety infrastructure, we hope to expedite the search for coronavirus 3CL protease inhibitors, to address the current epidemic and future ones that will inevitably arise.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Samuel J Resnick", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Sho Iketani", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Seo Jung Hong", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Arie Zask", + "author_inst": "Columbia University" + }, + { + "author_name": "Hengrui Liu", + "author_inst": "Columbia University" + }, + { + "author_name": "Sungsoo Kim", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Schuyler Melore", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Manoj S Nair", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Yaoxing Huang", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Nicholas E S Tay", + "author_inst": "Columbia University" + }, + { + "author_name": "Tomislav Rovis", + "author_inst": "Columbia University" + }, + { + "author_name": "Hee Won Yang", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Brent R Stockwell", + "author_inst": "Columbia University" + }, + { + "author_name": "David D Ho", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Alejandro Chavez", + "author_inst": "Columbia University Irving Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.29.257360", "rel_title": "The SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humans.", @@ -1219429,113 +1220054,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.08.27.267716", - "rel_title": "The immunodominant and neutralization linear epitopes for SARS-CoV-2", - "rel_date": "2020-08-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.27.267716", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) becomes a tremendous threat to global health. Although vaccines against the virus are under development, the antigen epitopes on the virus and their immunogenicity are poorly understood. Here, we simulated the three-dimensional structures of SARS-CoV-2 proteins with high performance computer, predicted the B cell epitopes on spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins of SARS-CoV-2 using structure-based approaches, and then validated the epitope immunogenicity by immunizing mice. Almost all 33 predicted epitopes effectively induced antibody production, six of which were immunodominant epitopes in patients identified via the binding of epitopes with the sera from domestic and imported COVID-19 patients, and 23 were conserved within SARS-CoV-2, SARS-CoV and bat coronavirus RaTG13. We also found that the immunodominant epitopes of domestic SARS-CoV-2 were different from that of the imported, which may be caused by the mutations on S (G614D) and N proteins. Importantly, we validated that eight epitopes on S protein elicited neutralizing antibodies that blocked the cell entry of both D614 and G614 pseudo-virus of SARS-CoV-2, three and nine epitopes induced D614 or G614 neutralizing antibodies, respectively. Our present study shed light on the immunodominance, neutralization, and conserved epitopes on SARS-CoV-2 which are potently used for the diagnosis, virus classification and the vaccine design tackling inefficiency, virus mutation and different species of coronaviruses.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Shuai Lu", - "author_inst": "Institute of Process Engineering, Chinese Academy of Sciences" - }, - { - "author_name": "Xi-xiu Xie", - "author_inst": "Institute of Process Engineering, Chinese Academy of Sciences" - }, - { - "author_name": "Lei Zhao", - "author_inst": "The fifth hospital of Shijiazhuang" - }, - { - "author_name": "Bin Wang", - "author_inst": "Institute of Process Engineering, Chinese Academy of Sciences" - }, - { - "author_name": "Jie Zhu", - "author_inst": "Institute of Process Engineering, Chinese Academy of Sciences" - }, - { - "author_name": "Ting-rui Yang", - "author_inst": "Institute of Process Engineering, Chinese Academy of Sciences" - }, - { - "author_name": "Guang-wen Yang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Mei Ji", - "author_inst": "Institute of Process Engineering, Chinese Academy of Sciences" - }, - { - "author_name": "Cui-ping Lv", - "author_inst": "Institute of Process Engineering, Chinese Academy of Sciences" - }, - { - "author_name": "Jian Xue", - "author_inst": "The fifth hospital of Shijiazhuang" - }, - { - "author_name": "Er-hei Dai", - "author_inst": "The fifth hospital of Shijiazhuang" - }, - { - "author_name": "Xi-ming Fu", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Dong-qun Liu", - "author_inst": "Institute of Process Engineering, Chinese Academy of Sciences" - }, - { - "author_name": "Lun Zhang", - "author_inst": "Institute of Process Engineering, Chinese Academy of Sciences" - }, - { - "author_name": "Sheng-jie Hou", - "author_inst": "Institute of Process Engineering, Chinese Academy of Sciences" - }, - { - "author_name": "Xiao-lin Yu", - "author_inst": "Institute of Process Engineering, Chinese Academy of Sciences" - }, - { - "author_name": "Yu-ling Wang", - "author_inst": "The fifth hospital of Shijiazhuang" - }, - { - "author_name": "Hui-xia Gao", - "author_inst": "The fifth hospital of Shijiazhuang" - }, - { - "author_name": "Xue-han Shi", - "author_inst": "The fifth hospital of Shijiazhuang" - }, - { - "author_name": "Chang-wen Ke", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Bi-xia Ke", - "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" - }, - { - "author_name": "Chun-guo Jiang", - "author_inst": "Beijing Chaoyang Hospital" - }, - { - "author_name": "Rui-tian Liu", - "author_inst": "Institute of Process Engineering, Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.26.269159", "rel_title": "Rethinking Remdesivir: Synthesis of Lipid Prodrugs that Substantially Enhance Anti-Coronavirus Activity", @@ -1219807,6 +1220325,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.27.270637", + "rel_title": "Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion", + "rel_date": "2020-08-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.27.270637", + "rel_abs": "The molecular basis for the severity and rapid spread of the COVID-19 disease caused by SARS-CoV-2 is largely unknown. ORF8 is a rapidly evolving accessory protein that has been proposed to interfere with immune responses. The crystal structure of SARS-CoV-2 ORF8 was determined at 2.04 [A] resolution by x-ray crystallography. The structure reveals a ~60 residue core similar to SARS-CoV ORF7a with the addition of two dimerization interfaces unique to SARS-CoV-2 ORF8. A covalent disulfide-linked dimer is formed through an N-terminal sequence specific to SARS-CoV-2, while a separate non-covalent interface is formed by another SARS-CoV-2-specific sequence, 73YIDI76. Together the presence of these interfaces shows how SARS-CoV-2 ORF8 can form unique large-scale assemblies not possible for SARS-CoV, potentially mediating unique immune suppression and evasion activities.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Thomas G Flower", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Cosmo Z Buffalo", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Richard M Hooy", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Marc Allaire", + "author_inst": "Lawrence Berkeley National Laboratory" + }, + { + "author_name": "Xuefeng Ren", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "James H Hurley", + "author_inst": "UC Berkeley" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.08.26.267781", "rel_title": "Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades", @@ -1220883,237 +1221440,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.08.25.256339", - "rel_title": "Highly potent anti-SARS-CoV-2 multi-DARPin therapeutic candidates", - "rel_date": "2020-08-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.25.256339", - "rel_abs": "Globally accessible therapeutics against SARS-CoV-2 are urgently needed. Here, we report the generation of the first anti-SARS-CoV-2 DARPin molecules with therapeutic potential as well as rapid large-scale production capabilities. Highly potent multivalent DARPin molecules with low picomolar virus neutralization efficacies were generated by molecular linkage of three different monovalent DARPin molecules. These multivalent DARPin molecules target various domains of the SARS-CoV-2 spike protein, thereby limiting possible viral escape. Cryo-EM analysis of individual monovalent DARPin molecules provided structural explanations for the mode of action. Analysis of the protective efficacy of one multivalent DARPin molecule in a hamster SARS-CoV-2 infection model demonstrated a significant reduction of pathogenesis. Taken together, the multivalent DARPin molecules reported here, one of which has entered clinical studies, constitute promising therapeutics against the COVID-19 pandemic.", - "rel_num_authors": 54, - "rel_authors": [ - { - "author_name": "Marcel Walser", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Sylvia Rothenberger", - "author_inst": "Spiez Laboratory" - }, - { - "author_name": "Daniel L. Hurdiss", - "author_inst": "Utrecht University" - }, - { - "author_name": "Anja Schlegel", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Valerie Calabro", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Simon Fontaine", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Denis Villemagne", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Maria Paladino", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Tanja Hospodarsch", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Alexandra Neculcea", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Andreas Cornelius", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Patricia Schildknecht", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Mirela Matzner", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Martin Haenggi", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Marco Franchini", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Yvonne Kaufmann", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Doris Schaible", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Iris Schlegel", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Chloe Iss", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Thamar Looser", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Susanne Mangold", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Christel Herzog", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Dieter Schiegg", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Christian Reichen", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Filip Radom", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Andreas Bosshart", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Andreas Lehmann", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Micha A. Haeuptle", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Alexander Zuercher", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Toni Vagt", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Gabriel Sigrist", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Marcel Straumann", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Karl Proba", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Niina Veitonmaki", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Keith M. Dawson", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Christof Zitt", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Jennifer Mayor", - "author_inst": "Spiez Laboratory" - }, - { - "author_name": "Sarah Ryter", - "author_inst": "Spiez Laboratory" - }, - { - "author_name": "Heyrhyoung Lyoo", - "author_inst": "Utrecht University" - }, - { - "author_name": "Chunyan Wang", - "author_inst": "Utrecht University" - }, - { - "author_name": "Wentao Li", - "author_inst": "Utrecht University" - }, - { - "author_name": "Ieva Drulyte", - "author_inst": "Thermo Fisher Scientific" - }, - { - "author_name": "Wenjuan Du", - "author_inst": "Utrecht University" - }, - { - "author_name": "H. Kaspar Binz", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Leon de Waal", - "author_inst": "Viroclinics Xplore" - }, - { - "author_name": "Koert J. Stittelaar", - "author_inst": "Viroclinics Xplore" - }, - { - "author_name": "Sarah Taplin", - "author_inst": "Integrated Biologix" - }, - { - "author_name": "Seth Lewis", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Daniel Steiner", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Frank J.M. van Kuppeveld", - "author_inst": "Utrecht University" - }, - { - "author_name": "Olivier Engler", - "author_inst": "Spiez Laboratory" - }, - { - "author_name": "Berend-Jan Bosch", - "author_inst": "Utrecht University" - }, - { - "author_name": "Michael T. Stumpp", - "author_inst": "Molecular Partners AG" - }, - { - "author_name": "Patrick Amstutz", - "author_inst": "Molecular Partners AG" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.25.267658", "rel_title": "Global and Local Mutations in Bangladeshi SARS-CoV-2 Genomes", @@ -1221421,6 +1221747,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.26.266825", + "rel_title": "Multi-species ELISA for the detection of antibodies against SARS-CoV-2 in animals", + "rel_date": "2020-08-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.26.266825", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic with millions of infected humans and hundreds of thousands of fatalities. As the novel disease - referred to as COVID-19 - unfolded, occasional anthropozoonotic infections of animals by owners or caretakers were reported in dogs, felid species and farmed mink. Further species were shown to be susceptible under experimental conditions. The extent of natural infections of animals, however, is still largely unknown. Serological methods will be useful tools for tracing SARS-CoV-2 infections in animals once test systems are validated for use in different species. Here, we developed an indirect multi-species ELISA based on the receptor-binding domain (RBD) of SARS-CoV-2. The newly established ELISA was validated using 59 sera of infected or vaccinated animals including ferrets, raccoon dogs, hamsters, rabbits, chickens, cattle and a cat, and a total of 220 antibody-negative sera of the same animal species. Overall, a diagnostic specificity of 100.0% and sensitivity of 98.31% was achieved, and the functionality with every species included in this study could be demonstrated. Hence, a versatile and reliable ELISA protocol was established that enables high-throughput antibody detection in a broad range of animal species, which may be used for outbreak investigations, to assess the seroprevalence in susceptible species or to screen for reservoir or intermediate hosts.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Kerstin Wernike", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Andrea Aebischer", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Anna Michelitsch", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Donata Hoffmann", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Conrad Freuling", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Anne Balkema-Buschmann", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Annika Graaf", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Thomas Mueller", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Nikolaus Osterrieder", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Melanie Rissmann", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Dennis Rubbenstroth", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Jacob Schoen", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Claudia Schulz", + "author_inst": "University of Veterinary Medicine Hannover" + }, + { + "author_name": "Jakob Trimpert", + "author_inst": "Freie Universitaet Berlin" + }, + { + "author_name": "Lorenz Ulrich", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Asisa Volz", + "author_inst": "University of Veterinary Medicine Hannover" + }, + { + "author_name": "Thomas Mettenleiter", + "author_inst": "Friedrich-Loeffler-Institut" + }, + { + "author_name": "Martin Beer", + "author_inst": "Friedrich-Loeffler-Institut" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.25.267328", "rel_title": "A unique view of SARS-CoV-2 through the lens of ORF8 protein", @@ -1223121,57 +1223534,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.23.20180281", - "rel_title": "Epidemiologically most successful SARS-CoV-2 variant: concurrent mutations in RNA-dependent RNA polymerase and spike protein", - "rel_date": "2020-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20180281", - "rel_abs": "The D614G mutation of the Spike protein is thought to be relevant for SARS-CoV-2 infection. Here we report biological and epidemiological aspects of this mutation. Using pseudotyped lentivectors, we were able to confirm that the G614 variant of the Spike protein is markedly more infectious than the ancestral D614 variant. We demonstrate by molecular modelling that the replacement of aspartate by glycine in position 614 facilitates the transition towards an open state of the Spike protein. To understand whether the increased infectivity of the D614 variant explains its epidemiological success, we analysed the evolution of 27,086 high-quality SARS-CoV-2 genome sequences from GISAID. We observed striking coevolution of D614G with the P323L mutation in the viral polymerase. Importantly, exclusive presence of G614 or L323 did not become epidemiologically relevant. In contrast, the combination of the two mutations gave rise to a viral G/L variant that has all but replaced the initial D/P variant. There was no significant correlation between reported COVID mortality in different countries and the prevalence of the Wuhan versus G/L variant. However, when comparing the speed of emergence and the ultimate predominance in individual countries, the G/L variant displays major epidemiological supremacy. Our results suggest that the P323L mutation, located in the interface domain of the RNA-dependent RNA polymerase (RdRp), is a necessary alteration that led to the epidemiological success of the present variant of SARS-CoV-2.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sten Ilmj\u00e4rv", - "author_inst": "University of Geneva" - }, - { - "author_name": "Fabien Abdul", - "author_inst": "Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva" - }, - { - "author_name": "Silvia Acosta-Guti\u00e9rrez", - "author_inst": "Department of Chemistry, University College London; Institute for the Physics of Living Systems, University College London; Institute of Structural and Molecula" - }, - { - "author_name": "Carolina Estarellas", - "author_inst": "Department of Chemistry, University College London" - }, - { - "author_name": "Ioannis Galdadas", - "author_inst": "Department of Chemistry, University College London" - }, - { - "author_name": "Marina Casimir", - "author_inst": "Neurix SA" - }, - { - "author_name": "Marco Alessandrini", - "author_inst": "Department of Pathology and Immunology, Faculty of Medicine, University of Geneva" - }, - { - "author_name": "Francesco Luigi Gervasio", - "author_inst": "Department of Chemistry, University College London; Institute of Structural and Molecular Biology, University College London; School of Pharmaceutical Sciences," - }, - { - "author_name": "Karl-Heinz Krause", - "author_inst": "Department of Pathology and Immunology, Faculty of Medicine, University of Geneva; Division of Infectious Disease and Dept. of Diagnostics, Geneva University Ho" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.23.20180174", "rel_title": "The Futures of the Pandemic in the USA : A Timed Intervention Model", @@ -1223367,6 +1223729,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.23.20180307", + "rel_title": "Hesitant or not? A global survey of potential acceptance of a COVID-19 vaccine", + "rel_date": "2020-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20180307", + "rel_abs": "A number of COVID-19 vaccines are under development, with one or more possibly becoming available in 2021. We conducted a global survey in June 2020 of 13,426 people in 19 countries to determine potential acceptance rates of a COVID-19 vaccine and factors influencing acceptance. We ran univariate logistic regressions to examine the associations with demographic variables. 71.5% reported they would be very or somewhat likely to take a COVID-19 vaccine; 61.4% reported they would accept their employers recommendation to take a COVID-19 vaccine. Differences in acceptance across countries ranged from almost 9 in 10 (China) to fewer than 6 in 10 (Russia). Respondents reporting higher levels of trust in information from government sources were more likely to accept a vaccine, and take their employers advice to do so. Targeted interventions addressing age, sex, income, and education level are required to increase and sustain public acceptance of a COVID-19 vaccine.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jeffrey V Lazarus", + "author_inst": "Barcelona Institute for Global Health (ISGlobal)" + }, + { + "author_name": "Scott Ratzan", + "author_inst": "City University of New York (CUNY) Graduate School of Public Health & Health Policy, New York, USA" + }, + { + "author_name": "Adam Palayew", + "author_inst": "Barcelona Institute for Global Health (ISGlobal)" + }, + { + "author_name": "Lawrence O Gostin", + "author_inst": "Georgetown University, Washington, DC, USA" + }, + { + "author_name": "Heidi J Larson", + "author_inst": "London School of Hygiene and Tropical Medicine, London, United Kingdom" + }, + { + "author_name": "Kenneth Rabin", + "author_inst": "City University of New York (CUNY) Graduate School of Public Health & Health Policy, New York, USA" + }, + { + "author_name": "Spencer Kimball", + "author_inst": "Emerson College, Boston, Mass, USA" + }, + { + "author_name": "Ayman El-Mohandes", + "author_inst": "City University of New York (CUNY) Graduate School of Public Health & Health Policy, New York, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.23.20180513", "rel_title": "3D Printed N95 Equivalent for PPE Shortages: The Kansas City Mask", @@ -1224698,49 +1225107,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.24.260901", - "rel_title": "The SARS-CoV-2 Envelope and Membrane proteins modulate maturation and retention of the Spike protein, allowing optimal formation of VLPs in presence of Nucleoprotein", - "rel_date": "2020-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.24.260901", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a {beta}-coronavirus, is the causative agent of the COVID-19 pandemic. Like for other coronaviruses, its particles are composed of four structural proteins, namely Spike S, Envelope E, Membrane M and Nucleoprotein N proteins. The involvement of each of these proteins and their interplays during the assembly process of this new virus are poorly-defined and are likely {beta}-coronavirus-type different. Therefore, we sought to investigate how SARS-CoV-2 behaves for its assembly by expression assays of S, in combination with E, M and/or N. By combining biochemical and imaging assays, we showed that E and M regulate intracellular trafficking of S and hence its furin-mediated processing. Indeed, our imaging data revealed that S remains at ERGIC or Golgi compartments upon expression of E or M, like for SARS-CoV-2 infected cells. By studying a mutant of S, we showed that its cytoplasmic tail, and more specifically, its C-terminal retrieval motif, is required for the M-mediated retention in the ERGIC, whereas E induces S retention by modulating the cell secretory pathway. We also highlighted that E and M induce a specific maturation of S N-glycosylation, which is observed on particles and lysates from infected cells independently of its mechanisms of intracellular retention. Finally, we showed that both M, E and N are required for optimal production of virus-like-proteins. Altogether, our results indicated that E and M proteins influence the properties of S proteins to promote assembly of viral particles. Our results therefore highlight both similarities and dissimilarities in these events, as compared to other {beta}-coronaviruses.\n\nAuthor SummaryThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Its viral particles are composed of four structural proteins, namely Spike S, Envelope E, Membrane M and Nucleoprotein N proteins, though their involvement in the virion assembly remain unknown for this particular coronavirus. Here we showed that presence of E and M influence the localization and maturation of S protein, in term of cleavage and N-glycosylation maturation. Indeed, E protein is able to slow down the cell secretory pathway whereas M-induced retention of S requires the retrieval motif in S C-terminus. We also highlighted that E and M might regulate the N glycosylation maturation of S independently of its intracellular retention mechanism. Finally, we showed that the four structural proteins are required for optimal formation of virus-like particles, highlighting the involvement of N, E and M in assembly of infectious particles. Altogether, our results highlight both similarities and dissimilarities in these events, as compared to other {beta}-coronaviruses.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Bertrand Boson", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Vincent Legros", - "author_inst": "Centre International de Recherche en Infectiologie, VetAgro Sup" - }, - { - "author_name": "Bingjie Zhou", - "author_inst": "Institut Pasteur of Shanghai, Chinese Academy of Sciences; University of Chinese Academy of Sciences" - }, - { - "author_name": "Cyrille Mathieu", - "author_inst": "Centre International de Recherche en Infectiologie" - }, - { - "author_name": "Fran\u00e7ois-Lo\u00efc Cosset", - "author_inst": "INSERM, ENS, Universit\u00e9 de Lyon" - }, - { - "author_name": "Dimitri Lavillette", - "author_inst": "CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences Pasteurien College" - }, - { - "author_name": "Solene Denolly", - "author_inst": "Centre International de Recherche en Infectiologie" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.24.264192", "rel_title": "Pathogenicity, immunogenicity, and protective ability of an attenuated SARS-CoV-2 variant with a deletion at the S1/S2 junction of the spike protein", @@ -1225128,6 +1225494,57 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.08.24.264077", + "rel_title": "An hACE2 peptide mimic blocks SARS-CoV-2 Pulmonary Cell Infection", + "rel_date": "2020-08-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.24.264077", + "rel_abs": "In the light of the recent accumulated knowledge on SARS-CoV-2 and its mode of human cells invasion, the binding of viral spike glycoprotein to human Angiotensin Converting Enzyme 2 (hACE2) receptor plays a central role in cell entry. We designed a series of peptides mimicking the N-terminal helix of hACE2 protein which contains most of the contacting residues at the binding site and have a high helical folding propensity in aqueous solution. Our best peptide mimics bind to the virus spike protein with high affinity and are able to block SARS-CoV-2 human pulmonary cell infection with an inhibitory concentration (IC50) in the nanomolar range. These first in class blocking peptide mimics represent powerful tools that might be used in prophylactic and therapeutic approaches to fight the coronavirus disease 2019 (COVID-19).", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Philippe Karoyan", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Vincent Vieillard", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Estelle Odile", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Alexis Denis", + "author_inst": "Oncodesign" + }, + { + "author_name": "amelie guihot", + "author_inst": "Assistance Publique Hopitaux de Paris Hopital Pitie Salpetriere Service de Medecine Intensive Reanimation Institut de Cardiologie 75013, Paris, France" + }, + { + "author_name": "charles edouard luyt", + "author_inst": "Assistance Publique Hopitaux de Paris, Hopital Pitie Salpetriere, Service de Medecine Intensive Reanimation, Institut de Cardiologie 75013 Paris France" + }, + { + "author_name": "Luis Gomes-Morales", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Pascal Grondin", + "author_inst": "Oncodesign" + }, + { + "author_name": "Olivier Lequin", + "author_inst": "Sorbonne Universite" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.08.24.264630", "rel_title": "SARS-CoV-2 neutralizing human antibodies protect against lower respiratory tract disease in a hamster model", @@ -1226396,41 +1226813,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "orthopedics" }, - { - "rel_doi": "10.1101/2020.08.21.20178855", - "rel_title": "Modeling Hospital Energy and Economic Costs for COVID-19 Infection Control Interventions", - "rel_date": "2020-08-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.21.20178855", - "rel_abs": "The objective of this study was to assess the energy demand and economic cost of two hospital-based COVID-19 infection control interventions. The intervention control measures evaluated include use of negative pressure (NP) treatment rooms and xenon pulsed ultraviolet (XP-UV) infection control equipment. After projecting COVID-19 hospitalizations, a Hospital Energy Model and Infection De-escalation Models are applied to quantify increases in energy demand and reductions in secondary infections. The scope of the interventions consisted of implementing NP in 11, 22, and 44 rooms (at small, medium, and large hospitals) while the XP-UV equipment was used eight, nine, and ten hours a day, respectively. The annum kilowatt-hours (kWh) for NP (and costs were at $0.1015 per kWh) were 116,700 ($11,845), 332,530 ($33,752), 795,675 ($80,761) for small, medium, and large hospitals ($1,077, $1,534 $1,836 added annum energy cost per NP room). For XP-UV, the annum kilowatt-hours and costs were 438 ($45), 493 ($50), 548 ($56) for small, medium, and large hospitals. There are other initial costs associated with the purchase and installation of the equipment, with XP-UV having a higher initial cost. XP-UV had a greater reduction in secondary COVID-19 infections in large and medium hospitals. NP rooms had a greater reduction in secondary SARS-CoV-2 transmission in small hospitals. Early implementation of interventions can result in realized cost savings through reduced hospital-acquired infections.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Marietta M. Squire", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Megashnee Munsamy", - "author_inst": "Mangosuthu University of Technology" - }, - { - "author_name": "Gary Lin", - "author_inst": "Center for Disease Dynamics, Economics & Policy" - }, - { - "author_name": "Arnesh Telukdarie", - "author_inst": "University of Johannesburg" - }, - { - "author_name": "Takeru Igusa", - "author_inst": "Johns Hopkins University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.08.21.20179416", "rel_title": "Impact of population density on Covid 19 infected and mortality rate in India", @@ -1226714,6 +1227096,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.23.255364", + "rel_title": "Antiviral activity of lambda-carrageenan against influenza viruses in mice and severe acute respiratory syndrome coronavirus 2 in vitro", + "rel_date": "2020-08-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.23.255364", + "rel_abs": "Influenza virus and coronavirus, belonging to enveloped RNA viruses, are major causes of human respiratory diseases. The aim of this study was to investigate the broad spectrum antiviral activity of a naturally existing sulfated polysaccharide, lambda-carrageenan ({lambda}-CGN), purified from marine red algae. Cell culture-based assays revealed that the macromolecule efficiently inhibited both influenza A and B viruses, as well as currently circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with EC50 values ranging from 0.3-1.4 g/ml. No toxicity to host cells was observed at concentrations up to 300 g/ml. Plaque titration and western blot analysis verified that {lambda}-CGN reduced expression of viral proteins in cell lysates and suppressed progeny virus production in culture supernatants in a dose-dependent manner. This polyanionic compound exerts antiviral activity by targeting viral attachment to cell surface receptors and preventing entry. Moreover, intranasal administration to mice during influenza A viral challenge not only alleviated infection-mediated reductions in body weight but also protected 60% of mice from virus-induced mortality. Thus, {lambda}-CGN could be a promising antiviral agent for preventing infection by several respiratory viruses.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ye Jin Jang", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Heegwon Shin", + "author_inst": "Korea Advanced Institute of Science and Technology" + }, + { + "author_name": "Myoung Kyu Lee", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Oh Seung Kwon", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Jin Soo Shin", + "author_inst": "Korea Research Institute of Chemical Technology" + }, + { + "author_name": "Yongil Kim", + "author_inst": "Hanmi Pharmaceutical Co." + }, + { + "author_name": "Meehyein Kim", + "author_inst": "Korea Research Institute of Chemical Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.20.20178723", "rel_title": "Automatic analysis system of COVID-19 radiographic lung images (XrayCoviDetector)", @@ -1228070,69 +1228495,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.19.20171868", - "rel_title": "Whether Early Pulse Steroid dose is associated with lower mortality in COVID-19 critically ill Patients- A retrospective Chart Review", - "rel_date": "2020-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20171868", - "rel_abs": "IntroductionSteroids have shown its usefulness in critically ill COVID19 patients. However time of starting steroid and dose tailored to severity remains a matter of inquiry due to still emerging evidences and wide-ranging concerns of benefits and harms. We did a retrospective record analysis in an apex teaching hospital ICU setting to explore optimal doses and duration of steroid therapy which can decrease mortality.\n\nMethodology114 adults with COVID19-ARDS admitted to ICU between 20thMarch-15thAugust2020 were included in chart review. We did preliminary exploratory analysis(rooted in steroid therapy matrix categorized by dose and duration) to understand the effect of several covariates on survival. This was followed by univariate and multivariate Cox proportion hazard regression analysis and model diagnostics.\n\nResultsExploratory analysis and visualization indicated age, optimal steroid, severity (measured in P/F) of disease and infection status as potential covariates for survival. Univariate cox regression analysis showed significant positive association of age>60 years{2.6 (1.5-4.7)} and protective effect of optimum steroid{0.38(0.2-0.72)} on death (hazard) in critically ill patients. Multivariate cox regression analysis after adjusting effect of age showed protective effect of optimum steroid on hazard defined as death {0.46(0.23-0.87),LR=17.04,(p=2e- 04)}.The concordance was 0.70 and model diagnostics fulfilled the assumption criteria for proportional hazard model.\n\nConclusionOptimal dose steroid as per defined optimum (<24 hours and doses tailored to P/F at presentation) criteria can offer protective effect from mortality which persists after adjusting for age. This protective effect was not found to be negatively influenced by the risk of infection.\n\nNo funding was taken for this paper.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Abhishek Goyal", - "author_inst": "All India INstitute of Medical Sciences Bhopal" - }, - { - "author_name": "Saurabh Saigal", - "author_inst": "All India institute of medical sciences Bhopal" - }, - { - "author_name": "Ankur Joshi", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "Dodda Brahmam", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "Yogesh Niwariya", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "Alkesh Khurana", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "Pooja Singh", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "Sunaina Tejpal Karna", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "Jaiprakash Sharma", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "G Sai Pavan Jr.", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "Sagar Khadanga", - "author_inst": "AIIMS Bhopal" - }, - { - "author_name": "Arun Mitra", - "author_inst": "AIIMS Bhopal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.18.20177717", "rel_title": "Absence of relevant QT interval prolongation in not critically ill COVID-19 patients.", @@ -1228400,6 +1228762,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.19.20178129", + "rel_title": "Epidemic Analysis of COVID-19 in Egypt, Qatar and Saudi Arabia using the Generalized SEIR Model", + "rel_date": "2020-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20178129", + "rel_abs": "BackgroundSince its emergence in late December 2019 and its declaration as a global pandemic by World Health Organization (WHO) on March 11, 2020, the novel coronavirus disease known as (COVID-19) has attracted global attention. The process of modeling and predicting the pandemic behavior became crucial as the different states needed accurate predictions to be able to adopt suitable policies to minimize the pressure on their health care systems. Researchers have employed modified variants of classical SIR/SEIR models to describe the dynamics of this pandemic. In this paper, after proven effective in numerous countries, a modified variant of SEIR is implemented to predict the behavior of COVID-19 in Egypt and other countries in the Middle East and North Africa region (MENA).\n\nMethodsWe built MATLAB simulations to fit the real data of COVID-19 Active, recovered and death Cases in Egypt, Qatar and Saudi Arabia to the modified SEIR model via Nelder-Mead algorithm to be able to estimate the future dynamics of the pandemic.\n\nFindingsWe estimate several characteristics of COVID-19 future dynamics in Egypt, Qatar and Saudi Arabia. We also estimate that the pandemic will resolve in the countries under investigation in February 2021, January 2021 and 28th August 2020 With total death cases of 9,742, 5,600, 185 and total cases of 187,600, 490,000, 120,000, respectively.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ahmed E Fahmy", + "author_inst": "Zewail University of Science and Technology" + }, + { + "author_name": "Mohammed M Eldesouky", + "author_inst": "Zewail University of Science and Technology" + }, + { + "author_name": "Ahmed S.A. Mohamed", + "author_inst": "Zewail University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.19.20177956", "rel_title": "Disparities in COVID-19 Hospitalizations and Mortality among Black and Hispanic Patients: Cross-Sectional Analysis from the Greater Houston Metropolitan Area", @@ -1229532,65 +1229921,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.08.20.20178558", - "rel_title": "Engagement and adherence trade-offs for SARS-CoV-2 contact tracing", - "rel_date": "2020-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20178558", - "rel_abs": "Contact tracing is an important tool for allowing countries to ease lock-down policies introduced to combat SARS-CoV-2. For contact tracing to be effective, those with symptoms must self-report themselves while their contacts must self-isolate when asked. However, policies such as legal enforcement of self-isolation can create trade-offs by dissuading individuals from self-reporting. We use an existing branching process model to examine which aspects of contact tracing adherence should be prioritised. We consider an inverse relationship between self-isolation adherence and self-reporting engagement, assuming that increasingly strict self-isolation policies will result in fewer individuals self-reporting to the programme. We find that policies that increase the average duration of self-isolation, or that increase the probability that people self-isolate at all, at the expense of reduced self-reporting rate, will not decrease the risk of a large outbreak and may increase the risk, depending on the strength of the trade-off. These results suggest that policies to increase self-isolation adherence should be implemented carefully. Policies that increase self-isolation adherence at the cost of self-reporting rates should be avoided.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Tim C D Lucas", - "author_inst": "University of Oxford" - }, - { - "author_name": "Emma L Davis", - "author_inst": "University of Oxford" - }, - { - "author_name": "Diepreye Ayabina", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anna Borlase", - "author_inst": "University of Oxford" - }, - { - "author_name": "Thomas Crellen", - "author_inst": "University of Oxford" - }, - { - "author_name": "Li Pi", - "author_inst": "University of Oxford" - }, - { - "author_name": "Graham Medley", - "author_inst": "LSHTM" - }, - { - "author_name": "Lucy Yardley", - "author_inst": "University of Bristol, University of Southampton" - }, - { - "author_name": "Petra Klepac", - "author_inst": "LSHTM" - }, - { - "author_name": "Julia Gog", - "author_inst": "University of Cambridge" - }, - { - "author_name": "T D\u00e9irdre Hollingsworth", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.20.20178533", "rel_title": "High SARS-CoV-2 Seroprevalence in Children and Adults in the Austrian Ski Resort Ischgl", @@ -1229922,6 +1230252,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.17.20176735", + "rel_title": "Comparing the Fit of N95, KN95, Surgical, and Cloth Face Masks and Assessing the Accuracy of Fit Checking", + "rel_date": "2020-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20176735", + "rel_abs": "IntroductionThe COVID-19 pandemic has made well-fitting face masks a critical piece of protective equipment for healthcare workers and civilians. While the importance of wearing face masks has been acknowledged, there remains a lack of understanding about the role of good fit in rendering protective equipment useful. In addition, supply chain constraints have caused some organizations to abandon traditional quantitative or qualitative fit testing, and instead, have implemented subjective fit checking. Our study seeks to quantitatively evaluate the level of fit offered by various types of masks, and most importantly, assess the accuracy of implementing fit checks by comparing fit check results to quantitative fit testing results.\n\nMethodsSeven participants first evaluated N95 and KN95 masks by performing a fit check. Participants then underwent quantitative fit testing wearing five N95 masks, a KN95 mask, a surgical mask, and fabric masks.\n\nResultsN95 masks offered higher degrees of protection than the other categories of masks tested; however, it should be noted that most N95 masks failed to fit the participants adequately. Fit check responses had poor correlation with quantitative fit scores. All non-N95 masks achieved low fit scores.\n\nConclusionFit is critical to the level of protection offered by masks. For an N95 mask to provide the promised protection, it must fit the participant. Performing a fit check was an unreliable way of determining fit.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Eugenia O'Kelly", + "author_inst": "Cambridge University" + }, + { + "author_name": "Anmol Arora", + "author_inst": "Cambridge University" + }, + { + "author_name": "Sophia Pirog", + "author_inst": "Northwestern University" + }, + { + "author_name": "James Ward", + "author_inst": "Cambridge University" + }, + { + "author_name": "P John Clarkson", + "author_inst": "Cambridge University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.17.20175117", "rel_title": "Real-time spatial health surveillance: mapping the UK COVID-19 epidemic", @@ -1231322,37 +1231687,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.08.21.261347", - "rel_title": "Covidex: an ultrafast and accurate tool for virus subtyping", - "rel_date": "2020-08-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.21.261347", - "rel_abs": "Covidex is an open-source, alignment-free machine learning subtyping tool for viral species. It is a shiny app that allows a fast and accurate classification in pre-defined clusters for SARS-CoV-2 and FMDV genome sequences. The user can also build its own classification models with the Covidex model generator.\n\nAvailabilityCovidex is open-source, cross-platform compatible, and is available under the terms of the GNU General Public License v3 (http://www.gnu.org/licenses/gpl.txt). Covidex is available via SourceForge https://sourceforge.net/projects/covidex or the web application https://cacciabue.shinyapps.io/shiny2/\n\nContactcacciabue.marco@inta.gob.ar; marcocacciabue@yahoo.com", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Marco Cacciabue", - "author_inst": "Instituto de Agrobiotecnolog\u00eda y Biolog\u00eda Molecular (IABIMO), Instituto Nacional de Tecnolog\u00eda Agropecuaria (INTA), Consejo Nacional de Investigaciones Cient\u00edfi" - }, - { - "author_name": "Pablo Aguilera", - "author_inst": "Instituto de Agrobiotecnolog\u00eda y Biolog\u00eda Molecular (IABIMO), Instituto Nacional de Tecnolog\u00eda Agropecuaria (INTA), Consejo Nacional de Investigaciones Cient\u00edfi" - }, - { - "author_name": "Mar\u00eda In\u00e9s Gismondi", - "author_inst": "Instituto de Agrobiotecnolog\u00eda y Biolog\u00eda Molecular (IABIMO), Instituto Nacional de Tecnolog\u00eda Agropecuaria (INTA), Consejo Nacional de Investigaciones Cient\u00edfi" - }, - { - "author_name": "Oscar Taboga", - "author_inst": "Instituto de Agrobiotecnolog\u00eda y Biolog\u00eda Molecular (IABIMO), Instituto Nacional de Tecnolog\u00eda Agropecuaria (INTA), Consejo Nacional de Investigaciones Cient\u00edfi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.08.21.260745", "rel_title": "Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic \u03b2-CoVs", @@ -1231560,6 +1231894,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.20.260190", + "rel_title": "Astodrimer sodium, dendrimer antiviral, inhibits replication of SARS-CoV-2 in vitro", + "rel_date": "2020-08-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.20.260190", + "rel_abs": "An effective response to the ongoing coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will involve a range of complementary preventive modalities. The current studies were conducted to evaluate the in vitro SARS-CoV-2 antiviral and virucidal activity of astodrimer sodium, a dendrimer with broad spectrum antimicrobial activity, including against enveloped viruses in in vitro and in vivo models, that is marketed for antiviral and antibacterial applications. We report that astodrimer sodium inhibits replication of SARS-CoV-2 in Vero E6 and Calu-3 cells, with 50% effective concentrations (EC50) for i) reducing virus-induced cytopathic effect of 0.002 to 0.012 mg/mL in Vero E6 cells, and ii) infectious virus release by plaque assay of 0.019 to 0.031 mg/mL in Vero E6 cells and 0.031 to 0.045 mg/mL in Calu-3 cells. The selectivity index (SI) in these assays was as high as 2197. Astodrimer sodium was also virucidal, reducing SARS-CoV-2 infectivity by >99.9% (>3 log10) within 1 minute of exposure, and up to >99.999% (>5 log10) shown at astodrimer sodium concentrations of 10 to 30 mg/mL in Vero E6 and Calu-3 cell lines. Astodrimer sodium also inhibited infection in a primary human airway epithelial cell line. The data were similar for all investigations and were consistent with the potent antiviral and virucidal activity of astodrimer sodium being due to inhibition of virus-host cell interactions, as previously demonstrated for other viruses. Further studies will confirm if astodrimer sodium binds to SARS-CoV-2 spike protein and physically blocks initial attachment of the virus to the host cell. Given the in vitro effectiveness and significantly high SI, astodrimer sodium warrants further investigation for potential as a nasally administered or inhaled antiviral agent for SARS-CoV-2 prevention and treatment applications.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jeremy R.A. Paull", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Graham P. Heery", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Michael D Bobardt", + "author_inst": "Scripps Research Institute" + }, + { + "author_name": "Alex Castellarnau", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Carolyn A. Luscombe", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Jacinth K. Fairley", + "author_inst": "Starpharma Pty Ltd" + }, + { + "author_name": "Philippe A Gallay", + "author_inst": "Scripps Research Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.21.261289", "rel_title": "Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses", @@ -1232944,25 +1233321,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.08.18.20175521", - "rel_title": "Machine learning and AI aided tool to differentiate COVID 19 and non-COVID 19 lung CXR", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20175521", - "rel_abs": "One of the main challenges in dealing with the current COVID 19 pandemic is how to detect and distinguish between the COVID 19 and non COVID 19 cases. This problem arises since COVID 19 symptoms resemble with other cases. One of the golden standards is by examining the lung using the chest X ray radiograph (CXR). Currently there is growing COVID 19 cases followed by the CXR images waiting to be analyzed and this may outnumber the health capacity. Learning from that current situation and to fulfill the demand for CXRs analysis, a novel solution is required. The tool is expected can detect and distinguish the COVID 19 case lung rely on CXR. Respectively, this study aims to propose the use of AI and machine learning aided tool to distinguish the COVID 19 and non COVID 19 cases based on the CXR lung image. The compared non COVID 19 CXR cases in this study include normal (healthy), influenza A, tuberculosis, and active smoker. The results confirm that the machine learning tool is able to distinguish the COVID 19 CXR lungs based on lung consolidation. Moreover, the tool is also able to recognize an abnormality of COVID 19 lung in the form of patchy ground glass opacity.\n\nTo conclude, AI and machine learning may be considered as a detection tool to identify and distinguish between COVID 19 and non COVID 19 cases in particular epidemic areas.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Andrio Adwibowo", - "author_inst": "University of Indonesia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.08.21.261909", "rel_title": "Limited window for donation of convalescent plasma with high live-virus neutralizing antibodies for COVID-19 immunotherapy", @@ -1233290,6 +1233648,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.16.20175901", + "rel_title": "Air pollution, SARS-CoV-2 transmission, and COVID-19 outcomes: A state-of-the-science review of a rapidly evolving research area", + "rel_date": "2020-08-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.16.20175901", + "rel_abs": "BackgroundAs the coronavirus pandemic rages on, 692,000 (August 7, 2020) human lives and counting have been lost worldwide to COVID-19. Understanding the relationship between short- and long-term exposure to air pollution and adverse COVID-19 health outcomes is crucial for developing solutions to this global crisis.\n\nObjectivesTo conduct a scoping review of epidemiologic research on the link between short- and long-term exposure to air pollution and COVID-19 health outcomes.\n\nMethodWe searched PubMed, Web of Science, Embase, Cochrane, MedRxiv, and BioRxiv for preliminary epidemiological studies of the association between air pollution and COVID-19 health outcomes. 28 papers were finally selected after applying our inclusion/exclusion criteria; we categorized these studies as long-term studies, short-term time-series studies, or short-term cross-sectional studies. One study included both short-term time-series and a cross-sectional study design.\n\nResults27 studies of the 28 reported evidence of statistically significant positive associations between air pollutant exposure and adverse COVID-19 health outcomes; 11 of 12 long-term studies and all 16 short-term studies reported statistically significant positive associations. The 28 identified studies included various confounders, spatial and temporal resolutions of pollution concentrations, and COVID-19 health outcomes.\n\nDiscussionWe discuss methodological challenges and highlight additional research areas based on our findings. Challenges include data quality issues, ecological study design limitations, improved adjustment for confounders, exposure errors related to spatial resolution, geographic variability in testing, mitigation measures and pandemic stage, clustering of health outcomes, and a lack of publicly available data and code.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anushka Bhaskar", + "author_inst": "Harvard University" + }, + { + "author_name": "Jay Chandra", + "author_inst": "Harvard University" + }, + { + "author_name": "Danielle Braun", + "author_inst": "Harvard TH Chan School of Public Health" + }, + { + "author_name": "Jacqueline Cellini", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Francesca Dominici", + "author_inst": "Harvard TH Chan School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.08.19.257493", "rel_title": "Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2", @@ -1234962,57 +1235355,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.17.20176610", - "rel_title": "Evidence and magnitude of seasonality in SARS-CoV-2 transmission: Penny wise, pandemic foolish?", - "rel_date": "2020-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20176610", - "rel_abs": "ImportanceIntensity and duration of the COVID-19 pandemic, and planning required to balance concerns of saving lives and avoiding economic collapse, could depend significantly on whether SARS-CoV-2 transmission is sensitive to seasonal changes.\n\nObjectiveHypothesis is that increasing temperature results in reduced SARS CoV-2 transmission and may help slow the increase of cases over time.\n\nSettingFifty representative Northern Hemisphere countries meeting specific criteria had sufficient COVID-19 case and meteorological data for analysis.\n\nMethodsRegression was used to find relationship between the log of number of COVID-19 cases and temperature over time in 50 representative countries. To summarize the day-day variability, and reduce dimensionality, we selected a robust measure, Coefficient of Time (CT), for each location. The resulting regression coefficients were then used in a multivariable regression against meteorological, country-level and demographic covariates.\n\nResultsMedian minimum daily temperature showed the strongest correlation with the reciprocal of CT (which can be considered as a rate associated with doubling time) for confirmed cases (adjusted R2 = 0.610, p = 1.45E-06). A similar correlation was found using median daily dewpoint, which was highly colinear with temperature, and therefore was not used in the analysis. The correlation between minimum median temperature and the rate of increase of the log of confirmed cases was 47% and 45% greater than for cases of death and recovered cases of COVID-19, respectively. This suggests the primary influence of temperature on SARS-CoV2 transmission more than COVID-19 morbidity. Based on the correlation between temperature and the rate of increase in COVID-19, it can be estimated that, between the range of 30 to 100 degrees Fahrenheit, a one degree increase leads to a 1% decrease--and a one degree decrease leads to a 3.7% increase--in the rate of increase of the log of daily confirmed cases.\n\nConclusionThe results suggest that boreal summer months are associated with slower rates of COVID-19 transmission, with the reverse true in winter months. Knowledge of COVID-19 seasonality could prove useful in local planning for phased reductions social interventions and help to prepare for the timing of possible pandemic resurgence during cooler months.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Adam Ian Kaplin", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Caesar Junker", - "author_inst": "Joint Artificial Intelligence Center" - }, - { - "author_name": "Anupama Kumar", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Mary Anne de Amorim Ribeiro", - "author_inst": "PUPA" - }, - { - "author_name": "Eileen Yu", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Michael Wang", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Ted Smith", - "author_inst": "University of Louisville School of Medicine" - }, - { - "author_name": "Shesh Nath Rai", - "author_inst": "University of Louisville School of Medicine" - }, - { - "author_name": "Aruni Bhatnager", - "author_inst": "University of Louisville School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.17.20176842", "rel_title": "Healthcare workers high COVID-19 infection rate: the source of infections and potential for respirators and surgical masks to reduce occupational infections", @@ -1235236,6 +1235578,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.17.20174821", + "rel_title": "Quantifying the efficiency of non-pharmaceutical interventions against SARS-COV-2 transmission in Europe", + "rel_date": "2020-08-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20174821", + "rel_abs": "Since the emergence of SARS-CoV-2, governments around the World have implemented a combination of public health responses based on non-pharmaceutical interventions (NPIs), with significant social and economic consequences. Though most European countries have overcome the first epidemic wave, it remains of high priority to quantify the efficiency of different NPIs to inform preparedness for an impending second wave. In this study, combining capture-recapture methods with Bayesian inference in an age-structured mathematical model, we use a unique European dataset compiled by the European Centre for Disease Control (ECDC) to quantify the efficiency of 24 NPIs and their combinations (referred to as public health responses, PHR) in reducing SARS-Cov-2 transmission rates in 32 European countries. Of 166 unique PHR tested, we found that median decrease in viral transmission was 74%, which is enough to suppress the epidemic. PHR efficiency was positively associated with the number of NPIs implemented. We found that bans on mass gatherings had the largest effect among NPIs, followed by school closures, teleworking, and stay home orders. Partial implementation of most NPIs resulted in lower than average response efficiency. This first large-scale estimation of NPI and PHR efficiency against SARS-COV-2 transmission in Europe suggests that a combination of NPIs targeting different population groups should be favored to control future epidemic waves.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Andres Garchitorena", + "author_inst": "Institut de Recherche pour le Developpement" + }, + { + "author_name": "Hugo Gruson", + "author_inst": "IRD" + }, + { + "author_name": "Bernard Cazelles", + "author_inst": "Sorbonne Universite" + }, + { + "author_name": "Tommi Karki", + "author_inst": "European Centre for Disease Control" + }, + { + "author_name": "Bertrand Sudre", + "author_inst": "European Centre for Disese Control" + }, + { + "author_name": "Benjamin ROCHE", + "author_inst": "IRD" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.17.20176552", "rel_title": "SARS-CoV-2 antibody responses in children with MIS-C and mild and severe COVID-19", @@ -1236832,85 +1237213,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.08.18.255810", - "rel_title": "SARS-CoV-2 Infection and Transmission Depends on Heparan Sulfates and Is Blocked by Low Molecular Weight Heparins", - "rel_date": "2020-08-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.18.255810", - "rel_abs": "The current pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and outbreaks of new variants highlight the need for preventive treatments. Here we identified heparan sulfate proteoglycans as attachment receptors for SARS-CoV-2. Notably, neutralizing antibodies against SARS-CoV-2 isolated from COVID-19 patients interfered with SARS-CoV-2 binding to heparan sulfate proteoglycans, which might be an additional mechanism of antibodies to neutralize infection. SARS-CoV-2 binding to and infection of epithelial cells was blocked by low molecular weight heparins (LMWH). Although dendritic cells (DCs) and mucosal Langerhans cells (LCs) were not infected by SARS-CoV-2, both DC subsets efficiently captured SARS-CoV-2 via heparan sulfate proteoglycans, and transmitted the virus to ACE2-positive cells. Moreover, human primary nasal cells were infected by SARS-CoV-2 and infection was blocked by pre-treatment with LMWH. These data strongly suggest that heparan sulfate proteoglycans are important attachment receptors facilitating infection and transmission, and support the use of LMWH as prophylaxis against SARS-CoV-2 infection.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Marta Bermejo-Jambrina", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - }, - { - "author_name": "Julia Eder", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - }, - { - "author_name": "Tanja M Kaptein", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - }, - { - "author_name": "John L van Hamme", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - }, - { - "author_name": "Leanne C Helgers", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - }, - { - "author_name": "Killian E Vlaming", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Philip J Brouwer", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - }, - { - "author_name": "Alexander P Vlaar", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - }, - { - "author_name": "Frank E.H.P van Baarle", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - }, - { - "author_name": "Marcel Spaargaren", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Godelieve J de Bree", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - }, - { - "author_name": "Bernadien Maartje Nijmeijer", - "author_inst": "Amsterdam Medical Centres, University of Amsterdam" - }, - { - "author_name": "Neeltje A Kootstra", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - }, - { - "author_name": "Marit J van Gils", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - }, - { - "author_name": "Rogier W Sanders", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - }, - { - "author_name": "Teunis B.H. Geijtenbeek", - "author_inst": "Amsterdam Medical Centers, University of Amsterdam" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.08.17.255166", "rel_title": "Seeding of outbreaks of COVID-19 by contaminated fresh and frozen food", @@ -1237098,6 +1237400,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.15.20175513", + "rel_title": "Behavioral preventive measures and the use of medicines and herbal products among the public in response to Covid-19 in Bangladesh: A cross-sectional study", + "rel_date": "2020-08-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.15.20175513", + "rel_abs": "The present study was conducted to assess the behavioral preventive measures and the use of medicines and herbal foods/products among the public in response to Covid-19. A cross-sectional survey was conducted from 27 June to 20 July 2020, and 1222 people participated. Kruskal-Wallis test was used to identify the differences in behavioral preventive practices across different demographic categories. To identify the factors associated with the use of preventive medicines and herbal foods/products, multivariable logistic regression was performed. Most participants adopted the recommended preventive practices such as washing hands more frequently (87.5%), staying home more often (85.5%), avoiding crowds (86%), and wearing masks (91.6%). About half of the smokers reported a decreased rate of smoking during the pandemic. Also, 14.8% and 57.6% of the participants took medicines and herbal foods/products as preventive measures against Covid-19. Arsenicum album and Zinc supplements were the most commonly used preventive medicines. Gender, age, and fear of Covid-19 were significantly associated with the use of both preventive medicines and herbal products. For the management of Covid-19 related symptoms, Paracetamols, Fexofenadine, and Zinc supplements were used most often. Most participants sought information from non-medical sources while using medicines and herbal products. Moreover, potentially inappropriate and unnecessary use of drugs were identified.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Iftekhar Ahmed", + "author_inst": "Department of Pharmacy, Jahangirnagar University, Dhaka, Bangladesh" + }, + { + "author_name": "Maruf Hasan", + "author_inst": "Department of Pharmacy, Jahangirnagar University, Dhaka, Bangladesh" + }, + { + "author_name": "Rahima Akter", + "author_inst": "Department of Pharmacy, World University of Bangladesh, Dhaka, Bangladesh" + }, + { + "author_name": "Bidduth Kumar Sarkar", + "author_inst": "Department of Pharmacy, Ranada Prasad Shaha University, Narayanganj, Bangladesh" + }, + { + "author_name": "Marufa Rahman", + "author_inst": "Department of Pharmacy, Jahangirnagar University, Savar, Dhaka, Bangladesh" + }, + { + "author_name": "Md Samun Sarker", + "author_inst": "Bangladesh Livestock Research Institute (BLRI), Savar, Dhaka, Bangladesh" + }, + { + "author_name": "Mohammed A. Samad", + "author_inst": "Bangladesh Livestock Research Institute (BLRI), Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.15.20175786", "rel_title": "Universal PCR and antibody testing demonstrate little to no transmission of SARS-CoV-2 in a rural community", @@ -1238558,33 +1238903,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.14.20175265", - "rel_title": "Assessment of physiological signs associated with COVID-19 measured using wearable devices", - "rel_date": "2020-08-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20175265", - "rel_abs": "Respiration rate, heart rate, and heart rate variability are some health metrics that are easily measured by consumer devices and which can potentially provide early signs of illness. Furthermore, mobile applications which accompany wearable devices can be used to collect relevant self-reported symptoms and demographic data. This makes consumer devices a valuable tool in the fight against the COVID-19 pandemic. We considered two approaches to assessing COVID-19 - a symptom-based approach, and a physiological signs based technique. Firstly, we trained a Logistic Regression classifier to predict the need for hospitalization of COVID-19 patients given the symptoms experienced, age, sex, and BMI. Secondly, we trained a neural network classifier to predict whether a person is sick on any specific day given respiration rate, heart rate, and heart rate variability data for that day and and for the four preceding days. Data on 1,181 subjects diagnosed with COVID-19 (active infection, PCR test) were collected from May 21 - July 14, 2020. 11.0% of COVID-19 subjects were asymptomatic, 47.2% of subjects recovered at home by themselves, 33.2% recovered at home with the help of someone else, 8.16% of subjects required hospitalization without ventilation support, and 0.448% required ventilation. Fever was present in 54.8% of subjects. Based on self-reported symptoms alone, we obtained an AUC of 0.77 {+/-} 0.05 for the prediction of the need for hospitalization. Based on physiological signs, we obtained an AUC of 0.77 {+/-} 0.03 for the prediction of illness on a specific day with 4 previous days of history. Respiration rate and heart rate are typically elevated by illness, while heart rate variability is decreased. Measuring these metrics can help in early diagnosis, and in monitoring the progress of the disease.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Aravind Natarajan", - "author_inst": "Fitbit" - }, - { - "author_name": "Hao-Wei Su", - "author_inst": "Fitbit" - }, - { - "author_name": "Conor Heneghan", - "author_inst": "Fitbit" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.14.20175018", "rel_title": "Socio-demographic, clinical, hospital admission and oxygen requirement characteristics of COVID-19 patients of Bangladesh", @@ -1238780,6 +1239098,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.14.20170878", + "rel_title": "Estimating the epidemic growth dynamics within the first week", + "rel_date": "2020-08-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20170878", + "rel_abs": "Information about the early growth of infectious outbreaks are indispensable to estimate the epidemic spreading. A large number of mathematical tools have been developed to this end, facing as much large number of different dynamic evolutions, ranging from sub-linear to super-exponential growth. Of course, the crucial point is that we do not have enough data during the initial outbreak phase to make reliable inferences. Here we propose a methodology to estimate the epidemic growth dynamics from the infected cumulative data of just a week, provided a surveillance system is available over the whole territory. The methodology, based on the Newcomb-Benford Law, is applied to Italian covid 19 case-study. Results show that it is possible to discriminate the epidemic dynamics using the first seven data points collected over fifty Italian cities. Moreover, the form of the most probable approximating function of the growth, within a six weeks epidemic scenario, is identified.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "VINCENZO FIORITI", + "author_inst": "ENEA" + }, + { + "author_name": "IVAN ROSELLI", + "author_inst": "ENEA" + }, + { + "author_name": "MARTA CHINNICI", + "author_inst": "ENEA" + }, + { + "author_name": "ANDREA ARBORE", + "author_inst": "ICT CONSULTANT" + }, + { + "author_name": "NICOLA SIGISMONDI", + "author_inst": "ICT CONSULTANT" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.14.20175190", "rel_title": "Bidirectional associations between COVID-19 and psychiatric disorder: a study of 62,354 COVID-19 cases", @@ -1240496,29 +1240849,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.12.20173294", - "rel_title": "Epidemics forecast from SIR-modeling, verification and calculated effects of lockdown and lifting of interventions", - "rel_date": "2020-08-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20173294", - "rel_abs": "Due to the current COVID-19 epidemic plague hitting the worldwide population it is of utmost medical, economical and societal interest to gain reliable predictions on the temporal evolution of the spreading of the infectious diseases in human populations. Of particular interest are the daily rates and cumulative number of new infections, as they are monitored in infected societies, and the influence of non-pharmaceutical interventions due to different lockdown measures as well as their subsequent lifting on these infections. Estimating quantitatively the influence of a later lifting of the interventions on the resulting increase in the case numbers is important to discriminate this increase from the onset of a second wave. The recently discovered new analytical solutions of Susceptible-Infectious-Recovered (SIR) model allow for such forecast and the testing of lockdown and lifting interventions as they hold for arbitrary time dependence of the infection rate. Here we present simple analytical approximations for the rate and cumulative number of new infections.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Reinhard Schlickeiser", - "author_inst": "Institute for Theoretical Physics and Astrophysics, Christian-Albrechts-University Kiel, Leibnizstr. 15, D-24118 Kiel, Germany" - }, - { - "author_name": "Martin Kroger", - "author_inst": "ETH Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.12.20173682", "rel_title": "Efficacy of Tocilizumab in Covid 19: A metanalysis of case series studies", @@ -1240790,6 +1241120,97 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.08.14.248880", + "rel_title": "In plain sight: the role of alpha-1-antitrypsin in COVID-19 pathogenesis and therapeutics.", + "rel_date": "2020-08-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.14.248880", + "rel_abs": "RationaleSARS-CoV-2 entry into host cells is facilitated by endogenous and exogenous proteases that proteolytically activate the spike glycoprotein and antiproteases inhibiting this process. Understanding the key actors in viral entry is crucial for advancing knowledge of virus tropism, pathogenesis, and potential therapeutic targets.\n\nObjectivesWe aimed to investigate the role of naive serum and alpha-1-antitrypsin (AAT) in inhibiting protease-mediated SARS-CoV-2 entry and explore the implications of AAT deficiency on susceptibility to different SARS-CoV-2 variants.\n\nFindingsOur study demonstrates that naive serum exhibits significant inhibition of SARS-CoV-2 entry, with AAT identified as the major serum protease inhibitor potently restricting entry. Using pseudoparticles, replication-competent pseudoviruses, and authentic SARS-CoV-2, we show that AAT inhibition occurs at low concentrations compared with those in serum and bronchoalveolar tissues, suggesting physiological relevance. Furthermore, sera from subjects with an AAT-deficient genotype show reduced ability to inhibit entry of both Wuhan-Hu-1 (WT) and B.1.617.2 (Delta) but exhibit no difference in inhibiting B.1.1.529 (Omicron) entry.\n\nConclusionsAAT may have a variant-dependent therapeutic potential against SARS-CoV-2. Our findings highlight the importance of further investigating the complex interplay between proteases, antiproteases, and spike glycoprotein activation in SARS-CoV-2 and other respiratory viruses to identify potential therapeutic targets and improve understanding of disease pathogenesis.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Christian S Stevens", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kasopefoluwa Y Oguntuyo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Shreyas Kowdle", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Aditya Gowlikar", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Mohammed NA Siddiquey", + "author_inst": "Louisiana State University Health Sciences Center Shreveport" + }, + { + "author_name": "Joshua A Acklin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Griffin Haas", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Robert M Schilke", + "author_inst": "Louisiana State University Health Sciences Center Shreveport" + }, + { + "author_name": "Matthew D Woolard", + "author_inst": "Louisiana State University Health Sciences Center-Shreveport" + }, + { + "author_name": "Hongbo Zhang", + "author_inst": "Louisiana State University Health Sciences Center-Shreveport" + }, + { + "author_name": "Luca Brambilla", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Satoshi Ikegame", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Chuan-tien Hung", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jean K Lim", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Robert W Cross", + "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" + }, + { + "author_name": "Thomas W Geisbert", + "author_inst": "University of Texas Medical Branch-Galveston National Laboratory" + }, + { + "author_name": "Stanimir S Ivanov", + "author_inst": "Louisiana State University Health Sciences Center-Shreveport" + }, + { + "author_name": "Jeremy P Kamil", + "author_inst": "Louisiana State University Health Sciences Center Shreveport" + }, + { + "author_name": "Benhur Lee", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.13.20174508", "rel_title": "Data Mining Approach to Analyze Covid19 Dataset of Brazilian Patients", @@ -1242010,101 +1242431,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.11.20172742", - "rel_title": "Post-discharge health status and symptoms in patients with severe COVID-19", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20172742", - "rel_abs": "BackgroundLittle is known about long-term recovery from severe COVID-19 disease. Here, we characterize overall health, physical health and mental health of patients one month after discharge for severe COVID-19.\n\nMethodsThis was a prospective single health system observational cohort study of patients [≥]18 years hospitalized with laboratory-confirmed COVID-19 disease who required at least 6 liters of oxygen during admission, had intact baseline cognitive and functional status and were discharged alive. Participants were enrolled between 30 and 40 days after discharge. Outcomes were elicited through validated survey instruments: the PROMIS(R) Dyspnea Characteristics and PROMIS(R) Global Health-10.\n\nResultsA total of 161 patients (40.6% of eligible) were enrolled; 152 (38.3%) completed the survey. Median age was 62 years (interquartile range [IQR], 50-67); 57 (37%) were female. Overall, 113/152 (74%) participants reported shortness of breath within the prior week (median score 3 out of 10 [IQR 0-5]), vs. 47/152 (31%) pre-COVID-19 infection (0, IQR 0-1), p<0.001. Participants also rated their physical health and mental health as worse in their post-COVID state (43.8, standard deviation 9.3; mental health 47.3, SD 9.3) compared to their pre-COVID state, (54.3, SD 9.3; 54.3, SD 7.8, respectively), both p <0.001. A total of 52/148 (35.1%) patients without pre-COVID oxygen requirements needed home oxygen after hospital discharge; 20/148 (13.5%) reported still using oxygen at time of survey.\n\nConclusionsPatients with severe COVID-19 disease typically experience sequelae affecting their respiratory status, physical health and mental health for at least several weeks after hospital discharge.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Himali Weerahandi", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Katherine A. Hochman", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Emma Simon", - "author_inst": "David Geffen School of Medicine at UCLA" - }, - { - "author_name": "Caroline Blaum", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Joshua Chodosh", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Emily Duan", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Kira Garry", - "author_inst": "Penn State College of Medicine" - }, - { - "author_name": "Tamara Kahan", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Savannah Karmen-Tuohy", - "author_inst": "New York University Grossman School of Medicine" - }, - { - "author_name": "Hannah Karpel", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Felicia Mendoza", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Alexander M. Prete", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Lindsey Quintana", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Jennifer Rutishauser", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Leticia Santos Martinez", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Kanan Shah", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Sneha Sharma", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Elias Simon", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Ana Stirniman", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Leora Horwitz", - "author_inst": "NYU Langone Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.10.20162412", "rel_title": "Acquired decrease of the C3b/C4b Receptor (CR1, CD35) and C4d deposits on Erythrocytes from ICU COVID-19 Patients", @@ -1242292,6 +1242618,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.11.20145086", + "rel_title": "Face Coverings and Respiratory Tract Droplet Dispersion", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20145086", + "rel_abs": "Respiratory droplets are the primary transmission route for SARS-CoV-2. Evidence suggests that virus transmission can be reduced by face coverings, but robust evidence for how mask usage might affect safe distancing parameters is lacking. Accordingly, we investigate the effectiveness of surgical masks and single-layer cotton masks on mitigating dispersion of large respiratory droplets (i.e. non aerosol). We tested a manikin ejecting fluorescent droplets and human volunteers in speaking and coughing conditions. We quantified the number of droplets in flight using laser sheet illumination and UV-light for those that had landed at table height at up to 2m. For human volunteers, expiratory droplets were caught on a microscope slide 5cm from the mouth. Whether manikin or human, wearing a face covering decreased the number of projected droplets by >1000-fold. We estimated that a person standing 2m from someone coughing without a mask is exposed to over 1000 times more respiratory droplets than from someone standing 5 cm away wearing a basic single layer mask. Our results indicate that face coverings show consistent efficacy at blocking respiratory droplets. If aerosol transmission is later determined to be a significant driver of infection, then our findings may overestimate the effectiveness of face coverings.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Lucia Bandiera", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Geethanjali Pavar", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Gabriele Pisetta", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Shuji Otomo", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Enzo Mangano", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Jonathan R. Seckl", + "author_inst": "Queen`s Medical Research Institute, University of Edinburgh" + }, + { + "author_name": "Paul Digard", + "author_inst": "The Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Emanuela Molinari", + "author_inst": "School of Informatics, University of Edinburgh" + }, + { + "author_name": "Filippo Menolascina", + "author_inst": "School of Engineering, University of Edinburgh" + }, + { + "author_name": "Ignazio Maria Viola", + "author_inst": "School of Engineering, University of Edinburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.11.20173062", "rel_title": "Quantitative analysis of SARS-CoV-2 RNA from wastewater solids in communities with low COVID-19 incidence and prevalence", @@ -1243700,53 +1244081,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2020.08.12.20173468", - "rel_title": "Immediate Effects of COVID-19 Outbreak on Psychiatric Outpatients: Posttraumatic Stress and Influencing Factors", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20173468", - "rel_abs": "We aimed to investigate the effects of COVID-19 outbreak and public health measures on the psychological well-being of patients with psychiatric disorders. This cross-sectional study assessed 436 outpatients recruited from a tertiary psychiatry clinic in Istanbul, Turkey, nearly one month after the government introduced strict measures of lockdown against the ongoing outbreak. Respondents completed a web-based survey on sociodemographic data, subjective sleep quality, and a range of psychiatric symptoms using the Impact of Events Scale-Revised (IES-R), and Hospital Anxiety and Depression Scale (HADS). Respondents reported high frequencies of clinically significant posttraumatic stress disorder (PTSD) (32.6%, IES-R score [≥] 33), anxiety (36.4%, HADS anxiety score > 10), and depression (51%, HADS depression score > 10). 20.5% of respondents described that their psychological status worsened during the COVID-19 outbreak, and 12.1% of respondents described poor or very poor sleep in the prior month. Positive predictors of increased PTSD symptoms included the chronic medical diseases, knowing someone in the social vicinity diagnosed with the COVID-19 infection, job loss or being on temporary leave after the outbreak, and increased exposure time to TV or social media. In contrast, male gender, older age, higher educational attainment, and the psychiatric diagnoses of schizophrenia and (to a lesser degree) bipolar disorder were the negative predictors. Our results suggest that patients with psychiatric disorders are prone to substantial psychological distress during the COVID-19 outbreak, and various individual, behavioral, and social factors mediate this effect.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Burc Cagri Poyraz", - "author_inst": "Department of Psychiatry, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey." - }, - { - "author_name": "Cana Aksoy Poyraz", - "author_inst": "Department of Psychiatry, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey." - }, - { - "author_name": "Senol Turan", - "author_inst": "Department of Psychiatry, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey." - }, - { - "author_name": "Omer Faruk Demirel", - "author_inst": "Department of Psychiatry, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey." - }, - { - "author_name": "Yasin Kavla", - "author_inst": "Department of Psychiatry, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey." - }, - { - "author_name": "Ersel Bulu", - "author_inst": "Department of Psychiatry, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey." - }, - { - "author_name": "Irem Hacisalihoglu", - "author_inst": "Department of Psychiatry, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey." - }, - { - "author_name": "Elif Burcu Ersungur", - "author_inst": "Department of Psychiatry, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Istanbul, Turkey." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.08.12.20173476", "rel_title": "Superspreading k-cores at the center of COVID-19 pandemic persistence", @@ -1244062,6 +1244396,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.13.20174060", + "rel_title": "Comprehensive Systematic Review to Identify putative COVID-19 Treatments: Roles for Immunomodulator and Antiviral Treatments", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174060", + "rel_abs": "ObjectivesTo identify putative COVID-19 treatments and identify the roles of immunomodulators and antivirals in disease management.\n\nDesignSystematic review.\n\nData sourcesPubMed, bioRxiv.org and medRxiv.org were searched for studies suggestive of effective treatments for COVID-19. Additional studies were identified via a snowballing method applied to the references of retrieved papers as well as a subsequent targeted search for drug names.\n\nReview methodsInclusion criteria included any case series or randomised control trials in any language that were published from 18th December 2019 to 18th April 2020 and described COVID-19 treatment. Of an initial 2140 studies identified from the initial search, 29 studies were found to meet the inclusion criteria and included in this comprehensive systematic review.\n\nResults19 studies of antiviral treatments for COVID-19 have been reported and seven studies for immunomodulatory treatments. Six randomised controlled trials have been published with one positive trial for Hydroxychloroquine. This small study consisted of 31 patients though subsequent studies showed contradictory findings. All the remaining studies were observational studies, retrospective case reviews or non-randomised trials and these results are difficult to interpret due to methodological issues.\n\nConclusionsTo date, an impressive number of studies have been performed in a short space of time, indicative of a resilient clinical trials infrastructure. However, there is a lack of high quality evidence to support any novel treatments for COVID-19 to be incorporated into the current standard of care. The majority of the studies of treatments for COVID-19 could only be found in pre-print servers. Future clinical reviews should therefore be Comprehensive Systematic Reviews involving pre-print studies to prevent potential unnecessary replications of clinical studies.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Thomas Hill", + "author_inst": "Department of Oncology, Queen Elizabeth Hospital Birmingham, Mindelsohn Way, Edgbaston, B152GW" + }, + { + "author_name": "Mark Baker", + "author_inst": "Birmingham Medical School, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT" + }, + { + "author_name": "Lawrence Isherwood", + "author_inst": "Birmingham Medical School, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT" + }, + { + "author_name": "Lennard YW Lee", + "author_inst": "Department of Oncology, Queen Elizabeth Hospital Birmingham, Mindelsohn Way, Edgbaston B15 2GW, United Kingdom. Institute of Cancer and Genomic Sciences, Univer" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.12.20173104", "rel_title": "First report of tocilizumab use in a cohort of Latin American patients hospitalized for severe COVID-19 pneumonia", @@ -1245094,37 +1245459,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "ophthalmology" }, - { - "rel_doi": "10.1101/2020.08.13.20166975", - "rel_title": "The cost-effectiveness of common strategies for the prevention of transmission of SARS-CoV-2 in universities.", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20166975", - "rel_abs": "BackgroundThe added value of interventions to prevent the transmission of SARS-CoV-2 among university affiliates is uncertain but needed as universities attempt to remain open.\n\nMethodsWe use a decision-analytic simulation to examine the cost-effectiveness of common interventions to reduce SARS-CoV-2 transmission. We use Columbia University for reference values but our approach centers around an online model that allows users to tailor the model and interventions to their local conditions and existing strategies. All interventions are compared relative to implementing the Centers for Disease Control and Prevention (CDC) guidelines alone. Results. At prevalence rate of actively infectious cases of COVID-19 in the community surrounding the university of 0.1%, using a symptom-checking mobile application is cost-saving relative to CDC guidelines alone and the university can expect to remain open. At a prevalence of 1%, standardizing masks will be cost-saving. At a prevalence rate of 2%, thermal imaging cameras cost $965,070 (95% credible interval [CrI] = $198,821, $2.15 million)/quality-adjusted life year (QALY) gained. One-time testing on entry costs $1.08 million (95% CrI = $170,703, $3.33 million)/QALY gained. Weekly testing costs $820,119 (95% CrI = $452,673, $1.68 million)/QALY gained. Upgrades to ventilation systems or installation of far-ultraviolet C lighting systems will be cost-effective at a willingness-to-pay threshold of $200,000/QALY gained only if aerosols account for 86-90% of all on-campus transmission of SARS-CoV-2.\n\nConclusionsThe value of interventions to prevent transmission of SARS-CoV-2 vary greatly with the prevalence rate of actively infectious cases of COVID-19 in the community surrounding the university.\n\nKey PointsUniversities are struggling to remain open in the face of COVID-19 infections among affiliates. There are a number of modalities to reduce the transmission of SARS-CoV-2, but it is unclear which are worthwhile investments for any given university.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Zafar Zafari", - "author_inst": "University of Maryland" - }, - { - "author_name": "Katia Korvizhkin", - "author_inst": "Johns Hopkins" - }, - { - "author_name": "Lee Goldman", - "author_inst": "Columbia University" - }, - { - "author_name": "Peter Muennig", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.08.13.20174201", "rel_title": "Efficacy of Corticosteroids in COVID-19 Patients: A Systematic Review and Meta-Analysis", @@ -1245424,6 +1245758,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.12.20172726", + "rel_title": "Testing of Healthcare Workers Exposed to COVID19 with Rapid Antigen Detection", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20172726", + "rel_abs": "There is a need to develop safe and cost-effective ways to test healthcare workers for COVID19. Here we describe a rapid antigen testing strategy in a cohort of 497 Healthcare workers exposed to SARS-CoV-2 that can be applied by systems facing a surge of COVID19 cases, increased number of exposures in their workforce and limited RT-PCR availability. Our findings support an expanded use for antigen testing beyond its current indication and highlights the importance of further evaluating this modality for the diagnosis of COVID19 on asymptomatic individuals.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Victor Herrera", + "author_inst": "Adventhealth" + }, + { + "author_name": "Vincent Hsu", + "author_inst": "AdventHealth" + }, + { + "author_name": "Ademola Adewale", + "author_inst": "Adventhealth" + }, + { + "author_name": "Timothy Hendrix", + "author_inst": "AdventHealth" + }, + { + "author_name": "Lee Johnson", + "author_inst": "Adventhealth" + }, + { + "author_name": "Jeffrey Kuhlman", + "author_inst": "Adventhealth" + }, + { + "author_name": "Neil Finkler", + "author_inst": "Adventhealth" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.13.20170068", "rel_title": "A novel approach for evaluating contact patterns and risk mitigation strategies for COVID-19 in English Primary Schools with application of Structured Expert Judgement", @@ -1246892,49 +1247269,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2020.08.09.20171173", - "rel_title": "Effects of universal masking on Massachusetts healthcare workers' COVID-19 incidence", - "rel_date": "2020-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.09.20171173", - "rel_abs": "BackgroundHealthcare workers (HCWs) and other essential workers are at risk for occupational infection during the COVID-19 pandemic. Several infection control strategies have been implemented. Particularly, evidence shows that universal masking can mitigate COVID-19 infection, though existing research is limited by secular trend bias.\n\nAimsTo investigate the effect of hospital universal masking on COVID-19 incidence among HCWs compared to the general community population.\n\nMethodsWe compared the 7-day averaged incidence rates between a Massachusetts (USA) healthcare system and Massachusetts residents statewide. The study period was from March 17 (the date of first incident case in the healthcare system) to May 6 (the date Massachusetts implemented public masking). The healthcare system implemented universal masking on March 26, we allotted a 5-day lag for effect onset, and peak COVID-19 incidence in Massachusetts was April 20. Thus, we categorized March 17-31 as the pre-intervention phase, April 1-20 the intervention phase, and April 21-May 6 the post-intervention phase. Temporal incidence trends (i.e. 7-day average slopes) were compared using standardized coefficients from linear regression models.\n\nResultsThe standardized coefficients were similar between the healthcare system and the state in both the pre- and post-intervention phases. During the intervention phase, the healthcare systems epidemic slope became negative (standardized {beta}: -0.68, 95% CI: -1.06 - -0.31), while Massachusetts slope remained positive (standardized {beta}: 0.99, 95% CI: 0.94 - 1.05).\n\nConclusionsUniversal masking at the healthcare system was associated with flattening the COVID-19 curve among HCWs, while the infection rate continued to rise in the surrounding community.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Fan-Yun Lan", - "author_inst": "Department of Environmental Health, Harvard University T.H. Chan School of Public Health, Boston, MA, USA" - }, - { - "author_name": "Costas A Christophi", - "author_inst": "Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus" - }, - { - "author_name": "Jane Buley", - "author_inst": "Department of Occupational Medicine, Cambridge Health Alliance, Harvard Medical School, Cambridge MA, USA" - }, - { - "author_name": "Eirini Iliaki", - "author_inst": "Department of Occupational Medicine, Cambridge Health Alliance, Harvard Medical School, Cambridge MA, USA" - }, - { - "author_name": "Lou Ann Bruno-Murtha", - "author_inst": "Infection Prevention & Infectious Diseases, Cambridge Health Alliance, Harvard Medical School, Cambridge MA, USA" - }, - { - "author_name": "Assaad J. Sayah", - "author_inst": "Cambridge Department of Public Health, Cambridge MA, USA" - }, - { - "author_name": "Stefanos N. Kales", - "author_inst": "Department of Environmental Health, Harvard University T.H. Chan School of Public Health, Boston, MA, USA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.08.09.20171041", "rel_title": "A city-level analysis of air pollution, climate and COVID-19 early spread during the Spanish lockdown", @@ -1247198,6 +1247532,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.07.20166868", + "rel_title": "Factors Associated with Disease Severity and Mortality among Patients with Coronavirus Disease 2019: A Systematic Review and Meta-Analysis", + "rel_date": "2020-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20166868", + "rel_abs": "BackgroundUnderstanding the factors associated with disease severity and mortality in Coronavirus disease (COVID-19) is imperative to effectively triage patients. We performed a systematic review to determine the demographic, clinical, laboratory and radiological factors associated with severity and mortality in COVID-19.\n\nMethodsWe searched PubMed, Embase and WHO database for English language articles from inception until May 8, 2020. We included Observational studies with direct comparison of clinical characteristics between a) patients who died and those who survived or b) patients with severe disease and those without severe disease. Data extraction and quality assessment were performed by two authors independently.\n\nResultsAmong 15680 articles from the literature search, 109 articles were included in the analysis. The risk of mortality was higher in patients with increasing age, male gender (RR 1.45, 95%CI 1.23-1.71), dyspnea (RR 2.55, 95%CI 1.88-2.46), diabetes (RR 1.59, 95%CI 1.41-1.78), hypertension (RR 1.90, 95%CI 1.69-2.15). Congestive heart failure (OR 4.76, 95%CI 1.34-16.97), hilar lymphadenopathy (OR 8.34, 95%CI 2.57-27.08), bilateral lung involvement (OR 4.86, 95%CI 3.19-7.39) and reticular pattern (OR 5.54, 95%CI 1.24-24.67) were associated with severe disease. Clinically relevant cut-offs for leukocytosis(>10.0 x109/L), lymphopenia(< 1.1 x109/L), elevated C-reactive protein(>100mg/L), LDH(>250U/L) and D-dimer(>1mg/L) had higher odds of severe disease and greater risk of mortality.\n\nConclusionKnowledge of the factors associated of disease severity and mortality identified in our study may assist in clinical decision-making and critical-care resource allocation for patients with COVID-19.\n\nPrimary Funding SourceNone.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Vignesh Chidambaram", + "author_inst": "Johns Hopkins Bloomberg school of Public health" + }, + { + "author_name": "Nyan Lynn Tun", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Waqas Haque", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Marie Gilbert Majella", + "author_inst": "Department of Preventive and Social Medicine, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry, India" + }, + { + "author_name": "Ranjith Kumar Sivakumar", + "author_inst": "Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong, China" + }, + { + "author_name": "Amudha Kumar", + "author_inst": "Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA" + }, + { + "author_name": "Angela Ting-Wei Hsu", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Izza Ishak", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Aqsha Nur", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Samuel Ayeh", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Emmanuella Salia", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Ahsan Zil-E-Ali", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Muhammad Saeed", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Ayu Sarena", + "author_inst": "Bhayangkara Setukpa Hospital, Sukabumi, Indonesia" + }, + { + "author_name": "Bhavna Seth", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Muzzammil Ahmadzada", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Eman Haque", + "author_inst": "Southern Methodist University, Dallas, TX, USA" + }, + { + "author_name": "Pranita Neupane", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Kuang-Heng Wang", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Tzu-Miao Pu", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Syed Ali", + "author_inst": "Fatima Memorial Hospital, Lahore, Pakistan" + }, + { + "author_name": "Muhammad Arshad", + "author_inst": "Nishtar Hospital, Multan, Pakistan" + }, + { + "author_name": "Lin Wang", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Sheriza Baksh", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Petros Karakousis", + "author_inst": "Johns Hopkins School of Medicine" + }, + { + "author_name": "Panagis Galiatsatos", + "author_inst": "Johns Hopkins School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.26.20162008", "rel_title": "COVID-19 mild cases determination from correlating COVID-line calls to reported cases", @@ -1248358,81 +1248811,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.11.20145458", - "rel_title": "Oncologic Immunomodulatory Agents in Patients with Cancer and COVID-19", - "rel_date": "2020-08-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20145458", - "rel_abs": "BackgroundCorticosteroids, anti-CD20 agents, immunotherapies, and cytotoxic chemotherapy are commonly used in the treatment of patients with cancer. How these agents impact patients with cancer who are infected with SARS-CoV-2 remains unclear.\n\nMethodsWe retrospectively investigated associations between SARS-CoV-2-associated respiratory failure or death with receipt of the aforementioned medications and with pre-COVID-19 neutropenia. The study included all cancer patients diagnosed with SARS-CoV-2 at Memorial Sloan Kettering Cancer Center until June 2, 2020 (N=820). We controlled for cancer-related characteristics known to predispose to worse COVID-19. To address that more acutely ill patients receive therapeutic corticosteroids, we examined patient subsets based on different levels of respiratory support: [≤]2 L/min supplemental oxygen, >2L/min supplemental oxygen, and advanced respiratory support prior to death.\n\nResultsCorticosteroid administration was associated with worse outcomes in the pre-2L supplemental oxygen cohort; no statistically significant difference was observed in the >2L/min supplemental oxygen and post-critical cohorts. Interleukin-6 (IL-6) and C-reactive protein (CRP) levels were lower, and ferritin levels were higher, after corticosteroid administration. In patients with metastatic thoracic cancer, 9 of 25 (36%) and 10 of 31 (32%) had respiratory failure or death among those who did and did not receive immunotherapy, respectively. Seven of 23 (30%) and 52 of 187 (28%) patients with hematologic cancer had respiratory failure or death among those who did and did not receive anti-CD20 therapy, respectively. Chemotherapy itself was not associated with worse outcomes, but pre-COVID-19 neutropenia was associated with worse COVID-19 course. Relative prevalence of chemotherapy-associated neutropenia in previous studies may account for different conclusions regarding the risks of chemotherapy in patients with COVID-19. In the absence of prospective studies and evidence-based guidelines, our data may aid providers looking to assess the risks and benefits of these agents in caring for cancer patients in the COVID-19 era.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Justin Jee", - "author_inst": "MSKCC" - }, - { - "author_name": "Aaron J Stonestrom", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Sean Devlin", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Teresa Nguyentran", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Beatriz Wills", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Varun Narendra", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Michael B Foote", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Melissa Lumish", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Santosha Vardhana", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Stephen Pastores", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Neha Korde", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Dhwani Patel", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Steven Horwitz", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Michael Scordo", - "author_inst": "Memorial Sloan Kettering Cancer Center" - }, - { - "author_name": "Anthony Daniyan", - "author_inst": "Memorial Sloan Kettering Cancer Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.08.10.20171637", "rel_title": "Hospital length of stay for severe COVID-19: implications for Remdesivir's value", @@ -1248704,6 +1249082,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.10.20171371", + "rel_title": "Impaired cellular immunity to SARS-CoV-2 in severe COVID-19 patients", + "rel_date": "2020-08-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171371", + "rel_abs": "The World Health Organization has declared SARS-CoV-2 virus outbreak a world-wide pandemic. Individuals infected by the virus exhibited different degrees of symptoms, the basis of which remains largely unclear. Currently, though convalescent individuals have been shown with both cellular and humoral immune responses, there is very limited understanding on the immune responses, especially adaptive immune responses, in patients with severe COVID-19. Here, we examined 10 blood samples from COVID-19 patients with acute respiratory distress syndrome (ARDS). The majority of them (70%) mounted SARS-CoV-2-specific humoral immunity with production of neutralizing antibodies. However, compared to healthy controls, the percentages and absolute numbers of both NK cells and CD8+ T cells were significantly reduced, accompanied with decreased IFN{gamma} expression in CD4+ T cells in peripheral blood from severe patients. Most notably, we failed in detecting SARS-CoV-2-specific IFN{gamma} production by peripheral blood lymphocytes from these patients. Our work thus indicates that COVID-19 patients with severe symptoms are associated with defective cellular immunity, which not only provides insights on understanding the pathogenesis of COVID-19, but also has implications in developing an effective vaccine to SARS-CoV-2.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Ling Ni", + "author_inst": "Institute for Immunology and School of Medicine,Tsinghua University" + }, + { + "author_name": "Meng-Li Cheng", + "author_inst": "College of Basic Medical Science, Jilin University" + }, + { + "author_name": "Hui Zhao", + "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" + }, + { + "author_name": "Yu Feng", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Jingyuan Liu", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases," + }, + { + "author_name": "Fang Ye", + "author_inst": "Department of Hematology, Chui Yang Liu Hospital affiliated to Tsinghua University" + }, + { + "author_name": "Qing Ye", + "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences," + }, + { + "author_name": "Gengzhen Zhu", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Xiaoli Li", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Pengzhi Wang", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Jing Shao", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Yong-qiang Deng", + "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" + }, + { + "author_name": "Peng Wei", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + }, + { + "author_name": "Fang Chen", + "author_inst": "Department of Cardiology, Chui Yang Liu Hospital affiliated to Tsinghua University" + }, + { + "author_name": "Cheng-feng Qin", + "author_inst": "Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" + }, + { + "author_name": "Guoqing Wang", + "author_inst": "College of Basic Medical Science, Jilin University" + }, + { + "author_name": "Fan Li", + "author_inst": "College of Basic Medical Science, Jilin University" + }, + { + "author_name": "Hui Zeng", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, and Beijing Key Laboratory of Emerging Infectious Diseases" + }, + { + "author_name": "Chen Dong", + "author_inst": "Institute for Immunology and School of Medicine, Tsinghua University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.08.10.20171439", "rel_title": "Extended SEIQR type model for COVID-19 epidemic and data analysis", @@ -1250144,25 +1250613,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.07.20169904", - "rel_title": "Model to Describe Fast Shutoff of CoVID-19 Pandemic Spread", - "rel_date": "2020-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20169904", - "rel_abs": "Early CoVID-19 growth obeys: [Formula], with Ko = [(ln 2)/(tdbl)], where tdbl is the pandemic growth doubling time. Given [Formula], the daily number of new CoVID-19 cases is [Formula]. Implementing society-wide Social Distancing increases the tdbl doubling time, and a linear function of time for tdbl was used in our Initial Model: O_FD O_INLINEFIG[Formula]C_INLINEFIGC_FD to describe these changes, with Go = [KA/{gamma}o]. However, this equation could not easily model some quickly decreasing{rho} [t] cases, indicating that a second Social Distancing process was involved. This second process is most evident in the initial CoVID-19 data from China, South Korea, and Italy. The Italy data is analyzed here in detail as representative of this second process. Modifying Zo[t] to allow exponential cutoffs: O_FD O_INLINEFIG[Formula]C_INLINEFIGC_FD provides a new Enhanced Initial Model (EIM), which significantly improves datafits, where [Formula]. Since large variations are present in{rho} data [t], these models were generalized into an orthogonal function series, to provide additional data fitting parameters:\n\nO_FD O_INLINEFIG[Formula]C_INLINEFIGC_FD\n\nIts first term can give No[t] or NE [t], for Z[t] [->] Zo[t] or Z[t] [->] Ze[t]. The Lm(Z) are Laguerre Polynomials, with L0(Z) = 1, and {gm; m = 0,MF} are constants derived from each dataset. When{rho} [t] = dN[t]/dt gradually decreases, using Zo[t] provided good datafits at small MF values, but was inadequate if{rho} [t] decreased faster. For those cases, ZE[t] was used in the above N(Z) series to give the most general Enhanced Orthogonal Function [EOF] model developed here. Even with MF = 0, qo = 0, this EOF model fit the Italy CoVID-19 data for{rho} [t] = dN[t]/dt fairly well.\n\nWhen the{rho} [t] post-peak behavior is not Gaussian, then ZE[t] with{delta} o = 0, qo = 0; which we call ZA[t], is also likely to be a sufficient extension of the Zo[t] model. The EOF model also can model a gradually decreasing{rho} [t] tail using small {{delta}o, qo} values [with 6 Figures].", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Genghmun Eng", - "author_inst": "Retired Scientist" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.09.20171223", "rel_title": "Markedly heterogeneous COVID-19 testing plans among US colleges and universities", @@ -1250522,6 +1250972,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.07.20161737", + "rel_title": "LamPORE: rapid, accurate and highly scalable molecular screening for SARS-CoV-2 infection, based on nanopore sequencing", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20161737", + "rel_abs": "LamPORE is a rapid way of testing/screening large numbers of samples for the presence or absence of SARS-CoV-2, the virus causing COVID-19. It combines barcoded multi-target amplification, 15-minute barcoded library preparation and real-time nanopore sequencing. Starting with extracted RNA, results can be obtained from 12 samples in approximately an hour and from 96 samples in under 2 hours. High scalability is achieved by combinatorial barcoding. Performance characteristics are currently being established and regulatory clearance to market is underway.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Phillip James", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "David Stoddart", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Eoghan D Harrington", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "John Beaulaurier", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Lynn Ly", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Stuart Reid", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Daniel J Turner", + "author_inst": "Oxford Nanopore Technologies" + }, + { + "author_name": "Sissel Juul", + "author_inst": "Oxford Nanopore Technologies" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.07.20170407", "rel_title": "Model-based projections for COVID-19 outbreak size and student-days lost to closure in Ontario childcare centres and primary schools", @@ -1251870,45 +1252367,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.10.20171777", - "rel_title": "The effectiveness of tests to detect the presence of SARS-CoV-2 virus, and antibodies to SARS-CoV-2, to inform COVID-19 diagnosis: a rapid systematic review", - "rel_date": "2020-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171777", - "rel_abs": "STRUCTURED ABSTRACTO_ST_ABSObjectivesC_ST_ABSWe undertook a rapid systematic review with the aim of identifying evidence that could be used to answer the following research questions: (1) What is the clinical effectiveness of tests that detect the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to inform COVID-19 diagnosis? (2) What is the clinical effectiveness of tests that detect the presence of antibodies to the SARS-CoV-2 virus to inform COVID-19 diagnosis?\n\nDesignsystematic review and meta-analysis of studies of diagnostic test accuracy. We systematically searched for all published evidence on the effectiveness of tests for the presence of SARS-Cov-2 virus, or antibodies to SARS-CoV-2, up to 4 May 2020, and assessed relevant studies for risks of bias using the QUADAS-2 framework.\n\nMain outcome measuresmeasures of diagnostic accuracy (sensitivity, specificity, positive/negative predictive value) were the main outcomes of interest. We also included studies that reported influence of testing on subsequent patient management, and that reported virus/antibody detection rates where these facilitated comparisons of testing in different settings, different populations, or using different sampling methods.\n\nResults38 studies on SARS-CoV-2 virus testing and 25 studies on SARS-CoV-2 antibody testing were identified. We identified high or unclear risks of bias in the majority of studies, most commonly as a result of unclear methods of patient selection and test conduct, or because of the use of a reference standard that may not definitively diagnose COVID-19. The majority were in hospital settings, in patients with confirmed or suspected COVID-19 infection. Pooled analysis of 16 studies (3818 patients) estimated a sensitivity of 87.8% (95% confidence interval 81.5% to 92.2%) for an initial reverse-transcriptase polymerase chain reaction test. For antibody tests, ten studies reported diagnostic accuracy outcomes: sensitivity ranged from 18.4% to 96.1% and specificity 88.9% to 100%. However, the lack of a true reference standard for SARS-CoV-2 diagnosis makes it challenging to assess the true diagnostic accuracy of these tests. Eighteen studies reporting different sampling methods suggest that for virus tests, the type of sample obtained/type of tissue sampled could influence test accuracy. Finally we searched for, but did not identify, any evidence on how any test influences subsequent patient management.\n\nConclusionsEvidence is rapidly emerging on the effectiveness of tests for COVID-19 diagnosis and management, but important uncertainties about their effectiveness and most appropriate application remain. Estimates of diagnostic accuracy should be interpreted bearing in mind the absence of a definitive reference standard to diagnose or rule out COVID-19 infection. More evidence is needed about the effectiveness of testing outside of hospital settings and in mild or asymptomatic cases. Implementation of public health strategies centred on COVID-19 testing provides opportunities to explore these important areas of research.\n\nSUMMARY BOXO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LITests for the presence of the SARS-CoV-2 virus, and antibodies to the virus, are being deployed rapidly and at scale as part of the global response to COVID-19.\nC_LIO_LIAt the outset of this work (March 2020), no high-quality evidence reviews on the effectiveness of SARS-CoV-2 virus or antibody tests were available.\nC_LIO_LIHigh-quality evidence reviews are required to help decision makers deploy and interpret these tests effectively.\nC_LI\n\nWhat are the new findings?O_LIHere, we synthesise evidence on the diagnostic accuracy of all known tests for SARS-CoV-2, as well as tests for antibodies to SARS-CoV-2.\nC_LIO_LIWe also systematically summarise evidence on the influence of tissue sample site on virus test detection rates, and the influence of test timing relative to disease course on antibody detection. The results suggest that both these factors could influence test results.\nC_LIO_LIWe conclude that evidence on SARS-CoV-2 virus and antibody tests is nascent and significant uncertainties remain in the evidence base regarding their clinical and public health application. We also note that potential risks of bias exist within many of the available studies.\nC_LI\n\nHow might it impact on clinical practice in the foreseeable future?O_LIIn a rapidly developing pandemic, the widespread use of testing is an essential element in the development of effective public health strategies, but it is important to acknowledge the gaps and limitations that exist in the current evidence base and that, where possible, these should be addressed in future studies.\nC_LIO_LIIn particular, more evidence is needed on the performance of point-of-care or near-patient tests compared to their laboratory equivalents, and results of testing in people with no or minimal symptoms in community-based settings needs further analysis.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "David Jarrom", - "author_inst": "Health Technology Wales, Velindre University NHS Trust" - }, - { - "author_name": "Lauren Elston", - "author_inst": "Health Technology Wales, Velindre University NHS Trust" - }, - { - "author_name": "Jennifer Washington", - "author_inst": "Velindre University NHS Trust" - }, - { - "author_name": "Matthew Prettyjohns", - "author_inst": "Health Technology Wales, Velindre University NHS Trust" - }, - { - "author_name": "Kimberley Cann", - "author_inst": "Health Technology Wales, Velindre University NHS Trust" - }, - { - "author_name": "Susan Myles", - "author_inst": "Health Technology Wales, Velindre University NHS Trust" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.08.07.20163402", "rel_title": "A Large-Scale Clinical Validation Study Using nCapp Cloud Plus Terminal by Frontline Doctors for the Rapid Diagnosis of COVID-19 and COVID-19 pneumonia in China", @@ -1252304,6 +1252762,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.10.20172155", + "rel_title": "EPIDEMIC ANALYSIS OF COVID-19 IN ALGERIA BY A GENERALIZED SEIR MODEL", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20172155", + "rel_abs": "The novel coronavirus diseases 2019 (COVID-19) in Wuhan is continuing to impress the world by its fast spread and the number of affected persons attracting an unprecedented attention. In this article, we used the classical SEIR model and a generalized SEIR model called SEIRDP model inspired in a model previously used during the outbreak in China to predict the evolution of COVID-19 in Algeria for a future period of 100 days using official reported data from early April to early August, 2020. Initial evaluation showed that thetwo models had a net correspondence with the reported data during this period for cumulative infected cases but the number of cumulative deaths was underestimated with the classical SEIR model. Model prediction with the SEIRDP concluded that the number of cumulative infected cases will increase in the next days reaching a number of about 60 k in middle November with a median of about 300 daily cases. Also, the number of estimated deaths will be around 2k. These results suggest that the COVID-19 is ongoing to infect more persons which may push national authorities to carefully act in the probable leaving of containment.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Mohamed LOUNIS Sr.", + "author_inst": "University of Ziane Achour Djelfa" + }, + { + "author_name": "Juarez dos Santos AZEVEDO Sr.", + "author_inst": "Universidade Federal da Bahia (UFBA)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.10.20172189", "rel_title": "Janus Kinase-Inhibitor and Type I Interferon Ability to Produce Favorable Clinical Outcomes in COVID-19 Patients: A Systematic Review and Meta-Analysis", @@ -1253860,41 +1254341,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.08.10.244756", - "rel_title": "The interplay of SARS-CoV-2 evolution and constraints imposed by the structure and functionality of its proteins", - "rel_date": "2020-08-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.10.244756", - "rel_abs": "Fast evolution of the SARS-CoV-2 virus provides us with unique information about the patterns of genetic changes in a single pathogen in the timescale of months. This data is used extensively to track the phylodynamic of the pandemics spread and its split into distinct clades. Here we show that the patterns of SARS-CoV-2 virus mutations along its genome are closely correlated with the structural features of the coded proteins. We show that the foldability of proteins 3D structures and conservation of their functions are the universal factors driving evolutionary selection in protein-coding genes. Insights from the analysis of mutation distribution in the context of the SARS-CoV-2 proteins structures and functions have practical implications including evaluating potential antigen epitopes or selection of primers for PCR-based COVID-19 tests.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Lukasz Jaroszewski", - "author_inst": "University of California Riverside School of Medicine" - }, - { - "author_name": "Mallika Iyer", - "author_inst": "Sanford Burnham Prebys Medical Discovery Institute" - }, - { - "author_name": "Arghavan Alisoltani", - "author_inst": "University of California Riverside School of Medicine" - }, - { - "author_name": "Mayya Sedova", - "author_inst": "University of California Riverside School of Medicine" - }, - { - "author_name": "Adam Godzik", - "author_inst": "University of California Riverside School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2020.08.08.238469", "rel_title": "An ultra-high affinity synthetic nanobody blocks SARS-CoV-2 infection by locking Spike into an inactive conformation", @@ -1254450,6 +1254896,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.09.242867", + "rel_title": "A potent neutralizing nanobody against SARS-CoV-2 with inhaled delivery potential", + "rel_date": "2020-08-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.09.242867", + "rel_abs": "The outbreak of COVID-19 has emerged as a global pandemic. The unprecedented scale and severity call for rapid development of effective prophylactics or therapeutics. We here reported Nanobody (Nb) phage display libraries derived from four camels immunized with the SARS-CoV-2 spike receptor-binding domain (RBD), from which 381 Nbs were identified to recognize SARS-CoV-2-RBD. Furthermore, seven Nbs were shown to block interaction of human angiotensin converting enzyme 2 (ACE2) with SARS-CoV-2-RBD-variants, bat-SL-CoV-WIV1-RBD and SARS-CoV-1-RBD. Among the seven candidates, Nb11-59 exhibited the highest activity against authentic SARS-CoV-2 with ND50 of 0.55 g/mL. Nb11-59 can be produced on a large-scale in Pichia pastoris, with 20 g/L titer and 99.36% purity. It also showed good stability profile, and nebulization did not impact its stability. Overall, Nb11-59 might be a promising prophylactic and therapeutic molecule against COVID-19, especially through inhalation delivery.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC=\"FIGDIR/small/242867v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (42K):\norg.highwire.dtl.DTLVardef@e4434org.highwire.dtl.DTLVardef@9fee79org.highwire.dtl.DTLVardef@1e15bb1org.highwire.dtl.DTLVardef@4adb0c_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Junwei Gai", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Linlin Ma", + "author_inst": "Shanghai University of Medicine and Health Sciences" + }, + { + "author_name": "Guanghui Li", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Min Zhu", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Peng Qiao", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Xiaofei Li", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Haiwei Zhang", + "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Yanmin Zhang", + "author_inst": "School of Science, China Pharmaceutical University" + }, + { + "author_name": "Yadong Chen", + "author_inst": "School of Science, China Pharmaceutical University" + }, + { + "author_name": "Weiwei Ji", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Hao Zhang", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Huanhuan Cao", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Xionghui Li", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + }, + { + "author_name": "Rui Gong", + "author_inst": "Wuhan Institute of Virology Chinese Academy of Sciences" + }, + { + "author_name": "Yakun Wan", + "author_inst": "Shanghai Novamab Biopharmaceuticals Co., Ltd." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.08.04.20168054", "rel_title": "SARS-CoV-2 and the Role of Orofecal Transmission: Systematic Review", @@ -1255906,41 +1256427,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2020.08.06.20168294", - "rel_title": "Quickly And Simply Detection For Coronavirus Including SARS-CoV-2 On The Mobile Real-Time PCR Device And Without RNA Extraction", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20168294", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was reported to WHO as an outbreak in Wuhan City, Hubei Province, China on end of 2019, afterwards epidemic in many countries, and pandemic on the worldwide in 2020.\n\nUsually detection of coronavirus including SARS-CoV-2 was detected by real-time RT-PCR method, but it must be long time that RNA is treated by extraction, concentration and purification, and detected by RT-PCR method. We modified various methods, of which evaluated if each method is short and simple enough.\n\nIn one point of the evaluations, real-time RT-PCR could be finished in very short time with using mobile real-time PCR device PCR1100 (Nippon Sheet Glass Co. Ltd.). It was able to detect positive control RNA for 20 minutes by each method according to the National Institute of Infections Disease in Japan (NIID), and less than 13.5 minutes according to the Centers for Disease Control and Prevention in USA (CDC).\n\nIn another point of the evaluations, surprisingly, Human coronavirus 229E, which was substituted for SARS-CoV-2, could be detected in crude state without treatment in advance of RNA. As that was, it was possible to detect coronavirus with direct RT-PCR. Therefore, it might eliminate wasteful time, avoid secondary infection and risk of contamination.\n\nIn light of the above two points, SARS-CoV-2 might be detected more quickly and more simply. With using this mobile real-time PCR, these methods should be suitable for not only SARS-CoV-2 but also other various viruses and might save time compared to earlier detection methods.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Masaaki Muraoka", - "author_inst": "Business Innovation Center, Nippon Sheet Glass Co., Ltd., Japan" - }, - { - "author_name": "Yukiko Tanoi", - "author_inst": "Business Innovation Center, Nippon Sheet Glass Co., Ltd., Japan" - }, - { - "author_name": "Tetsutaro Tada", - "author_inst": "Business Innovation Center, Nippon Sheet Glass Co., Ltd., Japan" - }, - { - "author_name": "Mikio Mizukoshi", - "author_inst": "Certified Non-Profit Organization Biomedical Science Association, Japan" - }, - { - "author_name": "Osamu Kawaguchi", - "author_inst": "Business Innovation Center, Nippon Sheet Glass Co., Ltd., Japan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.08.06.20169854", "rel_title": "Genetic and Phenotypic Evidence for the Causal Relationship Between Aging and COVID-19", @@ -1256264,6 +1256750,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.07.20169961", + "rel_title": "Neutralizing antibody response in non-hospitalized SARS-CoV-2 patients", + "rel_date": "2020-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20169961", + "rel_abs": "The majority of infections with SARS-CoV-2 are asymptomatic or mild without the necessity of hospitalization. It is of importance to reveal if these patients develop an antibody response against SARS-CoV-2 and to define which antibodies confer virus neutralization. We conducted a comprehensive serological survey of 49 patients with a mild course of disease and quantified neutralizing antibody responses against a clinical SARS-CoV-2 isolate employing human cells as targets.\n\nFour patients (8%), even though symptomatic, did not develop antibodies against SARS-CoV-2 and two other patients (4%) were only positive in one of the six serological assays employed. For the remainder, antibody response against the S-protein correlated with serum neutralization whereas antibodies against the nucleocapsid were poor predictors of virus neutralization. Regarding neutralization, only six patients (12%) could be classified as highly neutralizers. Furthermore, sera from several individuals with fairly high antibody levels had only poor neutralizing activity. In addition, employing a novel serological Western blot system to characterize antibody responses against seasonal coronaviruses, we found that antibodies against the seasonal coronavirus 229E might contribute to SARS-CoV-2 neutralization.\n\nAltogether, we show that there is a wide breadth of antibody responses against SARS-CoV-2 in patients that differentially correlate with virus neutralization. This highlights the difficulty to define reliable surrogate markers for immunity against SARS-CoV-2.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Natalia Ruetalo", + "author_inst": "Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen" + }, + { + "author_name": "Ramona Businger", + "author_inst": "Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen" + }, + { + "author_name": "Karina Althaus", + "author_inst": "Institute for Transfusion Medicine, University Hospital Tuebingen" + }, + { + "author_name": "Simon Fink", + "author_inst": "NMI, Reutlingen" + }, + { + "author_name": "Felix Ruoff", + "author_inst": "NMI, Reutlingen" + }, + { + "author_name": "Klaus Hamprecht", + "author_inst": "Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen" + }, + { + "author_name": "Bertram Flehmig", + "author_inst": "Mediagnost GmbH, Reutlingen" + }, + { + "author_name": "Tamam Bakchoul", + "author_inst": "Institute for Transfusion Medicine, University Hospital Tuebingen" + }, + { + "author_name": "Markus F Templin", + "author_inst": "NMI, Reutlingen" + }, + { + "author_name": "Michael Schindler", + "author_inst": "University Hospital Tuebingen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.05.20168476", "rel_title": "Specificity and Performance of Nucleocapsid and Spike-based SARS-CoV-2 Serologic Assays", @@ -1257848,33 +1258389,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.08.05.20168781", - "rel_title": "Groundbreaking predictions about COVID-19 pandemic duration, number of infected and dead: A novel mathematical approach never used in epidemiology", - "rel_date": "2020-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20168781", - "rel_abs": "Hundreds of predictions about the duration of the pandemic and the number of infected and dead have been carried out using traditional epidemiological tools (i.e. SIR, SIRD models, etc.) or new procedures of big-data analysis. However, the extraordinary complexity of the disease and the lack of knowledge about the pandemic (i.e. R value, mortality rate, etc.) create uncertainty about the accuracy of these estimates. However, several elegant mathematical approaches, based on physics and probability principles, like the Delta-t argument, Lindys Law or the Doomsday principle-Carters catastrophe, which have been successfully applied by scientists to unravel complex phenomena characterized by their great uncertainty (i.e. Human races longevity; How many more humans will be born before extinction) allow predicting parameters of the Covid-19 pandemic. These models predict that the COVID-19 pandemic will hit us until at least September-October 2021, but will likely last until January-September 2022, causing a minimum of 36,000,000 infected and most likely 60,000,000, as well as 1,400,000 dead at best and most likely 2,333,000.\n\nCompeting Interest Statement\n\nThe authors have declared no competing interest.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Javier Garcia Garcia de Alcaniz", - "author_inst": "Veterinary Faculty Complutense University Madrid Genetics Department;" - }, - { - "author_name": "Victoria Lopez-Rodas", - "author_inst": "Veterinary Faculty Complutense University Madrid Genetics Department;" - }, - { - "author_name": "Eduardo Costas", - "author_inst": "Veterinary Faculty UCM" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.04.20168344", "rel_title": "Performing Qualitative Mask Fit Testing without a Commercial Kit: Fit Testing Which can be Performed at Home and at Work", @@ -1258006,6 +1258520,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.05.20168799", + "rel_title": "COVID-19 Test & Trace Success Determinants: Modeling On A Network", + "rel_date": "2020-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20168799", + "rel_abs": "What determines the success of a COVID-19 Test & Trace policy? We use an SEIR agent-based model on a graph, with realistic epidemiological parameters. Simulating variations in certain parameters of Testing & Tracing, we find that important determinants of successful containment are: (i) the time from symptom onset until a patient is self-isolated and tested, and (ii) the share of contacts of a positive patient who are successfully traced. Comparatively less important is (iii) the time of test analysis and contact tracing. When the share of contacts successfully traced is higher, the Test & Trace Time rises somewhat in importance. These results are robust to a wide range of values for how infectious presymptomatic patients are, to the amount of asymptomatic patients, to the network degree distribution and to base epidemic growth rate. We also provide mathematical arguments for why these simulation results hold in more general settings. Since real world Test & Trace systems and policies could affect all three parameters, Symptom Onset to Test Time should be considered, alongside test turnaround time and contact tracing coverage, as a key determinant of Test & Trace success.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ofir Reich", + "author_inst": "Google" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.04.20168518", "rel_title": "Phylodynamics reveals the role of human travel and contact tracing in controlling COVID-19 in four island nations", @@ -1259766,49 +1260299,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.05.20169086", - "rel_title": "An Examination of School Reopening Strategies during the SARS-CoV-2 Pandemic", - "rel_date": "2020-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20169086", - "rel_abs": "The SARS-CoV-2 pandemic led to closure of nearly all K-12 schools in the United States of America in March 2020. Although reopening K-12 schools for in-person schooling is desirable for many reasons, officials understand that risk reduction strategies and detection of cases are imperative in creating a safe return to school. Furthermore, consequences of reclosing recently opened schools are substantial and impact teachers, parents, and ultimately educational experiences in children. To address competing interests in meeting educational needs with public safety, we compare the impact of physical separation through school cohorts on SARS-CoV-2 infections against policies acting at the level of individual contacts within classrooms. Using an age-stratified Susceptible-Exposed-Infected-Removed model, we explore influences of reduced class density, transmission mitigation, and viral detection on cumulative prevalence. We consider several scenarios over a 6-month period including (1) multiple rotating cohorts in which students cycle through in-person instruction on a weekly basis, (2) parallel cohorts with in-person and remote learning tracks, (3) the impact of a hypothetical testing program with ideal and imperfect detection, and (4) varying levels of aggregate transmission reduction. Our mathematical model predicts that reducing the number of contacts through cohorts produces a larger effect than diminishing transmission rates per contact. Specifically, the latter approach requires dramatic reduction in transmission rates in order to achieve a comparable effect in minimizing infections over time. Further, our model indicates that surveillance programs using less sensitive tests may be adequate in monitoring infections within a school community by both keeping infections low and allowing for a longer period of instruction. Lastly, we underscore the importance of factoring infection prevalence in deciding when a local outbreak of infection is serious enough to require reverting to remote learning.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alfonso Landeros", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Xiang Ji", - "author_inst": "Tulane University" - }, - { - "author_name": "Kenneth L. Lange", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Timothy C. Stutz", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Jason Xu", - "author_inst": "Duke University" - }, - { - "author_name": "Mary E. Sehl", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Janet S. Sinsheimer", - "author_inst": "University of California, Los Angeles" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.05.20169094", "rel_title": "U.S. Field Hospitals: A Study on Public Health Emergency Response to COVID-19", @@ -1259976,6 +1260466,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.06.239798", + "rel_title": "IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection", + "rel_date": "2020-08-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.06.239798", + "rel_abs": "The novel virus SARS-CoV-2 has infected more than 14 million people worldwide resulting in the Coronavirus disease 2019 (COVID-19). Limited information on the underlying immune mechanisms that drive disease or protection during COVID-19 severely hamper development of therapeutics and vaccines. Thus, the establishment of relevant animal models that mimic the pathobiology of the disease is urgent. Rhesus macaques infected with SARS-CoV-2 exhibit disease pathobiology similar to human COVID-19, thus serving as a relevant animal model. In the current study, we have characterized the transcriptional signatures induced in the lungs of juvenile and old rhesus macaques following SARS-CoV-2 infection. We show that genes associated with Interferon (IFN) signaling, neutrophil degranulation and innate immune pathways are significantly induced in macaque infected lungs, while pathways associated with collagen formation are downregulated. In COVID-19, increasing age is a significant risk factor for poor prognosis and increased mortality. We demonstrate that Type I IFN and Notch signaling pathways are significantly upregulated in lungs of juvenile infected macaques when compared with old infected macaques. These results are corroborated with increased peripheral neutrophil counts and neutrophil lymphocyte ratio in older individuals with COVID-19 disease. In contrast, pathways involving VEGF are downregulated in lungs of old infected macaques. Using samples from humans with SARS-CoV-2 infection and COVID-19, we validate a subset of our findings. Finally, neutrophil degranulation, innate immune system and IFN gamma signaling pathways are upregulated in both tuberculosis and COVID-19, two pulmonary diseases where neutrophils are associated with increased severity. Together, our transcriptomic studies have delineated disease pathways to improve our understanding of the immunopathogenesis of COVID-19 to facilitate the design of new therapeutics for COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Bruce A. Rosa", + "author_inst": "Washington University in Saint Louis School of Medicine" + }, + { + "author_name": "Mushtaq Ahmed", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Dhiraj K. Singh", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jose Alberto Choreno-Parra", + "author_inst": "Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias" + }, + { + "author_name": "Journey Cole", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Luis Armando Jimenez-Alvarez", + "author_inst": "Laboratory of Immunobiology and Genetics, Instituto Nacional de Enfermedades Respiratorias" + }, + { + "author_name": "Tatiana Sofia Rodriguez-Reyna", + "author_inst": "Department of Immunology and Rheumatology, Instituto Nacional de Ciencias Medicas y Nutricion" + }, + { + "author_name": "Bindu Singh", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Olga Golzalez", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Ricardo Carrion", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Larry S. Schlesinger", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "John Martin", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Joaquin Zuniga", + "author_inst": "Escuela Nacional de Ciencias Biologicas, Instituto Politecnico Nacional" + }, + { + "author_name": "Makedonka Mitreva", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Shabaana A Khader", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Deepak Kaushal", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.08.06.240333", "rel_title": "Computational Hot-Spot Analysis of the SARS-CoV-2 Receptor Binding Domain / ACE2 Complex", @@ -1261504,33 +1262073,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.31.20165662", - "rel_title": "Optimal lockdown strategies for SARS-CoV2 mitigation--- an Indian perspective", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20165662", - "rel_abs": "We sought to identify optimal temporal windows for lockdown-based mitigation strategies on infectious disease spreads. An age-structured multi-compartmental Susceptible- Infected-Recovered (SIR) model was used to estimate infection spreads under parametric variation of lockdown intensity and duration from the data of SARS-CoV2 cases in India between January to July, 2020. The resulting parameter values were used to simulate lockdown outcomes for a wide range of start times and durations. Lockdowns were simulated as intervention strategies that modified weights assigned to social contact matrices for work, school and other places. Lockdown efficacy was assessed by the maximum number of infections recorded during a simulation run. Our analysis shows that lockdown outcomes depend sensitively on the timing of imposition and that it is possible to minimize lockdown durations while limiting case loads to numbers below the hospitalization thresholds. Such timing based effects arise naturally from the non-linear nature of SIR dynamics.\n\nNotationN Total Population\n\nS Number of susceptible individuals\n\nI Number of infected individuals\n\nR Number of recovered/removed individuals\n\n{beta} Per-individual disease transmission rate\n\n{gamma}Recovery rate\n\n{tau}Lockdown start-time\n\n {Delta}Duration of lockdown\n\np Post-lockdown coefficient\n\nh Total number of hospital beds\n\n{xi}Maximum fraction of infected individuals\n\n{xi}0 Hospitalization threshold", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Anagh Pathak", - "author_inst": "National Brain Research Centre" - }, - { - "author_name": "Varun Madan Mohan", - "author_inst": "National Brain Research Centre" - }, - { - "author_name": "Arpan Banerjee", - "author_inst": "National Brain Research Centre" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.30.20165571", "rel_title": "An Exploration of Impact of COVID 19 on mental health -Analysis of tweets using Natural Language Processing techniques", @@ -1261898,6 +1262440,177 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.31.20163055", + "rel_title": "SARS-CoV-2 Seroprevalence Across a Diverse Cohort of Healthcare Workers", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20163055", + "rel_abs": "ImportanceAntibody testing is important for understanding patterns of exposure and potential immunity to SARS-CoV-2. Prior data on seroprevalence have been subject to variations in selection of individuals and nature as well as timing of testing in relation to exposures.\n\nObjectiveWe sought to determine the extent of SARS-CoV-2 seroprevalance and the factors associated with seroprevelance across a diverse cohort of healthcare workers.\n\nDesignObservational cohort study of healthcare workers, including SARS-CoV-2 serology testing and participant questionaires.\n\nParticipantsA diverse and unselected population of adults (n=6,062) employed in a multi-site healthcare delivery system located in Los Angeles County, including individuals with direct patient contact and others with non-patient-oriented work functions.\n\nExposureExposure and infection with the SARS-CoV-2 virus, as determined by seropositivity.\n\nMain OutcomesUsing Bayesian and multi-variate analyses, we estimated seroprevalence and factors associated with seropositivity and antibody titers, including pre-existing demographic and clinical characteristics; potential Covid-19 illness related exposures; and, symptoms consistent with Covid-19 infection.\n\nResultsWe observed a seroprevalence rate of 4.1%, with anosmia as the most prominently associated self-reported symptom in addition to fever, dry cough, anorexia, and myalgias. After adjusting for potential confounders, pre-existing medical conditions were not associated with antibody positivity. However, seroprevalence was associated with younger age, Hispanic ethnicity, and African-American race, as well as presence of either a personal or household member having a prior diagnosis of Covid-19. Importantly, African American race and Hispanic ethnicity were associated with antibody positivity even after adjusting for personal Covid-19 diagnosis status, suggesting the contribution of unmeasured structural or societally factors. Notably, number of people, or children, in the home was not associated with antibody positivity.\n\nConclusion and RelevanceThe demographic factors associated with SARS-CoV-2 seroprevalence among our healthcare workers underscore the importance of exposure sources beyond the workplace. The size and diversity of our study population, combined with robust survey and modeling techniques, provide a vibrant picture of the demographic factors, exposures, and symptoms that can identify individuals with susceptibility as well as potential to mount an immune response to Covid-19.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat is the SARS-CoV-2 IgG seroprevalence rate across a large and diverse healthcare worker population, and which clinical, envionrmental, and symptom-based measures are associated with seropositivity?\n\nFindingsWe observed a seroprevalence rate of 4.1%. Adjusting for potential confounders, seropositivity was associated with younger age, Hispanic ethnicity, African-American race, and the symptom of anosmia, while not significantly associated with any pre-existing medical conditions.\n\nMeaningFactors associated with SARS-CoV-2 seroprevalence among our healthcare workers underscore the importance of exposure sources beyond the workplace.", + "rel_num_authors": 39, + "rel_authors": [ + { + "author_name": "Joseph Ebinger", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Gregory J. Botwin", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Christine M. Albert", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Mona Alotaibi", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Moshe Arditi", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Anders H. Berg", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Aleksandra Binek", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Patrick G. Botting", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Justyna Fert-Bober", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Jane C. Figueiredo", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Jonathan D. Grein", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Wohaib Hasan", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Mir Henglin", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Shehnaz K. Hussain", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Mohit Jain", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Sandy Joung", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Michael Karin", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Elizabeth H Kim", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Dalin Li", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Yunxian Liu", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Eric Luong", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Dermot P.B. McGovern", + "author_inst": "Cedars Sinai Medical Center" + }, + { + "author_name": "Akil Merchant", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Noah M. Merin", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Peggy B. Miles", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Margo Minissian", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Trevor-Trung Nguyen", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Koen Raedschelders", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Mohamad A. Rashid", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Celine E. Riera", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Richard V. Riggs", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Sonia Sharma", + "author_inst": "La Jolla Institute" + }, + { + "author_name": "Sarah Sternbach", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Nancy Sun", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Warren G. Tourtellotte", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Jennifer E. Van Eyk", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Kimia Sobhani", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Jonathan G. Braun", + "author_inst": "Cedars-Sinai Medical Center" + }, + { + "author_name": "Susan Cheng", + "author_inst": "Cedars-Sinai Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.31.20165738", "rel_title": "Early clinical characteristics of Covid-19: scoping review", @@ -1263366,45 +1264079,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.31.20166116", - "rel_title": "Face masks prevent transmission of respiratory diseases: a meta-analysis of randomized controlled trials", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20166116", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSObjectiveC_ST_ABSTo examine the effect of face mask intervention in respiratory infections across different exposure settings and age groups.\n\nDesignSystematic review and meta-analysis.\n\nData sourcesPubMed, Cochrane Central Register of Controlled Trials, and Web of Science were searched for randomized controlled trials investigating the effect of face masks on respiratory infections published by November 18th, 2020. We followed PRISMA guidelines.\n\nEligibility criteria for selecting studiesRandomized controlled trials investigating face masks in respiratory infections across different exposure settings. Two reviewers performed the search, extracted data, and assessed the risk of bias. Random effects meta-analysis with risk ratio, adjusted odds ratios, and number needed to treat were performed. Findings by source control or wearer protection, age groups, exposure settings, and role of non-compliance were evaluated.\n\nResultsSeventeen studies were included, (N=11,601 cases and N=10,286 controls, follow-up from 4 days to 19 months). Fourteen trials included adults and children and three trials included children only. Twelve studies showed non-compliance in treatment and eleven in control group. Four studies supported the use of face masks. Meta-analysis across all studies with risk ratios found no association with number of infections (RR=0.957 [0.810 - 1.131], p=0.608). Meta-analysis using odds ratios adjusted for age, sex, and vaccination (when available) showed protective effect of face masks (OR=0.850 [0.736 - 0.982], p=0.027). Subgroup meta-analysis with adjusted odds ratios found a decrease in respiratory infections among adults (14 studies, OR = 0.829 [0.709 - 0.969], p=0.019) in source control setting (OR = 0.845 [0.7375 - 0.969], p=0.0159) and when face masks were used together with hand hygiene OR = 0.690 [0.568 - 0.838], p=0.0002). Overall between-study heterogeneity was large also in the subgroup analyses.\n\nConclusionDespite the large between study heterogeneity, compliance bias and differences by environmental settings, the findings support the use of face masks to prevent respiratory infections. PROSPERO registration number CRD42020205523.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Hanna M Ollila", - "author_inst": "Institute for Molecular Medicine Finland, University of Helsinki" - }, - { - "author_name": "Markku Partinen", - "author_inst": "Helsinki Sleep Clinic, Vitalmed Research Center and Department of Clinical Neurosciences, University of Helsinki, Helsinki, Finland" - }, - { - "author_name": "Jukka Koskela", - "author_inst": "Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland" - }, - { - "author_name": "Riikka Savolainen", - "author_inst": "Newcastle University Business School, \t Newcastle-upon-Tyne, United Kingdom" - }, - { - "author_name": "Anna Rotkirch", - "author_inst": "Population Research Institute, Vaestoliitto - The Family Federation of Finland" - }, - { - "author_name": "Liisa T Laine", - "author_inst": "Department of Medical Ethics and Health Policy, The Perelman School of Medicine, Philadelphia, PA, USA" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.31.20143016", "rel_title": "The characteristics of multi-source mobility datasets and how they reveal the luxury nature of social distancing in the U.S. during the COVID-19 pandemic", @@ -1263628,6 +1264302,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2020.08.03.20167320", + "rel_title": "Retrospective SARS-CoV-2 Real-Time PCR Testing of Stored Bronchoalveolar Lavage Samples from February 2020", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167320", + "rel_abs": "Bronchoalveolar lavage samples (n=34) collected in February, 2020 prior to the wide availability of molecular testing for SARS-CoV-2 were retrospectively assayed for presence of viral RNA. None of these patients qualified for SARS-CoV-2 testing based on Centers for Disease Control criteria at the time. None of the samples tested positive for SARS-CoV-2, suggesting that the virus was not yet widespread in Minnesota at the time these samples were obtained.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Douglas W Challener", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Aditya Shah", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Matthew Binnicker", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew Badley", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "John O'Horo", + "author_inst": "Mayo Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.02.20166256", "rel_title": "Clinical characteristics and antibody response to SARS-CoV-2 spike 1 protein using the VITROS Anti-SARS-CoV-2 antibody tests in COVID-19 patients in Japan", @@ -1264864,41 +1265573,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.03.20165589", - "rel_title": "Stepwise School Opening Online and Off-line and an Impact on the Epidemiology of COVID-19 in the Pediatric Population", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20165589", - "rel_abs": "BackgroundData on SARS-CoV-2 transmission from a pediatric index patient to others at the school setting are limited. Epidemiologic data on pediatric COVID-19 cases after school opening is warranted.\n\nMethodsWe analyzed data of the pediatric patients with COVID-19 collected from the press release of the Korea Centers for Disease Control and Prevention. Information on the school opening delay and re-opening policies were achieved from the press release from Korean Ministry of Education.\n\nFindingsThe school openings were delayed three times in March 2020. Online classes started from April 9, and off-line classes started from May 20 to June 8 at four steps in different grades of students. There was no sudden increase in pediatric cases after the school opening, and the proportion of pediatric cases remained around 7.0% to 7.1%. As of July 11, 45 children from 40 schools and kindergartens were diagnosed with COVID-19 after off-line classes started. More than 11,000 students and staff were tested; only one additional student was found to be infected in the same classroom. Among those 45, 32 (71.1%) patients had available information for the source of infection. Twenty-five (25/45, 55.6%) were infected by the family members. The proportions of pediatric patients without information on infection sources were higher in older age group (middle and high school students) than in younger age group (kindergarten and elementary school students) (47.6% vs 12.5%, p=0.010). In the younger age group, 79.1% of children were infected by family members, while only 28.6% of adolescents in the older age group were infected by family members (p<0.001).\n\nInterpretationKorea had a successful transition from school closure to re-opening with online and off-line classes. Although partial, off-line school opening did not cause significant school-related outbreak among pediatric population although young children and adolescents may have different epidemiologic features.\n\nFundingNone.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yoonsun Yoon", - "author_inst": "Department of Pediatrics, Samsung Medical Center" - }, - { - "author_name": "Kyung-Ran Kim", - "author_inst": "Department of pediatrics, Samsung medical center" - }, - { - "author_name": "Hwanhee Park", - "author_inst": "Department of Pediatrics, Samsung medical center" - }, - { - "author_name": "So young Kim", - "author_inst": "Department of Mathematics, Konkuk University" - }, - { - "author_name": "Yae-Jean Kim", - "author_inst": "Department of Pediatrics, Samsung Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.01.20166405", "rel_title": "Physical activity, BMI and COVID-19: an observational and Mendelian randomisation study", @@ -1265190,6 +1265864,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.03.20165233", + "rel_title": "Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20165233", + "rel_abs": "Most currently approved strategies for the collection of saliva for COVID-19 diagnostics require specialized tubes containing buffers promoted for the stabilization of SARS-CoV-2 RNA and virus inactivation. Yet many of these are expensive, in limited supply, and not necessarily validated specifically for viral RNA. While saliva is a promising sample type as it can be reliably self-collected for the sensitive detection of SARS-CoV-2, the expense and availability of these collection tubes are prohibitive to mass testing efforts. Therefore, we investigated the stability of SARS-CoV-2 RNA and infectious virus detection from saliva without supplementation. We tested RNA stability over extended periods of time (2-25 days) and at temperatures representing at-home storage and elevated temperatures which might be experienced when cold chain transport may be unavailable. We found SARS-CoV-2 RNA in saliva from infected individuals is stable at 4{degrees}C, room temperature ([~]19{degrees}C), and 30{degrees}C for prolonged periods and found limited evidence for viral replication in stored saliva samples. This work demonstrates that expensive saliva collection options involving RNA stabilization and virus inactivation buffers are not always needed, permitting the use of cheaper collection options. Affordable testing methods are urgently needed to meet current testing demands and for continued surveillance in reopening strategies.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Isabel M Ott", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Madison S Strine", + "author_inst": "Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Anne E Watkins", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Maikel Boot", + "author_inst": "Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Chaney C Kalinich", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Christina A Harden", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Chantal B.F. Vogels", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Arnau Casanovas-Massana", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Adam J Moore", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "M. Catherine Muenker", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Maura Nakahata", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Maria Tokuyama", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Allison Nelson", + "author_inst": "Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "John Fournier", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Santos Bermejo", + "author_inst": "Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Melissa Campbell", + "author_inst": "Department of Pediatrics, Division of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Rupak Datta", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "- the Yale IMPACT Research team", + "author_inst": "" + }, + { + "author_name": "Charles S Dela Cruz", + "author_inst": "Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Shelli F Farhadian", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Albert I Ko", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA; Department of Medicine, Section of Infectious Diseases" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT, 06510, USA; Howard Hughes Medical Institute, New Haven, CT 06510, USA" + }, + { + "author_name": "Nathan D Grubaugh", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + }, + { + "author_name": "Craig B Wilen", + "author_inst": "Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, 06510, USA" + }, + { + "author_name": "Anne Louise Wyllie", + "author_inst": "Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06510, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.03.20167304", "rel_title": "Correlation between daily infections and fatality rate due to Covid-19 in Germany", @@ -1266494,49 +1267283,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.04.20168013", - "rel_title": "Analysis of COVID-19 and comorbidity co-infection Model with Optimal Control", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20168013", - "rel_abs": "The new coronavirus disease 2019 (COVID-19) infection is a double challenge for people infected with comorbidities such as cardiovascular and cerebrovascular diseases and diabetes. Comorbidities have been reported to be risk factors for the complications of COVID-19. In this work, we develop and analyze a mathematical model for the dynamics of COVID-19 infection in order to assess the impacts of prior comorbidity on COVID-19 complications and COVID-19 re-infection. The model is simulated using data relevant to the dynamics of the diseases in Lagos, Nigeria, making predictions for the attainment of peak periods in the presence or absence of comorbidity. The model is shown to undergo the phenomenon of backward bifurcation caused by the parameter accounting for increased susceptibility to COVID-19 infection by comorbid susceptibles as well as the rate of re-infection by those who have recovered from a previous COVID-19 infection. Sensivity analysis of the model when the population of individuals co-infected with COVID-19 and comorbidity is used as response function revealed that the top ranked parameters that drive the dynamics of the co-infection model are the effective contact rate for COVID-19 transmission, {beta}CV, the parameter accounting for increased sucseptibility to COVID-19 by comorbid susceptibles,{chi} CM, the comorbidity development rate,{theta} CM, the detection rate for singly infected and co-infected individuals,{eta} 1 and{eta} 2, as well as the recovery rate from COVID-19 for co-infected individuals,{varphi} I2. Simulations of the model reveal that the cumulative confirmed cases (without comorbidity) may get up to 180,000 after 200 days, if the hyper susceptibility rate of comorbid susceptibles is as high as 1.2 per day. Also, the cumulative confirmed cases (including those co-infected with comorbidity) may be as high as 1000,000 cases by the end of November, 2020 if the re-infection rates for COVID-19 is 0.1 per day. It may be worse than this if the re-infection rates increase higher. Moreover, if policies are strictly put in place to step down the probability of COVID-19 infection by comorbid susceptibles to as low as 0.4 per day and step up the detection rate for singly infected individuals to 0.7 per day, then the reproduction number can be brought very low below one, and COVID-19 infection eliminated from the population. In addition, optimal control and cost-effectiveness analysis of the model reveal that the the strategy that prevents COVID-19 infection by comorbid susceptibles has the least ICER and is the most cost-effective of all the control strategies for the prevention of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Andrew Omame", - "author_inst": "Federal University of Technology Owerri, Nigeria" - }, - { - "author_name": "Ndolane Sene", - "author_inst": "University Cheikh Anta Diop" - }, - { - "author_name": "Ikenna Nometa", - "author_inst": "University of Hawaii Manoa" - }, - { - "author_name": "Cosmas Ifeanyi Nwakanma", - "author_inst": "Kumoh National Institute of Technology Gumi, Korea" - }, - { - "author_name": "Emmanuel Ugochukwu Nwafor", - "author_inst": "Federal University of Technology Owerri, Nigeria" - }, - { - "author_name": "Nneka Onyinyechi Iheonu", - "author_inst": "Federal University of Technology Owerri, Nigeria" - }, - { - "author_name": "Daniel Okuonghae", - "author_inst": "University of Benin, Nigeria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.03.234989", "rel_title": "Binding Ligands that Straddle an Important Contact Site on the RBD of the Covid-19 Spike Protein", @@ -1267032,6 +1267778,20 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.04.234880", + "rel_title": "SCV-2000bp: a primer panel for SARS-CoV-2 full-genome sequencing", + "rel_date": "2020-08-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.04.234880", + "rel_abs": "Here we provide technical data for amplifying the complete genome of SARS-CoV-2 from clinical samples using only seventeen pairs of primers. We demonstrate that the [C]V2000bp primer panel successfully produces genomes when used with the residual total RNA extracts from positive clinical samples following diagnostic RT-PCRs (with Ct in the range from 13 to 20). The library preparation method reported here includes genome amplification of ~1750-2000 bp fragments followed by ultrasonic fragmentation combined with the introduction of Illumina compatible adapters. Using the SCV2000bp panel, 25 complete SARS-CoV-2 virus genome sequences were sequenced from clinical samples of COVID-19 patients from Moscow obtained in late March - early April.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nc_nd", + "type": "confirmatory results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.08.04.236653", "rel_title": "Pathogenetic Perspective of Missense Mutations of ORF3a Protein of SARS-CoV2", @@ -1268616,65 +1269376,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.30.20165415", - "rel_title": "Loneliness, physical activity and mental health during Covid-19: a longitudinal analysis of depression and anxiety between 2015 and 2020.", - "rel_date": "2020-08-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20165415", - "rel_abs": "BackgroundLoneliness and physical activity are important targets for research into the impact of COVID-19 because they have established links with mental health, could be exacerbated by social distancing policies and are potentially modifiable.\n\nMethodWe analysed mental health data collected during COVID-19 from adults aged 50 and over alongside comparable annual data collected between 2015 and 2019 from the same sample. Trajectories of depression (PHQ-9) and anxiety (GAD-7) were analysed with respect to loneliness, physical activity levels and a number of socioeconomic and demographic characteristics using zero-inflated negative binomial regression.\n\nResults3,281 people completed the COVID-19 mental health questionnaire, all had at least one data point prior to 2020. In 2020, the adjusted PHQ-9 score for loneliness was 3.2. (95% CI: 3.0-3.4), an increase of one point on previous years and 2 points higher than people not rated lonely, whose score did not change in 2020 (1.2, 95% CI: 1.1-1.3). PHQ-9 was 2.6 (95% CI: 2.4-2.8) in people with decreased physical activity, an increase of 0.5 on previous years. In contrast, PHQ-9 in 2020 for people whose physical activity had not decreased was 1.7 (95% CI: 1.6-1.8), similar to previous years. A similar relationship was observed for GAD-7 though the differences were smaller and the absolute burden of symptoms lower.\n\nConclusionsAfter accounting for pre-COVID-19 trends, we show that experiencing loneliness and decreased physical activity are risk factors for worsening mental health during the pandemic. Our findings highlight the need to examine policies which target these potentially modifiable risk factors.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Byron Creese", - "author_inst": "University of Exeter" - }, - { - "author_name": "Zunera Khan", - "author_inst": "King's College London" - }, - { - "author_name": "William Henley", - "author_inst": "University of Exeter" - }, - { - "author_name": "Siobhan ODwyer", - "author_inst": "University of Exeter" - }, - { - "author_name": "Anne Corbett", - "author_inst": "University of Exeter" - }, - { - "author_name": "Miguel Vasconcelos Da Silva", - "author_inst": "King's College London" - }, - { - "author_name": "Kathryn Mills", - "author_inst": "University of Exeter" - }, - { - "author_name": "Natalie Wright", - "author_inst": "Public Health England" - }, - { - "author_name": "Ingelin Testad", - "author_inst": "Stavanger University Hospital" - }, - { - "author_name": "Dag Aarsland", - "author_inst": "King's College London" - }, - { - "author_name": "Clive Ballard", - "author_inst": "University of Exeter" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.07.30.20165423", "rel_title": "Microbial contamination of powered air purifying respirators (PAPR) used during the COVID-19 pandemic: an in situ microbiological study", @@ -1269202,6 +1269903,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.30.20163824", + "rel_title": "Clinical Utility of a Highly Sensitive Lateral Flow Immunoassay as determined by Titer Analysis for the Detection of anti-SARS-CoV-2 Antibodies at the Point-of-Care", + "rel_date": "2020-08-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20163824", + "rel_abs": "Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), became a pandemic in early 2020. Lateral flow immunoassays for antibody testing have been viewed as a cheap and rapidly deployable method for determining previous infection with SARS-CoV-2; however, these assays have shown unacceptably low sensitivity. We report on nine lateral flow immunoassays currently available and compare their titer sensitivity in serum to a best-practice enzyme-linked immunosorbent assay (ELISA) and viral neutralization assay. For a small group of PCR-positive, we found two lateral flow immunoassay devices with titer sensitivity roughly equal to the ELISA; these devices were positive for all PCR-positive patients harboring SARS-CoV-2 neutralizing antibodies. One of these devices was deployed in Northern Italy to test its sensitivity and specificity in a real-world clinical setting. Using the device with fingerstick blood on a cohort of 27 hospitalized PCR-positive patients and seven hospitalized controls, ROC curve analysis gave AUC values of 0.7646 for IgG. For comparison, this assay was also tested with saliva from the same patient population and showed reduced discrimination between cases and controls with AUC values of 0.6841 for IgG. Furthermore, during viral neutralization testing, one patient was discovered to harbor autoantibodies to ACE2, with implications for how immune responses are profiled. We show here through a proof-of-concept study that these lateral flow devices can be as analytically sensitive as ELISAs and adopted into hospital protocols; however, additional improvements to these devices remain necessary before their clinical deployment.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Amanda Haymond", + "author_inst": "George Mason University" + }, + { + "author_name": "Claudius Mueller", + "author_inst": "George Mason University" + }, + { + "author_name": "Hannah Steinberg", + "author_inst": "University of Illinois, Chicago" + }, + { + "author_name": "K. Alex Hodge", + "author_inst": "George Mason University" + }, + { + "author_name": "Caitlin W Lehman", + "author_inst": "George Mason University" + }, + { + "author_name": "Shih-Chao Lin", + "author_inst": "George Mason University" + }, + { + "author_name": "Lucia Collini", + "author_inst": "Santa Chiara Hospital" + }, + { + "author_name": "Heather Branscome", + "author_inst": "George Mason University" + }, + { + "author_name": "Tuong Vi Nguyen", + "author_inst": "George Mason University" + }, + { + "author_name": "Sally Rucker", + "author_inst": "George Mason University" + }, + { + "author_name": "Lauren Panny", + "author_inst": "George Mason University" + }, + { + "author_name": "Rafaela Flor", + "author_inst": "George Mason University" + }, + { + "author_name": "Raouf Guirguis", + "author_inst": "George Mason University" + }, + { + "author_name": "Richard Hoefer", + "author_inst": "Sentara Dorothy G. Hoefer Comprehensive Breast Center" + }, + { + "author_name": "Giovanni Lorenzin", + "author_inst": "Santa Chiara Hospital" + }, + { + "author_name": "Emanuel Petricoin", + "author_inst": "George Mason University" + }, + { + "author_name": "Fatah Kashanchi", + "author_inst": "George Mason University" + }, + { + "author_name": "Kylene Kehn-Hall", + "author_inst": "George Mason University" + }, + { + "author_name": "Paolo Lanzafame", + "author_inst": "Santa Chiara Hospital" + }, + { + "author_name": "Lance Liotta", + "author_inst": "George Mason University" + }, + { + "author_name": "Alessandra Luchini", + "author_inst": "George Mason University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.30.20114959", "rel_title": "Impact of tocilizumab administration on mortality in severe COVID-19", @@ -1270522,57 +1271322,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.29.20164665", - "rel_title": "Rapid real-time tracking of non-pharmaceutical interventions and their association SARS-CoV-2 positivity: The COVID-19 Pandemic Pulse Study", - "rel_date": "2020-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164665", - "rel_abs": "BackgroundCurrent mitigation strategies for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rely on population-wide adoption of non-pharmaceutical interventions (NPIs). Collecting demographically and geographically resolved data on NPIs and their association with SARS-CoV-2 infection history can provide critical information related to reopening geographies.\n\nMethodsWe sampled 1,030 individuals in Maryland from June 17 - June 28, 2020 to capture socio-demographically and geographically resolved information about NPI adoption, access to SARS-CoV-2 testing, and examine associations with self-reported SARS-CoV-2 positivity.\n\nResultsMedian age of the sample was 43 years and 45% were men; Whites and Blacks/African Americans represented 60% and 23%, respectively. Overall, 96% of the sample reported traveling outside their home for non-employment related services: most commonly cited reasons were essential services (92%) and visiting friends/family (66%). Use of public transport was reported by 18% of respondents. 68% reported always social distancing indoors and 53% always wearing masks indoors; indoor social distancing was significantly less common among younger vs. older individuals, and race/ethnicity and income were significantly associated with mask use (p<0.05 for all). 55 participants (5.3%) self-reported ever testing positive for SARS-CoV-2 with strong dose-response relationships between movement frequency and SARS-CoV-2 positivity that were significantly attenuated by social distancing. In multivariable analysis, history of SARS-CoV-2 infection was negatively associated with the practice of social distancing (adjusted Odd Ratio [aOR]: 0.10; 95% Confidence Interval: 0.03 - 0.33); the only travel associated with higher likelihood of SARS-CoV-2 infection was use of public transport (aOR for [≥]7 times vs. never: 4.29) and visiting a place of worship (aOR for [≥]3 times vs. never: 16.0) after adjusting for social distancing.\n\nConclusionsUsing a rapid cost-efficient approach, we highlight the role of movement and social distancing on SARS-CoV-2 transmission risk. Continued monitoring of NPI uptake, access to testing, and the subsequent impact on SARS-CoV-2 transmission will be critical for pandemic control and decisions about reopening geographies.\n\nKey PointsO_ST_ABSWhat we didC_ST_ABSO_LIWe utilized an online survey approach to sample residents of Maryland consistent with the distributions of age, gender, race/ethnicity, and income in the state.\nC_LIO_LIWe asked questions about places (and the frequency) visited for essential and nonessential services in the prior 2 weeks, practice of non-pharmaceutical interventions (NPIs) while visiting various places, and access to SARS-CoV-2 testing.\nC_LIO_LIWe characterized how movement and adoption of NPIs differed by key demographics (age, race, gender, income) and how these were associated with self-reported SARS-CoV-2 positivity.\nC_LI\n\nWhat we foundO_LI96% of the sample reported traveling for either essential or non-essential services in the prior 2 weeks; 82% reported traveling for non-essential services.\nC_LIO_LIThe adoption of NPIs varied by age, race/ethnicity, and income.\nC_LIO_LISelf-reported SARS-CoV-2 positivity was highest among Latinos followed by Blacks/African Americans and then Whites.\nC_LIO_LIThe more frequently a person traveled/visited places for non-essential services, the more likely they were to report ever having tested positive for SARS-CoV-2.\nC_LIO_LIThe strict practice of social distancing was associated with a lower likelihood of ever having tested positive for SARS-CoV-2; moreover, strict social distancing attenuated the association between most forms of movement and SARS CoV-2 positivity\nC_LIO_LIUsing public transport and attending places of worship remained associated with a higher likelihood of having tested positive for SARS-CoV-2 even when practicing social distancing.\nC_LIO_LIAbout 70% of people who wanted a SARS-CoV-2 test were able to get a test but there were delays of a week or more from wanting a test to getting a result among the majority of the sample.\nC_LI\n\nWhat it meansO_LIThe more people move the more likely they are to test positive for SARS-CoV-2; if you must travel, practice social distancing as it reduces the likelihood of testing positive.\nC_LIO_LIAvoid public transport to the extent possible.\nC_LIO_LIStrategies to reduce time from wanting a test to getting a result are critical to enhance early case detection and isolation to curb transmission.\nC_LI", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Steven J. Clipman", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Amy P. Wesolowski", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Dustin G. Gibson", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Smisha Agarwal", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Anastasia S. Lambrou", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Gregory D. Kirk", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Alain B. Labrique", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Shruti H. Mehta", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Sunil S. Solomon", - "author_inst": "Johns Hopkins University School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.29.20164822", "rel_title": "Clinical Outcomes From COVID-19 Following Use of Angiotensin-Converting Enzyme Inhibitors or Angiotensin-Receptor Blockers Among Patients with Hypertension in South Korea: A nationwide study", @@ -1270876,6 +1271625,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2020.07.31.231746", + "rel_title": "Engineered ACE2 receptor traps potently neutralize SARS-CoV-2", + "rel_date": "2020-08-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.31.231746", + "rel_abs": "An essential mechanism for SARS-CoV-1 and -2 infection begins with the viral spike protein binding to the human receptor protein angiotensin-converting enzyme II (ACE2). Here we describe a stepwise engineering approach to generate a set of affinity optimized, enzymatically inactivated ACE2 variants that potently block SARS-CoV-2 infection of cells. These optimized receptor traps tightly bind the receptor binding domain (RBD) of the viral spike protein and prevent entry into host cells. We first computationally designed the ACE2-RBD interface using a two-stage flexible protein backbone design process that improved affinity for the RBD by up to 12-fold. These designed receptor variants were affinity matured an additional 14-fold by random mutagenesis and selection using yeast surface display. The highest affinity variant contained seven amino acid changes and bound to the RBD 170-fold more tightly than wild-type ACE2. With the addition of the natural ACE2 collectrin domain and fusion to a human Fc domain for increased stabilization and avidity, the most optimal ACE2 receptor traps neutralized SARS-CoV-2 pseudotyped lentivirus and authentic SARS-CoV-2 virus with half-maximal inhibitory concentrations (IC50) in the 10-100 ng/ml range. Engineered ACE2 receptor traps offer a promising route to fighting infections by SARS-CoV-2 and other ACE2-utilizing coronaviruses, with the key advantage that viral resistance would also likely impair viral entry. Moreover, such traps can be pre-designed for viruses with known entry receptors for faster therapeutic response without the need for neutralizing antibodies isolated or generated from convalescent patients.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Anum Glasgow", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jeff Edward Glasgow", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Daniel Limonta", + "author_inst": "University of Alberta" + }, + { + "author_name": "Paige Solomon", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Irene Lui", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Yang Zhang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew A Nix", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Nicholas J Rettko", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Shion A Lim", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Shoshana Zha", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Rachel Yamin", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Kevin Kao", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Oren S Rosenberg", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jeffrey V Ravetch", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Arun P Wiita", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kevin K Leung", + "author_inst": "UCSF" + }, + { + "author_name": "Xin X Zhou", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Tom C Hobman", + "author_inst": "University of Alberta" + }, + { + "author_name": "Tanja K Kortemme", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "James A. Wells", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2020.07.31.190454", "rel_title": "Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy", @@ -1272256,41 +1273100,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.31.230607", - "rel_title": "Biochemical and mathematical lessons from the evolution of the SARS-CoV-2 virus: paths for novel antiviral warfare", - "rel_date": "2020-07-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.31.230607", - "rel_abs": "In the fight against the spread of COVID-19 the emphasis is on vaccination or on reactivating existing drugs used for other purposes. The tight links that necessarily exist between the virus as it multiplies and the metabolism of its host are systematically ignored. Here we show that the metabolism of all cells is coordinated by the availability of a core building block of the cells genome, cytidine triphosphate (CTP). This metabolite is also the key to the synthesis of the viral envelope and to the translation of its genome into proteins. This unique role explains why evolution has led to the early emergence in animals of an antiviral immunity enzyme, viperin, that synthesizes a toxic analogue of CTP. The constraints arising from this dependency guide the evolution of the virus. With this in mind, we explored the real-time experiment taking place before our eyes using probabilistic modelling approaches to the molecular evolution of the virus. We have thus followed, almost on a daily basis, the evolution of the composition of the viral genome to link it to the progeny produced over time, particularly in the form of blooms that sparked a firework of viral mutations. Some of those certainly increase the propagation of the virus. This led us to make out the critical role in this evolution of several proteins of the virus, such as its nucleocapsid N, and more generally to begin to understand how the virus ties up the host metabolism to its own benefit. A way for the virus to escape CTP-dependent control in cells would be to infect cells that are not expected to grow, such as neurons. This may account for unexpected body sites of viral development in the present epidemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Nicolas Cluzel", - "author_inst": "Tremplin Carnot SMILES, 4 Place Jussieu, 75005 Paris, France" - }, - { - "author_name": "Amaury Lambert", - "author_inst": "Laboratoire de Probabilites, Statistique & Modelisation (LPSM), Sorbonne Universite, Universite de Paris, CNRS UMR8001, 4 place Jussieu, 75005 Paris, France" - }, - { - "author_name": "Yvon Maday", - "author_inst": "Tremplin Carnot SMILES, 4 Place Jussieu, 75005 Paris, France" - }, - { - "author_name": "Gabriel Turinici", - "author_inst": "Ceremade, Universite Paris Dauphine - PSL" - }, - { - "author_name": "Antoine Danchin", - "author_inst": "Kodikos Labs / Stellate Therapeutics, Institut Cochin, 24 rue du Faubourg Saint-Jacques, 75014 Paris, France" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.31.230888", "rel_title": "Computer Simulations of the interaction between SARS-CoV-2 spike glycoprotein and different surfaces", @@ -1272558,6 +1273367,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.31.231472", + "rel_title": "New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release", + "rel_date": "2020-07-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.31.231472", + "rel_abs": "The massive worldwide spread of the SARS-CoV-2 virus is fueling the COVID-19 pandemic. Since the first whole-genome sequence was published in January 2020, a growing database of tens of thousands of viral genomes has been constructed. This offers opportunities to study pathways of molecular change in the expanding viral population that can help identify molecular culprits of virulence and virus spread. Here we investigate the genomic accumulation of mutations at various time points of the early pandemic to identify changes in mutationally highly active genomic regions that are occurring worldwide. We used the Wuhan NC_045512.2 sequence as a reference and sampled 15,342 indexed sequences from GISAID, translating them into proteins and grouping them by month of deposition. The per-position amino acid frequencies and Shannon entropies of the coding sequences were calculated for each month, and a map of intrinsic disorder regions and binding sites was generated. The analysis revealed dominant variants, most of which were located in loop regions and on the surface of the proteins. Mutation entropy decreased between March and April of 2020 after steady increases at several sites, including the D614G mutation site of the spike (S) protein that was previously found associated with higher case fatality rates and at sites of the NSP 12 polymerase and the NSP13 helicase proteins. Notable expanding mutations include R203K and G204R of the nucleocapsid (N) protein inter-domain linker region and G251V of the viroporin encoded by ORF3a between March and April. The regions spanning these mutations exhibited significant intrinsic disorder, which was enhanced and decreased by the N-protein and viroporin 3a protein mutations, respectively. These results predict an ongoing mutational shift from the spike and replication complex to other regions, especially to encoded molecules known to represent major {beta}-interferon antagonists. The study provides valuable information for therapeutics and vaccine design, as well as insight into mutation tendencies that could facilitate preventive control.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tre Tomaszewski", + "author_inst": "University of Illinois" + }, + { + "author_name": "Ryan S DeVries", + "author_inst": "University of Illinois" + }, + { + "author_name": "Mengyi Dong", + "author_inst": "University of Illinois" + }, + { + "author_name": "Gitanshu Bhatia", + "author_inst": "University of Illinois" + }, + { + "author_name": "Miles D Norsworthy", + "author_inst": "University of Illinois" + }, + { + "author_name": "Xuying Zheng", + "author_inst": "University of Illinois" + }, + { + "author_name": "Gustavo Caetano-Anolles", + "author_inst": "University of Illinois" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.31.230730", "rel_title": "Biomechanical Characterization of SARS-CoV-2 Spike RBD and Human ACE2 Protein-Protein Interaction", @@ -1273854,45 +1274706,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.28.20163634", - "rel_title": "Mechanistic modelling of coronavirus infections and the impact of confined neighbourhoods on a short time scale", - "rel_date": "2020-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163634", - "rel_abs": "BackgroundTo mitigate the spread of the COVID-19 coronavirus, some countries have adopted more stringent non-pharmaceutical interventions in contrast to those widely used (for e.g. the state of Kuwait). In addition to standard practices such as enforcing curfews, social distancing, and closure of non-essential service industries, other non-conventional policies such as the total confinement of highly populated areas has also been implemented.\n\nMethodsIn this paper, we model the movement of a host population using a mechanistic approach based on random walks, which are either diffusive or super-diffusive. Infections are realised through a contact process, whereby a susceptible host may be infected if in close spatial proximity of the infectious host. Our focus is only on the short-time scale prior to the infectious period, so that no further transmission is assumed.\n\nResultsWe find that the level of infection depends heavily on the population dynamics, and increases in the case of slow population diffusion, but remains stable for a high or super-diffusive population. Also, we find that the confinement of homogeneous or overcrowded sub-populations has minimal impact in the short term.\n\nConclusionsOur results indicate that on a short time scale, confinement restrictions or complete lock down of whole residential areas may not be effective. Finally, we discuss the possible implications of our findings for total confinement in the context of the current situation in Kuwait.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Danish A Ahmed", - "author_inst": "Gulf University for Science and Technology" - }, - { - "author_name": "Ali R Ansari", - "author_inst": "Gulf University for Science and Technology" - }, - { - "author_name": "Mudassar Imran", - "author_inst": "Gulf University for Science and Technology" - }, - { - "author_name": "Kamaludin Dingle", - "author_inst": "Gulf University for Science and Technology" - }, - { - "author_name": "Naveed Ahmed", - "author_inst": "Gulf University for Science and Technology" - }, - { - "author_name": "Michael A Bonsall", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.29.20164343", "rel_title": "Performance of Abbott Architect, Ortho Vitros, and Euroimmun Assays in Detecting Prior SARS-CoV-2 Infection", @@ -1274236,6 +1275049,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.28.20163816", + "rel_title": "Multimorbidity patterns among COVID-19 deaths: considerations for a better medical practice", + "rel_date": "2020-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163816", + "rel_abs": "Medical care of individuals diagnosed with severe COVID-19 is complex, especially when patients are older adults with multimorbidity. The objective of this study was to describe patterns of multimorbidity among fatal cases of COVID-19. Data of Colombian confirmed deaths of COVID-19 until June 11, 2020, were included in this analysis (1488 deaths). Relationships between COVID-19, combinations of health conditions and age were explored using locally weighted polynomial regressions. Some multimorbidity patterns increase probability of death among older individuals, whereas other patterns are not age-related, or decreases the probability of death among older people. Consider multimorbidity in the medical management of COVID-19 patients is important to determine the more adequate medical interventions. In addition to the co-occurrence of COVID-19 with diseases of high prevalence in the world, in Colombia there are cases more complex with COVID-19 co-occur with endemic and orphan tropical diseases. In these cases, although its occurrence may be low, clinical management requires adjusting to its complex clinical condition.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Julian Alfredo Fernandez-Nino", + "author_inst": "Fundacion Universidad del Norte" + }, + { + "author_name": "Jhon A Guerra-Gomez", + "author_inst": "Northeastern University, Silicon Valle" + }, + { + "author_name": "Alvaro Javier Idrovo-Velandia", + "author_inst": "Universidad Industrial de Santander" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.28.20163980", "rel_title": "Stochastic modelling of the effects of human-mobility restriction and viral infection characteristics on the spread of COVID-19", @@ -1275564,49 +1276404,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.07.30.229187", - "rel_title": "A dynamic regulatory interface on SARS-CoV-2 RNA polymerase", - "rel_date": "2020-07-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.30.229187", - "rel_abs": "The RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 is the core machinery responsible for the viral genome replication and transcription and also a major antiviral target. Here we report the cryo-electron microscopy structure of a post-translocated SARS-CoV-2 RdRp core complex, comprising one nsp12, one separate nsp8(I) monomer, one nsp7-nsp8(II) subcomplex and a replicating RNA substrate. Compared with the recently reported SARS-CoV-2 RdRp complexes, the nsp8(I)/nsp7 interface in this RdRp complex shifts away from the nsp12 polymerase. Further functional characterizations suggest that specific interactions between the nsp8(I) and nsp7, together with the rearrangement of nsp8(I)/nsp7 interface, ensure the efficient and processive RNA synthesis by the RdRp complex. Our findings provide a mechanistic insight into how nsp7 and nsp8 cofactors regulate the polymerase activity of nsp12 and suggest a potential new intervention interface, in addition to the canonical polymerase active center, in RdRp for antiviral design.\n\nAuthor summarySince it was first discovered and reported in late 2019, the coronavirus disease 2019 (COVID-19) pandemic caused by highly contagious SARS-CoV-2 virus is wreaking havoc around the world. Currently, no highly effective and specific antiviral drug is available for clinical treatment. Therefore, the threat of COVID-19 transmission necessitates the discovery of more effective antiviral strategies. Viral RNA-dependent RNA polymerase (RdRp) is an important antiviral drug target. Here, our cryo-EM structure of a SARS-CoV-2 RdRp/RNA replicating complex reveals a previously uncharacterized overall shift of the cofactor nsp8(I)/nsp7 interface, leading to its rearrangement. Through in vitro functional test, we found that the specific interactions on the interface are important to the efficient RNA polymerase activity of SARS-CoV-2 RdRp. These observations let us to suggest this interface as a potential new drug intervention site, outside of the canonical polymerase active center, in RdRp for antiviral design. Our findings would provide new insights into regulatory mechanism of this novel SARS-CoV-2 RdRp, contribute to the design of antiviral drugs against SARS-CoV-2, and benefit the global public health.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Wei Shi", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Ming Chen", - "author_inst": "University of Chinese Academy of Sciences" - }, - { - "author_name": "Yang Yang", - "author_inst": "Yale University" - }, - { - "author_name": "Wei Zhou", - "author_inst": "University of Chinese Academy of Sciences" - }, - { - "author_name": "Shiyun Chen", - "author_inst": "Wuhan Institute of Virology" - }, - { - "author_name": "Yangbo Hu", - "author_inst": "Wuhan Institute of Virology" - }, - { - "author_name": "Bin Liu", - "author_inst": "University of Minnesota" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.07.30.227470", "rel_title": "Ad26-vector based COVID-19 vaccine encoding a prefusion stabilized SARS-CoV-2 Spike immunogen induces potent humoral and cellular immune responses", @@ -1275966,6 +1276763,45 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2020.07.17.20156463", + "rel_title": "SARS-CoV-2 Infection and Stroke: Coincident or Causal?", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156463", + "rel_abs": "Neurological manifestations of SARS-CoV-2 infection described in isolated case reports and single institutions do not accurately reflect the clinical spectrum of disease across all geographies in a global pandemic. Data collected during peak of the Covid-19 pandemic from stroke centers in five states reveal few similarities to what has recently been published. Given the diversity in phenotype, we caution policymakers and health care providers when considering cerebrovascular complications from SARS-CoV-2 infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Melanie Walker", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Christopher C. Young", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Malveeka Sharma", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Michael R Levitt", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "David L Tirschwell", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "- WWAMI Stroke Investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.07.23.20160887", "rel_title": "Divide in Vaccine Belief in COVID-19 Conversations: Implications for Immunization Plans", @@ -1277198,97 +1278034,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.26.20162529", - "rel_title": "Impact of SARS-CoV-2 pandemic among health care workers in a secondary teaching hospital in Spain.", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20162529", - "rel_abs": "BackgroundThe COVID-19 pandemic has posed a huge challenge to healthcare systems and their personnel worldwide. The study of the impact of SARS-CoV-2 infection among healthcare workers, through prevalence studies, will let us know viral expansion, individuals at most risk and the most exposed areas. The aim of this study is to gauge the impact of SARS-CoV-2 pandemic in our hospital workforce and identify groups and areas at increased risk.\n\nMethods and FindingsThis is a cross-sectional and longitudinal study carried out on healthcare workers based on molecular and serological diagnosis of SARS-CoV-2 infection. Of the 3013 HCW invited to participate, finally 2439 (80.9%) were recruited, including 674 (22.4%) who had previously consulted at the OHS for confirmed exposure and/or presenting symptoms suggestive of COVID-19. A total of 411 (16.9%) and 264 (10.8%) healthcare workers were SARS-CoV-2 IgG and rRT-PCR positive, respectively. The cumulative prevalence considering all studies (IgG positive HCW and/or rRT-PCR positive detection) has been 485 (19.9%). SARS-CoV-2 IgG-positive patients in whom the virus was not detected were 221 (9.1%); up to 151 of them (68.3%) did not report any compatible symptoms nor consult at the OHS for this reason. Men became more infected than women (25% vs 18.5%, p=0.0009), including when data were also classified by age. COVID-19 cumulative prevalence among the HCW assigned to medical departments was higher (25.2%) than others, as well as among medical staff (25.4%) compared with other professional categories (p<0.01).\n\nConclusionsGlobal impact of the COVID-19 pandemic on HCW of our centre has been 19.9%. Doctors and medical services personnel have had the highest prevalence of SARS-CoV-2 infection, but many of them have not presented compatible symptoms. This emphasizes the performance of continuous surveillance methods of the most exposed health personnel and not only based on the appearance of symptoms.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Javier Garralda Fernandez", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Ignacio Molero Vilches", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Alfredo Bermejo Rodriguez", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Isabel Cano de Torres", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Elda I Colino Romay", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Isabel Garcia-Arata", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Jeronimo Jaqueti Aroca", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Rosa Lillo", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Daniel Lopez Lacomba", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Luis Mazon Cuadrado", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Laura M Molina Esteban", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Luis J Morales Garcia", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Laura Moratilla Monzo", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Elva Nieto-Borrajo", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Maria Pacheco Delgado", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Santiago Prieto Menchero", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Cristina Sanchez Hernandez", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Eva Sanchez Testillano", - "author_inst": "Hospital Universitario de Fuenlabrada" - }, - { - "author_name": "Jesus Garcia-Martinez", - "author_inst": "Hospital Universitario de Fuenlabrada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.27.20044990", "rel_title": "Severity detection for the coronavirus disease 2019 (COVID-19) patients using a machine learning model based on the blood and urine tests", @@ -1277516,6 +1278261,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.27.20149757", + "rel_title": "Children with COVID-19 like symptoms in Italian Pediatric Surgeries: the dark side of the coin", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20149757", + "rel_abs": "BackgroundSymptoms of SARS-CoV-2 infection in children are nonspecific and shared with other common acute viral illnesses (fever, respiratory or gastrointestinal symptoms, and cutaneous signs), thus making clinical differential diagnosis tricky. In Italy, first line management of pediatric care is handed over to Primary Care Pediatricians (PCPs), who were not allowed to directly perform diagnostic tests during the recent COVID-19 outbreak. Without a confirmatory diagnosis, PCPs could only collect information on \"COVID-19 like symptoms\" rather than identify typical COVID-19 symptoms.\n\nAimTo evaluate the prevalence of COVID-19 like symptoms in outpatient children, during Italian lockdown. To provide PCPs a risk score to be used in clinical practice during the differential diagnosis process.\n\nMethodsA survey was submitted to 50 PCPs (assisting 47,500 children) from 7 different Italian regions between the 4th of March and the 23rd of May 2020 (total and partial lockdown period). COVID-19 like symptoms in the assisted children were recorded, as well as presence of confirmed/suspected cases in childrens families, which was taken as proxy of COVID-19. Multivariable logistic regression was accomplished to estimate the risk of having suspected/confirmed cases in families, considering symptoms as potential determinants.\n\nResults2,300 children (4.8% of overall survey population) fell ill with COVID-19 like symptoms, 3.1% and 1.7% during total and partial lockdown period respectively. The concurrent presence of fatigue, cough, and diarrhea in children, in absence of sore throat/earache and abnormal skin signs, represents the maximum risk level of having a suspected/confirmed case of COVID-19 at home.\n\nConclusionsThe percentage of children presenting COVID-19 like symptoms at home has been remarkable also during the total lockdown period. The present study identified a pattern of symptoms which could help, in a cost-effective perspective, PCPs in daily clinical practice to define priorities in addressing children to the proper diagnostic procedure.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Gianfranco Trapani", + "author_inst": "Alfred Nobel's Friends International Association Study Center and Primary Care Pediatrician, Sanremo (IM), Italy" + }, + { + "author_name": "Vassilios Fanos", + "author_inst": "Neonatal Intensive Care Unit, Department of Surgical Sciences, University of Cagliari, Cagliari, Italy" + }, + { + "author_name": "Enrico Bertino", + "author_inst": "Neonatal Care Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy" + }, + { + "author_name": "Giulia Maiocco", + "author_inst": "Neonatal Care Unit, Department of Public Health and Pediatric Sciences, University of Turin, Turin, Italy" + }, + { + "author_name": "Osama Al Jamal", + "author_inst": "Alfred Nobel's Friends International Association Study Center and Primary Care Pediatrician, Cagliari, Italy" + }, + { + "author_name": "Michele Fiore", + "author_inst": "Primary Care Pediatrician, Genoa, Italy" + }, + { + "author_name": "VIncenzo Bembo", + "author_inst": "Primary Care Pediatrician, Frosinone, Italy" + }, + { + "author_name": "Domenico Careddu", + "author_inst": "Alfred Nobel's Friends International Association Study Center and Primary Care Pediatrician, Novara, Italy" + }, + { + "author_name": "Lando Barberio", + "author_inst": "Primary Care Pediatrician, Taggia (IM), Italy" + }, + { + "author_name": "Luisella Zanino", + "author_inst": "Alfred Nobel's Friends International Association Study Center and Primary Care Pediatrician, Turin, Italy" + }, + { + "author_name": "Giuseppe Verlato", + "author_inst": "Unit of Epidemiology and Medical Statistics, Department of Diagnostics & Public Health, University of Verona, Verona, Italy" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.07.27.20162057", "rel_title": "Predicting PPE use, post-traumatic stress, and physical symptoms during the early weeks of COVID-19 lockdowns in the USA", @@ -1278988,57 +1279792,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.28.20163386", - "rel_title": "DPP4 inhibitors and respiratory infection, a systematic review and meta-analysis of the CardioVascular Outcomes Trials conducted before the pandemic and implications for the management of diabetes during COVID-19", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163386", - "rel_abs": "BackgroundAssociation between DPP4 inhibitors and respiratory infection remains unclear. CardioVascular Outcomes Trials (CVOTs) conducted before the COVID-19 pandemic are available. We aimed to estimate the effect of DPP4 inhibitors on the risk of respiratory infections.\n\nMethodsWe updated a previous systematic review and meta-analysis, searching for CVOTs assessing a DPP4 inhibitor in patients with type 2 diabetes mellitus. We focused on placebo-controlled CVOTs. Our primary outcome was any respiratory infection. We added a sensitivity analysis integrating non-CVOTs and active-controlled CVOTs.\n\nFindingsWe included 47 714 patients in five placebo-controlled CVOTs. Median follow-up ranged from 1{middle dot}5 years to 3 years. 4 369 events of overall respiratory infection were reported (rate of 9{middle dot}2%). DPP4 inhibitors were not associated with a different risk compared to placebo (RR = 0{middle dot}99 [95% CI: 0{middle dot}93; 1{middle dot}04]). The sensitivity analysis integrating the non-CVOTs studies and the active-controlled CVOT reached 11 349 events among 82 644 participants (rate of 13{middle dot}7%). DPP4 inhibitors were not associated with a different risk of overall respiratory infection (RR = 1{middle dot}00 [95% CI: 0{middle dot}97; 1{middle dot}03]).\n\nInterpretationOur up-dated meta-analysis provides the most powerful and least biased estimation of the association of DPP4 inhibitors and the risk of overall (non COVID-19) respiratory infection. We did not find any effect of the DPP4 inhibitors on the risk of respiratory infection. Our results support the recently published practical recommendations for the management of diabetes in patients with COVID-19, suggesting that DPP4 inhibitors should not be discontinued regarding the COVID-19 pandemic.\n\nFundingNo source of funding\n\nPanel: Research in contextO_ST_ABSEvidence before this studyC_ST_ABSFrom before the COVID19 pandemic, respiratory infections are considered potential adverse effects of DPP4 inhibitors. Randomized trials assessing DPP4 inhibitors in patients with type 2 diabetes (T2D), their meta-analyses and pharmacovigilance studies reported conflicting results. Since the last meta-analyses assessing the risk of infections with DPP4 inhibitors, powerful cardiovascular outcomes randomized trials (CVOTs) became available. Recent practical recommendations for the management of diabetes during COVID-19 suggested that DPP4 inhibitors could be continued. We updated our previous meta-analysis of CVOTs and focused to the overall risk of respiratory infection associated with DPP4 inhibitors. We searched for published and unpublished CVOTs in Medline, the Cochrane Central Register of Controlled Trials (CENTRAL), and ClinicalTrials.gov, up to January 27, 2020, using key word as \"diabetes mellitus\", \"hypoglycemic agents\", \"glucose control\", \"randomized controlled trial\", \"cardiovascular diseases\".\n\nAdded value of this studyWe included CVOTs comparing a DPP4 inhibitor versus placebo, in people with T2D, and analysed the risk of respiratory infection with DPP4 inhibitors. We focused on placebo-controlled CVOTs to avoid the pitfalls of small study effect and heterogeneous comparators. We added a sensitivity analysis integrating non-CVOTs and non-placebo CVOTs to challenge our results and to increase the statistical power. Our meta-analysis provides the most powerful and least biased estimation of the association of DPP4 inhibitors and the risk of overall (non COVID-19) respiratory infection. Our analyses integrated 11 349 events of any respiratory infections through 82 644 patients from randomized trials. Our results did not find any association between DPP4 inhibitors use and risk of non-COVID respiratory infections.\n\nImplications of all the available evidenceThe current COVID-19 pandemic has raised some questions about pros and cons of certain cardiovascular drugs. Our results support the recent practical recommendations for the management of diabetes in patients with COVID-19, suggesting that DPP4 inhibitors should not be discontinued regarding the COVID-19 pandemic.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Guillaume Grenet", - "author_inst": "Hospices Civils de Lyon" - }, - { - "author_name": "Samia Mekhaldi", - "author_inst": "Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France" - }, - { - "author_name": "Sabine MAINBOURG", - "author_inst": "Hospices Civils de Lyon, Hopital Lyon Sud, Service de Medecine Interne et Vasculaire, Lyon, France" - }, - { - "author_name": "Marine AUFFRET", - "author_inst": "Hospices Civils de Lyon, Pole Sante Publique, Service hospitalo-universitaire de pharmacotoxicologie, Lyon, France" - }, - { - "author_name": "Catherine Cornu", - "author_inst": "CIC1407 INSERM, Hospices Civils de Lyon, Lyon, France" - }, - { - "author_name": "Jean-Luc Cracowski", - "author_inst": "Univ. Grenoble Alpes, INSERM, HP2, and centre regional de pharmacovigilance de Grenoble, F-38000 Grenoble, France" - }, - { - "author_name": "Francois Gueyffier", - "author_inst": "Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France" - }, - { - "author_name": "Jean-Christophe Lega", - "author_inst": "Hospices Civils de Lyon, Hopital Lyon Sud, Service de Medecine Interne et Vasculaire, Lyon, France" - }, - { - "author_name": "Michel CUCHERAT", - "author_inst": "Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2020.07.28.225649", "rel_title": "Intradermal-delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 challenge model", @@ -1279558,6 +1280311,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.28.225581", + "rel_title": "Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis", + "rel_date": "2020-07-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.28.225581", + "rel_abs": "The novel betacoronavirus named Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) caused a worldwide pandemic (COVID-19) after initially emerging in Wuhan, China. Here we applied a novel, comprehensive bioinformatic strategy to public RNA sequencing and viral genome sequencing data, to better understand how SARS-CoV-2 interacts with human cells. To our knowledge, this is the first meta-analysis to predict host factors that play a specific role in SARS-CoV-2 pathogenesis, distinct from other respiratory viruses. We identified differentially expressed genes, isoforms and transposable element families specifically altered in SARS-CoV-2 infected cells. Well-known immunoregulators including CSF2, IL-32, IL-6 and SERPINA3 were differentially expressed, while immunoregulatory transposable element families were overexpressed. We predicted conserved interactions between the SARS-CoV-2 genome and human RNA-binding proteins such as hnRNPA1, PABPC1 and eIF4b, which may play important roles in the viral life cycle. We also detected four viral sequence variants in the spike, polymerase, and nonstructural proteins that correlate with severity of COVID-19. The host factors we identified likely represent important mechanisms in the disease profile of this pathogen, and could be targeted by prophylactics and/or therapeutics against SARS-CoV-2.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC=\"FIGDIR/small/225581v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@15ca5a6org.highwire.dtl.DTLVardef@17f455forg.highwire.dtl.DTLVardef@a39f50org.highwire.dtl.DTLVardef@306ec1_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Mariana G. Ferrarini", + "author_inst": "University of Lyon, INSA-Lyon, INRAE, BF2I" + }, + { + "author_name": "Avantika Lal", + "author_inst": "NVIDIA" + }, + { + "author_name": "Rita Rebollo", + "author_inst": "University of Lyon, INSA-Lyon, INRAE, BF2I" + }, + { + "author_name": "Andreas Gruber", + "author_inst": "Oxford Big Data Institute, Nuffield Department of Medicine, University of Oxford" + }, + { + "author_name": "Andrea Guarracino", + "author_inst": "Centre for Molecular Bioinformatics, Department of Biology, University Of Rome Tor Vergata" + }, + { + "author_name": "Itziar Martinez Gonzalez", + "author_inst": "Netherlands\tAmsterdam UMC" + }, + { + "author_name": "Taylor Floyd", + "author_inst": "Center for Neurogenetics, Weill Cornell Medicine, Cornell University" + }, + { + "author_name": "Daniel Siqueira de Oliveira", + "author_inst": "Laboratoire de Biometrie et Biologie Evolutive, Universite de Lyon, CNRS" + }, + { + "author_name": "Justin Shanklin", + "author_inst": "Brigham Young University" + }, + { + "author_name": "Ethan Beausoleil", + "author_inst": "Brigham Young University" + }, + { + "author_name": "Taneli Pusa", + "author_inst": "Luxembourg Centre for Systems Biomedicine" + }, + { + "author_name": "Brett Pickett", + "author_inst": "Brigham Young University" + }, + { + "author_name": "Vanessa Aguiar-Pulido", + "author_inst": "Center for Neurogenetics, Weill Cornell Medicine, Cornell University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.29.227389", "rel_title": "On the molecular mechanism of SARS-CoV-2 retention in the upper respiratory tract", @@ -1280650,109 +1281470,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.28.223784", - "rel_title": "A Speedy Route to Multiple Highly Potent SARS-CoV-2 Main Protease Inhibitors", - "rel_date": "2020-07-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.28.223784", - "rel_abs": "The COVID-19 pathogen, SARS-CoV-2, requires its main protease (SC2MPro) to digest two of its translated polypeptides to form a number of mature proteins that are essential for viral replication and pathogenesis. Inhibition of this vital proteolytic process is effective in preventing the virus from replication in infected cells and therefore provides a potential COVID-19 treatment option. Guided by previous medicinal chemistry studies about SARS-CoV-1 main protease (SC1MPro), we have designed and synthesized a series of SC2MPro inhibitors that contain {beta}-(S-2-oxopyrrolidin-3-yl)-alaninal (Opal) for the formation of a reversible covalent bond with the SC2MPro active site cysteine C145. All inhibitors display high potency with IC50 values at or below 100 nM. The most potent compound MPI3 has as an IC50 value as 8.5 nM. Crystallographic analyses of SC2MPro bound to 7 inhibitors indicated both formation of a covalent bond with C145 and structural rearrangement from the apoenzyme to accommodate the inhibitors. Virus inhibition assays revealed that several inhibitors have high potency in inhibiting the SARS-CoV-2-induced cytopathogenic effect in both Vero E6 and A549 cells. Two inhibitors MP5 and MPI8 completely prevented the SARS-CoV-2-induced cytopathogenic effect in Vero E6 cells at 2.5-5 M and A549 cells at 0.16-0.31 M. Their virus inhibition potency is much higher than some existing molecules that are under preclinical and clinical investigations for the treatment of COVID-19. Our study indicates that there is a large chemical space that needs to be explored for the development of SC2MPro inhibitors with extreme potency. Due to the urgent matter of the COVID-19 pandemic, MPI5 and MPI8 may be quickly advanced to preclinical and clinical tests for COVID-19.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Wenshe Ray Liu", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Kai S Yang", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Xinyu R. Ma", - "author_inst": "Texas A and M University" - }, - { - "author_name": "Yuyin Ma", - "author_inst": "Texas A and M University" - }, - { - "author_name": "Yugenda R. Alugubelli", - "author_inst": "Texas A and M University" - }, - { - "author_name": "Danielle A. Scott", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Erol Can Vatansever", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Aleksandra K Drelich", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Zhi Z Geng", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Lauren R. Blankenship", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Banumathi Sankaran", - "author_inst": "Laurence Berkeley National Laboratory" - }, - { - "author_name": "Hannah E Ward", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Yan J. Sheng", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Jason C Hsu", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Kaci K Kratch", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Baoyu Zhao", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Jin Liu", - "author_inst": "University of North Texas System College of Pharmacy" - }, - { - "author_name": "Pingwei Li", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Carol A. Fierke", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Chien-Te K. Tseng", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Shiqing Xu", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Hamed S Hayatshahi", - "author_inst": "University of North Texas Health Science Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.07.28.224733", "rel_title": "SARS-CoV-2 in-vitro neutralization assay reveals inhibition of virus entry by iota-carrageenan", @@ -1281140,6 +1281857,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.28.224386", + "rel_title": "Comparative Analysis of Human Coronaviruses Focusing on Nucleotide Variability and Synonymous Codon Usage Pattern", + "rel_date": "2020-07-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.28.224386", + "rel_abs": "Prevailing pandemic across the world due to SARSCoV-2 drawing great attention towards discovering its evolutionary origin. We perform an exploratory study to understand the variability of the whole coding region of possible proximal evolutionary neighbours of SARSCoV-2. We consider seven (07) human coronavirus strains from six different species as a candidate for our study.\n\nFirst, we observe a good variability of nucleotides across candidate strains. We did not find a significant variation of GC content across the strains for codon position first and second. However, we interestingly see huge variability of GC-content in codon position 3rd (GC3), and pairwise mean GC-content (SARSCoV, MERSCoV), and (SARSCoV-2, hCoV229E) are quite closer. While observing the relative abundance of dinucleotide feature, we find a shared typical genetic pattern, i.e., high usage of GC and CT nucleotide pair at the first two positions (P12) of codons and the last two positions (P23) of codons, respectively. We also observe a low abundance of CG pair that might help in their evolution bio-process. Secondly, Considering RSCU score, we find a substantial similarity for mild class coronaviruses, i.e., hCoVOC43, hCoVHKU1, and hCoVNL63 based on their codon hit with high RSCU value ([≥] 1.5), and minim number of codons hit (count-9) is observed for MERSCoV. We see seven codons ATT, ACT, TCT, CCT, GTT, GCT and GGT with high RSCU value, which are common in all seven strains. These codons are mostly from Aliphatic and Hydroxyl amino acid group. A phylogenetic tree built using RSCU feature reveals proximity among hCoVOC43 and hCoV229E (mild). Thirdly, we perform linear regression analysis among GC content in different codon position and ENC value. We observe a strong correlation (significant p-value) between GC2 and GC3 for SARSCoV-2, hCoV229E and hCoVNL63, and between GC1 and GC3 for hCoV229E, hCoVNL63, SARSCoV. We believe that our findings will help in understanding the mechanism of human coronavirus.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Jayanta Das", + "author_inst": "Johns Hopkins University, MD-21205, USA" + }, + { + "author_name": "Swarup Roy", + "author_inst": "Sikkim University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.07.22.20154542", "rel_title": "Prophylaxis with tetracyclines in ARDS: Potential therapy for COVID-19-induced ARDS?", @@ -1282456,81 +1283196,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.25.20161968", - "rel_title": "Assessing the quality of nontraditional N95 filtering face-piece respirators available during the COVID-19 pandemic", - "rel_date": "2020-07-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.25.20161968", - "rel_abs": "BackgroundDuring the current COVID-19 pandemic, supply chains for Personal Protective Equipment (PPE) have been severely disrupted and many products, particularly surgical N95 filtering facepiece respirators (FFRs; \"masks\") are in short supply. As a consequence, an Emergency Use Authorization (EUA) from the FDA has allowed importation of N95-type masks manufactured to international standards; these include KN95 masks from China and FFP2 masks from the European Union.\n\nMethodsWe conducted a survey of mask in the inventory of major academic medical centers in Boston, MA to determine provenance and manufacturer. We then assembled a simple apparatus for performing a necessary (but not sufficient) test of filtration performance and tested masks from the inventory; an accompanying website shows how to build and use the testing apparatus.\n\nResultsOur survey showed that, seven months after the start of the COVID-19 pandemic, over 100 different makes and models of N95-type masks are in the inventory of local hospitals as opposed to 2-5 models under normal circumstances. A substantial number of unfamiliar masks are from unknown manufacturers. Many did not perform to accepted standards and are likely to be counterfeit. Due to the absence of publicly available information on mask suppliers in the FDA EUA and confusing or inconsistent labeling of KN95 masks, it is difficult to distinguish legitimate and counterfeit products.\n\nConclusionsMany of the FFR masks available for procurement during the COVID-19 pandemic do not provide levels of fit and filtration similar to those of N95 masks and are not acceptable for use in healthcare settings. Based on these results, and in consultation with occupational health officers, we make six recommendations for end users to assist in acquiring legitimate products. In particular, institutions should always assess masks from non-traditional supply chains by checking their markings and manufacturer information against data provided by NIOSH and the latest FDA EUA Appendix A. In the absence of verifiable information on the legitimacy of mask source, institutions should consider measuring mask fit and filtration directly. We also make suggestions for U.S and Chinese regulatory agencies with regard to labeling and public disclosure aimed at increase pandemic resilience.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Deborah Plana", - "author_inst": "Harvard-MIT Division of Health Sciences & Technology; Harvard Ludwig Cancer Research Center and Department of Systems Biology, Harvard Medical School" - }, - { - "author_name": "Enze Tian", - "author_inst": "Department of Building Science, Tsinghua University; Department of Nuclear Science and Engineering and Department of Materials Science and Engineering, MIT" - }, - { - "author_name": "Avilash K. Cramer", - "author_inst": "Harvard-MIT Division of Health Sciences & Technology" - }, - { - "author_name": "Helen Yang", - "author_inst": "Harvard-MIT Center for Regulatory Science, Harvard Medical School" - }, - { - "author_name": "Mary M. Carmack", - "author_inst": "Harvard-MIT Center for Regulatory Science, Harvard Medical School; Computational Health Informatics Program, Boston Children's Hospital" - }, - { - "author_name": "Michael S. Sinha", - "author_inst": "Harvard-MIT Center for Regulatory Science, Harvard Medical School" - }, - { - "author_name": "Florence T. Bourgeois", - "author_inst": "Harvard-MIT Center for Regulatory Science, Harvard Medical School; Computational Health Informatics Program, Boston Children's Hospital" - }, - { - "author_name": "Sherry H. Yu", - "author_inst": "Department of Dermatology, Yale University School of Medicine" - }, - { - "author_name": "Peter Masse", - "author_inst": "Environmental Affairs, Brigham & Women's Hospital" - }, - { - "author_name": "Jon Boyer", - "author_inst": "Environmental Affairs, Brigham & Women's Hospital" - }, - { - "author_name": "Minjune Kim", - "author_inst": "Department of Nuclear Science and Engineering and Department of Materials Science and Engineering, MIT" - }, - { - "author_name": "Jinhan Mo", - "author_inst": "Department of Building Science, Tsinghua University" - }, - { - "author_name": "Nicole R. LeBoeuf", - "author_inst": "Department of Dermatology, Center for Cutaneous Oncology, Brigham and Women's Hospital; Dana-Farber Cancer Institute" - }, - { - "author_name": "Ju Li", - "author_inst": "Department of Nuclear Science and Engineering and Department of Materials Science and Engineering, MIT" - }, - { - "author_name": "Peter K. Sorger", - "author_inst": "Harvard Ludwig Cancer Research Center, Department of Systems Biology, and Harvard-MIT Center for Regulatory Science; Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.07.23.20160804", "rel_title": "A High-throughput Anti-SARS-CoV-2 IgG Testing Platform for COVID-19", @@ -1282938,6 +1283603,105 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.27.223495", + "rel_title": "Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals", + "rel_date": "2020-07-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.27.223495", + "rel_abs": "The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity and provided evidence of expression of ORF10. Heterogeneous allelic frequencies along the 20kb ORF1ab gene suggested the presence of a defective interfering viral RNA species subpopulation in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Harsha Vardhan Doddapaneni", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Sara Javornik Cregeen", + "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Richard Sucgang", + "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Qingchang Meng", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Xiang Qing", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Vasanthi Avadhanula", + "author_inst": "Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Hsu Chao", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Vipin Menon", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Erin Nicholson", + "author_inst": "Department of Molecular Virology and Microbiology, and Pediatrics , Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "David Henke", + "author_inst": "Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Felipe-Andres Piedra", + "author_inst": "Department of Molecular Virology and Microbiology , Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Anubama Rajan", + "author_inst": "Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Zeineen Momin", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Kavya Kottapalli", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Kristi L. Hoffman", + "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Fritz J Sedlazeck", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Ginger Metcalf", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Pedro A Piedra", + "author_inst": "Department of Molecular Virology and Microbiology and Pediatrics , Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Donna M Muzny", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Joseph F Petrosino", + "author_inst": "Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA, 77030" + }, + { + "author_name": "Richard A Gibbs", + "author_inst": "Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA, 77030" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.07.27.222836", "rel_title": "Targeting the endolysosomal host-SARS-CoV-2 interface by the clinically licensed antidepressant fluoxetine", @@ -1284374,41 +1285138,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.20.20157784", - "rel_title": "INDEPENDENT ASSOCIATION OF METEOROLOGICAL CHARACTERISTICS WITH INITIAL SPREAD OF COVID-19 IN INDIA", - "rel_date": "2020-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20157784", - "rel_abs": "Whether weather plays a part in the transmissibility of the novel COronaVIrus Disease-19 (COVID-19) is still not established. We tested the hypothesis that meteorological factors (air temperature, relative humidity, air pressure, wind speed and rainfall) are independently associated with transmissibility of COVID-19 quantified using the basic reproduction rate (R0). We used publicly available datasets on daily COVID-19 case counts (total n = 108,308), three-hourly meteorological data and community mobility data over a three-month period. Estimated R0 varied between 1.15-1.28. Mean daily air temperature (inversely) and wind speed (positively) were significantly associated with time dependent R0, but the contribution of countrywide lockdown to variability in R0 was over three times stronger as compared to that of temperature and wind speed combined. Thus, abating temperatures and easing lockdown may concur with increased transmissibility of COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Hemant Kulkarni", - "author_inst": "M&H Research, LLC" - }, - { - "author_name": "Harshwardhan Vinod Khandait", - "author_inst": "Government Medical College, Nagpur, India" - }, - { - "author_name": "Uday Wasudeorao Narlawar", - "author_inst": "Government Medical College, Nagpur, India" - }, - { - "author_name": "Pragati G Rathod", - "author_inst": "Government Medical College, Nagpur, india" - }, - { - "author_name": "Manju Mamtani", - "author_inst": "M&H Research, LLC" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.20.20157792", "rel_title": "Comparison of viral levels in individuals with or without symptoms at time of COVID-19 testing among 32,480 residents and staff of nursing homes and assisted living facilities in Massachusetts.", @@ -1284676,6 +1285405,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.07.21.20156711", + "rel_title": "Healthcare Workers' Mental Health and Wellbeing During the COVID-19 Pandemic in the UK: Contrasting Guidelines with Experiences in Practice", + "rel_date": "2020-07-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20156711", + "rel_abs": "BackgroundSubstantial evidence has highlighted the importance of considering healthcare workers (HCW) mental health during the COVID-19 pandemic, and several organisations have issued guidelines with recommendations. However, the definition of wellbeing and the evidence-base behind such guidelines remains unclear.\n\nObjectivesAssessing the applicability of wellbeing guidelines in practice; identifying unaddressed HCWs needs; and providing recommendations for supporting frontline staff during the current and future pandemics.\n\nMethods and DesignThis paper discusses the findings of a qualitative study based on interviews with frontline healthcare staff in the UK and examines them in relation to a rapid review of wellbeing guidelines developed in response to the COVID-19 pandemic.\n\nResults14 guidelines were included in the rapid review and 33 interviews with HCWs were conducted in the qualitative study. As a whole, the guidelines placed greater emphasis on wellbeing at an individual level, while HCWs placed greater emphasis on structural conditions at work, such as understaffing and the invaluable support of the community. This in turn had implications for the focus of wellbeing intervention strategies; staff reported an increased availability of formal mental health support, however, understaffing or clashing schedules prevented them from participating in these activities.\n\nConclusionHCWs expressed wellbeing needs which align with social-ecological conceptualisations of wellbeing related to quality of life. This approach to wellbeing has been highlighted in literature about HCWs support in previous health emergencies, yet it has not been monitored during this pandemic. Wellbeing guidelines should explore staffs needs and contextual characteristics affecting the implementation of recommendations.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Norha Vera San Juan", + "author_inst": "Insitute of Psychiatry, Psychology and Neuroscience. King's College London" + }, + { + "author_name": "David Aceituno", + "author_inst": "Institute of Psychiatry, Psychology and Neuroscience. King's College London" + }, + { + "author_name": "Nehla Djellouli", + "author_inst": "Institute for Global Health. University College London" + }, + { + "author_name": "Kirsi Sumray", + "author_inst": "Institute of Epidemiology and Health Care. University College London" + }, + { + "author_name": "Nina Regenold", + "author_inst": "Institute of Epidemiology and Health Care. University College London" + }, + { + "author_name": "Aron Syversen", + "author_inst": "Institute of Epidemiology and Health Care. University College London" + }, + { + "author_name": "Sophie Mulcahy Symmons", + "author_inst": "Institute of Epidemiology and Health Care. University College London" + }, + { + "author_name": "Anna Dowrick", + "author_inst": "Institute of Population Health and Science. Queen Mary University of London" + }, + { + "author_name": "Lucy Mitchinson", + "author_inst": "Marie Cuerie Pallatieve Care Research Department. University College London" + }, + { + "author_name": "Georgina Singleton", + "author_inst": "Health Services Research Centre. University College London" + }, + { + "author_name": "Cecilia Vindrola-Padros", + "author_inst": "Rapid Research, Evaluation and Appraisal Lab. University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.07.20.20157149", "rel_title": "Association of contact to small children with mild course of COVID-19", @@ -1286656,49 +1287444,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.22.20159731", - "rel_title": "Alternative Approaches for Modelling COVID-19:High-Accuracy Low-Data Predictions", - "rel_date": "2020-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20159731", - "rel_abs": "BackgroundNumerous models have tried to predict the spread of COVID-19. Many involve myriad assumptions and parameters which cannot be reliably calculated under current conditions. We describe machine-learning and curve-fitting based models using fewer assumptions and readily available data.\n\nMethodsInstead of relying on highly parameterized models, we design and train multiple neural networks with data on a national and state level, from 9 COVID-19 affected countries, including Indian and US states and territories. Further, we use an array of curve-fitting techniques on government-reported numbers of COVID-19 infections and deaths, separately projecting and collating curves from multiple regions across the globe, at multiple levels of granularity, combining heavily-localized extrapolations to create accurate national predictions.\n\nFindingsWe achieve an R2 of 0{middle dot}999 on average through the use of curve-fits and fine-tuned statistical learning methods on historical, global data. Using neural network implementations, we consistently predict the number of reported cases in 9 geographically- and demographically-varied countries and states with an accuracy of 99{middle dot}53% for 14 days of forecast and 99{middle dot}1% for 24 days of forecast.\n\nInterpretationWe have shown that curve-fitting and machine-learning methods applied on reported COVID-19 data almost perfectly reproduce the results of far more complex and data-intensive epidemiological models. Using our methods, several other parameters may be established, such as the average detection rate of COVID-19. As an example, we find that the detection rate of cases in India (even with our most lenient estimates) is 2.38% - almost a fourth of the world average of 9% [1].", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Dewang K Agarwal", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Soham De", - "author_inst": "Ashoka University" - }, - { - "author_name": "Ojas Shukla", - "author_inst": "DPS International Gurgaon" - }, - { - "author_name": "Archit Checker", - "author_inst": "Ashoka University" - }, - { - "author_name": "Apoorvi Mittal", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Ankita Borah", - "author_inst": "Ashoka University" - }, - { - "author_name": "Debayan Gupta", - "author_inst": "Ashoka University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.22.20159293", "rel_title": "Air pollution, sociodemographic and health conditions effects on COVID-19 mortality in Colombia: an ecological study", @@ -1286906,6 +1287651,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.07.18.20156828", + "rel_title": "Local public health officials and COVID-19: Evidence from China", + "rel_date": "2020-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.18.20156828", + "rel_abs": "Local public health authorities are at the forefront of fighting COVID-19. They monitor its spread in the local population and advise the local government on whether to close schools and businesses. Examining their role in battling COVID-19 will inform the public how best to prepare for a public health emergency. This study examined whether more competent local public health officials in China are more effective in fighting COVID-19, where competence was measured by the public health officials professional background. Only 38% of the heads of the public health departments of Chinese cities have a medical background. Cities with medical professionals as the head of public health departments had lower infection rates and death rates from COVID-19. The results were significant only at the start of the outbreak. Our results suggest that we should staff local public health authorities with competent professionals to better combat a pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "John Jiang", + "author_inst": "Michigan State University" + }, + { + "author_name": "Maobin Wang", + "author_inst": "The University of International Business and Economics" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.07.23.20158980", "rel_title": "Prevalence of mask wearing in northern Vermont in response to SARS-CoV-2", @@ -1288290,65 +1289058,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.20.20158071", - "rel_title": "Evaluating temperature and humidity gradients of COVID-19 infection rates in light of Non-Pharmaceutical Interventions", - "rel_date": "2020-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20158071", - "rel_abs": "We evaluate potential temperature and humidity impact on the infection rate of COVID-19 with a data up to June 10th 2020, which comprises a large geographical footprint. It is critical to analyse data from different countries or regions at similar stages of the pandemic in order to avoid picking up false gradients. The degree of severity of NPIs is found to be a good gauge of the stage of the pandemic for individual countries. Data points are classified according to the stringency index of the NPIs in order to ensure that comparisons between countries are made on equal footing. We find that temperature and relative humidity gradients dont significantly deviate from the zero-gradient hypothesis. Upper limits on the absolute value of the gradients are set. The procedure chosen here yields 6 10-3 {degrees}C-1 and 3.3 10-3 (%)-1 upper limits on the absolute values of the temperature and relative humidity gradients, respectively, with a 95% Confidence Level. These findings do not preclude existence of seasonal effects and are indicative that these are likely to be nuanced.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Joshua Choma", - "author_inst": "University of the Witwatersrand (ZA)" - }, - { - "author_name": "Bruce Mellado", - "author_inst": "University of the Witwatersrand (ZA)" - }, - { - "author_name": "Benjamin Lieberman", - "author_inst": "University of the Witwatersrand (ZA)" - }, - { - "author_name": "Fabio Correa", - "author_inst": "Rhodes University" - }, - { - "author_name": "Caroline Maslo", - "author_inst": "Netcare Hospitals" - }, - { - "author_name": "Jacques Naude", - "author_inst": "University of the Witwatersrand (ZA)" - }, - { - "author_name": "Xifeng Ruan", - "author_inst": "University of the Witwatersrand (ZA)" - }, - { - "author_name": "Kentaro Hayashi", - "author_inst": "University of the Witwatersrand (ZA)" - }, - { - "author_name": "Kgomotso Monnakgotla", - "author_inst": "University of the Witwatersrand (ZA)" - }, - { - "author_name": "Salah-Eddine Dahbi", - "author_inst": "University of the Witwatersrand (ZA)" - }, - { - "author_name": "Finn D Stevenson", - "author_inst": "University of the Witwatersrand (ZA)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.20.20158345", "rel_title": "A vulnerability analysis for the management of and response to the COVID-19 epidemic in the second most populous state in Brazil", @@ -1288556,6 +1289265,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.22.20159830", + "rel_title": "Clustering, diffusion and evolution of COVID19 infections during lock-down", + "rel_date": "2020-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20159830", + "rel_abs": "Epidemics such as the spreading of the SARS-CoV-2 virus are highly non linear, and therefore difficult to predict. In the present pandemic as time evolves, it appears more and more clearly that a clustered dynamics is a key element of description. This means that the disease rapidly evolves within spatially localized networks, that diffuse and eventually create new clusters. We improve upon the simplest possible compartmental model, the SIR model, by adding an additional compartment associated with the clustered individuals. The so-obtained SBIR model compares satisfactorily with results on the pandemic propagation in a number of European countries, during and immediately after lock-down. Especially, the decay exponent of the number of new cases after the first peak of the epidemic, is observed to be very similar for countries in which a strict lock-down was applied. We derive an analytical expression for the value of this exponent.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Wouter Bos", + "author_inst": "CNRS" + }, + { + "author_name": "Jean-Pierre Bertoglio", + "author_inst": "CNRS" + }, + { + "author_name": "Louis Gostiaux", + "author_inst": "CNRS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.25.217158", "rel_title": "High neutralizing potency of swine glyco-humanized polyclonal antibodies against SARS-CoV-2", @@ -1289856,69 +1290592,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.22.20159673", - "rel_title": "SARS-CoV-2 antibodies, serum inflammatory biomarkers and clinical severity of hospitalized COVID-19 Patients", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20159673", - "rel_abs": "BackgroundThe involvement of SARS-CoV-2 antibodies in mediating immunopathogenetic events in COVID-19 patients has been suggested. By using several experimental approaches, we investigated the potential association between SARS-CoV-2 IgGs recognizing the spike (S) protein receptor-binding domain (RBD), neutralizing antibodies (NtAb) targeting S, and COVID-19 severity.\n\nPatients and MethodsThis unicenter, retrospective, observational study included 51 hospitalized patients (24 at the intensive care unit; ICU). A total of 93 sera from these patients collected at different time points from the onset of symptoms were analyzed. SARS-CoV-2 RBD IgGs were quantitated by ELISA and NtAb50 titers were measured in a GFP reporter-based pseudotyped virus platform. Demographic and clinical data, complete blood counts, as well as serum levels of ferritin, Dimer-D, C reactive protein (CRP), lactose dehydrogenase (LDH), and interleukin-6 (IL-6) were retrieved from clinical charts.\n\nResultsThe overall correlation between levels of both antibody measurements was good (Rho=0.79; P=0<0.001). SARS-CoV-2 RBD IgG and NtAb50 levels in sera collected up to day 30 after the onset of symptoms were comparable between ICU and non-ICU patients (P=>0.1). The percentage of patients who exhibited high NtAb50 titers ([≥] 160) was similar (P=0.20) in ICU (79%) and non-ICU (60%) patients. Four ICU patients died; two of these achieved NtAb50 titers [≥] 1/160 while the other two exhibited a 1/80 titer. Very weak (Rho=>0.0-<0.2) or weak (Rho=>0.2-<0.4) correlations were observed between anti-RBD IgGs, NtAb50, and serum levels pro-inflammatory biomarkers.\n\nConclusionsThe data presented herein do not support an association between SARS-CoV-2 RBD IgG or NtAb50 levels and COVID-19 severity.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Roberto Gozalbo-Rovira", - "author_inst": "Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain." - }, - { - "author_name": "Estela Gimenez", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain" - }, - { - "author_name": "Victor Latorre", - "author_inst": "Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, 46980 Valencia, Spain" - }, - { - "author_name": "Clara Frances-Gomez", - "author_inst": "Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, 46980 Valencia, Spain" - }, - { - "author_name": "Eliseo Albert", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Javier Buesa", - "author_inst": "Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain. Microbiology Service, Clinic University Hospital, INCLIVA Health Resear" - }, - { - "author_name": "Alberto Marina", - "author_inst": "Department of Genomics and Proteomics, Instituto de Biomedicina de Valencia (IBV-CSIC) and CIBER de Enfermedades Raras (CIBERER-ISCIII), Valencia, Spain" - }, - { - "author_name": "Maria Luisa Blasco", - "author_inst": "Medical Intensive Care Unit, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Jaime Signes-Costa", - "author_inst": "Pneumology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain" - }, - { - "author_name": "Jesus Rodriguez-Diaz", - "author_inst": "Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain." - }, - { - "author_name": "Ron Geller", - "author_inst": "Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, 46980 Valencia, Spain." - }, - { - "author_name": "David Navarro", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain. Department of Microbiology, School of Medicine, University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.23.218529", "rel_title": "Immuno-informatics approach for multi-epitope vaccine designing against SARS-CoV-2", @@ -1290154,6 +1290827,65 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.07.24.217562", + "rel_title": "Identification, Mapping and Relative Quantitation of SARS-Cov2 Spike Glycopeptides by Mass-Retention Time Fingerprinting", + "rel_date": "2020-07-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.24.217562", + "rel_abs": "We describe a novel analytical method for rapid and robust identification, mapping and relative quantitation of glycopeptides from SARS-CoV-2 Spike protein. The method may be executed using any LC-TOF mass spectrometer, requires no specialised knowledge of glycan analysis and makes use of the differential resolving power of reversed phase HPLC. While this separation technique resolves peptides with high efficiency, glycans are resolved poorly, if at all. Consequently, glycopeptides consisting of the same peptide bearing different glycan structures will all possess very similar retention times and co-elute. While this has previously been viewed as a disadvantage, we show that shared retention time can be used to map multiple glycan species to the same peptide and location. In combination with MSMS and pseudo MS3, we have constructed a detailed mass-retention time database for Spike. This database allows any ESI-TOF equipped lab to reliably identify and quantify spike glycans from a single overnight elastase protein digest in less than 90 minutes.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Rod Chalk", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "William Greenland", + "author_inst": "Agilent Technologies, Lakeside, Cheadle Royal Business Park, Cheadle, Cheshire, SK8 3GR, UK" + }, + { + "author_name": "Tiago Moreira", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Jesse Coker", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Shubhashish Mukhopadhyay", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Eleanor Williams", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Charlotte Manning", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Tina Bohstedt", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Rama McCrorie", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Alejandra Fernandez-Cid", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + }, + { + "author_name": "Nicola A Burgess-Brown", + "author_inst": "Centre for Medicines Discovery, ORCRB, Oxford University, OX3 7DQ, UK" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.07.24.219139", "rel_title": "Tissue-specific and interferon-inducible expression of non-functional ACE2 through endogenous retrovirus co-option", @@ -1291326,37 +1292058,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.24.20161414", - "rel_title": "Complement C3 identified as a unique Risk Factor for Disease Severity among Young COVID-19 Patients in Wuhan", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161414", - "rel_abs": "BackgroundGiven that a substantial proportion of the subgroup of COVID-19 patients that face a severe disease course are younger than 60 years, it is critical to understand the disease-specific characteristics of young COVID-19 patients. Risk factors for a severe disease course for young COVID-19 patients and possibly non-linear influences remain unknown.\n\nMethodsData of COVID-19 patients with clinical outcome in a designated hospital in Wuhan, China, collected retrospectively from Jan 24th to Mar 27th, were analyzed. Clinical, demographic, treatment and laboratory data were collected from patients medical records. Uni- and multivariable analysis using logistic regression and random forest, with the latter allowing the study of non-linear influences, were performed to investigate and exploit the clinical characteristics of a severe disease course.\n\nResultsA total of 762 young patients (median age 47 years, interquartile ranges [IQR] 38 - 55, range 16 - 60; 55.9% female) were included, as well as 714 elderly patients as a comparison group. Among the young patients, 362 (47.5%) had a severe/critical disease course and the mean age was significantly higher in the severe subgroup than in the mild subgroup (59.3 vs. 56.0, Students t-test: p < 0.001). The uni- and multivariable analysis suggested that several covariates such as elevated levels of ASS, CRP and LDH, and decreased lymphocyte counts are influential on disease severity independent of age. Elevated levels of complement C3 (odds ratio [OR] 15.6, 95% CI 2.41-122.3; p=0.039) are particularly associated with the risk for the development of severity specifically in young patients, where no such influence seems to exist for elderly patients. Additional analysis suggests that the influence of complement C3 in young patients is independent of age, gender, and comorbidities. Variable importance values and partial dependence plots obtained using random forests delivered additional insights, in particular indicating non-linear influences of risk factors on disease severity.\n\nConclusionIn young patients with COVID-19, the levels of complement C3 correlated with disease severity and tended to be a good predictor of adverse outcome.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Weiting Cheng Sr.", - "author_inst": "Wuhan No.1 Hospital" - }, - { - "author_name": "Roman Hornung", - "author_inst": "Ludwig-Maximillian-University Munchen Institute of Medical Information, Biometry and Epidemiology" - }, - { - "author_name": "Kai Xu", - "author_inst": "Tongji hospital, Huazhong University of Science and Technology" - }, - { - "author_name": "Jian Li", - "author_inst": "Ludwig-Maximilian-Univeristy Munchen Institute of Medical Information, Biometry and Epidemiology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.23.218198", "rel_title": "Host transcriptional responses and SARS-CoV-2 isolates from the nasopharyngeal samples of Bangladeshi COVID-19 patients", @@ -1291524,6 +1292225,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.23.20160564", + "rel_title": "Modelling Palliative and End of Life resource requirements during COVID-19: implications for quality care", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20160564", + "rel_abs": "BackgroundThere were between 84,891 and 113,139 all-cause excess deaths in the United States (US) from February 1st to 25th May 2020. These deaths are widely attributed directly and indirectly to the COVID-19 pandemic. This surge in death necessitates a matched health system response to relieve serious health related suffering at the end of life (EoL) and achieve a dignified death, through timely and appropriate expertise, medication and equipment. Identifying the human and material resource needed relies on modelling resource and understanding anticipated surges in demand.\n\nMethodsA Discrete Event Simulation model designed in collaboration with health service funders, health providers, clinicians and modellers in the South West of England was created to estimate the resources required during the COVID-19 pandemic to care for deaths from COVID-19 in the community for a geographical area of nearly 1 million people. While our analysis focused on the UK setting, the model is flexible to changes in demand and setting.\n\nResultsThe model predicts that a mean of 11.97 hours (0.18 hours Standard Error (SE), up to a max of 28 hours) of additional community nurse time, up to 33 hours of care assistant time (mean 9.17 hours, 0.23 hours SE), and up to 30 hours additional care from care assistant night-sits (mean of 5.74 hours per day, 0.22 hours SE) will be required per day as a result of out of hospital COVID-19 deaths. Specialist palliative care demand is predicted to increase up to 19 hours per day (mean of 9.32 hours per day, 0.12 hours SE). An additional 286 anticipatory medicine bundles or just in case prescriptions per month will be necessary to alleviate physical symptoms at the EoL care for patients with COVID-19: an average additional 10.21 bundles (0.06 SE) of anticipatory medication per day. An average additional 9.35 syringe pumps (0.11 SE) could be needed to be in use per day (between 1 and 20 syringe pumps).\n\nConclusionModelling provides essential data to prepare, plan and deliver a palliative care pandemic response tailored to local work patterns and resource. The analysis for a large region in the South West of England shows the significant additional physical and human resource required to relieve suffering at the EoL as part of a pandemic response.\n\nWhy Was This Study Done?The resource required for the relief of suffering at the EoL in the community setting has been poorly described. The stark mortality resulting from the COVID-19 pandemic has highlighted the essential requirement to better understand the demand and available supply of EoL resource to prepare, plan and deliver a palliative care pandemic response.\n\nWhat Did the Researchers Do and Find?This manuscript describes the first open access model to describe EoL resource need during COVID-19 and presents an analysis based on a UK population of nearly 1 million people. The model identified a large increase in need for staff time, including registered community nurses, health care assistants and specialist palliative care nurses and doctors, as well as pressure on resources including syringe pumps and anticipatory medication (such as opioids) used at the EoL for symptom relief from breathlessness and delirium.\n\nWhat Do These Findings Mean?The model findings are critical in planning for a second wave of COVID-19. The open-access nature of the model allows researchers to tailor their analysis to low and middle income or high-income settings worldwide. The model ensures that EoL care is not an afterthought in pandemic planning, but an opportunity to ensure that the relief of suffering at the EoL is available to all.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Daniel Chalk", + "author_inst": "University of Exeter Medical School" + }, + { + "author_name": "Sara Robbins", + "author_inst": "University Hospitals Bristol and Weston NHS Foundation Trust" + }, + { + "author_name": "Rohan Kandasamy", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Kate Rush", + "author_inst": "Sirona Care and Health" + }, + { + "author_name": "Ajay Aggarwal", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Richard Sullivan", + "author_inst": "Kings College London" + }, + { + "author_name": "Charlotte Chamberlain", + "author_inst": "Bristol Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "palliative medicine" + }, { "rel_doi": "10.1101/2020.07.22.20160333", "rel_title": "The COVID-19 Pandemic Impact on Primary Health Care services: An Experience from Qatar", @@ -1292572,41 +1293316,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.22.20160226", - "rel_title": "Pediatric intensive care unit admissions for COVID-19: insights using state level data", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20160226", - "rel_abs": "IntroductionIntensive care has played a pivotal role during the COVID-19 pandemic as many patients developed severe pulmonary complications. The availability of information in pediatric intensive care (PICUs) remains limited. The purpose of this study is to characterize COVID-19 positive admissions (CPAs) in the United States and to determine factors that may impact those admissions.\n\nMaterials and MethodsThis is a retrospective cohort study using data from the COVID-19 dashboard virtual pediatric system containing information regarding respiratory support and comorbidities for all CPAs between March and April 2020. The state level data contained 13 different factors from population density, comorbid conditions and social distancing score. The absolute CPAs count was converted to frequency using the states population. Univariate and multivariate regression analyses were performed to assess the association between CPAs frequency and endpoints.\n\nResultsA total of 205 CPAs were reported by 167 PICUs across 48 states. The estimated CPAs frequency was 2.8 per million children. A total of 3,235 tests were conducted with 6.3% positive tests. Children above 11 years of age comprised 69.7% of the total cohort and 35.1% had moderated or severe comorbidities. The median duration of a CPA was 4.9 days [1.25-12.00 days]. Out of the 1,132 total CPA days, 592 [52.2%] were for mechanical ventilation. The inpatient mortalities were 3 [1.4%]. Multivariate analyses demonstrated an association between CPAs with greater population density [beta-coefficient 0.01, p<0.01] and increased percent of children receiving the influenza vaccination [beta-coefficient 0.17, p=0.01].\n\nConclusionsInpatient mortality during PICU CPAs is relatively low at 1.4%. CPA frequency seems to be impacted by population density while characteristics of illness severity appear to be associated with ultraviolet index, temperature, and comorbidities such as Type 1 diabetes. These factors should be included in future studies using patient-level data.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Rohit S. Loomba", - "author_inst": "Advocate Childre's Hospital" - }, - { - "author_name": "Enrique G. Villarreal", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud" - }, - { - "author_name": "Juan S. Farias", - "author_inst": "Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud" - }, - { - "author_name": "Ronald A. Bronicki", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Saul Flores", - "author_inst": "Baylor College of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.22.20159863", "rel_title": "Sentiment Informed Timeseries Analyzing AI (SITALA) to curb the spread of COVID-19 in Houston", @@ -1292754,6 +1293463,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.07.17.20156075", + "rel_title": "A national consensus management pathway for Paediatric Inflammatory Multisystem Syndrome - Temporally associated with SARS-CoV-2 (PIMS-TS): The results of a national Delphi process", + "rel_date": "2020-07-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156075", + "rel_abs": "ObjectiveTo develop a consensus management pathway for children with Paediatric Inflammatory Multisystem Syndrome - Temporally associated with SARS-CoV-2 (PIMS-TS).\n\nDesignA three-phase online Delphi process and virtual consensus meeting sought consensus over the investigation, management and research priorities from 98 multidisciplinary participants caring for children with PIMS-TS. 46 participants (47%) completed all three phases. Participants were grouped into three panels and scored each statement from 1 (disagree) to 9 (strongly agree). In phase two participants were shown their panels scores, and in phase three all panels scores.\n\nConsensus agreement was defined as [≥]70% of participants in each panel scoring the statement 7-9, and <15% scoring 1-3, and consensus disagreement was the opposite of this. Statements which achieved consensus in 2/3 panels were discussed at the consensus meeting, and when [≥]70% participants agreed with the statement it achieved consensus.\n\nResults255 statements were assessed, with consensus agreement achieved for 111 (44%), consensus disagreement for 29 (11%), and no consensus for 115 (45%). The 140 consensus statements were used to derive the consensus management pathway.\n\nConclusionsA national consensus pathway has been developed for children suspected of having the novel syndrome PIMS-TS in a timely, cost-efficient manner, in the midst of a global pandemic. Use of a rapid online Delphi process has made this consensus process possible. Future evidence will inform updates to this guidance, which in the interim provides a solid framework to support clinicians caring for children with PIMS-TS.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Rachel Harwood", + "author_inst": "Department of Paediatric Surgery, Alder Hey Childrens Hospital, Eaton Road, Liverpool, L12 2AP" + }, + { + "author_name": "Benjamin Allin", + "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Health, University of Oxford, Old Road Campus, Oxford, OX3 9DU" + }, + { + "author_name": "Christine E Jones", + "author_inst": "NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust and Faculty of Medicine and Ins" + }, + { + "author_name": "Elizabeth Whittaker", + "author_inst": "Department of Paediatrics, Imperial College Healthcare NHS Trust, London, UK" + }, + { + "author_name": "Padmanabhan Ramnarayan", + "author_inst": "Childrens Acute Transport Service, Great Ormond Street Hospital for Children, London, UK" + }, + { + "author_name": "Athimalaipet Ramanan", + "author_inst": "Bristol Royal Hospital for Children, Upper Maudlin Street Bristol, BS2 8BJ, UK" + }, + { + "author_name": "Musa Kaleem", + "author_inst": "Department of Paediatric Radiology, Alder Hey Childrens Hospital Eaton Road, Liverpool, L12 2AP, UK" + }, + { + "author_name": "Robert Tulloh", + "author_inst": "Bristol Royal Hospital for Children, Upper Maudlin Street Bristol, BS2 8BJ, UK" + }, + { + "author_name": "Mark J Peters", + "author_inst": "UCL Great Ormond St Institute of Child Health and Great Ormond St Hospital NHS Trust, NIHR Biomedical Research Centre, UK" + }, + { + "author_name": "Sarah Almond", + "author_inst": "Department of Paediatric Surgery, Alder Hey Childrens Hospital, Eaton Road, Liverpool, L12 2AP" + }, + { + "author_name": "Peter J Davis", + "author_inst": "Bristol Royal Hospital for Children, Upper Maudlin Street Bristol, BS2 8BJ, UK" + }, + { + "author_name": "Michael Levin", + "author_inst": "Department of Paediatrics, Imperial College Healthcare NHS Trust, London, UK" + }, + { + "author_name": "Saul N Faust", + "author_inst": "NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust and Faculty of Medicine and Ins" + }, + { + "author_name": "Marian Knight", + "author_inst": "University of Oxford" + }, + { + "author_name": "Simon Kenny", + "author_inst": "NHS England/Improvement, PO Box 16738, Redditch, B97 9PT, UK" + }, + { + "author_name": "- PIMS-TS National Consensus Management Study Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.16.20155531", "rel_title": "Safety of Hydroxychloroquine among Outpatient Clinical Trial Participants for COVID-19", @@ -1294186,25 +1294974,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.20.20158436", - "rel_title": "Optimal Size of COVID-19 Testing Pools", - "rel_date": "2020-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20158436", - "rel_abs": "This research note investigates the optimal size of pools for pooled, COVID-19 testing when positive pools will be followed up by individual tests of pool members. Formulae for the optimum are derived and provided. The analysis indicates that\n\nO_LIoptimal pool sizes are unlikely to exceed about 20 individuals in realistic situations,\nC_LIO_LIoptimal pool size is influenced by prevalence in the population and the extent to which infection is clustered within the population, and,\nC_LIO_LIpools are most efficiently comprised of people with homogeneous risk, with heterogeneity across pools.\nC_LI", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "jon D cohen", - "author_inst": "JCM Analytics" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.07.20.20158410", "rel_title": "Rapid quantitative screening assay for SARS-CoV-2 neutralizing antibodies using HiBiT-tagged virus-like particles", @@ -1294716,6 +1295485,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.15.20154955", + "rel_title": "The effect of border controls on the risk of COVID-19 reincursion from international arrivals", + "rel_date": "2020-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154955", + "rel_abs": "In an attempt to maintain elimination of COVID-19 in New Zealand, all international arrivals are required to spend 14 days in government-managed quarantine and to return a negative test result before being released. We model the testing, isolation and transmission of COVID-19 within quarantine facilities to estimate the risk of community outbreaks being seeded at the border. We use a simple branching process model for COVID-19 transmission that includes a time-dependent probability of a false negative test result. We show that the combination of 14-day quarantine with two tests reduces the risk of releasing an infectious case to around 0.1% per infected arrival. Shorter quarantine periods, or reliance on testing only with no quarantine, substantially increases this risk. We calculate the fraction of cases detected in the second week of their two week stay and show that this may be a useful indicator of the likelihood of transmission occurring within quarantine facilities. Frontline staff working at the border risk exposure to infected individuals and this has the potential to lead to a community outbreak. We use the model to test surveillance strategies and evaluate the likely size of the outbreak at the time it is first detected. We conclude with some recommendations for managing the risk of potential future outbreaks originating from the border.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nicholas Steyn", + "author_inst": "University of Auckland" + }, + { + "author_name": "Michael J Plank", + "author_inst": "University of Canterbury" + }, + { + "author_name": "Alex James", + "author_inst": "University of Canterbury, NZ" + }, + { + "author_name": "Rachelle N Binny", + "author_inst": "Manaaki Whenua" + }, + { + "author_name": "Shaun C Hendy", + "author_inst": "University of Auckland" + }, + { + "author_name": "Audrey Lustig", + "author_inst": "Manaaki Whenua" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.21.214759", "rel_title": "Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants", @@ -1295872,41 +1296680,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.19.20157248", - "rel_title": "Disparity in the quality of COVID-19 data reporting across India", - "rel_date": "2020-07-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.19.20157248", - "rel_abs": "BackgroundTransparent and accessible reporting of COVID-19 data is critical for public health efforts. Each state and union territory (UT) of India has its own mechanism for reporting COVID-19 data, and the quality of their reporting has not been systematically evaluated. We present a comprehensive assessment of the quality of COVID-19 data reporting done by the Indian state and union territory governments. This assessment informs the public health efforts in India and serves as a guideline for pandemic data reporting by other governments.\n\nMethodsWe designed a semi-quantitative framework to assess the quality of COVID-19 data reporting done by the states and union territories of India. This framework is based on 45 indicators that capture four key aspects of public health data reporting - availability, accessibility, granularity, and privacy. We then used this framework to calculate a COVID-19 Data Reporting Score (CDRS, ranging from 0 to 1) for 29 statesi based on the quality of COVID-19 data reporting done by the state during the two-week period from 19 May to 1 June, 2020. States that reported less than 10 total confirmed cases as of May 18, were excluded from the study.\n\nFindingsOur results indicate a strong disparity in the quality of COVID-19 data reporting done by the state governments in India. CDRS varies from 0.61 (good) in Karnataka to 0.0 (poor) in Bihar and Uttar Pradesh, with a median value of 0.26. Only ten states provide a visual representation of the trend in COVID-19 data. Ten states do not report any data stratified by age, gender, comorbidities or districts. In addition, we identify that Punjab and Chandigarh compromised the privacy of individuals under quarantine by releasing their personally identifiable information on the official websites. Across the states, the CDRS is positively associated with the states sustainable development index for good health and well-being (Pearson correlation: r = 0.630, p = 0.0003).\n\nInterpretationThe disparity in CDRS across states highlights three important findings at the national, state, and individual level. At the national level, it shows the lack of a unified framework for reporting COVID-19 data in India, and highlights the need for a central agency to monitor or audit the quality of data reporting done by the states. Without a unified framework, it is difficult to aggregate the data from different states, gain insights from them, and coordinate an effective nationwide response to the pandemic. Moreover, it reflects the inadequacy in coordination or sharing of resources among the states in India. Coordination among states is particularly important as more people start moving across states in the coming months. The disparate reporting score also reflects inequality in individual access to public health information and privacy protection based on the state of residence.\n\nFundingJ.Z. is supported by NSF CCF 1763191, NIH R21 MD012867-01, NIH P30AG059307, NIH U01MH098953 and grants from the Silicon Valley Foundation and the Chan-Zuckerberg Initiative.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Varun Vasudevan", - "author_inst": "Stanford University" - }, - { - "author_name": "Abeynaya Gnanasekaran", - "author_inst": "Stanford University" - }, - { - "author_name": "Varsha Sankar", - "author_inst": "Independent Researcher" - }, - { - "author_name": "Siddarth A. Vasudevan", - "author_inst": "Independent Researcher" - }, - { - "author_name": "James Zou", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.18.20157008", "rel_title": "Adjunctive Corticosteroids for COVID-19: A Retrospective Cohort Study", @@ -1296222,6 +1296995,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.07.20.20157602", + "rel_title": "The COVID-19 outbreak in Sichuan, China: epidemiology and impact of interventions", + "rel_date": "2020-07-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20157602", + "rel_abs": "In January 2020, a COVID-19 outbreak was detected in Sichuan Province of China. The aim of this work is to characterize the epidemiology of the Sichuan outbreak and estimate the impact of the performed interventions. We analyzed patient records for all laboratory-confirmed cases reported in the province for the period of January 21 to March 16, 2020. To estimate the basic and daily reproduction numbers, we used a Bayesian framework. In addition, we estimate the number of cases averted by the implemented control strategies. The outbreak resulted in 539 confirmed cases, lasted less than two months, and no further local transmission was detected after February 27. The median age of local cases was 8 years older than that of imported cases. Severity of symptoms increased with age. We estimated R0 at 2.4 (95% CI: 1.6-3.7). The epidemic was self-sustained for about 3 weeks before going below the epidemic threshold 3 days after the declaration of a public health emergency by Sichuan authorities. Our findings indicate that, were the control measures be adopted four weeks later, the epidemic could have lasted 49 days longer (95%CI: 31-68 days), causing 9,216 (95%CI: 1,317-25,545) more cases and possibly overwhelming Sichuan healthcare system.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Quanhui Liu", + "author_inst": "Sichuan University, Chengdu, China" + }, + { + "author_name": "Ana I Bento", + "author_inst": "Indiana University" + }, + { + "author_name": "Kexin Yang", + "author_inst": "Sichuan University" + }, + { + "author_name": "Hang Zhang", + "author_inst": "Sichuan University" + }, + { + "author_name": "Xiaohan Yang", + "author_inst": "Department of Engineering and Computer Science, New York University Shanghai, Shanghai, China" + }, + { + "author_name": "Stefano Merler", + "author_inst": "Bruno Kessler Foundation, Trento, Italy" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Jiancheng Lv", + "author_inst": "Sichuan University" + }, + { + "author_name": "Hongjie Yu", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Wei Zhang", + "author_inst": "Sichuan University" + }, + { + "author_name": "Tao Zhou", + "author_inst": "University of Electronic Science and Technology of China, Chengdu, China" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, IN, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.18.20156695", "rel_title": "A preliminary model to describe the transmission dynamics of Covid-19 between two neighboring cities or countries", @@ -1297558,85 +1298394,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2020.07.20.211789", - "rel_title": "A human disease model of SARS-CoV-2-induced lung injury and immune responses with a microengineered organ chip", - "rel_date": "2020-07-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.20.211789", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that seriously endangers human health. There is an urgent need to build physiological relevant human models for deep understanding the complex organ-level disease processes and facilitating effective therapeutics for COVID-19. Here, we first report the use of microengineered alveolus chip to create a human disease model of lung injury and immune responses induced by native SARS-CoV-2 at organ-level. This biomimetic system is able to reconstitute the key features of human alveolar-capillary barrier by co-culture of alveolar epithelial and microvascular endothelial cells under microfluidic flow. The epithelial cells on chip showed higher susceptibility to SARS-CoV-2 infection than endothelial cells identified by viral spike protein expression. Transcriptional analysis showed distinct responses of two cell types to SARS-CoV-2 infection, including activated type I interferon (IFN-I) signaling pathway in epithelium and activated JAK-STAT signaling pathway in endothelium. Notably, in the presence of circulating immune cells, a series of alveolar pathological changes were observed, including the detachment of endothelial cells, recruitment of immune cells, and increased production of inflammatory cytokines (IL-6, IL-8, IL-1{beta} and TNF-). These new findings revealed a crucial role of immune cells in mediating lung injury and exacerbated inflammation. Treatment with antiviral compound remdesivir could suppress viral copy and alleviate the disruption of alveolar barrier integrity induced by viral infection. This bioengineered human organ chip system can closely mirror human-relevant lung pathogenesis and immune responses to SARS-CoV-2 infection, not possible by other in vitro models, which provides a promising and alternative platform for COVID-19 research and preclinical trials.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Min Zhang", - "author_inst": "Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China." - }, - { - "author_name": "Peng Wang", - "author_inst": "Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China." - }, - { - "author_name": "Ronghua Luo", - "author_inst": "Kunming National High-level Bio-safety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy " - }, - { - "author_name": "Yaqing Wang", - "author_inst": "Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China; University of Chinese A" - }, - { - "author_name": "Zhongyu Li", - "author_inst": "Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China." - }, - { - "author_name": "Yaqiong Guo", - "author_inst": "Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China; University of Chinese A" - }, - { - "author_name": "Yulin Yao", - "author_inst": "Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy o" - }, - { - "author_name": "Minghua Li", - "author_inst": "Kunming National High-level Bio-safety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy " - }, - { - "author_name": "Tingting Tao", - "author_inst": "Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China; University of Chinese A" - }, - { - "author_name": "Wenwen Chen", - "author_inst": "Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China; University of Chinese A" - }, - { - "author_name": "Jianbao Han", - "author_inst": "Kunming National High-level Bio-safety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy " - }, - { - "author_name": "Haitao Liu", - "author_inst": "Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China; University of Chinese A" - }, - { - "author_name": "Kangli Cui", - "author_inst": "Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China; University of Chinese A" - }, - { - "author_name": "Xu Zhang", - "author_inst": "Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China." - }, - { - "author_name": "Yongtang Zheng", - "author_inst": "Kunming National High-level Bio-safety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy " - }, - { - "author_name": "Jianhua Qin", - "author_inst": "Division of Biotechnology, CAS Key Laboratory of SSAC, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China; Institute for Stem Cell" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.07.11.20148486", "rel_title": "COVID-19, Race, and Redlining", @@ -1297960,6 +1298717,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.15.20154336", + "rel_title": "Epidemiological Profile and Transmission Dynamics of COVID-19 in the Philippines", + "rel_date": "2020-07-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154336", + "rel_abs": "The Philippines confirmed local transmission of COVID-19 on 7 March 2020. We described the characteristics and epidemiological time-to-event distributions for laboratory-confirmed cases in the Philippines. The median age of 8,212 cases was 46 years (IQR: 32-61), with 46.2% being female and 68.8% living in the National Capital Region. Health care workers represented 24.7% of all detected infections. Mean length of hospitalization for those who were discharged or died were 16.00 days (95% CI: 15.48, 16.54) and 7.27 days (95% CI: 6.59, 8.24). Mean duration of illness was 26.66 days (95% CI: 26.06, 27.28) and 12.61 days (95% CI: 11.88, 13.37) for those who recovered or died. Mean serial interval was 6.90 days (95% CI: 5.81, 8.41). Epidemic doubling time pre-quarantine (11 February and 19 March) was 4.86 days (95% CI: 4.67, 5.07) and the reproductive number was 2.41 (95% CI: 2.33, 2.48). During quarantine (March 20 to April 9), doubling time was 12.97 days (95% CI: 12.57, 13.39) and the reproductive number was 0.89 (95% CI: 0.78, 1.02).", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Nel Jason Ladiao Haw", + "author_inst": "Ateneo de Manila University" + }, + { + "author_name": "Jhanna Uy", + "author_inst": "Ateneo de Manila University" + }, + { + "author_name": "Karla Therese L. Sy", + "author_inst": "Boston University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.18.20152256", "rel_title": "Providing breastfeeding support during the COVID-19 pandemic: Concerns of mothers who contacted the Australian Breastfeeding Association", @@ -1299184,49 +1299968,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.07.17.20156505", - "rel_title": "Geographic access to COVID-19 healthcare in Brazil using a balanced float catchment area approach", - "rel_date": "2020-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156505", - "rel_abs": "The rapid spread of the new coronavirus across the world has raised concerns about the responsiveness of cities and healthcare systems during pandemics. Recent studies try to model how the number of COVID-19 infections will likely grow and impact the demand for hospitalization services at national and regional levels. However, less attention has been paid to the geographic access to COVID-19 healthcare services and to the response capacity of hospitals at the local level, particularly in urban areas in the Global South. This paper shows how transport accessibility analysis can provide actionable information to help improve healthcare coverage and responsiveness. It analyzes accessibility to COVID-19 healthcare at high spatial resolution in the 20 largest cities of Brazil. Using network-distance metrics, we estimate the vulnerable population living in areas with poor access to healthcare facilities that could either screen or hospitalize COVID-19 patients. We then use a new balanced floating catchment area (BFCA) indicator to estimate spatial, income and racial inequalities in access to hospitals with intensive care unit (ICU) beds and mechanical ventilators while taking into account congestion effects. Based on this analysis, we identify substantial social and spatial inequalities in access to health services during the pandemic. The availability of ICU equipment varies considerably between cities and it is substantially lower among black and poor communities. The study maps territorial inequalities in healthcare access and reflects on different policy lessons that can be learned for other countries based on the Brazilian case.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Rafael H. M. Pereira", - "author_inst": "Institute for Applied Economic Research (Ipea)" - }, - { - "author_name": "Carlos Kaue Vieira Braga", - "author_inst": "Institute for Applied Economic Research - Ipea" - }, - { - "author_name": "Luciana Mendes Servo", - "author_inst": "Institute for Applied Economic Research - Ipea" - }, - { - "author_name": "Bernardo Serra", - "author_inst": "Institute for Transport Policy & Development - ITDP Brazil" - }, - { - "author_name": "Pedro Amaral", - "author_inst": "Centre for Development and Regional Planning (CEDEPLAR) at Universidade Federal de Minas Gerais (UFMG), Brazil" - }, - { - "author_name": "Nelson Gouveia", - "author_inst": "Department of Preventive Medicine, University of Sao Paulo Medical School (FMUSP)" - }, - { - "author_name": "Antonio Paez", - "author_inst": "School of Earth, Environment, and Society, McMaster University, Canada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.17.20156497", "rel_title": "UV-C decontamination for N95 emergency reuse: Quantitative dose validation with photochromic indicators", @@ -1299466,6 +1300207,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.17.20156513", + "rel_title": "Large-scale Multi-omic Analysis of COVID-19 Severity", + "rel_date": "2020-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156513", + "rel_abs": "We performed RNA-Seq and high-resolution mass spectrometry on 128 blood samples from COVID-19 positive and negative patients with diverse disease severities. Over 17,000 transcripts, proteins, metabolites, and lipids were quantified and associated with clinical outcomes in a curated relational database, uniquely enabling systems analysis and cross-ome correlations to molecules and patient prognoses. We mapped 219 molecular features with high significance to COVID-19 status and severity, many involved in complement activation, dysregulated lipid transport, and neutrophil activation. We identified sets of covarying molecules, e.g., protein gelsolin and metabolite citrate or plasmalogens and apolipoproteins, offering pathophysiological insights and therapeutic suggestions. The observed dysregulation of platelet function, blood coagulation, acute phase response, and endotheliopathy further illuminated the unique COVID-19 phenotype. We present a web-based tool (covid-omics.app) enabling interactive exploration of our compendium and illustrate its utility through a comparative analysis with published data and a machine learning approach for prediction of COVID-19 severity.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Katherine A Overmyer", + "author_inst": "Morgridge Institute for Research" + }, + { + "author_name": "Evgenia Shishkova", + "author_inst": "University of Wisconsin-Madison, Madison, WI USA" + }, + { + "author_name": "Ian Miller", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Joseph Balnis", + "author_inst": "Albany Medical College, Albany NY, USA" + }, + { + "author_name": "Matthew N. Bernstein", + "author_inst": "Morgridge Institute for Research" + }, + { + "author_name": "Trenton M. Peters-Clarke", + "author_inst": "University of Wisconsin-Madison, Madison, WI USA" + }, + { + "author_name": "Jesse G. Meyer", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Qiuwen Quan", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Laura K. Muehlbauer", + "author_inst": "University of Wisconsin-Madison, Madison, WI, USA" + }, + { + "author_name": "Edna A. Trujillo", + "author_inst": "University of Wisconsin-Madison, Madison, WI, USA" + }, + { + "author_name": "Yuchen He", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Amit Chopra", + "author_inst": "Albany Medical Center, Albany NY, USA" + }, + { + "author_name": "Hau Chieng", + "author_inst": "Albany Medical Center, Albany NY, USA" + }, + { + "author_name": "Anupama Tiwari", + "author_inst": "Albany Medical Center, Albany NY, USA" + }, + { + "author_name": "Marc A. Judson", + "author_inst": "Albany Medical College, Albany NY, USA" + }, + { + "author_name": "Brett Paulson", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Dain R. Brademan", + "author_inst": "University of Wisconsin-Madison, Madison, WI, USA" + }, + { + "author_name": "Yunyun Zhu", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Lia R. Serrano", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Vanessa Linke", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Lisa A. Drake", + "author_inst": "Albany Medical College, Albany NY, USA" + }, + { + "author_name": "Alejandro P. Adam", + "author_inst": "Albany Medical College, Albany NY, USA" + }, + { + "author_name": "Bradford S. Schwartz", + "author_inst": "Morgridge Institute for Research, Madison WI, USA" + }, + { + "author_name": "Harold A. Singer", + "author_inst": "Albany Medical College, Albany NY, USA" + }, + { + "author_name": "Scott Swanson", + "author_inst": "Morgridge Institute for Research, Madison WI, USA" + }, + { + "author_name": "Deane F. Mosher", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Ron Stewart", + "author_inst": "Morgridge Institute For Research, Madison WI, USA." + }, + { + "author_name": "Joshua J. Coon", + "author_inst": "University of Wisconsin-Madison, Madison WI, USA" + }, + { + "author_name": "Ariel Jaitovich", + "author_inst": "Albany Medical College, Albany NY, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.17.20156539", "rel_title": "Quantifying SARS-CoV-2 infection risk within the Apple/Google exposure notification framework to inform quarantine recommendations", @@ -1300878,33 +1301750,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.16.20155721", - "rel_title": "Forecasting hospital demand in metropolitan areas during the current COVID-19 pandemic and estimates of lockdown-induced 2nd waves", - "rel_date": "2020-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155721", - "rel_abs": "We present a forecasting model aim to predict hospital occupancy in metropolitan areas during the current COVID-19 pandemic. Our SEIRD type model features asymptomatic and symptomatic infections with detailed hospital dynamics. We model explicitly branching probabilities and non-exponential residence times in each latent and infected compartments. Using both hospital admittance confirmed cases and deaths, we infer the contact rate and the initial conditions of the dynamical system, considering breakpoints to model lockdown interventions and the increase in effective population size due to lockdown relaxation. The latter features let us model lockdown-induced 2nd waves. Our Bayesian approach allows us to produce timely probabilistic forecasts of hospital demand. We have applied the model to analyze more than 70 metropolitan areas and 32 states in Mexico.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Marcos A Capistran", - "author_inst": "CIMAT" - }, - { - "author_name": "Antonio Capella", - "author_inst": "UNAM" - }, - { - "author_name": "J. Andres Christen", - "author_inst": "CIMAT" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.16.20155622", "rel_title": "DETERMINANTS OF BURNOUT AND OTHER ASPECTS OF PSYCHOLOGICAL WELL-BEING IN HEALTHCARE WORKERS DURING THE COVID-19 PANDEMIC: A MULTINATIONAL CROSS-SECTIONAL STUDY", @@ -1301172,6 +1302017,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.07.16.20155630", + "rel_title": "Emerging Mental Health Challenges, Strategies and Opportunities in the context of the COVID-19 Pandemic: Perspectives from South American Decision-makers.", + "rel_date": "2020-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155630", + "rel_abs": "BackgroundMental health awareness has increased during the COVID-19 pandemic. Although international guidelines address the mental health and psychosocial support (MHPSS) response to emergencies, regional recommendations on COVID-19 are still insufficient. We identified emerging mental health problems, strategies to address them, and opportunities to reform mental health systems during the COVID-19 pandemic in South America.\n\nMethodsAn anonymous online questionnaire was sent to mental health decision-makers of Ministries of Health in 10 South American countries in mid-April 2020. The semi-structured questionnaire had 12 questions clustered into 3 main sections: emerging challenges in mental health, current and potential strategies to face the pandemic, and, key elements for mental health reform. We identified keywords and themes for each section through summative content analysis.\n\nFindingsAn increasing mental health burden and emerging needs are arising as direct and indirect consequences of the pandemic among health care providers and the general population. National lockdowns challenge the delivery and access to mental health treatment and care. Strategies to meet these health needs rely heavily on timely and adequate responses by strengthened mental health governance and systems, availability of services, virtual platforms, and appropriate capacity building for service providers. Short- and medium-term strategies focused on bolstering community-based mental health networks and telemedicine for high-risk populations. Opportunities for long-term mental health reform entail strengthening legal frameworks, redistribution of financial resources and collaboration with local and international partners.\n\nInterpretationMental health and psychosocial support have been identified as a priority area by South American countries in the COVID-19 response. The pandemic has generated specific needs that require appropriate actions including: implementing virtual based interventions, orienting capacity building towards protection of users and health providers, strengthening evidence-driven decision making and integrating MHPSS in high-level mechanisms guiding the response to COVID-19.\n\nFundingNone.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe COVID-19 pandemic has affected mental health and wellbeing as well as its determinants. General population have reported anxiety and stress while health professionals fear, and bereavement. Mental health services have also been overburdened as the health needs increase as consequence of the pandemic and the isolation measures in place. The WHO General director has recognized mental health and psychological support (MHPPS) as a major pillar in the overall health response to the COVID-19 pandemic. Likewise, the Inter Agency Standing Committee (IASC) published a global briefing recommending eight MHPPS interventions to be implement during the crisis. Nonetheless, evidence to guide action at regional and sub-regional levels is still insufficient.\n\nAdded value of this studyThis study provides expert perspectives of decision-makers about mental health burden and actions during the COVID-19 in South America, currently the most serious hub of infection worldwide. Health services have reported an increase of anxiety, stress and fear among the general population emerging during the pandemic. The pandemic has generated specific needs that require appropriate actions including implementing virtual based interventions, bolstering community-based mental health networks, and integrating MHPSS in high-level mechanisms guiding the response to COVID-19. Decision-makers identified opportunities to seize for long-term mental health reform such as strengthening legal frameworks, redistribution of financial resources and collaboration with local and international partners.\n\nImplications of all the available evidenceThe importance of this research goes beyond documenting the status quo of mental health at country level, but implies fostering, enhancing and expanding collaborations in the Sub-region to strengthen the mental health response to the COVID-19 pandemic. Country-cooperation initiatives in mental health have been an important strategy to improve local mental health systems and services. Our findings are expected to better orient next steps in making decisions on mental health policies and services in South America, but also to inform public health key leaders and mental health experts within and beyond the Region of the Americas.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Daniel A Antiporta", + "author_inst": "Johns Hopkins School of Public Health" + }, + { + "author_name": "Andrea Bruni", + "author_inst": "Pan American Health Organization" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.16.20155572", "rel_title": "Probability of aerosol transmission of SARS-CoV-2", @@ -1302936,65 +1303804,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.07.15.20149559", - "rel_title": "Risk Adjusted Non-Pharmaceutical Interventions for the Management of COVID-19 in South Africa", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20149559", - "rel_abs": "A global analysis of the impact of non-pharmaceutical interventions (NPIs) on the dynamics of the spread of the COVID-19 indicates that these can be classified using the stringency index proposed by the Oxford COVID-19 Government Response Tracker (OxCGRT) team. The world average for the coefficient that linearises the level of transmission with respect to the OxCGRT stringency index is s = 0.01{+/-}0.0017 (95% C.I.). The corresponding South African coefficient is s = 0.0078 {+/-} 0.00036 (95% C.I.), compatible with the world average. Here, we implement the stringency index for the recently announced 5-tier regulatory alert system. Predictions are made for the spread of the virus for each alert level. Assuming constant rates of recovery and mortality, it is essential to increase s. For the system to remain sub-critical, the rate with which s increases should outpace that of the decrease of the stringency index. Monitoring of s becomes essential to controlling the post-lockdown phase. Data from the Gauteng province obtained in May 2020 has been used to re-calibrate the model, where s was found increase by 20% with respect to the period before lockdown. Predictions for the province are made in this light.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Finn D Stevenson", - "author_inst": "University of Witwaterstrand" - }, - { - "author_name": "Bruce Mellado", - "author_inst": "University of Witwaterstrand" - }, - { - "author_name": "Joshua Choma", - "author_inst": "University of Witwaterstrand" - }, - { - "author_name": "Benjamin Lieberman", - "author_inst": "University of Witwaterstrand" - }, - { - "author_name": "F\u00e1bio Corr\u00eaa", - "author_inst": "Rhodes University" - }, - { - "author_name": "Salah-Eddine Dahbi", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Kentaro Hayashi", - "author_inst": "University of Witwaterstrand" - }, - { - "author_name": "Kgomotso Monnakgotla", - "author_inst": "University of Witwaterstrand" - }, - { - "author_name": "Jacques Naude", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Xifeng Ruan", - "author_inst": "University of Witwaterstrand" - }, - { - "author_name": "Caroline Maslo", - "author_inst": "Netcare Hospital Division" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.07.16.20155143", "rel_title": "Anti-SARS-CoV-2 IgG antibodies in adolescent students and their teachers in Saxony, Germany (SchoolCoviDD19): very low seropraevalence and transmission rates", @@ -1303470,6 +1304279,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.15.20153098", + "rel_title": "Public's perceived importance of non-pharmacological interventions for COVID-19 control in Greece: preliminary evidence from a cross-sectional study", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20153098", + "rel_abs": "BackgroundIn the early stages of coronavirus disease 2019 (COVID-19) pandemic, while effective pharmaceutical approaches are pending, COVID-19 management relies primarily on non-pharmaceutical interventions (NPIs), such as social distancing, which requirepublics engagement and behavioral adjustment. This study aims to evaluate publics perceived importance of the NPIs imposed for COVID-19 control in personal and public health protection in Greece.\n\nMethodsThis cross-sectional online study, enrolled 657 participants of the general Greek population in order to assess their beliefs and evaluate possible factors that influence their perceptions as regards NPI importance in personal and public health protection.\n\nResultsOverall, Greeks considered NPIs important for health protection. The participants who were less likely to consider NPIs important were men (OR versus females=1.64, 95% CI:1.15 to 2.36, p=0.007), people younger than 40 years old (OR between ages over 40 versus ages below 40=0.48, 95% CI:0.34 to 0.68, p<0.001), and people who did not chose the Hellenic National Public Health Organization (EODY) to get informed about COVID-19 (OR of EODY versus other sources of information = 0.65, 95% CI:0.46-0.92, p= 0.014).\n\nConclusionsThis study profiled Greek people who do and do not consider NPIs important, mainly as of their demographic features. Focused communicational strategies in certain population subgroups are recommended.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Eleni C. Boutsikari", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Anna Christakou", + "author_inst": "University of West Attica" + }, + { + "author_name": "Michail Elpidoforou", + "author_inst": "University of West Attica" + }, + { + "author_name": "Ioannis Kopsidas", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Nicholas Nikolovienis", + "author_inst": "University of West Attica" + }, + { + "author_name": "Despina Kardara", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Chrissoula C. Boutsikari", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Christos Triantafyllou", + "author_inst": "National and Kapodistrian University of Athens" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.15.20147041", "rel_title": "A systematic review uncovers a wide-gap between COVID-19 in humans and animal models", @@ -1304862,57 +1305718,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.07.16.205799", - "rel_title": "Development of a simple in vitro assay to identify and evaluate nucleotide analogs against SARS-CoV-2 RNA-dependent RNA polymerase", - "rel_date": "2020-07-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.16.205799", - "rel_abs": "Nucleotide analogs targeting viral RNA polymerase have been approved to be an effective strategy for antiviral treatment and are attracting antiviral drugs to combat the current SARS-CoV-2 pandemic. In this report, we develop a robust in vitro nonradioactive primer extension assay to evaluate the incorporation efficiency of nucleotide analog by SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) quantitively. Our results show that many nucleotide analogs can be incorporated into RNA by SARS-CoV-2 RdRp, and that the incorporation of some of them leads to chain termination. The discrimination values of nucleotide analog over those of natural nucleotide were measured to evaluate the incorporation efficiency of nucleotide analog by RdRp. We found that the incorporation efficiency of Remdesivir-TP is higher than ATP, and we did not observe chain termination or delayed chain termination caused by single Remdesivir-TP incorporation, while multiple incorporations of Remdesivir-TP caused chain termination in our assay condition. The incorporation efficiency of Ribavirin-TP and Favipiravir-TP is very low either as ATP or GTP analogs, which suggested that mutagenesis may not be the mechanism of action of those two drugs against SARS-CoV-2. Incorporation of Sofosbuvir-TP is also very low suggesting that sofosbuvir may not be very effective in treating SARS-CoV-2 infection. As a comparison, 2-C-Methyl-GTP can be incorporated into RNA efficiently, and the derivative of 2-C-Methyl-GTP may have therapeutic application in treating SARS-CoV-2 infection. This report provides a simple screening method that should be useful in evaluating nucleotide-based drugs targeting SARS-CoV-2 RdRp, and for studying the mechanism of action of selected nucleotide analog.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Gaofei Lu", - "author_inst": "Global Health Drug Discovery Institute" - }, - { - "author_name": "Xi Zhang", - "author_inst": "Global Health Drug Discovery Institute" - }, - { - "author_name": "Weinan Zheng", - "author_inst": "Global Health Drug Discovery Institute" - }, - { - "author_name": "Jialei Sun", - "author_inst": "Global Health Drug Discovery Institute" - }, - { - "author_name": "Lan Hua", - "author_inst": "Global Health Drug Discovery Institute" - }, - { - "author_name": "Lan Xu", - "author_inst": "Global Health Drug Discovery Institute" - }, - { - "author_name": "Xin-jie Chu", - "author_inst": "Global Health Drug Discovery Institute" - }, - { - "author_name": "Sheng Ding", - "author_inst": "Global Health Drug Discovery Institute" - }, - { - "author_name": "Wen Xiong", - "author_inst": "Global Health Drug Discovery Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.07.16.207308", "rel_title": "Systematic modeling of SARS-CoV-2 protein structures", @@ -1305336,6 +1306141,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.17.20156117", + "rel_title": "Training and reployment of non-specialists is an effective solution for the shortage of health care workers in the COVID-19 pandemic", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156117", + "rel_abs": "ImportanceIn the COVID-19 pandemic many countries encounter problems arising from shortage of specialists. Short intensive training and reployment of non-specialists is an option but the effectiveness is unknown.\n\nObjectiveTo investigate whether there was difference in in-hospital mortality rates between COVID-19 patients managed by a mixed team (including non-specialists who had short intensive training and operated to a strict protocol) and those managed by a specialist team of health care workers.\n\nDesignCohort study, from January 26, 2020 to April 7, 2020, follow up to April 7, 2020.\n\nSettingMulticenter - Wuhan Hankou Hospital and Wuhan Xiehe Hospital, Wuhan, China.\n\nParticipants261 HCWs deployed to Wuhan from Guangdong emergency rescue team and the 269 COVID-19 patients they treated.\n\nExposureAmong 261 health care workers, 130 were in the specialist team and included 33 physicians, 32 of whom (97.0%) of whom were from relevant specialties. Each physician was in charge of 25-27 beds, with a 6-hour shift time. The mixed team included 131 health care workers, with 7 of the 28 physicians (25.0%) from relevant specialties. Each physician managed 12-13 beds, with a 4-hour shift time.\n\nNon-specialists received short-term intensive training and then followed strict management protocols. Specialists practiced as normal.\n\nMain Outcomes and MeasuresMain outcome was in-hospital mortality of COVID-19 patients. Another outcome was rate of SARS-CoV-2 infection in health care workers.\n\nResultsA total of 269 patients were included (144 male). In-hospital mortality rate of patients treated by the specialist teams and the mixed teams was 12.6% (20/159) and 12.7% (14/110) respectively (Difference = -0.1%, 95% CI -8.2% to 7.9%, p=.97). None of the health care workers were infected.\n\nConclusions and RelevanceTraining and reployment of non-specialists is an effective solution for the shortage of health care workers in the COVID-19 pandemic.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWas there difference in mortality rates between COVID-19 patients managed by a mixed team (including non-specialists who had short intensive training and operated to a strict protocol) and those managed by a specialist team of health care workers (HCWs)?\n\nFindingsIn-hospital mortality rate among patients managed by specialist team (130 HCWs, 159 patients) and mixed team (131 HCWs, 110 patients) was 12.6% (20/159) and 12.7% (14/110) respectively (Difference = -0.1%, 95% CI -8.2% to 7.9%, p=.97).\n\nMeaningWith shortage of specialist HCWs, training and reployment of non-specialists is an effective option in the management of COVID-19 patients.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ming Kuang", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen Univeristy" + }, + { + "author_name": "Jianfeng Wu", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Yifeng Luo", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Han Xiao", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Ruiming Liang", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Wenjie Hu", + "author_inst": "The First Affiliate Hospital of Sun Yat-sen University" + }, + { + "author_name": "Shouzhen Cheng", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Qian Zhou", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Sui Peng", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "KarKeung Cheng", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Haipeng Xiao", + "author_inst": "The First Affiliated Hospital of Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.17.20156158", "rel_title": "Multisectoral collaboration for pandemic response and operational support of critical care and emergency departments", @@ -1306792,69 +1307656,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.15.20154930", - "rel_title": "Home-based and remote exercise testing in chronic respiratory disease, during the COVID-19 pandemic and beyond: a rapid review", - "rel_date": "2020-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154930", - "rel_abs": "ObjectivesTo identify exercise tests that are suitable for home-based or remote administration in people with chronic lung disease.\n\nMethodsRapid review of studies that reported home-based or remote administration of an exercise test in people with chronic lung disease, and studies reporting their clinimetric properties.\n\nResults84 studies were included. Tests used at home were the 6-minute walk test (6MWT, 2 studies), sit-to-stand tests (STS, 5 studies), Timed Up and Go (TUG, 4 studies) and step tests (2 studies). Exercise tests administered remotely were the 6MWT (2 studies) and step test (1 study). Compared to centre-based testing the 6MWT distance was similar when performed outdoors but shorter when performed at home (2 studies). The STS, TUG and step tests were feasible, reliable (intra-class correlation coefficients >0.80), valid (concurrent and known groups validity) and moderately responsive to pulmonary rehabilitation (medium effect sizes). These tests elicited less desaturation than the 6MWT, and validated methods to prescribe exercise were not reported.\n\nDiscussionThe STS, step and TUG tests can be performed at home, but do not accurately document desaturation with walking or allow exercise prescription. Patients at risk of desaturation should be prioritised for centre-based exercise testing when this is available.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Anne E Holland", - "author_inst": "Monash University and Alfred Health" - }, - { - "author_name": "Carla Malaguti", - "author_inst": "Federal University of Juiz de Fora, Brazil" - }, - { - "author_name": "Mariana Hoffman", - "author_inst": "Monash University" - }, - { - "author_name": "Aroub Lahham", - "author_inst": "Monash University" - }, - { - "author_name": "Angela T Burge", - "author_inst": "Monash University and Alfred Health" - }, - { - "author_name": "Leona Dowman", - "author_inst": "Monash University and Austin Health" - }, - { - "author_name": "Anthony K May", - "author_inst": "Monash University and Deakin University" - }, - { - "author_name": "Janet Bondarenko", - "author_inst": "Alfred Health" - }, - { - "author_name": "Marnie Graco", - "author_inst": "Alfred Health and Institute for Breathing and Sleep" - }, - { - "author_name": "Gabriella Tikellis", - "author_inst": "Monash University" - }, - { - "author_name": "Joanna Y.T. Lee", - "author_inst": "Monash University" - }, - { - "author_name": "Narelle S Cox", - "author_inst": "Monash University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.07.15.20154567", "rel_title": "Estimate of airborne transmission of SARS-CoV-2 using real time tracking of health care workers.", @@ -1307206,6 +1308007,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.15.20154906", + "rel_title": "Higher Comorbidities and Early Death is Characteristic of Hospitalized African-American Patients with COVID-19", + "rel_date": "2020-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154906", + "rel_abs": "BackgroundAfrican-Americans/Blacks have suffered higher morbidity and mortality from COVID-19 than all other racial groups. This study aims to identify the causes of this health disparity, determine prognostic indicators, and assess efficacy of treatment interventions.\n\nMethodWe performed a retrospective cohort study of clinical features and laboratory data of COVID-19 patients admitted over a five-week period at the height of the pandemic in the United States. This study was performed at an urban academic medical center in New York City, declared a COVID-only facility, serving a majority Black population\n\nResultOf the 1,070 consecutive patients who tested positive for COVID-19, 496 critically ill patients were hospitalized and included in the study. 88% of patients were Black; and a majority (53%) were 61-80 years old with a mean body mass index in the \"obese\" range. 97% had one or more comorbidities. Hypertension was the most common (84%) pre-existing condition followed by diabetes mellitus (57%) and chronic kidney disease (24%). Patients with chronic kidney disease and end-stage renal disease who received hemodialysis were found to have significantly lower mortality, then those who did not receive it, suggesting benefit from hemodialysis (11%, OR, 0.35, CI, 0.17 - 0.69 P=0.001). Age >60 years and coronary artery disease were independent predictors of mortality in multivariate analysis. Cox Proportional Hazards modeling for time to death demonstrated a significantly high ratio for COPD/Asthma, and favorable effects on outcomes for pre-admission ACE inhibitors and ARBs. CRP (180, 283 mg/L), LDH (551, 638 U/L), glucose (182, 163 mg/dL), procalcitonin (1.03, 1.68 ng/mL), and neutrophil / lymphocyte ratio (8.5, 10.0) were predictive of mortality on admission and at 48-96 hrs. Of the 496 inpatients, 48% died, one third of patients died within the first three days of admission. 54/488 patients received invasive mechanical ventilation, of which 87% died and of the remaining patients, 32% died.\n\nCONCLUSIONSCOVID-19 patients in our predominantly Black neighborhood had higher mortality, likely due to higher prevalence of comorbidities. Early dialysis and pre-admission intake of ACE inhibitors/ARBs improved patient outcomes. Early escalation of care based on comorbidities and key laboratory indicators is critical for improving outcomes in African-American patients.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Raavi Gupta", + "author_inst": "State University of New York, Downstate Medical Center" + }, + { + "author_name": "Raag Agrawal", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Zaheer Bukhari", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Absia Jabbar", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Donghai Wang", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "John Diks", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Mohamed Alshal", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Dokpe Yvonne Emechebe", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "F. Charles Brunicardi", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Jason M Lazar", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Robert Chamberlain", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "Aaliya Burza", + "author_inst": "SUNY Downstate Medical Center" + }, + { + "author_name": "M. A. Haseeb", + "author_inst": "SUNY Downstate Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.15.20154971", "rel_title": "Time-dependent dynamic transmission potential and instantaneous reproduction number of COVID-19 pandemic in India.", @@ -1308330,57 +1309198,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.07.14.20153858", - "rel_title": "Community-level SARS-CoV-2 Seroprevalence Survey in urban slum dwellers of Buenos Aires City, Argentina: a participatory research.", - "rel_date": "2020-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.14.20153858", - "rel_abs": "BackgroundBy July 1st, the incidence rate of RT-qPCR SARS-CoV-2 infection was 5.9% in Barrio Padre Mugica, one of the largest slums in Buenos Aires City. This study aimed to establish the seroprevalence of SARS-CoV-2 three months after the first case was reported.\n\nMethodsBetween June 10th and July 1st, a cross-sectional design was carried out on people over 14 years old, selected from a probabilistic sample of households. A finger prick sample was tested by ELISA to detect IgG-class antibodies against SARS-CoV-2. Multilevel model was applied to understand sector, household and individual conditions associated with seroconvert.\n\nResultsPrevalence based on IgG was 53.4% (95%IC 52.8% to 54.1%). Among the IgG positive cases, 15% reported having compatible symptoms at some point in the past two months. There is evidence of within-household clustering effect (rho=0.52; 95% IC 0.36-0.67); living with a PCR-confirmed case doubled the chance of being SARS-CoV2 IgG positive (OR 2.13; 95% IC 1.17-3.85). The highest risk of infection was found in one of the most deprived areas of the slum, the \"Bajo autopista\" sector.\n\nDiscussionHigh seroprevalence is shown, for each symptomatic RT-qPCR-confirmed diagnosis, 9 people were IgG positive, indicating a high rate of undetected (probable asymptomatic) infections. Given that transmission among family members is a leading driver of the diseases spread, it is unsurprising that crowded housing situations in slums are directly associated with higher risk of infection and consequently high seroprevalence levels.\n\nThis study contributes to the understanding of population immunity against SARS-CoV2, its relation to living conditions and viral spread, for future decision making.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Silvana Figar", - "author_inst": "Hospital Italiano de Buenos Aires" - }, - { - "author_name": "Vanina Pagotto", - "author_inst": "Hospital Italiano de Buenos Aires, Argentina" - }, - { - "author_name": "Lorena Luna", - "author_inst": "Salud Comunitaria, Ministerio de Salud de la Ciudad de Buenos Aires, Argentina" - }, - { - "author_name": "Julieta Salto", - "author_inst": "Salud Comunitaria, Ministerio de Salud de la Ciudad de Buenos Aires, Argentina" - }, - { - "author_name": "Magdalena Wagner Manslau", - "author_inst": "Ministerio de Salud de la Ciudad de Buenos Aires, Argentina" - }, - { - "author_name": "Alicia Mistchenko", - "author_inst": "Laboratorio de Virologia, Hospital de Ni\u00f1os Dr R. Gutierrez, Buenos Aires, Argentina" - }, - { - "author_name": "ANDREA GAMARNIK", - "author_inst": "FUNDACION INSTITUTO LELOIR" - }, - { - "author_name": "Ana Maria Gomez Saldano", - "author_inst": "Atencion Primaria, Ministerio de Salud de la Ciudad de Buenos Aires, Argentina." - }, - { - "author_name": "Fernan Quiros", - "author_inst": "Ministro de Salud, Ministerio de Salud de la Ciudad de Buenos Aires, Argentina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.15.20154039", "rel_title": "COVID-19 effective reproductive ratio determination: An application, and analysis of issues and influential factors", @@ -1308640,6 +1309457,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.07.13.20152231", + "rel_title": "A Quantitative Lung Computed Tomography Image Feature for Multi-Center Severity Assessment of COVID-19", + "rel_date": "2020-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152231", + "rel_abs": "The COVID-19 pandemic has affected millions and congested healthcare systems globally. Hence an objective severity assessment is crucial in making therapeutic decisions judiciously. Computed Tomography (CT)-scans can provide demarcating features to identify severity of pneumonia --commonly associated with COVID-19--in the affected lungs. Here, a quantitative severity assessing chest CT image feature is demonstrated for COVID-19 patients. An open-source multi-center Italian database1 was used, among which 60 cases were incorporated in the study (age 27-86, 71% males) from 27 CT imaging centers. Lesions in the form of opacifications, crazy-paving patterns, and consolidations were segmented. The severity determining feature --Lnorm was quantified and established to be statistically distinct for the three --mild, moderate, and severe classes (p-value<0.0001). The thresholds of Lnorm for a 3-class classification were determined based on the optimum sensitivity/specificity combination from Receiver Operating Characteristic (ROC) analyses. The feature Lnorm classified the cases in the three severity categories with 86.88% accuracy. Substantial to almost-perfect intra-rater and inter-rater agreements were achieved involving expert and non-expert based evaluations ({kappa}-score 0.79-0.97). We trained machine learning based classification models and showed Lnorm alone has a superior diagnostic accuracy over standard image intensity and texture features. Classification accuracy was further increased when Lnorm was used for 2-class classification i.e. to delineate the severe cases from non-severe ones with a high sensitivity (97.7%), and specificity (97.49%). Therefore, key highlights of this severity assessment feature are accuracy, lower dependency on expert availability, and wide utility across different imaging centers.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Biswajoy Ghosh", + "author_inst": "Indian Institute of Technology Kharagpur" + }, + { + "author_name": "Nikhil Kumar", + "author_inst": "Indian Institute of Technology Kharagpur" + }, + { + "author_name": "Nitisha Singh", + "author_inst": "National Institute of Technology Durgapur" + }, + { + "author_name": "Anup K Sadhu", + "author_inst": "EKO CT and MRI Scan Centre, Medical College and Hospitals Campus, Kolkata" + }, + { + "author_name": "Nirmalya Ghosh", + "author_inst": "Indian Institute of Technology Kharagur" + }, + { + "author_name": "Pabitra Mitra", + "author_inst": "Indian Institute of Technology Kharagur" + }, + { + "author_name": "Jyotirmoy Chatterjee", + "author_inst": "Indian Institute of Technology Kharagur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.07.13.20153130", "rel_title": "Asthma in COVID-19: An extra chain fitting around the neck?", @@ -1309896,29 +1310756,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.13.20152991", - "rel_title": "Climate & BCG: Effects on COVID-19 DeathGrowth Rates", - "rel_date": "2020-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152991", - "rel_abs": "Multiple studies have suggested the spread of COVID-19 is affected by factors such as climate, BCG vaccinations, pollution and blood type. We perform a joint study of these factors using the death growth rates of 40 regions worldwide with both machine learning and Bayesian methods. We find weak, non-significant (< 3{sigma}) evidence for temperature and relative humidity as factors in the spread of COVID-19 but little or no evidence for BCG vaccination prevalence or PM2.5 pollution. The only variable detected at a statistically significant level (>3{sigma}) is the rate of positive COVID-19 tests, with higher positive rates correlating with higher daily growth of deaths.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Chris Finlay", - "author_inst": "South Africa Radio Astronomy Observatory" - }, - { - "author_name": "Bruce A Bassett", - "author_inst": "University of Cape Town" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.12.20152074", "rel_title": "Association between epidemic dynamics of Covid-19 infection and ABO blood group types", @@ -1310222,6 +1311059,33 @@ "type": "confirmatory results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.15.176933", + "rel_title": "Alignment-free machine learning approaches for the lethality prediction of potential novel human-adapted coronavirus using genomic nucleotide", + "rel_date": "2020-07-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.15.176933", + "rel_abs": "A newly emerging novel coronavirus appeared and rapidly spread worldwide and World Health Organization declared a pandemic on March 11, 2020. The roles and characteristics of coronavirus have captured much attention due to its power of causing a wide variety of infectious diseases, from mild to severe on humans. The detection of the lethality of human coronavirus is key to estimate the viral toxicity and provide perspective for treatment. We developed alignment-free machine learning approaches for an ultra-fast and highly accurate prediction of the lethality of potential human-adapted coronavirus using genomic nucleotide. We performed extensive experiments through six different feature transformation and machine learning algorithms in combination with digital signal processing to infer the lethality of possible future novel coronaviruses using previous existing strains. The results tested on SARS-CoV, MERS-Cov and SARS-CoV-2 datasets show an average 96.7% prediction accuracy. We also provide preliminary analysis validating the effectiveness of our models through other human coronaviruses. Our study achieves high levels of prediction performance based on raw RNA sequences alone without genome annotations and specialized biological knowledge. The results demonstrate that, for any novel human coronavirus strains, this alignment-free machine learning-based approach can offer a reliable real-time estimation for its viral lethality.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rui YIN", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Zihan Luo", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Chee Keong Kwoh", + "author_inst": "Nanyang Technological University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.14.203463", "rel_title": "Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: An endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations", @@ -1311682,145 +1312546,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.14.201616", - "rel_title": "SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2", - "rel_date": "2020-07-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.14.201616", - "rel_abs": "We show that SARS-CoV-2 spike protein interacts with cell surface heparan sulfate and angiotensin converting enzyme 2 (ACE2) through its Receptor Binding Domain. Docking studies suggest a putative heparin/heparan sulfate-binding site adjacent to the domain that binds to ACE2. In vitro, binding of ACE2 and heparin to spike protein ectodomains occurs independently and a ternary complex can be generated using heparin as a template. Contrary to studies with purified components, spike protein binding to heparan sulfate and ACE2 on cells occurs codependently. Unfractionated heparin, non-anticoagulant heparin, treatment with heparin lyases, and purified lung heparan sulfate potently block spike protein binding and infection by spike protein-pseudotyped virus and SARS-CoV-2 virus. These findings support a model for SARS-CoV-2 infection in which viral attachment and infection involves formation of a complex between heparan sulfate and ACE2. Manipulation of heparan sulfate or inhibition of viral adhesion by exogenous heparin may represent new therapeutic opportunities.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Thomas Mandel Clausen", - "author_inst": "Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA." - }, - { - "author_name": "Daniel R Sandoval", - "author_inst": "Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA." - }, - { - "author_name": "Charlotte B Spliid", - "author_inst": "Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA." - }, - { - "author_name": "Jessica Pihl", - "author_inst": "Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA." - }, - { - "author_name": "Chelsea D Painter", - "author_inst": "Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA." - }, - { - "author_name": "Bryan E Thacker", - "author_inst": "TEGA Therapeutics, Inc., 3550 General Atomics Court, G02-102, San Diego, CA 92121, USA." - }, - { - "author_name": "Charles A Glass", - "author_inst": "TEGA Therapeutics, Inc., 3550 General Atomics Court, G02-102, San Diego, CA 92121, USA." - }, - { - "author_name": "Anoop Narayanan", - "author_inst": "Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA." - }, - { - "author_name": "Sydney A Majowicz", - "author_inst": "Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA." - }, - { - "author_name": "Yang Zhang", - "author_inst": "Copenhagen Center for Glycomics, Department of Molecular and Cellular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark." - }, - { - "author_name": "Jonathan L Torres", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Gregory J Golden", - "author_inst": "Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA." - }, - { - "author_name": "Ryan Porell", - "author_inst": "Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA." - }, - { - "author_name": "Aaron F Garretson", - "author_inst": "Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." - }, - { - "author_name": "Logan Laubach", - "author_inst": "Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA." - }, - { - "author_name": "Xin Yin", - "author_inst": "Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute 10901 North Torrey Pines Road," - }, - { - "author_name": "Yuan Pu", - "author_inst": "Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute 10901 North Torrey Pines Road," - }, - { - "author_name": "Blake Hauser", - "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge MA 02139, USA." - }, - { - "author_name": "Timothy M Caradonna", - "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge MA 02139, USA." - }, - { - "author_name": "Benjamin P Kellman", - "author_inst": "Department of Bioengineering, University of California, San Diego." - }, - { - "author_name": "Cameron Martino", - "author_inst": "Department of Bioengineering, University of California, San Diego." - }, - { - "author_name": "Philip L.S.M. Gordts", - "author_inst": "Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." - }, - { - "author_name": "Sandra L Leibel", - "author_inst": "Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA 92093, USA." - }, - { - "author_name": "Summit K Chanda", - "author_inst": "Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute 10901 North Torrey Pines Road," - }, - { - "author_name": "Aaron G Schmidt", - "author_inst": "Ragon Institute of MGH, MIT and Harvard, Cambridge MA 02139, USA." - }, - { - "author_name": "Kamil Godula", - "author_inst": "Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA." - }, - { - "author_name": "Joyce Jose", - "author_inst": "Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA." - }, - { - "author_name": "Kevin D Corbett", - "author_inst": "Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA." - }, - { - "author_name": "Andrew B Ward", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Aaron F Carlin", - "author_inst": "Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." - }, - { - "author_name": "Jeffrey D Esko", - "author_inst": "Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.13.201509", "rel_title": "SARS-CoV-2 uses clathrin-mediated endocytosis to gain access into cells", @@ -1312024,6 +1312749,73 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.07.14.202549", + "rel_title": "Targeting heparan sulfate proteoglycan-assisted endocytosis as a COVID-19 therapeutic option", + "rel_date": "2020-07-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.14.202549", + "rel_abs": "The cell entry of SARS-CoV-2 has emerged as an attractive drug repurposing target for COVID-19. Here we combine genetics and chemical perturbation to demonstrate that ACE2-mediated entry of SARS-CoV and CoV-2 requires the cell surface heparan sulfate (HS) as an assisting cofactor: ablation of genes involved in HS biosynthesis or incubating cells with a HS mimetic both inhibit Spike-mediated viral entry. We show that heparin/HS binds to Spike directly, facilitates the attachment of viral particles to the cell surface to promote cell entry. We screened approved drugs and identified two classes of inhibitors that act via distinct mechanisms to target this entry pathway. Among the drugs characterized, Mitoxantrone is a potent HS inhibitor, while Sunitinib and BNTX disrupt the actin network to indirectly abrogate HS-assisted viral entry. We further show that drugs of the two classes can be combined to generate a synergized activity against SARS-CoV-2-induced cytopathic effect. Altogether, our study establishes HS as an attachment factor that assists SARS coronavirus cell entry, and reveals drugs capable of targeting this important step in the viral life cycle.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Qi Zhang", + "author_inst": "NIH" + }, + { + "author_name": "Catherine Chen", + "author_inst": "NIH" + }, + { + "author_name": "Manju Swaroop", + "author_inst": "NIH" + }, + { + "author_name": "Miao Xu", + "author_inst": "NIH" + }, + { + "author_name": "Lihui Wang", + "author_inst": "NIH" + }, + { + "author_name": "Juhyung Lee", + "author_inst": "NIH" + }, + { + "author_name": "Manisha Pradhan", + "author_inst": "NIH" + }, + { + "author_name": "Min Shen", + "author_inst": "NIH" + }, + { + "author_name": "Zhiji Luo", + "author_inst": "NIH" + }, + { + "author_name": "Yue Xu", + "author_inst": "NIH" + }, + { + "author_name": "Wenwei Huang", + "author_inst": "NIH" + }, + { + "author_name": "Wei Zheng", + "author_inst": "NIH" + }, + { + "author_name": "Yihong Ye", + "author_inst": "NIH" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.07.13.20152793", "rel_title": "At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR based tests?: A systematic review of individual participant data", @@ -1313240,33 +1314032,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.11.20151035", - "rel_title": "Knowledge and Behaviors towards COVID-19 among University of Aleppo Students: An Online Cross-sectional Survey", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.11.20151035", - "rel_abs": "BackgroundCoronavirus Disease 2019 (COVID-19) is an infection caused by a novel coronavirus that affects respiratory tract. Peoples awareness and knowledge of, and behavior and attitude toward COVID-19 are scarcely investigated, making medical literature related to this point poor. we aim to measure the knowledge of, and the reaction to COVID-19 among University of Aleppo students in Syria, and the determinants of their awareness and behavior regarding this disease.\n\nMaterials and MethodsThis was an online, questionnaire-based cross-sectional study, that was conducted from 21st March to 30 March 2020. We included undergraduate students of the University of Aleppo (Syria). The questionnaire consisted of three sections: Demographics,knowledge and behaviours. Every participants knowledge was scored from 0-13 depending on the number of correct answers in the knowledge section. The correctness was judged depending on WHO recommendations at the time of questionnaire administration. P-value of 0.05 was considered significant.\n\nResultsAmong this well-educated and predominantly medical and health-related students, 682 (45.4%) students had a good knowledge level, which is somehow disappointing. The current study shows that 1st year students and non-medical specialties students and smokers had significantly lower knowledge levels than others. On contrary, residing with less people-which may indicate a higher socioeconomic status-, was associated with a higher knowledge level. We also found that commitment to preventive measures was in general satisfying and correlated significantly with knowledge level and gender in most cases.\n\nConclusionJunior students, non-medical specialties, smokers and those who live with high number of people are vulnerable to less knowledge level and awareness campaigns should concentrate on them. Increasing awareness is useful to increase commitment to preventive measures, and groups that have less adherence to preventive measures, as described in detail, should be taken into consideration while designing public health responses. Finally, we should be aware of the negative impact of quarantine on public health to take it into consideration for current campaigns and future policies.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "aos mohammed alhamid", - "author_inst": "university of aleppo" - }, - { - "author_name": "Ahmad Mohammed Alhamid", - "author_inst": "university of aleppo" - }, - { - "author_name": "ziad aljarad", - "author_inst": "Aleppo University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.11.20150193", "rel_title": "Impact of COVID-19 Lockdown Policy on Homicide, Suicide, and Motor Vehicle Deaths in Peru", @@ -1313602,6 +1314367,233 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.07.13.20152355", + "rel_title": "State-level tracking of COVID-19 in the United States", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152355", + "rel_abs": "As of 1st June 2020, the US Centers for Disease Control and Prevention reported 104,232 confirmed or probable COVID-19-related deaths in the US. This was more than twice the number of deaths reported in the next most severely impacted country. We jointly modelled the US epidemic at the state-level, using publicly available death data within a Bayesian hierarchical semi-mechanistic framework. For each state, we estimate the number of individuals that have been infected, the number of individuals that are currently infectious and the time-varying reproduction number (the average number of secondary infections caused by an infected person). We used changes in mobility to capture the impact that non-pharmaceutical interventions and other behaviour changes have on the rate of transmission of SARS-CoV-2. Nationally, we estimated 3.7% [3.4%-4.0%] of the population had been infected by 1st June 2020, with wide variation between states, and approximately 0.01% of the population was infectious. We also demonstrated that good model forecasts of deaths for the next 3 weeks with low error and good coverage of our credible intervals.", + "rel_num_authors": 53, + "rel_authors": [ + { + "author_name": "H Juliette T Unwin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Swapnil Mishra", + "author_inst": "Imperial College London" + }, + { + "author_name": "Valerie C Bradley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Axel Gandy", + "author_inst": "Imperial College London" + }, + { + "author_name": "Thomas A Mellan", + "author_inst": "Imperial College" + }, + { + "author_name": "Helen Coupland", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jonathan Ish-Horowicz", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michaela Andrea Christine Vollmer", + "author_inst": "Imperial College London" + }, + { + "author_name": "Charles Whittaker", + "author_inst": "Imperial College London" + }, + { + "author_name": "Sarah L Filippi", + "author_inst": "Imperial College London" + }, + { + "author_name": "Xiaoyue Xi", + "author_inst": "Imperial College London" + }, + { + "author_name": "M\u00e9lodie Monod", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver Ratmann", + "author_inst": "Imperial College London" + }, + { + "author_name": "Michael Hutchinson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Fabian Valka", + "author_inst": "None" + }, + { + "author_name": "Harrison Zhu", + "author_inst": "Imperial College London" + }, + { + "author_name": "Iwona Hawryluk", + "author_inst": "Imperial College London" + }, + { + "author_name": "Philip Milton", + "author_inst": "Imperial College London" + }, + { + "author_name": "Kylie E C Ainslie", + "author_inst": "Imperial College London" + }, + { + "author_name": "Marc Baguelin", + "author_inst": "Imperial College London" + }, + { + "author_name": "Adhiratha Boonyasiri", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nick F Brazeau", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lorenzo Cattarino", + "author_inst": "Imperial College London" + }, + { + "author_name": "Zulma M Cucunub\u00e1", + "author_inst": "Imperial College London" + }, + { + "author_name": "Gina Cuomo-Dannenburg", + "author_inst": "Imperial College London" + }, + { + "author_name": "Ilaria Dorigatti", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver D Eales", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jeffrey W Eaton", + "author_inst": "Imperial College London" + }, + { + "author_name": "Sabinee L van Elsland", + "author_inst": "Imperial College London" + }, + { + "author_name": "Richard G FitzJohn", + "author_inst": "Imperial College London" + }, + { + "author_name": "Katy A M Gaythorpe", + "author_inst": "Imperial College London" + }, + { + "author_name": "William Green", + "author_inst": "Imperial College London" + }, + { + "author_name": "Wes Hinsley", + "author_inst": "Imperial College London" + }, + { + "author_name": "Benjamin Jeffrey", + "author_inst": "Imperial College London" + }, + { + "author_name": "Edward Knock", + "author_inst": "Imperial College London" + }, + { + "author_name": "Daniel J Laydon", + "author_inst": "Imperial College London" + }, + { + "author_name": "John Lees", + "author_inst": "Imperial College London" + }, + { + "author_name": "Gemma Nedjati-Gilani", + "author_inst": "Imperial College London" + }, + { + "author_name": "Pierre Nouvellet", + "author_inst": "University of Sussex" + }, + { + "author_name": "Lucy C Okell", + "author_inst": "Imperial College London" + }, + { + "author_name": "Kris V Parag", + "author_inst": "Imperial College London" + }, + { + "author_name": "Igor Siveroni", + "author_inst": "Imperial College London" + }, + { + "author_name": "Hayley A Thompson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Patrick Walker", + "author_inst": "Imperial College London" + }, + { + "author_name": "Caroline E Walters", + "author_inst": "Imperial College London" + }, + { + "author_name": "Oliver J Watson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Lilith K Whittles", + "author_inst": "Imperial College London" + }, + { + "author_name": "Azra Ghani", + "author_inst": "Imperial College London" + }, + { + "author_name": "Neil M Ferguson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Steven Riley", + "author_inst": "Dept Inf Dis Epi, Imperial College" + }, + { + "author_name": "Christl A. Donnelly", + "author_inst": "Imperial College London" + }, + { + "author_name": "Samir Bhatt", + "author_inst": "Imperial College London" + }, + { + "author_name": "Seth Flaxman", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.12.20152157", "rel_title": "Quantifying Respiratory Airborne Particle Dispersion Control Through Improvised Reusable Masks", @@ -1314814,45 +1315806,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.13.200188", - "rel_title": "Single-cell analysis reveals the function of lung progenitor cells in COVID-19 patients", - "rel_date": "2020-07-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.13.200188", - "rel_abs": "The high mortality of severe 2019 novel coronavirus disease (COVID-19) cases is mainly caused by acute respiratory distress syndrome (ARDS), which is characterized by increased permeability of the alveolar epithelial barriers, pulmonary edema and consequently inflammatory tissue damage. Some but not all patients showed full functional recovery after the devastating lung damage, and so far there is little knowledge about the lung repair process1. Here by analyzing the bronchoalveolar lavage fluid (BALF) of COVID-19 patients through single cell RNA-sequencing (scRNA-Seq), we found that in severe (or critical) cases, there is remarkable expansion of TM4SF1+ and KRT5+ lung progenitor cells. The two distinct populations of progenitor cells could play crucial roles in alveolar cell regeneration and epithelial barrier re-establishment, respectively. In order to understand the function of KRT5+ progenitors in vivo, we transplanted a single KRT5+ cell-derived cell population into damaged mouse lung. Time-course single-cell transcriptomic analysis showed that the transplanted KRT5+ progenitors could long-term engrafted into host lung and differentiate into HOPX+ OCLN+ alveolar barrier cell which restored the epithelial barrier and efficiently prevented inflammatory cell infiltration. Similar barrier cells were also identified in some COVID-19 patients with massive leukocyte infiltration. Altogether this work uncovered the mechanism that how various lung progenitor cells work in concert to prevent and replenish alveoli loss post severe SARS-CoV-2 infection.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Wei Zuo", - "author_inst": "Tongji University" - }, - { - "author_name": "Zixian Zhao", - "author_inst": "Tongji University" - }, - { - "author_name": "Yu Zhao", - "author_inst": "Tongji University" - }, - { - "author_name": "Yueqing Zhou", - "author_inst": "Tongji University" - }, - { - "author_name": "Xiaofan Wang", - "author_inst": "Tongji University" - }, - { - "author_name": "Ting Zhang", - "author_inst": "Regend Therapeutics" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.07.12.199687", "rel_title": "Modulating the transcriptional landscape of SARS-CoV-2 as an effective method for developing antiviral compounds", @@ -1315048,6 +1316001,33 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2020.07.12.199364", + "rel_title": "Flexibility and mobility of SARS-CoV-2-related protein structures", + "rel_date": "2020-07-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.12.199364", + "rel_abs": "The worldwide CoVid-19 pandemic has led to an unprecedented push across the whole of the scientific community to develop a potent antiviral drug and vaccine as soon as possible. Existing academic, governmental and industrial institutions and companies have engaged in large-scale screening of existing drugs, in vitro, in vivo and in silico. Here, we are using in silico modelling of SARS-CoV-2 drug targets, i.e. SARS-CoV-2 protein structures as deposited on the Protein Databank (PDB). We study their flexibility, rigidity and mobility, an important first step in trying to ascertain their dynamics for further drug-related docking studies. We are using a recent protein flexibility modelling approach, combining protein structural rigidity with possible motion consistent with chemical bonds and sterics. For example, for the SARS-CoV-2 spike protein in the open configuration, our method identifies a possible further opening and closing of the S1 subunit through movement of SB domain. With full structural information of this process available, docking studies with possible drug structures are then possible in silico. In our study, we present full results for the more than 200 thus far published SARS-CoV-2-related protein structures in the PDB.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rudolf A Roemer", + "author_inst": "University of Warwick" + }, + { + "author_name": "Navodya Sophie Roemer", + "author_inst": "University of Lincoln" + }, + { + "author_name": "Anne Katrine Wallis", + "author_inst": "University of Warwick" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.07.10.20150045", "rel_title": "Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka", @@ -1316164,41 +1317144,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.10.20151175", - "rel_title": "Epidemiological characteristics of COVID-19 patients in Samarinda, East Kalimantan, Indonesia", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20151175", - "rel_abs": "IntroductionCoronavirus Disease (COVID-19) is caused by SARS-CoV-2 infection. Indonesia announced the first COVID-19 case on 2 March 2020. East Kalimantan has been determined as the new capital of Indonesia since 2019. This makes Samarinda as the capital of East Kalimantan has been focused for its capability of handling COVID-19 patients. We report the epidemiological characteristics and immunofluorescence assay results of these patients.\n\nMethodsAll patients with positive confirmed COVID-19 by RT-PCR were admitted to hospitals and quarantine center in Samarinda. We retrospectively analyzed data from the daily report of the Samarinda City and East Kalimantan Health Office information system.\n\nResultsBy June 25, 2020, 64 patients had been identified as having positive confirmed COVID-19. The mean age of the patients was 37.3 {+/-} 13.8 years. Most of the patients were men (57 [90.6%] patients). Thirty-nine COVID-19 patients were imported cases with a history of traveling from South Sulawesi. Most of the patients were admitted to the Quarantine Center of Samarinda City. The mean duration from the first hospital admission for isolation to discharge was 25.6 {+/-} 13.1 days. There was only one death case of COVID-19 patients in Samarinda. There were the highest confirmed cases of COVID-19 in Samarinda in early June 2020. There was a declining trend in the age of COVID-19 patients and the duration of isolation time in the hospital.\n\nDiscussionImported cases still contributed to the increase of COVID-19 cases in Samarinda. Younger age of COVID-19 patients was more involved in frequent mobility which makes them cause the spread of the disease. Activation of the national reference laboratory for the COVID-19 examination in Samarinda has reduced the length of time patients treated in hospitals.\n\nConclusionThe epidemiological characteristics of COVID-19 patients show the ability of local governments to deal with this pandemic. This can be seen from the low case fatality rate in Samarinda.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Swandari Paramita", - "author_inst": "Mulawarman University" - }, - { - "author_name": "Ronny Isnuwardana", - "author_inst": "Mulawarman University" - }, - { - "author_name": "Anton Rahmadi", - "author_inst": "Mulawarman University" - }, - { - "author_name": "Osa Rafshodia", - "author_inst": "Samarinda City Health Office" - }, - { - "author_name": "Ismid Kusasih", - "author_inst": "Samarinda City Health Office" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.10.20150755", "rel_title": "Serology in Children with Multisystem Inflammatory Syndrome (MIS-C) associated with COVID-19", @@ -1316578,6 +1317523,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.11.20151365", + "rel_title": "Decreased serum levels of inflammaging marker miR-146a are associated with clinical response to tocilizumab in COVID-19 patients", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.11.20151365", + "rel_abs": "BackgroundCurrent COVID-19 pandemic poses an unprecedented threat to global health and healthcare systems. At least in western countries, the most amount of the death toll is accounted by old people affected by age-related diseases. In this regard, we proposed that COVID-19 severity may be tightly related to inflammaging, i.e. the age-related onset of inflammation, which is responsible for age-related diseases. It has been reported that systemic hyper-inflammation may turn to be detrimental in COVID-19 patients.\n\nObjectiveHere, we exploited a recently closed clinical trial (NCT04315480) on the anti-IL-6 drug tocilizumab to assess whether microRNAs regulating inflammaging can be assessed as biomarkers of drug response and outcome.\n\nMethodsSerum levels of miR-146a-5p, -21-5p, and -126-3p were quantified by RT-PCR and Droplet Digital PCR by two independent laboratories on 30 patients with virologically confirmed COVID-19, characterized by multifocal interstitial pneumonia confirmed by CT-scan and requiring oxygen therapy, and 29 age- and gender-matched healthy control subjects. COVID-19 patients were treated with a single-dose intravenous infusion of 8 mg/kg tocilizumab and categorized into responders and non-responders.\n\nResultsWe showed that COVID-19 patients who did not respond to tocilizumab have lower serum levels of miR-146a-5p after the treatment (p=0.007). Moreover, among non-responders, those with the lowest serum levels of miR-146a-5p experienced the most adverse outcome (p=0.008).\n\nConclusionOur data show that blood-based biomarkers, such as miR-146a-5p, can provide a molecular link between inflammaging and COVID-19 clinical course, thus allowing to enlarge the drug armory against this worldwide health threat.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jacopo Sabbatinelli", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Angelica Giuliani", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Giulia Matacchione", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Silvia Latini", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Noemi Laprovitera", + "author_inst": "University of Bologna" + }, + { + "author_name": "Giovanni Pomponio", + "author_inst": "Azienda Ospedaliera \"Ospedali Riuniti\" di Ancona" + }, + { + "author_name": "Alessia Ferrarini", + "author_inst": "Azienda Ospedaliera \"Ospedali Riuniti\" di Ancona" + }, + { + "author_name": "Silvia Svegliati Baroni", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Marianna Pavani", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Marco Moretti", + "author_inst": "Azienda Ospedaliera \"Ospedali Riuniti\" di Ancona" + }, + { + "author_name": "Armando Gabrielli", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Antonio Domenico Procopio", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + }, + { + "author_name": "Manuela Ferracin", + "author_inst": "University of Bologna" + }, + { + "author_name": "Massimiliano Bonaf\u00e8", + "author_inst": "University of Bologna" + }, + { + "author_name": "Fabiola Olivieri", + "author_inst": "Universit\u00e0 Politecnica delle Marche" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.10.20150904", "rel_title": "Serological Tests for SARS-CoV-2 Coronavirus by Commercially Available Point-of-Care and Laboratory Diagnostics in Pre-COVID-19 Samples in Japan", @@ -1317826,45 +1318846,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.07.10.20133801", - "rel_title": "COVID-19 causing HELLP-like syndrome in pregnancy and role of angiogenic factors for differential diagnosis", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20133801", - "rel_abs": "ImportanceThe clinical presentation of hemolysis, elevated liver enzymes, and low platelet count (HELLP) syndrome is one of the more severe forms of preeclampsia. COVID-19 infection exhibits signs that are shared with preeclampsia and HELLP syndrome, which may lead to needless interventions and iatrogenic preterm delivery.\n\nObjectiveWe evaluated the prevalence of HELLP-like signs in pregnant women admitted for COVID-19 and the value of angiogenic factors to rule out preeclampsia.\n\nMethodsa consecutive series of 27 pregnant women beyond 20 weeks of gestation, with symptomatic COVID-19. Clinical and analytical features were recorded and those cases with signs of HELLP syndrome were tested for sFlt-1/PlGF ratio.\n\nResultsSeven patients (25.9%) presented at least one sign of suspected HELLP syndrome, of which 2 (7.4%) were diagnosed clinically with PE because of hypertension and high transaminases and 5 (18.5%) had only elevated transaminases. sFlt-1/PlGF ratio was normal in 6 of 7.\n\nConclusionSymptomatic COVID-19 may simulate severe preeclampsia in pregnancy. Angiogenic factors may be essential to avoid false diagnosis and needless interventions.\n\nKEY-POINTSO_ST_ABSQuestionC_ST_ABSDo pregnant women with symptomatic COVID-19 infection exhibit signs shared with preeclampsia and HELLP syndrome? Are these conditions ruled out by the measurement of angiogenic factors?\n\nFindingsIn series of 27 pregnancies with symptomatic COVID-19 infection, 7 presented at least one sign of suspected HELLP syndrome. In 6 of them, the level of angiogenic factors ruled out preeclampsia.\n\nMeaningSymptomatic COVID-19 may simulate severe pregnancy in pregnancy. Angiogenic factors may be essential to avoid false diagnosis and needless interventions.\n\nThese data were presented in a Virtual Symposium on Covid-19 and Pregnancy on 17 April: 2020:(http://medicinafetalbarcelona.org/simposiocovid19/ [Spanish] and https://medicinafetalbarcelona.org/symposiumcovid19/ [English]", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Francesc Figueras", - "author_inst": "Hospital Clinic. University of Barcelona" - }, - { - "author_name": "Elisa LLurba", - "author_inst": "Servei de Ginecologia i Obstetricia. Hospital de la Santa Creu i Sant Pau" - }, - { - "author_name": "Raigam Martinez-Portilla", - "author_inst": "Fetal i+D Fetal Medicine Research Center, BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clinic and Hospital Sant Joan de Deu), I" - }, - { - "author_name": "Josefina Mora", - "author_inst": "Servei de Bioquimica Clinica. Hospital de la Santa Creu i Sant Pau" - }, - { - "author_name": "Fatima Crispi", - "author_inst": "Fetal i+D Fetal Medicine Research Center, BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clinic and Hospital Sant Joan de Deu), I" - }, - { - "author_name": "Eduard Gratacos", - "author_inst": "Fetal i+D Fetal Medicine Research Center, BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clinic and Hospital Sant Joan de Deu), I" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2020.07.08.20147561", "rel_title": "SARS-CoV-2 RNA extraction using magnetic beads for rapid large-scale testing by RT-qPCR and RT-LAMP", @@ -1318232,6 +1319213,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.11.198770", + "rel_title": "ACE2-expressing endothelial cells in aging mouse brain", + "rel_date": "2020-07-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.11.198770", + "rel_abs": "Angiotensin-converting enzyme 2 (ACE2) is a key receptor mediating the entry of SARS-CoV-2 into the host cell. Through a systematic analysis of publicly available mouse brain sc/snRNA-seq data, we found that ACE2 is specifically expressed in small sub-populations of endothelial cells and mural cells, namely pericytes and vascular smooth muscle cells. Further, functional changes in viral mRNA transcription and replication, and impaired blood-brain barrier regulation were most prominently implicated in the aged, ACE2-expressing endothelial cells, when compared to the young adult mouse brains. Concordant EC transcriptomic changes were further found in normal aged human brains. Overall, this work reveals an outline of ACE2 distribution in the mouse brain and identify putative brain host cells that may underlie the selective susceptibility of the aging brain to viral infection.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "SU Bin Lim", + "author_inst": "Johns Hopkins University, School of Medicine" + }, + { + "author_name": "Valina L. Dawson", + "author_inst": "Johns Hopkins University, School of Medicine" + }, + { + "author_name": "Ted M. Dawson", + "author_inst": "Johns Hopkins University, School of Medicine" + }, + { + "author_name": "Sung-Ung Kang", + "author_inst": "Johns Hopkins University, School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2020.07.06.20147827", "rel_title": "Clinical Features of Hemodialysis (HD) patients confirmed with Coronavirus Disease 2019 (COVID-19): a Retrospective Case-Control Study", @@ -1319700,69 +1320712,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.07.09.20149849", - "rel_title": "Severe SAR-CoV-2 infection in humans is defined by a shift in the serum lipidome resulting indysregulation of eicosanoid immune mediators", - "rel_date": "2020-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20149849", - "rel_abs": "Introductory ParagraphThe COVID-19 pandemic has affected more than 10 million people worldwide with mortality exceeding half a million patients. Risk factors associated with severe disease and mortality include advanced age, hypertension, diabetes, and obesity.1 Clear mechanistic understanding of how these comorbidities converge to enable severe infection is lacking. Notably each of these risk factors pathologically disrupts the lipidome and this disruption may be a unifying feature of severe COVID-19.1-7 Here we provide the first in depth interrogation of lipidomic changes, including structural-lipids as well as the eicosanoids and docosanoids lipid mediators (LMs), that mark COVID-19 disease severity. Our data reveal that progression from moderate to severe disease is marked by a loss of specific immune regulatory LMs and increased pro-inflammatory species. Given the important immune regulatory role of LMs, these data provide mechanistic insight into the immune balance in COVID-19 and potential targets for therapy with currently approved pharmaceuticals.8", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Benjamin Schwarz", - "author_inst": "Rocky Mountain Laboratories/NIAID/NIH" - }, - { - "author_name": "Lokesh Sharma", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Lydia Roberts", - "author_inst": "Rocky Mountain Laboratories/NIAID/NIH" - }, - { - "author_name": "Xiaohua Peng", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Santos Bermejo", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Ian Leighton", - "author_inst": "Rocky Mountain Laboratories/NIAID/NIH" - }, - { - "author_name": "Arnau Casanovas Massana", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Shelli Farhadian", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Albert Ko", - "author_inst": "Yale University School of Public Health" - }, - { - "author_name": "- IMPACT Yale IMPACT team", - "author_inst": "" - }, - { - "author_name": "Charles DelaCruz", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Catharine M Bosio", - "author_inst": "Rocky Mountain Laboratories" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.09.20149864", "rel_title": "Comparison of SARS-CoV-2 serological tests with different antigen targets", @@ -1320142,6 +1321091,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.08.20149146", + "rel_title": "Recurrent Neural Reinforcement Learning for Counterfactual Evaluation of Public Health Interventions on the Spread of Covid-19 in the world", + "rel_date": "2020-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20149146", + "rel_abs": "As the Covid-19 pandemic soars around the world, there is urgent need to forecast the expected number of cases worldwide and the length of the pandemic before receding and implement public health interventions for significantly stopping the spread of Covid-19. Widely used statistical and computer methods for modeling and forecasting the trajectory of Covid-19 are epidemiological models. Although these epidemiological models are useful for estimating the dynamics of transmission of epidemics, their prediction accuracies are quite low. Alternative to the epidemiological models, the reinforcement learning (RL) and causal inference emerge as a powerful tool to select optimal interventions for worldwide containment of Covid-19. Therefore, we formulated real-time forecasting and evaluation of multiple public health intervention problems into off-policy evaluation (OPE) and counterfactual outcome forecasting problems and integrated RL and recurrent neural network (RNN) for exploring public health intervention strategies to slow down the spread of Covid-19 worldwide, given the historical data that may have been generated by different public health intervention policies. We applied the developed methods to real data collected from January 22, 2020 to July 30, 2020 for real-time forecasting the confirmed cases of Covid-19 across the world. We observed that the number of new cases of Covid-19 worldwide reached a peak (407,205) on July 24, 2020 and forecasted that the number of laboratory-confirmed cumulative cases of Covid-19 will pass 20 million as of August 22, 2020. The results showed that outbreak of Covid-19 worldwide has peaked and is on the decline", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Qiyang Ge", + "author_inst": "Fudan University" + }, + { + "author_name": "Zixin Hu", + "author_inst": "fudan University" + }, + { + "author_name": "Kai Zhang", + "author_inst": "University of Texas School of Public Health" + }, + { + "author_name": "Shudi Li", + "author_inst": "University of Texas School of Public Health" + }, + { + "author_name": "Wei Lin", + "author_inst": "Fudan University" + }, + { + "author_name": "Li Jin", + "author_inst": "Fudan University" + }, + { + "author_name": "Momiao Xiong", + "author_inst": "University of Texas School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.08.20148742", "rel_title": "Disproportionate incidence of COVID-19 in African Americans correlates with dynamic segregation", @@ -1321510,89 +1322502,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.07.20148569", - "rel_title": "Risk Factors Prediction, Clinical Outcomes, and Mortality of COVID-19 Patients", - "rel_date": "2020-07-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20148569", - "rel_abs": "BackgroundPreventing communicable diseases requires understanding the spread, epidemiology, clinical features, progression, and prognosis of the disease. Early identification of risk factors and clinical outcomes might help to identify critically ill patients, provide proper treatment and prevent mortality.\n\nMethodsWe conducted a prospective study in patients with flu-like symptoms referred to the imaging department of a tertiary hospital in IRAN between 3 March 2020 and 8 April 2020. Patients with COVID- 19 were followed up to check their health condition after two months. The categorical data between groups were analyzed by Fishers exact test and continuous data by Wilcoxon Rank-Sum Test.\n\nFindings319 patients (mean age 45.48{+/-}18.50 years, 177 women) were enrolled. Fever, dyspnea, weakness, shivering, C-reactive protein (CRP), fatigue, dry cough, anorexia, anosmia, ageusia, dizziness, sweating and age were the most important symptoms of COVID-19 infection. Traveling in past three months, asthma, taking corticosteroids, liver disease, rheumatological disease, cough with sputum, eczema, conjunctivitis, tobacco use, and chest pain did not have any relationship with COVID-19.\n\nO_TEXTBOXResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched Google scholar, PUBMED and Scopus for articles that investigated the recent epidemic of COVID-19, especially those that investigate effective risk factors. We found that there is not enough research in this field, especially the risk factor that is effective in finding the rate of mortality of this disease.\n\nAdded value of this studyWe determined some of the most important effective risk factors on prediction, clinical outcome and mortality rate of COVID-19 infection. To the best of our knowledge, some of these risk factors are investigated in this work for the first time. Our findings could provide good insight into the early prediction of the disease, its clinical outcomes, and suggest a cost-effective method for mortality prediction.\n\nImplication of all the available evidenceCOVID-19 can transmit human-to-human and lead to severe symptoms and high mortality. Early prediction of this disease and the risk of mortality can help the physicians to better manage this worldwide health problem.\n\nC_TEXTBOX\n\nInterpretationFinding clinical symptoms for early diagnosis of COVID-19 is a critical part of prevention. These symptoms can help in the assessment of disease progression. To the best of our knowledge, some of the effective features on the mortality due to COVID-19 are investigated for the first time in this research.\n\nFundingNone", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Roohallah Alizadehsani", - "author_inst": "Deakin University" - }, - { - "author_name": "Zahra Alizadeh sani", - "author_inst": "Omid hospital, Cardiac MRI department,Tehran, IRAN" - }, - { - "author_name": "Mohaddeseh Behjati", - "author_inst": "Rajaei Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Zahra Roshanzamir", - "author_inst": "Pediatric Respiratory and Sleep Medicine Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Sadiq Hussain", - "author_inst": "System Administrator at Dibrugarh University, Assam, India, 786004." - }, - { - "author_name": "Niloofar Abedini", - "author_inst": "Tehran University of Medical Science, Imam Khomeini Hospital Complex, Tehran, Iran." - }, - { - "author_name": "Fereshteh Hasanzadeh", - "author_inst": "Omid hospital, Cardiac MRI department,Tehran, IRAN." - }, - { - "author_name": "Abbas Khosravi", - "author_inst": "Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Victoria 3217, Australia." - }, - { - "author_name": "Afshin Shoeibi", - "author_inst": "Computer Engineering Department, Ferdowsi University of Mashhad, Mashhad, Iran." - }, - { - "author_name": "Mohamad Roshanzamir", - "author_inst": "Department of Engineering, Fasa Branch, Islamic Azad University, Post Box No 364, Fasa, Fars 7461789818, Iran" - }, - { - "author_name": "Pardis Moradnejad", - "author_inst": "Rajaei Cardiovascular Medical and Research Center, Iran University of Medical Sciences, Tehran, Iran." - }, - { - "author_name": "Saeid Nahavandi", - "author_inst": "Institute for Intelligent Systems Research and Innovation (IISRI), Deakin University, Victoria 3217, Australia." - }, - { - "author_name": "Fahime Khozeimeh", - "author_inst": "Mashhad University of Medical Science, Mashhad, Iran." - }, - { - "author_name": "Assef Zare", - "author_inst": "Faculty of Electrical Engineering, Gonabad Branch, Islamic Azad University, Gonabad, Iran." - }, - { - "author_name": "Maryam Panahiazar", - "author_inst": "University of California San Francisco, San Francisco, CA, USA." - }, - { - "author_name": "U. Rajendra Acharya", - "author_inst": "Department of Electronics and Computer Engineering, Ngee Ann Polytechnic, Singapore 599489, Singapore." - }, - { - "author_name": "Sheikh Mohammed Shariful Islam", - "author_inst": "Institute for Physical Activity and Nutrition, Deakin University, Melbourne, Australia." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.08.20148783", "rel_title": "SARS-CoV-2 virus culture from the upper respiratory tract: Correlation with viral load, subgenomic viral RNA and duration of illness.", @@ -1322288,6 +1323197,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.09.194639", + "rel_title": "Decline of humoral responses against SARS-CoV-2 Spike in convalescent individuals", + "rel_date": "2020-07-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.09.194639", + "rel_abs": "In the absence of effective vaccines and with limited therapeutic options, convalescent plasma is being collected across the globe for potential transfusion to COVID-19 patients. The therapy has been deemed safe and several clinical trials assessing its efficacy are ongoing. While it remains to be formally proven, the presence of neutralizing antibodies is thought to play a positive role in the efficacy of this treatment. Indeed, neutralizing titers of [≥]1:160 have been recommended in some convalescent plasma trials for inclusion. Here we performed repeated analyses at one-month interval on 31 convalescent individuals to evaluate how the humoral responses against the SARS-CoV-2 Spike, including neutralization, evolve over time. We observed that receptor-binding domain (RBD)-specific IgG slightly decreased between six and ten weeks after symptoms onset but RBD-specific IgM decreased much more abruptly. Similarly, we observed a significant decrease in the capacity of convalescent plasma to neutralize pseudoparticles bearing SARS-CoV-2 S wild-type or its D614G variant. If neutralization activity proves to be an important factor in the clinical efficacy of convalescent plasma transfer, our results suggest that plasma from convalescent donors should be recovered rapidly after symptoms resolution.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Guillaume Beaudoin-Bussi\u00e8res", + "author_inst": "CRCHUM" + }, + { + "author_name": "Annemarie Laumaea", + "author_inst": "Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Sai Priya Anand", + "author_inst": "CRCHUM / McGill" + }, + { + "author_name": "J\u00e9r\u00e9mie Pr\u00e9vost", + "author_inst": "CRCHUM / Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Romain Gasser", + "author_inst": "Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Guillaume Goyette", + "author_inst": "CRCHUM" + }, + { + "author_name": "Halima Medjahed", + "author_inst": "CRCHUM" + }, + { + "author_name": "Jos\u00e9ee Perreault", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Tony Tremblay", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Antoine Lewin", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Laurie Gokool", + "author_inst": "CRCHUM" + }, + { + "author_name": "Chantal Morrisseau", + "author_inst": "CRCHUM" + }, + { + "author_name": "Philippe B\u00e9gin", + "author_inst": "CHU Ste-Justine" + }, + { + "author_name": "Cecile Tremblay", + "author_inst": "CRCHUM" + }, + { + "author_name": "Val\u00e9rie Martel-Laferri\u00e8re", + "author_inst": "CRCHUM" + }, + { + "author_name": "Jonathan Richard", + "author_inst": "Centre de Recherche du CHUM" + }, + { + "author_name": "Ren\u00e9e Bazin", + "author_inst": "H\u00e9ma-Qu\u00e9bec" + }, + { + "author_name": "Andr\u00e9s Finzi", + "author_inst": "CRCHUM, Universit\u00e9 de Montr\u00e9al" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.07.08.194456", "rel_title": "Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2", @@ -1323763,29 +1324759,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.06.20147181", - "rel_title": "Predicting Health Disparities in Regions at Risk of Severe Illness to inform Healthcare Resource Allocations during Pandemics", - "rel_date": "2020-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147181", - "rel_abs": "Pandemics including COVID-19 have disproportionately affected socioeconomically vulnerable populations. To create a repeatable modelling process to identify regional population centers with pandemic vulnerability, readily available COVID-19 and socioeconomic variable datasets were compiled, and linear regression models were built during the early days of the COVID-19 pandemic. The models were validated later in the pandemic timeline using actual COVID-19 mortality rates in states with high population densities, with New York, New Jersey, Connecticut, Massachusetts, Louisiana, Michigan and Pennsylvania showing the strongest predictive results. Our models have been shared with the Department of Health Commissioners of each of these states as input into a much needed \"pandemic playbook\" for local healthcare agencies in allocating medical testing and treatment resources.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Tara Fusillo", - "author_inst": "John F. Kennedy High School" - }, - { - "author_name": "Tara Fusillo", - "author_inst": "John F. Kennedy High School" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.07.20148148", "rel_title": "Atypical Presentations of COVID-19 in Care Home Residents presenting to Secondary Care: A UK Single Centre Study", @@ -1324209,6 +1325182,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2020.07.07.20148304", + "rel_title": "COVID-19 Mortality Risk Assessment: An International Multi-Center Study", + "rel_date": "2020-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20148304", + "rel_abs": "BackgroundTimely identification of COVID-19 patients at high risk of mortality can significantly improve patient management and resource allocation within hospitals. This study seeks to develop and validate a data-driven personalized mortality risk calculator for hospitalized COVID-19 patients.\n\nMethodsDe-identified data was obtained for 3,927 COVID-19 positive patients from six independent centers, comprising 33 different hospitals. Demographic, clinical, and laboratory variables were collected at hospital admission. The COVID-19 Mortality Risk (CMR) tool was developed using the XGBoost algorithm to predict mortality. Its discrimination performance was subsequently evaluated on three validation cohorts.\n\nFindingsThe derivation cohort of 3,062 patients has an observed mortality rate of 26.84%. Increased age, decreased oxygen saturation ([≤] 93%), elevated levels of C-reactive protein ([≥] 130 mg/L), blood urea nitrogen ([≥] 18 mg/dL), and blood creatinine ([≥] 1.2 mg/dL) were identified as primary risk factors, validating clinical findings. The model obtains out-of-sample AUCs of 0.90 (95% CI, 0.87-0.94) on the derivation cohort. In the validation cohorts, the model obtains AUCs of 0.92 (95% CI, 0.88-0.95) on Seville patients, 0.87 (95% CI, 0.84-0.91) on Hellenic COVID-19 Study Group patients, and 0.81 (95% CI, 0.76-0.85) on Hartford Hospital patients. The CMR tool is available as an online application at covidanalytics.io/mortality_calculator and is currently in clinical use.\n\nInterpretationThe CMR model leverages machine learning to generate accurate mortality predictions using commonly available clinical features. This is the first risk score trained and validated on a cohort of COVID-19 patients from Europe and the United States.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, BioRxiv, MedRxiv, arXiv, and SSRN for peer-reviewed articles, preprints, and research reports in English from inception to March 25th, 2020 focusing on disease severity and mortality risk scores for patients that had been infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Earlier investigations showed promise at predicting COVID-19 disease severity using data at admission. However, existing work was limited by its data scope, either relying on a single center with rich clinical information or broader cohort with sparse clinical information. No analysis has leveraged Electronic Health Records data from an international multi-center cohort from both Europe and the United States.\n\nAdded value of this studyWe present the first multi-center COVID-19 mortality risk study that uses Electronic Health Records data from 3,062 patients across four different countries, including Greece, Italy, Spain, and the United States, encompassing 33 hospitals. We employed state-of-the-art machine learning techniques to develop a personalized COVID-19 mortality risk (CMR) score for hospitalized patients upon admission based on clinical features including vitals, lab results, and comorbidities. The model validates clinical findings of mortality risk factors and exhibits strong performance, with AUCs ranging from 0.81 to 0.92 across external validation cohorts. The model identifies increased age as a primary mortality predictor, consistent with observed disease trends and subsequent public health guidelines. Additionally, among the vital and lab values collected at admission, decreased oxygen saturation ([≤] 93%) and elevated levels of C-reactive protein ([≥] 130 mg/L), blood urea nitrogen ([≥] 18 mg/dL), blood creatinine ([≥] 1.2 mg/dL), and blood glucose ([≥]180 mg/dL) are highlighted as key biomarkers of mortality risk. These findings corroborate previous studies that link COVID-19 severity to hypoxemia, impaired kidney function, and diabetes. These features are also consistent with risk factors used in severity risk scores for related respiratory conditions such as community-acquired pneumonia.\n\nImplications of all the available evidenceOur work presents the development and validation of a personalized mortality risk score. We take a data-driven approach to derive insights from Electronic Health Records data spanning Europe and the United States. While many existing papers on COVID-19 clinical characteristics and risk factors are based on Chinese hospital data, the similarities in our findings suggest consistency in the disease characteristics across international cohorts. Additionally, our machine learning model offers a novel approach to understanding the disease and its risk factors. By creating a single comprehensive risk score that integrates various admission data components, the calculator offers a streamlined way of evaluating COVID-19 patients upon admission to augment clinical expertise. The CMR model provides a valuable clinical decision support tool for patient triage and care management, improving risk estimation early within admission, that can significantly affect the daily practice of physicians.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Dimitris Bertsimas", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Galit Lukin", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Luca Mingardi", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Omid Nohadani", + "author_inst": "Benefits Science Technologies" + }, + { + "author_name": "Agni Orfanoudaki", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Bartolomeo Stellato", + "author_inst": "Princeton University" + }, + { + "author_name": "Holly Wiberg", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Sara Gonzalez-Garcia", + "author_inst": "Institute of Biomedicine of Seville (IBIS), Virgen del Rocio University Hospital, CSIC, University of Seville" + }, + { + "author_name": "Carlos Luis Parra-Calderon", + "author_inst": "Institute of Biomedicine of Seville (IBIS), Virgen del Rocio University Hospital, CSIC, University of Seville" + }, + { + "author_name": "- The Hellenic COVID-19 Study Group", + "author_inst": "" + }, + { + "author_name": "Kenneth Robinson", + "author_inst": "Hartford HealthCare" + }, + { + "author_name": "Michelle Schneider", + "author_inst": "Hartford HealthCare" + }, + { + "author_name": "Barry Stein", + "author_inst": "Hartford HealthCare" + }, + { + "author_name": "Alberto Estirado", + "author_inst": "HM Hospitals" + }, + { + "author_name": "Lia a Beccara", + "author_inst": "Azienda Socio-Sanitaria Territoriale di Cremona" + }, + { + "author_name": "Rosario Canino", + "author_inst": "Azienda Socio-Sanitaria Territoriale di Cremona" + }, + { + "author_name": "Martina Dal Bello", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Federica Pezzetti", + "author_inst": "Azienda Socio-Sanitaria Territoriale di Cremona" + }, + { + "author_name": "Angelo Pan", + "author_inst": "Azienda Socio-Sanitaria Territoriale di Cremona" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.07.20148213", "rel_title": "No evidence of viral polymorphisms associated with Paediatric Inflammatory Multisystem Syndrome Temporally Associated With SARS-CoV-2 (PIMS-TS).", @@ -1325581,61 +1326645,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.06.20147264", - "rel_title": "Clinical characteristics and epidemiology survey of lung transplantation recipients accepting surgeries during the COVID-19 pandemic:from area near Hubei Province", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147264", - "rel_abs": "Lung transplantation recipients (LTx) were susceptible to severe acute respiratory syndrome-corona virus-2 (SARS-Cov-2) and suffered a higher mortality risk than healthy subjects. Here we aim to analyze whether it was appropriate or and valuable to maintain lung transplant programs in medical institutions accepting coronavirus disease 2019 (COVID-19) patients. In this study, the clinical characteristics, laboratory testing and epidemiology survey results of 10 LTx recipients undergoing allograft lung transplantation surgeries in the First Affiliated Hospital of Zhengzhou University during the COVID-19 pandemic were collected. A web-based epidemiology questionnaire was used to collect the information of LTx recipients after discharge. Up to now, none of the LTx recipients or their family members get infected with SARS-CoV-2 during the novel coronavirus pandemic. In conclusion, under the premise of taking appropriate preventive measures during hospitalization and after discharge, the lung transplant program can be maintained in the medical institution that accepts patients with COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Lingxiao Qiu", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Shanshan Chen", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Cong Wang", - "author_inst": "King's College London" - }, - { - "author_name": "Caihong Liu", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Huaqi Wang", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Xiaoguang Zhao", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Zeming Fang", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Siyuan Chang", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Gaofeng Zhao", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - }, - { - "author_name": "Guojun Zhang", - "author_inst": "The First Affiliated Hospital of Zhengzhou University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "transplantation" - }, { "rel_doi": "10.1101/2020.07.06.20147629", "rel_title": "Are men dying more than women by COVID-19?", @@ -1325867,6 +1326876,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.07.06.182972", + "rel_title": "Unique transcriptional changes in coagulation cascade genes in SARS-CoV-2-infected lung epithelial cells: A potential factor in COVID-19 coagulopathies", + "rel_date": "2020-07-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.06.182972", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global pandemic. In addition to the acute pulmonary symptoms of COVID-19 (the disease associated with SARS-CoV-2 infection), pulmonary and distal coagulopathies have caused morbidity and mortality in many patients. Currently, the molecular pathogenesis underlying COVID-19 associated coagulopathies are unknown. While there are many theories for the cause of this pathology, including hyper inflammation and excess tissue damage, the cellular and molecular underpinnings are not yet clear. By analyzing transcriptomic data sets from experimental and clinical research teams, we determined that changes in the gene expression of genes important in the extrinsic coagulation cascade in the lung epithelium may be important triggers for COVID-19 coagulopathy. This regulation of the extrinsic blood coagulation cascade is not seen with influenza A virus (IAV)-infected NHBEs suggesting that the lung epithelial derived coagulopathies are specific to SARS-Cov-2 infection. This study is the first to identify potential lung epithelial cell derived factors contributing to COVID-19 associated coagulopathy.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC=\"FIGDIR/small/182972v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (42K):\norg.highwire.dtl.DTLVardef@93cfb7org.highwire.dtl.DTLVardef@2a23c9org.highwire.dtl.DTLVardef@93623borg.highwire.dtl.DTLVardef@161e25_HPS_FORMAT_FIGEXP M_FIG C_FIG AUTHOR SUMMARYO_ST_ABSWhy was this study done?C_ST_ABSO_LISevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly become a global pandemic.\nC_LIO_LIIn addition to the acute pulmonary symptoms of COVID-19 (the disease associated with SARS-CoV-2 infection), pulmonary and distal coagulopathies have caused morbidity and mortality in many patients.\nC_LIO_LICurrently, the molecular pathogenesis underlying COVID-19 associated coagulopathies are unknown. Understanding the molecular basis of dysregulated blood coagulation during SARS-CoV-2 infection may help promote new therapeutic strategies to mitigate these complications in COVID-19 patients.\nC_LI\n\nWhat did the researchers do and find?O_LIWe analyzed three publicly available RNA sequencing datasets to identify possible molecular etiologies of COVID-19 associated coagulopathies. These data sets include sequencing libraries from clinically isolated samples of bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMCs) from SARS-CoV-2 positive patients and healthy controls. We also analyzed a publicly available RNA sequencing dataset derived from in vitro SARS-CoV-2 infected primary normal human bronchial epithelial (NHBE) cells and mock infected samples.\nC_LIO_LIPathway analysis of both NHBE and BALF differential gene expression gene sets. We found that SARS-CoV-2 infection induces the activation of the extrinsic blood coagulation cascade and suppression of the plasminogen activation system in both NHBEs and cells isolated from the BALF. PBMCs did not differentially express genes regulating blood coagulation.\nC_LIO_LIComparison with influenza A virus (IAV)-infected NHBEs revealed that the regulation of the extrinsic blood coagulation cascade is unique to SARS-CoV-2, and not seen with IAV infection.\nC_LI\n\nWhat do these findings mean?O_LIThe hyper-activation of the extrinsic blood coagulation cascade and the suppression of the plasminogen activation system in SARS-CoV-2 infected epithelial cells may drive diverse coagulopathies in the lung and distal organ systems.\nC_LIO_LIThe gene transcription pattern in SARS-CoV-2 infected epithelial cells is distinct from IAV infected epithelial cells with regards to the regulation of blood coagulation.\nC_LI", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ethan S. FitzGerald", + "author_inst": "Brown University" + }, + { + "author_name": "Amanda M. Jamieson", + "author_inst": "Brown University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.07.07.192005", "rel_title": "A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex", @@ -1326931,29 +1327963,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.06.20147033", - "rel_title": "The relative power of individual distancing efforts and public policies to curb the COVID-19 epidemics", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147033", - "rel_abs": "Lockdown curbs the COVID-19 epidemics but at huge costs. Public debates question its impact compared with reliance on individual responsibility. We aim at understanding how rationally chosen self-protective behavior impacts the spread of the epidemics. We want to, first, assess the value of lockdown compared to a counterfactual that incorporates self-protection efforts under unknown disease prevalence; and second, assess how individual behavior modify the epidemic dynamics when mandatory policies are relaxed. We couple an SLIAR model, that includes asymptomatic transmission, with utility maximization: Individuals trade off economic and wellbeing costs from physical distancing with a lower infection risk. Effort depends on risk aversion, perceptions, and the value of contacts. In a Nash equilibrium, individual uncoordinated efforts yield average contact intensity, which drives epidemic transmission. Equilibrium effort differs markedly from constant, stochastic or proportional contacts reduction. It adjusts to reported cases in a way that creates a slightly decreasing plateau in epidemic prevalence. Calibration on French data shows that the number of deaths with no lockdown but equilibrium efforts is only 1/6 to 1/10 of the number predicted with business-as-usual. However, lockdown saves at least 50% more lives than individual efforts alone. Prolonged weaker restrictions prevent an exponential rebound. Public policies post-lockdown have a limited impact as they partly crowd out individual efforts. Compulsory mask wearing helps resume activity but has no impact on the epidemic. Communication that increases risk salience is more effective.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Cecile Aubert", - "author_inst": "University of Bordeaux" - }, - { - "author_name": "Emmanuelle Augeraud-Veron", - "author_inst": "University of Bordeaux" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.05.20146647", "rel_title": "An SEIR Model with Contact Tracing and Age-Structured Social Mixing for COVID-19 outbreak", @@ -1327109,6 +1328118,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.07.06.20147751", + "rel_title": "COVID-19 presenting as anosmia and dysgeusia in New York City emergency departments, March - April, 2020", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147751", + "rel_abs": "BackgroundIncreasing evidence has been emerging of anosmia and dysgeusia as frequently reported symptoms in COVID-19. Improving our understanding of these presenting symptoms may facilitate the prompt recognition of the disease in emergency departments and prevent further transmission.\n\nMethodsWe examined a cross-sectional cohort using New York City emergency department syndromic surveillance data for March and April 2020. Emergency department visits for anosmia and/or dysgeusia were identified and subsequently matched to the Electronic Clinical Laboratory Reporting System to determine testing results for SARS-CoV-2.\n\nResultsOf the 683 patients with anosmia and/or dysgeusia included, SARS-CoV-2 testing was performed for 232 (34%) and 168 (72%) were found to be positive. Median age of all patients presenting with anosmia and/or dysgeusia symptoms was 38, and 54% were female. Anosmia and/or dysgeusia was the sole complaint of 158 (23%) patients, of whom 35 were tested for SARS-CoV-2 and 23 (66%) were positive. While the remaining patients presented with at least one other symptom, nearly half of all patients (n=334, 49%) and more than a third of those who tested positive (n=62, 37%) did not have any of the CDC-established symptoms used for screening of COVID-19 such as fever, cough, shortness of breath, or sore throat.\n\nConclusions and RelevanceAnosmia and/or dysgeusia have been frequent complaints among patients presenting to emergency departments during the COVID-19 pandemic, and, while only a small proportion of patients ultimately underwent testing for SARS-CoV-19, the majority of patients tested have been positive. Anosmia and dysgeusia likely represent underrecognized symptoms of COVID-19 but may have important future implications in disease diagnosis and surveillance.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tina Z. Wang", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Jessica Sell", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Don Weiss", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Ramona Lall", + "author_inst": "New York City Department of Health and Mental Hygiene" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.06.20147702", "rel_title": "COVID-19 screening strategies that permit the safe re-opening of college campuses", @@ -1328173,53 +1329213,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.07.04.20146530", - "rel_title": "Global pattern of COVID-19 research", - "rel_date": "2020-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.04.20146530", - "rel_abs": "Since the COVID-19 outbreak began, a large number of studies have been conducted in a short period. However, it is unclear whether countries involved in this crisis have made adequate efforts and allocated resources to cutting-edge SARS-CoV-2 research. We analyzed the dynamics of and professional fields represented by papers about this novel coronavirus published before June 15, 2020. High-infection countries produced more scientific output than low-infection countries, and high-income and upper-middle-income countries were the main contributors. However, the research areas overlapped substantially, indicating a waste of resources. Our findings also suggest that international cooperation among countries is still relatively lacking, and all countries should make better use of their strengths to face the epidemic jointly.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Xunzhi Zhu", - "author_inst": "Institute of Botany Jiangsu Province and Chinese Academy of Sciences" - }, - { - "author_name": "Qi Jin", - "author_inst": "Institute of Occupational Diseases, Hangzhou Medical College" - }, - { - "author_name": "Xiyi Jiang", - "author_inst": "Institute of Occupational Diseases, Hangzhou Medical College" - }, - { - "author_name": "Yuanyuan Dan", - "author_inst": "School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology" - }, - { - "author_name": "Aimin Zhang", - "author_inst": "School of Computer, Jiangsu University of Science and Technology" - }, - { - "author_name": "Guangming Qiu", - "author_inst": "School of Computer, Jiangsu University of Science and Technology" - }, - { - "author_name": "Jianlin Lou", - "author_inst": "Institute of Occupational Diseases, Hangzhou Medical College" - }, - { - "author_name": "Hualong Yu", - "author_inst": "School of Computer, Jiangsu University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.07.04.20145334", "rel_title": "Global Assessment of the Relationship between Government Response Measures and COVID-19 Deaths", @@ -1328531,6 +1329524,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.03.20145797", + "rel_title": "Dengue antibodies can cross-react with SARS-CoV-2 and vice versa-Antibody detection kits can give false-positive results for both viruses in regions where both COVID-19 and Dengue co-exist", + "rel_date": "2020-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145797", + "rel_abs": "Five of thirteen Dengue antibody-positive serum samples, dated 2017 (pre-dating the COVID-19 outbreak) produced false-positive results in SARS-CoV-2 IgG/IgM rapid strip tests. Our results emphasize the importance of NAT and/or virus antigen tests to complement sero-surveillance for definitive diagnosis of COVID-19/Dengue in regions where both viruses are co-endemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Himadri Nath", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "Abinash Mallick", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "Subrata Roy", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + }, + { + "author_name": "Soumi Sukla", + "author_inst": "NIPER, Kolkata" + }, + { + "author_name": "Keya Basu", + "author_inst": "IPGMER, Kolkata (Department of Pathology)" + }, + { + "author_name": "Abhishek De", + "author_inst": "Calcutta National Medical College, Kolkata (Department of Dermatology)" + }, + { + "author_name": "Subhajit Biswas", + "author_inst": "CSIR-Indian Institute of Chemical Biology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.29.20131367", "rel_title": "Evaluation of Viasure SARS-CoV-2 RT-qPCR kit (CerTest Biotec) using CDC FDA EUA RT-qPCR kit as a gold standard.", @@ -1329543,37 +1330579,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.01.20144592", - "rel_title": "Genetic risk factors for death with SARS-CoV-2 from the UK Biobank", - "rel_date": "2020-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20144592", - "rel_abs": "We present here genetic risk factors for survivability from infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) responsible for coronavirus disease 19 (COVID-19). At the time of writing it is too early to determine comprehensively and without doubt all risk factors, but there is an urgency due to the global pandemic crisis that merits this early analysis. We have nonetheless discovered 5 novel risk variants in 4 genes, discovered by examining 193 deaths from 1,412 confirmed infections in a group of 5,871 UK Biobank participants tested for the virus. We also examine the distribution of these genetic variants across broad ethnic groups and compare it to data from the UK Office of National Statistics for increased risk of death from SARS-CoV-2. We confidently identify the gene ERAP2 with a high-risk variant, as well as three other genes of potential interest. Although mostly rare, a common theme of genetic risk factors affecting survival might be the inability to launch or modulate an effective immune and stress response to infection from the SARS-CoV-2 virus.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Chang Lu", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "Rihab Gam", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "Arun Prasad Pandurangan", - "author_inst": "MRC Laboratory of Molecular Biology" - }, - { - "author_name": "Julian Gough", - "author_inst": "MRC Laboratory of Molecular Biology" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.02.20145045", "rel_title": "Prediction of COVID-19 Active and Total Cases After a Fall and Rise of Cases", @@ -1329737,6 +1330742,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.02.20143032", + "rel_title": "Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients", + "rel_date": "2020-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20143032", + "rel_abs": "BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus disease 2019 (COVID-19). However, microbial composition of the respiratory tract and other infected tissues, as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear.\n\nMethodBetween January 27 and February 26, 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients (requiring ICU admission and mechanical ventilation), in the Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. Co-infection rates, the prevalence and abundance of microbial communities in these COVID-19 patients were determined.\n\nFindingsNotably, respiratory microbial co-infections were exclusively found in 84.6% of severely ill patients (11/13), among which viral and bacterial co-infections were detected by sequencing in 30.8% (4/13) and 69.2% (9/13) of the patients, respectively. In addition, for 23.1% (3/13) of the patients, bacterial co-infections with Burkholderia cepacia complex (BCC) and Staphylococcus epidermidis were also confirmed by bacterial culture. Further, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes in one severely ill patient was demonstrated, which might be the primary cause of his disease deterioration and death one month after ICU admission.\n\nInterpretationOur findings identified distinct patterns of co-infections with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking of BCC-associated nosocomial infections are recommended to improve the pre-emptive treatment regimen and reduce fatal outcomes of hospitalized patients infected with SARS-CoV-2.\n\nFundingNational Science and Technology Major Project of China, National Major Project for Control and Prevention of Infectious Disease in China, the emergency grants for prevention and control of SARS-CoV-2 of Ministry of Science and Technology and Guangdong province, Guangdong Provincial Key Laboratory of Genome Read and Write, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, and Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Huanzi Zhong", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China. Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denma" + }, + { + "author_name": "Yanqun Wang", + "author_inst": "Guangzhou Institute of Respiratory Health" + }, + { + "author_name": "Zhun Shi", + "author_inst": "BGI-Shenzhen,Shenzhen 518083,China" + }, + { + "author_name": "Lu Zhang", + "author_inst": "Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China 510060." + }, + { + "author_name": "Huahui Ren", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Weiqun He", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Zhaoyong Zhang", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Airu Zhu", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Jingxian Zhao", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Fei Xiao", + "author_inst": "Department of Infectious Diseases, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imag" + }, + { + "author_name": "Fangming Yang", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Tianzhu Liang", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Feng Ye", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Bei Zhong", + "author_inst": "The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong, China" + }, + { + "author_name": "Shicong Ruan", + "author_inst": "Yangjiang People's Hospital, Yangjiang, Guangdong, China" + }, + { + "author_name": "Mian Gan", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Jiahui Zhu", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Fang Li", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Fuqiang Li", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Daxi Wang", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Jiandong Li", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Peidi Ren", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Shida Zhu", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Huanming Yang", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Jian Wang", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Karsten Kristiansen", + "author_inst": "BGI-Shenzhen, Shenzhen, 518083, China." + }, + { + "author_name": "Hein M Tun", + "author_inst": "HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China." + }, + { + "author_name": "Weijun Chen", + "author_inst": "BGI PathoGenesis Pharmaceutical Technology, Shenzhen, China." + }, + { + "author_name": "Nanshan Zhong", + "author_inst": "State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University" + }, + { + "author_name": "Xun Xu", + "author_inst": "BGI-shenzhen" + }, + { + "author_name": "Yi-min Li", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + }, + { + "author_name": "Junhua LI", + "author_inst": "BGI-Shenzhen" + }, + { + "author_name": "Jincun Zhao", + "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.02.20145052", "rel_title": "Modeling COVID-19 for lifting non-pharmaceutical interventions", @@ -1330953,29 +1332105,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.07.02.20145391", - "rel_title": "Laboratory findings that predict a poor prognosis in COVID-19 patients with diabetes: A meta-analysis", - "rel_date": "2020-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20145391", - "rel_abs": "Diabetes is one of the main comorbidities in patients infected with the SARS-CoV-2 virus, the causative agent of the new coronavirus disease 2019 (COVID-19). Because the presence of diabetes and COVID-19 in the same patient is related to a poor clinical prognosis and a high probability of death, it is necessary to determine what findings allow us to predict a good or bad resolution of the disease in order to opt for a traditional treatment or a more incisive one. In this way, in the present work we analyze which laboratory parameters showed differences in patients with COVID-19 and diabetes who recovered and in those who had complications or died.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Francisco Alejandro Lagunas-Rangel", - "author_inst": "Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional" - }, - { - "author_name": "Venice Ch\u00e1vez-Valencia", - "author_inst": "Instituto Mexicano del Seguro Social" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2020.07.02.20145508", "rel_title": "Firearm Purchasing and Firearm Violence in the First Months of the Coronavirus Pandemic in the United States", @@ -1331159,6 +1332288,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.03.20145672", + "rel_title": "A Novel Approach for Estimating the Final Outcome of Global Diseases Like COVID-19", + "rel_date": "2020-07-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145672", + "rel_abs": "The existence of a universal law which maps the bell curve of daily cases to a sigmoid curve for cumulative ones is used for making robust estimations about the final outcome of a disease. Computations of real time effective reproduction rate are presented and its limited usefulness is derived. After using methods ESE & EDE we are able to find the inflection point of the cumulative curve under consideration and study its time evolution. Since mortality processes tend to follow a Gompertz distribution, we apply the properties of it and introduce novel estimations for both the time remaining after inflection time and the capacity of the curve. Special properties of sigmoid curves are used for assessing the quality of estimation and as indices for the cycle completion. Application is presented for COVID-19 evolution for most affected countries and the World.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Demetris T Christopoulos", + "author_inst": "National and Kapodistrian University of Athens" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.03.20146167", "rel_title": "Serial interval, basic reproduction number and prediction of COVID-19 epidemic size in Jodhpur, India", @@ -1332367,37 +1333515,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.06.30.20143347", - "rel_title": "Rapid detection of SARS-CoV-2 infection by multicapillary column coupled ion mobility spectrometry (MCC-IMS) of breath. A proof of concept study", - "rel_date": "2020-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20143347", - "rel_abs": "There is an urgent need for screening of patients having a communicable viral disease to cut infection chains.\n\nWe could recently demonstrate that MCC-IMS of breath is able to identify Influenza-A infected patients. With decreasing Influenza epidemic and upcoming SARS-CoV-2 infections we went on and also analysed patients with suspected SARS-CoV-2 infections.\n\n75 patients, 34m, 41f, aged 64.4 {+/-} 15.4 years, 14 positive for Influenza-A, 16 positive for SARS-CoV-2, the remaining 44 patients were used as controls. In one patient RT-PCR was highly suspicious of SARS-CoV-2 but initially inconclusive.\n\nBesides RT-PCR analysis of nasopharyngeal swabs all patients underwent MCC-IMS analysis of breath. There was no difference in gender or age according to the groups.\n\n97.3% of the patients could be correctly classified to the respective group by discriminant analysis. Even the inconclusive patient could be mapped to the SARS-CoV-2 group applying the discrimination function.\n\nConclusionMCC-IMS is able to detect SARS-CoV-2 infection and Influenza-A infection in breath. As this method provides exact, fast non-invasive diagnosis it should be further developed for screening of communicable viral diseases.\n\nTrial registration: ClinicalTrial.gov, NCT04282135 Registered 20 February 2020 - Retrospectively registered, https://clinicaltrials.gov/ct2/show/NCT04282135?term=IMS&draw=2&rank=1", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Claus Steppert", - "author_inst": "Department of Pulmonology and Thoracic Oncology, Bayreuth General Hospital, Bayreuth, Germany" - }, - { - "author_name": "Isabel Steppert", - "author_inst": "Institute for Biochemistry and Biology, Potsdam University, Germany" - }, - { - "author_name": "William Sterlacci", - "author_inst": "Institute for Pathology, Bayreuth General Hospital, Bayreuth, Germany" - }, - { - "author_name": "Thomas Bollinger", - "author_inst": "Institute for Microbiology and Laboratory Medicine, Bayreuth General Hospital, Bayreuth, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.06.30.20143354", "rel_title": "Disruption of the renal service during COVID-19 pandemic, physicians survey responses from 5 countries", @@ -1332725,6 +1333842,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.01.20129882", + "rel_title": "Retrospective Clinical Evaluation of Four Lateral Flow Assays for the Detection of SARS-CoV-2 Antibodies", + "rel_date": "2020-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20129882", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is a potentially life-threatening respiratory infection caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), for which numerous serologic assays are available. In a CLIA laboratory setting, we used a retrospective sample set (n = 457) to evaluate two lateral flow immunoassays (LFIAs; two iterations of Rapid Response COVID-19 Test Cassette, BTNX Inc.) and a subset of to evaluate SARS-COV-2 IgG/IgM Rapid Test, ACON Laboratories (n = 200); and Standard Q COVID-19 IgM/IgG Duo, SD BIOSENSOR (n = 155) for their capacity to detect of SARS-CoV-2 IgG. In a cohort of primarily hospitalized patients with RT-PCR confirmed COVID-19, the BTNX assays demonstrated 95% and 92% agreement with the Abbott SARS-CoV-2 IgG assay and sensitivity was highest at [≥] 14 days from symptom onset [BTNX kit 1, 95%; BTNX kit 2, 91%]. ACON and SD assays demonstrated 99% and 100% agreement with the Abbott assay at [≥] 14 days from symptom onset. Specificity was measured using 74 specimens collected prior to SARS-CoV-2 circulation in the United States and 31 \"cross-reactivity challenge\" specimens, including those from patients with a history of seasonal coronavirus infection and was 98% for BTNX kit 1 and ACON and 100% for BTNX kit 2 and SD. Taken with data from EUA assays, these results suggest that LFIAs may provide adequate results for rapid detection of SARS-CoV-2. Replicating these results in fingerstick blood in outpatient populations, would further support the possibility that LFIAs may be useful to increase access to serologic testing", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kathrine McAulay", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew Bryan", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Francisca Grill", + "author_inst": "Arizona State University" + }, + { + "author_name": "Douglas F. Lake", + "author_inst": "Arizona State University" + }, + { + "author_name": "Erin J. Kaleta", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Thomas E Grys", + "author_inst": "Mayo Clinic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.01.20144667", "rel_title": "Numerical Analysis of Disastrous Effect of Reopening Too Soon in Georgia, USA", @@ -1333841,53 +1335001,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.01.20144105", - "rel_title": "Associations of exercise and social support with mental health during quarantine and social-distancing measures during the COVID-19 pandemic: A cross-sectional survey in Germany", - "rel_date": "2020-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20144105", - "rel_abs": "IntroductionSocial distancing and quarantine measures applied during the COVID-19 pandemic might result in mental health problems. In this cross-sectional study we examined if perceived social support, exercise in minutes per week and change in exercise are protective factors regarding symptoms of depression, anxiety, and sleeping disorders.\n\nMethodIn April 2020, n = 4271 German adults completed an online survey including mental health questionnaires regarding depression (PHQ-D), anxiety (PHQ-D) and sleep (PSQI), as well as questionnaires related to protective factors such as exercise (BSA-F), physical activity-related health competence (PAHCO) and social support (F-SozU).\n\nResultsComplete case analysis (n = 3700; mean age 33.13 {+/-} 11.73 years, 78.6 % females) resulted in elevated prevalence of depressive disorder (31.4%), panic disorder (5.7%) and other anxiety disorders (7.4%). 58.3% reported symptoms of insomnia. Three separate models of multiple regression were conducted. Perceived social support was associated with lower values of anxiety (beta = -0.10; t(19) = -6.46; p >0.001), lower values of depressive symptoms (beta = -0.22; t(19) = -15.71; p < .001) and lower values of sleeping disorder symptoms (beta = -0.15; t(19) = -9.55; p < .001). Change towards less exercise compared to the time before Covid-19 was associated with and higher values of anxiety (beta = -0.05; t(19) = -2.85; p= .004), higher values of depressive symptoms (beta = -0.08; t(19) = - 5.69; p < .001), and higher values of sleeping disorder symptoms (beta = -0.07; t(19) = -4.54; p < .000). Post-hoc analysis (ANOVAs) revealed that a change towards less exercise was significantly associated with more depressive, anxiety and sleeping disorder symptoms whereas a positive change was not. No significant association was found for exercise in minutes per week for all outcomes.\n\nConclusionThe COVID-19 pandemic seems to have a negative impact on mental health in the German population. Social Support and a stable amount of exercise might attenuate these negative mental health consequences. Ongoing monitoring of the impact of the pandemic on mental health and possible protective factors is needed in order to create a basis for the development of appropriate prevention and intervention measures.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Leonie Louisa Bauer", - "author_inst": "University of Tuebingen" - }, - { - "author_name": "Britta Seiffer", - "author_inst": "University of Tuebingen" - }, - { - "author_name": "Clara Deinhart", - "author_inst": "University of Tuebingen" - }, - { - "author_name": "Beatrice Atrott", - "author_inst": "University of Tuebingen" - }, - { - "author_name": "Gorden Sudeck", - "author_inst": "University of Tuebingen" - }, - { - "author_name": "Martin Hautzinger", - "author_inst": "University of Tuebingen" - }, - { - "author_name": "Inka R\u00f6sel", - "author_inst": "University Hospital of Tuebingen" - }, - { - "author_name": "Sebastian Wolf", - "author_inst": "University of Tuebingen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.30.20143867", "rel_title": "ROX Index Predicts Intubation in Patients with COVID-19 Pneumonia and Moderate to Severe Hypoxemic Respiratory Failure Receiving High Flow Nasal Therapy.", @@ -1334279,6 +1335392,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.30.20143651", + "rel_title": "Identifying main and interaction effects of risk factors to predict intensive care admission in patients hospitalized with COVID-19: a retrospective cohort study in Hong Kong", + "rel_date": "2020-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20143651", + "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) has become a pandemic, placing significant burdens on the healthcare systems. In this study, we tested the hypothesis that a machine learning approach incorporating hidden nonlinear interactions can improve prediction for Intensive care unit (ICU) admission.\n\nMethodsConsecutive patients admitted to public hospitals between 1st January and 24th May 2020 in Hong Kong with COVID-19 diagnosed by RT-PCR were included. The primary endpoint was ICU admission.\n\nResultsThis study included 1043 patients (median age 35 (IQR: 32-37; 54% male). Nineteen patients were admitted to ICU (median hospital length of stay (LOS): 30 days, median ICU LOS: 16 days). ICU patients were more likely to be prescribed angiotensin converting enzyme inhibitors/angiotensin receptor blockers, anti-retroviral drugs lopinavir/ritonavir and remdesivir, ribavirin, steroids, interferon-beta and hydroxychloroquine. Significant predictors of ICU admission were older age, male sex, prior coronary artery disease, respiratory diseases, diabetes, hypertension and chronic kidney disease, and activated partial thromboplastin time, red cell count, white cell count, albumin and serum sodium. A tree-based machine learning model identified most informative characteristics and hidden interactions that can predict ICU admission. These were: low red cells with 1) male, 2) older age, 3) low albumin, 4) low sodium or 5) prolonged APTT. A five-fold cross validation confirms superior performance of this model over baseline models including XGBoost, LightGBM, random forests, and multivariate logistic regression.\n\nConclusionsA machine learning model including baseline risk factors and their hidden interactions can accurately predict ICU admission in COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jiandong Zhou", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Gary Tse", + "author_inst": "Tianjin Medical University" + }, + { + "author_name": "Sharen Lee", + "author_inst": "Laboratory of Cardiovascular Physiology" + }, + { + "author_name": "Tong Liu", + "author_inst": "Tianjin Medical University" + }, + { + "author_name": "William KK Wu", + "author_inst": "LKS Institute of Health Sciences" + }, + { + "author_name": "zhidong cao", + "author_inst": "Institute of Automation, Chinese Academy of Sciences" + }, + { + "author_name": "Dajun Zeng", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Ian CK Wong", + "author_inst": "HKU" + }, + { + "author_name": "Qingpeng Zhang", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Bernard MY Cheung", + "author_inst": "HKU" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.01.20144030", "rel_title": "Broad phenotypic alterations and potential dysfunctions of lymphocytes in COVID-19 recovered individuals", @@ -1335363,125 +1336531,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.07.02.184093", - "rel_title": "Interleukin-3 is a predictive marker for severity and outcome during SARS-CoV-2 infections", - "rel_date": "2020-07-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.02.184093", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a worldwide health threat. Here, we report that low plasma interleukin-3 (IL-3) levels were associated with increased severity and mortality during SARS-CoV-2 infections. IL-3 promoted the recruitment of antiviral circulating plasmacytoid dendritic cells (pDCs) into the airways by stimulating CXCL12 secretion from pulmonary CD123+ epithelial cells. This study identifies IL-3 as a predictive disease marker and potential therapeutic target for SARS-CoV-2 infections.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Alan Benard", - "author_inst": "Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Anne Jacobsen", - "author_inst": "Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Maximilian Brunner", - "author_inst": "Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Christian Krautz", - "author_inst": "Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Bettina Klosch", - "author_inst": "Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Izabela Swierzy", - "author_inst": "Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Elisabeth Naschberger", - "author_inst": "Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Torsten Birkholz", - "author_inst": "Department of Anesthesiology, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Ixchel Castellanos", - "author_inst": "Department of Anesthesiology, Friedrich-Alexander University (FAU) Erlangen-\tNurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Denis Trufa", - "author_inst": "Department of Thoracic Surgery, Friedrich-Alexander University (FAU) Erlangen-\tNurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Horia Sirbu", - "author_inst": "Department of Thoracic Surgery, Friedrich-Alexander University (FAU) Erlangen-\tNurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Marcel Vetter", - "author_inst": "Department of Internal Medicine 1 - Gastroenterology, Pneumology and Endocrinology, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklini" - }, - { - "author_name": "Andreas E. Kremer", - "author_inst": "Department of Internal Medicine 1 - Gastroenterology, Pneumology and Endocrinology, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklini" - }, - { - "author_name": "Kai Hildner", - "author_inst": "Department of Internal Medicine 1 - Gastroenterology, Pneumology and Endocrinology, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklini" - }, - { - "author_name": "Andreas Hecker", - "author_inst": "Department of Surgery, University Hospital, Giessen" - }, - { - "author_name": "Fabian Edinger", - "author_inst": "Department of Surgery, University Hospital, Giessen" - }, - { - "author_name": "Matthias Tenbusch", - "author_inst": "Institute of Clinical and Molecular Virology, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Enrico Richter", - "author_inst": "Institute of \tVirology, University Hospital, Bonn" - }, - { - "author_name": "Hendrik Streeck", - "author_inst": "Institute of \tVirology, University Hospital, Bonn" - }, - { - "author_name": "Marc M. Berger", - "author_inst": "Department of Anesthesiology and Intensive Care Medicine, Essen University Hospital" - }, - { - "author_name": "Thorsten Brenner", - "author_inst": "Department of Anesthesiology and Intensive CAre Medicine, Essen University Hospital" - }, - { - "author_name": "Markus A. Weigand", - "author_inst": "Department of Anesthesiology, Heidelberg University Hospital" - }, - { - "author_name": "Filip K. Swirski", - "author_inst": "Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School" - }, - { - "author_name": "Georg Schett", - "author_inst": "Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and Universitatsklinikum Erlangen" - }, - { - "author_name": "Robert Grutzmann", - "author_inst": "Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and \tUniversitatsklinikum Erlangen" - }, - { - "author_name": "Georg F. Weber", - "author_inst": "Department of Surgery, Friedrich-Alexander University (FAU) Erlangen-Nurnberg and \tUniversitatsklinikum Erlangen" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.01.183236", "rel_title": "Development of a Synthetic Poxvirus-Based SARS-CoV-2 Vaccine", @@ -1335841,6 +1336890,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.23.20132522", + "rel_title": "The advantages of the simplest pandemic models", + "rel_date": "2020-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20132522", + "rel_abs": "As a pandemic of coronavirus spreads across the globe, people debate policies to mitigate its severity. Many complex, highly detailed models have been developed to help policy setters make better decisions. However, the basis of these models is unlikely to be understood by non-experts.\n\nWe describe the advantages of simple models for covid-19. We say a model is \"simple\" if its only parameter is the rate of contact between people in the population. This contact rate can vary over time, depending on choices by policy setters. Such models can be understood by a broad audience, and thus can be helpful in explaining the policy decisions to the public. They can be used to evaluate outcomes of different policy strategies. However, simple models have a disadvantage when dealing with inhomogeneous populations.\n\nTo augment the power of a simple model to evaluate complicated situations, we add what we call \"satellite\" equations that do not change the original model. For example, with the help of a satellite equation, one could know what his/her chance is of remaining uninfected through the end of epidemic. Satellite equations can model the effect of the epidemic on high-risk individuals, or death rates, or on nursing homes, and other isolated populations.\n\nTo compare simple models with complex models, we introduce our \"slightly complex\" Model J. We find the conclusions of simple and complex models can be quite similar. But, for each added complexity, a modeler may have to choose additional parameter values describing who will infect whom under what conditions, choices for which there is often little rationale but that can have a big impact on predictions. Our simulations suggest that the added complexity offers little predictive advantage.\n\nAuthor SummaryThere is a large variety of available data about the coronavirus pandemic, but we still lack data about some important factors. Who is likely to infect whom and under what conditions and how long after becoming infected? These factors are the essence of transmission dynamics. Two groups using identical complex models can be expected to make different predictions simply because they make different choices for such transmission parameters in the model. The audience has no way to choose between their predictions. We explain how simple models can be used to answer complex questions by adding what we call satellite equations, addressing questions involving age groups, death rates, and likelihood of transmission to nursing homes and to uninfected, isolated populations. Simple models are ideal for seeing what kinds of interventions are needed to achieve goals of policy setters.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sana Jahedi", + "author_inst": "University of New Brunswick" + }, + { + "author_name": "James Yorke", + "author_inst": "University of Maryland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.24.20138644", "rel_title": "Strong Correlation Between Prevalence of Severe Vitamin D Deficiency and Population Mortality Rate from COVID-19 in Europe", @@ -1337337,49 +1338409,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.06.30.181446", - "rel_title": "Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2", - "rel_date": "2020-07-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.30.181446", - "rel_abs": "BackgroundThe detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples.\n\nMethodsA virus panel based on the principle of biotinylated RNA-baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2 positive samples. Libraries generated from complex samples were sequenced via generic HTS and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted.\n\nResultsThe VirBaits set consists of 177,471 RNA-baits (80-mer) based on about 18,800 complete viral genomes targeting 35 epizootic and zoonotic viruses. In all tested samples, viruses with both DNA and RNA genomes were clearly enriched ranging from about 10-fold to 10,000-fold for viruses including distantly related viruses with at least 72% overall identity to viruses represented in the bait set. Viruses showing a lower overall identity (38% and 46%) to them were not enriched but could nonetheless be detected based on capturing conserved genome regions. The internal proficiency test supports the improved virus detection using the combination of HTS plus targeted enrichment but also point to the risk of carryover between samples.\n\nConclusionsThe VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector or research question. The risk of carryover needs to be taken into consideration. The application of the RNA-baits principle turned out to be user-friendly, and even non-experts (without sophisticated bioinformatics skills) can easily use the VirBait workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible without any problems as shown for SARS-CoV-2.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Claudia Wylezich", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Sten Calvelage", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Kore Schlottau", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Ute Ziegler", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Anne Pohlmann", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Dirk Hoeper", - "author_inst": "Friedrich-Loeffler-Institut" - }, - { - "author_name": "Martin Beer", - "author_inst": "Friedrich-Loeffler-Institut" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.07.01.150805", "rel_title": "Identification of peptide candidate against COVID-19 through reverse vaccinology: An immunoinformatics approach", @@ -1337643,6 +1338672,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.30.181297", + "rel_title": "If the link missed\uff1aCould inflammatory skin disorders with barrier dysfunction increase the risk of COVID-19?", + "rel_date": "2020-07-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.30.181297", + "rel_abs": "Since the end of 2019, COVID-19 pandemic caused by the SARS-CoV-2 emerged globally. The angiotensin-converting enzyme 2 (ACE2) on the cell surface is crucial for SARS-COV-2 entering into the cells. We use SARS-COV-2 pseudo virus and humanized ACE2 mice to mimic the possible transmitting of SARS-COV-2 through skin based on the data we found that skin ACE2 level is associated with skin pre-existing cutaneous conditions in human and mouse models and inflammatory skin disorders with barrier dysfunction increased the penetration of topical FITC conjugated spike protein into the skin. Our study indicated the possibility that the pre-existing cutaneous conditions could increase the risk for SARS-COV-2 infection.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC=\"FIGDIR/small/181297v4_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (33K):\norg.highwire.dtl.DTLVardef@14cef60org.highwire.dtl.DTLVardef@1f78c65org.highwire.dtl.DTLVardef@1224834org.highwire.dtl.DTLVardef@1b27475_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Qiannan Xu", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Lihong Chen", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Li Zhang", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Mengyan Hu", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Xiaopan Wang", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Qi Yang", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Yunchen Le", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Feng Xue", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Xia Li", + "author_inst": "Shanghai Ruijin Hospital" + }, + { + "author_name": "Jie Zheng", + "author_inst": "Shanghai Ruijin Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.06.24.20134288", "rel_title": "A retrospective study evaluating efficacy and safety of compassionate use of tocilizumab in 13 patients with severe-to-critically ill COVID-19: analysis of well-responding cases and rapidly-worsening cases after tocilizumab administration", @@ -1339295,29 +1340379,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.29.20142448", - "rel_title": "Using past and current data to estimate potential crisis service use in mental healthcare after the COVID-19 lockdown: South London and Maudsley data", - "rel_date": "2020-06-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142448", - "rel_abs": "The lockdown policy response to the COVID-19 pandemic in the UK has a potentially important impact on provision of mental healthcare with uncertain consequences over the 12 months ahead. Past activity may provide a means to predict future demand. Taking advantage of the Clinical Record Interactive Search (CRIS) data resource at the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for 1.2m residents in south London), we carried out a range of descriptive analyses to inform the Trust on patient groups who might be most likely to require inpatient and home treatment team (HTT) crisis care. We considered the 12 months following UK COVID-19 lockdown policy on 16th March, drawing on comparable findings from previous years, and quantified levels of change in service delivery to those most likely to receive crisis care. For 12-month crisis days from 16th March in 2015-19, we found that most (over 80%) were accounted for by inpatient care (rather than HTT), most (around 75%) were used by patients who were current or recent Trust patients at the commencement of follow-up, and highest numbers were used by patients with a previously recorded schizophreniform disorder diagnosis. For current/recent patients on 16th March there had been substantial reductions in use of inpatient care in the following 31 days in 2020, more than previous years; changes in total non-inpatient contact numbers did not differ in 2020 compared to previous years, although there had been a marked switch from face-to-face to virtual contacts.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Robert Stewart", - "author_inst": "King's College London" - }, - { - "author_name": "Matthew Broadbent", - "author_inst": "South London and Maudsley NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.06.29.20142554", "rel_title": "Citywide Nucleic Acid Screening of SARS-CoV-2 Infections in Post-lockdown Wuhan, China: Results and Implications", @@ -1339673,6 +1340734,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.29.20140129", + "rel_title": "Assessment of a Diagnostic Strategy Based on Chest Computed Tomography in Patients Hospitalized for COVID-19 Pneumonia: an observational study", + "rel_date": "2020-06-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20140129", + "rel_abs": "ObjectivesTo assess the relevance of a diagnostic strategy for COVID-19 based on chest computed tomography (CT) in patients with hospitalization criteria.\n\nSettingObservational study with retrospective analysis in a French emergency department (ED).\n\nParticipants and interventionFrom March 3 to April 2, 2020, 385 adult patients presenting to the ED for suspected COVID-19 underwent an evaluation that included history, physical examination, blood tests, real-time reverse transcription-polymerase chain reaction (RT-PCR) and chest CT. When the time-interval between chest CT and RT-PCR assays was longer than 7 days, patients were excluded from the study. Only patients with hospitalization criteria were included. Diagnosis accuracy was assessed using the sensitivity and specificity of RT-PCR.\n\nOutcomesSensitivity and specificity of RT-PCR, chest CT (also accompanied by lymphopenia) were measured and were also analyzed by subgroups of age and sex.\n\nResultsAmong 377 included subjects, RT-PCR was positive in 36%, while chest CT was compatible with a COVID-19 diagnosis in 59%. In the population with positive RT-PCR, there were more men (55% vs 37%, p=0.015), a higher frequency of reticular and, or, interlobular septal thickening (53% vs 31%, p=0.02) as well as a higher frequency of bilateral lesion distribution (98% vs 86%, p=0.01) compared to the population with negative RT-PCR. The proportion of lymphopenia was higher in men vs women (47% vs 39%, p=0.03) and varies between patients >80 versus 50-80 and p<0.001).\n\nUsing CT as reference, RT-PCR obtained a sensitivity of 61%, specificity of 93%. There was a significant difference between CT and RT-PCR diagnosis performance (p<0.001). When CT was accompanied by lymphopenia, sensitivity and specificity of RT-PCR were respectively 71% and 94%. CT abnormalities and lymphopenia provided diagnosis in 29% of patients with negative PCR.\n\nConclusionsChest CT had a superior yield than RT-PCR in COVID-19 hospitalized patients, especially when accompanied by lymphopenia.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Marine Thieux", + "author_inst": "Medipole Hopital Mutualiste Clinical Research Unit" + }, + { + "author_name": "Anne Charlotte Kalenderian", + "author_inst": "Medipole Hopital Mutualiste Imapole" + }, + { + "author_name": "Aurelie Chabrol", + "author_inst": "Medipole Hopital Mutualiste Imapole" + }, + { + "author_name": "Laurent Gendt", + "author_inst": "Medipole Hopital Mutualiste Eurofins CBM 69" + }, + { + "author_name": "Emma Giraudier", + "author_inst": "Lyon 2 University Masters Degree in Medical Translation and Scientific Writing" + }, + { + "author_name": "Herve Lelievre", + "author_inst": "Medipole Hopital Mutualiste Eurofins CBM 69" + }, + { + "author_name": "Samir Lounis", + "author_inst": "Medipole Hopital Mutualiste Imapole" + }, + { + "author_name": "Yves Mataix", + "author_inst": "Medipole Hopital Mutualiste Department of Medicine" + }, + { + "author_name": "Emeline Moderni", + "author_inst": "Lyon 2 University Masters Degree in Medical Translation and Scientific Writing" + }, + { + "author_name": "Laetitia Paradisi", + "author_inst": "Medipole Hopital Mutualiste Clinical Research Unit" + }, + { + "author_name": "Guillaume Ranchon", + "author_inst": "Medipole Hopital Mutualiste Emergency Department" + }, + { + "author_name": "Carlos El Khoury", + "author_inst": "Medipole Hopital Mutualiste Clinical Research Unit" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.28.20141838", "rel_title": "SARS-CoV-2 serological testing using electrochemiluminescence reveals arapid onset of seroconversion in severe COVID-19 patients", @@ -1341237,77 +1342361,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.26.20140731", - "rel_title": "SARS-CoV-2 in human sewage in Santa Catalina, Brazil, November 2019", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20140731", - "rel_abs": "We analysed human sewage located in Florianopolis (Santa Catalina, Brazil) from late October until the Brazil lockdown on early March. We detected SARS-CoV-2 in two samples collected independently on 27th November 2019 (5.49{+/-}0.02 log genome copies/L). Subsequent samplings were positive until 4th March 2020 (coinciding with the first COVID-19 case reported in Santa Catalina), with a SARS-CoV-2 RNA increase of one log (6.68{+/-}0.02 log genome copies/L). Our results show that SARS-CoV-2 has been circulating in Brazil since late November 2019, much earlier than the first reported case in the Americas (21st January 2020, USA).", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Gislaine Fongaro", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Patricia Hermes Stoco", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Doris Sobral Marques Souza", - "author_inst": "Federal University of Santa Catarina," - }, - { - "author_name": "Edmundo Carlos Grisard", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Maria Elisa Magri", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Paula Rogovski", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Marcos Andre Schorner", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Fernando Hartmann Barazzetti", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Ana Paula Christoff", - "author_inst": "BiomeHub" - }, - { - "author_name": "Luiz Felipe Valter de Oliveira", - "author_inst": "BiomeHub" - }, - { - "author_name": "Maria Luiza Bazzo", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Glauber Wagner", - "author_inst": "Federal University of Santa Catarina" - }, - { - "author_name": "Marta Hernandez", - "author_inst": "University of Burgos" - }, - { - "author_name": "David Rodriguez-Lazaro", - "author_inst": "University of Burgos" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.26.20141127", "rel_title": "From predictions to prescriptions: A data-drivenresponse to COVID-19", @@ -1341651,6 +1342704,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.06.27.20141689", + "rel_title": "Estimating the infection fatality risk of COVID-19 in New York City, March 1-May 16, 2020", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.27.20141689", + "rel_abs": "During March 1-May 16, 2020, 191,392 laboratory-confirmed COVID-19 cases were diagnosed and reported and 20,141 confirmed and probable COVID-19 deaths occurred among New York City (NYC) residents. We applied a network model-inference system developed to support the Citys pandemic response to estimate underlying SARS-CoV-2 infection rates. Based on these estimates, we further estimated the infection fatality risk (IFR) for 5 age groups (i.e. <25, 25-44, 45-64, 65-74, and 75+ years) and all ages overall, during March 1-May 16, 2020. We estimated an overall IFR of 1.45% (95% Credible Interval: 1.09-1.87%) in NYC. In particular, weekly IFR was estimated as high as 6.1% for 65-74 year-olds and 17.0% for 75+ year-olds. These results are based on more complete ascertainment of COVID-19-related deaths in NYC and thus likely more accurately reflect the true, higher burden of death due to COVID-19 than previously reported elsewhere. It is thus crucial that officials account for and closely monitor the infection rate and population health outcomes and enact prompt public health responses accordingly as the pandemic unfolds.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Wan Yang", + "author_inst": "Columbia University" + }, + { + "author_name": "Sasikiran Kandula", + "author_inst": "Columbia University" + }, + { + "author_name": "Mary Huynh", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Sharon K Greene", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Gretchen Van Wye", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Wenhui Li", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Hiu Tai Chan", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Emily McGibbon", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Alice Yeung", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Don Olson", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Anne Fine", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Jeffrey Shaman", + "author_inst": "Columbia University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.26.20131144", "rel_title": "The scale and dynamics of COVID-19 epidemics across Europe", @@ -1342799,57 +1343915,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.28.20142232", - "rel_title": "EVALUATION OF THE ROCHE ELECSYS ANTI-SARS-COV-2 ASSAY.", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.28.20142232", - "rel_abs": "BackgroundLittle is known about the performance of the Roche novel severe acute respiratory syndrome coronavirus 2 antibody (anti-SARS-CoV-2) assay. We provide an extensive evaluation of this fully automated assay on the Cobas e801/e602 immunoassay analysers.\n\nMethodsWe assessed the linearity, precision, and throughput of the Roche anti-SARS-CoV-2 assay. Sensitivity was calculated from 349 SARS-CoV-2 polymerase chain reaction (PCR) positive samples; specificity was determined from 714 coronavirus disease 2019 (COVID-19)-naive samples. We examined cross-reactivity against other antibody positive samples (syphilis, RF, ANA, ds-DNA, influenza, dengue, HBV, HCV) and the anti-SARS-CoV-2 kinetics.\n\nResultsThe assay cut-off index (COI) was linear up to 90.7. The inter-assay precision was 2.9% for a negative control (COI=0.1) and 5.1% for a positive control (COI=3.0). Assay time is 18min and results are available 1 minute later; throughput for 300 samples was 76 minutes. No cross-reactivity was observed with other antibody positive samples; specificity was 100%. The assay has a sensitivity of 97.1% 14 days after PCR positivity (POS) and 100% at [≥]21 days POS; 48.2% of cases had anti-SARS-CoV-2 within 6 days POS. In 11 subjects in whom serum was available prior to a positive antibody signal (COI [≥]1.0) the interval between the last negative and first positive COI (time to \"sero-conversion\") on average is 3 days (range 1-6 days) and 4 more days (range 1-7) for the anti-SARS-CoV-2 to plateau.\n\nConclusionThe Roche anti-SARS-CoV-2 assay shows excellent performance with minimal cross-reactivity from other viral and confounding antibodies. Antibody development and sero-conversion appears quite early.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "CS Lau", - "author_inst": "Changi General Hospital" - }, - { - "author_name": "SP Hoo", - "author_inst": "Changi General Hospital" - }, - { - "author_name": "SF Yew", - "author_inst": "Changi General Hospital" - }, - { - "author_name": "SK Ong", - "author_inst": "Sengkang General Hospital" - }, - { - "author_name": "LT Lum", - "author_inst": "Sengkang General Hospital" - }, - { - "author_name": "PY Heng", - "author_inst": "Khoo Teck Puat Hospital" - }, - { - "author_name": "JG Tan", - "author_inst": "Khoo Teck Puat Hospital" - }, - { - "author_name": "MS Wong", - "author_inst": "Khoo Teck Puat Hospital" - }, - { - "author_name": "TC Aw", - "author_inst": "Changi General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.28.20141945", "rel_title": "A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples", @@ -1343125,6 +1344190,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.29.20142281", + "rel_title": "Early Hemoglobin kinetics in response to ribavirin: Safety lesson learned from Hepatitis C to CoVID-19 therapy", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142281", + "rel_abs": "BackgroundRibavirin (RBV) is been used for SARS-CoV-2 infection. This drug is associated with a wide range of side effects, mainly anemia, so its use in patients with potential respiratory affectation could not be appropriate. The evidences of adverse events associated with RBV-use has mainly been derived in the context of hepatitis C (HCV) treatment, however the possible use of RBV in CoVID-19 patients could be limited to 14 days.\n\nMethodsLongitudinal study including HIV/HCV coinfected patients. We evaluate the hemoglobin dynamics and reductions as well as evaluate the development rate of anemia during the first 2 weeks of therapy in HCV infected patients.\n\nResults189 patients were included in the study. The median hemoglobin levels were 14.6 g/dL (IQR: 13.2-15.6 g/dL) and 13.5 g/dL (IQR: 12.3-14.5 g/dL) at weeks 1 and 2 of therapy, respectively. A cumulative number of 27 (14.2%) patients developed anemia (23 grade 1 [12.1%] and 4 grade 2 [2.1%]). We identify a baseline hemoglobin levels of 14 g/dL as the better cut-off to identify those patients with a high chance to develop anemia. Of the 132 patients with baseline hemoglobin level >14 g/dL, 8 developed anemia (6.1%) compared with 19 of 57 (33.3%) with hemoglobin levels lower than 14 g/dL (p < 0.001).\n\nConclusionsOur study shows valuable information about the early hemoglobin kinetic timing in patients on RBV-therapy, that could be useful to tailor CoVID-19 treatment if RBV use is considered.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Antonio Rivero-Juarez", + "author_inst": "IMIBIC" + }, + { + "author_name": "Mario Frias", + "author_inst": "IMIBIC" + }, + { + "author_name": "Isabel Machuca", + "author_inst": "IMIBIC" + }, + { + "author_name": "Marina Gallo", + "author_inst": "IMIBIC" + }, + { + "author_name": "Pedro Lopez-Lopez", + "author_inst": "IMIBIC" + }, + { + "author_name": "Angela Camacho", + "author_inst": "IMIBIC" + }, + { + "author_name": "Antonio Rivero", + "author_inst": "IMIBIC" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "toxicology" + }, { "rel_doi": "10.1101/2020.06.28.20141960", "rel_title": "Data presented by the UK government as lockdown was eased shows the transmission of COVID-19 had already increased.", @@ -1344281,57 +1345389,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.26.20141085", - "rel_title": "Identification of SARS-CoV-2 RNA in Healthcare Heating, Ventilation, and Air Conditioning Units", - "rel_date": "2020-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20141085", - "rel_abs": "Available information on Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) transmission by small particle aerosols continues to evolve rapidly. To assess the potential role of heating, ventilation, and air conditioning (HVAC) systems in airborne viral transmission, this study sought to determine the viral presence, if any, on air handling units in a healthcare setting where Coronavirus Disease 2019 (COVID-19) patients were being treated. The presence of SARS-CoV-2 RNA was detected in approximately 25% of samples taken from nine different locations in multiple air handlers. While samples were not evaluated for viral infectivity, the presence of viral RNA in air handlers raises the possibility that viral particles can enter and travel within the air handling system of a hospital, from room return air through high efficiency MERV-15 filters and into supply air ducts. Although no known transmission events were determined to be associated with these specimens, the findings suggest the potential for HVAC systems to facilitate transmission by environmental contamination via shared air volumes with locations remote from areas where infected persons reside. More work is needed to further evaluate the risk of SARS-CoV-2 transmission via HVAC systems and to verify effectiveness of building operations mitigation strategies for the protection of building occupants. These results are important within and outside of healthcare settings and may present a matter of some urgency for building operators of facilities that are not equipped with high-efficiency filtration.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Patrick F Horve", - "author_inst": "University of Oregon" - }, - { - "author_name": "Leslie Dietz", - "author_inst": "University of Oregon" - }, - { - "author_name": "Mark Fretz", - "author_inst": "University of Oregon" - }, - { - "author_name": "David A Constant", - "author_inst": "Oregon Health and Science University" - }, - { - "author_name": "Andrew Wilkes", - "author_inst": "Oregon Health and Science University" - }, - { - "author_name": "John M Townes", - "author_inst": "Oregon Health and Science University" - }, - { - "author_name": "Robert G Martindale", - "author_inst": "Oregon Health and Science University" - }, - { - "author_name": "William B Messer", - "author_inst": "Oregon Health and Science University" - }, - { - "author_name": "Kevin Van Den Wymelenberg", - "author_inst": "University of Oregon" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.26.20141341", "rel_title": "A Streamlined CyTOF Workflow To Facilitate Standardized Multi-Site Immune Profiling of COVID-19 Patients", @@ -1344515,6 +1345572,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.26.20140616", + "rel_title": "The impact of SARS-CoV-2 transmission fear and COVID-19 pandemic on the mental health of patients with primary immunodeficiency disorders, severe asthma, and other high-risk groups", + "rel_date": "2020-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20140616", + "rel_abs": "BackgroundThe adverse effects of COVID-19 pandemic on the mental health of high-risk group patients for morbidity and mortality and its impact on public health in the long term have not been clearly determined.\n\nObjectiveTo determine the level of COVID-19 related transmission fear and anxiety in healthcare workers and patients with primary immunodeficiency disorder (PID), severe asthma, and the ones with other comorbidities.\n\nMethodsThe healthcare workers and patients with PID, severe asthma (all patients receiving biological agent treatment), malignancy, cardiovascular disease, hypertension (90% of patients receiving ACEI or ARB therapy), diabetes mellitus (42 % of patients receiving DPP-4 inhibitor therapy) were included in the study. A total of 560 participants, 80 individuals in each group, were provided. The hospital anxiety and depression scale (HADS) and Fear of illness and virus evaluation (FIVE) scales were applied to the groups with face to face interview methods.\n\nResultsThe mean age was 49.30 {+/-} 13.74 years and 306 (55 %) were female. The FIVE Scale and HADS-A scale scores of health care workers were significantly higher than other groups scores (p = 0.001 and 0.006). The second-highest scores belonged to patients with PID. There was no significant difference between the groups for the HADS-D score (p=0.07). The lowest score in all scales was observed in patients with hypertension.\n\nConclusionsThis study demonstrated that in the pandemic process, patients with primary immunodeficiency, asthma patients, and other comorbid patients, especially healthcare workers, should be referred to the centers for the detection and treatment of mental health conditions.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Fatih Colkesen", + "author_inst": "Department of Clinical Immunology and Allergy, Necmettin Erbakan University Meram Faculty of Medicine," + }, + { + "author_name": "Oguzhan Kilincel", + "author_inst": "Department of Psychiatry, Sakarya Yenikent State Hospital" + }, + { + "author_name": "Mehmet Sozen", + "author_inst": "Department of Endocrinology and Metabolism, Kocaeli University Faculty of Medicine" + }, + { + "author_name": "Eray Yildiz", + "author_inst": "Department of Clinical Immunology and Allergy, Necmettin Erbakan University Meram Faculty of Medicine" + }, + { + "author_name": "Sengul Beyaz", + "author_inst": "Division of Clinical Immunology and Allergy, Department of Internal Medicine, Istanbul Faculty of Medicine, Istanbul University" + }, + { + "author_name": "Fatma Colkesen", + "author_inst": "Department of Infectious Diseases and Clinical Microbiology, University of Health Sciences, Konya Training and Research Hospital" + }, + { + "author_name": "Gokhan Aytekin", + "author_inst": "Department of Clinical Immunology and Allergy, University of Health Sciences, Konya Training and Research Hospital" + }, + { + "author_name": "Mehmet Zahit Kocak", + "author_inst": "Department of Medical Oncology, Meram Faculty of Medicine, Necmettin Erbakan University" + }, + { + "author_name": "Yakup Alsancak", + "author_inst": "Department of Cardiology , Meram Faculty of Medicine, Necmettin Erbakan University" + }, + { + "author_name": "Murat Araz", + "author_inst": "Department of Medical Oncology, Meram Faculty of Medicine, Necmettin Erbakan University" + }, + { + "author_name": "Sevket Arslan", + "author_inst": "Department of Clinical Immunology and Allergy, Necmettin Erbakan University Meram Faculty of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.06.25.20139907", "rel_title": "Teach, and teach and teach: does the average citizen use masks correctly during daily activities? Results from an observational study with more than 12,000 participants", @@ -1345735,197 +1346851,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.22.20133413", - "rel_title": "Tocilizumab and steroid treatment in patients with severe Covid-19 pneumonia.", - "rel_date": "2020-06-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20133413", - "rel_abs": "IntroductionCoronavirus disease 2019 (COVID-19) can lead to respiratory failure due to severe immune response. Treatment targeting this immune response might be beneficial but there is limited evidence on its efficacy.\n\nThe aim of this study was to determine if early treatment of patients with COVID-19 pneumonia with tocilizumab and/or steroids was associated with better outcome.\n\nMethodsThis observational single-center study included patients with COVID-19 pneumonia who were not intubated and received either standard of care (SOC, controls) or SOC plus early (within 3 days from hospital admission) anti-inflammatory treatment. SOC consisted of hydroxychloroquine 400mg bid plus, in those admitted before March 24th, also darunavir/ritonavir. Anti-inflammatory treatment consisted of either tocilizumab (8mg/kg intravenously or 162mg subcutaneously) or methylprednisolone 1 mg/kg for 5 days or both. Failure was defined as intubation or death, and the endpoints were failure-free survival (primary endpoint) and overall survival (secondary) at day 30. Difference between the groups was estimated as Hazard Ratio by a propensity score weighted Cox regression analysis (HROW).\n\nResultsOverall, 196 adults were included in the analyses. They were mainly male (67.4%), with comorbidities (78.1%) and severe COVID-19 pneumonia (83.7%). Median age was 67.9 years (range, 30-100) and median PaO2/FiO2 200 mmHg (IQR 133-289). Among them, 130 received early anti-inflammatory treatment with: tocilizumab (n=29, 22.3%), methylprednisolone (n=45, 34.6%), or both (n=56, 43.1%). The adjusted failure-free survival among tocilizumab/methylprednisolone/SOC treated patients vs. SOC was 80.8% (95%CI, 72.8-86.7) vs. 64.1% (95%CI, 51.3-74.0), HROW 0.48, 95%CI, 0.23-0.99; p=0.049. The overall survival among tocilizumab/methylprednisolone/SOC patients vs. SOC was 85.9% (95%CI, 80.7-92.6) vs. 71.9% (95%CI, 46-73), HROW 0.41, 95%CI: 0.19-0.89, p=0.025.\n\nConclusionEarly adjunctive treatment with tocilizumab, methylprednisolone or both may improve outcomes in non-intubated patients with COVID-19 pneumonia.", - "rel_num_authors": 44, - "rel_authors": [ - { - "author_name": "Malgorzata Mikulska", - "author_inst": "University of Genova" - }, - { - "author_name": "Laura Ambra Nicolini", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Alessio Signori", - "author_inst": "Section of Biostatistics, Department of Health Sciences, University of Genova, Genova, Italy" - }, - { - "author_name": "Antonio Di Biagio", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy; Division of Infectious Diseases, IRCCS Ospedale Poli" - }, - { - "author_name": "Chiara Sepulcri", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Chiara Russo", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Silvia Dettori", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Marco Berruti", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Maria Pia Sormani", - "author_inst": "Section of Biostatistics, Department of Health Sciences, University of Genova, Genova, Italy" - }, - { - "author_name": "Daniele Roberto Giacobbe", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy; Division of Infectious Diseases, IRCCS Ospedale Poli" - }, - { - "author_name": "Antonio Vena", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Andrea De Maria", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy; Division of Infectious Diseases, IRCCS Ospedale Poli" - }, - { - "author_name": "Chiara Dentone", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Lucia Taramasso", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Michele Mirabella", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy; Division of Infectious Diseases, IRCCS Ospedale Poli" - }, - { - "author_name": "Laura Magnasco", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy; Division of Infectious Diseases, IRCCS Ospedale Poli" - }, - { - "author_name": "Sara Mora", - "author_inst": "Department of Informatics, Bioengineering, Robotics and System Engineering, University of Genoa, Genoa, Italy" - }, - { - "author_name": "Emanuele Delfino", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Federica Toscanini", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Elisa Balletto", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy; Division of Infectious Diseases, IRCCS Ospedale Poli" - }, - { - "author_name": "Anna Ida Alessandrini", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Federico Baldi", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Federica Briano", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Marco Camera", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Ferdinando Dodi", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Antonio Ferrazin", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Laura Labate", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Giovanni Mazzarello", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Rachele Pincino", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Federica Portunato", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Stefania Tutino", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy" - }, - { - "author_name": "Emanuela Barisione", - "author_inst": "Interventional Pulmonology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Bianca Bruzzone", - "author_inst": "Hygiene Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy" - }, - { - "author_name": "Andrea Orsi", - "author_inst": "Hygiene Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy; Department of Health Sciences, University of Genoa" - }, - { - "author_name": "Eva Schenone", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Nirmala Rosseti", - "author_inst": "Division of Infectious Diseases, IRCCS Ospedale Policlinico San Martino, Genoa, Italy" - }, - { - "author_name": "Elisabetta Sasso", - "author_inst": "Pharmacy Complex Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy" - }, - { - "author_name": "Giorgio Da Rin", - "author_inst": "Medicine Laboratory, IRCCS Ospedale Policlinico San Martino, Genova, Italy" - }, - { - "author_name": "Paolo Pelosi", - "author_inst": "Department of Surgical Sciences and Integrated Diagnostics, University of Genova, Genova, Italy; Anesthesia and Intensive Care, San Martino Policlinico Hospital" - }, - { - "author_name": "Sabrina Beltramini", - "author_inst": "Pharmacy Complex Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy" - }, - { - "author_name": "Mauro Giacomini", - "author_inst": "Department of Informatics, Bioengineering, Robotics and System Engineering, University of Genoa, Genoa, Italy" - }, - { - "author_name": "Giancarlo Icardi", - "author_inst": "Hygiene Unit, IRCCS Ospedale Policlinico San Martino, Genova, Italy; Department of Health Sciences, University of Genoa" - }, - { - "author_name": "Angelo Gratarola", - "author_inst": "Department of Emergency and Urgency, San Martino Policlinico Hospital, IRCCS for Oncology and Neurosciences, Genoa, Italy" - }, - { - "author_name": "Matteo Bassetti", - "author_inst": "Division of Infectious Diseases, Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy; Division of Infectious Diseases, IRCCS Ospedale Poli" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.23.20134072", "rel_title": "Treatment of ARDS and hyperinflammation in COVID-19 with IL-6 antagonist Tocilizumab: a tertiary care experience from Pakistan", @@ -1346125,6 +1347050,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.23.20138222", + "rel_title": "Phylogenomics and phylodynamics of SARS-CoV-2 retrieved genomes from India", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20138222", + "rel_abs": "The ongoing SARS-CoV-2 pandemic is one of the biggest outbreaks after the Spanish flu of 1918. Understanding the epidemiology of viral outbreaks is the first step towards vaccine development programs. This is the first phylodynamics study attempted on of SARS-CoV-2 genomes from India to infer its current evolution in the context of an ongoing pandemic. Out of 286 retrieved SARS-CoV-2 whole genomes from India, 138 haplotypes were generated and analyzed. Median-joining network was built to investigate the relatedness of SARS-CoV-2 haplotypes in India. The BDSIR package of BEAST2 was used to calculate the reproduction number (R0) and the infectious rate of the virus. Past and current population trend was investigated using the stamp date method in coalescent Bayesian skyline plot, implemented in BEAST2 and by exponential growth prior in BEAST 1.10.4. Median-joining network reveals two distinct ancestral clusters A and B showing genetic affinities with Wuhan outbreak sample. The network also illustrates the autochthonous development of isolates in a few instances. High basic reproduction number of SARS-nCoV-2 in India points towards the phase of active community transmission. The Bayesian skyline plot revel exponential rise in the effective population size (Ne) of Indian isolates from the first week of January to the first week of April 2020. More genome sequencing and analyses of the virus will be required in coming days to monitor COVID19 after the upliftment of lock down in India.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sameera Farah", + "author_inst": "Department of Zoology, Laboratory of Molecular and Conservation Genetics, Govt. Vidarbha Institute of Science and Humanities, Amravati-444604-India; Department " + }, + { + "author_name": "Ashwin Atkulwar", + "author_inst": "Department of Zoology, Laboratory of Molecular and Conservation Genetics, Govt. Vidarbha Institute of Science and Humanities, VMV Road, Amravati-444604-Indial; " + }, + { + "author_name": "Manas Ranjan Praharaj", + "author_inst": "National Institute of Animal Biotechnology, Gowlidoddy, Hyderabad, Telangana-500032-India." + }, + { + "author_name": "Raja Khan", + "author_inst": "Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P - 243122, India." + }, + { + "author_name": "Ravikumar Gandham", + "author_inst": "National Institute of Animal Biotechnology, Gowlidoddy, Hyderabad, Telangana-500032-India." + }, + { + "author_name": "Mumtaz Baig", + "author_inst": "Department of Zoology, Laboratory of Molecular and Conservation Genetics, Govt. Vidarbha Institute of Science and Humanities, Amravati-444604-India; Department " + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.22.20134130", "rel_title": "Impact of public health interventions on the COVID-19 epidemic: a stochastic model based on data from an African island", @@ -1347185,29 +1348149,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.25.20139865", - "rel_title": "A Logistic Curve in the SIR Model and Its Application to Deaths by COVID-19 in Japan", - "rel_date": "2020-06-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20139865", - "rel_abs": "Approximate solutions of SIR equations are given, based on a logistic growth curve in the Biology. These solutions are applied to fix the basic reproduction number and the removed ratio c, especially from data of accumulated number of deaths in Japan COVID-19. We then discuss the end of the epidemic. These logistic curve results are compared with the exact results of the SIR model.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Kazuyasu Shigemoto", - "author_inst": "Tezukayama University" - }, - { - "author_name": "Takesi Saito", - "author_inst": "Kwansei Gakuin University" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.25.20139782", "rel_title": "An Epidemic Model SIPHERD and its application for prediction of the spread of COVID-19 infection in India", @@ -1347419,6 +1348360,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.24.20139329", + "rel_title": "A Decision Analytic Approach for Social Distancing Policies During the COVID-19 Pandemic", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139329", + "rel_abs": "The COVID-19 pandemic has become a crucial public health issue in many countries including the United States. In the absence of the right vaccine strain and sufficient antiviral stockpiles on hand, non-pharmaceutical interventions have become valuable public health tools at the early stages of the pandemic and they are employed by many countries across the globe. These interventions are designed to increase social distancing between individuals to reduce the transmission of the virus and eventually dampen the burden on the healthcare system. The virus transmissibility is a function of the average number of contacts individuals have in their communities and it is highly dependent on population density and daily mobility patterns, along with other social factors. These show significant variation across the United States. In this article, we study the effectiveness of social distancing measures in communities with different population density. Specifically, first we show how the empirical estimation of reproduction number differs for two completely different states, thus the experience of the COVID-19 outbreak is drastically different, suggesting different outbreak growth rates in practice. Second, we develop an age-structured compartmental model for simulating the disease spread in order to demonstrate the variation in the observed outbreak characteristics. We find that early trigger and late trigger options present a trade-off between the peak magnitude and the overall death toll of the outbreak which may also vary across different populations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Zeynep Ertem", + "author_inst": "University of Southern California" + }, + { + "author_name": "Ozgur Araz", + "author_inst": "University of Nebraska" + }, + { + "author_name": "Maytee Cruz-Aponte", + "author_inst": "University of Puerto Rico" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.25.20140384", "rel_title": "Seroprevalence of Antibodies to SARS-CoV-2 in Six Sites in the United States, March 23-May 3, 2020", @@ -1348751,141 +1349719,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.06.26.173203", - "rel_title": "Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2", - "rel_date": "2020-06-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.26.173203", - "rel_abs": "The emergence of the novel human coronavirus, SARS-CoV-2, causes a global COVID-19 (coronavirus disease 2019) pandemic. Here, we have characterized and compared viral populations of SARS-CoV-2 among COVID-19 patients within and across households. Our work showed an active viral replication activity in the human respiratory tract and the co-existence of genetically distinct viruses within the same host. The inter-host comparison among viral populations further revealed a narrow transmission bottleneck between patients from the same households, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions.\n\nAuthor summaryIn this study, we compared SARS-CoV-2 populations of 13 Chinese COVID-19 patients. Those viral populations contained a considerable proportion of viral sub-genomic messenger RNAs (sgmRNA), reflecting an active viral replication activity in the respiratory tract tissues. The comparison of 66 identified intra-host variants further showed a low viral genetic distance between intra-household patients and a narrow transmission bottleneck size. Despite the co-existence of genetically distinct viruses within the same host, most intra-host minor variants were not shared between transmission pairs, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions. Furthermore, the narrow bottleneck and active viral activity in the respiratory tract show that the passage of a small number of virions can cause infection. Our data have therefore delivered a key genomic resource for the SARS-CoV-2 transmission research and enhanced our understanding of the evolutionary dynamics of SARS-CoV-2.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Daxi Wang", - "author_inst": "BGI" - }, - { - "author_name": "Yanqun Wang", - "author_inst": "First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Wanying Sun", - "author_inst": "BGI" - }, - { - "author_name": "Lu Zhang", - "author_inst": "First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Jingkai Ji", - "author_inst": "BGI" - }, - { - "author_name": "Zhaoyong Zhang", - "author_inst": "First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Xinyi Cheng", - "author_inst": "BGI" - }, - { - "author_name": "Yimin Li", - "author_inst": "First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Fei Xiao", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-Sen University" - }, - { - "author_name": "Airu Zhu", - "author_inst": "First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Jiandong Li", - "author_inst": "BGI" - }, - { - "author_name": "Peidi Ren", - "author_inst": "BGI" - }, - { - "author_name": "Zhihua Ou", - "author_inst": "BGI" - }, - { - "author_name": "Minfeng Xiao", - "author_inst": "BGI" - }, - { - "author_name": "Min Li", - "author_inst": "BGI" - }, - { - "author_name": "Ziqing Deng", - "author_inst": "BGI" - }, - { - "author_name": "Huanzi Zhong", - "author_inst": "BGI" - }, - { - "author_name": "Fuqiang Li", - "author_inst": "BGI" - }, - { - "author_name": "Weijun Chen", - "author_inst": "BGI" - }, - { - "author_name": "Shida Zhu", - "author_inst": "BGI" - }, - { - "author_name": "Wenjing Wang", - "author_inst": "BGI" - }, - { - "author_name": "Yongwei Zhang", - "author_inst": "BGI" - }, - { - "author_name": "Xun Xu", - "author_inst": "BGI" - }, - { - "author_name": "Xin Jin", - "author_inst": "BGI" - }, - { - "author_name": "Jingxian Zhao", - "author_inst": "First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Nanshan Zhong", - "author_inst": "First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Wenwei Zhang", - "author_inst": "BGI" - }, - { - "author_name": "Jincun Zhao", - "author_inst": "First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Junhua Li", - "author_inst": "BGI" - }, - { - "author_name": "Yonghao Xu", - "author_inst": "First Affiliated Hospital of Guangzhou Medical University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.06.26.174193", "rel_title": "A cytosine-to-uracil change within the programmed -1 ribosomal frameshift signal of SARS-CoV-2 results in structural similarities with the MERS-CoV signal", @@ -1349109,6 +1349942,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.24.20138982", + "rel_title": "Modeling the Covid-19 Pandemic Response of the US States", + "rel_date": "2020-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20138982", + "rel_abs": "BackgroundThe United States of America (USA) has been the country worst affected, in absolute terms, by the Covid-19 pandemic. The country comprises 50 states under a federal system. The impact of the pandemic has resulted in different responses at the state level, which are driven by differing intervention policies, demographics, connectedness and other factors. Understanding the dynamics of the Covid-19 pandemic at the state level is essential in predicting its future evolution.\n\nObjectiveOur objective is to identify and characterize multiple waves of the pandemic by analyzing the reported infected population curve in each of the 50 US states. Based on the intensity of the waves, characterized by declining, stationary, or increasing strengths, each states response can be inferred and quantified.\n\nMethodsWe apply a recently proposed multiple-wave model to fit the infected population data for each state in USA, and use the proposed Pandemic Response Index to quantify their response to the Covid-19 pandemic.\n\nResultsWe have analyzed reported infected cases from each one of the 50 USA states and the District of Columbia, based on the multiple-wave model, and present the relevant parameters. Multiple waves have been identified and this model is found to describe the data better. Each of the states can be classified into one of three distinct classes characterized by declining, increasing, or stationary strength of the waves following the initial one. The effectiveness of intervention measures can be inferred by the peak intensities of the waves, and states with similar population characteristics can be directly compared. We estimate how much lower the number of infections might have been, if early and strict intervention measures had been imposed to stop the disease spread at the first wave, as was the case for certain states. Based on our models results, we compute the value of the Pandemic Response Index, a recently introduced metric for quantifying in an objective manner the response to the pandemic.\n\nConclusionsOur results reveal a series of epidemic waves, characterizing USAs pandemic response at the state level, and also infer to what extent the imposition of early intervention measures could have had on the spread and impact of the disease. As of June 11, 2020, only 19 states and the District of Columbia (40% of the total) clearly exhibit declining trends in the numbers of reported infected cases, while 13 states exhibit stationary and 18 states increasing trends in the numbers of reported cases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Georgios Neofotistos", + "author_inst": "Institute for Applied Computational Science (IACS), John A. Paulson School of Engineering and Applied Sciences, Harvard University" + }, + { + "author_name": "Efthimios Kaxiras", + "author_inst": "Institute for Applied Computational Science (IACS), John A. Paulson School of Engineering and Applied Sciences, Harvard University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.24.20139196", "rel_title": "How Many Lives Has Lockdown Saved in the UK?", @@ -1350332,133 +1351188,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.06.24.162156", - "rel_title": "CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes using Nanopore sequencing", - "rel_date": "2020-06-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.24.162156", - "rel_abs": "The COVID-19 pandemic has spread to almost every country in the world since it started in China in late 2019. Controlling the pandemic requires a multifaceted approach including whole genome sequencing to support public health interventions at local and national levels. One of the most widely used methods for sequencing is the ARTIC protocol, a tiling PCR approach followed by Oxford Nanopore sequencing (ONT) of up to 96 samples at a time. There is a need, however, for a flexible, platform agnostic, method that can provide multiple throughput options depending on changing requirements as the pandemic peaks and troughs. Here we present CoronaHiT, a method capable of multiplexing up to 96 small genomes on a single MinION flowcell or >384 genomes on Illumina NextSeq, using transposase mediated addition of adapters and PCR based addition of barcodes to ARTIC PCR products. We demonstrate the method by sequencing 95 and 59 SARS-CoV-2 genomes for routine and rapid outbreak response runs, respectively, on Nanopore and Illumina platforms and compare to the standard ARTIC LoCost nanopore method. Of the 154 samples sequenced using the three approaches, genomes with [≥] 90% coverage (GISAID criteria) were generated for 64.3% of samples for ARTIC LoCost, 71.4% for CoronaHiT-ONT, and 76.6% for CoronaHiT-Illumina and have almost identical clustering on a maximum likelihood tree. In conclusion, we demonstrate that CoronaHiT can multiplex up to 96 SARS-CoV-2 genomes per MinION flowcell and that Illumina sequencing can be performed on the same libraries, which will allow significantly higher throughput. CoronaHiT provides increased coverage for higher Ct samples, thereby increasing the number of high quality genomes that pass the GISAID QC threshold. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally, to help control the pandemic.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "David J Baker", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Alp Aydin", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Thanh Le-Viet", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Gemma L Kay", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Steven Rudder", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Leonardo de Oliveira Martins", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Ana P Tedim", - "author_inst": "Quadram Institute Bioscience, Grupo de Investigacion Biomedica en Sepsis - BioSepsis. Hospital Universitario Rio Hortega/Instituto de Investigacion Biomedica de" - }, - { - "author_name": "Anastasia Kolyva", - "author_inst": "Quadram Institute Bioscience, Norfolk and Norwich University Hospital" - }, - { - "author_name": "Maria Diaz", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Nabil-Fareed Alikhan", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Lizzie Meadows", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Andrew Bell", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Ana Victoria Gutierrez", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Alexander J Trotter", - "author_inst": "Quadram Institute Bioscience, University of East Anglia" - }, - { - "author_name": "Nicholas M Thomson", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Rachel Gilroy", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Luke Griffith", - "author_inst": "University of East Anglia" - }, - { - "author_name": "Evelien M Adriaenssens", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Rachael Stanley", - "author_inst": "Norfolk and Norwich University Hospital" - }, - { - "author_name": "Ian G Charles", - "author_inst": "Quadram Institute Bioscience, University of East Anglia" - }, - { - "author_name": "Ngozi Elumogo", - "author_inst": "Quadram Institute Bioscience, Norfolk and Norwich University Hospital" - }, - { - "author_name": "John Wain", - "author_inst": "Quadram Institute Bioscience, University of East Anglia" - }, - { - "author_name": "Reenesh Prakash", - "author_inst": "Norfolk and Norwich University Hospital" - }, - { - "author_name": "Emma Meader", - "author_inst": "Norfolk and Norwich University Hospital" - }, - { - "author_name": "Alison E Mather", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Mark A Webber", - "author_inst": "Quadram Institute Bioscience" - }, - { - "author_name": "Samir Dervisevic", - "author_inst": "Norfolk and Norwich University Hospital" - }, - { - "author_name": "Andrew J Page", - "author_inst": "Quadram Institute Bioscience" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.06.24.169334", "rel_title": "Pixatimod (PG545), a clinical-stage heparan sulfate mimetic, is a potent inhibitor of the SARS-CoV-2 virus", @@ -1350750,6 +1351479,37 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.06.24.168534", + "rel_title": "Lung expression of genes encoding SARS-CoV-2 cell entry molecules and antiviral restriction factors: interindividual differences are associated with age and germline variants", + "rel_date": "2020-06-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.24.168534", + "rel_abs": "Germline variants in genes involved in SARS-CoV-2 cell entry (i.e. ACE2 and TMPRSS2) may influence the susceptibility to infection, as may polymorphisms in genes involved in the innate host response to viruses (e.g. APOBEC3 family). We searched for polymorphisms acting, in lung tissue, as expression quantitative trait loci (eQTLs) for 15 candidate COVID-19 susceptibility genes, selected for their roles in virus cell entry and host antiviral responses. No significant eQTLs were identified for ACE2 and TMPRSS2 genes, whose expression levels did not associate with either sex or age of the 408 patients whose non-diseased lung tissue was analyzed. Instead, we identified seven cis-eQTLs (FDR<0.05) for APOBEC3D and APOBEC3G (rs139296, rs9611092, rs139331, rs8177832, rs17537581, rs61362448, and rs738469). The genetic control of the expression of APOBEC3 genes, which encode enzymes that interfere with virus replication, may explain interindividual differences in risk or severity of viral infections. Future studies should investigate the role of host genetics in COVID-19 patients using a genome-wide approach, to identify other genes whose expression levels are associated with susceptibility to SARS-CoV-2 infection or COVID-19 severity.\n\nAuthor summaryIdentification of expression quantitative trait loci (eQTLs) has become commonplace in functional studies on the role of individual genetic variants in susceptibility to diseases. In COVID-19, it has been proposed that individual variants in SARS-CoV-2 cell entry and innate host response genes may influence the susceptibility to infection. We searched for polymorphisms acting, in non-diseased lung tissue of 408 patients, as eQTLs for 15 candidate COVID-19 susceptibility genes, selected for their roles in virus cell entry and host antiviral responses. Seven cis-eQTLs were detected for APOBEC3D and APOBEC3G genes, which encode enzymes that interfere with virus replication. No significant eQTLs were identified for ACE2 and TMPRSS2 genes. Therefore, the identified eQTLs may represent candidate loci modulating interindividual differences in risk or severity of SARS-CoV-2 virus infection.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Chiara E. Cotroneo", + "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy" + }, + { + "author_name": "Nunzia Mangano", + "author_inst": "Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy" + }, + { + "author_name": "Tommaso A. Dragani", + "author_inst": "Fondazione IRCCS Istituto Nazionale Tumori" + }, + { + "author_name": "Francesca Colombo", + "author_inst": "Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate (MI), Italy" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.06.23.167791", "rel_title": "N-glycosylation network construction and analysis to modify glycans on the spike S glycoprotein of SARS-CoV-2.", @@ -1351765,25 +1352525,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.24.20138800", - "rel_title": "Analysis and Forecast of COVID-19 Pandemic in Pakistan", - "rel_date": "2020-06-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20138800", - "rel_abs": "The COVID-19 infections in Pakistan are spreading at an exponential rate and a point may soon be reached where rigorous prevention measures would need to be adopted. Mathematical models can help define the scale of an epidemic and the rate at which an infection can spread in a community. I used ARIMA Model, Diffusion Model, SIRD Model and Prophet Model to forecast the magnitude of the COVID-19 pandemic in Pakistan and compared the numbers with the reported cases on the national database. Results depicts that Pakistan could hit peak number of infectious cases between June 2020 and July, 2020.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Abdul Bari Malik", - "author_inst": "Micromerger Pvt Ltd." - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.23.20138685", "rel_title": "HAS COUNTRYWIDE LOCKDOWN WORKED AS A FEASIBLE MEASURE IN BENDING THE COVID-19 CURVE IN DEVELOPING COUNTRIES?", @@ -1351975,6 +1352716,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.15.20117747", + "rel_title": "SARS-CoV-2 titers in wastewater foreshadow dynamics and clinical presentation of new COVID-19 cases", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20117747", + "rel_abs": "Current estimates of COVID-19 prevalence are largely based on symptomatic, clinically diagnosed cases. The existence of a large number of undiagnosed infections hampers population-wide investigation of viral circulation. Here, we use longitudinal wastewater analysis to track SARS-CoV-2 dynamics in wastewater at a major urban wastewater treatment facility in Massachusetts, between early January and May 2020. SARS-CoV-2 was first detected in wastewater on March 3. Viral titers in wastewater increased exponentially from mid-March to mid-April, after which they began to decline. Viral titers in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 4-10 days earlier in wastewater than in clinical data. We inferred viral shedding dynamics by modeling wastewater viral titers as a convolution of back-dated new clinical cases with the viral shedding function of an individual. The inferred viral shedding function showed an early peak, likely before symptom onset and clinical diagnosis, consistent with emerging clinical and experimental evidence. Finally, we found that wastewater viral titers at the neighborhood level correlate better with demographic variables than with population size. This work suggests that longitudinal wastewater analysis can be used to identify trends in disease transmission in advance of clinical case reporting, and may shed light on infection characteristics that are difficult to capture in clinical investigations, such as early viral shedding dynamics.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Fuqing Wu", + "author_inst": "MIT" + }, + { + "author_name": "Amy Xiao", + "author_inst": "MIT" + }, + { + "author_name": "Jianbo Zhang", + "author_inst": "MIT" + }, + { + "author_name": "Katya Moniz", + "author_inst": "MIT" + }, + { + "author_name": "Noriko Endo", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Federica Armas", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Richard Bonneau", + "author_inst": "New York University" + }, + { + "author_name": "Megan A Brown", + "author_inst": "New York University" + }, + { + "author_name": "Mary Bushman", + "author_inst": "Harvard University" + }, + { + "author_name": "Peter R Chai", + "author_inst": "Harvard University" + }, + { + "author_name": "Claire Duvallet", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Timothy B Erickson", + "author_inst": "Harvard University" + }, + { + "author_name": "Katelyn Foppe", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Newsha Ghaeli", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Xiaoqiong Gu", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "William P Hanage", + "author_inst": "Harvard University" + }, + { + "author_name": "Katherine H Huang", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Wei Lin Lee", + "author_inst": "Singapore-MIT Alliance for Research and Technology" + }, + { + "author_name": "Mariana Matus", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Kyle A McElroy", + "author_inst": "Biobot Analytics, Inc." + }, + { + "author_name": "Jonathan Nagler", + "author_inst": "Center for Data Science NYU" + }, + { + "author_name": "Steven F Rhode", + "author_inst": "Massachusetts Water Resources Authority, Boston, MA" + }, + { + "author_name": "Mauricio Santillana", + "author_inst": "Harvard University" + }, + { + "author_name": "Joshua A Tucker", + "author_inst": "Center for Data Science NYU" + }, + { + "author_name": "Stefan Wuertz", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Shijie Zhao", + "author_inst": "MIT" + }, + { + "author_name": "Janelle Thompson", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Eric J Alm", + "author_inst": "Massachusetts Institute of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.22.20132910", "rel_title": "Insufficient social distancing may be related to a future COVID-19 outbreak in Ijui-Brazil: Predictions of further social interventions.", @@ -1353063,45 +1353931,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.22.20137075", - "rel_title": "The validation of the original and modified Caprini score in COVID-19 patients", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20137075", - "rel_abs": "ObjectiveThe study aimed to validate the original Caprini score and its modifications considering coronavirus disease (COVID-19) as a severe prothrombotic condition in patients admitted to the hospital with confirmed infection.\n\nMethodsThe relevant data were extracted from the electronic medical records with the implemented Caprini score and were evaluated retrospectively. The score was calculated twice: by the physician at the admission and by the investigator at discharge or after death. The second calculation at discharge, considered additional risk factors that occurred during inpatient treatment. Besides the original Caprini score (a version of 2005), the modified version added the elevation of D-dimer and specific scores for COVID-19 as follows: 2 points for asymptomatic, 3 points for symptomatic and 5 points for symptomatic infection with positive D-dimer, were evaluated in a retrospective manner. The primary endpoint was symptomatic venous thromboembolism (VTE) confirmed by appropriate imaging testing or dissection. The secondary endpoint included the unfavorable outcome as a combination of symptomatic VTE, admission to the intensive care unit, the requirement for invasive mechanical ventilation, and death. The association of eight different versions of the Caprini score with outcomes was evaluated.\n\nResultsTotally 168 patients (83 males and 85 females at the age of 58.3{+/-}12.7 years old) were admitted to the hospital between April 30 and May 29, 2020, and were discharged or died up to the time of data analysis. The original Caprini score varied between 2-12 (5.4{+/-}1.8) at the admission and between 2-15 (5.9{+/-}2.5) at discharge or death. The presence of the virus increased these scores and resulted in an increased score with the maximal value for those including COVID-19 points (10.0{+/-}3.0). Patients received prophylactic (2.4%), intermediate (76.8%), or therapeutic (20.8%) doses of enoxaparin. Despite this, the symptomatic VTE was detected in 11 (6.5%) and unfavorable outcomes in 31 (18.5%) patients. The Caprini score of all eight versions demonstrated a significant association with VTE with the highest predictability for the original scale when assessed at discharge. Supplementation of the original score by elevated D-dimer improved predictability only at the admission. Four versions of the Caprini score calculated at the admission had a significant correlation with the unfavorable outcome with the minor advantages of specific COVID-19 points.\n\nConclusionThe study identified a significant correlation between the Caprini score and the risk of VTE or unfavorable outcomes in COVID-19 patients. All models, including specific COVID-19 scores, showed high predictability with minor differences.\n\nARTICLE HIGHLIGHTSO_ST_ABSType of ResearchC_ST_ABSA single-center retrospective analysis of prospectively collected data.\n\nKey FindingsThe original version of the Caprini score and its modifications considering the elevation of D-dimer and specific COVID-19 points demonstrated a significant association with symptomatic VTE and unfavorable outcome in 168 hospitalized COVID-19 patients, of whom 6.5% developed symptomatic VTE and 18.5% - unfavorable outcome despite routine pharmacoprophylaxis.\n\nTake Home MessageThe Caprini score allows stratification of COVID-19 inpatients according to their VTE risk and identification of subjects at extremely high risk.\n\nTABLE OF CONTENTS SUMMARYThis retrospective analysis of prospectively collected data demonstrates the significant association between the original and modified Caprini score and symptomatic VTE or unfavorable outcome in 168 patients with confirmed COVID-19. The Caprini score may be used for VTE risk assessment, and identification of persons at extremely high risk among COVID-19 patients admitted to the hospital.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sergey Tsaplin", - "author_inst": "Pirogov Russian National Research Medical University, Moscow, Russian Federation" - }, - { - "author_name": "Ilya Schastlivtsev", - "author_inst": "Pirogov Russian National Research Medical University, Moscow, Russian Federation" - }, - { - "author_name": "Kirill Lobastov", - "author_inst": "Pirogov Russian National Research Medical University" - }, - { - "author_name": "Sergey Zhuravlev", - "author_inst": "Clinical Hospital no.1 (Volynskaya) of the President's Administration of the Russian Federation, Moscow, Russian Federation" - }, - { - "author_name": "Victor Barinov", - "author_inst": "Clinical Hospital no.1 (Volynskaya) of the President's Administration of the Russian Federation, Moscow, Russian Federation" - }, - { - "author_name": "Joseph Caprini", - "author_inst": "University of Chicago Pritzker School of Medicine, Chicago, IL, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "surgery" - }, { "rel_doi": "10.1101/2020.06.22.20136838", "rel_title": "First results from the UK COVID-19 Serology in Oncology Staff Study (CSOS)", @@ -1353341,6 +1354170,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.21.20136937", + "rel_title": "A Statistical and Dynamical Model for Forecasting COVID-19 Deaths based on a Hybrid Asymmetric Gaussian and SEIR Construct", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20136937", + "rel_abs": "BackgroundThe limitations of forecasting (real-time statistical) and predictive (dynamic epidemiological) models have become apparent as COVID-19 has progressed from a rapid exponential ascent to a slower decent, which is dependent on unknowable parameters such as extent of social distancing and easing. We present a means to optimize a forecasting model by functionalizing our previously reported Asymmetric Gaussian model with SEIR-like parameters. Conversely, SEIR models can be adapted to better incorporate real-time data.\n\nMethodsOur previously reported asymmetric Gaussian model was shown to greatly improve on forecasting accuracy relative to use of symmetric functions, such as Gaussian and error functions for death rates and cumulative deaths, respectively. However, the reported asymmetric Gaussian implementation, which fitted well to the ascent and much of the recovery side of the real death rate data, was not agile enough to respond to changing social behavior that is resulting in persistence of infections and deaths in the later stage of recovery. We have introduced a time-dependent {sigma}(t) parameter to account for transmission rate variability due to the effects of behavioral changes such as social distancing and subsequent social easing. The {sigma}(t) parameter is analogous to the basic reproduction number R0 (infection factor) that is evidently not a constant during the progression of COVID-19 for a particular population. The popularly used SEIR model and its many variants are also incorporating a time dependent R0(t) to better describe the effects of social distancing and social easing to improve predictive capability when extrapolating from real-time data.\n\nResultsComparisons are given for the previously reported Asymmetric Gaussian model and to the revised, what we call, SEIR Gaussian model. We also have developed an analogous model based on R0(t) that we call SEIR Statistical model to show the correspondence that can be attained. It is shown that these two models can replicate each other and therefore provide similar forecasts based on fitting to the same real-time data. We show the results for reported U.S. death rates up to June 12, 2020 at which time the cumulative death count was 113,820. The forecasted cumulative deaths for these two models and compared to the University of Washington (UW) IHME model are 140,440, 139,272, and 149,690 (for 8/4/20) and 147,819, 148, 912, and 201,129 (for 10/1/20), respectively. We also show how the SEIR asymmetric Gaussian model can also account for various scenarios of social distancing, social easing, and even re-bound outbreaks where the death and case rates begin climbing again.\n\nConclusionsForecasting models, based on real-time data, are essential for guiding policy and human behavior to minimize the deadly impact of COVID-19 while balancing the need to socialize and energize the economy. It is becoming clear that changing social behavior from isolation to easing requires models that can adapt to the changing transmission rate in order to more accurately forecast death and case rates. We believe our asymmetric Gaussian approach has advantages over modified SEIR models in offering simpler governing equations that are dependent on fewer variables.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jack A. Syage", + "author_inst": "ImmunogenX" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.21.20136929", "rel_title": "Derivation and Validation of Clinical Prediction Rule for COVID-19 Mortality in Ontario, Canada", @@ -1354581,89 +1355429,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.23.20138081", - "rel_title": "A primary care approach to the COVID-19 pandemic: clinical features and natural history of 2,073 suspected cases in the Corona Sao Caetano programme, Sao Paulo, Brazil", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20138081", - "rel_abs": "BackgroundDespite most cases not requiring hospital care, there are limited community-based clinical data on COVID-19.\n\nMethods and findingsThe Corona Sao Caetano program is a primary care initiative offering COVID-19 care to all residents of Sao Caetano do Sul, Brazil. After triage of potentially severe cases, consecutive patients presenting between 13th April and 13th May 2020 were tested at home with SARS-CoV-2 reverse transcriptase (RT) PCR; positive patients were followed up for 14 days. RT-PCR-negative patients were offered SARS-CoV-2 serology. We describe the clinical features, virology and natural history of this prospective population-based cohort. Of 2,073 suspected COVID-19 cases, 1,583 (76{middle dot}4%) were tested by RT-PCR, of whom 444 (28{middle dot}0%, 95%CI: 25{middle dot}9% - 30{middle dot}3%) were positive; 604/1,136 (53%) RT-PCR-negative patients underwent serology, of whom 52 (8{middle dot}6%) tested SARS-CoV-2 seropositive. The most common symptoms of COVID-19 were cough, fatigue, myalgia and headache; whereas self-reported fever, anosmia, and ageusia were most associated with a positive COVID-19 diagnosis. RT-PCR cycle thresholds were lower in men, older patients, those with fever and arthralgia, and around symptom onset. The rates of hospitalization and death among 444 RT-PCR-positive cases were 6{middle dot}7% and 0{middle dot}7%, respectively, with older age and obesity more frequent in the hospitalized group.\n\nConclusionsCOVID-19 presents similarly to other mild respiratory disease in primary care. Some symptoms assist the differential diagnosis. Most patients can be managed at home.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Fabio E Leal", - "author_inst": "Universidade Municipal de Sao Caetano do Sul (USCS), Sao Caetano do Sul, Brazil" - }, - { - "author_name": "Maria C Mendes-Correa", - "author_inst": "Instituto de Medicina Tropical (LIM-52, LIM-46, LIM-49) and Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sao" - }, - { - "author_name": "Lewis F Buss", - "author_inst": "Instituto de Medicina Tropical (LIM-52, LIM-46, LIM-49) and Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sa" - }, - { - "author_name": "Silvia F Costa", - "author_inst": "Instituto de Medicina Tropical (LIM-52, LIM-46, LIM-49) and Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sao" - }, - { - "author_name": "Joao CS Bizario", - "author_inst": "Universidade Municipal de Sao Caetano do Sul (USCS), Sao Caetano do Sul, Brazil" - }, - { - "author_name": "Sonia RP Souza", - "author_inst": "Universidade Municipal de Sao Caetano do Sul (USCS), Sao Caetano do Sul, Brazil" - }, - { - "author_name": "Osorio Thomaz", - "author_inst": "Instituto de Pesquisas Tecnologicas do Estado de Sao Paulo - IPT" - }, - { - "author_name": "Tania R Tozetto-Mendoza", - "author_inst": "Instituto de Medicina Tropical (LIM-52, LIM-46, LIM-49) and Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sao" - }, - { - "author_name": "Lucy S Villas-Boas", - "author_inst": "Instituto de Medicina Tropical (LIM-52, LIM-46, LIM-49) and Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sao" - }, - { - "author_name": "Lea CO Silva", - "author_inst": "Instituto de Medicina Tropical (LIM-52, LIM-46, LIM-49) and Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sao" - }, - { - "author_name": "Regina MZ Grespan", - "author_inst": "Universidade Municipal de Sao Caetano do Sul (USCS), Rua Santo Antonio, Sao Caetano do Sul, Brazil" - }, - { - "author_name": "Ligia Capuani", - "author_inst": "Modular Research System, Sao Paulo, Brazil" - }, - { - "author_name": "Renata Buccheri", - "author_inst": "Instituto de Medicina Tropical (LIM-52, LIM-46, LIM-49) and Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sao" - }, - { - "author_name": "Helves Domingues", - "author_inst": "Modular Research System, Sao Paulo, Brazil" - }, - { - "author_name": "Neal DE Alexander", - "author_inst": "London School of Hygiene and Tropical Medicine, London, United Kingdom" - }, - { - "author_name": "Philippe Mayaud", - "author_inst": "London School of Hygiene and Tropical Medicine, London, United Kingdom" - }, - { - "author_name": "Ester C Sabino", - "author_inst": "Instituto de Medicina Tropical (LIM-52, LIM-46, LIM-49) and Departamento de Molestias Infecciosas e Parasitarias da Faculdade de Medicina da Universidade de Sa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2020.06.23.20137901", "rel_title": "Factors associated with self-reported anxiety, depression, and general health during the UK lockdown; a cross-sectional survey", @@ -1354819,6 +1355584,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.23.20137596", + "rel_title": "Platelets can contain SARS-CoV-2 RNA and are hyperactivated in COVID-19", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20137596", + "rel_abs": "RationaleIn addition to the overwhelming lung inflammation that prevails in COVID-19, hypercoagulation and thrombosis contribute to the lethality of subjects infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Platelets are chiefly implicated in thrombosis. Moreover, they can interact with viruses and are an important source of inflammatory mediators. While a lower platelet count is associated with severity and mortality, little is known about platelet function during COVID-19.\n\nObjectiveTo evaluate the contribution of platelets to inflammation and thrombosis in COVID-19 patients.\n\nMethods and ResultsWe document the presence of SARS-CoV-2 RNA in platelets of COVID-19 patients. Exhaustive assessment of cytokines in plasma and in platelets revealed the modulation of platelet-associated cytokine levels in COVID-19, pointing to a direct contribution of platelets to the plasmatic cytokine load. Moreover, we demonstrate that platelets release their alpha- and dense-granule contents and phosphatidylserine-exposing extracellular vesicles. Functionally, platelets were hyperactivated in COVID-19 subjects, with aggregation occurring at suboptimal thrombin concentrations. Furthermore, platelets adhered more efficiently onto collagen-coated surfaces under flow conditions.\n\nConclusionsThese data suggest that platelets could participate in the dissemination of SARS-CoV-2 and in the overwhelming thrombo-inflammation observed in COVID-19. Thus, blockade of platelet activation pathways may improve outcomes in this disease.\n\nKEY POINTSPlatelets are a source of inflammatory cytokines and degranulate in COVID-19 Platelets contain SARS-CoV-2 RNA molecules and are prone to activation in COVID-19\n\nSubject termsInfectious diseases/Emerging infectious diseases, SARS-CoV-2, COVID-19, Hematology, Platelets", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Younes Zaid", + "author_inst": "Cheikh Zaid Hospital; Mohammed V University" + }, + { + "author_name": "Florian Puhm", + "author_inst": "Universite Laval" + }, + { + "author_name": "Isabelle Allaeys", + "author_inst": "Universite Laval" + }, + { + "author_name": "Abdallah Naya", + "author_inst": "Hassan II University" + }, + { + "author_name": "Mounia Oudghiri", + "author_inst": "Hassan II University" + }, + { + "author_name": "Loubna Khalki", + "author_inst": "Mohammed VI University of Health Sciences (UM6SS)" + }, + { + "author_name": "Youness Limami", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Nabil Zaid", + "author_inst": "Mohammed V University" + }, + { + "author_name": "Khalid Sadki", + "author_inst": "Mohammed V University" + }, + { + "author_name": "Rafiqua Ben El Haj", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Wissal Maher", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Lamiae Belayachi", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Bouchra Belefquih", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Amina Benouda", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Amine Cheikh", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Yahia Cherrah", + "author_inst": "Cheikh Zaid Hospital" + }, + { + "author_name": "Louis Flamand", + "author_inst": "Universite Laval" + }, + { + "author_name": "Fadila Guessous", + "author_inst": "Mohammed VI University of Health Sciences (UM6SS); University of Virginia" + }, + { + "author_name": "Eric Boilard", + "author_inst": "Universite Laval" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.23.20137521", "rel_title": "SARS CoV-2 Serosurvey in Addis Ababa, Ethiopia", @@ -1356075,53 +1356931,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.21.20129049", - "rel_title": "Estimation of fatality rate in Africa through the behavior of COVID-19 in Italy relevance to age profiles", - "rel_date": "2020-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20129049", - "rel_abs": "The emergence and pandemic of COVID-19 has rapidly become a global concern. In Italy, on 27 March 2020, there were 8165 deaths and 80539 confirmed cases of COVID-19. Demographic situations, like age profiles is reported to be the cause of high case fatality rate (CFR) in Italy. In Africa, the COVID-19 pandemic has not yet grasped epic proportion, but the estimation of CFR is still needed. We compared the CFR observed in Italy with the age profiles in 46 Africa countries and 2 territories which are already confirmed COVID-19 case. The estimation of the CFR in Africa ranges between (1.0%-5.4%) while in Italy is 10.1%. The five highest CFR countries and territories in Africa are Reunion (5.4%), Mauritius (5.1%), Tunisia (3.9%), Seychelles (3.8%) and Morocco (3.3%). The last three countries with low CFR are Uganda (1.0%), Zambia (1.1%) and Angola (1.1%). The observed difference is related to the age profiles.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "NZUNGIZE LAMBERT", - "author_inst": "Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, " - }, - { - "author_name": "Diane UMUHOZA", - "author_inst": "State Key Laboratory of Silkworm Genome Biology, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest Univer" - }, - { - "author_name": "Yongdong Dai", - "author_inst": "Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of EcoEnvironment and Bio-Resource of the Three Gorges Area, Ministry of Education, S" - }, - { - "author_name": "Stech A E. NZAOU", - "author_inst": "Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, " - }, - { - "author_name": "Mohammed Asaad", - "author_inst": "Department of Biotechnology, Faculty of Science and Technology, Omdurman Islamic University, Sudan" - }, - { - "author_name": "M. A. Abokadoum", - "author_inst": "Department of Microbiology and Immunology, Al-Azhar University, Egypt" - }, - { - "author_name": "Ulrich Aymard Ekomi Moure", - "author_inst": "Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, " - }, - { - "author_name": "Jianping Xie", - "author_inst": "Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Ministry of Education, " - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.18.20134619", "rel_title": "Epidemiological and clinical characteristics in patients with SARS-CoV-2 antibody negative probable COVID-19 in Wuhan", @@ -1356397,6 +1357206,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.20.20134387", + "rel_title": "A systematic review and meta-analysis reveals long and dispersive incubation period of COVID-19", + "rel_date": "2020-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.20.20134387", + "rel_abs": "BackgroundThe incubation period of SARS-CoV-2 remains uncertain, which has important implications for estimating transmission potential, forecasting epidemic trends, and decision-making in prevention and control.\n\nPurposeTo estimate the central tendency and dispersion for incubation period of COVID-19 and, in turn, assess the effect of a certain length of quarantine for close contacts in active monitoring.\n\nData SourcesPubMed, Embase, medRxiv, bioRxiv, and arXiv, searched up to April 26, 2020\n\nStudy SelectionCOVID-19 studies that described either individual-level incubation period data or summarized statistics for central tendency and dispersion measures of incubation period were recruited.\n\nData ExtractionFrom each recruited study, either individual-level incubation period data or summarized statistics for central tendency and dispersion measures were extracted, as well as population characteristics including sample size, average age, and male proportion.\n\nData SynthesisFifty-six studies encompassing 4 095 cases were included in this meta-analysis. The estimated median incubation period for general transmissions was 5.8 days [95% confidence interval (95%CI), 5.3 to 6.2 d]. Median and dispersion were higher for SARS-CoV-2 incubation compared to other viral respiratory infections. Furthermore, about 20 in 10 000 contacts in active monitoring would develop symptoms after 14 days, or below 1 in 10 000 for young-age infections or asymptomatic transmissions.\n\nLimitationSmall sample sizes for subgroups; some data were possibly used repeatedly in different studies; limited studies for outside mainland China; non-negligible intra-study heterogeneity.\n\nConclusionThe long, dispersive incubation period of SARS-CoV-2 contributes to the global spread of COVID-19. Yet, a 14-day quarantine period is sufficient to trace and identify symptomatic infections, which while could be justified according to a better understanding of the crucial parameters.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yongyue Wei", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Liangmin Wei", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Yihan Liu", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Lihong Huang", + "author_inst": "Zhongshan Hospital Fudan University" + }, + { + "author_name": "Sipeng Shen", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Ruyang Zhang", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Jiajin Chen", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Yang Zhao", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Hongbing Shen", + "author_inst": "Nanjing Medical University" + }, + { + "author_name": "Feng Chen", + "author_inst": "Nanjing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.18.20132571", "rel_title": "Transcriptomic profiling of disease severity in patients with COVID-19 reveals role of blood clotting and vasculature related genes", @@ -1357449,121 +1358313,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.21.163394", - "rel_title": "Endemic human coronaviruses induce distinct antibody repertoires in adults and children", - "rel_date": "2020-06-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.21.163394", - "rel_abs": "Four endemic human coronaviruses (HCoVs) are commonly associated with acute respiratory infection in humans. B cell responses to these \"common cold\" viruses remain incompletely understood. Here we report a comprehensive analysis of CoV-specific antibody repertoires in 231 children and 1168 adults using phage-immunoprecipitation sequencing. Seroprevalence of antibodies to endemic HCoVs ranged between ~4 and 27% depending on the species and cohort. We identified at least 136 novel linear B cell epitopes. Antibody repertoires against endemic HCoVs were qualitatively different between children and adults in that anti-HCoV IgG specificities more frequently found among children targeted functionally important and structurally conserved regions of the spike, nucleocapsid and matrix proteins. Moreover, antibody specificities targeting the highly conserved fusion peptide region and S2 cleavage site of the spike protein were broadly cross-reactive with peptides of epidemic human and non-human coronaviruses. In contrast, an acidic tandem repeat in the N-terminal region of the Nsp3 subdomain of the HCoV-HKU1 polyprotein was the predominant target of antibody responses in adult donors. Our findings shed light on the dominant species-specific and pan-CoV target sites of human antibody responses to coronavirus infection, thereby providing important insights for the development of prophylactic or therapeutic monoclonal antibodies and vaccine design.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Taushif Khan", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Mahbuba Rahman", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Fatima Al Ali", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Susie SY Huang", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Manar Ata", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Qian Zhang", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Paul Bastard", - "author_inst": "INSERM U1163, Necker Hospital for Sick Children" - }, - { - "author_name": "Zhiyong Liu", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Emmanuelle Jouanguy", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Vivien Beziat", - "author_inst": "INSERM U1163, Necker Hospital for Sick Children" - }, - { - "author_name": "Aurelie Cobat", - "author_inst": "INSERM U1163, Necker Hospital for Sick Children" - }, - { - "author_name": "Gheyath K Nasrallah", - "author_inst": "Qatar University" - }, - { - "author_name": "Hadi Yassine", - "author_inst": "Qatar University" - }, - { - "author_name": "Maria Smatti", - "author_inst": "Qatar University" - }, - { - "author_name": "Amira Sayeed", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Isabelle Vandernoot", - "author_inst": "Hopital Erasme" - }, - { - "author_name": "Jean-Christophe Goffard", - "author_inst": "Hopital Erasme" - }, - { - "author_name": "Guillaume Smits", - "author_inst": "Hopital Erasme" - }, - { - "author_name": "Isabelle Migeotte", - "author_inst": "Hopital Erasme" - }, - { - "author_name": "Filomeen Haerynck", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Isabelle Meyts", - "author_inst": "University Hospitals Leuven" - }, - { - "author_name": "Laurent Abel", - "author_inst": "INSERM U1163, Necker Hospital for Sick Children" - }, - { - "author_name": "Jean-Laurent Casanova", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Mohammad R Hasan", - "author_inst": "Sidra Medicine" - }, - { - "author_name": "Nico Marr", - "author_inst": "Sidra Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.06.22.164442", "rel_title": "Pathogenicity, tissue tropism and potential vertical transmission of SARSr-CoV-2 in Malayan pangolins", @@ -1357754,6 +1358503,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.21.162396", + "rel_title": "Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis", + "rel_date": "2020-06-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.21.162396", + "rel_abs": "COVID-19, the disease caused by SARS-CoV-2 (1), was declared a pandemic by the World Health Organization (WHO) in March 2020 (2). While awaiting a vaccine, several antivirals are being used to manage the disease with limited success (3, 4). To expand this arsenal, we screened 4 compound libraries: a United States Food and Drug Administration (FDA) approved drug library, an angiotensin converting enzyme-2 (ACE2) targeted compound library, a flavonoid compound library as well as a natural product library. Of the 121 compounds identified with activity against SARS-CoV-2, 7 were shortlisted for validation. We show for the first time that the active form of Vitamin D, calcitriol, exhibits significant potent activity against SARS-CoV-2. This finding paves the way for consideration of host-directed therapies for ring prophylaxis of contacts of SARS-CoV-2 patients.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Chee Keng Mok", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Yan Ling Ng", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Bintou Ahmadou Ahidjo", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Regina Ching Hua Lee", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Marcus Wing Choy Loe", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Jing Liu", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Kai Sen Tan", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Parveen Kaur", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Wee Joo Chng", + "author_inst": "National University of Singapore" + }, + { + "author_name": "John Eu Li Wong", + "author_inst": "National University of Singapore" + }, + { + "author_name": "De Yun Wang", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Er Wei Hao", + "author_inst": "Guangxi University of Chinese Medicine, China" + }, + { + "author_name": "Xiaotao Hao", + "author_inst": "Guangxi University of Chinese Medicine" + }, + { + "author_name": "Yong Wah Tan", + "author_inst": "Agency for Science, Technology and Research, Singapore" + }, + { + "author_name": "Tze Minn Mak", + "author_inst": "National Public Health Laboratory, Singapore" + }, + { + "author_name": "Cui Lin", + "author_inst": "National Public Health Laboratory, Singapore" + }, + { + "author_name": "Raymond V.T.P Lin", + "author_inst": "National Public Health Laboratory, Singapore" + }, + { + "author_name": "Paul A Tambyah", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Jiagang Deng", + "author_inst": "Guangxi University of Chinese Medicine, China" + }, + { + "author_name": "Justin Jang Hann Chu", + "author_inst": "National University of Singapore" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.22.133355", "rel_title": "Companion vaccine Bioinformatic design tool reveals limited functional genomic variability of SARS-Cov-2 Spike Receptor Binding Domain", @@ -1359346,33 +1360190,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.20.163030", - "rel_title": "Engineered human mesenchymal stem cells as new vaccine platform for COVID-19", - "rel_date": "2020-06-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.20.163030", - "rel_abs": "Recently, there are several routes for COVID-19 vaccine research, yet their weaknesses lie in low efficiency, tolerability, immune adaptability and safety. We describe a new approach to COVID-19 based on engineered human mesenchymal stem cells(hu-MSC), which is like a small protein antigen response device, but will be gradually cleared and degraded by bodys immune system among recognization process. The antibody response results show that this is effective and fast. Furthermore, after several antibody response tests, we obtained an injection of a set of cocktail-like modified human mesenchymal stem cell line. This strategy opened a new avenue for vaccine design against COVID-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Junhua Liu", - "author_inst": "Shenyang University of Chemical Technology" - }, - { - "author_name": "Huping Jiao", - "author_inst": "Jilin University" - }, - { - "author_name": "Xiushan Yin", - "author_inst": "Shenyang University of Chemical Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.19.20135392", "rel_title": "Half of children entitled to free school meals do not have access to the scheme during the COVID-19 lockdown in the UK.", @@ -1359628,6 +1360445,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.20.162560", + "rel_title": "Multi-Omics and Integrated Network Approach to Unveil Evolutionary Patterns, Mutational Hotspots, Functional Crosstalk and Regulatory Interactions in SARS-CoV-2", + "rel_date": "2020-06-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.20.162560", + "rel_abs": "SARS-CoV-2 pandemic resulted in 92 million cases in a span of one year. The study focuses on understanding population specific variations attributing its high rate of infections in specific geographical regions particularly in USA. Rigorous phylogenomic network analysis of complete SARS-CoV-2 genomes (245) inferred five central clades named a (ancestral), b, c, d and e (subtype e1 & e2). The clade d & e2 were found exclusively comprising of USA. Clades were distinguished by 10 co-mutational combinations in Nsp3, ORF8, Nsp13, S, Nsp12, Nsp2 and Nsp6. Our analysis revealed that only 67.46% of SNP mutations were at amino acid level. T1103P mutation in Nsp3 was predicted to increase protein stability in 238 strains except 6 strains which were marked as ancestral type; whereas co-mutation (P409L & Y446C) in Nsp13 were found in 64 genomes from USA highlighting its 100% co-occurrence. Docking highlighted mutation (D614G) caused reduction in binding of Spike proteins with ACE2, but it also showed better interaction with TMPRSS2 receptor contributing to high transmissibility among USA strains. We also found host proteins, MYO5A, MYO5B, MYO5C had maximum interaction with viral proteins (N, S, M). Thus, blocking the internalization pathway by inhibiting MYO5 proteins which could be an effective target for COVID-19 treatment. The functional annotations of the HPI network were found to be closely associated with hypoxia and thrombotic conditions confirming the vulnerability and severity of infection. We also screened CpG islands in Nsp1 & N conferring ability of SARS-CoV-2 to enter and trigger ZAP activity inside host cell.\n\nImportanceIn the current study we presented a global view of mutational pattern observed in SARS-CoV-2 virus transmission. This provided a who-infect-whom geographical model since the early pandemic. This is hitherto the most comprehensive comparative genomics analysis of full-length genomes for co-mutations at different geographical regions specially in USA strains. Compositional structural biology results suggested that mutations have balance of contrary forces effect on pathogenicity suggesting only few mutations to effective at translation level but not all. Novel HPI analysis and CpG predictions elucidates the proof of concept of hypoxia and thrombotic conditions in several patients. Thus, the current study focuses the understanding of population specific variations attributing high rate of SARS-CoV-2 infections in specific geographical regions which may eventually be vital for the most severely affected countries and regions for sharp development of custom-made vindication strategies.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Vipin Gupta", + "author_inst": "PHIXGEN PVT. LTD" + }, + { + "author_name": "Shazia Haider", + "author_inst": "Jaypee Institute of Information Technology, Noida" + }, + { + "author_name": "Mansi Verma", + "author_inst": "Sri Venkateswara College, University of Delhi" + }, + { + "author_name": "Nirjara Singhvi", + "author_inst": "University of Delhi" + }, + { + "author_name": "Kalaiarasan Ponnusamy", + "author_inst": "Jawaharlal Nehru University" + }, + { + "author_name": "Md. Zubbair Malik", + "author_inst": "Jawaharlal Nehru University, New Delhi, India." + }, + { + "author_name": "Helianthous Verma", + "author_inst": "Ramjas College, University of Delhi" + }, + { + "author_name": "Roshan Kumar", + "author_inst": "Magadh University, Bodh Gaya, Bihar" + }, + { + "author_name": "Utkarsh Sood", + "author_inst": "The Energy and Resources Institute" + }, + { + "author_name": "Princy Hira", + "author_inst": "Maitreyi College, University of Delhi." + }, + { + "author_name": "Shiva Satija", + "author_inst": "Sri Venkateswara College, University of Delhi" + }, + { + "author_name": "Rup Lal", + "author_inst": "The Energy and Resources Institute" + }, + { + "author_name": "Yogendra Singh", + "author_inst": "University of Delhi" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.19.20135996", "rel_title": "The support needs of Australian primary health care nurses during the COVID-19 pandemic", @@ -1360752,53 +1361636,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.06.18.20134395", - "rel_title": "SARS-CoV-2 in human milk is inactivated by Holder pasteurization but not cold storage", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134395", - "rel_abs": "As the COVID-19 pandemic evolves, human milk banks worldwide continue to provide donor human milk to vulnerable infants who lack access to mothers own milk. Under these circumstances, ensuring the safety of donor human milk is paramount, as the risk of vertical transmission of SARS-CoV-2 is not well understood. Here, we investigate the inactivation of SARS-CoV-2 in human milk by pasteurisation, and the stability of SARS-CoV-2 in human milk under cold storage (freezing or refrigeration). Following heating to 63{degrees}C or 56{degrees}C for 30 minutes, SARS-CoV-2 replication competent (i.e. live) virus was undetected in both human milk and the control medium. Cold storage of SARS-CoV-2 in human milk (either at 4{degrees}C or - 30{degrees}C) did not significantly impact infectious viral load over a 48 hour period. Our findings demonstrate that SARS-CoV-2 can be effectively inactivated by Holder pasteurisation, and confirm that existing milk bank processes will effectively mitigate the risk of transmission of SARS-COV-2 to vulnerable infants through pasteurised donor human milk.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Gregory J Walker", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Vanessa Clifford", - "author_inst": "Australian Red Cross Lifeblood" - }, - { - "author_name": "Nidhi Bansal", - "author_inst": "University of Queensland" - }, - { - "author_name": "Alberto Ospina Stella", - "author_inst": "Kirby Institute, University of New South Wales" - }, - { - "author_name": "Stuart Turville", - "author_inst": "Kirby Institute, University of New South Wales" - }, - { - "author_name": "Sacha Stelzer-Braid", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Laura D Klein", - "author_inst": "Australian Red Cross Lifeblood" - }, - { - "author_name": "William Rawlinson", - "author_inst": "University of New South Wales" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.18.20134304", "rel_title": "THE USE OF DENATURING SOLUTION AS COLLECTION AND TRANSPORT MEDIA TO IMPROVE SARS-COV-2 RNA DETECTION AND REDUCE INFECTION OF LABORATORY PERSONNEL", @@ -1361034,6 +1361871,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.18.20134700", + "rel_title": "Predictable county-level estimates of R0 for COVID-19 needed for public health planning in the USA", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134700", + "rel_abs": "The basic reproduction number, R0, determines the rate of spread of a communicable disease and therefore gives fundamental information needed to plan public health interventions. Estimated R0 values are only useful, however, if they accurately predict the future potential rate of spread. Using mortality records, we estimated the rate of spread of COVID-19 among 160 counties and county-aggregates in the USA. Most of the high among-county variance in the rate of spread was explained by four factors: the timing of the county-level outbreak (partial R2 = 0.093), population size (partial R2 = 0.34), population density (partial R2 = 0.13), and spatial location (partial R2 = 0.42). Of these, the effect of timing is explained by early steps that people and governments took to reduce transmission, and population size is explained by the sample size of deaths that affects the statistical ability to estimate R0. For predictions of future spread, population density is important, likely because it scales the average contact rate among people. To generate support for a possible explanation for the importance of spatial location, we show that SARS-CoV-2 strains containing the G614 mutation to the spike gene are associated with higher rates of spread (P = 0.016). The high predictability of R0 based on population density and spatial location allowed us to extend estimates to all 3109 counties in the lower 48 States. The high variation of R0 among counties argues for public health policies that are enacted at the county level for controlling COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Anthony R Ives", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Claudio Bozzuto", + "author_inst": "Wildlife Analysis GmbH, Zurich, Switzerland" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.18.20134346", "rel_title": "The Relationship between the Global Burden of Influenza from 2017-2019 and COVID-19", @@ -1362886,165 +1363746,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.18.160655", - "rel_title": "A single dose of recombinant VSV-{triangleup}G-spike vaccine provides protection against SARS-CoV-2 challenge", - "rel_date": "2020-06-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.18.160655", - "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 that emerged in December 2019 in China resulted in over 7.8 million infections and over 430,000 deaths worldwide, imposing an urgent need for rapid development of an efficient and cost-effective vaccine, suitable for mass immunization. Here, we generated a replication competent recombinant VSV-{Delta}G-spike vaccine, in which the glycoprotein of VSV was replaced by the spike protein of the SARS-CoV-2. In vitro characterization of the recombinant VSV-{Delta}G-spike indicated expression and presentation of the spike protein on the viral membrane with antigenic similarity to SARS-CoV-2. A golden Syrian hamster in vivo model for COVID-19 was implemented. We show that vaccination of hamsters with recombinant VSV-{Delta}G-spike results in rapid and potent induction of neutralizing antibodies against SARS-CoV-2. Importantly, single-dose vaccination was able to protect hamsters against SARS-CoV-2 challenge, as demonstrated by the abrogation of body weight loss of the immunized hamsters compared to unvaccinated hamsters. Furthermore, whereas lungs of infected hamsters displayed extensive tissue damage and high viral titers, immunized hamsters lungs showed only minor lung pathology, and no viral load. Taken together, we suggest recombinant VSV-{Delta}G-spike as a safe, efficacious and protective vaccine against SARS-CoV-2 infection.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Yfat Yahalom-Ronen", - "author_inst": "IIBR" - }, - { - "author_name": "Hadas Tamir", - "author_inst": "IIBR" - }, - { - "author_name": "Sharon Melamed", - "author_inst": "IIBR" - }, - { - "author_name": "Boaz Politi", - "author_inst": "IIBR" - }, - { - "author_name": "Ohad Shifman", - "author_inst": "IIBR" - }, - { - "author_name": "Hagit Achdout", - "author_inst": "IIBR" - }, - { - "author_name": "Einat B. Vitner", - "author_inst": "IIBR" - }, - { - "author_name": "Ofir Israeli", - "author_inst": "IIBR" - }, - { - "author_name": "Elad Milrot", - "author_inst": "IIBR" - }, - { - "author_name": "Dana Stein", - "author_inst": "IIBR" - }, - { - "author_name": "Inbar Cohen-Gihon", - "author_inst": "IIBR" - }, - { - "author_name": "Shlomi Lazar", - "author_inst": "IIBR" - }, - { - "author_name": "Hila Gutman", - "author_inst": "IIBR" - }, - { - "author_name": "Itai Glinert", - "author_inst": "IIBR" - }, - { - "author_name": "Lilach Cherry", - "author_inst": "IIBR" - }, - { - "author_name": "Yaron Vagima", - "author_inst": "IIBR" - }, - { - "author_name": "Shirley Lazar", - "author_inst": "IIBR" - }, - { - "author_name": "Shay Weiss", - "author_inst": "IIBR" - }, - { - "author_name": "Amir Ben-Shmuel", - "author_inst": "IIBR" - }, - { - "author_name": "Roy Avraham", - "author_inst": "IIBR" - }, - { - "author_name": "Reut Puni", - "author_inst": "IIBR" - }, - { - "author_name": "Edith Lupu", - "author_inst": "IIBR" - }, - { - "author_name": "Elad Bar David", - "author_inst": "IIBR" - }, - { - "author_name": "Assa Sittner", - "author_inst": "IIBR" - }, - { - "author_name": "Noam Erez", - "author_inst": "IIBR" - }, - { - "author_name": "Ran Zichel", - "author_inst": "IIBR" - }, - { - "author_name": "Emanuelle Mamroud", - "author_inst": "IIBR" - }, - { - "author_name": "Ohad Mazor", - "author_inst": "IIBR" - }, - { - "author_name": "Haim Levy", - "author_inst": "IIBR" - }, - { - "author_name": "Orly Laskar", - "author_inst": "IIBR" - }, - { - "author_name": "Shmuel Yitzhaki", - "author_inst": "IIBR" - }, - { - "author_name": "Shmuel C. Shapira", - "author_inst": "IIBR" - }, - { - "author_name": "Anat Zvi", - "author_inst": "IIBR" - }, - { - "author_name": "Adi Beth-Din", - "author_inst": "IIBR" - }, - { - "author_name": "Nir Paran", - "author_inst": "IIBR" - }, - { - "author_name": "Tomer Israely", - "author_inst": "IBR" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.19.161042", "rel_title": "Drug repurposing screens reveal FDA approved drugs active against SARS-Cov-2", @@ -1363360,6 +1364061,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.19.161687", + "rel_title": "Cytosine deamination in SARS-CoV-2 leads to progressive CpG depletion.", + "rel_date": "2020-06-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.19.161687", + "rel_abs": "RNA viruses use CpG reduction to evade the host cell defense, but the driving mechanisms are still largely unknown. In an attempt to address this we used a rapidly growing genomic dataset of SARS-CoV-2 with relevant metadata information. Remarkably, by simply ordering SARS-CoV-2 genomes by their date of collection, we find a progressive increase of C-to-U substitutions resulting in 5'-UCG-3' motif reduction that in turn have reduced the CpG frequency over just a few months of observation. This is consistent with APOBEC-mediated RNA editing resulting in CpG reduction, thus allowing the virus to escape ZAP-mediated RNA degradation. Our results thus link the dynamics of target sequences in the viral genome for two known host molecular defense mechanisms, mediated by the APOBEC and ZAP proteins.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Mukhtar Sadykov", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Tobias Mourier", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Qingtian Guan", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Arnab Pain", + "author_inst": "King Abdullah University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.19.158717", "rel_title": "No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia.", @@ -1364612,69 +1365344,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.16.156166", - "rel_title": "Evaluation of the performance of SARS-CoV-2 serological tools and their positioning in COVID-19 diagnostic strategies.", - "rel_date": "2020-06-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.156166", - "rel_abs": "Rapid and accurate diagnosis is crucial for successful outbreak containment. During the current coronavirus disease 2019 (COVID-19) public health emergency, the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection diagnosis is the detection of viral RNA by reverse transcription (RT)-PCR. Additional diagnostic methods enabling the detection of current or past SARS-CoV-2 infection would be highly beneficial to ensure the timely diagnosis of all infected and recovered patients. Here, we investigated several serological tools, i.e., two immunochromatographic lateral flow assays (LFA-1 (Biosynex COVID-19 BSS) and LFA-2 (COVID-19 Sign IgM/IgG)) and two enzyme-linked immunosorbent assays (ELISAs) detecting IgA (ELISA-1 Euroimmun), IgM (ELISA-2 EDI) and/or IgG (ELISA-1 and ELISA-2) based on well-characterized panels of serum samples from patients and healthcare workers with PCR-confirmed COVID-19 and from SARS-CoV-2-negative patients. A total of 272 serum samples were used, including 62 serum samples from hospitalized patients (panel 1 and panel 3), 143 serum samples from healthcare workers (panel 2) diagnosed with COVID-19 and 67 serum samples from negative controls. Diagnostic performances of each assay were assessed according to days after symptom onset (dso) and the antigenic format used by manufacturers. We found overall sensitivities ranging from 69% to 93% on panels 1 and 2 and specificities ranging from 83% to 98%. The clinical sensitivity varied greatly according to the panel tested and the dso. The assays we tested showed poor mutual agreement. A thorough selection of serological assays for the detection of ongoing or past infections is advisable.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Aur\u00e9lie Velay", - "author_inst": "H\u00f4pitaux Universitaires de Strasbourg" - }, - { - "author_name": "Floriane Gallais", - "author_inst": "H\u00f4pitaux Universitaires de Strasbourg" - }, - { - "author_name": "Ilies Benotmane", - "author_inst": "H\u00f4pitaux Universitaires de Strasbourg" - }, - { - "author_name": "Marie-Josee Wendling", - "author_inst": "Hopitaux Universtaires" - }, - { - "author_name": "Fran\u00e7ois Danion", - "author_inst": "H\u00f4pitaux Universitaires de Strasbourg" - }, - { - "author_name": "Olivier Collange", - "author_inst": "H\u00f4pitaux Universitaires de Strasbourg" - }, - { - "author_name": "Jerome De Seze", - "author_inst": "H\u00f4pitaux Universitaires de Strasbourg" - }, - { - "author_name": "Catherine Schmidt-Mutter", - "author_inst": "H\u00f4pitaux Universitaires de Strasbourg" - }, - { - "author_name": "Francis Schneider", - "author_inst": "Hopitaux de Strasbourg" - }, - { - "author_name": "Pascal Bilbault", - "author_inst": "H\u00f4pitaux Universitaires de Strasbourg" - }, - { - "author_name": "Ferhat Meziani", - "author_inst": "H\u00f4pitaux Universitaires de Strasbourg" - }, - { - "author_name": "Samira Fafi-Kremer", - "author_inst": "H\u00f4pitaux Universitaires de Strasbourg, Inserm 1109, Labex Transplantex, F\u00e9d\u00e9ration de M\u00e9decine Translationnelle, Universit\u00e9 de Strasbourg" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.16.20132985", "rel_title": "Estimation of the incubation period of COVID-19 using viral load data", @@ -1364858,6 +1365527,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.16.20132423", + "rel_title": "Seroprevalence and epidemiological characteristics of immunoglobulin M and G antibodies against SARS-CoV-2 in asymptomatic people in Wuhan, China", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20132423", + "rel_abs": "ObjectivesPopulation screening for IgG and IgM against SARS-CoV-2 was initiated on March 25 and was open to all residents of Wuhan who were symptom-free. All ages with no fever, headache or other symptoms of COVID-19 among residents in Wuhan were included.\n\nMethodsThis study adopted a cross-sectional study. Pearson Chi-square test, T-test, and Mann-Whitney test were used in comparison between different groups. To correct the effects of gender and age, the seroprevalence of IgM positivity, IgG positivity, and IgM and/or IgG positivity were standardized according to the gender and age-specific population of Wuhan in 2017.\n\nResultsThe seroprevalence of IgG and IgM standardized for age and gender in Wuhan showed a downward trend. No significant correlation was observed between the seroprevalence of IgG and the different age groups. The seroprevalence was significantly higher for females than males (x2 =35.702, p < 0.001), with an odds ratio of 1.36 (95% CI: 1.24-1.48). A significant difference was seen in the seroprevalence of IgG among people from different geographic areas and different types of workplaces (respectively, x2 = 42.871, p < 0.001 and x2 = 202.43, p < 0.001). The IgG antibody-positive cases had a greater number of abnormalities in CT imaging than IgG-negative cases (30.7% vs 19.7%).\n\nConclusionsOur work found the reported number of confirmed patients in Wuhan only represents a small proportion of the total number of infections. There was a significant aggregation of asymptomatic infections in individuals from some occupations, and based on CT and laboratory findings, some damage may have occurred in asymptomatic individuals positive for IgG antibody.\n\nO_LSTStrengths and limitations of this studyC_LSTO_LIThis study has the important feature of having been designed as repeated five-day serosurveys, which allowed for the monitoring of seroprevalence progression.\nC_LIO_LIThis study applied scientific statistical methods accounting for the demographic structure of the general population and imperfect diagnostic tests to estimate seroprevalence in the overall population.\nC_LIO_LIThis study had selection bias since the analyzed medical records were based on examinees directed by their work units.\nC_LIO_LIPeople under the age of 19 and over age 65 were too few to be fully covered in analyses.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ruijie Ling", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Yihan Yu", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Jiayu He", + "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Jixian Zhang", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Sha Xu", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Renrong Sun", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Wangcai Zhu", + "author_inst": "Hubei Provincial Hospital of Integrated Chinese & Western Medicine, Wuhan, Hubei, China" + }, + { + "author_name": "Mingfeng Chen", + "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Tao Li", + "author_inst": "National Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Honglong Ji", + "author_inst": "Department of Cellular and Molecular Biology, University of Texas Health Science Centre at Tyler, Tyler, Texas, USA" + }, + { + "author_name": "Huanqiang Wang", + "author_inst": "National Institute of Occupational Health and Poisons Control,Chinese CDC" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.16.20133207", "rel_title": "Downsides of face masks and possible mitigation strategies: a systematic review and meta-analysis", @@ -1366042,105 +1366770,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.16.20132597", - "rel_title": "Hydroxychloroquine with or without azithromycin and in-hospital mortality or discharge in patients hospitalized for COVID-19 infection: a cohort study of 4,642 in-patients in France", - "rel_date": "2020-06-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20132597", - "rel_abs": "ObjectiveTo assess the clinical effectiveness of oral hydroxychloroquine (HCQ) with or without azithromycin (AZI) in preventing death or leading to hospital discharge.\n\nDesignRetrospective cohort study.\n\nSettingAn analysis of data from electronic medical records and administrative claim data from the French Assistance Publique - Hopitaux de Paris (AP-HP) data warehouse, in 39 public hospitals, Ile-de-France, France.\n\nParticipantsAll adult inpatients with at least one PCR-documented SARS-CoV-2 RNA from a nasopharyngeal sample between February 1st, 2020 and April 6th, 2020 were eligible for analysis. The study population was restricted to patients who did not receive COVID-19 treatments assessed in ongoing trials, including antivirals and immunosuppressive drugs. End of follow-up was defined as the date of death, discharge home, day 28 after admission, whichever occurred first, or administrative censoring on May 4, 2020.\n\nInterventionPatients were further classified into 3 groups: (i) receiving HCQ alone, (ii) receiving HCQ together with AZI, and (iii) receiving neither HCQ nor AZI. Exposure to a HCQ/AZI combination was defined as a simultaneous prescription of the 2 treatments (more or less one day).\n\nMain outcome measuresThe primary outcome was all-cause 28-day mortality as a time-to-event endpoint under a competing risks survival analysis framework. The secondary outcome was 28-day discharge home. Augmented inverse probability of treatment weighted (AIPTW) estimates of the average treatment effect (ATE) were computed to account for confounding.\n\nResultsA total of 4,642 patients (mean age: 66.1 {+/-} 18; males: 2,738 (59%)) were included, of whom 623 (13.4%) received HCQ alone, 227 (5.9%) received HCQ plus AZI, and 3,792 (81.7%) neither drug. Patients receiving HCQ alone or HCQ plus AZI were more likely younger, males, current smokers and overall presented with slightly more co-morbidities (obesity, diabetes, any chronic pulmonary diseases, liver diseases), while no major difference was apparent in biological parameters. After accounting for confounding, no statistically significant difference was observed between the HCQ and Neither drug groups for 28-day mortality: AIPTW absolute difference in ATE was +1.24% (-5.63 to 8.12), ratio in ATE 1.05 (0.77 to 1.33). 28-day discharge rates were statistically significantly higher in the HCQ group: AIPTW absolute difference in ATE (+11.1% [3.30 to 18.9]), ratio in ATE (1.25 [1.07 to 1.42]). As for the HCQ+AZI vs neither drug, trends for significant differences and ratios in AIPTW ATE were found suggesting higher mortality rates in the former group (difference in ATE +9.83% [-0.51 to 20.17], ratio in ATE 1.40 [0.98 to 1.81];p=0.062).\n\nConclusionsUsing a large non-selected population of inpatients hospitalized for COVID-19 infection in 39 hospitals in France and robust methodological approaches, we found no evidence for efficacy of HCQ or HCQ combined with AZI on 28-day mortality. Our results suggested a possible excess risk of mortality associated with HCQ combined with AZI, but not with HCQ alone. Significantly higher rates of discharge home were observed in patients treated by HCQ, a novel finding warranting further confirmation in replicative studies. Altogether, our findings further support the need to complete currently undergoing randomized clinical trials.\n\nWHAT THIS PAPER ADDS?O_ST_ABSWhat is already known on this subjectC_ST_ABS- The use of Hydroxychloroquine (HCQ) or HCQ with azithromycin (AZI) has been associated with viral load reduction at 6 days in COVID-19 infected patients\n- No difference between HCQ and no-HCQ groups in terms of risk of death or need for mechanical ventilation was found in two large cohorts of hospitalized COVID-19 infected patients\n\n\nWhat this study adds- Using a large non-selected population of inpatients hospitalized for COVID-19 infection in 39 hospitals in France and robust methodological approaches, we found no evidence for efficacy of HCQ on 28-day mortality\n- Our results suggest an excess risk of mortality in patients treated by a combination of HCQ and AZI, but not with HCQ alone\n- Significantly higher rates of discharge home were observed in patients treated by HCQ, a novel finding warranting further confirmation in replicative studies", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Emilie Sbidian", - "author_inst": "APHP hospital" - }, - { - "author_name": "Julie Josse", - "author_inst": "Polytechnique" - }, - { - "author_name": "Guillaume Lemaitre", - "author_inst": "INRIA" - }, - { - "author_name": "Imke Mayer", - "author_inst": "EHESS" - }, - { - "author_name": "Melodie Bernaux", - "author_inst": "APHP" - }, - { - "author_name": "Alexandre Gramfort", - "author_inst": "INRIA" - }, - { - "author_name": "Nathanael Lapidus", - "author_inst": "INRIA" - }, - { - "author_name": "Nicolas Paris", - "author_inst": "APHP" - }, - { - "author_name": "Antoine Neuraz", - "author_inst": "Necker-Enfants Malades Hospital" - }, - { - "author_name": "Ivan Lerner", - "author_inst": "APHP" - }, - { - "author_name": "Nicolas Garcelon", - "author_inst": "APHP" - }, - { - "author_name": "Bastien Rance", - "author_inst": "APHP" - }, - { - "author_name": "Olivier Grisel", - "author_inst": "INRIA" - }, - { - "author_name": "Thomas Moreau", - "author_inst": "APHP" - }, - { - "author_name": "Ali Bellamine", - "author_inst": "APHP" - }, - { - "author_name": "Pierre Wolkenstein", - "author_inst": "APHP" - }, - { - "author_name": "Gael Varoquaux", - "author_inst": "INRIA" - }, - { - "author_name": "Eric Caumes", - "author_inst": "APHP" - }, - { - "author_name": "Marc Lavielle", - "author_inst": "INRIA" - }, - { - "author_name": "Armand Mekontso Dessap", - "author_inst": "APHP" - }, - { - "author_name": "Etienne Audureau", - "author_inst": "APHP" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2020.06.16.20133280", "rel_title": "The effectiveness of interventions to reduce COVID-19 transmission in a large urban jail", @@ -1366368,6 +1366997,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.06.17.20133611", + "rel_title": "Knowledge, Attitudes, and Fear of COVID-19 during the Rapid Rise Period in Bangladesh", + "rel_date": "2020-06-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.17.20133611", + "rel_abs": "ObjectivesTo determine the level of Knowledge, Attitude, and Practice (KAP) related to COVID-19 preventive health habits and perception of Fear towards COVID-19 in subjects living in Bangladesh.\n\nDesignProspective, cross-sectional survey of (n= 2157) male and female subjects, 13-90 years of age, living in Bangladesh.\n\nMethodsEthical Approval and Trial registration were obtained prior to the commencement of the study. Subjects who volunteered to participate and signed the informed consent were enrolled in the study and completed the \"Fear of COVID-19 Scale\" (FCS).\n\nResultsTwenty-eight percent (28.69%) of subjects reported one or more COVID-19 symptoms and 21.4% of subjects reported one or more comorbidities. Knowledge scores were slightly higher in males (8.75{+/-} 1.58) than females (8.66{+/-} 1.70). Knowledge was significantly correlated with age (p<.005), an education level (p<.001), Attitude (p<.001), and urban location (p=<.001). Knowledge scores showed an inverse correlation with Fear scores (p=<.001). Eighty-three percent (83.7%) of subjects with COVID-19 symptoms reported wearing a mask in public and 75.4% of subjects reported staying away from crowded places. Subjects with one or more symptoms reported higher Fear compared to subjects without (18.73{+/-} 4.6; 18.45{+/-} 5.1).\n\nConclusionsOverall, Bangladeshis reported a high prevalence of self-isolation, positive preventive health behaviors related to COVID-19, and moderate to high fear levels. Higher Knowledge and Practice were found in males, higher education levels, older age, and urban location. \"Fear\" of COVID-19 was more prevalent in female and elderly subjects. Positive \"Attitude\" was reported for the majority of subjects, reflecting the belief that COVID-19 was controllable and containable.\n\nEthical approvalEthical permission obtained from the Institutional review board (BPA-IPRR/IRB/29/03/2020/021) of Institute of Physiotherapy, Rehabilitation, and Research (IPRR), the academic organization of the Bangladesh Physiotherapy Association.\n\nWHO Trial registryThe trial registration obtained prospectively from a primary trial registry of WHO (CTRI/2020/04/024413).\n\nData AvailabilityThe data are available regarding this study and can be viewed upon request", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Mohammad Anwar Hossain", + "author_inst": "Centre for the Rehabilitation of the Paralysed" + }, + { + "author_name": "K M Amran Hossain", + "author_inst": "Bangladesh Health Professions Institute" + }, + { + "author_name": "Lori Maria Walton", + "author_inst": "University of Scranton" + }, + { + "author_name": "Zakir Uddin", + "author_inst": "McGill University" + }, + { + "author_name": "Md. Obaidul Haque", + "author_inst": "Bangladesh Health Professions Institute" + }, + { + "author_name": "Md. Feroz Kabir", + "author_inst": "Jashore University of Science and Technology" + }, + { + "author_name": "S. M. Yasir Arafat", + "author_inst": "Enam Medical College & Hospital" + }, + { + "author_name": "Mohamed Sakel", + "author_inst": "East Kent University NHS Hospital" + }, + { + "author_name": "Rafey Faruqui", + "author_inst": "Kent & Medway NHS and Social care Partnership Trust" + }, + { + "author_name": "Ikbal Kabir Jahid", + "author_inst": "Jashore University of Science and Technology" + }, + { + "author_name": "Zahid Hossain", + "author_inst": "Bangladesh Health Professions Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.16.20133215", "rel_title": "The first proof of the capability of wastewater surveillance for COVID-19 in India through the detection of the genetic material of SARS-CoV-2", @@ -1367960,61 +1368648,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.06.17.156554", - "rel_title": "Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs", - "rel_date": "2020-06-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.17.156554", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes the coronavirus disease 2019 (COVID-19). SARS-CoV-2 encodes three putative ion channels: E, 8a, and 3a1,2. 3a is expressed in SARS patient tissue and anti-3a antibodies are observed in patient plasma3-6. 3a has been implicated in viral release7, inhibition of autophagy8, inflammasome activation9, and cell death10,11 and its deletion reduces viral titer and morbidity in mice1, raising the possibility that 3a could be an effective vaccine or therapeutic target3,12. Here, we present the first cryo-EM structures of SARS-CoV-2 3a to 2.1 [A] resolution and demonstrate 3a forms an ion channel in reconstituted liposomes. The structures in lipid nanodiscs reveal 3a dimers and tetramers adopt a novel fold with a large polar cavity that spans halfway across the membrane and is accessible to the cytosol and the surrounding bilayer through separate water- and lipid-filled openings. Electrophysiology and fluorescent ion imaging experiments show 3a forms Ca2+-permeable non-selective cation channels. We identify point mutations that alter ion permeability and discover polycationic inhibitors of 3a channel activity. We find 3a-like proteins in multiple Alphacoronavirus and Betacoronavirus lineages that infect bats and humans. These data show 3a forms a functional ion channel that may promote COVID-19 pathogenesis and suggest targeting 3a could broadly treat coronavirus diseases.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "David M Kern", - "author_inst": "Department of Molecular and Cell Biology, University of California Berkeley; Helen Wills Neuroscience Institute; California Institute for Quantitative Biology (" - }, - { - "author_name": "Ben Sorum", - "author_inst": "Department of Molecular and Cell Biology, University of California Berkeley; Helen Wills Neuroscience Institute; California Institute for Quantitative Biology (" - }, - { - "author_name": "Sonali S Mali", - "author_inst": "Department of Molecular & Cell Biology, University of California Berkeley; Helen Wills Neuroscience Institute" - }, - { - "author_name": "Christopher M Hoel", - "author_inst": "Department of Molecular and Cell Biology, University of California Berkeley; Helen Wills Neuroscience Institute; California Institute for Quantitative Biology (" - }, - { - "author_name": "Savitha Sridharan", - "author_inst": "Department of Molecular and Cell Biology, University of California Berkeley; Helen Wills Neuroscience Institute" - }, - { - "author_name": "Jonathan P Remis", - "author_inst": "California Institute for Quantitative Biology (QB3)" - }, - { - "author_name": "Daniel B Toso", - "author_inst": "California Institute for Quantitative Biology (QB3)" - }, - { - "author_name": "Abhay Kotecha", - "author_inst": "Materials and Structural Analysis Division, Thermo Fisher Scientific, Eindhoven, The Netherlands" - }, - { - "author_name": "Diana M Bautista", - "author_inst": "Department of Molecular & Cell Biology, University of California Berkeley; Helen Wills Neuroscience Institute, University of California Berkeley" - }, - { - "author_name": "Stephen G Brohawn", - "author_inst": "Department of Molecular and Cell Biology, University of California Berkeley; Helen Wills Neuroscience Institute; California Institute for Quantitative Biology (" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.06.18.158154", "rel_title": "Early temporal dynamics of cellular responses to SARS-CoV-2", @@ -1368242,6 +1368875,25 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.06.16.154559", + "rel_title": "in-silica Analysis of SARS-CoV-2 viral strain using Reverse Vaccinology Approach: A Case Study for USA", + "rel_date": "2020-06-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.154559", + "rel_abs": "The recent pandemic of COVID19 that has struck the world is yet to be battled by a potential cure. Countless lives have been claimed due to the existing pandemic and the societal normalcy has been damaged permanently. As a result, it becomes crucial for academic researchers in the field of bioinformatics to combat the existing pandemic. The study involved collecting the virulent strain sequence of SARS-nCoV19 for the country USA against human host through publically available bioinformatics databases. Using in-silica analysis and reverse vaccinology, two leader proteins were identified to be potential vaccine candidates for development of a multi-epitope drug. The results of this study can provide further researchers better aspects and direction on developing vaccine and immune responses against COVID19. This work also aims at promoting the use of existing bioinformatics tools to faster streamline the pipeline of vaccine development.\n\nThe Situation of COVID19A new infection respiratory disease was first observed in the month of December 2019, in Wuhan, situated in the Hubei province, China. Studies have indicated that the reason of this disease was the emergence of a genetically-novel coronavirus closely related to SARS-CoV. This coronavirus, now named as nCoV-19, is the reason behind the spread of this fatal respiratory disease, now named as COVID-19. The initial group of infections is supposedly linked with the Huanan seafood market, most likely due to animal contact. Eventually, human-to-human interaction occurred and resulted in the transmission of the virus to humans. [13].\n\nSince then, nCoV-19 has been rapidly spreading within China and other parts of World. At the time of writing this article (mid-March 2020), COVID-19 has spread across 146 countries. A count of 164,837 cases have been confirmed of being diagnosed with COVID-19, and a total of 6470 deaths have occurred. The cumulative cases have been depicting a rising trend and the numbers are just increasing. WHO has declared COVID-19 to be a \"global health emergency\". [14].\n\nCurrent Scenario and ObjectivesCurrently, research is being conducted on a massive level to understand the immunology and genetic characteristics of the disease. However, no cure or vaccine of nCoV-19 has been developed at the time of writing this article.\n\nThough, nCoV-19 and SARS-CoV are almost genetically similar, the respiratory syndrome caused by both of them, COVID-19 and SARS respectively, are completely different. Studies have indicated that -\n\n\"SARS was more deadly but much less infectious than COVID-19\".\n\n-World Health Organization", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ajay Agarwal", + "author_inst": "DIT University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.06.15.20130328", "rel_title": "Can we trust the prediction model? Demonstrating the importance of external validation by investigating the COVID-19 Vulnerability (C-19) Index across an international network of observational healthcare datasets", @@ -1369718,33 +1370370,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.15.20132134", - "rel_title": "Prevalence of Chemosensory Dysfunction in COVID-19 Patients: A Systematic Review and Meta-analysis Reveals Significant Ethnic Differences", - "rel_date": "2020-06-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20132134", - "rel_abs": "A significant fraction of people who test positive for COVID-19 have chemosensory deficits. However, the reported prevalence of these deficits in smell and/or taste varies widely, and the reason for the differences between studies is unclear. We determined the pooled prevalence of such chemosensory deficits in a systematic review. We searched the COVID-19 portfolio of the National Institutes of Health for all studies that reported the prevalence of smell and/or taste deficits in patients diagnosed with COVID-19. Forty-two studies reporting on 23,353 patients qualified and were subjected to a systematic review and meta-analysis. Estimated random prevalence of olfactory dysfunction was 38.5%, of taste dysfunction was 30.4% and of overall chemosensory dysfunction was 50.2%. We examined the effects of age, disease severity, and ethnicity on chemosensory dysfunction. The effect of age did not reach significance, but anosmia/hypogeusia decreased with disease severity, and ethnicity was highly significant: Caucasians had a 3-6 times higher prevalence of chemosensory deficits than East Asians. The finding of ethnic differences points to genetic, ethnicity-specific differences of the virus-binding entry proteins in the olfactory epithelium and taste buds as the most likely explanation, with major implications for infectivity, diagnosis and management of the COVID-19 pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Christopher S von Bartheld", - "author_inst": "University of Nevada, Reno" - }, - { - "author_name": "Molly M Hagen", - "author_inst": "University of Nevada, Reno" - }, - { - "author_name": "Rafal Butowt", - "author_inst": "Nicolaus Copernicus University, Bydgoszcz" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "otolaryngology" - }, { "rel_doi": "10.1101/2020.06.15.20132357", "rel_title": "Predictive Modeling on the Number of Covid-19 Death Toll in the United States Considering the Effects of Coronavirus-Related Changes and Covid-19 Recovered Cases", @@ -1369904,6 +1370529,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.06.16.151555", + "rel_title": "Decoding of persistent multiscale structures in complex biological networks", + "rel_date": "2020-06-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.151555", + "rel_abs": "In any omics study, the scale of analysis can dramatically affect the outcome. For instance, when clustering single-cell transcriptomes, is the analysis tuned to discover broad or specific cell types? Likewise, protein communities revealed from protein networks can vary widely in sizes depending on the method. Here we use the concept of \"persistent homology\", drawn from mathematical topology, to identify robust structures in data at all scales simultaneously. Application to mouse single-cell transcriptomes significantly expands the catalog of identified cell types, while analysis of SARS-COV-2 protein interactions suggests hijacking of WNT. The method, HiDeF, is available via Python and Cytoscape.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Fan Zheng", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "She Zhang", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Christopher Churas", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Dexter Pratt", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Ivet Bahar", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Trey Ideker", + "author_inst": "University of California, San Diego" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.06.17.157982", "rel_title": "Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding", @@ -1371388,101 +1372052,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.13.20127605", - "rel_title": "Longitudinal immune profiling reveals distinct features of COVID-19 pathogenesis", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20127605", - "rel_abs": "BackgroundThe pathogenesis of COVID-19, caused by a novel strain of coronavirus (SARS-CoV-2), involves a complex host-virus interaction and is characterised by an exaggerated immune response, the specific components of which are poorly understood. Here we report the outcome of a longitudinal immune profiling study in hospitalised patients during the peak of the COVID-19 pandemic in the UK and show the relationship between immune responses and severity of the clinical presentation.\n\nMethodsThe Coronavirus Immune Response and Clinical Outcomes (CIRCO) study was conducted at four hospitals in Greater Manchester. Patients with SARS-CoV-2 infection, recruited as close to admission as possible, provided peripheral blood samples at enrolment and sequentially thereafter. Fresh samples were assessed for immune cells and proteins in whole blood and serum. Some samples were also stimulated for 3 hours with LPS and analysed for intracellular proteins. Results were stratified based on patient-level data including severity of symptoms and date of reported symptom onset.\n\nFindingsLongitudinal analysis showed a very high neutrophil to T cell ratio and abnormal activation of monocytes in the blood, which displayed high levels of the cell cycle marker, Ki67 and low COX-2. These properties all reverted in patient with good outcome. Unexpectedly, multiple aspects of inflammation were diminished as patients progressed in severity and time, even in ITU patients not recovering.\n\nInterpretationThis is the first detailed longitudinal analysis of COVID-19 patients of varying severity and outcome, revealing common features and aspects that track with severity. Patients destined for a severe outcome can be identified at admission when still displaying mild-moderate symptoms. We provide clues concerning pathogenesis that should influence clinical trials and therapeutics. Targeting pathways involved in neutrophil and monocyte release from the bone marrow should be tested in patients with COVID-19.\n\nFundingThe Kennedy Trust for Rheumatology Research, The Wellcome Trust, The Royal Society, The BBSRC, National Institute for Health Research (NIHR) Biomedical Research Centres (BRC).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSAnalysis of the literature before the study via pubmed and bioRxiv searches using the terms COVID-19, SARS-CoV2, immune and inflammation (with the last search performed on 27th April 2020) showed evidence of an overactive immune response in a handful of studies in cross-sectional analyses all done at a single time point.\n\nAdded value of this studyTo determine the role of the immune response in a disease process, it is necessary to correlate immune activity with clinical parameters dynamically. In this study patients presented to hospital at different stages of disease so we took samples at different time-points to provide an accurate picture of the relevant pathobiology. In order to avoid loss of large components of the immune system due to the processes of storage, longitudinal samples were interrogated in real time to reveal the full immune alterations in COVID-19.\n\nImplications of all the available evidenceRespiratory viruses continue to cause devastating global disease. The finding of altered myelopoiesis, with excess neutrophils and altered monocyte function, as dominant features in our study provides an incentive for clinical testing of therapeutics that specifically target this pathobiology. Given that inflammation is greatest prior to admission to intensive care, trials of specific immune-modulating therapies should be considered earlier in admission. Future studies of COVID-19 mechanisms should place more emphasis on longitudinal analyses since disease changes dramatically over time.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Elizabeth R Mann", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester; Maternal and Fetal Health Centre, St Mary's Hospital" - }, - { - "author_name": "Madhvi Menon", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Sean Blandin Knight", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester; Respiratory Department, Salford Royal NHS Foundation Trust" - }, - { - "author_name": "Joanne E Konkel", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Christopher Jagger", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Tovah N Shaw", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Siddarth Krishnan", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Magnus Rattray", - "author_inst": "Division of Informatics, Imaging and Data Sciences, University of Manchester" - }, - { - "author_name": "Andrew Ustianowski", - "author_inst": "Regional Infectious Diseases Unit, North Manchester General Hospital" - }, - { - "author_name": "Nawar Diar Bakerly", - "author_inst": "Respiratory Department, Salford Royal NHS Foundation Trust" - }, - { - "author_name": "Paul Dark", - "author_inst": "Intensive Care Department, Salford Royal NHS Foundation Trust" - }, - { - "author_name": "Graham Lord", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Angela Simpson", - "author_inst": "Division of Infection, Immunity and Respiratory Medicine, University of Manchester; Manchester NIHR BRC, Education and Research Centre, Wythenshawe Hospital" - }, - { - "author_name": "Timothy Felton", - "author_inst": "Division of Infection, Immunity and Respiratory Medicine, University of Manchester; Manchester NIHR BRC, Education and Research Centre, Wythenshawe Hospital" - }, - { - "author_name": "Ling-Pei Ho", - "author_inst": "MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford" - }, - { - "author_name": "- NIHR Respiratory TRC", - "author_inst": "" - }, - { - "author_name": "Marc Feldmann", - "author_inst": "Kennedy Institute of Rheumatology, Botnar Research Centre, Headington, Oxford" - }, - { - "author_name": "- CIRCO", - "author_inst": "" - }, - { - "author_name": "John Grainger", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Tracy Hussell", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.11.20127332", "rel_title": "Low and high infection dose transmission of SARS-CoV-2 in the first COVID-19 clusters in Northern Germany", @@ -1371718,6 +1372287,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.13.20130062", + "rel_title": "Guillain Barr e syndrome in COVID-19:A scoping review", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130062", + "rel_abs": "IntroductionThe novel corona virus (COVID19) can result in several neurological complications. Guillain-Barre Syndrome (GBS) is one of them and has been reported from different parts of the world in this pandemic. It is an acute post infectious polyneuropathy. The review aims to summarize the demographic features, clinical presentation, diagnostics workup, and management strategies of COVID-19 associated GBS reported in literature.\n\nMaterial and methodWe searched Medline, PubMed Central, SCOPUS and Google Scholar using pre-defined keywords, with no time limits and in English language only. We aimed to include all kind of manuscripts. Last search was done on 18th May 2020.\n\nDemographics, clinical features, diagnostic workup, management, and outcomes were documented in the data sheet.\n\nResultsWe identified 24 cases of COVID-19 associated GBS. Most of the cases were reported from Italy followed by USA. Majority were males (18 /24) The age ranged from 23 -84 years. The clinical presentation was typical sensory-motor GBS in most. Nine patients had facial palsy of which five had bilateral involvement. Two patients had bilateral abducent nerve palsy while two presented as paraparetic GBS variant with autonomic dysfunction. Electrodiagnostics was performed in 17 patients only and 12 had typical features of acute inflammatory demyelinating polyneuropathy.. Intravenous immunoglobulins were the preferred mode of treatment in most of the patient. There was one death, and most were discharged to rehabilitation or home.\n\nConclusionGBS is a frequent neurological complication associated with COVID-19. There is no clear causative relationship between GBS, and COVID-19 at present and more data are needed to establish the casualty. However, most cases have a post-infectious onset with male preponderance. Most of the cases have a typical presentation but some may present in an atypical way. Prognosis is generally good.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Imran Ahmad", + "author_inst": "Bahria University Medical and Dental College" + }, + { + "author_name": "Farooq Azam Rathore", + "author_inst": "Bahria University Medical and Dental College" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.06.13.20130310", "rel_title": "COVID-19: a crash test for biomedical publishing?", @@ -1372602,33 +1373194,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.13.20130120", - "rel_title": "Evaluating the Mental Health Impacts of the COVID-19 Pandemic in Urban South Africa: Perceived Risk of COVID-19 Infection and Childhood Trauma Predict Adult Depressive Symptoms", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130120", - "rel_abs": "South Africas national lockdown introduced serious threats to public mental health in a society where one in three individuals develop a psychiatric disorder during their life. We aimed to evaluate the mental health impacts of the COVID-19 pandemic using a mixed methods design. This longitudinal study drew from a preexisting sample of 957 adults living in Soweto, a major township near Johannesburg. Psychological assessments were administered across two waves: between August 2019-March 2020 and during the first six weeks of the lockdown (late March-early May 2020). Interviews on COVID-19 experiences were administered in the second wave. Multiple regression models examined relationships between perceived COVID-19 risk and depression. Full data on perceived COVID-19 risk, depression, and covariates were available in 221 adults. 14.5% of adults were at risk for depression. Higher perceived COVID-19 risk predicted greater depressive symptoms (p < 0.001) particularly among adults with histories of childhood trauma, though this effect was marginally significant (p = 0.062). Adults were two times more likely to experience significant depressive symptoms for every one unit increase in perceived COVID-19 risk (p = 0.016; 95% CI [1.14, 3.49]). Qualitative data identified potent experiences of anxiety, financial insecurity, fear of infection, and rumination. Higher perceived risk of COVID-19 infection is associated with greater depressive symptoms among adults with histories of childhood trauma during the first six weeks of quarantine. High rates of severe mental illness and low availability of mental healthcare amidst COVID-19 emphasize the need for immediate and accessible psychological resources in South Africa.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Andrew Wooyoung Kim", - "author_inst": "Department of Anthropology, Northwestern University" - }, - { - "author_name": "Tawanda Nyengerai", - "author_inst": "School of Public Health, University of the Witwatersrand" - }, - { - "author_name": "Emily Mendenhall", - "author_inst": "Edmund A. Walsh School of Foreign Service, Georgetown University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.13.20130138", "rel_title": "Impact Of Temperature and Sunshine Duration on Daily New Cases and Death due to COVID-19", @@ -1372824,6 +1373389,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.13.20130617", + "rel_title": "Is tracking and modeling Covid-19 infection dynamics for Bangladesh using daily data feasible?", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130617", + "rel_abs": "Given the low Covid-19 testing coverage in the country, this study tested whether the daily change in the number of new Covid-19 cases is due to increase (or decrease) in the number of tests done daily. We performed Granger causality test based on vector autoregressive models on Bangladeshs case and test numbers between 8 March and 5 June 2020, using publicly available data. The test results show that the daily number of tests Granger-cause the number of new cases (p <0.001), meaning the daily number of new cases is perhaps due to an increase in test capacity rather than a change in the infection rates. From the results of this test we can infer that if the number of daily tests does not increase substantially, data on new infections will not give much information for understanding covid-19 infection dynamics in Bangladesh.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Karar Zunaid Ahsan", + "author_inst": "Gillings School of Global Public Health, the University of North Carolina at Chapel Hill, NC, USA" + }, + { + "author_name": "Rashida Ijdi", + "author_inst": "Carolina Population Center, University of North Carolina at Chapel Hill, NC, USA" + }, + { + "author_name": "Peter Kim Streatfield", + "author_inst": "Health Systems and Population Studies Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.13.20130088", "rel_title": "Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia. When late administration is too late.", @@ -1374228,65 +1374820,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.13.150243", - "rel_title": "Catch and kill airborne SARS-CoV-2 to control spread of COVID-19 by a heated air disinfection system", - "rel_date": "2020-06-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.13.150243", - "rel_abs": "Airborne transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) via air-conditioning systems poses a significant threat for the continued escalation of the current coronavirus disease (COVID-19) pandemic. Considering that SARS-CoV-2 cannot tolerate temperatures above 70 {degrees}C, here we designed and fabricated efficient air disinfection systems based on heated nickel (Ni) foam to catch and kill SARS-CoV-2. Virus test results revealed that 99.8% of the aerosolized SARS-CoV-2 was caught and killed by a single pass through a Ni-foam-based filter when heated up to 200 {degrees}C. Additionally, the same filter was also used to catch and kill 99.9% of Bacillus anthracis, an airborne spore. This study paves the way for preventing transmission of SARS-CoV-2 and other highly infectious airborne agents in closed environments.\n\nOne Sentence SummaryHeated Ni-foam filters are capable of effectively catching and killing airborne SARS-CoV-2 and Bacillus anthracis spores.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Luo Yu", - "author_inst": "University of Houston" - }, - { - "author_name": "Garrett K. Peel", - "author_inst": "Medistar Corporation" - }, - { - "author_name": "Faisal H. Cheema", - "author_inst": "University of Houston College of Medicine" - }, - { - "author_name": "William S. Lawrence", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Natalya Bukreyeva", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Christopher W. Jinks", - "author_inst": "Medistar Corporation" - }, - { - "author_name": "Jennifer E. Peel", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Johnny W. Peterson", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Slobodan Paessler", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "Monzer Hourani", - "author_inst": "Medistar Corporation" - }, - { - "author_name": "Zhifeng Ren", - "author_inst": "University of Houston" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.15.153916", "rel_title": "Cell entry of SARS-CoV-2 conferred by angiotensin-converting enzyme 2 (ACE2) of different species", @@ -1374622,6 +1375155,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.15.153692", + "rel_title": "Bio-JOIE: Joint Representation Learning of Biological Knowledge Bases", + "rel_date": "2020-06-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.15.153692", + "rel_abs": "The widespread of Coronavirus has led to a worldwide pandemic with a high mortality rate. Currently, the knowledge accumulated from different studies about this virus is very limited. Leveraging a wide-range of biological knowledge, such as gene on-tology and protein-protein interaction (PPI) networks from other closely related species presents a vital approach to infer the molecular impact of a new species. In this paper, we propose the transferred multi-relational embedding model Bio-JOIE to capture the knowledge of gene ontology and PPI networks, which demonstrates superb capability in modeling the SARS-CoV-2-human protein interactions. Bio-JOIE jointly trains two model components. The knowledge model encodes the relational facts from the protein and GO domains into separated embedding spaces, using a hierarchy-aware encoding technique employed for the GO terms. On top of that, the transfer model learns a non-linear transformation to transfer the knowledge of PPIs and gene ontology annotations across their embedding spaces. By leveraging only structured knowledge, Bio-JOIE significantly outperforms existing state-of-the-art methods in PPI type prediction on multiple species. Furthermore, we also demonstrate the potential of leveraging the learned representations on clustering proteins with enzymatic function into enzyme commission families. Finally, we show that Bio-JOIE can accurately identify PPIs between the SARS-CoV-2 proteins and human proteins, providing valuable insights for advancing research on this new disease.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Junheng Hao", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Chelsea Jui-Ting Ju", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Muhao Chen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Yizhou Sun", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Carlo Zaniolo", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Wei Wang", + "author_inst": "University of California, Los Angeles" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.06.16.153403", "rel_title": "Oral drug repositioning candidates and synergistic remdesivir combinations for the prophylaxis and treatment of COVID-19", @@ -1376206,65 +1376778,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.15.151779", - "rel_title": "Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry", - "rel_date": "2020-06-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.15.151779", - "rel_abs": "The causative agent of the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is steadily mutating during continuous transmission among humans. Such mutations can occur in the spike (S) protein that binds to the angiotensin-converting enzyme-2 (ACE2) receptor and is cleaved by transmembrane protease serine 2 (TMPRSS2). However, whether S mutations affect SARS-CoV-2 infectivity remains unknown. Here, we show that naturally occurring S mutations can reduce or enhance cell entry via ACE2 and TMPRSS2. A SARS-CoV-2 S-pseudotyped lentivirus exhibits substantially lower entry than SARS-CoV S. Among S variants, the D614G mutant shows the highest cell entry, as supported by structural observations. Nevertheless, the D614G mutant remains susceptible to neutralization by antisera against prototypic viruses. Taken together, these data indicate that the D614G mutation enhances viral infectivity while maintaining neutralization susceptibility.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Seiya Ozono", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Yanzhao Zhang", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Hirotaka Ode", - "author_inst": "Clinical Research Center, National Hospital Organization Nagoya Medical Center" - }, - { - "author_name": "Toong Seng Tan", - "author_inst": "Joint Research Center for Human Retrovirus Infection, Kumamoto University" - }, - { - "author_name": "Kazuo Imai", - "author_inst": "Self-Defense Forces Central Hospital" - }, - { - "author_name": "Kazuyasu Miyoshi", - "author_inst": "Self-Defense Forces Central Hospital" - }, - { - "author_name": "Satoshi Kishigami", - "author_inst": "University of Yamanashi" - }, - { - "author_name": "Takamasa Ueno", - "author_inst": "Joint Research Center for Human Retrovirus Infection, Kumamoto University" - }, - { - "author_name": "Yasumasa Iwatani", - "author_inst": "Clinical Research Center, National Hospital Organization Nagoya Medical Center" - }, - { - "author_name": "Tadaki Suzuki", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Kenzo Tokunaga", - "author_inst": "National Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.14.151381", "rel_title": "Pulmonary toxicity and inflammatory response of e-cigarettes containing medium-chain triglyceride oil and vitamin E acetate: Implications in the pathogenesis of EVALI but independent of SARS-COV-2 COVID-19 related proteins", @@ -1376464,6 +1376977,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.11.20128330", + "rel_title": "Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador.", + "rel_date": "2020-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128330", + "rel_abs": "SARS-CoV-2, the etiological agent of COVID-19 was first described in Wuhan in December 2019 and has now spread globally. Ecuador was the second country in South America to report confirmed cases. The first case reported in Quito, the capital city of Ecuador, was a tourist who came from the Netherlands and presented symptoms on March 10th, 2020 (index case). In this work we used the MinION platform (Oxford Nanopore Technologies) to sequence the metagenome of the bronchoalveolar lavage (BAL) from this case reported, and subsequently we sequenced the whole genome of the index case and other three patients using the ARTIC network protocols. Our data from the metagenomic approach confirmed the presence of SARS-CoV-2 coexisting with pathogenic bacteria suggesting coinfection. Relevant bacteria found in the BAL metagenome were Streptococcus pneumoniae, Mycobacterium tuberculosis, Staphylococcus aureus and Chlamydia spp. Lineage assignment of the four whole genomes revealed three different origins. The variant HEE-01 was imported from the Netherlands and was assigned to B lineage, HGSQ-USFQ-018, belongs to the B.1 lineage showing nine nucleotide differences with the reference strain and grouped with sequences from the United Kingdom, and HGSQ-USFQ-007 and HGSQ-USFQ-010 belong to the B lineage and grouped with sequences from Scotland. All genomes show mutations in their genomes compared to the reference strain, which could be important to understand the virulence, severity and transmissibility of the virus. Our findings also suggest that there were at least three independent introductions of SARS-CoV-2 to Ecuador.\n\nIMPORTANCECOVID-19, an infectious disease caused by SARS-CoV-2, has spread globally including Latin American countries including Ecuador. The first strain of SARS-CoV-2 sequenced was from Wuhan, which is considered as the reference strain. There were no data about the SARS-CoV-2 lineages in Ecuador, and the purpose of this study was to find out the origin of the different lineages circulating in the population. We also were interested in the mutations present in these genomes as they can influence virulence, transmission and infectivity.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Sully Marquez", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Belen Prado-Vivar", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Juan Jose Guadalupe", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Laboratorio de Biotecnologia Vegetal" + }, + { + "author_name": "Bernardo Gutierrez Granja", + "author_inst": "Department of Zoology, University of Oxford" + }, + { + "author_name": "Manuel Jibaja", + "author_inst": "Hospital Eugenio Espejo, Quito" + }, + { + "author_name": "Milton Tobar", + "author_inst": "Hospital Eugenio Espejo, Quito" + }, + { + "author_name": "Francisco Mora", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Juan Gaviria", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Maria Garcia", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Edison Ligna", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Franklin Espinosa", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Jorge Reyes", + "author_inst": "Hospital General Sur de Quito, IESS" + }, + { + "author_name": "Veronica Barragan", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Patricio Rojas-Silva", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Gabriel Trueba", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + }, + { + "author_name": "Michelle Grunauer", + "author_inst": "Universidad San Francisco de Quito, Escuela de Medicina, COCSA" + }, + { + "author_name": "Paul Cardenas", + "author_inst": "Universidad San Francisco de Quito, COCIBA, Instituto de Microbiologia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.12.20129098", "rel_title": "Laboratory Testing Implications of Risk-Stratification and Management for Improving Clinical Outcomes of COVID-19 Patients", @@ -1377784,25 +1378380,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.12.20129197", - "rel_title": "COVID-19 Spread in India: Dynamics, Modeling, and Future Projections", - "rel_date": "2020-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129197", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWCOVID-19 is an extremely infectious disease with a relatively large virus incubation period in the affected people who may be asymptomatic. Therefore, to reduce the transmission of this pathogen, several countries have taken many intervention measures. In this paper, we show that the impact of these measures in India is different from several other countries. It is shown that an early lockdown in late March 2020 changed the initial exponential growth curve of COVID-19 to a linear one, but a surge in the number of cases from late April 2020 brought India back to a quadratic trajectory. A regional analysis shows the disparate impact of the intervention in different states. It is further shown that the number of reported infections correlates with the number of tests, and therefore regions with limited diagnostics resources may not have a realistic estimate of the virus spread. This insufficiency of diagnostic test data is also reflected in an increasing positivity rate for India nearly 2.5 months after the lockdown, inconsistent with the trends observed for other geographical regions. Nonetheless, future projections are made using different epidemiological models based on the available data, and a comparative study is presented. In the absence of a reliable estimate of the true number of infections, these projections will have a limited accuracy: with that limitation, the most optimistic prediction suggests a continuing virus transmission through September 2020.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Rajesh Ranjan", - "author_inst": "The Ohio State University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.12.20129825", "rel_title": "National Smoking Rates Correlate Inversely with COVID-19 Mortality", @@ -1377974,6 +1378551,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.11.20127241", + "rel_title": "Critical Questions when Interpreting Coronavirus PCR Diagnostics", + "rel_date": "2020-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20127241", + "rel_abs": "The results of PCR measurements are regarded as unquestionable. This statement must be put into perspective. This relativization is particularly important in connection with the interpretation of SARS-CoV-2 results. Members of the critical infrastructure, such as nurses, may be quarantined although this is not necessary and are therefore missing from patient care. With our small but impressive comparison of methods and transport media for SARS-CoV-2, we not only show the different sensitivity of common routine systems and media in laboratory medicine. Further, we would like to inform clinically working physicians, who are not familiar with the technical weaknesses of the PCR investigation, about gaps and present solutions for their daily work.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Juergen Durner", + "author_inst": "Department of Operative/Restorative Dentistry, Periodontology and Pedodontics, Ludwig- Maximilians-" + }, + { + "author_name": "Siegfried Burggraf", + "author_inst": "Laboratory Becker & Colleagues" + }, + { + "author_name": "Ludwig Czibere", + "author_inst": "Laboratory Becker & Colleagues" + }, + { + "author_name": "Tobias Fleige", + "author_inst": "Laboratory Becker & Colleagues" + }, + { + "author_name": "Michael Spannagl", + "author_inst": "Haemophilia Treatment Centre, Ludwig-Maximilians-University of Munich" + }, + { + "author_name": "David Watts", + "author_inst": "School of Medical Sciences and Photon Science Institute, University of Manchester, UK" + }, + { + "author_name": "Marc Becker", + "author_inst": "Laboratory Becker & Colleagues" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.11.20128991", "rel_title": "Transformed time series analysis of first-wave COVID-19: universal similarities found in the Group of Twenty (G20) Countries", @@ -1379130,29 +1379750,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.06.12.20129908", - "rel_title": "A Logistic Model for Age-Specific COVID-19 Case-Fatality Rates", - "rel_date": "2020-06-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129908", - "rel_abs": "ObjectivesTo develop a mathematical model to characterize age-specific case-fatality rates (CFR) of COVID-19.\n\nMaterials and MethodBased on two large-scale Chinese and Italian CFR data, a logistic model was derived to provide quantitative insight on the dynamics between CFR and age.\n\nResults and DiscussionWe inferred that CFR increased faster in Italy than in China, as well as in females over males. In addition, while CFR increased with age, the rate of growth eventually slowed down, with a predicted theoretical upper limit for males (32%), females (21%), and the general population (23%).\n\nConclusionOur logistic model provided quantitative insight on the dynamics of CFR.\n\nLay SummaryRecently published studies have qualitatively shown that the COVID-19 case-fatality rates increased with age, with elder people at higher risk of fatality than younger ones. In our study, we presented a quantitative mathematical modeling approach to re-analyze those published data. Specifically, we were able to derive a logistic model to characterize age-specific CFRs. The derived mathematical model uncovered novel quantitative insights on the dynamics between CFR and age. Specifically, we inferred from the model that while CFR increased with age, the rate of growth eventually slowed down, with a predicted theoretical upper limit of 23% for the general population.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Xiang Gao", - "author_inst": "Loyola University Chicago" - }, - { - "author_name": "Qunfeng Dong", - "author_inst": "Loyola University Chicago" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.13.20129569", "rel_title": "The BCG dilemma: linear versus non-linear correlation models over the time of the COVID-19 pandemic", @@ -1379320,6 +1379917,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.11.20107086", + "rel_title": "COVID-19: Comparison between 8-days and extended 4-weeks outbreak periods through socioeconomic and natural factors", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20107086", + "rel_abs": "Since mid-March 2020, global COVID-19 pandemic has experienced an exponential growth in process from sporadic to sudden outbreaks. This paper selects the 8-day surge data of daily cases, death and recovery rates (March 19-26, 2020) from 18 countries with severe pandemic situation to discuss the impact of 9 factors of both socioeconomic and natural on the pathogen outbreak. Moreover, the paper also elaborates analysis and comparison of relatively slow 4-week (February 1-29, 2020) data of Chinas surge cases to determine the relationship between social and natural factors and on the spread of pandemic, which provides an effective reference for delaying and controlling the pandemic development.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Sana Ullah", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Jianghua ZHENG", + "author_inst": "College of Resources and Environment Science, Xinjiang University, Urumqi, 830046, China" + }, + { + "author_name": "Zhengkang ZUO", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Feizhou ZHANG", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Ke SHANG", + "author_inst": "School of Geophysics and Information Technology, China University of Geosciences, Beijing, 100083, China." + }, + { + "author_name": "Wenjie YU", + "author_inst": "College of Resources and Environment Science, Xinjiang University, Urumqi, 830046, China." + }, + { + "author_name": "Yu FU", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Chuqiao HAN", + "author_inst": "College of Resources and Environment Science, Xinjiang University, Urumqi, 830046, China." + }, + { + "author_name": "Yi LIN", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Kaiwen JIANG", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Shanlin SUN", + "author_inst": "College of Electronic Information and Automation, Guilin University of Aerospace Technology, Guilin 541004, Guangxi Province China." + }, + { + "author_name": "Yiyuan SUN", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Shoujiang ZHAO", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + }, + { + "author_name": "Lei YAN", + "author_inst": "School of Earth and Space Science, Peking University, Beijing, 100871, China." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.09.20120139", "rel_title": "Prevalence and Predictors of General Psychiatric Disorders and Loneliness during COVID-19 in the United Kingdom: Results from the Understanding Society UKHLS", @@ -1380460,29 +1381128,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.08.20125781", - "rel_title": "Remarks on pooling Coronavirus tests", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125781", - "rel_abs": "Diagnostic testing for the novel Coronavirus is an important tool to fight the Covid-19 pandemic. However, testing capacities are limited. A modified testing protocol, whereby a number of probes are \"pooled\" (that is, grouped), is known to increase the capacity for testing. Here, we model pooled testing with a double-average model, which we think to be close to reality for Covid-19 testing. The optimal pool size and the effect of test errors are considered. Results show that the best pool size is three to five, under reasonable assumptions. Pool testing even reduces the number of false positives in the absence of dilution effects.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Alexander Pikovski", - "author_inst": "self-employed" - }, - { - "author_name": "Kajetan Bentele", - "author_inst": "no institution" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.08.20125534", "rel_title": "Interregional SARS-CoV-2 spread from a single introduction outbreak in a meat-packing plant in northeast Iowa", @@ -1380670,6 +1381315,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.09.20126086", + "rel_title": "Private Health Sector in India: Ready and willing, yet underutilized in the Covid-19 pandemic.", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126086", + "rel_abs": "BackgroundThe private medical sector is a resource that must be estimated for efficient inclusion into public healthcare during pandemics.\n\nMethodsA survey was conducted among private healthcare workers to ascertain their views on the potential resources that can be accessed from the private sector and methods to do the same.\n\nResultsThere were 213 respondents, 80% of them being doctors. Nearly half (47.4%) felt that the contribution from the private medical sector has been suboptimal. Areas suggested for improved contributions by the private sector related to patient care (71.8%) and provision of equipment (62.4%), with fewer expectations (39.9%) on the research front. Another area of deemed support was maintaining continuity of care for non-COVID patients using virtual consultation services (77.4%), tele-consultation being the preferred option (60%). 58.2% felt that the Government had not involved the private sector adequately; and 45.1% felt they should be part of policy-making.\n\nConclusionA streamlined pathway to facilitate the private sector to join hands with the public sector for a national cause is the need of the hour. Through our study, we have identified gaps in the current contribution by the private sector and identified areas in which they could contribute, by their own admission.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Samira Davalbhakta", + "author_inst": "Byramjee Jeejeebhoy Government Medical College and Sassoon General Hospitals" + }, + { + "author_name": "Supriya Sharma", + "author_inst": "Department of Surgical Gastroenterology Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + }, + { + "author_name": "Shefali Gupta", + "author_inst": "Department of Microbiology Maharishi Markandeshwar Institute of Medical Sciences and Research (MMIMSR) Haryana, India" + }, + { + "author_name": "Vishwesh Agarwal", + "author_inst": "Mahatma Gandhi Missions Medical College" + }, + { + "author_name": "Gaurav Pandey", + "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + }, + { + "author_name": "Durga Prasanna Misra", + "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + }, + { + "author_name": "Bijaya Nanda Naik", + "author_inst": "Dept of Community Medicine NAMO Medical Education and Research Institute, Silvassa, DNH" + }, + { + "author_name": "Ashish Goel", + "author_inst": "University College Of Medical Sciences, New Delhi" + }, + { + "author_name": "Latika Gupta", + "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + }, + { + "author_name": "Vikas Agarwal", + "author_inst": "Sanjay Gandhi Postgraduate Institute of Medical Sciences Lucknow, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.10.20127266", "rel_title": "Resource requirements for reintroducing elective surgery in England during the COVID-19 pandemic: a modelling study", @@ -1381926,61 +1382626,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.10.20127845", - "rel_title": "At-home self-collection of saliva, oropharyngeal swabs and dried blood spots for SARS-CoV-2 diagnosis and serology: post-collection acceptability of specimen collection process and patient confidence in specimens", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127845", - "rel_abs": "BackgroundOptions to increase the ease of testing for SARS-CoV-2 infection and immune response are needed. Self-collection of diagnostic specimens at home offers an avenue to allow people to test for SARS-CoV-2 infection or immune response without traveling to a clinic or laboratory. Before this study, survey respondents indicated willingness to self-collect specimens for COVID-related tests, but hypothetical willingness can differ from post-collection acceptability after participants collect specimens.\n\nMethods153 US adults were enrolled in a study of the willingness and feasibility of patients to self-collect three diagnostic specimens (saliva, oropharyngeal swab (OPS) and dried blood spot (DBS) card) while observed by a clinician through a telehealth session. After the specimens were collected, 148 participants participated in a survey about the acceptability of the collection, packing and shipping process, and their confidence in the samples collected for COVID-related laboratory testing.\n\nResultsA large majority of participants (>84%) reported that collecting, packing and shipping of saliva, OPS, and DBS specimens were acceptable. Nearly nine in 10 (87%) reported being confident or very confident that the specimens they collected were sufficient for laboratory analysis. There were no differences in acceptability for any specimen type, packing and shipping, or confidence in samples by gender, age, race/ethnicity, or educational level.\n\nConclusionsSelf-collection of specimens for SARS-CoV-2 testing and preparing and shipping specimens for analysis were acceptable in a diverse group of US adults. Further refinement of materials and instructions to support self-collection of saliva, OPS and DBS specimens for COVID-related testing is needed.\n\nTrial registrationNo intervention was tested in this study", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mariah Valentine-Graves", - "author_inst": "Emory University" - }, - { - "author_name": "Eric Hall", - "author_inst": "Emory University" - }, - { - "author_name": "Jodie Lynn Guest", - "author_inst": "Emory University" - }, - { - "author_name": "Elizabeth Adam", - "author_inst": "Emory University" - }, - { - "author_name": "Rachel Valencia", - "author_inst": "Emory University" - }, - { - "author_name": "Isabel Hardee", - "author_inst": "Emory University" - }, - { - "author_name": "Kaitlin Shinn", - "author_inst": "Emory University" - }, - { - "author_name": "Travis Howard Sanchez", - "author_inst": "Emory University" - }, - { - "author_name": "Aaron J Siegler", - "author_inst": "Emory University" - }, - { - "author_name": "Patrick S Sullivan", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.10.20127084", "rel_title": "The role of remdesivir in South Africa: preventing COVID-19 deaths through increasing ICU capacity", @@ -1382196,6 +1382841,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.11.20127894", + "rel_title": "A scenario modeling pipeline for COVID-19 emergency planning", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20127894", + "rel_abs": "Coronavirus disease 2019 (COVID-19) has caused strain on health systems worldwide due to its high mortality rate and the large portion of cases requiring critical care and mechanical ventilation. During these uncertain times, public health decision makers, from city health departments to federal agencies, sought the use of epidemiological models for decision support in allocating resources, developing non-pharmaceutical interventions, and characterizing the dynamics of COVID-19 in their jurisdictions. In response, we developed a flexible scenario modeling pipeline that could quickly tailor models for decision makers seeking to compare projections of epidemic trajectories and healthcare impacts from multiple intervention scenarios in different locations. Here, we present the components and configurable features of the COVID Scenario Pipeline, with a vignette detailing its current use. We also present model limitations and active areas of development to meet ever-changing decision maker needs.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Joseph Chadi Lemaitre", + "author_inst": "EPFL" + }, + { + "author_name": "Kyra H Grantz", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Joshua Kaminsky", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Hannah R Meredith", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Shaun A Truelove", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Stephen A Lauer", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Lindsay T Keegan", + "author_inst": "University of Utah" + }, + { + "author_name": "Sam Shah", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Josh Wills", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Kathryn Kaminsky", + "author_inst": "Unaffiliated" + }, + { + "author_name": "Javier Perez-Saez", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Justin Lessler", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Elizabeth C Lee", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.10.20127589", "rel_title": "Effect of social distancing on COVID-19 incidence and mortality in the US", @@ -1383256,57 +1383968,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.11.20128561", - "rel_title": "Determinants of COVID-19 incidence and mortality: A cross-country analysis", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128561", - "rel_abs": "The authors have withdrawn this manuscript because the source data was last updated at the end of March, and hence the authors believe that the results derived and conclusions drawn in the manuscript may not hold true now. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Gursimer Jeet", - "author_inst": "Post Graduate Institute of Medical Education and Research, Chandigarh, India" - }, - { - "author_name": "Atul Sharma", - "author_inst": "Post Graduate Institute of Medical Education and Research, Chandigarh, India" - }, - { - "author_name": "Aarti Goyal", - "author_inst": "Post Graduate Institute of Medical Education and Research, Chandigarh, India" - }, - { - "author_name": "Shankar Prinja", - "author_inst": "Post Graduate Institute of Medical Education and Research, Chandigarh, India" - }, - { - "author_name": "Arvind Pandey", - "author_inst": "Indian Council of Medical Research, New Delhi, India" - }, - { - "author_name": "Sandip Mandal", - "author_inst": "Indian Council of Medical Research, New Delhi, India" - }, - { - "author_name": "Mendu V Rao", - "author_inst": "National Institute of Medical Statistics, New Delhi, India" - }, - { - "author_name": "Sumit Aggarwal", - "author_inst": "Indian Council of Medical Research, New Delhi, India" - }, - { - "author_name": "Narendra K Arora", - "author_inst": "The INCLEN Trust International, New Delhi, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.11.20128918", "rel_title": "They stumble that run fast: the economic and COVID-19 transmission impacts of reopening industries in the US", @@ -1383570,6 +1384231,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.11.20128389", + "rel_title": "Profiling the positive detection rate of SARS-CoV-2 using polymerase chain reaction in different types of clinical specimens: a systematic review and meta-analysis", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128389", + "rel_abs": "BackgroundTesting is one of the commendable preventive measures against coronavirus disease (COVID-19), and needs to be done using both most appropriate specimen and an accurate diagnostic test like real time reverse transcription polymerase chain reaction (qRT-PCR). However, the detection rate of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from different clinical specimens after onset of symptoms is not yet well established. For guiding the selection of specimens for clinical diagnosis of COVID-19, a systematic review aiming at profiling the positive detection rate from different clinical specimens using PCR was conducted.\n\nMethodsThe systematic search was done using PubMed/MEDLINE, Science direct, Google Scholar, among others. The search included studies on laboratory diagnosis of SARS-CoV-2 from different clinical specimens using PCR. Data extraction was done using Microsoft Excel spread sheet 2010 and reported according to PRISMA-P guidelines. Using Open Meta Analyst software, DerSimonian-Laird random effects analysis was performed to determine a summary estimate (positive rate [PR]/proportions) and their 95% confidence interval (95%CI).\n\nResultsA total of 8136 different clinical specimens were analyzed to detect SARS-CoV-2, with majority being nasopharyngeal swabs (69.6%). Lower respiratory tract (LRT) specimens had a PR of 71.3% (95%CI:60.3%-82.3%) while no virus was detected from the urinogenital specimens. Bronchoalveolar lavage fluid (BLF) specimen had the PR of 91.8% (95%CI:79.9-103.7%), followed by rectal swabs, 87.8 % (95%CI:78.6%-96.9%) then sputum, 68.1% (95%CI:56.9%-79.4%). Low PR was observed in oropharyngeal swabs, 7.6% (95%CI:5.7%-9.6%) and blood samples, 1.0% (95%CI: -0.1%-2.1%), whilst no SARS-CoV-2 was detected in urine samples. Nasopharyngeal swab, a widely used specimen had a PR of 45.5% (95%CI:31.2%-59.7%).\n\nConclusionIn this study, SARS-CoV-2 was highly detected in lower respiratory tract specimens while there was no detected virus in urinogenital specimens. Regarding the type of clinical specimens, bronchoalveolar lavage fluid had the highest positive rate followed by rectal swab then sputum. Nasopharyngeal swab which is widely used had a moderate detection rate. Low positive rate was recorded in oropharyngeal swab and blood sample while no virus was found in urine samples. More importantly, the virus was detected in feces, suggesting SARS-CoV-2 transmission by the fecal route.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "George M. Bwire", + "author_inst": "School of Pharmacy, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania." + }, + { + "author_name": "Mtebe V. Majigo", + "author_inst": "School of Medicine, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania" + }, + { + "author_name": "Belinda J. Njiro", + "author_inst": "School of Medicine, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania" + }, + { + "author_name": "Akili Mawazo", + "author_inst": "Institute of Allied Health Sciences, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.11.20128165", "rel_title": "Easing social distancing index after COVID-19 pandemic", @@ -1385114,33 +1385806,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.11.146332", - "rel_title": "Validation and performance of a quantitative IgG assay for the screening of SARS-CoV-2 antibodies", - "rel_date": "2020-06-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.11.146332", - "rel_abs": "The current COVID-19 epidemic imposed an unpreceded challenge to the scientific community in terms of treatment, epidemiology, diagnosis, social interaction, fiscal policies and many other areas. The development of accurate and reliable diagnostic tools (high specificity and sensitivity) is crucial in the current period, the near future and in the long term. These assays should provide guidance to identify immune presumptive protected persons, potential plasma, and/or B cell donors and vaccine development among others. Also, such assays will be contributory in supporting prospective and retrospective studies to identify the prevalence and incidence of COVID-19 and to characterize the dynamics of the immune response. As of today, only thirteen serological assays have received the Emergency Use Authorization (EUA) by the U.S. Federal Drug Administration (FDA). In this work we describe the development and validation of a quantitative IgG enzyme-linked immunoassay (ELISA) using the recombinant SARS-CoV-2 Spike Protein S1 domain, containing the receptor-binding domain (RBD), showing 98% sensitivity, 98.9% specificity and positive and negative predictive values of 100% and 99.2%, respectively. The assay showed to be useful to test for SARS-CoV-2 IgG antibodies in plasma samples from COVID-19-recovered subjects as potential donors for plasmapheresis. This assay is currently under review by the Federal Drug Administration for an Emergency Use Authorization request (Submission Number EUA201115).", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ana M Espino", - "author_inst": "Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico 00936, USA." - }, - { - "author_name": "Petraleigh Pantoja", - "author_inst": "Unit of Comparative Medicine, Caribbean Primate Research Center, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico 00952, USA. Department" - }, - { - "author_name": "Carlos A Sariol", - "author_inst": "Department of Microbiology and Medical Zoology, University of Puerto Rico-Medical Sciences Campus, San Juan, PR, USA, Unit of Comparative Medicine, Caribbean Pr" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.12.146290", "rel_title": "Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients", @@ -1385456,6 +1386121,137 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.10.20127175", + "rel_title": "Excess deaths in people with cardiovascular diseases during the COVID-19 pandemic.", + "rel_date": "2020-06-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127175", + "rel_abs": "BackgroundCardiovascular diseases(CVD) increase mortality risk from coronavirus infection(COVID-19), but there are concerns that the pandemic has affected supply and demand of acute cardiovascular care. We estimated excess mortality in specific CVDs, both \"direct\", through infection, and \"indirect\", through changes in healthcare.\n\nMethodsWe used population-based electronic health records from 3,862,012 individuals in England to estimate pre- and post-COVID-19 mortality risk(\"direct\" effect) for people with incident and prevalent CVD. We incorporated: (i)pre-COVID-19 risk by age, sex and comorbidities, (ii)estimated population COVID-19 prevalence, and (iii)estimated relative impact of COVID-19 on mortality(relative risk, RR: 1.5, 2.0 and 3.0). For \"indirect\" effects, we analysed weekly mortality and emergency department data for England/Wales and monthly hospital data from England(n=2), China(n=5) and Italy(n=1) for CVD referral, diagnosis and treatment until 1 May 2020.\n\nFindingsCVD service activity decreased by 60-100% compared with pre-pandemic levels in eight hospitals across China, Italy and England during the pandemic. In China, activity remained below pre-COVID-19 levels for 2-3 months even after easing lockdown, and is still reduced in Italy and England. Mortality data suggest indirect effects on CVD will be delayed rather than contemporaneous(peak RR 1.4). For total CVD(incident and prevalent), at 10% population COVID-19 rate, we estimated direct impact of 31,205 and 62,410 excess deaths in England at RR 1.5 and 2.0 respectively, and indirect effect of 49932 to 99865 excess deaths.\n\nInterpretationSupply and demand for CVD services have dramatically reduced across countries with potential for substantial, but avoidable, excess mortality during and after the COVID-19 pandemic.\n\nFundingNIHR, HDR UK, Astra Zeneca", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Amitava Banerjee", + "author_inst": "University College London" + }, + { + "author_name": "Suliang Chen", + "author_inst": "University College London" + }, + { + "author_name": "Laura Pasea", + "author_inst": "University College London" + }, + { + "author_name": "Alvina Lai", + "author_inst": "University College London" + }, + { + "author_name": "Michail Katsoulis", + "author_inst": "UCL" + }, + { + "author_name": "Spiros Denaxas", + "author_inst": "University College London" + }, + { + "author_name": "Vahe Nafilyan", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Bryan Williams", + "author_inst": "UCL" + }, + { + "author_name": "Wai Keong Wong", + "author_inst": "University College London Hospitals NHS Trust" + }, + { + "author_name": "Ameet Bakhai", + "author_inst": "Royal Free Hospitals NHS Trust" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "University of Leicester" + }, + { + "author_name": "Deenan Pillay", + "author_inst": "UCL" + }, + { + "author_name": "Mahdad Noursadeghi", + "author_inst": "UCL" + }, + { + "author_name": "Honghan Wu", + "author_inst": "UCL" + }, + { + "author_name": "Nilesh Pareek", + "author_inst": "King's College Hospital" + }, + { + "author_name": "Daniel Bromage", + "author_inst": "Kings College London" + }, + { + "author_name": "Theresa Mcdonagh", + "author_inst": "Kings College London" + }, + { + "author_name": "Jonathan Byrne", + "author_inst": "Kings London NHS Trust" + }, + { + "author_name": "James T Teo", + "author_inst": "Kings College Hospital NHS Foundation Trust" + }, + { + "author_name": "Ajay Shah", + "author_inst": "King's College London" + }, + { + "author_name": "Ben Humberstone", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Liang V Tang", + "author_inst": "Huazhong University of Science and Technology, Wuhan, China" + }, + { + "author_name": "Anoop SV Shah", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Andrea Rubboli", + "author_inst": "Ospedale S. Maria delle Croci, Ravenna, Italy" + }, + { + "author_name": "Yutao Guo", + "author_inst": "PLA General Hospital, Beijing, China." + }, + { + "author_name": "Yu Hu", + "author_inst": "Huazhong University of Science and Technology, Wuhan, China." + }, + { + "author_name": "Cathie LM Sudlow", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Gregory YH Lip", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Harry Hemingway", + "author_inst": "UCL" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.06.10.20127258", "rel_title": "Knowledge, attitudes, and practices among the general population during COVID-19 outbreak in Iran: A national cross-sectional survey", @@ -1386828,29 +1387624,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.09.20126128", - "rel_title": "Poorly known aspects of flattening the curve of COVID-19", - "rel_date": "2020-06-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126128", - "rel_abs": "This work concerns the too-often mentioned flattening of the curve of COVID-19. The diffusion of the virus is analyzed with logistic-curve fits on the 25 countries most affected at the time of the writing and in which the diffusion curve was more than 95% completed. A negative correlation observed between the final number of infections and the slope of the logistic curve corroborates a result obtained long time ago via an extensive simulation study. There is both theoretical arguments and experimental evidence for the existence of such correlations. The flattening of the curve results in a retardation of the curves midpoint, which entails an increase in the final number of infections. It is possible that more lives are lost at the end by this process. Our analysis also permits evaluation of the various governments interventions in terms of rapidity of response, efficiency of the actions taken (the amount of flattening achieved), and the number of days by which the curve was delayed. Not surprisingly, early decisive response proves to be the optimum strategy among the countries studied.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Alain Debecker", - "author_inst": "Institut de Maintien \u00e0 Domicile" - }, - { - "author_name": "Theodore Modis", - "author_inst": "Growth Dynamics" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.09.20125724", "rel_title": "Estimating Force of Infection from Serologic Surveys with Imperfect Tests", @@ -1387014,6 +1387787,73 @@ "type": "confirmatory results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.06.10.144816", + "rel_title": "Remdesivir but not famotidine inhibits SARS-CoV-2 replication in human pluripotent stem cell-derived intestinal organoids", + "rel_date": "2020-06-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.10.144816", + "rel_abs": "Gastrointestinal symptoms in COVID-19 are associated with prolonged symptoms and increased severity. We employed human intestinal organoids derived from pluripotent stem cells (PSC-HIOs) to analyze SARS-CoV-2 pathogenesis and to validate efficacy of specific drugs in the gut. Certain, but not all cell types in PSC-HIOs express SARS-CoV-2 entry factors ACE2 and TMPRSS2, rendering them susceptible to SARS-CoV-2 infection. Remdesivir, a promising drug to treat COVID-19, effectively suppressed SARS-CoV-2 infection of PSC-HIOs. In contrast, the histamine-2-blocker famotidine showed no effect. Thus, PSC-HIOs provide an interesting platform to study SARS-CoV-2 infection and to identify or validate drugs.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jan Krueger", + "author_inst": "Ulm University" + }, + { + "author_name": "Ruediger Gross", + "author_inst": "Ulm University" + }, + { + "author_name": "Carina Conzelmann", + "author_inst": "Ulm University" + }, + { + "author_name": "Janis A Mueller", + "author_inst": "Ulm University" + }, + { + "author_name": "Lennart Koepke", + "author_inst": "Ulm University" + }, + { + "author_name": "Konstantin Sparrer", + "author_inst": "Ulm University" + }, + { + "author_name": "Desiree Schuetz", + "author_inst": "Ulm University" + }, + { + "author_name": "Thomas Seufferlein", + "author_inst": "Ulm University" + }, + { + "author_name": "Thomas F.E. Barth", + "author_inst": "Ulm University" + }, + { + "author_name": "Steffen Stenger", + "author_inst": "Ulm University" + }, + { + "author_name": "Sandra Heller", + "author_inst": "Ulm University" + }, + { + "author_name": "Alexander Kleger", + "author_inst": "Ulm University" + }, + { + "author_name": "Jan Muench", + "author_inst": "Ulm University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.11.140285", "rel_title": "ROBOCOV: An affordable open-source robotic platform for COVID-19 testing by RT-qPCR", @@ -1388510,33 +1389350,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.06.09.082834", - "rel_title": "SARS-CoV-2 sequence typing, evolution and signatures of selection using CoVa, a Python-based command-line utility", - "rel_date": "2020-06-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.09.082834", - "rel_abs": "The current global pandemic COVID-19, caused by SARS-CoV-2, has resulted in millions of infections worldwide in a few months. Global efforts to tackle this situation have produced a tremendous body of genomic data, which can be used for tracing transmission routes, characterization of isolates, and monitoring variants with potential for unusual virulence. Several groups have analyzed these genomes using different approaches. However, as new data become available, the research community needs a pipeline to perform a set of routine analyses, that can quickly incorporate new genome sequences and update the analysis reports. We developed a programmatic tool, CoVa, with this objective. It is a fast, accurate and user-friendly utility to perform a variety of genome analyses on hundreds of SARS-CoV-2 sequences. Using CoVa, we define a modified sequence typing nomenclature and identify sites under positive selection. Further analysis identified some peptides and sites showing geographical patterns of selection. Specifically, we show differences in sequence type distribution between sequences from India and those from the rest of the world. We also show that several sites show signatures of positive selection uniquely in sequences from India. Preliminary evolutionary analysis, using features that will be incorporated into CoVa in the near future, show a mutation rate of 7.4 x 10-4 substitutions/site/year, confirm a temporal signal with a November 2019 origin of SARS-CoV-2, and a heterogeneity in the geographical distribution of Indian samples.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Farhan Ali", - "author_inst": "National Centre for Biological Sciences, TIFR, Bangalore" - }, - { - "author_name": "Mohak Sharda", - "author_inst": "National Centre for Biological Sciences, TIFR" - }, - { - "author_name": "Aswin Sai Narain Seshasayee", - "author_inst": "Tata Institute of Fundamental Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.06.09.134585", "rel_title": "Global cataloguing of variations in untranslated regions of viral genome and prediction of key host RNA binding protein-microRNA interactions modulating genome stability in SARS-CoV2", @@ -1388856,6 +1389669,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.08.20125658", + "rel_title": "Temporal evolution of COVID-19 in the states of India using SIQR Model", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125658", + "rel_abs": "COVID 19 entered during the last week of April 2020 in India has caused 3,546 deaths with 1,13,321 number of reported cases. Indian government has taken many proactive steps, including strict lockdown of the entire nation for more than 50 days, identification of hotspots, app-based tracking of citizens to track infected. This paper investigated the evolution of COVID 19 in five states of India (Maharashtra, UP, Gujrat, Tamil Nadu, and Delhi) from 1st April 2020 to 20th May 2020. Variation of doubling rate and reproduction number (from SIQR) with time is used to analyse the performance of the majorly affected Indian states. It has been determined that Uttar Pradesh is one of the best performers among five states with the doubling rate crossing 18 days as of 20th May. Tamil Nadu has witnessed the second wave of infections during the second week of May. Maharashtra is continuously improving at a steady rate with its doubling rate reaching to 12.67 days. Also these two states are performing below the national average in terms of infection doubling rate. Gujrat and Delhi have reported the doubling rate of 16.42 days and 15.49 days respectively. Comparison of these states has also been performed based on time-dependent reproduction number. Recovery rate of India has reached to 40 % as the day paper is written.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "ALOK TIWARI", + "author_inst": "IIT BOMBAY" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.08.20125062", "rel_title": "Principles and Practice of SARS-CoV-2 Decontamination of N95 Masks with UV-C", @@ -1390400,85 +1391232,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.06.08.141267", - "rel_title": "Structural basis of a public antibody response to SARS-CoV-2", - "rel_date": "2020-06-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.08.141267", - "rel_abs": "Molecular-level understanding of human neutralizing antibody responses to SARS-CoV-2 could accelerate vaccine design and facilitate drug discovery. We analyzed 294 SARS-CoV-2 antibodies and found that IGHV3-53 is the most frequently used IGHV gene for targeting the receptor binding domain (RBD) of the spike (S) protein. We determined crystal structures of two IGHV3-53 neutralizing antibodies +/- Fab CR3022 ranging from 2.33 to 3.11 [A] resolution. The germline-encoded residues of IGHV3-53 dominate binding to the ACE2 binding site epitope with no overlap with the CR3022 epitope. Moreover, IGHV3-53 is used in combination with a very short CDR H3 and different light chains. Overall, IGHV3-53 represents a versatile public VH in neutralizing SARS-CoV-2 antibodies, where their specific germline features and minimal affinity maturation provide important insights for vaccine design and assessing outcomes.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Meng Yuan", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Hejun Liu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Nicholas C. Wu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Chang-Chun D. Lee", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Xueyong Zhu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Fangzhu Zhao", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Deli Huang", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Wenli Yu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Yuanzi Hua", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Henry Tien", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Thomas F. Rogers", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Elise Landais", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Devin Sok", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Joseph G. Jardine", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Dennis R. Burton", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Ian A. Wilson", - "author_inst": "The Scripps Research Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.08.141077", "rel_title": "Cholesterol 25-hydroxylase suppresses SARS-CoV-2 replication by blocking membrane fusion", @@ -1390809,6 +1391562,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.08.139477", + "rel_title": "An Inexpensive RT-PCR Endpoint Diagnostic Assay for SARS-CoV-2 Using Nested PCR: Direct Assessment of Detection Efficiency of RT-qPCR Tests and Suitability for Surveillance", + "rel_date": "2020-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.08.139477", + "rel_abs": "With a view to extending testing capabilities for the ongoing SARS-CoV-2 pandemic we have developed a test that lowers cost and does not require real time quantitative reverse transcription polymerase chain reaction (RT-qPCR). We developed a reverse transcription nested PCR endpoint assay (RT-nPCR) and showed that RT-nPCR has comparable performance to the standard RT-qPCR test. In the course of comparing the results of both tests, we found that the standard RT-qPCR test can have low detection efficiency (less than 50%) in a real testing scenario which may be only partly explained by low viral representation in many samples. This finding points to the importance of directly monitoring detection efficiency in test environments. We also suggest measures that would improve detection efficiency.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jayeshkumar Narsibhai Davda", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Keith Frank", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Sivakumar Prakash", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Gunjan Purohit", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Devi Prasad Vijayashankar", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Dhiviya Vedagiri", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Karthik Bharadwaj Tallapaka", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Krishnan Harinivas Harshan", + "author_inst": "CSIR-Centre for Cellular and Molecular Biollgy" + }, + { + "author_name": "Archana Bharadwaj Siva", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Rakesh Kumar Mishra", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Jyotsna Dhawan", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Imran Siddiqi", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.06.07.20121939", "rel_title": "Mortality Analysis of COVID-19 Confirmed cases in Pakistan", @@ -1392413,41 +1393229,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.07.20124776", - "rel_title": "Analysis of the effect of proton pump inhibitors on the course of common COVID-19", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.07.20124776", - "rel_abs": "Background/aimsTo evaluate the effect of proton pump inhibitors on the course of common COVID-19.\n\nMethodsClinical data of common COVID-19 patients admitted to the Shanghai public health clinical center for treatment from January 20, 2020 to March 16, 2020 were collected. A retrospective study was conducted and the patients were divided into two groups according to whether they used proton pump inhibitors or not. The differences in SARS-CoV-2 clearance and hospital stay between the two groups were compared by univariate and multivariate analyses.\n\nResultsA total of 154 COVID-19 common cases were included in this study, including 80 males (51.9%), 35 patients (22.7%) in the proton pump inhibitors group, and 119 patients (77.3%) in the control group. In the proton pump inhibitors group and the control group, the duration of SARS-CoV-2 clearance were 7(6-9) and 7(6-11) days, and the duration of hospital stay was 21(16-25) and 20(15-26) days, respectively. There was no significant difference between the two groups in the cumulative incidence of SARS-CoV-2 clearance and the cumulative incidence of discharge, and the same after Propensity Score Match, all P > 0.05. Multivariate analysis suggested that chronic gastropathy prolonged the duration of SARS-CoV-2 clearance, the HR was 20.924(3.547-123.447). Hypertension, chronic obstructive pulmonary disease, chronic liver disease and malignant tumor all increased the duration of hospital stay for COVID-19, and the HR were 1.820 (1.073-3.085), 4.370 (1.205-15.844), 9.011 (2.681-30.290) and 5.270 (1.237-22.456), respectively; the duration of hospital stay in COVID-19 patients was shortened by SARS-CoV-2 clearance, and the HR was 0.907 (0.869-0.947); all P < 0.05.\n\nConclusionProton pump inhibitors use have no effect on the prolonging or shortening of the course of adults hospitalized with COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Xiao-Yu Zhang", - "author_inst": "Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Hai-Bing Wu", - "author_inst": "Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Yun Ling", - "author_inst": "Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Zhi-Ping Qian", - "author_inst": "Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Liang Chen", - "author_inst": "Shanghai Public Health Clinical Center, Fudan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.07.20124677", "rel_title": "Repurposing of drugs for Covid-19: a systematic review and meta-analysis", @@ -1392659,6 +1393440,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.08.20125377", + "rel_title": "Weather variables impact on COVID-19 incidence", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125377", + "rel_abs": "We test the hypothesis of COVID-19 contagion being influenced by meteorological parameters such as temperature or humidity. We analysed data at high spatial resolution (regions in Italy and counties in the USA) and found that while at low resolution this might seem the case, at higher resolution no correlation is found. Our results are consistent with a poor outdoors transmission of the disease. However, a possible indirect correlation between good weather and a decrease in disease spread may occur, as people spend longer time outdoors.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Javier G. Corripio", + "author_inst": "meteoexploration.com" + }, + { + "author_name": "Lorna Raso", + "author_inst": "meteoexploration.com" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.08.20124305", "rel_title": "Time-series plasma cell-free DNA analysis reveals disease severity of COVID-19 patients", @@ -1393679,77 +1394483,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.05.20116624", - "rel_title": "Associations between COVID-19 infection, tobacco smoking and nicotine use, common respiratory conditions and inhaled corticosteroids: a prospective QResearch-Case Mix Programme data linkage study January-May 2020", - "rel_date": "2020-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20116624", - "rel_abs": "IntroductionEpidemiological and laboratory research seems to suggest that smoking and perhaps nicotine alone could reduce the severity of COVID-19. Likewise, there is some evidence that inhaled corticosteroids could also reduce its severity, opening the possibility that nicotine and inhaled steroids could be used as treatments.\n\nMethodsIn this prospective cohort study, we will link English general practice records from the QResearch database to Public Health Englands database of SARS-CoV-2 positive tests, Hospital Episode Statistics, admission to intensive care units, and death from COVID-19 to identify our outcomes: hospitalisation, ICU admission, and death due to COVID. Using Cox regression, we will perform sequential adjustment for potential confounders identified by separate directed acyclic graphs to:\n\nO_LIAssess the association between smoking and COVID-19 disease severity, and how that changes on adjustment for smoking-related comorbidity.\nC_LIO_LIMore closely characterise the association between smoking and severe COVID-19 disease by assessing whether the association is modified by age (as a proxy of length of smoking), gender, ethnic group, and whether people have asthma or COPD.\nC_LIO_LIAssess for evidence of a dose-response relation between smoking intensity and disease severity, which would help create a case for causality.\nC_LIO_LIExamine the association between former smokers who are using NRT or are vaping and disease severity.\nC_LIO_LIExamine whether pre-existing respiratory disease is associated with severe COVID-19 infection.\nC_LIO_LIAssess whether the association between chronic obstructive pulmonary disease (COPD) and asthma and COVID-19 disease severity is modified by age, gender, ethnicity, and smoking status.\nC_LIO_LIAssess whether the use of inhaled corticosteroids is associated with severity of COVID-19 disease.\nC_LIO_LITo assess whether the association between use of inhaled corticosteroids and severity of COVID-19 disease is modified by the number of other airways medications used (as a proxy for severity of condition) and whether people have asthma or COPD.\nC_LI\n\nConclusionsThis representative population sample will, to our knowledge, present the first comprehensive examination of the association between smoking, nicotine use without smoking, respiratory disease, and severity of COVID-19. We will undertake several sensitivity analyses to examine the potential for bias in these associations.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Paul Aveyard", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicola Lindson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Min Gao", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jamie Hartmann-Boyce", - "author_inst": "University of Oxford" - }, - { - "author_name": "Margaret Smith", - "author_inst": "University of Oxford" - }, - { - "author_name": "Duncan Young", - "author_inst": "University of Oxford" - }, - { - "author_name": "Carol Coupland", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Pui San Tan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ashley K Clift", - "author_inst": "University of Oxford" - }, - { - "author_name": "David Harrison", - "author_inst": "Intensive Care National Audit & Research Centre (icnarc)" - }, - { - "author_name": "Doug W Gould", - "author_inst": "Intensive Care National Audit & Research Centre (icnarc)" - }, - { - "author_name": "Ian Pavord", - "author_inst": "University of Oxford" - }, - { - "author_name": "Peter Watkinson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Julia Hippisley-Cox", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.06.05.20107011", "rel_title": "A COVID-19 outbreak in a rheumatology department upon the early days of the pandemic", @@ -1394041,6 +1394774,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.06.20124149", + "rel_title": "Hawkes process modeling of COVID-19 with mobility leading indicators and spatial covariates", + "rel_date": "2020-06-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20124149", + "rel_abs": "Hawkes processes are used in machine learning for event clustering and causal inference, while they also can be viewed as stochastic versions of popular compartmental models used in epidemiology. Here we show how to develop accurate models of COVID-19 transmission using Hawkes processes with spatial-temporal covariates. We model the conditional intensity of new COVID-19 cases and deaths in the U.S. at the county level, estimating the dynamic reproduction number of the virus within an EM algorithm through a regression on Google mobility indices and demographic covariates in the maximization step. We validate the approach on short-term forecasting tasks, showing that the Hawkes process outperforms several benchmark models currently used to track the pandemic, including an ensemble approach and a SEIR-variant. We also investigate which covariates and mobility indices are most important for building forecasts of COVID-19 in the U.S.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Wen-Hao Chiang", + "author_inst": "Indiana University-Purdue University Indianapolis" + }, + { + "author_name": "Xueying Liu", + "author_inst": "Indiana University-Purdue University Indianapolis" + }, + { + "author_name": "George Mohler", + "author_inst": "Indiana University-Purdue University Indianapolis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.04.20122325", "rel_title": "Sub-weekly cycle uncovers the hidden link of 1atmospheric pollution to Kawasaki Disease", @@ -1395609,69 +1396369,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.06.08.140459", - "rel_title": "Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide", - "rel_date": "2020-06-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.08.140459", - "rel_abs": "The COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), was declared on March 11, 2020 by the World Health Organization. As of the 31st of May, 2020, there have been more than 6 million COVID-19 cases diagnosed worldwide and over 370,000 deaths, according to Johns Hopkins. Thousands of SARS-CoV-2 strains have been sequenced to date, providing a valuable opportunity to investigate the evolution of the virus on a global scale. We performed a phylogenetic analysis of over 1,225 SARS-CoV-2 genomes spanning from late December 2019 to mid-March 2020. We identified a missense mutation, D614G, in the spike protein of SARS-CoV-2, which has emerged as a predominant clade in Europe (954 of 1,449 (66%) sequences) and is spreading worldwide (1,237 of 2,795 (44%) sequences). Molecular dating analysis estimated the emergence of this clade around mid-to-late January (10 - 25 January) 2020. We also applied structural bioinformatics to assess D614G potential impact on the virulence and epidemiology of SARS-CoV-2. In silico analyses on the spike protein structure suggests that the mutation is most likely neutral to protein function as it relates to its interaction with the human ACE2 receptor. The lack of clinical metadata available prevented our investigation of association between viral clade and disease severity phenotype. Future work that can leverage clinical outcome data with both viral and human genomic diversity is needed to monitor the pandemic.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sandra Isabel", - "author_inst": "The Hospital for Sick Children" - }, - { - "author_name": "Lucia Grana-Miraglia", - "author_inst": "University of Toronto" - }, - { - "author_name": "Jahir M Gutierrez", - "author_inst": "Layer 6 AI" - }, - { - "author_name": "Cedoljub Bundalovic-Torma", - "author_inst": "University of Toronto" - }, - { - "author_name": "Helen E Groves", - "author_inst": "University of Toronto" - }, - { - "author_name": "Marc R Isabel", - "author_inst": "Universite Laval" - }, - { - "author_name": "Alireza Eshaghi", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Samir N Patel", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Jonathan B Gubbay", - "author_inst": "Publich Health Ontario" - }, - { - "author_name": "Tomi Poutanen", - "author_inst": "Layer 6 AI" - }, - { - "author_name": "David S Guttman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Susan M Poutanen", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.06.05.20123711", "rel_title": "Prevention of household transmission crucial to stop the catastrophic spread of COVID-19 in cities", @@ -1395863,6 +1396560,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2020.06.05.20123117", + "rel_title": "Serology confirms SARS-CoV-2 infection in PCR-negative children presenting with Paediatric Inflammatory Multi-System Syndrome", + "rel_date": "2020-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123117", + "rel_abs": "BackgroundDuring the COVID-19 outbreak, reports have surfaced of children who present with features of a multisystem inflammatory syndrome with overlapping features of Kawasaki disease and toxic shock syndrome - Paediatric Inflammatory Multisystem Syndrome-temporally associated with SARS-CoV-2 pandemic (PIMS-TS). Initial reports find that many of the children are PCR-negative for SARS-CoV-2, so it is difficult to confirm whether this syndrome is a late complication of viral infection in an age group largely spared the worst consequences of this infection, or if this syndrome reflects enhanced surveillance.\n\nMethodsChildren hospitalised for symptoms consistent with PIMS-TS between 28 April and 8 May 2020, and who were PCR-negative for SARS-CoV-2, were tested for antibodies to viral spike glycoprotein using an ELISA test.\n\nResultsEight patients (age range 7-14 years, 63% male) fulfilled case-definition for PIMS-TS during the study period. Six of the eight patients required admission to intensive care. All patients exhibited significant IgG and IgA responses to viral spike glycoprotein. Further assessment showed that the IgG isotypes detected in children with PIMS-TS were of the IgGl and lgG3 subclasses, a distribution similar to that observed in samples from hospitalised adult COVID-19 patients. In contrast, lgG2 and lgG4 were not detected in children or adults. IgM was not detected in children, which contrasts with adult hospitalised adult COVID-19 patients of whom all had positive IgM responses.\n\nConclusionsStrong IgG antibody responses can be detected in PCR-negative children with PIMS-TS. The low detection rate of IgM in these patients is consistent with infection having occurred weeks previously and that the syndrome onset occurs well after the control of SARS-CoV-2 viral load. This implies that the disease is largely immune-mediated. Lastly, this indicates that serology can be an appropriate diagnostic tool in select patient groups.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Marisol Perez-Toledo", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Sian E. Faustini", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Sian E. Jossi", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Adrian Shields", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Hari Krishnan Kanthimathinathan", + "author_inst": "Birmingham Women and Children's NHS Foundation Trust" + }, + { + "author_name": "Joel D. Allen", + "author_inst": "University of Southampton" + }, + { + "author_name": "Yasunori Watanabe", + "author_inst": "University of Southampton" + }, + { + "author_name": "Margaret Goodall", + "author_inst": "University of Birmingham" + }, + { + "author_name": "David C. Wraith", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Tonny V. Veenith", + "author_inst": "University Hospitals Birmingham NHS Trust" + }, + { + "author_name": "Mark T. Drayson", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Deepthi Jyothish", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Eslam Al-Abadi", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Ashish Chikermane", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Steven Welch", + "author_inst": "University Hospitals Birmingham" + }, + { + "author_name": "Kavitha Masilamani", + "author_inst": "Birmingham Women's and Children's NHS Foundation Trust" + }, + { + "author_name": "Scott Hackett", + "author_inst": "University Hospitals Birmingham" + }, + { + "author_name": "Max Crispin", + "author_inst": "University of Southampton" + }, + { + "author_name": "Barnaby Scholefield", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Adam F. Cunningham", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Alex G. Richter", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.05.20123745", "rel_title": "Combined oropharyngeal/nasal swab is equivalent to nasopharyngeal sampling for SARS-CoV-2 diagnostic PCR", @@ -1396775,77 +1397571,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.06.20122689", - "rel_title": "The impact of COVID-19 control measures on social contacts and transmission in Kenyan informal settlements", - "rel_date": "2020-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.06.20122689", - "rel_abs": "BackgroundMany low- and middle-income countries have implemented control measures against coronavirus disease 2019 (COVID-19). However, it is not clear to what extent these measures explain the low numbers of recorded COVID-19 cases and deaths in Africa. One of the main aims of control measures is to reduce respiratory pathogen transmission through direct contact with others. In this study we collect contact data from residents of informal settlements around Nairobi, Kenya to assess if control measures have changed contact patterns, and estimate the impact of changes on the basic reproduction number (R0).\n\nMethodsWe conducted a social contact survey with 213 residents of five informal settlements around Nairobi in early May 2020, four weeks after the Kenyan government introduced enhanced physical distancing measures and a curfew between 7pm and 5am. Respondents were asked to report all direct physical and non-physical contacts made the previous day, alongside a questionnaire asking about the social and economic impact of COVID-19 and control measures. We examined contact patterns by demographic factors, including socioeconomic status. We described the impact of COVID-19 and control measures on income and food security. We compared contact patterns during control measures to patterns from non-pandemic periods to estimate the change in R0.\n\nFindingsWe estimate that control measures reduced physical and non-physical contacts, reducing the R0 from around 2.6 to between 0.5 and 0.7, depending on the pre-COVID-19 comparison matrix used. Masks were worn by at least one person in 92% of contacts. Respondents in the poorest socioeconomic quintile reported 1.5 times more contacts than those in the richest. 86% of respondents reported a total or partial loss of income due to COVID-19, and 74% reported eating less or skipping meals due to having too little money for food.\n\nInterpretationCOVID-19 control measures have had a large impact on direct contacts and therefore transmission, but have also caused considerable economic and food insecurity. Reductions in R0 are consistent with the linear epidemic growth in Kenya and other sub-Saharan African countries that implemented similar, early control measures. However, negative and inequitable impacts on economic and food security may mean control measures are not sustainable in the longer term.\n\nResearch in context Evidence before this studyWe conducted a PubMed search on 6 June 2020 with no language restrictions for studies published since inception, using the search terms (\"social mix*\" OR \"social cont*\" OR \"contact pattern*) AND (\"covid*\"). The search yielded 53 articles, two of which reported changes in social contacts after COVID-19 control measures. The first study reported changes in contact patterns in Wuhan and Shanghai, and the second changes in contact patterns in the UK. We found no studies examining changes in contact patterns due to control measures in sub-Saharan Africa, and no studies disaggregating contacts by socioeconomic status.\n\nAdded value of this studyThis is the first study to estimate the reproduction number of COVID-19 under control measures in sub-Saharan Africa using primary contact data. This study also moves beyond existing work to i) measure contacts in densely populated informal settlements, ii) explore how social contacts vary across socioeconomic status, and iii) assess the impact of control measures on economic and food security in these areas.\n\nImplications of all the evidenceCOVID-19 control measures have substantially reduced social contacts and disease transmission. People of lower socioeconomic status face greater transmission risk as they report more contacts. Control measures have led to considerable economic and food insecurity, and may not be sustainable in the long term without efforts to reduce the burden of control measures on households.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Matthew Quaife", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Kevin van Zandvoort", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Amy Gimma", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Kashvi Shah", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Nicky McCreesh", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Kiesha Prem", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Edwine Barasa", - "author_inst": "KEMRI-Wellcome Trust Research Programme" - }, - { - "author_name": "Daniel Mwanga", - "author_inst": "Population Council, Kenya" - }, - { - "author_name": "Beth Kangwana", - "author_inst": "Population Council, Kenya" - }, - { - "author_name": "Jessie Pinchoff", - "author_inst": "Population Council, USA" - }, - { - "author_name": "- LSHTM Centre for Mathematical Modelling of Infectious Disease COVID-19 working group", - "author_inst": "" - }, - { - "author_name": "John Edmunds", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Christopher I Jarvis", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Karen Austrian", - "author_inst": "Population Council, Kenya" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.05.20121962", "rel_title": "TRACKing Excess Deaths (TRACKED): an interactive online tool to monitor excess deaths associated with COVID-19 pandemic in the United Kingdom", @@ -1397041,6 +1397766,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.04.20122317", + "rel_title": "Heart Disease Deaths during the Covid-19 Pandemic", + "rel_date": "2020-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122317", + "rel_abs": "The SARS-CoV-2 pandemic is associated with a reduction in hospitalization for an acute cardiovascular conditions. In a major health system in Massachusetts, there was a 43% reduction in these types of hospitalizations in March 2020 compared with March 2019.4 Whether mortality rates from heart disease have changed over this period is unknown.\n\nWe assembled information from the National Center for Health Statistics (Centers for Disease Control and Prevention) for 118,356,533 person-weeks from Week 1 (ending January 4) through Week 17 (ending April 25) of 2020 for the state of Massachusetts. We found that heart disease deaths are unchanged during the Covid-19 pandemic period as compared to the corresponding period of 2019. This is despite reports that admissions for acute myocardial infarction have fallen during this time.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jeremy Faust", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Zhenqiu Lin", + "author_inst": "Yale-New Haven Hospital, Center for Outcomes Research and Evaluation" + }, + { + "author_name": "Harlan Krumholz", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.07.137802", "rel_title": "Neuropilin-1 facilitates SARS-CoV-2 cell entry and provides a possible pathway into the central nervous system", @@ -1398769,29 +1399521,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.03.20120113", - "rel_title": "Discrete SIRIR modelling using empirical infection data shows that SARS-CoV-2 infection provides short-term immunity", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20120113", - "rel_abs": "The novel coronavirus SARS-CoV-2, which causes the COVID-19 disease, is now a global pandemic. Since December 2019, it has infected millions of people, caused the deaths of hundreds of thousands, and resulted in incalculable social and economic damage. Understanding the infectivity and transmission dynamics of the virus is essential for understanding how best to reduce mortality whilst ensuring minimal social restrictions to the lives of the general population. Anecdotal evidence is available, but detailed studies have not yet revealed whether infection with the virus results in immunity. In this work, we have extended the generic SIR framework to analyse empirical infection and fatality data from different regions to investigate the reinfection frequency of the disease. Our model predicts that cases of reinfection should have been observed by now if primary SARS-CoV-2 infection did not protect from subsequent exposure in the short term, however, no such cases have been documented. This work, therefore, provides a useful insight for serological testing strategies, lockdown easing and vaccine design.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Andrew McMahon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicole C. Robb", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.04.20117911", "rel_title": "Side by side comparison of three fully automated SARS-CoV-2 antibody assays with a focus on specificity", @@ -1399063,6 +1399792,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.02.20117499", + "rel_title": "Emergency calls are early indicators of ICU bed requirement during the COVID-19 epidemic", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20117499", + "rel_abs": "BackgroundAlthough the number of intensive care unit (ICU) beds is crucial during the COVID-19 epidemic caring for the most critically ill infected patients, there is no recognized early indicator to anticipate ICU bed requirements.\n\nMethodsIn the Ile-de-France region, from February 20 to May 5, 2020, emergency medical service (EMS) calls and the response provided (ambulances) together the percentage of positive reverse transcriptase polymerase chain reaction (RT-PCR) tests, general practitioner (GP) and emergency department (ED) visits, and hospital admissions of COVID-19 patients were recorded daily and compared to the number of COVID-19 ICU patients. Correlation curve analysis was performed to determine the best correlation coefficient (R), depending on the number of days the indicator has been shifted. A delay [≥]7 days was considered as an early alert, and a delay [≥]14 days a very early alert.\n\nFindingsEMS calls, percentage of positive RT-PCR tests, ambulances used, ED and GP visits of COVID-19 patients were strongly associated with COVID-19 ICU patients with an anticipation delay of 23, 15, 14, 13, and 12 days respectively. Hospitalization did not anticipate ICU bed requirement.\n\nInterpretationThe daily number of COVID19-related telephone calls received by the EMS and corresponding dispatch ambulances, and the proportion of positive RT-PCR tests were the earliest indicators of the number of COVID19 patients requiring ICU care during the epidemic crisis in the Ile-de-France region, rapidly followed by ED and GP visits. This information may help health authorities to anticipate a future epidemic, including a second wave of COVID19 or decide additional social measures.\n\nFundingOnly institutional funding was provided.\n\nResearch in contextO_ST_ABSEvidence before the studyC_ST_ABSWe searched PubMed and preprint archives for articles published up to May 17, 2020, that contained information about the anticipation of intensive care unit (ICU) bed requirement during the COVID-19 outbreak using the terms \"coronavirus\", \"2009-nCOV\", \"COVID-19\", SARS-CoV2\", \"prediction\" \"resource\" and \"intensive care\". We also reviewed relevant references in retrieved articles and the publicly available publication list of the COVID-19 living systematic review.22 This list contains studies on covid-19 published on PubMed and Embase through Ovid, bioRxiv, and medRxiv, and is continuously updated. Although many studies estimated the number of patients who would have severe COVID-19 requiring ICU, very few contained assessment for early signals (from internet or social media), and we retrieved no study whose data came from suspected or infected patients.\n\nAdded values of this studyDuring the COVID-19 epidemic, emergency medical system (EMS) calls, percentage of positive reverse transcriptase polymerase chain reaction (RT-PCR) tests, ambulance dispatch, emergency department (ED) and general practitioner (GP) visits of COVID-19 patients were strongly associated with COVID-19 ICU patients with an anticipation delay of 23, 15, 14, 13, and 12 days respectively. Hospitalization did not anticipated COVID-19 ICU bed requirement.\n\nImplication of all available evidenceEMS calls and ambulance dispatch, percent of positive RT-PCR, and ED and GP visits could be valuable tools as daily alert signals to set up plan to face the burden of ICU bed requirement during the initial wave of the COVID-19 epidemic, and may possibly also help anticipating a second wave. These results are important since mortality has been reported being correlated to health care resources.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "- The COVID-19 APHP-Universities-INRIA-INSERM Group", + "author_inst": "" + }, + { + "author_name": "Bruno Riou", + "author_inst": "Sorbonne Universite and Assistance Publique-Hopitaux de Paris, Paris, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.06.01.20119560", "rel_title": "Covid-19 Epidemiological Factor Analysis: Identifying Principal Factors with Machine Learning", @@ -1400107,77 +1400859,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.04.20119784", - "rel_title": "Clinical Management and Mortality among COVID-19 Cases in Sub-Saharan Africa: A retrospective study from Burkina Faso and simulated case data analysis", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20119784", - "rel_abs": "BackgroundAbsolute numbers of COVID-19 cases and deaths reported to date in the sub-Saharan Africa (SSA) region have been significantly lower than those across the Americas, Asia, and Europe. As a result, there has been limited information about the demographic and clinical characteristics of deceased cases in the region, as well as the impacts of different case management strategies.\n\nMethodsData from deceased cases reported across SSA through May 10, 2020 and from hospitalized cases in Burkina Faso through April 15, 2020 were analyzed. Demographic, epidemiological, and clinical information on deceased cases in SSA was derived through a line-list of publicly available information and, for cases in Burkina Faso, from aggregate records at the Center Hospitalier Universitaire de Tengandogo in Ouagadougou. A synthetic case population was derived probabilistically using distributions of age, sex, and underlying conditions from populations of West African countries to assess individual risk factors and treatment effect sizes. Logistic regression analysis was conducted to evaluate the adjusted odds of survival for patients receiving oxygen therapy or convalescent plasma, based on therapeutic effectiveness observed for other respiratory illnesses.\n\nResultsAcross SSA, deceased cases for which demographic data are available have been predominantly male (63/103, 61.2%) and over 50 years of age (59/75, 78.7%). In Burkina Faso, specifically, the majority of deceased cases either did not seek care at all or were hospitalized for a single day (59.4%, 19/32); hypertension and diabetes were often reported as underlying conditions. After adjustment for sex, age, and underlying conditions in the synthetic case population, the odds of mortality for cases not receiving oxygen therapy was significantly higher than those receiving oxygen, such as due to disruptions to standard care (OR: 2.07; 95% CI: 1.56 - 2.75). Cases receiving convalescent plasma had 50% reduced odds of mortality than those who did not (95% CI: 0.24 - 0.93).\n\nConclusionInvestment in sustainable production and maintenance of supplies for oxygen therapy, along with messaging around early and appropriate use for healthcare providers, caregivers, and patients could reduce COVID-19 deaths in SSA. Further investigation into convalescent plasma is warranted, as data on its effectiveness specifically in treating COVID-19 becomes available. The success of supportive or curative clinical interventions will depend on earlier treatment seeking, such that community engagement and risk communication will be critical components of the response.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Laura Skrip", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Karim Derra", - "author_inst": "IRSS - Clinical Research Unit of Nanoro, Burkina Faso" - }, - { - "author_name": "Mikaila Kabor\u00e9", - "author_inst": "Ministry of Health, Teaching Hospital Yalgado Ouedraogo, Ouagadougou, Burkina Faso; Ministry of Health, Teaching Hospital Tengandogo, Ouagadougou, Burkina Faso" - }, - { - "author_name": "Navideh Noori", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Adama Gansan\u00e9", - "author_inst": "Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso; Ministry of Health, Ouagadougou, Burkina Faso" - }, - { - "author_name": "Innocent Val\u00e9a", - "author_inst": "IRSS - Clinical Research Unit of Nanoro, Burkina Faso" - }, - { - "author_name": "Halidou Tinto", - "author_inst": "IRSS - Clinical Research Unit of Nanoro, Burkina Faso" - }, - { - "author_name": "Bicaba W. Brice", - "author_inst": "Centre des Operations de R\u00e9ponses aux Urgences Sanitaires, Ouagadougou, National Public Heath Institute" - }, - { - "author_name": "Mollie Van Gordon", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Brittany Hagedorn", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Herv\u00e9 Hien", - "author_inst": "Centre MURAZ, Institut National de Sante Publique, Ouagadougou, Burkina Faso" - }, - { - "author_name": "Benjamin Muir Althouse", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Edward Wenger", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Andr\u00e9 Lin Ou\u00e9draogo", - "author_inst": "Institute for Disease Modeling" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.03.20121137", "rel_title": "Review of published systematic reviews and meta-analyses on COVID-19", @@ -1400405,6 +1401086,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.06.03.20121590", + "rel_title": "Deep Learning and Holt-Trend Algorithms for predicting COVID-19 pandemic", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20121590", + "rel_abs": "According to WHO, more than one million individuals are infected with COVID-19, and around 20000 people have died because of this infectious disease around the world. In addition, COVID-19 epidemic poses serious public health threat to the world where people with little or no pre-existing human immunity can be more vulnerable to the effects of the effects of the coronavirus. Thus, developing surveillance systems for predicting COVID-19 pandemic in an early stage saves millions of lives. In this study, the deep learning algorithm and Holt-trend model is proposed to predict coronavirus. The Long-Short Term Memory (LSTM) algorithm and Holt-trend were applied to predict confirmed numbers and death cases. The real time data have been collected from the World Health Organization (WHO). In the proposed research, we have considered three countries to test the proposed model namely Saudi Arabia, Spain and Italy. The results suggest that the LSTM models showed better performance in predicting the cases of coronavirus patients. Standard measure performance MSE, RMSE, Mean error and correlation are employed to estimate the results of the proposed models. The empirical results of the LSTM by using correlation metric are 99.94%, 99.94% and 99.91 to predict number of confirmed cases on COVID-19 in three countries. Regarding the prediction results of LSTM model to predict the number of death on COVID-19 are 99.86%, 98.876% and 99.16 with respect to the Saudi Arabia, Italy and Spain respectively. Similarly the experimented results of Holt-Trend to predict the number of confirmed cases on COVID-19 by using correlation metrics are 99.06%, 99.96% and 99.94, whereas the results of Holt-Trend to predict the number of death cases are 99.80%, 99.96 and 99.94 with respect to the Saudi Arabia, Italy and Spain respectively. The empirical results indicate the efficient performance of the presented model in predicting the number of confirmed and death cases of COVID-19 in these countries. Such findings provide better insights about the future of COVID-19 in general. The results were obtained by applying the time series models which needs to be considered for the sake of saving the lives of many people.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Theyazn H.H Aldhyani", + "author_inst": "Department of Computer Science and Information at king faisal University, Kingdom of Saudi Arabia" + }, + { + "author_name": "Melfi Alrasheed Sr.", + "author_inst": "Department of Quantitative Methods, School of Business, King Faisal University. Saudi" + }, + { + "author_name": "Ahmed i Abdullah Alqarn Sr.", + "author_inst": "Department of Computer Sciences and Information Technology, Albaha University," + }, + { + "author_name": "Mohammed Y. Alzahrani", + "author_inst": "Department of Computer Sciences and Information Technology, Albaha University" + }, + { + "author_name": "Ahmed H., Alahmadi", + "author_inst": "Department of Computer Science and Information at Taibah University," + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.06.04.20121848", "rel_title": "An Agent Based Model methodology for assessing spread and health systems burden for Covid-19 using a synthetic population from India", @@ -1402309,73 +1403025,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.06.05.135699", - "rel_title": "SARS-CoV-2 proteases cleave IRF3 and critical modulators of inflammatory pathways (NLRP12 and TAB1): implications for disease presentation across species and the search for reservoir hosts.", - "rel_date": "2020-06-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.05.135699", - "rel_abs": "The genome of SARS-CoV-2 (SARS2) encodes for two viral proteases (NSP3/ papain-like protease and NSP5/ 3C-like protease or major protease) that are responsible for cleaving viral polyproteins for successful replication. NSP3 and NSP5 of SARS-CoV (SARS1) are known interferon antagonists. Here, we examined whether the protease function of SARS2 NSP3 and NSP5 target proteins involved in the host innate immune response. We designed a fluorescent based cleavage assay to rapidly screen the protease activity of NSP3 and NSP5 on a library of 71 human innate immune proteins (HIIPs), covering most pathways involved in human innate immunity. By expressing each of these HIIPs with a genetically encoded fluorophore in a cell-free system and titrating in the recombinant protease domain of NSP3 or NSP5, we could readily detect cleavage of cognate HIIPs on SDS-page gels. We identified 3 proteins that were specifically and selectively cleaved by NSP3 or NSP5: IRF-3, and NLRP12 and TAB1, respectively. Direct cleavage of IRF3 by NSP3 could explain the blunted Type- I IFN response seen during SARS-CoV-2 infections while NSP5 mediated cleavage of NLRP12 and TAB1 point to a molecular mechanism for enhanced production of IL-6 and inflammatory response observed in COVID-19 patients. Surprisingly, both NLRP12 and TAB1 have each two distinct cleavage sites. We demonstrate that in mice, the second cleavage site of NLRP12 is absent. We pushed this comparative alignment of IRF-3 and NLRP12 homologs and show that the lack or presence of cognate cleavage motifs in IRF-3 and NLRP12 could contribute to the presentation of disease in cats and tigers, for example. Our findings provide an explanatory framework for in-depth studies into the pathophysiology of COVID-19 and should facilitate the search or development of more effective animal models for severe COVID-19. Finally, we discovered that one particular species of bats, Davids Myotis, possesses the five cleavage sites found in humans for NLRP12, TAB1 and IRF3. These bats are endemic from the Hubei province in China and we discuss its potential role as reservoir for the evolution of SARS1 and SASR2.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Mehdi Moustaqil", - "author_inst": "The University of New South Wales" - }, - { - "author_name": "Emma Ollivier", - "author_inst": "The University of New South Wales" - }, - { - "author_name": "Hsin-Ping Chiu", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Paulina Rudolffi-Soto", - "author_inst": "The University of New South Wales and EMBL Australia Node for Single Molecule Science" - }, - { - "author_name": "Sarah Van Tol", - "author_inst": "The University of Texas Medical Branch" - }, - { - "author_name": "Christian Stevens", - "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Akshay Bhumkar", - "author_inst": "The University of New South Wales and EMBL Australia Node for Single Molecule Science" - }, - { - "author_name": "Dominic J.B. Hunter", - "author_inst": "The University of New South Wales and EMBL Australia Node for Single Molecule Science and IMB, University of Queensland" - }, - { - "author_name": "Alexander N. Freiberg", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "David Jacques", - "author_inst": "The University of New South Wales and EMBL Australia Node for Single Molecule Science" - }, - { - "author_name": "Benhur Lee", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Emma Sierecki", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Yann Gambin", - "author_inst": "EMBL Australia, The University of New South Wales" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.06.04.20122457", "rel_title": "HIGH LIVER FAT ASSOCIATES WITH HIGHER RISK OF DEVELOPING SYMPTOMATIC COVID-19 INFECTION - INITIAL UK BIOBANK OBSERVATIONS", @@ -1402562,6 +1403211,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.06.04.20122846", + "rel_title": "A tertiary center experience of multiple myeloma patients with COVID-19: lessons learned and the path forward", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122846", + "rel_abs": "BackgroundThe COVID-19 pandemic, caused by SARS-CoV-2 virus, has resulted in over 100,000 deaths in the United States. Our institution has treated over 2,000 COVID-19 patients during the pandemic in New York City. The pandemic directly impacted cancer patients and the organization of cancer care. Mount Sinai Hospital has a large and diverse multiple myeloma (MM) population. Herein, we report the characteristics of COVID-19 infection and serological response in MM patients in a large tertiary care institution in New York.\n\nMethodsWe performed a retrospective study on a cohort of 58 patients with a plasma-cell disorder (54 MM, 4 smoldering MM) who developed COVID-19 between March 1, 2020 and April 30, 2020. We report epidemiological, clinical and laboratory characteristics including persistence of viral detection by polymerase chain reaction (PCR) and anti-SARS-CoV-2 antibody testing, treatments initiated, and outcomes.\n\nResultsOf the 58 patients diagnosed with COVID-19, 36 were hospitalized and 22 were managed at home. The median age was 67 years; 52% of patients were male and 63% were non-white. Hypertension (64%), hyperlipidemia (62%), obesity (37%), diabetes mellitus (28%), chronic kidney disease (24%) and lung disease (21%) were the most common comorbidities. In the total cohort, 14 patients (24%) died. Older age (>70 years), male sex, cardiovascular risk, and patients not in complete remission (CR) or stringent CR were significantly (p<0.05) associated with hospitalization. Among hospitalized patients, laboratory findings demonstrated elevation of traditional inflammatory markers (CRP, ferritin, D-dimer) and a significant (p<0.05) association between elevated inflammatory markers, severe hypogammaglobulinemia, non-white race, and mortality. Ninety-six percent (22/23) of patients developed antibodies to SARS-CoV-2 at a median of 32 days after initial diagnosis. Median time to PCR negativity was 43 (range 19-68) days from initial positive PCR.\n\nConclusionsDrug exposure and MM disease status at the time of contracting COVID-19 had no bearing on mortality. Mounting a severe inflammatory response to SARS-CoV-2 and severe hypogammaglobulinemia were associated with higher mortality. The majority of patients mounted an antibody response to SARS-CoV-2. These findings pave a path to identification of vulnerable MM patients who need early intervention to improve outcome in future outbreaks of COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Bo Wang", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Oliver Van Oekelen", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Tarek Mouhieddine", + "author_inst": "Mount Sinai Hospital" + }, + { + "author_name": "Diane Marie Del Valle", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Joshua Richter", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Hearn Jay Cho", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Shambavi Richard", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Ajai Chari", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Sacha Gnjatic", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Miriam Merad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sundar Jagannath", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Samir Parekh", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + }, + { + "author_name": "Deepu Madduri", + "author_inst": "Icahn Mount Sinai Tisch Cancer Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2020.06.04.20122564", "rel_title": "Adverse effects of COVID-19 related lockdown on pain, physical activity and psychological wellbeing in people with chronic pain", @@ -1403546,29 +1404262,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.06.03.132506", - "rel_title": "Inhibition of Corona virus spike protein binding to ACE2", - "rel_date": "2020-06-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.03.132506", - "rel_abs": "In this paper, we investigate the molecular assembly processes of a Coronavirus Spike protein fragment, the hexapeptide YKYRYL on the ACE2 receptor and its inhibitory effect on the aggregation and activation of the CoV-2 spike receptor protein at the same receptor protein. In agreement with an experimental study, we find a high affinity of the hexapeptide to the binding interface between the spike receptor protein and ACE2, which we investigate using 20 independent equilibrium MD simulations over a total of 1 s and a 200 ns enhanced MD simulation. We then evaluate the effect of the hexapeptide on the aggregation process of the spike receptor protein to ACE2 in long-time enhanced MD simulations. In that set of simulations, we find that the spike receptor protein does not bind to ACE2 with the binding motif shown in experiments, but it rotates due to an electrostatic repulsion and forms a hydrophobic interface with ACE2. Surprisingly, we observe that the hexapeptide binds to the spike receptor domain, which has the effect that this protein only weakly attaches to ACE2, so that the activation of the spike protein receptor might be inhibited in this case. Our results indicate that the hexapeptide might be a possible treatment option which prevents the viral activation through the inhibition of the interaction between ACE2 and the spike receptor protein.\n\nSIGNIFICANCEA novel coronavirus, CoV-19 and a later phenotype CoV-2 were identified as primary cause for a severe acute respiratory syndrome (SARS CoV-2). The spike (S) protein of CoV-2 is one target for the development of a vaccine to prevent the viral entry into human cells. The inhibition of the direct interaction between ACE2 and the S-protein could provides a suitable strategy to prevent the membrane fusion of CoV-2 and the viral entry into human cells. Using MD simulations, we investigate the assembly process of a Coronavirus Spike protein fragment, the hexapeptide YKYRYL on the ACE2 receptor and its inhibitzory effect on the aggregation and activation of the CoV-2 spike receptor protein at the same receptor protein.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Emanuel Peter", - "author_inst": "Forschungszentrum J\u00fclich" - }, - { - "author_name": "Alexander Schug", - "author_inst": "Forschungszentrum J\u00fclich" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.06.02.20120782", "rel_title": "Substitutions in Spike and Nucleocapsid proteins of SARS-CoV-2 circulating in Colombia", @@ -1403872,6 +1404565,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.03.132639", + "rel_title": "Human iPSC-derived alveolar and airway epithelial cells can be cultured at air-liquid interface and express SARS-CoV-2 host factors", + "rel_date": "2020-06-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.03.132639", + "rel_abs": "Development of an anti-SARS-CoV-2 therapeutic is hindered by the lack of physiologically relevant model systems that can recapitulate host-viral interactions in human cell types, specifically the epithelium of the lung. Here, we compare induced pluripotent stem cell (iPSC)-derived alveolar and airway epithelial cells to primary lung epithelial cell controls, focusing on expression levels of genes relevant for COVID-19 disease modeling. iPSC-derived alveolar epithelial type II-like cells (iAT2s) and iPSC-derived airway epithelial lineages express key transcripts associated with lung identity in the majority of cells produced in culture. They express ACE2 and TMPRSS2, transcripts encoding essential host factors required for SARS-CoV-2 infection, in a minor subset of each cell sub-lineage, similar to frequencies observed in primary cells. In order to prepare human culture systems that are amenable to modeling viral infection of both the proximal and distal lung epithelium, we adapt iPSC-derived alveolar and airway epithelial cells to two-dimensional air-liquid interface cultures. These engineered human lung cell systems represent sharable, physiologically relevant platforms for SARS-CoV-2 infection modeling and may therefore expedite the development of an effective pharmacologic intervention for COVID-19.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Kristine M Abo", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Liang Ma", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Taylor Matte", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Jessie Huang", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Konstantinos D Alysandratos", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Rhiannon B Werder", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Aditya Mithal", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Mary Lou Beermann", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Jonathan Lindstrom-Vautrin", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Gustavo Mostoslavsky", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Laertis Ikonomou", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Darrell N Kotton", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Finn Hawkins", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Andrew Wilson", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + }, + { + "author_name": "Carlos Villacorta-Martin", + "author_inst": "Boston University School of Medicine and Boston Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.06.04.135012", "rel_title": "Olfactory transmucosal SARS-CoV-2 invasion as port of Central Nervous System entry in COVID-19 patients", @@ -1405256,85 +1406024,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.02.20120774", - "rel_title": "Quantifying the prevalence of SARS-CoV-2 long-term shedding among non-hospitalized COVID-19 patients", - "rel_date": "2020-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120774", - "rel_abs": "Analysis of 851 COVID-19 patients with a SARS-CoV-2-positive PCR at follow-up shows 99 patients remained SARS-CoV-2-positive after four weeks from initial diagnosis. Surprisingly, a majority of these long-term viral RNA shedders were not hospitalized (61 of 99), with variable PCR Crossing point values over the month post diagnosis. For the 851-patient cohort, the mean lower bound of viral RNA shedding was 17.3 days (SD: 7.8), and the mean upper bound of viral RNA shedding from 668 patients transitioning to confirmed PCR-negative status was 22.7 days (SD: 11.8). Among 104 patients with an IgG test result, 90 patients were seropositive to date, with mean upper bound of time to seropositivity from initial diagnosis being 37.8 days (95%CI: 34.3-41.3). Juxtaposing IgG/PCR tests revealed that 14 of 90 patients are non-hospitalized and seropositive yet shed viral RNA. This study emphasizes the need for monitoring viral loads and neutralizing antibody titers in long-term shedders.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Vineet Agarwal", - "author_inst": "nference" - }, - { - "author_name": "AJ Venkatakrishnan", - "author_inst": "nference" - }, - { - "author_name": "Arjun Puranik", - "author_inst": "nference" - }, - { - "author_name": "Christian Kirkup", - "author_inst": "nference" - }, - { - "author_name": "Agustin Lopez-Marquez", - "author_inst": "nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA 02142, USA" - }, - { - "author_name": "Douglas W. Challener", - "author_inst": "Mayo Clinic, Rochester MN, USA" - }, - { - "author_name": "John C. O Horo", - "author_inst": "Mayo Clinic, Rochester MN, USA" - }, - { - "author_name": "Matthew J Binnicker", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Walter K Kremers", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "William A Faubion", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Andrew D. Badley", - "author_inst": "Mayo Clinic, Rochester MN, USA" - }, - { - "author_name": "Amy W Williams", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Gregory J Gores", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "John D. Halamka", - "author_inst": "Mayo Clinic, Rochester MN, USA" - }, - { - "author_name": "William G. Morice II", - "author_inst": "Mayo Clinic, Rochester MN, USA; Mayo Clinic Laboratories, Rochester MN, USA" - }, - { - "author_name": "Venky Soundararajan", - "author_inst": "nference, inc., One Main Street, Suite 400, East Arcade, Cambridge, MA 02142, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.02.20120238", "rel_title": "Globally Coherent Weekly Periodicity in the Covid-19 Pandemic", @@ -1405494,6 +1406183,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.06.01.20119347", + "rel_title": "COVID-19 Public Sentiment Insights and MachineLearning for Tweets Classification", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119347", + "rel_abs": "Along with the Coronavirus pandemic, another crisis has manifested itself in the form of mass fear and panic phenomena, fueled by incomplete and often inaccurate information. There is therefore a tremendous need to address and better understand COVID-19s informational crisis and gauge public sentiment, so that appropriate messaging and policy decisions can be implemented. In this research article, we identify public sentiment associated with the pandemic using Coronavirus specific Tweets and R statistical software, along with its sentiment analysis packages. We demonstrate insights into the progress of fear-sentiment over time as COVID-19 approached peak levels in the United States, using descriptive textual analytics supported by necessary textual data visualizations. Furthermore, we provide a methodological overview of two essential machine learning (ML) classification methods, in the context of textual analytics, and compare their effectiveness in classifying Coronavirus Tweets of varying lengths. We observe a strong classification accuracy of 91% for short Tweets, with the Naive Bayes method. We also observe that the logistic regression classification method provides a reasonable accuracy of 74% with shorter Tweets, and both methods showed relatively weaker performance for longer Tweets. This research provides insights into Coronavirus fear sentiment progression, and outlines associated methods, implications, limitations and opportunities.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jim Samuel", + "author_inst": "University of Charleston, Charleston, WV" + }, + { + "author_name": "Ali G. G. Md. Nawaz", + "author_inst": "University of Charleston, Charleston, WV" + }, + { + "author_name": "Md Mokhlesur Rahman", + "author_inst": "University of North Carolina at Charlotte, Charlotte, NC; Khulna University of Engineering & Technology (KUET), Khulna, Bangladesh" + }, + { + "author_name": "Ek Esawi", + "author_inst": "University of Charleston, Charleston, WV" + }, + { + "author_name": "Yana Samuel", + "author_inst": "Northeastern University, Boston, MA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.29.20117143", "rel_title": "Detection of lung hypoperfusion in Covid-19 patients during recovery by digital imaging quantification", @@ -1406390,29 +1407114,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.05.30.20117838", - "rel_title": "The impact of the undetected COVID-19 cases on its transmission dynamics", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117838", - "rel_abs": "ObjectiveThe COVID-19 pandemic is currently ongoing. Presently, due to the unavailability of a definitive vaccine to decrease its acquiring, its essential to understand its transmissibility in the community by undetected cases to control its transmission. This study aims to study this context using mathematical modelling.\n\nMethodsA COVID-19 transmission model was framed that estimated the basic reproduction number (R0, a measurement of disease risk) using the next-generation method. It explored the contribution of exposed and infected (detected and undetected) individuals, and environmental pathogen to the overall risk of infection spreading, utilizing the publicly reported data of this infection in Maharashtra between March 22, 2020, and May 4, 2020. A sensitivity analysis was performed to study the effect of a rising number of undetected cases to R0.\n\nResultsThe estimated basic reproduction number is R0 = 4.63, which increases rapidly with the rise in the undetected COVID-19 cases. Although the exposed individuals made the largest contribution to infection transmission (R1 = 2.42), the contaminated environment also played a significant role.\n\nConclusionsIt is crucial to identify the individuals exposed and infected to COVID-19 disease and isolate them to control its transmission. The awareness of the role of fomites in infection transmission is also important in this regard.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Sujata Saha", - "author_inst": "Mankar College" - }, - { - "author_name": "Sumanta Saha", - "author_inst": "None" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.30.20117804", "rel_title": "Statistical methods for estimating cure fraction of COVID-19 patients in India", @@ -1406680,6 +1407381,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.30.20117853", + "rel_title": "Evaluating the Efficacy of Stay-At-Home Orders: Does Timing Matter?", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117853", + "rel_abs": "BACKGROUNDThe many economic, psychological, and social consequences of pandemics and social distancing measures create an urgent need to determine the efficacy of non-pharmaceutical interventions (NPIs), and especially those considered most stringent, such as stay-at-home and self-isolation mandates. This study focuses specifically on the efficacy of stay-at-home orders, both nationally and internationally, in the control of COVID-19.\n\nMETHODSWe conducted an observational analysis from April to May 2020 and included countries and US states with known stay-at-home orders. Our primary exposure was the time between the date of the first reported case of COVID-19 to an implemented stay-at-home mandate for each region. Our primary outcomes were the time from the first reported case to the highest number of daily cases and daily deaths. We conducted simple linear regression analyses, controlling for the case rate of the outbreak.\n\nRESULTSFor US states and countries, a larger number of days between the first reported case and stay-at-home mandates was associated with a longer time to reach the peak daily case and death counts. The largest effect was among regions classified as the latest 10% to implement a mandate, which in the US, predicted an extra 35.3 days to the peak number of cases (95 % CI: 18.2, 52.5), and 38.3 days to the peak number of deaths (95 % CI: 23.6, 53.0).\n\nCONCLUSIONSOur study supports the potential beneficial effect of earlier stay-at-home mandates, by shortening the time to peak case and death counts for US states and countries. Regions in which mandates were implemented late experienced a prolonged duration to reaching both peak daily case and death counts.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alexandra Medline, MPH", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Lamar Hayes, MPH", + "author_inst": "David Geffen School of Medicine" + }, + { + "author_name": "Farnoosh Vahedi", + "author_inst": "David Geffen School of Medicine" + }, + { + "author_name": "Katia Valdez", + "author_inst": "Fielding School of Public Health, University of California Los Angeles" + }, + { + "author_name": "Jake Sonnenberg", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Will Capell", + "author_inst": "David Geffen School of Medicine" + }, + { + "author_name": "Ami Hayashi", + "author_inst": "David Geffen School of Medicine" + }, + { + "author_name": "Zoe Glick", + "author_inst": "UC Berkeley" + }, + { + "author_name": "Jeffrey D. Klausner, MD, MPH", + "author_inst": "UCLA David Geffen School of Medicine and Fielding School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.31.20118315", "rel_title": "Cytokine biomarkers of COVID-19", @@ -1407660,57 +1408412,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.06.03.131474", - "rel_title": "Rapid detection of SARS-CoV-2 and other respiratory viruses by using LAMP method with Nanopore Flongle workflow", - "rel_date": "2020-06-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.03.131474", - "rel_abs": "The ongoing novel coronavirus (COVID-19) outbreak as a global public health emergency infected by SARC-CoV-2 has caused devastating loss around the world. Currently, a lot of diagnosis methods have been used to detect the infection. The nucleic acid (NA) testing is reported to be the clinical standard for COVID-19 infection. Evidence shows that a faster and more convenient method to detect in the early phase will control the spreading of SARS-CoV-2. Here, we propose a method to detect SARC-Cov-2 infection within two hours combined with Loop-mediated Isothermal Amplification (LAMP) reaction and nanopore Flongle workflow. In this approach, RNA reverse transcription and nucleic acid amplification reaction with one step in 30 minutes at 60-65{degrees}C constant temperature environment, nanopore Flongle rapidly adapter ligated within 10 minutes. Flongle flow cell sequencing and analysis in real-time. This method described here has the advantages of rapid amplification, convenient operation and real-time detection which is the most important for rapid and reliable clinical diagnosis of COVID-19. Moreover, this approach not only can be used for SARS-CoV-2 detection but also can be extended to other respiratory viruses and pathogens.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jingjing Li", - "author_inst": "Grandomics" - }, - { - "author_name": "Weipeng Quan", - "author_inst": "Grandomics" - }, - { - "author_name": "Shuge Yan", - "author_inst": "Grandomics" - }, - { - "author_name": "Shuangju Wu", - "author_inst": "Grandomics" - }, - { - "author_name": "Jianhu Qin", - "author_inst": "Grandomics" - }, - { - "author_name": "Tingting Yang", - "author_inst": "Grandomcis" - }, - { - "author_name": "Fan Liang", - "author_inst": "Grandomics" - }, - { - "author_name": "Depeng Wang", - "author_inst": "Grandomics" - }, - { - "author_name": "Yu Liang", - "author_inst": "Grandomics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.03.131755", "rel_title": "In silico design and characterization of multiepitopes vaccine for SARS-CoV from its Spike proteins", @@ -1407962,6 +1408663,37 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.06.03.129817", + "rel_title": "Closing coronavirus spike glycoproteins by structure-guided design", + "rel_date": "2020-06-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.03.129817", + "rel_abs": "The recent spillover of SARS-CoV-2 in the human population resulted in the ongoing COVID-19 pandemic which has already caused 4.9 million infections and more than 326,000 fatalities. To initiate infection the SARS-CoV-2 spike (S) glycoprotein promotes attachment to the host cell surface, determining host and tissue tropism, and fusion of the viral and host membranes. Although SARS-CoV- 2 S is the main target of neutralizing antibodies and the focus of vaccine design, its stability and conformational dynamics are limiting factors for developing countermeasures against this virus. We report here the design of a prefusion SARS-CoV-2 S ectodomain trimer construct covalently stabilized in the closed conformation. Structural and antigenicity analysis showed we successfully shut S in the closed state without otherwise altering its architecture. Finally, we show that this engineering strategy is applicable to other {beta}-coronavirus S glycoproteins and might become an important tool for vaccine design, structural biology, serology and immunology studies.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Matthew McCallum", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexandra C Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs Biomed SA, subsidiary of Vir Biotechnology" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.06.02.130955", "rel_title": "Sarbecovirus comparative genomics elucidates gene content of SARS-CoV-2 and functional impact of COVID-19 pandemic mutations", @@ -1409150,57 +1409882,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.06.01.20118943", - "rel_title": "Greater risk of severe COVID-19 in non-White ethnicities is not explained by cardiometabolic, socioeconomic, or behavioural factors, or by 25(OH)-vitamin D status: study of 1,326 cases from the UK Biobank", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20118943", - "rel_abs": "BackgroundWe examined whether the greater severity of coronavirus disease 2019 (COVID-19) amongst men and non-White ethnicities is explained by cardiometabolic, socio-economic, or behavioural factors.\n\nMethodsWe studied 4,510 UK Biobank participants tested for COVID-19 (positive, n = 1,326). Multivariate logistic regression models including age, sex, and ethnicity were used to test whether addition of: 1)cardiometabolic factors (diabetes, hypertension, high cholesterol, prior myocardial infarction, smoking, BMI); 2)25(OH)-vitamin D; 3)poor diet; 4)Townsend deprivation score; 5)housing (home type, overcrowding); or 6)behavioural factors (sociability, risk taking) attenuated sex/ethnicity associations with COVID-19 status.\n\nResultsThere was over-representation of men and non-White ethnicities in the COVID-19 positive group. Non-Whites had, on average, poorer cardiometabolic profile, lower 25(OH)-vitamin D, greater material deprivation, and were more likely to live in larger households and flats/apartments. Male sex, non-White ethnicity, higher BMI, Townsend deprivation score, and household overcrowding were independently associated with significantly greater odds of COVID-19. The pattern of association was consistent for men and women; cardiometabolic, socio-demographic and behavioural factors did not attenuate sex/ethnicity associations.\n\nConclusionsSex and ethnicity differential pattern of COVID-19 is not adequately explained by variations in cardiometabolic factors, 25(OH)-vitamin D levels, or socio-economic factors. Investigation of alternative biological pathways and different genetic susceptibilities is warranted.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Zahra Raisi-Estabragh", - "author_inst": "William Harvey Research Institute" - }, - { - "author_name": "Celeste McCracken", - "author_inst": "William Harvey Research Institute" - }, - { - "author_name": "Mae S Bethell", - "author_inst": "North West Anglia NHS Foundation Trust" - }, - { - "author_name": "Jackie Cooper", - "author_inst": "William Harvey Research Institute" - }, - { - "author_name": "Cyrus Cooper", - "author_inst": "MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK" - }, - { - "author_name": "Mark J Caulfield", - "author_inst": "William Harvey Research Institute" - }, - { - "author_name": "Patricia B Munroe", - "author_inst": "William Harvey Research Institute" - }, - { - "author_name": "Nicholas C Harvey", - "author_inst": "MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK" - }, - { - "author_name": "Steffen E Petersen", - "author_inst": "William Harvey Research Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.31.20118653", "rel_title": "Environmental and social analysis as risk factors for the spread of the novel coronavirus (SARS-CoV-2) using remote sensing, GIS and analytical hierarchy process (AHP): Case of Peru", @@ -1409612,6 +1410293,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.01.20118612", + "rel_title": "Modeling the Covid-19 Epidemic using Time Series Econometrics", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20118612", + "rel_abs": "The classic logistic model has provided a realistic model of the behavior of Covid-19 in China and many East Asian countries. Once these countries passed the peak, the daily case count fell back, mirroring its initial climb in a symmetric way, just as the classic model predicts. However, in Italy and Spain, and now the UK and many other Western countries, the experience has been very different. The daily count has fallen back gradually from the peak but remained stubbornly high. The reason for the divergence from the classical model remain unclear. We take an empirical stance on this issue and develop a model that is based upon the statistical characteristics of the time series. With the possible exception of China, the workhorse logistic model is decisively rejected against more flexible alternatives.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Peter D. Spencer", + "author_inst": "University of York" + }, + { + "author_name": "Adam Golinski", + "author_inst": "University of York" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.01.20118505", "rel_title": "Pulmonary Thromboembolic Disease in Patients with COVID-19 Undergoing Computed Tomography Pulmonary Angiography (CTPA): Incidence and Relationship with Pulmonary Parenchymal Abnormalities", @@ -1410740,117 +1411444,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.31.20115196", - "rel_title": "Detection of SARS-CoV-2 in Exhaled Breath from COVID-19 Patients Ready for Hospital Discharge", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20115196", - "rel_abs": "The COVID-19 pandemic has brought an unprecedented crisis to the global health sector1. When recovering COVID-19 patients are discharged in accordance with throat or nasal swab protocols using reverse transcription polymerase chain reaction (RT-PCR), the potential risk of re-introducing the infection source to humans and the environment must be resolved2,3,4. Here we show that 20% of COVID-19 patients, who were ready for a hospital discharge based on current guidelines, had SARS-CoV-2 in their exhaled breath ([~]105 RNA copies/m3). They were estimated to emit about 1400 RNA copies into the air per minute. Although fewer surface swabs (1.3%, N=318) tested positive, medical equipment frequently contacted by healthcare workers and the work shift floor were contaminated by SARS-CoV-2 in four hospitals in Wuhan. All air samples (N=44) appeared negative likely due to the dilution or inactivation through natural ventilation (1.6-3.3 m/s) and applied disinfection. Despite the low risk of cross environmental contamination in the studied hospitals, there is a critical need for strengthening the hospital discharge standards in preventing re-emergence of COVID-19 spread.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Lian Zhou", - "author_inst": "Department of Environment and Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China" - }, - { - "author_name": "Maosheng Yao", - "author_inst": "Peking University" - }, - { - "author_name": "Xiang Zhang", - "author_inst": "The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China" - }, - { - "author_name": "Bicheng Hu", - "author_inst": "The Clinical Laboratory, Wuhan No.1 Hospital, Wuhan, China" - }, - { - "author_name": "Xinyue Li", - "author_inst": "Peking University" - }, - { - "author_name": "Haoxuan Chen", - "author_inst": "Peking University" - }, - { - "author_name": "Lu Zhang", - "author_inst": "Peking University" - }, - { - "author_name": "Yun Liu", - "author_inst": "The First Affiliated Hospital of Nanjing Medical University (Jiangsu Province Hospital), Nanjing, China" - }, - { - "author_name": "Meng Du", - "author_inst": "Zhenjiang Center for Disease Control and Prevention, Zhenjiang, China" - }, - { - "author_name": "Bochao Sun", - "author_inst": "Yancheng Center for Disease Control and Prevention, Yancheng, China" - }, - { - "author_name": "Yunyu Jiang", - "author_inst": "Taizhou Center for Disease Control and Prevention, Taizhou, China" - }, - { - "author_name": "Kai Zhou", - "author_inst": "Suzhou Center for Disease Control and Prevention, Suzhou, China" - }, - { - "author_name": "Jie Hong", - "author_inst": "Department of Environment and Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China" - }, - { - "author_name": "Na Yu", - "author_inst": "The First Hospital of China Medical University, Shenyang, China" - }, - { - "author_name": "Zhen Ding", - "author_inst": "Department of Environment and Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China" - }, - { - "author_name": "Yan Xu", - "author_inst": "Department of Environment and Health, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China" - }, - { - "author_name": "Min Hu", - "author_inst": "Peking University" - }, - { - "author_name": "Lidia Morawska", - "author_inst": "Queensland University of Technology" - }, - { - "author_name": "Sergey A. Grinshpun", - "author_inst": "University of Cincinnati" - }, - { - "author_name": "Pratim Biswas", - "author_inst": "Washington University in St. Louis" - }, - { - "author_name": "Richard C. Flagan", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Baoli Zhu", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China" - }, - { - "author_name": "Wenqing Liu", - "author_inst": "Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei City, Anhui Province, China" - }, - { - "author_name": "Yuanhang Zhang", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.01.20119362", "rel_title": "Feeling Positive About Reopening?New Normal Scenarios from COVID-19 ReopenSentiment Analytics", @@ -1411078,6 +1411671,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.05.29.20114751", + "rel_title": "Syncope at SARS-CoV-2 onset due to impaired baroreflex response", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20114751", + "rel_abs": "We describe clinical and laboratory findings in 35 consecutive patients tested positive for SARS-CoV-2 by reverse transcriptase-polymerase chain reaction on nasopharyngeal swab that presented one or multiple syncopal events at disease onset. Neurological examination and electrocardiographic findings were normal. Chest computed tomography showed findings consistent with interstitial pneumonia. Arterial blood gas analysis showed low pO2, pCO2, and P/F ratio indicating hypocapnic hypoxemia, while patients did not show the expected compensatory heart rate increase. Such mechanism could have led to syncope. We speculate that SARS-CoV-2 could have caused angiotensin-converting enzyme-2 (ACE2) receptor internalization in the nucleus of the solitary tract (NTS), thus altering the baroreflex response and inhibiting the compensatory tachycardia during acute hypocapnic hypoxemia.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Ciro Canetta", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Silvia Accordino", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Elisabetta Buscarini", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Gianpaolo Benelli", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Giuseppe La Piana", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Alessandro Scartabellati", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Giovanni Vigano'", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Roberto Assandri", + "author_inst": "Ospedale Maggiore di Crema, Crema, Italy" + }, + { + "author_name": "Alberto Astengo", + "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy;" + }, + { + "author_name": "Chiara Benzoni", + "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy;" + }, + { + "author_name": "Gianfranco Gaudiano", + "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy;" + }, + { + "author_name": "Daniele Cazzato", + "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan, Italy" + }, + { + "author_name": "Sebastiano Davide Rossi", + "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan, Italy" + }, + { + "author_name": "Susanna Usai", + "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan, Italy" + }, + { + "author_name": "Irene Tramacere", + "author_inst": "Fondazione IRCCS Istituto Neurologico \"Carlo Besta\", Milan, Italy" + }, + { + "author_name": "Giuseppe Lauria", + "author_inst": "Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy; Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.05.29.20114199", "rel_title": "Effect of Dry Heat and Autoclave Decontamination Cycles on N95 FFRs", @@ -1412922,37 +1413594,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.10.20097634", - "rel_title": "Pulmonary alveolar regrowth in an adult COVID-19 patient", - "rel_date": "2020-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20097634", - "rel_abs": "We detected active alveolar regrowth in the lung of a 58-year-old COVID-19 patient who underwent lung transplantation due to severe lung hemorrhage. Specifically, immunohistological and scanning electronic microscopy analyses revealed that alveolar type II epithelial cells (AT2 cells) accumulate in response to viral pneumonia and that these AT2 cells actively proliferate and differentiate into squamous AT1-like alveolar epithelial cells. Thus, our work establishes that alveolar regrowth does occur in post-COVID-19 injury adult human lungs.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Jingyu Chen", - "author_inst": "Wuxi Lung Transplantation Center, Wuxi People Hospital affiliated to Nanjing Medical University," - }, - { - "author_name": "Huijuan Wu", - "author_inst": "School of Life Sciences, Tsinghua University, National Institute of Biological Sciences, Beijing" - }, - { - "author_name": "Yuanyuan Yu", - "author_inst": "School of Life Sciences, Tsinghua University, National Institute of Biological Sciences, Beijing" - }, - { - "author_name": "Nan Tang", - "author_inst": "National Institute of Biological Sciences, Beijing" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.05.28.122374", "rel_title": "ACE2 expression in human dorsal root ganglion sensory neurons: implications for SARS-CoV-2 virus-induced neurological effects", @@ -1413264,6 +1413905,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.01.20100461", + "rel_title": "Determining the optimal strategy for reopening schools, work and society in the UK: balancing earlier opening and the impact of test and trace strategies with the risk of occurrence of a secondary COVID-19 pandemic wave", + "rel_date": "2020-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20100461", + "rel_abs": "BackgroundIn order to slow down the spread of SARS-CoV-2, the virus causing the COVID-19 pandemic, the UK government has imposed strict physical distancing ( lockdown) measures including school dismissals since 23 March 2020. As evidence is emerging that these measures may have slowed the spread of the pandemic, it is important to assess the impact of any changes in strategy, including scenarios for school reopening and broader relaxation of social distancing. This work uses an individual-based model to predict the impact of a suite of possible strategies to reopen schools in the UK, including that currently proposed by the UK government.\n\nMethodsWe use Covasim, a stochastic agent-based model for transmission of COVID-19, calibrated to the UK epidemic. The model describes individuals contact networks stratified as household, school, work and community layers, and uses demographic and epidemiological data from the UK. We simulate a range of different school reopening strategies with a society-wide relaxation of lockdown measures and in the presence of different non-pharmaceutical interventions, to estimate the number of new infections, cumulative cases and deaths, as well as the effective reproduction number with different strategies. To account for uncertainties within the stochastic simulation, we also simulated different levels of infectiousness of children and young adults under 20 years old compared to older ages.\n\nFindingsWe found that with increased levels of testing of people (between 25% and 72% of symptomatic people tested at some point during an active COVID-19 infection depending on scenarios) and effective contact-tracing and isolation for infected individuals, an epidemic rebound may be prevented across all reopening scenarios, with the effective reproduction number (R) remaining below one and the cumulative number of new infections and deaths significantly lower than they would be if testing did not increase. If UK schools reopen in phases from June 2020, prevention of a second wave would require testing 51% of symptomatic infections, tracing of 40% of their contacts, and isolation of symptomatic and diagnosed cases. However, without such measures, reopening of schools together with gradual relaxing of the lockdown measures are likely to induce a secondary pandemic wave, as are other scenarios for reopening. When infectiousness of <20 year olds was varied from 100% to 50% of that of older ages, our findings remained unchanged.\n\nInterpretationTo prevent a secondary COVID-19 wave, relaxation of social distancing including reopening schools in the UK must be implemented alongside an active large-scale population-wide testing of symptomatic individuals and effective tracing of their contacts, followed by isolation of symptomatic and diagnosed individuals. Such combined measures have a greater likelihood of controlling the transmission of SARS-CoV-2 and preventing a large number of COVID-19 deaths than reopening schools and society with the current level of implementation of testing and isolation of infected individuals.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSSince the onset of COVID-19 pandemic, mathematical modelling has been at the heart of informing decision-making, including the imposing of the lockdown in the UK. As countries are now starting to plan modification of these measures, it is important to assess the impact of different lockdown exit strategies including whether and how to reopen schools and relax other social distancing measures.\n\nAdded value of this studyUsing mathematical modelling, we explored the impact of strategies to reopen schools and society in the UK, including that currently proposed by the UK government. We assessed the impact of opening all schools fully or in a phased way with only some school years going back, with a society-wide relaxation of lockdown measures and in the presence of a different levels of implementation of test-trace-isolate strategies. We projected the number of new COVID-19 infections, cumulative cases and deaths, as well as the temporal distribution in the effective reproduction number (R) across different strategies. Our study is the first to provide quantification of the amount of testing and tracing that would be needed to prevent a second wave of COVID-19 in the UK under different reopening scenarios. To account for uncertainties within the stochastic simulation, we also simulated different levels of infectiousness of children and young adults under 20 years old compared to older ages.\n\nImplications of all the available evidenceEvidence to date points to the need for additional testing, contact tracing, and isolation of individuals who have either been diagnosed with COVID-19, or who are considered to be at high risk of carrying infection due to their contact history or symptoms. Our study supports these conclusions and provides additional quantification of the amount of testing and tracing that would be needed to prevent a second wave of COVID-19 in the UK under different lockdown exit strategies. Reopening schools and society alongside active testing of the symptomatic population (between 25% and 72% of people with symptomatic COVID-19 infection depending on scenarios) and with an effective contact-tracing and rapid isolation of symptomatic and diagnosed individuals, will not only prevent a secondary pandemic wave, but is also likely to be able to control the transmission of SARS-CoV-2, via keeping the R value below 1, thus preventing a large number of COVID-19 cases and deaths. However, in the absence of fully implemented large-scale testing, contact-tracing and isolation strategy, plans for reopening schools, including those currently proposed by the UK government, and the associated increase in work and community contacts, are likely to induce a secondary pandemic wave of COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jasmina Panovska-Griffiths", + "author_inst": "UCL" + }, + { + "author_name": "Cliff Kerr", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Robyn Margaret Stuart", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Dina Mistry", + "author_inst": "Institute for Disease Modelling" + }, + { + "author_name": "Daniel Klein", + "author_inst": "Institute for Disease Modelling" + }, + { + "author_name": "Russell M Viner", + "author_inst": "UCL Great Ormond St. Institute of Child Health" + }, + { + "author_name": "Chris Bonell", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.01.20118885", "rel_title": "Modelling testing frequencies required for early detection of a SARS-CoV-2 outbreak on a university campus", @@ -1414284,101 +1414968,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2020.06.01.127605", - "rel_title": "SARS-CoV-2 infects and induces cytotoxic effects in human cardiomyocytes", - "rel_date": "2020-06-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.01.127605", - "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has emerged as global pandemic. SARS-CoV-2 infection can lead to elevated markers of cardiac injury associated with higher risk of mortality in COVID-19 patients. It is unclear whether cardiac injury may have been caused by direct infection of cardiomyocytes or is mainly secondary to lung injury and inflammation. Here we investigate whether human cardiomyocytes are permissive for SARS-CoV-2 infection.\n\nMethodsInfection was induced by two strains of SARS-CoV-2 (FFM1 and FFM2) in human induced pluripotent stem cells-derived cardiomyocytes (hiPS-CM) and in two models of human cardiac tissue.\n\nResultsWe show that SARS-CoV-2 infects hiPS-CM as demonstrated by detection of intracellular double strand viral RNA and viral spike glycoprotein protein expression. Increasing concentrations of virus RNA are detected in supernatants of infected cardiomyocytes, which induced infections in CaCo-2 cell lines documenting productive infections. SARS-COV-2 infection induced cytotoxic and pro-apoptotic effects and abolished cardiomyocyte beating. RNA sequencing confirmed a transcriptional response to viral infection as demonstrated by the up-regulation of genes associated with pathways related to viral response and interferon signaling, apoptosis and reactive oxygen stress. SARS-CoV-2 infection and cardiotoxicity was confirmed in a iPS-derived human 3D cardiosphere tissue models. Importantly, viral spike protein and viral particles were detected in living human heart slices after infection with SARS-CoV-2.\n\nConclusionsThe demonstration that cardiomyocytes are permissive for SARS-CoV-2 infection in vitro warrants the further in depth monitoring of cardiotoxic effects in COVID-19 patients.\n\nClinical PerspectiveO_ST_ABSWhat is New?C_ST_ABSO_LIThis study demonstrates that human cardiac myocytes are permissive for SARS-CoV-2 infection.\nC_LIO_LIThe study documents that SARS-CoV-2 undergoes a full replicatory circle and induces a cytotoxic response in cardiomyocytes.\nC_LIO_LIInfection was confirmed in two cardiac tissue models, including living human heart slices.\nC_LI\n\nWhat are the Clinical Implications?O_LIThe study may provide a rational to explain part of the cardiotoxicity observed in COVID-19 patients\nC_LIO_LIThe demonstration of direct cardiotoxicity induced by SARS-CoV-2 warrants an in depth further analysis of cardiac tissue of COVID-19 patients and a close monitoring for putative direct cardiomyocyte injury.\nC_LIO_LIThe established models can be used to test novel therapeutic approaches targeting COVID-19.\nC_LI", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Denisa Bojkova", - "author_inst": "University Frankfurt" - }, - { - "author_name": "Julian Wagner", - "author_inst": "University Frankfurt" - }, - { - "author_name": "Mariana Shumliakivska", - "author_inst": "University Frankfurt" - }, - { - "author_name": "Galip Aslan", - "author_inst": "University Frankfurt" - }, - { - "author_name": "Umber Saleem", - "author_inst": "UKE Hamburg" - }, - { - "author_name": "Arne Hansen", - "author_inst": "UKE Hamburg" - }, - { - "author_name": "Guillermo Luxan", - "author_inst": "Goethe University Frankfurt" - }, - { - "author_name": "Stefan Guenther", - "author_inst": "MPI Heart and Lung Research" - }, - { - "author_name": "Minh Duc Pham", - "author_inst": "University Frankfurt" - }, - { - "author_name": "Jaya Krishnan", - "author_inst": "University Frankfurt" - }, - { - "author_name": "Patrick Harter", - "author_inst": "University Frankfurt" - }, - { - "author_name": "Utz Ermel", - "author_inst": "University Frankfurt" - }, - { - "author_name": "Achilleas S Frangakis", - "author_inst": "Goethe University Frankfurt" - }, - { - "author_name": "Andreas Zeiher", - "author_inst": "University Frankfurt" - }, - { - "author_name": "Hendrik Milting", - "author_inst": "Clinic for Thoracic and Cardiovascular Surgery, Bad Oyenhausen" - }, - { - "author_name": "Jindrich Cinatl Jr.", - "author_inst": "Klinikum der Goethe-Universitaet" - }, - { - "author_name": "Andreas Dendorfer", - "author_inst": "Walter-Brendel-Centre, Hospital of the Ludwig-Maximilians-University Munich" - }, - { - "author_name": "Thomas Eschenhagen", - "author_inst": "UKE Hamburg" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Goethe Universtiy Frankfurt" - }, - { - "author_name": "Stefanie Dimmeler", - "author_inst": "Goethe University Frankfurt" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.05.29.123810", "rel_title": "Dose-dependent response to infection with SARS-CoV-2 in the ferret model: evidence of protection to re-challenge", @@ -1414685,6 +1415274,81 @@ "type": "confirmatory results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.31.116061", + "rel_title": "Origin and cross-species transmission of bat coronaviruses in China", + "rel_date": "2020-05-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.31.116061", + "rel_abs": "Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. We used a Bayesian statistical framework and sequence data from all known bat-CoVs (including 630 novel CoV sequences) to study their macroevolution, cross-species transmission, and dispersal in China. We find that host-switching was more frequent and across more distantly related host taxa in alpha-than beta-CoVs, and more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Alice Latinne", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Ben Hu", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Kevin J Olival", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Guangjian Zhu", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Libiao Zhang", + "author_inst": "Guangdong Institute of Applied Biological Resources" + }, + { + "author_name": "Hongying Li", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Aleksei A Chmura", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Hume E Field", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Carlos Zambrana-Torrelio", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Jonathan H Epstein", + "author_inst": "EcoHealth Alliance" + }, + { + "author_name": "Bei Li", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Wei Zhang", + "author_inst": "Wuhan Institute of Virology" + }, + { + "author_name": "Lin-Fa Wang", + "author_inst": "Duke-NUS Graduate Medical School" + }, + { + "author_name": "Zhengli Shi", + "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" + }, + { + "author_name": "Peter Daszak", + "author_inst": "EcoHealth Alliance" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.05.31.126136", "rel_title": "A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates", @@ -1415949,53 +1416613,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2020.05.28.20115311", - "rel_title": "A survey of the psychological status of primary school students who were quarantined at home during the coronavirus disease 2019 epidemic in Hangzhou China", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115311", - "rel_abs": "ObjectiveTo investigate the presence of social anxiety and depression and the risk factors for them among primary school students who were quarantined at home during the coronavirus disease 2019 (COVID-19) epidemic in Hangzhou China.\n\nMethodsA total of 1620 students who were quarantined at home for at least one month were recruited from two primary schools in Hangzhou. Students completed a questionnaire on a mobile App with help from their guardians; the measures included demographic and general information, the Social Anxiety Scale for Children (SASC), and the Depression Self-rating Scalefor Children (DSRSC).\n\nResultsThe mean SASC score of the participants was 3.90 {+/-} 3.73, which was higher than the mean norm score of Chinese urban children (3.48 {+/-} 3.47) (P < 0.01). The mean DSRSC score of the participants (5.67 {+/-} 4.97) was much lower than the mean norm score of Chinese urban children (9.84 {+/-} 4.73) (P < 0.05). A total of 279 (17.2%) students had social anxiety, with a mean score of 10.41 {+/-} 2.59, and 102 (6.3%) students had depression, with a mean score of 18.96 {+/-} 3.89. The following variables were found to be significant risk factors for social anxiety during home quarantine: deterioration of the parent-child relationship, increased conflicts with parents, irregular work and rest, and worrying more about being infected. Deterioration of the parent-child relationship, less physical activity, irregular work and rest, and negative mood during home quarantine were significant risk factors for depression.\n\nConclusionPrimary school students who were quarantined at home during the COVID-19 epidemic were more likely to have social anxiety but less likely to have depressive symptoms. Poor parent-child relationships, irregularity of work and rest, and epidemic-related problems were the main reasons for psychological problems. Families, schools, and social organizations need to pay more attention to the psychological status of primary school students quarantined at home.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yanghao Zheng", - "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" - }, - { - "author_name": "Jianhua Li", - "author_inst": "The Affiliated Xiaoshan First People's Hospital of Hangzhou Normal University" - }, - { - "author_name": "Maiyan Zhang", - "author_inst": "Beigan primary school of Xiaoshan District" - }, - { - "author_name": "Bicheng Jin", - "author_inst": "Greentown Yuhua Primary School of Hangzhou" - }, - { - "author_name": "Xiaoyi Li", - "author_inst": "Beigan primary school of Xiaoshan District" - }, - { - "author_name": "Zhiyong Cao", - "author_inst": "Greentown Yuhua Primary School of Hangzhou" - }, - { - "author_name": "Nanping Wu", - "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" - }, - { - "author_name": "Changzhong Jin", - "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.05.30.20117457", "rel_title": "Emotional distress and associated sociodemographic risk factors during the COVID-19 outbreak in Spain", @@ -1416279,6 +1416896,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.28.20115584", + "rel_title": "Prognostic value of visual quantification of lesion severity at initial chest CT in confirmed Covid-19 infection: a retrospective analysis on 216 patients", + "rel_date": "2020-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115584", + "rel_abs": "Rationale and ObjectivesStudies suggest an association between chest CT findings assessed with semi-quantitative CT score and gravity of Covid-19. The objective of this work is to analyze potential correlation between visual quantification of lesion severity at initial chest CT and clinical outcome in confirmed Covid-19 patients.\n\nMaterials and MethodsFrom March 5th to March 21st, 2020, all consecutive patients that underwent chest CT for clinical suspicion of Covid-19 at a single tertiary center were retrospectively evaluated for inclusion. Patients with lung parenchyma lesions compatible with Covid-19 and positive RT-PCR were included.\n\nGlobal extensiveness of abnormal lung parenchyma was visually estimated and classified independently by 2 readers, following the European Society of Thoracic Imaging Guidelines. Death and/or mechanical ventilation within 30 days following the initial chest CT was chosen as the primary hard endpoint.\n\nResults216 patients (124 men, 62 years-old {+/-} 16.5, range 22 - 94 yo) corresponding to 216 chest CT were included. Correlation between lesion severity and percentage of patients that met the primary endpoint was high, with a coefficient {rho} of 0.87 (p = 0.05).\n\nA greater than 25% involvement was significantly associated with a higher risk of mechanical ventilation or death at 30 days, with a Risk Ratio of 5.00 (95% CI [3.59-6.99]).\n\nConclusionThis retrospective cohort confirms a correlation between visual evaluation of lesions severity at initial chest CT and the 30 days clinical outcome of Covid-19 patients and suggests using a threshold of greater than 25% involvement to identify patients at risk.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Elias Taieb", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Aissam Labani", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Yvon Ruch", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Francois Danion", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Mathieu Oberlin", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Pascal Bilbault", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Pierre Leyendecker", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Catherine Roy", + "author_inst": "Hopitaux Universitaires de Strasbourg" + }, + { + "author_name": "Mickael Ohana", + "author_inst": "Hopitaux Universitaires de Strasbourg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.05.29.20116376", "rel_title": "Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report", @@ -1417459,57 +1418127,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2020.05.29.124123", - "rel_title": "Development Optimization and Validation of RT-LAMP based COVID-19 Facility in Pakistan", - "rel_date": "2020-05-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.29.124123", - "rel_abs": "The pandemic SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) has created a widespread panic across the globe especially in the developing countries like Pakistan. The lack of resources and technical staff are causing havoc challenges in the detection and prevention of this global outbreak. Therefore, a less expensive and massive screening of suspected individuals for COVID-19 is required. In this study, a user-friendly technique of reverse transcription-loop mediated isothermal amplification (RT-LAMP) was designed and validated to suggest a potential RT-qPCR alternate for rapid testing of COVID-19 suspected individuals. A total of 12 COVID-19 negative and 72 COVID-19 suspected individuals were analyzed. Both RT-qPCR and RT-LAMP assays were performed for all the individuals using open reading frame (ORF 1ab), nucleoprotein (N) and Spike (S) genes. All 12 specimens which were negative using RT-qPCR were also found negative using RT-LAMP assay. Overall 62 out of 72 positive samples (detected using RT-qPCR) were found COVID-19 positive using RT-LAMP assay. Interestingly all samples (45) having Ct values less than 30 showed 100% sensitivity. However, samples with weaker Ct values (i.e., => 35) showed 54% concordance, suggesting potential false negatives or false positives in RT-LAMP or RT-qPCR results, respectively.\n\nOverall comparative assessment showed that RT-LAMP assay showed strong sensitivity and specificity and can be used as an alternative strategy for rapid COVID-19 testing. Hence, based on fast processing time, minimal risk of specimens transfer and utilizing available resources, LAMP based detection of COVID-19 is strongly advocated especially for developing countries.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Farhan Haq Sr.", - "author_inst": "COMSATS University Islamabad" - }, - { - "author_name": "Salmaan Sharif Sr.", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Adnan Khurshid Sr.", - "author_inst": "National Institute of Health, Islamabad" - }, - { - "author_name": "Imran Shabbir Sr.", - "author_inst": "International Islamic University, Islamabad" - }, - { - "author_name": "Muhammad Salman Sr.", - "author_inst": "National Institute of Health, Islamabad" - }, - { - "author_name": "Nazish Badar Sr.", - "author_inst": "National Institute of Health, Islamabad" - }, - { - "author_name": "Aamir Ikram III", - "author_inst": "National Institute of Health, Islamabad" - }, - { - "author_name": "Abdul Ahad Sr.", - "author_inst": "National Institute of Health, Islamabad" - }, - { - "author_name": "Muhammad Faraz Malik Sr.", - "author_inst": "COMSATS University Islamabad" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.05.28.118729", "rel_title": "Expansion of SARS-CoV-2-specific Antibody-secreting Cells and Generation of Neutralizing Antibodies in Hospitalized COVID-19 Patients", @@ -1417809,6 +1418426,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.29.20116921", + "rel_title": "Time courses of COVID-19 infection and local variation in socioeconomic and health disparities in England", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20116921", + "rel_abs": "ObjectiveTo identify factors associated with local variation in the time course of COVID-19 case burden in England.\n\nMethodsWe analyzed laboratory-confirmed COVID-19 case data for 150 upper tier local authorities, from the period from January 30 to May 6, 2020, as reported by Public Health England. Using methods suitable for time-series data, we identified clusters of local authorities with distinct trajectories of daily cases, after adjusting for population size. We then tested for differences in sociodemographic, economic, and health disparity factors between these clusters.\n\nResultsTwo clusters of local authorities were identified: a higher case trajectory that rose faster over time to reach higher peak infection levels, and a lower case trajectory cluster that emerged more slowly, and had a lower peak. The higher case trajectory cluster (79 local authorities) had higher population density (p<0.001), higher proportion of Black and Asian residents (p=0.03; p=0.02), higher multiple deprivation scores (p<0.001), a lower proportions of older adults (p=0.005), and higher preventable mortality rates (p=0.03). Local authorities with higher proportions of Black residents were more likely to belong to the high case trajectory cluster, even after adjusting for population density, deprivation, proportion of older adults and preventable mortality (p=0.04).\n\nConclusionAreas belonging to the trajectory with significantly higher COVID-19 case burden were more deprived, and had higher proportions of ethnic minority residents. A higher proportion of Black residents in regions belonging to the high trajectory cluster was not fully explained by differences in population density, deprivation, and other overall health disparities between the clusters.\n\nWhat is already known on this subject?Emerging evidence suggests that the burden of COVID-19 infection is falling unequally across England, with provisional data suggesting higher overall infection and mortality rates for Black, Asian, and mixed race/ethnicity individuals.\n\nWhat does this study add?We found that regions with greater socioeconomic deprivation and poorer population health measures showed a faster rise in COVID-19 cases, and reached higher peak case levels. Areas with a higher proportion of Black residents were more likely to show this kind of time course, even after adjusting for multiple co-occurring factors, including population density. This finding merits further investigation in terms of the intersecting vulnerability factors Black and other minority ethnic individuals face in England (e.g. proportion of people working in service and caring roles, and the role of structural discrimination), and has implications for the ongoing allocation of public health resources, in order to better mitigate such inequalities.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shelley H. Liu", + "author_inst": "Icahn School of Medicine at Mount SInai" + }, + { + "author_name": "Bian Liu", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Yan Li", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Agnes Norbury", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.29.20116657", "rel_title": "Loneliness during lockdown: trajectories and predictors during the COVID-19 pandemic in 35,712 adults in the UK", @@ -1418761,33 +1419409,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.27.20114694", - "rel_title": "The association between treatment with heparin and survival in patients with Covid-19", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114694", - "rel_abs": "ObjectivesThis study investigates the association between the treatment with heparin and mortality in patients admitted with Covid-19.\n\nMethodsRoutinely recorded, clinical data, up to the 24th of April 2020, from the 2075 patients with Covid-19, admitted in 17 hospitals in Spain between the 1st of March and the 20th of April 2020 were used. The following variables were extracted for this study: age, gender, temperature, and saturation of oxygen on admission, treatment with heparin, hydroxychloroquine, azithromycin, steroids, tocilizumab, a combination of lopinavir with ritonavir, and oseltamivir, together with data on mortality. Multivariable logistic regression models were used to investigate the associations.\n\nResultsAt the time of collecting the data, 301 patients had died, 1447 had been discharged home from the hospitals, 201 were still admitted, and 126 had been transferred to hospitals not included in the study. Median follow up time was 8 (IQR:5-12) days. Heparin had been used in 1734 patients. Heparin was associated with lower mortality when the model was adjusted for age and gender, with OR (95%CI): 0.55 (0.37-0.82) p=0.003. This association remained significant when saturation of oxygen <90%, and temperature >37C were added to de model with OR: 0.54(0.36-0.82) p=0.003, and also when all the other drugs were included as covariates OR: 0.42 (0.26-0.66) p<0.001.\n\nConclusionsThe association between heparin and lower mortality observed in this study can be acknowledged by clinicians in hospitals and in the community. Randomized controlled trials to assess the causal effects of heparin in different therapeutic regimes are required.\n\n- The administration of heparin was associated with lower mortality in patients admitted with Covid-19.\n- Our findings support that there is a thrombotic component in the development of respiratory distress for these patients.\n- The positive effect of heparin seems consistent and its use, when indicated, could be considered in clinical settings.\n- Randomized controlled trials are necessary to complement observational studies, and assess the causal associations between heparin, in different therapeutic regimes, and clinical outcomes.\n- Heparin is easy to administer, its use in ambulatory patients, to prevent admissions, or reduce their duration, could also be considered by clinicians and future researchers.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Luis Ayerbe", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Carlos Risco", - "author_inst": "Hospital Universitario HM Sanchinarro" - }, - { - "author_name": "Salma Ayis", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.27.20115105", "rel_title": "The Association Between Biomarkers and Clinical Outcomes in Novel Coronavirus (COVID-19) Pneumonia in a U.S. Cohort", @@ -1418979,6 +1419600,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.27.20114819", + "rel_title": "Distinctive trajectories of COVID-19 epidemic by age and gender: a retrospective modeling of the epidemic in South Korea", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114819", + "rel_abs": "ObjectivesElderly people had suffered disproportional burden of COVID-19. We hypothesized that males and females in different age groups might have different epidemic trajectories.\n\nMethodsUsing publicly available data from South Korea, daily new COVID-19 cases were fitted with generalized additive models, assuming Poisson and negative binomial distributions. Epidemic dynamics by age and gender groups were explored with interactions between smoothed time terms and age and gender.\n\nResultsA negative binomial distribution fitted the daily case counts best. Interaction between the dynamic patterns of daily new cases and age groups was statistically significant (p<0.001), but not with gender group. People aged 20-39 years led the epidemic processes in the society with two peaks: one major peak around March 1 and a smaller peak around April 7, 2020. The epidemic process among people aged 60 or above was trailing behind that of younger people with smaller magnitude. After March 15, there was a consistent decline of daily new cases among elderly people, despite large fluctuations of case counts among young adults.\n\nConclusionsAlthough young people drove the COVID-19 epidemic in the whole society with multiple rebounds, elderly people could still be protected from virus infection after the peak of epidemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xinhua Yu", + "author_inst": "University of Memphis" + }, + { + "author_name": "Jiasong Duan", + "author_inst": "University of Memphis" + }, + { + "author_name": "Yu Jiang", + "author_inst": "University of Memphis" + }, + { + "author_name": "Hongmei Zhang", + "author_inst": "University of Memphis" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.27.20114728", "rel_title": "Lessons from movement ecology for the return to work: modeling contacts and the spread of COVID-19", @@ -1419991,125 +1420643,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.05.28.122291", - "rel_title": "SARS-CoV-2 infection induces EMT-like molecular changes, including ZEB1-mediated repression of the viral receptor ACE2, in lung cancer models", - "rel_date": "2020-05-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.28.122291", - "rel_abs": "COVID-19 is an infectious disease caused by SARS-CoV-2, which enters host cells via the cell surface proteins ACE2 and TMPRSS2. Using a variety of normal and malignant models and tissues from the aerodigestive and respiratory tracts, we investigated the expression and regulation of ACE2 and TMPRSS2. We find that ACE2 expression is restricted to a select population of highly epithelial cells. Notably, infection with SARS-CoV-2 in cancer cell lines, bronchial organoids, and patient nasal epithelium, induces metabolic and transcriptional changes consistent with epithelial to mesenchymal transition (EMT), including upregulation of ZEB1 and AXL, resulting in an increased EMT score. Additionally, a transcriptional loss of genes associated with tight junction function occurs with SARS-CoV-2 infection. The SARS-CoV-2 receptor, ACE2, is repressed by EMT via TGFbeta, ZEB1 overexpression and onset of EGFR TKI inhibitor resistance. This suggests a novel model of SARS-CoV-2 pathogenesis in which infected cells shift toward an increasingly mesenchymal state, associated with a loss of tight junction components with acute respiratory distress syndrome-protective effects. AXL-inhibition and ZEB1-reduction, as with bemcentinib, offers a potential strategy to reverse this effect. These observations highlight the utility of aerodigestive and, especially, lung cancer model systems in exploring the pathogenesis of SARS-CoV-2 and other respiratory viruses, and offer important insights into the potential mechanisms underlying the morbidity and mortality of COVID-19 in healthy patients and cancer patients alike.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "C. Allison Stewart", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Carl M. Gay", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Kavya Ramkumar", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Kasey R. Cargill", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Robert J. Cardnell", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Monique B. Nilsson", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Simon Heeke", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Elizabeth M. Park", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Samrat T. Kundu", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Lixia Diao", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Qi Wang", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Li Shen", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Yuanxin Xi", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Bingnan Zhang", - "author_inst": "University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Carminia Maria Della Corte", - "author_inst": "University of Campania Luigi Vanvitelli" - }, - { - "author_name": "Youhong Fan", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Kiran Kundu", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Curtis R Pickering", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Faye M Johnson", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Jianjun Zhang", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Humam Kadara", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "John D. Minna", - "author_inst": "The University of Texas Southwestern Medical Center" - }, - { - "author_name": "Don L. Gibbons", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Jing Wang", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "John V. Heymach", - "author_inst": "The University of Texas MD Anderson Cancer Center" - }, - { - "author_name": "Lauren Averett Byers", - "author_inst": "The University of Texas MD Anderson Cancer Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "cancer biology" - }, { "rel_doi": "10.1101/2020.05.28.120642", "rel_title": "Molecules inhibit the enzyme activity of 3-chymotrypsin-like cysteine protease of SARS-CoV-2 virus", @@ -1420253,6 +1420786,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.29.20117069", + "rel_title": "Regression Analysis of COVID-19 Spread in India and its Different States", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20117069", + "rel_abs": "Linear and polynomial regression model has been used to investigate the COVID-19 outbreak in India and its different states using time series epidemiological data up to 26th May 2020. The data driven analysis shows that the case fatality rate (CFR) for India (3.14% with 95% confidence interval of 3.12% to 3.16%) is half of the global fatality rate, while higher than the CFR of the immediate neighbors i.e. Bangladesh, Pakistan and Sri Lanka. Among Indian states, CFR of West Bengal (8.70%, CI: 8.21-9.18%) and Gujrat (6.05%, CI: 4.90-7.19%) is estimated to be higher than national rate, whereas CFR of Bihar, Odisha and Tamil Nadu is less than 1%. The polynomial regression model for India and its different states is trained with data from 21st March 2020 to 19th May 2020 (60 days). The performance of the model is estimated using test data of 7 days from 20th May 2020 to 26th May 2020 by calculating RMSE and % error. The model is then used to predict number of patients in India and its different states up to 16th June 2020 (21 days). Based on the polynomial regression analysis, Maharashtra, Gujrat, Delhi and Tamil Nadu are continue to remain most affected states in India.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Poonam Chauhan", + "author_inst": "Central University of Punjab, Bathinda" + }, + { + "author_name": "Ashok Kumar", + "author_inst": "Central University of Punjab" + }, + { + "author_name": "Pooja Jamdagni", + "author_inst": "Himachal Pradesh University, Shimla" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.28.121533", "rel_title": "Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies", @@ -1421521,57 +1422081,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.28.120709", - "rel_title": "\"Monoclonal-type\" plastic antibodies for SARS-CoV-2 based on Molecularly Imprinted Polymers", - "rel_date": "2020-05-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.28.120709", - "rel_abs": "Summary of the ideaOur idea is focused on the development of \u201cmonoclonal-type\u201d plastic antibodies based on Molecularly Imprinted Polymers (MIPs) able to selectively bind a portion of the novel coronavirus SARS-CoV-2 spike protein to block its function and, thus, the infection process. Molecular Imprinting, indeed, represents a very promising and attractive technology for the synthesis of MIPs characterized by specific recognition abilities for a target molecule. Given these characteristics, MIPs can be considered tailor-made synthetic antibodies obtained by a templating process.In the present study, the developed imprinted polymeric nanoparticles were characterized in terms of particles size and distribution by Dynamic Light Scattering (DLS) and the imprinting effect and selectivity were investigated by performing binding experiments using the receptor-binding domain (RBD) of the novel coronavirus and the RBD of SARS-CoV spike protein, respectively. Finally, the hemocompatibility of the prepared MIP-based plastic antibodies was also evaluated.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Francesco Puoci", - "author_inst": "Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende (CS), Italy. - Macrofarm s.r.l., c/o Department of Pharmacy, Health" - }, - { - "author_name": "Ortensia Ilaria Parisi", - "author_inst": "Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende (CS), Italy. - Macrofarm s.r.l., c/o Department of Pharmacy, Health" - }, - { - "author_name": "Marco Dattilo", - "author_inst": "Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende (CS), Italy." - }, - { - "author_name": "Francesco Patitucci", - "author_inst": "Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende (CS), Italy." - }, - { - "author_name": "Rocco Malivindi", - "author_inst": "Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende (CS), Italy. - Macrofarm s.r.l., c/o Department of Pharmacy, Health" - }, - { - "author_name": "Vincenzo Pezzi", - "author_inst": "Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende (CS), Italy. - Macrofarm s.r.l., c/o Department of Pharmacy, Health" - }, - { - "author_name": "Ida Perrotta", - "author_inst": "Department of Biology, Ecology and Earth Sciences, University of Calabria, 87036 Rende (CS), Italy." - }, - { - "author_name": "Mariarosa Ruffo", - "author_inst": "Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende (CS), Italy. - Macrofarm s.r.l., c/o Department of Pharmacy, Health" - }, - { - "author_name": "Fabio Amone", - "author_inst": "Macrofarm s.r.l., c/o Department of Pharmacy, Health and Nutrition Sciences, University of Calabria, 87036 Rende (CS), Italy." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "synthetic biology" - }, { "rel_doi": "10.1101/2020.05.27.120204", "rel_title": "Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays", @@ -1421807,6 +1422316,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.24.20101238", + "rel_title": "Single-cell RNA-seq and V(D)J profiling of immune cells in COVID-19 patients", + "rel_date": "2020-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20101238", + "rel_abs": "Coronavirus disease 2019 (COVID-19) has caused over 220,000 deaths so far and is still an ongoing global health problem. However, the immunopathological changes of key types of immune cells during and after virus infection remain unclear. Here, we enriched CD3+ and CD19+ lymphocytes from peripheral blood mononuclear cells of COVID-19 patients (severe patients and recovered patients at early or late stages) and healthy people (SARS-CoV-2 negative) and revealed transcriptional profiles and changes in these lymphocytes by comprehensive single-cell transcriptome and V(D)J recombination analyses. We found that although the T lymphocytes were decreased in the blood of patients with virus infection, the remaining T cells still highly expressed inflammatory genes and persisted for a while after recovery in patients. We also observed the potential transition from effector CD8 T cells to central memory T cells in recovered patients at the late stage. Among B lymphocytes, we analyzed the expansion trajectory of a subtype of plasma cells in severe COVID-19 patients and traced the source as atypical memory B cells (AMBCs). Additional BCR and TCR analyses revealed a high level of clonal expansion in patients with severe COVID-19, especially of B lymphocytes, and the clonally expanded B cells highly expressed genes related to inflammatory responses and lymphocyte activation. V-J gene usage and clonal types of higher frequency in COVID-19 patients were also summarized. Taken together, our results provide crucial insights into the immune response against patients with severe COVID-19 and recovered patients and valuable information for the development of vaccines and therapeutic strategies.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Xiaoying Fan", + "author_inst": "Guangzhou Regenerative Medicine and Health Guangdong Laboratory" + }, + { + "author_name": "Xiangyang Chi", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Wenji Ma", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Suijuan Zhong", + "author_inst": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University" + }, + { + "author_name": "Yunzhu Dong", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Wei Zhou", + "author_inst": "Guangzhou Regenerative Medicine and Health Guangdong Laboratory" + }, + { + "author_name": "Wenyu Ding", + "author_inst": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University" + }, + { + "author_name": "Hongyan Fan", + "author_inst": "Department of Clinical Laboratory, The 940th Hospital of PLA Joint Logistics Support Forces" + }, + { + "author_name": "Chonghai Yin", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Zhentao Zuo", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Yilong Yang", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Mengyao Zhang", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Qiang Ma", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Jianwei Liu", + "author_inst": "Guangzhou Regenerative Medicine and Health Guangdong Laboratory" + }, + { + "author_name": "Ting Fang", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Qian Wu", + "author_inst": "State Key Laboratory of Cognitive Neuroscience and Learning, Beijing Normal University" + }, + { + "author_name": "Wei Chen", + "author_inst": "Beijing Institute of Biotechnology, Academy of Military Medical Sciences" + }, + { + "author_name": "Xiaoqun Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.26.20111120", "rel_title": "THE LOW-HARM SCORE FOR PREDICTING MORTALITY IN PATIENTS DIAGNOSED WITH COVID-19: A MULTICENTRIC VALIDATION STUDY", @@ -1423011,37 +1423607,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.05.26.115261", - "rel_title": "Angiotensin-converting enzyme 2, a SARS-CoV-2 receptor, is upregulated by interleukin-6 via STAT3 signaling in rheumatoid synovium", - "rel_date": "2020-05-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.26.115261", - "rel_abs": "Detected in December 2019, the coronavirus disease 2019 (COVID-19) has since spread all over the world, resulting in a global pandemic. The disease is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), and its symptoms usually include cough, fever, and gastrointestinal problems. Although the prevalence of rheumatoid arthritis (RA) is about 1 % of the global population and RA patients naturally have a chance of acquiring COVID-19 in this pandemic, no studies have considered the expression of angiotensin-converting enzyme 2 (ACE2) (a receptor for SARS-CoV-2) in synovial tissues. Our presenting data revealed that ACE2 expression was elevated in active rheumatoid synovium, and siRNA against STAT3 was able to downregulate ACE2 expression, which was in turn induced by IL-6 signaling.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sho Mokuda", - "author_inst": "Hiroshima University Hospital" - }, - { - "author_name": "Tadahiro Tokunaga", - "author_inst": "Hiroshima University Hospital" - }, - { - "author_name": "Junya Masumoto", - "author_inst": "Ehime University Proteo-Science Center and Graduate School of Medicine" - }, - { - "author_name": "Eiji Sugiyama", - "author_inst": "Hiroshima University Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.26.115832", "rel_title": "Different pattern of pre-existing SARS-COV-2 specific T cell immunity in SARS-recovered and uninfected individuals", @@ -1423309,6 +1423874,41 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.05.27.119610", + "rel_title": "Assessment of ACE2, CXCL10 and Their co-expressed Genes: An In-silico Approach to Evaluate the Susceptibility and Fatality of Lung Cancer Patients towards COVID-19 Infection", + "rel_date": "2020-05-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.27.119610", + "rel_abs": "BackgroundCOVID-19 is a recent pandemic that started to spread out worldwide from Wuhan, China. This disease is caused by a newly discovered strain of the coronavirus, namely SARS CoV-2. Lung cancer patients are reported to be more susceptible to COVID-19 infection. To evaluate the probable reasons behind the excessive susceptibility and fatality of lung cancer patients to COVID-19 infection, we targeted two most crucial biomarkers of COVID-19, ACE2 and CXCL10. ACE2 plays a vital role in the SARS CoV-2 entry into the host cell while CXCL10 is a cytokine mainly responsible for the lung cell damage involving in a cytokine storm.\n\nMethodsFirstly, we used the TIMER, UALCAN and GEPIA2 databases to analyze the expression and correlation of ACE2 and CXCL10 in LUAD and LUSC. After that, using the cBioPortal database, we performed an analytical study to determine the genetic changes in ACE2 and CXCL10 protein sequences that are responsible for lung cancer development. Finally, we analyzed different functional approaches of ACE2, CXCL10 and their co-expressed genes associated with lung cancer and COVID-19 development by using the PANTHER database.\n\nResultsInitially, we observed that ACE2 and CXCL10 are mostly overexpressed in LUAD and LUSC. We also found the functional significance of ACE2 and CXCL10 in lung cancer development by determining the genetic alteration frequency in their amino acid sequences. Lastly, by doing the functional assessment of the targeted genes, we identified that ACE2 and CXCL10 along with their commonly co-expressed genes are respectively involved in the binding activity and immune responses in case of lung cancer and COVID-19 infection.\n\nConclusionsFinally, on the basis of this systemic analysis, we came to the conclusion that ACE2 and CXCL10 are possible biomarkers responsible for the higher susceptibility and fatality of lung cancer patients towards the COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Tousif Bin Mahmood", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Afrin Sultana Chowdhury", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Mehedee Hasan", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Md. Mezbah-Ul-Islam Aakil", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + }, + { + "author_name": "Mohammad Imran Hossan", + "author_inst": "Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.26.20109595", "rel_title": "Efficacy and harms of remdesivir for the treatment of COVID-19: a systematic review and meta-analysis", @@ -1424597,45 +1425197,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.22.20106294", - "rel_title": "High-throughput immunoassays for SARS-CoV-2, considerable differences in performance when comparing three methods", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20106294", - "rel_abs": "BackgroundThe recently launched high-throughput assays for the detection of antibodies against SARS-CoV-2 may change the managing strategies for the COVID-19 pandemic. This study aimed at investigating the performance of three high-throughput assays and one rapid lateral flow test relative to the recommended criteria defined by regulatory authorities.\n\nMethodsA total of 133 samples, including 100 pre-pandemic samples, 20 samples from SARS-CoV-2 RT-PCR positive individuals, and 13 potentially cross-reactive samples were analysed with SARS-CoV-2 IgG (Abbott), Elecsys Anti-SARS-CoV-2 (Roche), LIAISON SARS-CoV-2 S1/S2 IgG (DiaSorin) and 2019-nCOV IgG/IgM Rapid Test (Dynamiker Biotechnology Co).\n\nResultsAll assays performed with a high level of specificity; however, only Abbott reached 100% (95% CI 96.3-100). The pre-pandemic samples analysed with Roche, DiaSorin and Dynamiker Biotechnology resulted in two to three false-positive results per method (specificity 96.9-98.0%). Sensitivity differed more between the assays, Roche exhibiting the highest sensitivity (100%, CI 83.9-100). The corresponding figures for Abbott, DiaSorin and Dynamiker Biotechnology were 85.0%, 77.8% and 75.0%, respectively.\n\nConclusionsThe results of the evaluated SARS-CoV-2 assays vary considerably as well as their ability to fulfil the performance criteria proposed by regulatory authorities. Introduction into clinical use in low-prevalent settings, should therefore, be made with caution.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Oskar Ekelund", - "author_inst": "Region Kronoberg" - }, - { - "author_name": "Kim Ekblom", - "author_inst": "Department of Clinical Chemistry and Transfusion Medicine, Vaxjo Central Hospital, Vaxjo, Sweden" - }, - { - "author_name": "Sofia Somajo", - "author_inst": "Department of Clinical Microbiology, Blekinge County Hospital, Karlskrona, Sweden" - }, - { - "author_name": "Johanna Pattison-Granberg", - "author_inst": "Department of Clinical Chemistry and Transfusion Medicine, Vaxjo Central Hospital, Vaxjo, Sweden" - }, - { - "author_name": "Karl Olsson", - "author_inst": "Department of Clinical Microbiology, Blekinge County Hospital, Karlskrona, Sweden" - }, - { - "author_name": "Annika Petersson", - "author_inst": "Department of Clinical Chemistry and Transfusion Medicine, Vaxjo Central Hospital, Vaxjo, Sweden" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.22.20106328", "rel_title": "Diagnostic performances and thresholds: the key to harmonization in serological SARS-CoV-2 assays?", @@ -1424807,6 +1425368,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.26.20104497", + "rel_title": "Knowledge and attitude towards COVID-19 in Bangladesh: Population-level estimation and a comparison of data obtained by phone and online survey methods", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20104497", + "rel_abs": "Peoples adherence to the guidelines and measures suggested in fighting the ongoing COVID-19 pandemic is partly determined by the Knowledge, Attitude, and Practices (KAP) of the population. In this cross-sectional study, we primarily addressed two key issues. First, we tried to determine whether there is a significant difference in the estimated COVID-19 knowledge level from the online and phone survey methods. Second, we tried to quantify the knowledge and attitude of COVID-19 in Bangladeshi adult population. Data were collected through phone calls (April 14-23, 2020) and online survey (April 18-19, 2020) in Bangladesh. The questionnaire had 20 knowledge questions with each correct response getting one point and incorrect/dont know response getting no point (maximum total knowledge score 20). Participants scoring >17 were categorized as having good knowledge. The percentages of good knowledge holders were 57.6%, 75.1%, and 95.8% in the phone (n=1426), online non-medical (n=1097), and online medical participants (n=382), respectively. Comparison between phone and online survey showed that, overall, online survey might overestimate knowledge level than that of phone survey, although there was no difference for elderly, poor, and rural people. Male gender, higher education, living in town/urban areas, good financial condition, and use of internet were positively associated with good knowledge. However, higher knowledge was associated with having less confidence in the final control of COVID-19. Our adult population-level estimates showed that only 32.6% (95% CI 30.1-35.2%) had good knowledge. This study provides crucial information that could be useful for the researchers and policymakers to develop effective strategies.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Anwarul Karim", + "author_inst": "Department of Surgery, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Mastura Akter", + "author_inst": "Department of Biomedical Sciences, City University of Hong Kong, Hong Kong" + }, + { + "author_name": "AHM Thafikul Mazid", + "author_inst": "Department of Medicine, Dhaka Medical College and Hospital, Dhaka, Bangladesh" + }, + { + "author_name": "Orindom Shing Pulock", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Tasmiah Tahera Aziz", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Samira Hayee", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Nowrin Tamanna", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "GS Chuwdhury", + "author_inst": "Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Afsana Haque", + "author_inst": "Department of Urban Planning and Design, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Farhana Yeasmin", + "author_inst": "Department of Applied Food Science and Nutrition, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh" + }, + { + "author_name": "Mashkura Akter Mitu", + "author_inst": "Faculty of Agriculture, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh" + }, + { + "author_name": "Farjana Yeasmin", + "author_inst": "Department of Zoology, Government Hazi Mohammad Mohsin College, National University, Bangladesh" + }, + { + "author_name": "Humayun Rashid", + "author_inst": "Chattogram International Medical College, Chattogram, Bangladesh" + }, + { + "author_name": "Ashish Kumar Kuri", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Arni Das", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Koushik Majumder", + "author_inst": "Chittagong Medical College and Hospital, Chattogram, Bangladesh" + }, + { + "author_name": "Dipen Barua", + "author_inst": "Centre of Buddhist Studies, Faculty of Arts, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Md Mahabubur Rahaman", + "author_inst": "Infectious Disease Division, International Centre for Diarrhoeal Disease Research, Bangladesh" + }, + { + "author_name": "Sanjida Akter", + "author_inst": "Department of Social and Preventive Medicine, Faculty of Medicine, University Malaya, Malaysia" + }, + { + "author_name": "Nashid Niaz Munia", + "author_inst": "Chattogram International Medical College, Chattogram, Bangladesh" + }, + { + "author_name": "Jabin Sultana", + "author_inst": "Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangl" + }, + { + "author_name": "Faeeqa Usaila", + "author_inst": "Department of Biomedical Sciences, City University of Hong Kong, Hong Kong" + }, + { + "author_name": "Sabrina Sifat", + "author_inst": "Shaheed Suhrawardy Medical College and Hospital, Dhaka, Bangladesh" + }, + { + "author_name": "Nishat Anjum Nourin", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + }, + { + "author_name": "Md Forhad Uddin", + "author_inst": "Independent Researcher, Chattogram, Bangladesh" + }, + { + "author_name": "Mrinmoy Bhowmik", + "author_inst": "Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh" + }, + { + "author_name": "Tanvir Ahammed", + "author_inst": "Department of Statistics, Shahjalal University of Science and Technology, Sylhet, Bangladesh" + }, + { + "author_name": "Nabil Sharik", + "author_inst": "Upzila Health and Family Planning Office, Sadar, Gopalganj, Bangladesh" + }, + { + "author_name": "Quddus Mehnaz", + "author_inst": "School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong" + }, + { + "author_name": "Md Nur Hossain Bhuiyan", + "author_inst": "Department of Surgery, Chittagong Medical College and Hospital, Chattogram, Bangladesh" + }, + { + "author_name": "Tahmina Banu", + "author_inst": "Chittagong Research Institute for Children Surgery, Chattogram, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.19.20106492", "rel_title": "A modified SEIR Model with Confinement and Lockdown of COVID-19 for Costa Rica", @@ -1426087,93 +1426787,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.23.20111450", - "rel_title": "The Outcome Impact of Early vs Late HFNC Oxygen Therapy in Elderly Patients with COVID-19 and ARDS", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20111450", - "rel_abs": "Coronavirus disease-2019 (COVID-19) has rapidly spread worldwide. High-flow nasal cannula therapy (HFNC) is a major oxygen supporting therapy for severely ill patients, but information regarding the timing of HFNC application is scarce, especially in elderly patients. We retrospectively analyzed the clinical data of 110 elderly patients ([≥]65 years) who received HFNC from Renmin Hospital of Wuhan University, Peoples Hospital of Xiantao City and Chinese Medicine Hospital of Shishou City in Hubei Province, China, and from Affiliated Hospital of Guangdong Medical University, Peoples Hospital of Yangjiang City, Peoples Hospital of Maoming City in Guangdong Province, China.\n\nOf the 110 patients, the median age was 71 years (IQR, 68-78) and 59.1% was male. Thirty-eight patients received HFNC when 200 mmHg < PO2/FiO2 [≤] 300 mmHg (early HFNC group), and 72 patients received HFNC treatment when 100 mmHg < PaO2/FiO2 [≤] 200 mmHg (late HFNC group). Compared with the late HFNC group, patients in the early HFNC group had a lower likelihood of developing severe ARDS, longer time from illness onset to severe ARDS and shorter duration of viral shedding after illness onset, as well as shorter lengths of ICU and hospital stay. Twenty-four patients died during hospitalization, of whom 22 deaths (30.6%) were in the late HFNC group and 2(5.3%) in the early HFNC group. It is concluded that the Prognosis was better in severely ill elderly patients with COVID-19 receiving early compared to late HFNC. This suggests HFNC could be considered early in this disease process.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Liehua Deng", - "author_inst": "Department of Critical Care Medicine of affiliated hospital of Guangdong Medical University" - }, - { - "author_name": "Shaoqing Lei", - "author_inst": "Department of Anesthesiology, Renmin Hospital of Wuhan University" - }, - { - "author_name": "Fang Jiang", - "author_inst": "Department of Anesthesiology, The University of Hong Kong" - }, - { - "author_name": "David A. Lubarsky", - "author_inst": "Department of Anesthesiology and Pain Medicine, University of California Davis Health" - }, - { - "author_name": "Liangqing Zhang", - "author_inst": "The Department of Anesthesiology, Affiliated hospital of Guangdong Medical University" - }, - { - "author_name": "Danyong Liu", - "author_inst": "The Department of Anesthesiology, Affiliated hospital of Guangdong Medical University" - }, - { - "author_name": "Conghua Han", - "author_inst": "Department of Critical Care Medicine of Xiantao first people's Hospital of Xiantao City" - }, - { - "author_name": "Dunrong Zhou", - "author_inst": "Department of Critical Care Medicine of people's Hospital of Yangjiang City" - }, - { - "author_name": "Zheng Wang", - "author_inst": "Department of Critical Care Medicine of people's Hospital of Maoming City" - }, - { - "author_name": "Xiaocong Sun", - "author_inst": "Department of Critical Care Medicine of affiliated hospital of Guangdong Medical University" - }, - { - "author_name": "Yuanli Zhang", - "author_inst": "Department of Critical Care Medicine of affiliated hospital of Guangdong Medical University" - }, - { - "author_name": "Chi Wai Cheung", - "author_inst": "Department of Anesthesiology, The University of Hong Kong" - }, - { - "author_name": "Sheng Wang", - "author_inst": "Department of Anesthesiology, Guangdong provincial people Hospital, Guangdong Academy of Medical Sciences" - }, - { - "author_name": "Zhong-yuan Xia", - "author_inst": "Department of Anesthesiology, Renmin Hospital of Wuhan University" - }, - { - "author_name": "Richard L Applegate II", - "author_inst": "Department of Anesthesiology and Pain Medicine, University of California Davis Health" - }, - { - "author_name": "Hong Liu", - "author_inst": "Department of Anesthesiology and Pain Medicine, University of California Davis Health" - }, - { - "author_name": "Jing Tang", - "author_inst": "The Department of Anesthesiology, Affiliated hospital of Guangdong Medical University" - }, - { - "author_name": "Zhengyuan Xia", - "author_inst": "Department of Anesthesiology, University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.21.20107003", "rel_title": "Renin-angiotensin-aldosterone system inhibitors and mortality in patients with hypertension hospitalized for COVID-19: a systematic review and meta-analysis", @@ -1426377,6 +1426990,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2020.05.19.20107532", + "rel_title": "COVID-19 Datasets: A Survey and Future Challenges", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107532", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWIn December 2019, a novel virus named COVID-19 emerged in the city of Wuhan, China. In early 2020, the COVID-19 virus spread in all continents of the world except Antarctica causing widespread infections and deaths due to its contagious characteristics and no medically proven treatment. The COVID-19 pandemic has been termed as the most consequential global crisis after the World Wars. The first line of defense against the COVID-19 spread are the non-pharmaceutical measures like social distancing and personal hygiene. The great pandemic affecting billions of lives economically and socially has motivated the scientific community to come up with solutions based on computer-aided digital technologies for diagnosis, prevention, and estimation of COVID-19. Some of these efforts focus on statistical and Artificial Intelligence-based analysis of the available data concerning COVID-19. All of these scientific efforts necessitate that the data brought to service for the analysis should be open source to promote the extension, validation, and collaboration of the work in the fight against the global pandemic. Our survey is motivated by the open source efforts that can be mainly categorized as (a) COVID-19 diagnosis from CT scans, X-ray images, and cough sounds, (b) COVID-19 case reporting, transmission estimation, and prognosis from epidemiological, demographic, and mobility data, (c) COVID-19 emotional and sentiment analysis from social media, and (d) knowledge-based discovery and semantic analysis from the collection of scholarly articles covering COVID-19. We survey and compare research works in these directions that are accompanied by open source data and code. Future research directions for data-driven COVID-19 research are also debated. We hope that the article will provide the scientific community with an initiative to start open source extensible and transparent research in the collective fight against the COVID-19 pandemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Junaid Shuja", + "author_inst": "Umm Al-Qura University" + }, + { + "author_name": "Eisa Alanazi", + "author_inst": "Umm Al-Qura University" + }, + { + "author_name": "Waleed Alasmary", + "author_inst": "Umm Al-Qura University" + }, + { + "author_name": "Abdulaziz Alashaikh", + "author_inst": "University of Jeddah" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.24.20107193", "rel_title": "Using HoloLens\u2122 to reduce staff exposure to aerosol generating procedures during a global pandemic", @@ -1427465,125 +1428109,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.24.20111864", - "rel_title": "Patient trajectories and risk factors for severe outcomes among persons hospitalized for COVID-19 in the Maryland/DC region", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20111864", - "rel_abs": "BackgroundRisk factors for poor outcomes from COVID-19 are emerging among US cohorts, but patient trajectories during hospitalization ranging from mild-moderate, severe, and death and the factors associated with these outcomes have been underexplored.\n\nMethodsWe performed a cohort analysis of consecutive COVID-19 hospital admissions at 5 Johns Hopkins hospitals in the Baltimore/DC area between March 4 and April 24, 2020. Disease severity and outcomes were classified using the WHO COVID-19 disease severity ordinal scale. Cox proportional-hazards regressions were performed to assess relationships between demographics, clinical features and progression to severe disease or death.\n\nResults832 COVID-19 patients were hospitalized; 633 (76.1%) were discharged, 113 (13.6%) died, and 85 (10.2%) remained hospitalized. Among those discharged, 518 (82%) had mild/moderate and 116 (18%) had severe illness. Mortality was statistically significantly associated with increasing age per 10 years (adjusted hazard ratio (aHR) 1.54; 95%CI 1.28-1.84), nursing home residence (aHR 2.13, 95%CI 1.41-3.23), Charlson comorbidity index (1.13; 95% CI 1.02-1.26), respiratory rate (aHR 1.13; 95%CI 1.09-1.17), D-dimer greater than 1mg/dL (aHR 2.79; 95% 1.53-5.09), and detectable troponin (aHR 2.79; 95%CI 1.53-5.09). In patients under 60, only male sex (aHR 1.7;95%CI 1.11-2.58), increasing body mass index (BMI) (aHR1.25 1.14-1.37), Charlson score (aHR 1.27; 1.1-1.46) and respiratory rate (aHR 1.16; 95%CI 1.13-1.2) were associated with severe illness or death.\n\nConclusionsA combination of demographic and clinical features on admission is strongly associated with progression to severe disease or death in a US cohort of COVID-19 patients. Younger patients have distinct risk factors for poor outcomes.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Brian T Garibaldi", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Jacob Fiksel", - "author_inst": "Johns Hopkins University Bloomberg School of Public Health" - }, - { - "author_name": "John Muschelli", - "author_inst": "Johns Hopkins University Bloomberg School of Public Health" - }, - { - "author_name": "Matthew L Robinson", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Masoud Rouhizadeh", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Paul Nagy", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Josh H Gray", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Harsha Malapati", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Mariam Ghobadi-Krueger", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Timothy M Niessen", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Bo Soo Kim", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Peter M Hill", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "M. Shafeeq Ahmed", - "author_inst": "Howard Country General Hospital" - }, - { - "author_name": "Eric D Dobkin", - "author_inst": "Suburban Hospital, Johns Hopkins Medicine" - }, - { - "author_name": "Renee Blanding", - "author_inst": "Johns Hopkins Bayview Medical Center" - }, - { - "author_name": "Jennifer Abele", - "author_inst": "Sibley Memorial Hospital, Johns Hopkins Medicine" - }, - { - "author_name": "Bonnie Woods", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Kenneth Harkness", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "David R Thiemann", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Mary Grace Bowring", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Aalok B. Shah", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Mei Cheng Wang", - "author_inst": "Johns Hopkins University Bloomberg School of Medicine" - }, - { - "author_name": "Karen Bandeen-Roche", - "author_inst": "Johns Hopkins University Bloomberg School of Public Health" - }, - { - "author_name": "Antony Rosen", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Scott L Zeger", - "author_inst": "Johns Hopkins University Bloomberg School of Public Health" - }, - { - "author_name": "Amita Gupta", - "author_inst": "Johns Hopkins University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.22.20108290", "rel_title": "Knowledge, attitude, and practices of Community pharmacists about COVID-19: A cross-sectional survey in two provinces of Pakistan.", @@ -1427803,6 +1428328,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.20.20107755", + "rel_title": "BCG vaccination and socioeconomic variables vs Covid-19 global features: clearing up a controversial issue", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20107755", + "rel_abs": "BackgroundThe Covid-19 pandemic is characterized by extreme variability in the outcome distribution and mortality rates across different countries. Some recent studies suggested an inverse correlation with BCG vaccination at population level, while others denied this hypothesis. In order to address this controversial issue, we performed a strict epidemiological study collecting data available on a global scale, considering additional variables such as cultural-political factors and adherence to other vaccination coverages.\n\nMethodsData on 121 countries, accounting for about 99% of Covid-19 cases and deaths globally, were from Johns Hopkins Coronavirus Resource Center, World Bank, International Monetary Fund, United Nations, Human Freedom Report, and BCG Atlas. Statistical models used were Ordinary Least Squares, Tobit and Fractional Probit, implemented on Stata/MP16 software.\n\nResultsBased on our results, countries where BCG vaccination is or has been mandated in the last decades have seen a drastic reduction in Covid-19 diffusion (-80% on average) and mortality (-50% on average), even controlling for relative wealth of countries and their governmental health expenditure. A significant contribution to this reduction (respectively -50% and -13% on average) was also associated to the outbreak onset during summer, suggesting a possible influence of seasonality. Other variables turned out to be associated, though to a lesser extent.\n\nConclusionsRelying on a very large dataset and a wide array of control variables, our study confirms a strong and robust association between Covid-19 diffusion and mortality with BCG vaccination and a set socio-economic factors, opening new perspectives for clinical speculations and public health policies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Luigi Ventura", + "author_inst": "Department of Economy and Law, Sapienza University of Rome, Rome, Italy" + }, + { + "author_name": "Matteo Vitali", + "author_inst": "Department of Public Health and Infectious Diseases, Sapienza University of Rome, Italy" + }, + { + "author_name": "Vincenzo Romano Spica", + "author_inst": "Department of Movement, Human and Health Sciences, University of Rome \u201cForo Italico\u201d, Rome Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.25.20109470", "rel_title": "Seroprevalence of antibodies against SARS-CoV-2 among public community and health-care workers in Alzintan City of Libya", @@ -1429163,97 +1429715,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.22.20110544", - "rel_title": "IMPACT OF GLUCOCORTICOID TREATMENT IN SARS-COV-2 INFECTION MORTALITY: A RETROSPECTIVE CONTROLLED COHORT STUDY", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110544", - "rel_abs": "ObjectiveWe aim to determine the impact of steroid use in COVID-19 pneumonia in-hospital mortality.\n\nDesignWe performed a single-centre retrospective cohort study.\n\nSettingA University hospital in Madrid, Spain, during March 2020.\n\nParticipantsPatients admitted with SARS-CoV-2 pneumonia.\n\nExposuresPatients treated with steroids were compared to patients not treated with steroids. A propensity-score for steroid treatment was developed. Different steroid regimens were also compared, and adjusted with a second propensity score.\n\nMain Outcomes and MeasuresTo determine the role of steroids in in-hospital mortality, univariable and multivariable analyses were performed, and adjusted including the propensity score as a covariate. Survival times were compared using a log-rank test.\n\nResultsDuring the study period, 463 out of 848 hospitalized patients with COVID19 pneumonia fulfilled inclusion criteria. Among them, 396 (46.7%) consecutive patients were treated with steroids and 67 patients were assigned to the control cohort. Global mortality was 15.1%. Median time to steroid treatment from symptom onset was 10 days (IQR 8 to13). In-hospital mortality was lower in patients treated with steroids than in controls (13.9% [55/396] versus 23.9% [16/67], OR 0.51 [0.27 to 0.96], p= 0.044). Steroid treatment reduced mortality by 41.8% relative to no steroid treatment (RRR 0,42 [0.048 to 0.65). Initial treatment with 1 mg/kg/day of methylprednisolone (or equivalent) versus steroid pulses was not associated with in-hospital mortality (13.5% [42/310] versus 15.1% [13/86], OR 0.880 [0.449-1.726], p=0.710).\n\nConclusionsOur results show that survival of patients with SARS-CoV2 pneumonia is higher in patients treated with glucocorticoids than in those not treated. In-hospital mortality was not different between initial regimens of 1 mg/kg/day of methylprednisolone or equivalent and glucocorticoid pulses. These results support the use of glucocorticoids in SARS-CoV2 infection.\n\nSummaryWe investigated in-hospital mortality of patients with SARS-CoV-2 pneumonia in a large series of patients treated with steroids compared to controls, and adjusted using a propensity score. Our results show a beneficial impact of steroid treatment in SARS-CoV-2 pneumonia.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Ana Fernandez-Cruz", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Belen Ruiz-Antoran", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Ana Munoz-Gomez", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Aranzazu Sancho-Lopez", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Patricia Mills-Sanchez", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Gustavo Adolfo Centeno-Soto", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Silvia Blanco-Alonso", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Laura Javaloyes-Garachana", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Amy Galan-Gomez", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Angela Valencia-Alijo", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Javier Gomez-Irusta", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Concepcion Payares-Herrera", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Ignacio Morras-Torre", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Enrique Sanchez-Chica", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Laura Delgado-Tellez-de-Cepeda", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Alejandro Callejas-Diaz", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Antonio Ramos-Martinez", - "author_inst": "HU Puerta de Hierro-Majadahonda" - }, - { - "author_name": "Elena Munez-Rubio", - "author_inst": "Hospital Universitario Puerta de Hierro" - }, - { - "author_name": "Cristina Avendano-Sola", - "author_inst": "Hospital Universitario Puerta de Hierro" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.24.20110346", "rel_title": "Investigating SARS-CoV-2 surface and air contamination in an acute healthcare setting during the peak of the COVID-19 pandemic in London", @@ -1429533,6 +1429994,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.05.23.20111310", + "rel_title": "No evidence for allelic association between Covid-19 and ACE2 genetic variants by direct exome sequencing in 99 SARS-CoV-2 positive patients", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20111310", + "rel_abs": "BackgroundCoronaviruses (CoV) are a large family of viruses that are common in people and many animal species. Animal coronaviruses rarely infect humans with the exceptions of the Middle East Respiratory Syndrome (MERS-CoV), the Severe acute respiratory syndrome coronavirus (SARS-CoV), and now SARS-CoV-2, which is the cause of the ongoing pandemic of coronavirus disease 2019 (COVID-19). Many studies suggested that genetic variants in ACE2 gene may influence the host susceptibility/resistance to SARS-CoV-2 virus according to the functional role of ACE2 in human pathophysiology. However, all these studies have been conducted in silico based on epidemiological and population data. We therefore investigated the occurrence of ACE2 variants in a cohort of 99 Italian unrelated individuals clinically diagnosed with coronavirus disease 19 (COVID-19) to experimental demonstrate allelic association with disease severity.\n\nMethodsBy whole-exome sequencing we analysed 99 DNA samples of severely and extremely severely COVID-19 patients hospitalized at the University Hospital of Rome \"Tor Vergata\" and Bambino Gesu Hospital in Rome.\n\nResultsWe identified three different germline variants, one intronic (c.439+4G>A) and two missense (c.2158A>G, p.Asn720Asp; c.1888G>C, p.Asp630His), in 26 patients with a similar frequency between male and female and a not statistically different frequency, except for c.1888G>C, (p.Asp630His) with the ethnically matched populations (EUR).\n\nConclusionsOur results suggest that there is not any ACE2 exonic allelic association with disease severity. It is possible that rare susceptibility alleles are located in the non-coding region of the gene able to control ACE2 gene activity. It is therefore of interest, to explore the existence of ACE2 susceptibility alleles to SARS-Co-V2 in these regulatory regions. In addition, we found no significant evidence that ACE2 alleles is associated with disease severity/sex bias in the Italian population.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Antonio Novelli", + "author_inst": "Laboratory of Medical Genetics, Bambino Ges\u00f9 Children's Hospital, IRCCS, Rome, Italy" + }, + { + "author_name": "Michela Biancolella", + "author_inst": "Department of Biology, Tor Vergata University of Rome, 00133 Rome, Italy" + }, + { + "author_name": "Paola Borgiani", + "author_inst": "Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy" + }, + { + "author_name": "Dario Cocciadiferro", + "author_inst": "Laboratory of Medical Genetics, Bambino Ges\u00f9 Children's Hospital, IRCCS, Rome, Italy" + }, + { + "author_name": "Vito Luigi Colona", + "author_inst": "Medical Genetics Laboratory, Tor Vergata Hospital, Rome, Italy" + }, + { + "author_name": "Maria Rosaria D'Apice", + "author_inst": "Medical Genetics Laboratory, Tor Vergata Hospital, Rome, Italy" + }, + { + "author_name": "Paola Rogliani", + "author_inst": "Unit of Respiratory Medicine, Department of Experimental Medicine, University of Rome \"Tor Vergata\", Rome, Italy" + }, + { + "author_name": "Salvatore Zaffina", + "author_inst": "Occupational Medicine, Bambino Ges\u00f9 Children's Hospital, IRCCS, Rome, Italy" + }, + { + "author_name": "Francesca Leonardis", + "author_inst": "Intensive Care Unit, Tor Vergata University Hospital, Rome, Italy" + }, + { + "author_name": "Andrea Campana", + "author_inst": "Department of Pediatrics, IRCCS Bambino Ges\u00f9 Children's Hospital, Rome, Italy" + }, + { + "author_name": "Massimiliano Raponi", + "author_inst": "Medical Directorate, IRCCS Bambino Ges\u00f9 Children's Hospital, Rome, Italy" + }, + { + "author_name": "Massimo Andreoni", + "author_inst": "Infectious Diseases Clinic, Policlinico Tor Vergata, Rome, Italy" + }, + { + "author_name": "Sandro Grelli", + "author_inst": "Dept. of Experimental Medicine and Biochemical Sciences, University of Rome Tor Vergata, Italy" + }, + { + "author_name": "Giuseppe Novelli", + "author_inst": "Tor Vergata University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.05.25.20112938", "rel_title": "What Can We Learn from the Time Evolution of COVID-19 Epidemic in Slovenia?", @@ -1430413,85 +1430945,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.05.26.20113191", - "rel_title": "Improved detection of antibody against SARS-CoV-2 by microsphere-based antibody assay", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20113191", - "rel_abs": "ObjectiveCurrently available COVID-19 antibody tests using enzyme immunoassay (EIA) or immunochromatographic assay have variable sensitivity and specificity. Here, we developed and evaluated a novel microsphere-based antibody assay (MBA) for the detection of immunoglobulin G (IgG) against SARS-CoV-2 nucleoprotein (NP) and spike protein receptor binding domain (RBD).\n\nMethodWe developed a microsphere-based assay (MBA) to determine the levels of IgG against SARS-CoV-2 NP and spike RBD. The seropositive cut-off mean fluorescent intensity (MFI) was set using a cohort of 294 anonymous serum specimens collected in 2018. The specificity was assessed using serum specimens collected from organ donors or influenza patients before 2020. Seropositive rate was determined among patients with COVID-19. Time-to-seropositivity and signal-to-cutoff (S/CO) ratio were compared between MBA and EIA.\n\nResultsMBA had a specificity of 100% (93/93; 95% confidence interval [CI], 96-100%) for anti-NP IgG and 98.9% (92/93; 95% CI 94.2-100%) for anti-RBD IgG. The MBA seropositive rate for convalescent serum specimens of COVID-19 patients were 89.8% (35/39) for anti-NP IgG and 79.5% (31/39) for anti-RBD IgG. The time-to-seropositivity was shorter with MBA than that of EIA. When compared with EIA, MBA could better differentiate between COVID-19 patients and negative controls with significantly higher S/CO ratio for COVID-19 patients and lower S/CO ratio with negative controls. MBA also had fewer specimens in the equivocal range (S/CO 0.9-1.1) than EIA.\n\nConclusionMBA is robust and simple, and is suitable for clinical microbiology laboratory for the accurate determination of anti-SARS-CoV-2 antibody for retrospective diagnosis, serosurveillance, and vaccine trials.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Carol Ho Yan Fong", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Thrimendra Kaushika Dissanayake", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Lin-Lei Chen", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Charlotte Yee-Ki Choi", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Lok-Hin Wong", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Anthony Chin-Ki Ng", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Polly K.P Pang", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Deborah Tip-Yin Ho", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Rosana Wing-Shan Poon", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Tom Wai-Hin Chung", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Siddharth Sridhar", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Kwok-Hung Chan", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Jasper Fuk-Woo Chan", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Ivan Fan-Ngai Hung", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Kwok-Yung Yuen", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Kelvin Kai-Wang To", - "author_inst": "University of Hong Kong" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.23.20111401", "rel_title": "Association of Renin Angiotensin System Blockers with Outcomes in Patients with Covid-19: A Systematic Review and Meta-analysis", @@ -1430667,6 +1431120,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.23.112284", + "rel_title": "SciSight: Combining faceted navigation and research group detection for COVID-19 exploratory scientific search", + "rel_date": "2020-05-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.23.112284", + "rel_abs": "The COVID-19 pandemic has sparked unprecedented mobilization of scientists, generating a deluge of papers that makes it hard for researchers to keep track and explore new directions. Search engines are designed for targeted queries, not for discovery of connections across a corpus. In this paper, we present SciSight, a system for exploratory search of COVID-19 research integrating two key capabilities: first, exploring associations between biomedical facets automatically extracted from papers (e.g., genes, drugs, diseases, patient outcomes); second, combining textual and network information to search and visualize groups of researchers and their ties. SciSight1 has so far served over 15K users with over 42K page views and 13% returns.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Tom Hope", + "author_inst": "Allen Institute for AI" + }, + { + "author_name": "Jason Portenoy", + "author_inst": "University of Washington" + }, + { + "author_name": "Kishore Vasan", + "author_inst": "University of Washington" + }, + { + "author_name": "Jonathan Borchardt", + "author_inst": "Allen Institute for AI" + }, + { + "author_name": "Eric Horvitz", + "author_inst": "Microsoft Research" + }, + { + "author_name": "Daniel S. Weld", + "author_inst": "Allen Institute for AI" + }, + { + "author_name": "Marti A. Hearst", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Jevin West", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.23.20111443", "rel_title": "COVID-19 in Latin America: Contrasting phylodynamic inference with epidemiological surveillance.", @@ -1431719,165 +1432219,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.23.20100024", - "rel_title": "Single-Cell Analysis Reveals Macrophage-Driven T Cell Dysfunction in Severe COVID-19 Patients", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20100024", - "rel_abs": "The vastly spreading COVID-19 pneumonia is caused by SARS-CoV-2. Lymphopenia and cytokine levels are tightly associated with disease severity. However, virus-induced immune dysregulation at cellular and molecular levels remains largely undefined. Here, the leukocytes in the pleural effusion, sputum, and peripheral blood biopsies from severe and mild patients were analyzed at single-cell resolution. Drastic T cell hyperactivation accompanying elevated T cell exhaustion was observed, predominantly in pleural effusion. The mechanistic investigation identified a group of CD14+ monocytes and macrophages highly expressing CD163 and MRC1 in the biopsies from severe patients, suggesting M2 macrophage polarization. These M2-like cells exhibited up-regulated IL10, CCL18, APOE, CSF1 (M-CSF), and CCL2 signaling pathways. Further, SARS-CoV-2-specific T cells were observed in pleural effusion earlier than in peripheral blood. Together, our results suggest that severe SARS-CoV-2 infection causes immune dysregulation by inducing M2 polarization and subsequent T cell exhaustion. This study improves our understanding of COVID-19 pathogenesis.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Xiaoqing Liu", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Airu Zhu", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Jiangping He", - "author_inst": "Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL)" - }, - { - "author_name": "Zhao Chen", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Longqi Liu", - "author_inst": "BGI-Shenzhen, Shenzhen, China" - }, - { - "author_name": "Yuanda Xu", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Feng Ye", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Huijian Feng", - "author_inst": "Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangz" - }, - { - "author_name": "Lin Luo", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Baomei Cai", - "author_inst": "Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou, China" - }, - { - "author_name": "Yuanbang Mai", - "author_inst": "Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangz" - }, - { - "author_name": "Lihui Lin", - "author_inst": "Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangz" - }, - { - "author_name": "Zhekun Zhang", - "author_inst": "BGI-Shenzhen, Shenzhen, China" - }, - { - "author_name": "Sibei Chen", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Junjie Shi", - "author_inst": "Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou, China" - }, - { - "author_name": "Lilan Wen", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Yuanjie Wei", - "author_inst": "Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou, China" - }, - { - "author_name": "Jianfen Zhuo", - "author_inst": "Becton Dickinson Medical Devices (Shanghai) Co., Ltd, Guangzhou, Guangdong, China" - }, - { - "author_name": "Yingying Zhao", - "author_inst": "Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangz" - }, - { - "author_name": "Fang Li", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Xiaoyu Wei", - "author_inst": "BGI-Shenzhen, Shenzhen, China" - }, - { - "author_name": "Dingbin Chen", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Xinmei Zhang", - "author_inst": "Becton Dickinson Medical Devices (Shanghai) Co., Ltd, Guangzhou, Guangdong, China" - }, - { - "author_name": "Na Zhong", - "author_inst": "Becton Dickinson Medical Devices (Shanghai) Co., Ltd, Guangzhou, Guangdong, China" - }, - { - "author_name": "Yaling Huang", - "author_inst": "BGI-Shenzhen, Shenzhen, China" - }, - { - "author_name": "He Liu", - "author_inst": "Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou, China" - }, - { - "author_name": "Jinyong Wang", - "author_inst": "Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Xun Xu", - "author_inst": "BGI-Shenzhen, Shenzhen, China" - }, - { - "author_name": "Jie Wang", - "author_inst": "Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangz" - }, - { - "author_name": "Ruchong Chen", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Xinwen Chen", - "author_inst": "Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangz" - }, - { - "author_name": "Nanshan Zhong", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Jinxian Zhao", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Yimin Li", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease" - }, - { - "author_name": "Jincun Zhao", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Jiekai Chen", - "author_inst": "Guangzhou Regenerative Medicine and Health-Guangdong Laboratory (GRMH-GDL), Guangzhou, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.05.23.20099671", "rel_title": "Psychiatric Predictors of COVID-19 Outcomes in a Skilled Nursing Facility Cohort", @@ -1432101,6 +1432442,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.24.20104414", + "rel_title": "Risk of infection and hospitalization by Covid-19 in Mexico: a case-control study", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20104414", + "rel_abs": "ObjectiveDuring the onset of a novel epidemic, there are public health priorities that need to be estimated, such as risk factors for infection, hospitalization, and clinical severity to allocate resources and issue health policies. In this work we calculate the risk of infection and hospitalization by Covid-19 conferred by demographic, lifestyle, and co-morbidity factors.\n\nMaterial and methodsThis is a case-control study including the tested individuals for SARS-Cov-2 by RT-PCR officially reported by the Health Secretary of Mexico from January 01 to May 8, 2020 (102,875 subjects). Demographic (sex, age, foreign and immigrant status, native speaking, place of residence), life-style (smoking), and co-morbidities [diabetes, obesity, high blood pressure (HBP), asthma, immunosuppression, chronic obstructive pulmonary disease (COPD), cardiovascular disease other than HBP, chronic kidney disease (CKD), and other not specified diseases (other diseases)] variables were included in this study. The risk of infection and hospitalization conferred by each variable was calculated with univariate (ULR) and multivariate (MLR) logistic regression models.\n\nResultsThe place of residence (OR=4.91 living in Tijuana City), followed by advanced age (OR=6.71 in 61-70 years-old), suffering from diabetes (OR=1.87) or obesity (OR=1.61), being male (OR=1.55), having HBP (OR=1.52), and notoriously being indigenous (OR=1.49) conferred a higher risk of becoming infected by SARS-CoV-2 in Mexico. Unexpectedly, we found that having asthma (OR=0.63), immunosuppression (OR=0.65) or smoking (OR=0.85) are protective factors against infection, while suffering from COPD does not increase the risk for SARS-CoV-2 infection. In contrast, advanced age (OR=11.6 in [≥] 70 years-old) is the main factor for hospitalization due to Covid-19, followed by some co-morbidities, mainly diabetes (OR=3.69) and HBP (OR=2.79), being indigenous (OR=1.89), male sex (OR=1.67) and the place of residence (OR=4.22 for living in Juarez City). Unlike the protective risk against infection, immunosuppression (OR=2.69) and COPD (OR=3.63), contribute to the risk of being hospitalized, while having asthma (OR=0.7) also provides protection against hospitalization.\n\nConclusionsIn addition to confirming that older age, diabetes, HBP and obesity are the main risk of infection and hospitalization by Covid-19, we found that being indigenous, immunosuppression, smoking and asthma protect against infection, and the latter also against hospitalization.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jaime Berumen", + "author_inst": "Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Max Schmulson", + "author_inst": "Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Jesus Alegre", + "author_inst": "Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Guadalupe Guerrero", + "author_inst": "Hospital General de Mexico, Dr. Eduardo Liceaga, Mexico City, Mexico" + }, + { + "author_name": "Gustavo Olaiz", + "author_inst": "Centro de Investigacion en politicas, poblacion y salud, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Rosa M. Wong-Chew", + "author_inst": "Division de Investigacion, Facultad de Medicina, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico" + }, + { + "author_name": "Jorge Larriva-Sahd", + "author_inst": "Instituto de Neurobiologia, Universidad Nacional Autonoma de Mexico, Campus Juriquilla, Queretaro Mexico" + }, + { + "author_name": "Carlos Cantu-Brito", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico." + }, + { + "author_name": "Ana Ochoa-Guzman", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico." + }, + { + "author_name": "Adrian Garcilazo-Avila", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico." + }, + { + "author_name": "Carlos Gonzalez-Carballo", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran, Mexico City, Mexico." + }, + { + "author_name": "Erwin Chiquete", + "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.22.20102525", "rel_title": "Study on the expression levels of antibodies against SARS-CoV-2 at different period of disease and its related factors in 192 cases of COVID-19 patients", @@ -1433029,25 +1433433,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.20.20107912", - "rel_title": "Quantifying Effects, Forecasting Releases, and Herd Immunity of the Covid-19 Epidemic in S. Paulo, Brazil", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20107912", - "rel_abs": "A simple and well known epidemiological deterministic model was selected to estimate the main results for the basic dynamics of the Covid-19 epidemic breakout in the city of Sao Paulo - Brazil. The methodology employed the SEIR Model to characterize the epidemics outbreak and future outcomes. A time-dependent incidence weight on the SEIR reproductive basic number accounts for local Mitigation Policies (MP). The insights gained from analysis of these successful interventions were used to quantify shifts and reductions on active cases, casualties, and estimatives on required medical facilities (ITU). This knowledge can be applied to other Brazilian areas. The analysis was applied to forecast the consequences of releasing the MP over specific periods of time. Herd Immunity (HI) analysis allowed estimating how far we are from reaching the HI threshold value, and the price to be paid.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Sergio Celaschi", - "author_inst": "CTI Renato Archer" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.20.20107904", "rel_title": "Coronavirus (COVID-19) infection in children at a specialist centre: outcome and implications of underlying high-risk comorbidities in a paediatric population", @@ -1433319,6 +1433704,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.19.20107425", + "rel_title": "A Modelling Analysis of Strategies for Relaxing COVID-19 Social Distancing", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107425", + "rel_abs": "BackgroundThe ability of countries to contain and control COVID-19 virus transmission via social distancing is critical in the absence of a vaccine. Early activation of robust measures has been shown to control the daily infection rate, and consequential pressure on the health care system. As countries begin to control COVID-19 spread an understanding of how to ease social distancing measures to prevent a rebound in cases and deaths is required.\n\nMethodsUsing COVID-19 transmission data from the outbreak source in Hubei Province, China prior to activation of containment measures, we adapted an established individual-based simulation model of the city of Newcastle, Australia. Simulation of virus transmission in this model, with and without, social distancing measures activated permitted us to quantify social distancing effectiveness. Optimal strategies for relaxing social distancing were determined under two settings: with high numbers of daily cases, as in New York; and where early social distancing activation resulted in limited ongoing transmission, as in Perth, Australia.\n\nFindingsIn countries where strong social distancing measures were activated after the COVID-19 virus had spread widely, our study found these measures are required to be maintained for significant periods before being eased, to return to a situation where daily case numbers become low. In countries where early responses to the COVID-19 pandemic have been highly successful, as in Australia, we show that a staged relaxation of social distancing prevents a rebound in cases.\n\nInterpretationModelling studies and direct observation have shown that robust and timely social distancing have the most effect in containing the spread of the COVID-19 virus. Questions arise as to the duration of strong social distancing measures, given they are highly disruptive to society and economic activity. This study demonstrates the necessity of holding robust social distancing in place until COVID-19 virus transmission has significantly decreased, and how they may then be safely eased.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "George J Milne", + "author_inst": "University of Western Australia" + }, + { + "author_name": "Simon Xie", + "author_inst": "the University of Western Australia" + }, + { + "author_name": "Dana Poklepovich", + "author_inst": "University of Western Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.20.20107573", "rel_title": "Modelling information-dependent social behaviors in response to lockdowns: the case of COVID-19 epidemic in Italy", @@ -1434691,37 +1435103,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.25.20112482", - "rel_title": "Modeling the Dynamics of the COVID-19 Population in Australia: A Probabilistic Analysis", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20112482", - "rel_abs": "The novel Corona Virus COVID-19 arrived on Australian shores around 25 January 2020. This paper presents a novel method of dynamically modeling and forecasting the COVID-19 pandemic in Australia with a high degree of accuracy and in a timely manner using limited data; a valuable resource that can be used to guide government decision-making on societal restrictions on a daily and/or weekly basis. The \"partially-observable stochastic process\" used in this study predicts not only the future actual values with extremely low error, but also the percentage of unobserved COVID-19 cases in the population. The model can further assist policy makers to assess the effectiveness of several possible alternative scenarios in their decision-making processes.\n\nHighlightsO_LIThis work applies a novel and effective approach using a partially-observable stochastic process to study the dynamics of the COVID-19 population in Australia over the 1 March-22 May 2020 period.\nC_LIO_LIThe key contributions of this work include (but are not limited to):\nO_LIidentifying two structural break points in the numbers of new cases coinciding with where the dynamics of the COVID-19 population are altered: the first, a major break point, on 27 March 2020, is one week after implementing the \"lockdown restrictions\", and the second minor point on 18 April 2020, is one week after the \"Easter break\";\nC_LIO_LIforecasting the future daily numbers of new cases up to 28 days in advance with extremely low mean absolute percentage errors (MAPEs) using a relative paucity of data, namely, MAPE of 1.53% using 20 days of data to predict the number of new cases for the following 6 days, MAPE of 0.43% using 34 days of data to predict the number of new cases for the following 14 days, and MAPE of 0.20% using 55 days of data to predict the number of new cases for the following 28 days;\nC_LIO_LIestimating approximately 33% of COVID-19 cases as unobserved by 26 March 2020, reducing to less than 5% after implementing the Governments constructive restrictions;\nC_LIO_LIpredicting that the growth rate, prior to the Governments implementation of restrictions, was on a trajectory to infect numbers equal to Australias entire population by 24 April 2020;\nC_LIO_LIestimating the dynamics of the growth rate of the COVID-19 population to slow down to a rate of 0.820 after the first break point, with a slight rise to 0.979 after the second break point;\nC_LIO_LIAdvocating the outlined stochastic model as practically beneficial for policy makers when considering implementation and easing of virus restrictions due to the demonstrated sensitivity of the dynamics of the COVID-19 population in Australia to both major and minor system changes.\nC_LI\nC_LIO_LIThe model developed in this work may further assist policy makers to consider the impact of several potential scenarios in their decision-making processes.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ali Eshragh", - "author_inst": "University of Newcastle" - }, - { - "author_name": "Saed Alizamir", - "author_inst": "Yale University" - }, - { - "author_name": "Peter Howley", - "author_inst": "University of Newcastle" - }, - { - "author_name": "Elizabeth Stojanovski", - "author_inst": "University of Newcastle" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.25.20112433", "rel_title": "Understanding Spatial Heterogeneity of COVID-19 Pandemic Using Shape Analysis of Growth Rate Curves", @@ -1434997,6 +1435378,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.05.22.20109959", + "rel_title": "CLINICAL CHARACTERISTICS AND PROGNOSTIC FACTORS FOR ICU ADMISSION OF PATIENTS WITH COVID-19 USING MACHINE LEARNING AND NATURAL LANGUAGE PROCESSING", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20109959", + "rel_abs": "There remain many unknowns regarding the onset and clinical course of the ongoing COVID-19 pandemic. We used a combination of classic epidemiological methods, natural language processing (NLP), and machine learning (for predictive modeling), to analyse the electronic health records (EHRs) of patients with COVID-19.\n\nWe explored the unstructured free text in the EHRs within the SESCAM Healthcare Network (Castilla La-Mancha, Spain) from the entire population with available EHRs (1,364,924 patients) from January 1st to March 29th, 2020. We extracted related clinical information upon diagnosis, progression and outcome for all COVID-19 cases, focusing in those requiring ICU admission.\n\nA total of 10,504 patients with a clinical or PCR-confirmed diagnosis of COVID-19 were identified, 52.5% males, with age of 58.2{+/-}19.7 years. Upon admission, the most common symptoms were cough, fever, and dyspnoea, but all in less than half of cases. Overall, 6% of hospitalized patients required ICU admission. Using a machine-learning, data-driven algorithm we identified that a combination of age, fever, and tachypnoea was the most parsimonious predictor of ICU admission: those younger than 56 years, without tachypnoea, and temperature <39{degrees}C, (or >39{degrees}C without respiratory crackles), were free of ICU admission. On the contrary, COVID-19 patients aged 40 to 79 years were likely to be admitted to the ICU if they had tachypnoea and delayed their visit to the ER after being seen in primary care.\n\nOur results show that a combination of easily obtainable clinical variables (age, fever, and tachypnoea with/without respiratory crackles) predicts which COVID-19 patients require ICU admission.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jose Luis Izquierdo", + "author_inst": "Hospital Universitario de Guadalajara, Guadalajara, Spain" + }, + { + "author_name": "Julio Ancochea", + "author_inst": "Hospital Universitario de La Princesa, Madrid, Spain" + }, + { + "author_name": "- Savana COVID-19 Research Group", + "author_inst": "" + }, + { + "author_name": "Joan B Soriano", + "author_inst": "Hospital Universitario de La Princesa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.05.21.20108969", "rel_title": "ASSESSMENT OF WORKERS PERSONAL VULNERABILITY TO COVID-19 USING COVID-AGE", @@ -1436225,37 +1436637,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.05.22.20110700", - "rel_title": "Determinants of COVID-19 Vaccine Acceptance in the U.S.", - "rel_date": "2020-05-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110700", - "rel_abs": "BackgroundThe COVID-19 pandemic continues to adversely affect the U.S., which leads globally in total cases and deaths. As COVID-19 vaccines are under development, public health officials and policymakers need to create strategic vaccine-acceptance messaging to effectively control the pandemic and prevent thousands of additional deaths.\n\nMethodsUsing an online platform, we surveyed the U.S. adult population in May 2020 to understand risk perceptions about the COVID-19 pandemic, acceptance of a COVID-19 vaccine, and trust in sources of information. These factors were compared across basic demographics.\n\nFindingsOf the 672 participants surveyed, 450 (67%) said they would accept a COVID-19 vaccine if it is recommended for them. Males (72%), older adults ([≥]55 years; 78%), Asians (81%), and college and/or graduate degree holders (75%) were more likely to accept the vaccine. When comparing reported influenza vaccine uptake to reported acceptance of the COVID-19 vaccine: 1) participants who did not complete high school had a very low influenza vaccine uptake (10%), while 60% of the same group said they would accept the COVID-19 vaccine; 2) unemployed participants reported lower influenza uptake and lower COVID-19 vaccine acceptance when compared to those employed or retired; and, 3) black Americans reported lower influenza vaccine uptake and lower COVID-19 vaccine acceptance than nearly all other racial groups. Lastly, we identified geographic differences with Department of Health and Human Services regions 2 (New York) and 5 (Chicago) reporting less than 50 percent COVID-19 vaccine acceptance.\n\nInterpretationAlthough our study found a 67% acceptance of a COVID-19 vaccine, there were noticeable demographic and geographical disparities in vaccine acceptance. Before a COVID-19 vaccine is introduced to the U.S., public health officials and policymakers must prioritize effective COVID-19 vaccine-acceptance messaging for all Americans, especially those who are most vulnerable.\n\nFundingThe study was funded by the Yale Institute for Global Health.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Amyn A. Malik", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "SarahAnn M. McFadden", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Jad Elharake", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Saad B. Omer", - "author_inst": "Yale Institute for Global Health" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.22.20110627", "rel_title": "Predictors of misconceptions, knowledge, attitudes, and practices of COVID-19 pandemic among a sample of Saudi population and its impact: a cross-sectional study", @@ -1436435,6 +1436816,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.22.20110502", + "rel_title": "Conditions for a second wave of COVID-19 due to interactions between disease dynamics and social processes", + "rel_date": "2020-05-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110502", + "rel_abs": "In May 2020, many jurisdictions around the world began lifting physical distancing restrictions against the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), giving rise to concerns about a possible second wave of coronavirus disease 2019 (COVID-19). These restrictions were imposed as a collective population response to the presence of COVID-19 in communities. However, lifting restrictions is also a population response to their socio-economic impacts, and is expected to increase COVID-19 cases, in turn. This suggests that the COVID-19 pandemic exemplifies a coupled behaviour-disease system. Here we develop a minimal mathematical model of the interaction between social support for school and workplace closure and the transmission dynamics of SARS-CoV-2. We find that a second wave of COVID-19 occurs across a broad range of plausible model input parameters, on account of instabilities generated by behaviour-disease interactions. We conclude that second waves of COVID-19-should they materialize-can be interpreted as the outcomes of nonlinear interactions between disease dynamics and population behaviour.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sansao A Pedro", + "author_inst": "Universidade Eduardo Mondlane, Departamento de Matematica e Informatica, Maputo, Mozambique" + }, + { + "author_name": "Frank T Ndjomatchoua", + "author_inst": "International Rice Research Institute, Sustainable Impact Platform, Geospatial Science and Modelling cluster, DAPO Box 7777-1301, Metro Manila, Philippines" + }, + { + "author_name": "Peter Jentsch", + "author_inst": "University of Guelph, School of Environmental Sciences, Guelph, N1G 2W1, Canada and University of Waterloo, Department of Applied Mathematics, Waterloo, N2L 3G1" + }, + { + "author_name": "Jean M Tcheunche", + "author_inst": "Avenir Health, Glastonbury, CT, USA" + }, + { + "author_name": "Madhur Anand", + "author_inst": "University of Guelph, School of Environmental Sciences, Guelph, N1G 2W1, Canada" + }, + { + "author_name": "Chris T Bauch", + "author_inst": "University of Waterloo, Department of Applied Mathematics, Waterloo, N2L 3G1, Canada" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.22.20110551", "rel_title": "Anti-SARS-CoV-2 IgG antibodies are associated with reduced viral load", @@ -1437367,113 +1437787,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.21.108308", - "rel_title": "Systemic and mucosal antibody secretion specific to SARS-CoV-2 during mild versus severe COVID-19", - "rel_date": "2020-05-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.108308", - "rel_abs": "BackgroundInfection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes an acute illness termed coronavirus disease 2019 (COVID-19). Humoral immune responses likely play an important role in containing SARS-CoV-2, however, the determinants of SARS-CoV-2-specific antibody responses are unclear.\n\nMethodsUsing immunoassays specific for the SARS-CoV-2 spike protein, we determined SARS-CoV-2-specific immunoglobulin A (IgA) and immunoglobulin G (IgG) in sera and mucosal fluids of two cohorts, including patients with quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR)-confirmed SARS-CoV-2 infection (n = 56; median age 61 years) with mild versus severe COVID-19, and SARS-CoV-2-exposed healthcare workers (n = 109; median age 36 years) with or without symptoms and tested negative or positive by RT-qPCR.\n\nFindingsOn average, SARS-CoV-2-specific serum IgA titers in mild COVID-19 cases became positive eight days after symptom onset and were often transient, whereas serum IgG levels remained negative or reached positive values 9-10 days after symptom onset. Conversely, patients with severe COVID-19 showed a highly significant increase of SARS-CoV-2-specific serum IgA and IgG titers as a function of duration since symptom onset, independent of patient age and comorbidities. Very high levels of SARS-CoV-2-specific serum IgA correlated with severe acute respiratory distress syndrome (ARDS). Interestingly, some of the SARS-CoV-2-exposed healthcare workers with negative SARS-CoV-2-specific IgA and IgG serum titers had detectable SARS-CoV-2-specific IgA antibodies in their nasal fluids and tears. Moreover, SARS-CoV-2-specific IgA levels in nasal fluids of these healthcare workers were inversely correlated with patient age.\n\nInterpretationThese data show that systemic IgA and IgG production against SARS-CoV-2 develops mainly in severe COVID-19, with very high IgA levels seen in patients with severe ARDS, whereas mild disease may be associated with transient serum titers of SARS-CoV-2-specific antibodies but stimulate mucosal SARS-CoV-2-specific IgA secretion. The findings suggest four grades of antibody responses dependent on COVID-19 severity.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Carlo Cervia", - "author_inst": "Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland" - }, - { - "author_name": "Jakob Nilsson", - "author_inst": "Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland" - }, - { - "author_name": "Yves Zurbuchen", - "author_inst": "Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland" - }, - { - "author_name": "Alan Valaperti", - "author_inst": "Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland" - }, - { - "author_name": "Jens Schreiner", - "author_inst": "Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland" - }, - { - "author_name": "Aline Wolfensberger", - "author_inst": "Department of Infectious Diseases and Hospital Epidemiology, USZ, Zurich, Switzerland" - }, - { - "author_name": "Miro E. Raeber", - "author_inst": "Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland" - }, - { - "author_name": "Sarah Adamo", - "author_inst": "Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland" - }, - { - "author_name": "Marc Emmenegger", - "author_inst": "Institute of Neuropathology, USZ, Zurich, Switzerland" - }, - { - "author_name": "Sara Hasler", - "author_inst": "Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland" - }, - { - "author_name": "Philipp P. Bosshard", - "author_inst": "Department of Dermatology, USZ, Zurich, Switzerland" - }, - { - "author_name": "Elena De Cecco", - "author_inst": "Institute of Neuropathology, USZ, Zurich, Switzerland" - }, - { - "author_name": "Esther Baechli", - "author_inst": "Clinic for Internal Medicine, Uster Hospital, Uster, Switzerland" - }, - { - "author_name": "Alain Rudiger", - "author_inst": "Department of Medicine, Limmattal Hospital, Schlieren, Switzerland" - }, - { - "author_name": "Melina Stuessi-Helbling", - "author_inst": "Clinic for Internal Medicine, City Hospital Triemli Zurich, Zurich, Switzerland" - }, - { - "author_name": "Lars C. Huber", - "author_inst": "Clinic for Internal Medicine, City Hospital Triemli Zurich, Zurich, Switzerland" - }, - { - "author_name": "Annelies S. Zinkernagel", - "author_inst": "Department of Infectious Diseases and Hospital Epidemiology, USZ, Zurich, Switzerland" - }, - { - "author_name": "Dominik J. Schaer", - "author_inst": "Department of Internal Medicine, USZ, Zurich, Switzerland" - }, - { - "author_name": "Adriano Aguzzi", - "author_inst": "Institute of Neuropathology, USZ, Zurich, Switzerland" - }, - { - "author_name": "Ulrike Held", - "author_inst": "Department of Biostatistics, at Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Zurich, Switzerland" - }, - { - "author_name": "Elsbeth Probst-Mueller", - "author_inst": "Department of Immunology, University Hospital Zurich (USZ), Zurich, Switzerland" - }, - { - "author_name": "Silvana K. Rampini", - "author_inst": "Department of Infectious Diseases and Hospital Epidemiology, USZ, Zurich, Switzerland" - }, - { - "author_name": "Onur Boyman", - "author_inst": "Department of Immunology, University Hospital Zurich (USZ), Gloriastrasse 23, 8091 Zurich, Switzerland; Faculty of Medicine, University of Zurich, Zurich, Switz" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.22.111187", "rel_title": "Age-related expression of SARS-CoV-2 priming protease TMPRSS2 in the developing lung", @@ -1437829,6 +1438142,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.23.107334", + "rel_title": "Lung epithelial stem cells express SARS-CoV-2 entry factors: implications for COVID-19", + "rel_date": "2020-05-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.23.107334", + "rel_abs": "SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2. Thus, stem cells can be potentially infected by SARS-CoV-2, which may lead to defects in regeneration capacity partially accounting for the severity of SARS-CoV-2 infection and its consequences.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anna A. Valyaeva", + "author_inst": "Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University" + }, + { + "author_name": "Anastasia A. Zharikova", + "author_inst": "Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University" + }, + { + "author_name": "Artem S. Kasianov", + "author_inst": "The Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute)" + }, + { + "author_name": "Yegor S. Vassetzky", + "author_inst": "CNRS, UMR 9018, Universite Paris-Saclay, Institut Gustave Roussy" + }, + { + "author_name": "Eugene V. Sheval", + "author_inst": "Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2020.05.21.109322", "rel_title": "The emergence of SARS-CoV-2 in Europe and the US", @@ -1439173,29 +1439521,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.22.20109660", - "rel_title": "The effect of non-pharmaceutical interventions (NPIs) on the spread of COVID-19 pandemic in Japan: A modeling study", - "rel_date": "2020-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20109660", - "rel_abs": "Non-pharmaceutical interventions (NPIs) are founded to be effective to delay epidemic spread and to reduce the number of patients. Moderate NPIs took in Japan seemed to have reduced the COVID-19 patients and to lower death rates, thus, effects of those NPIs are worthy of investigation. We used open source data and divided the data into three periods: Jan 22 to Feb 25 (Period I), Feb 26 to Apr 6 (Period II), and Apr 7 to May 14 (Period III). We developed the SIRD model and applied the Monte Carlo Simulation to estimate a combination of optimal results, including the peak of infected cases, the peak date, and R0. For Period I, the estimated peak infected cases were smaller than the observed ones, the peak date was earlier than the observed one, and the R0 was about 4.66. For the other two periods, the estimated cases were more, and the peak dates were earlier than the observed ones. The R0 was 2.50 in Period II, and 1.79 in Period III. NPIs took in Japan might have reduced more than 50% of the daily contacts per people compared to that before COVID-19. Owing to the effects of NPIs, the Japanese society had avoided collapse of medical service. Nevertheless, the capacity of daily RT-PCR may have restricted the reported confirmed cases.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Yingying Sun", - "author_inst": "Institute for Disaster Management and Reconstruction, Sichuan University" - }, - { - "author_name": "Jikai Sun", - "author_inst": "Department of Architecture and Architectural Engineering, Kyoto University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.20.20108357", "rel_title": "Liver Function in Novel Coronavirus Disease (COVID-19): A Systematic Review and Meta-Analysis", @@ -1439443,6 +1439768,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.05.18.20105874", + "rel_title": "Early experiences with antibody testing in a Flemish nursing home during an acute COVID-19 outbreak: a retrospective cohort study.", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105874", + "rel_abs": "objectivesto assess the prevalence of COVID-19 (PCR-test) in residents and staff of a nursing home. To examine the presence of IgM and IgG antibodies in the sample and the relation between PCR and antibody test results.\n\ndesigncross-sectional and (retrospective) cohort study\n\nsettinga nursing home for the elderly Bessemerberg in Lanaken (Belgium) with up to 130 beds. Lanaken is situated in the Belgian province with the highest COVID-19 prevalence.\n\nparticipantsresidents (N=108) and staff members (N=93) of the nursing home\n\noutcomesPCR, IgM and IgG\n\nresultsthe prevalence of COVID-19, based on PCR test was 34% (N=40) for residents and 13% (N=11) for staff members, respectively. Of the residents, 13% showed positive IgM results and 15% positive IgG results. In 17% of the residents, at least one of the antibodies was positive. In total 13% of the staff members had positive IgM and 16% had a positive IgG. In 20% of the staff members at least one of these antibody tests was positive. In PCR positive residents, the percentage of IgM positive, IgG positive, and at least one of both was 28%, 34%, and 41%. In PCR positive staff, we found 30%, 60%, and 60%. Additional antibody tests were performed in nine residents between day 11 and 14 after the positive PCR test. Of those, 7 (78%) tested positive on at least one antibody. When retesting three weeks later, all remaining residents also tested positive.\n\nconclusionsRecently it was reported that in Belgium antibodies are present in 3-4% of the general population. Although, the prevalence in our residents is higher, the number is largely insufficient for herd immunity. In staff members of the regional hospital the prevalence of antibodies was 6%. The higher prevalence in nursing home staff (21%) may be related to the complete absence of good quality protection in the first weeks of the outbreak.\n\nArticle summaryO_LSTStrengths and limitations of this studyC_LST- This is the first study in Belgium examining the prevalence of COVID-19 and the presence of antibodies in residents and staff members of a nursing home\n- The internal procedural control was positive -with one exception- in all tests, which suggests good quality sampling and testing.\n- Some degree of selection bias should be assumed in residents, since some residents were absent; mostly from hospitalisation or death which can be related to the presence of COVID-related disease.\n- The study was set up in one nursing home and is consequently not representative for the whole of the Flemish community", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Frank Buntinx", + "author_inst": "University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium" + }, + { + "author_name": "Peter Claes", + "author_inst": "Woonzorgcentrum Bessemerberg, Lanaken, Belgium." + }, + { + "author_name": "Marjo Gulikers", + "author_inst": "Woonzorgcentrum Bessemerberg, Lanaken, Belgium." + }, + { + "author_name": "Jan Y Verbakel", + "author_inst": "University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium" + }, + { + "author_name": "Jan De Lepeleire", + "author_inst": "University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium" + }, + { + "author_name": "Michael Van der Elst", + "author_inst": "University of Leuven, Department of Public Health and Primary Care, Leuven, Belgium" + }, + { + "author_name": "Marc Van Ranst", + "author_inst": "University of Leuven, Laboratory of Clinical and Epidemiological Virology (Rega Institute), Leuven, Belgium" + }, + { + "author_name": "Pieter Vermeersch", + "author_inst": "Department of cardiovascular Sciences, KU Leuven, Leuven Belgium" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.18.20104703", "rel_title": "COVID-19 in China: Risk Factors and R0 Revisited", @@ -1440755,29 +1441127,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.05.21.108043", - "rel_title": "Open-source 3D printed Ventilation Device", - "rel_date": "2020-05-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.108043", - "rel_abs": "COVID-19 is an acute respiratory tract infection caused by a coronavirus known as SARS-CoV-2. The common signs of infection include respiratory symptoms such as shortness of breath, breathing difficulties, dry cough, fever, and in some patients, severe acute respiratory syndrome, kidney failure, and death. 312,009 deaths from COVID-19 has been reported as of today. While respiratory symptoms are commonly caused by the infection, the use of mechanical ventilation is required for some patients. The following is intended to review the development and testing of a 3D printed and open-source mechanical ventilation device that is capable of adjusting breathing rate, volume, and pressure simultaneously and was designed according to the latest clinical observations of the current pandemic. The intuitive design of this device along with the use of primarily 3D printed or readily available components allow the rapid manufacturing and transportation of this ventilation device to the impacted regions.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ahmad Faryami", - "author_inst": "Wayne State University" - }, - { - "author_name": "Carolyn A Harris", - "author_inst": "Wayne State University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.05.21.109637", "rel_title": "Electric-field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2", @@ -1441013,6 +1441362,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.21.109280", + "rel_title": "A previously uncharacterized gene in SARS-CoV-2 illuminates the functional dynamics and evolutionary origins of the COVID-19 pandemic", + "rel_date": "2020-05-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.109280", + "rel_abs": "Understanding the emergence of novel viruses requires an accurate and comprehensive annotation of their genomes. Overlapping genes (OLGs) are common in viruses and have been associated with pandemics, but are still widely overlooked. We identify and characterize ORF3d, a novel OLG in SARS-CoV-2 that is also present in Guangxi pangolin-CoVs but not other closely related pangolin-CoVs or bat-CoVs. We then document evidence of ORF3d translation, characterize its protein sequence, and conduct an evolutionary analysis at three levels: between taxa (21 members of Severe acute respiratory syndrome-related coronavirus), between human hosts (3978 SARS-CoV-2 consensus sequences), and within human hosts (401 deeply sequenced SARS-CoV-2 samples). ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients. However, it has been misclassified as the unrelated gene ORF3b, leading to confusion. Our results liken ORF3d to other accessory genes in emerging viruses and highlight the importance of OLGs.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Chase W. Nelson", + "author_inst": "American Museum of Natural History" + }, + { + "author_name": "Zachary Ardern", + "author_inst": "Chair for Microbial Ecology, Technical University of Munich, Freising, Germany" + }, + { + "author_name": "Tony L. Goldberg", + "author_inst": "Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI" + }, + { + "author_name": "Chen Meng", + "author_inst": "Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany" + }, + { + "author_name": "Chen-Hao Kuo", + "author_inst": "Biodiversity Research Center, Academia Sinica, Taipei, Taiwan" + }, + { + "author_name": "Christina Ludwig", + "author_inst": "Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Freising, Germany" + }, + { + "author_name": "Sergios-Orestis Kolokotronis", + "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, SUNY Downstate Health Sciences University, Brooklyn, NY" + }, + { + "author_name": "Xinzhu Wei", + "author_inst": "Departments of Integrative Biology and Statistics, University of California, Berkeley, CA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.05.21.109298", "rel_title": "Recombinant SARS-CoV-2 spike proteins for sero-surveillance and epitope mapping", @@ -1442237,29 +1442633,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.05.16.20104422", - "rel_title": "Contributions of Latin American researchers in the understanding the novel coronavirus outbreak: A literature review", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20104422", - "rel_abs": "This paper aimed to give the visibility of Latin American researchers contributions to the comprehension of COVID-19; our method was a literature review. Currently, the world is facing a health and socioeconomic crisis caused by the novel coronavirus, SARS-CoV-2, and its disease COVID-19. Therefore, in less than four months, researchers have published a significant number of articles related to this novel virus. For instance, a search focused on the Scopus database on April 10, 2020, showed 1224 documents published by authors with 1797 affiliations from 80 countries. 25.4%, 24.0%, and 12.6% of these national affiliations were from China, Europe, and the USA, respectively, making these regions leaders in COVID-19 research. In the case of Latin America, on April 10, 2020, we searched different databases, such as Scopus, PubMed, and Web of Science, finding that the contribution of this region was 2.7{+/-}0.6% of the total publications found. In other words, we found 153 publications related to COVID-19 with at least one Latin American researcher. We summarized and processed the information from these 153 publications, finding active participation in topics like medical, social, and environmental considerations, bioinformatics, and epidemiology.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Karen Y Fiesco-Sepulveda", - "author_inst": "Epidemiology Program, Faculty of Health Sciences, Universidad Surcolombiana, Neiva, Colombia." - }, - { - "author_name": "Luis Miguel Serrano-Bermudez", - "author_inst": "Bioprocesses and Bioprospecting Group, Universidad Nacional de Colombia, Bogota D.C., Colombia." - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.17.20104588", "rel_title": "COVID 19: Real-time Forecasts of Confirmed Cases, Active Cases, and Health Infrastructure Requirements for India and its Majorly Affected States using the ARIMA model.", @@ -1442711,6 +1443084,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.05.17.20104687", + "rel_title": "A DISSYMMETRY IN THE FIGURES RELATED TO THE COVID-19 PANDEMIC IN THE WORLD: WHAT FACTORS EXPLAIN THE DIFFERENCE BETWEEN AFRICA AND THE REST OF THE WORLD?", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104687", + "rel_abs": "Humanity has experienced outbreaks for millennia, from epidemics limited to pandemics that have claimed many victims and changed the course of civilizations. The advent of vaccines has eradicated some of the serious pathogens and reduced many others. However, pandemics are still part of our modern world, as we continue to have pandemics as devastating as HIV and as alarming as severe acute respiratory syndrome, Ebola and the Middle East respiratory syndrome. The Covid-19 epidemic with 0-exponential contamination curves reaching 3 million confirmed cases should not have come as a surprise, nor should it have been the last pandemic in the world. In this article, we try to summarize the lost opportunities as well as the lessons learned, hoping that we can do better in the future. The objective of this study is to relate the situation of Covid-19 in African countries with those of the countries most affected by the pandemic. It also allows us to verify how, according to the observed situation, the African ecosystem seems to be much more resilient compared to that of other continents where the number of deaths is in the thousands. To verify this, the diagnosed morbidity and mortality reported for different states of the world are compared to the ages of life and the average annual temperature of these states. The results show that the less dramatic balance of the African continent compared to other continents is partly linked to the relatively high temperatures on the continent but also to the relatively young character of its population.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Cheikh Faye Sr.", + "author_inst": "Assane Seck University of Ziguinchor" + }, + { + "author_name": "CheikhTidiane Wade Sr.", + "author_inst": "Assane Seck University of Ziguinchor" + }, + { + "author_name": "Ibrahima Demba Dione Sr.", + "author_inst": "Assane Seck University of Ziguinchor" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.20.20103200", "rel_title": "The Hybrid Forecasting Method SVR-ESAR forCovid-19", @@ -1443867,33 +1444267,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.18.20105528", - "rel_title": "Reproduction ratio and growth rates: measures for an unfolding pandemic", - "rel_date": "2020-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105528", - "rel_abs": "The initial exponential growth rate of an epidemic is an important measure that follows directly from data at hand, commonly used to infer the basic reproduction number. As the growth rates{lambda} (t) of tested positive COVID-19 cases have crossed the threshold in many countries, with negative numbers as surrogate for disease transmission deceleration, lockdowns lifting are linked to the behavior of the momentary reproduction numbers r(t), often called R0. Important to note that this concept alone can be easily misinterpreted as it is bound to many internal assumptions of the underlying model and significantly affected by the assumed recovery period. Here we present our experience, as part of the Basque Country Modeling Task Force (BMTF), in monitoring the development of the COVID-19 epidemic, by considering not only the behaviour of r(t) estimated for the new tested positive cases - significantly affected by the increased testing capacities, but also the momentary growth rates for hospitalizations, ICU admissions, deceased and recovered cases, in assisting the Basque Health Managers and the Basque Government during the lockdown lifting measures. Two different data sets, collected and then refined during the COVID-19 responses, are used as an exercise to estimate the momentary growth rates and reproducetion numbers over time in the Basque Country, and the implications of using those concepts to make decisions about easing lockdown and relaxing social distancing measures are discussed. These results are potentially helpful for task forces around the globe which are now struggling to provide real scientific advice for health managers and governments while the lockdown measures are relaxed.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Maira Aguiar", - "author_inst": "University of Trento, Italy; Basque Center for Applied Mathematics, Spain; Ikerbasque Foundation, Spain" - }, - { - "author_name": "Joseba Bidaurrazaga Van-Dierdonck", - "author_inst": "Public Health, Basque Health Departmen Rekalde Zumarkalea 39A - 48008, Bilbao, Spain" - }, - { - "author_name": "Nico Stollenwerk", - "author_inst": "Lisbon University, Portugal" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.18.20105411", "rel_title": "Dynamical model for social distancing in the U.S. during the COVID-19 epidemic", @@ -1444133,6 +1444506,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.17.20104968", + "rel_title": "Fuzzy Autocatalytic analysis of Covid-19 outbreak in Malaysia", + "rel_date": "2020-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104968", + "rel_abs": "The objective of this research is to demonstrate a mathematical technique to analyze the Covid-19 outbreak, particularly with respect to Malaysia. The technique is able to accommodate scarcity, quantity, and availability of the data set. The obtained results can offer descriptive insight for reflecting and strategizing actions in combating the pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Tahir Ahmad", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Azmirul Ashaari", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Siti Rahmah Awang", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Siti Salwana Mamat", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Wan Munirah Wan Mohamad", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Amirul Aizad Ahmad Fuad", + "author_inst": "Universiti Teknologi Malaysia" + }, + { + "author_name": "Nurfarhana Hassan", + "author_inst": "Universiti Teknologi Malaysia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.18.20105155", "rel_title": "The Dynamic Changes of Antibodies against SARS-CoV-2 during the Infection and Recovery of COVID-19", @@ -1445477,33 +1445893,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.19.20106914", - "rel_title": "The potential effect of the African population age structure on COVID-19 mortality", - "rel_date": "2020-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20106914", - "rel_abs": "Currently (mid May 2020), most active cases of COVID-19 are found in Europe and North America while it is still in the initial phases in Africa. As COVID-19 mortality occurs mainly in elderly and as Africa has a comparably young population, the death rates should be lower than on other continents.\n\nWe calculated standardised mortality ratios (SMR) using age-specific case fatality rates for COVID-19 and the age structure of the population of Africa and of other continents. Compared to a European or Northern American population, the standardised mortality ratio was only 0.22 and 0.25, respectively, corresponding to reduction of deaths rates to a quarter. Compared to the Asian and Latin American & Caribbean population, the SMR was 0.43 and 0.44, respectively, corresponding to half the death rate for Africa.\n\nIt is useful to quantify the isolated effect of the African age-structure on potential COVID-19 mortality for illustrative and communication purposes, keeping in mind the importance of public health measures that have been shown to be effective in reducing cases and deaths. The different aspect of age pyramids of a European and an African population are striking and the potential implications for the pandemic are often discussed but rarely quantified.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Fabrice Mougeni", - "author_inst": "Centre de Recherches Medicales de Lambarene (CERMEL), Gabon" - }, - { - "author_name": "Ance Mangaboula", - "author_inst": "Centre de Recherches Medicales de Lambarene (CERMEL), Gabon" - }, - { - "author_name": "Bertrand Lell", - "author_inst": "CERMEL and Department of Medicine I, Division of Infectious Diseases and Tropical Medicine, Medical University of Vienna, Vienna, Austria" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.18.20098863", "rel_title": "Changes in RT-PCR-positive SARS-CoV-2 rates in adults and children according to the epidemic stages", @@ -1445691,6 +1446080,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.18.20103283", + "rel_title": "Search for asymptomatic carriers of SARS-CoV-2 in healthcare workers during the pandemic: a Spanish experience", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20103283", + "rel_abs": "Objectivedetermine the percentage of healthcare workers (HCW) carrying SARS-CoV-2 in high exposure areas of the hospital.\n\nDesigncross-sectional study during April 15-24th in Hospital Costa del Sol (Marbella, Spain), excluding HCW with previous COVID19.\n\nSettinghospital based, focused on patient care areas COVID19.\n\nParticipants498 subjects, 80% women. Participation was offered to all the HCW of Emergencies, Intensive Care and Anesthesia, Internal Medicine and Pneumology. Other units not directly involved in the care of these patients were offered to participate.\n\nInterventionnaso and oropharyngeal PCR determination was performed together with IgG and IgM antibody determination by immunochromatography. On the day of sampling, a health questionnaire was answered, reporting symptoms on the same day and in the previous fourteen days.\n\nMain outcome measurespercentage of HCW with positive PCR for SARS-CoV-2, percentage of HCW with positive IgG for SARS-CoV-2.\n\nResultsTwo individuals were detected with PCR for SARS-CoV-2 positive (0.4%). Both were asymptomatic on the day of sampling, but one of them had had a CoVID-19 compatible picture in the previous two weeks and had positive IgG and IgM; therefore, only one subject was truly asymptomatic carrier (0.2%). 9 workers with positive IgG (1.8%) were detected.\n\nConclusionsthe prevalence of asymptomatic carriers among health workers of the services directly involved in the care of patients with CoVID-19 was very low in our center. This type of strategy can be one more tool in controlling the pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Julian Olalla", + "author_inst": "Unidad de Medicina Interna. Hospital Costa del Sol" + }, + { + "author_name": "Ana M Correa", + "author_inst": "Unidad de Microbiologia. Hospital Costa del Sol." + }, + { + "author_name": "Maria Dolores Martin-Escalante", + "author_inst": "Unidad de Medicina Interna. Hospital Costa del Sol." + }, + { + "author_name": "Maria Luisa Hortas", + "author_inst": "Area de Laboratorio. Hospital Costa del Sol." + }, + { + "author_name": "Maria Jesus Martin-Sendarrubias", + "author_inst": "Salud Laboral. Hospital Costa del Sol." + }, + { + "author_name": "Victor Fuentes", + "author_inst": "Medicina Preventiva. Hospital Costa del Sol." + }, + { + "author_name": "Gabriel Sena", + "author_inst": "Unidad de Microbiologia. Hospital Costa del Sol." + }, + { + "author_name": "Javier Garcia-Alegria", + "author_inst": "Unidad de Medicina Interna. Hospital Costa del Sol." + }, + { + "author_name": "ROBLE Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.15.20103531", "rel_title": "IL6 inhibition in critically ill COVID-19 patients is associated with increased secondary infections", @@ -1446627,41 +1447067,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.20.107052", - "rel_title": "Discovery of potent inhibitors of PLproCoV2 by screening libraries of selen-containing compounds", - "rel_date": "2020-05-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.20.107052", - "rel_abs": "A collection of twelve organoselenium compounds, structural analogues of antioxidant drug ebselen were screened for inhibition of the papain-like protease (PLpro) from the acute respiratory syndrome coronavirus 2 (SARS-CoV-2, CoV2). This cysteine protease, being responsible for the hydrolysis of peptide bonds between specific amino acids, plays a critical role in CoV2 replication and in assembly of new viral particles within human cells. The activity of the PLpro CoV2 is essential for the progression of coronavirus disease 2019 (COVID-19) and it constitutes a key target for the development of anti-COVID-19 drugs. Here, we identified four strong inhibitors that bind favorably to the PLpro CoV2 with the IC50 in the nanomolar range.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ewelina Weglarz-Tomczak", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Jakub M Tomczak", - "author_inst": "Vrije Universiteit Amsterdam" - }, - { - "author_name": "Miroslaw Giurg", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Malgorzata Burda-Grabowska", - "author_inst": "Wroclaw University of Science and Technology" - }, - { - "author_name": "Stanley Brul", - "author_inst": "University of Amsterdam" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.05.19.105437", "rel_title": "Type I and Type III IFN Restrict SARS-CoV-2 Infection of Human Airway Epithelial Cultures", @@ -1446969,6 +1447374,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.19.105445", + "rel_title": "Clinical And Analytical Performance Of An Automated Serological Test That Identifies S1/S2 Neutralizing IgG In Covid-19 Patients Semiquantitatively.", + "rel_date": "2020-05-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.19.105445", + "rel_abs": "BACKGROUNDIn the Covid-19 pandemic, highly selective serological testing is essential to define exposure to SARS-CoV-2 virus. Many tests have been developed, yet with variable speed to first result, and of unknown quality, particularly when considering the prediction of neutralizing capacity.\n\nOBJECTIVES/METHODSThe LIAISON(R) SARS-CoV-2 S1/S2 IgG assay was designed to measure antibodies against the SARS-CoV-2 native S1/S2 proteins in a standardized automated chemiluminescent assay. Clinical and analytical performance of the test were validated in an observational study using residual samples (>1500) with positive or negative Covid-19 diagnosis.\n\nRESULTSThe LIAISON(R) SARS-CoV-2 S1/S2 IgG assay proved highly selective and specific, and offers semiquantitative measures of serum or plasma levels of anti-S1/S2 IgG with neutralizing activity. The diagnostic sensitivity was 91.3% and 95.7% at >5 or [≥]15 days from diagnosis respectively, and 100% when assessed against a neutralizing assay. The specificity ranged between 97% and 98.5%. The average imprecision of the assay was <5 % coefficient of variation. Assay performance at 2 different cut-offs was evaluated to optimize predictive values in settings with different % disease prevalence. CONCLUSIONS. The automated LIAISON(R) SARS-CoV-2 S1/S2 IgG assay brings efficient, sensitive, specific, and precise serological testing to the laboratory, with the capacity to test large amounts of samples per day: first results are available within 35 minutes with a throughput of 170 tests/hour. The test also provides a semiquantitative measure to identify samples with neutralizing antibodies, useful also for a large scale screening of convalescent plasma for safe therapeutic use.\n\nIMPORTANCEWith the worldwide advance of the COVID-19 pandemic, efficient, reliable and accessible diagnostic tools are needed to support public health officials and healthcare providers in their efforts to deliver optimal medical care, and articulate sound demographic policy. DiaSorin has developed an automated serology based assay for the measurement of IgG specific to SARS CoV-2 Spike protein, and tested its clinical performance in collaboration with Italian health care professionals who provided access to large numbers of samples from infected and non-infected individuals. The assay delivers excellent sensitivity and specificity, and is able to identify samples with high levels of neutralizing antibodies. This will provide guidance in assessing the true immune status of subjects, as well as meeting the pressing need to screen donors for high titer convalescent sera for subsequent therapeutic and prophylactic use.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Fabrizio Bonelli", + "author_inst": "DiaSorin" + }, + { + "author_name": "Antonella Sarasini", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Claudia Zierold", + "author_inst": "DiaSorin" + }, + { + "author_name": "Mariella Calleri", + "author_inst": "DiaSorin" + }, + { + "author_name": "Alice Bonetti", + "author_inst": "Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Frank A Blocki", + "author_inst": "DiaSorin" + }, + { + "author_name": "Luca Pallavicini", + "author_inst": "DiaSorin" + }, + { + "author_name": "Alberto Chinali", + "author_inst": "DiaSorin" + }, + { + "author_name": "Daniela Campisi", + "author_inst": "ASST Niguarda Hospital" + }, + { + "author_name": "Elena Percivalle", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Anna Pia DiNapoli", + "author_inst": "Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Carlo Federico Perno", + "author_inst": "University of Milan" + }, + { + "author_name": "Fausto Balldanti", + "author_inst": "Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.05.20.105247", "rel_title": "A replication-competent vesicular stomatitis virus for studies of SARS-CoV-2 spike-mediated cell entry and its inhibition", @@ -1448173,37 +1448645,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.18.20082073", - "rel_title": "Early assessment of knowledge, attitudes, anxiety and behavioral adaptations of Connecticut residents to COVID-19", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20082073", - "rel_abs": "ObjectivesTo assess knowledge, attitudes, anxiety and behavioral adaptations to COVID-19.\n\nMethodsA cross-sectional study was conducted among non-healthcare-related participants after a stay-at-home directive was implemented. Multivariate logistic regression analysis was conducted to identify factors associated with anxiety, perceived seriousness of COVID-19 and loneliness.\n\nResultsA total of 464 participants responded to the survey. Most participants recognized cough, shortness of breath and fever as primary symptoms of COVID-19. Nearly 50% reported high levels of anxiety to COVID-19 and 48% reported being loneliness during the social isolation. Higher level of COVID-19 knowledge was associate with higher levels with anxiety. Being married had 1.79 times higher levels of anxiety about COVID-19. Women were less likely to report loneliness than men. Older age was associated with taking the pandemic seriously, and was also associated with loneliness during the social isolation.\n\nConclusionsIt is crucial for the public health authorities not only provide accurate and scientific information about the COVID-19 promoting protective behavior changes but also to minimize anxiety through supportive messages and recommendations for positive coping strategies and timely offering mental health counselling services for those in need.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Toan Ha", - "author_inst": "UConn School of Medicine" - }, - { - "author_name": "Stephen Schensul", - "author_inst": "Department of Public Health Sciences University of Connecticut School of Medicine" - }, - { - "author_name": "Judy Lewis", - "author_inst": "Department of Public Health Sciences University of Connecticut School of Medicine" - }, - { - "author_name": "Stacey Brown", - "author_inst": "Department of Public Health Sciences University of Connecticut School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.17.20082123", "rel_title": "Feasibility of non-invasive nitric oxide inhalation in acute hypoxic respiratory failure: potential role during the COVID-19 pandemic", @@ -1448359,6 +1448800,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.18.20101501", + "rel_title": "The impact of physical distancing measures against COVID-19 transmission on contacts and mixing patterns in the Netherlands: repeated cross-sectional surveys", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20101501", + "rel_abs": "BackgroundDuring the current pandemic of coronavirus (COVID-19) many countries have taken drastic measures to reduce transmission of SARS-CoV2. The measures often include physical distancing that aims to reduce the number of contacts in the population. Little is known about the actual reduction in number of contacts as a consequence of physical distancing measures.\n\nMethodsIn the Netherlands, a cross-sectional survey was carried out in 2016/2017 in which 8179 participants retrospectively reported the number, age and gender of different persons they had contacted (spoken to in person or touched) during the previous day. The survey was repeated among 2830 of the original participants, using the same questionnaire, in March and April 2020 after physical distancing measures had been implemented.\n\nResultsThe average number of contacts in the community was reduced from on average 12.5 (interquartile range: 2-17) to 3.7 (interquartile range: 0-4) different persons per participant, a reduction of 71% (95% confidence interval: 71-71). The reduction in the number of community contacts was highest for children and adolescents (between 5 and 20 years) and smallest for elderly persons of 80 years and older. The reduction in the effective number of total contacts, measured as the largest eigenvalue of the matrix with community and household contacts, was 62% (95% confidence interval: 48 - 72).\n\nConclusionThe substantial reduction in contacts has contributed greatly in halting the COVID-19 epidemic. This reduction was unevenly distributed over age groups, household sizes and occupations. These findings offer guidance for the lifting of age-group targeted measures.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jantien A. Backer", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Liesbeth Mollema", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Eric R. A. Vos", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Don Klinkenberg", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Fiona R.M. van der Klis", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Hester E. de Melker", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Susan van den Hof", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Jacco Wallinga", + "author_inst": "National Institute for Public Health and the Environment" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.15.20103077", "rel_title": "Mathematical Modeling and Simulation of SIR Model for COVID-2019 Epidemic Outbreak: A Case Study of India", @@ -1449431,49 +1449919,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.14.20102012", - "rel_title": "Mental health in the UK during the COVID-19 pandemic: early observations", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102012", - "rel_abs": "BackgroundPrevious pandemics have resulted in significant consequences for mental health. Here we report the mental health sequela of the COVID-19 pandemic on the UK population and examine modifiable and non-modifiable explanatory factors associated with mental health outcomes. We focus on the short-term consequences for mental health, as reported during the first four-six weeks of social distancing measures being introduced.\n\nMethodsA community cohort study was conducted with adults aged[≥]18 years recruited through a mainstream and social media campaign between 3/4/20-30/4/20. Consenting participants completed an online survey measuring depression, anxiety and stress and explanatory variables hypothesised to be related to these mental health outcomes.\n\nOutcomesN = 3097 eligible individuals participated. The cohort was predominantly female (85%); mean age forty-four years; 10% from minority ethnic groups; 50% described themselves as key-workers and 20% identified as having clinical risk factors putting them at increased risk of COVID-19. Mean scores for depression, stress and anxiety significantly exceeded population norms. Analysis of non-modifiable factors indicated that being younger and female were associated with all outcomes, with the final multivariable models accounting for 7-13% of variance. When adding modifiable factors, significant independent effects emerged for positive mood, perceived loneliness and worry about getting COVID-19 for all outcomes, with the final multivariable models accounting for 54-57% of variance.\n\nInterpretationIncreased psychological morbidity was evident in this UK cohort, with younger people and women at particular risk. Interventions targeting perceptions of: loneliness, risk of COVID-19, worry about COVID-19, and positive mood may be effective.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ru Jia", - "author_inst": "Division of Primary Care, University of Nottingham" - }, - { - "author_name": "Kieran Ayling", - "author_inst": "Division of Primary Care, University of Nottingham" - }, - { - "author_name": "Trudie Chalder", - "author_inst": "Department of Psychological Medicine, Institute of Psychiatry, Psychology & Neuroscience, King's College London" - }, - { - "author_name": "Adam Massey", - "author_inst": "Division of Primary Care, University of Nottingham" - }, - { - "author_name": "Elizabeth Broadbent", - "author_inst": "Department of Psychological Medicine, University of Auckland" - }, - { - "author_name": "Carol Coupland", - "author_inst": "Division of Primary Care, University of Nottingham" - }, - { - "author_name": "Kavita Vedhara", - "author_inst": "Division of Primary Care, University of Nottingham" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.14.20101998", "rel_title": "Obesity and COVID-19: The role of visceral adipose tissue", @@ -1449853,6 +1450298,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.13.20100495", + "rel_title": "Risk factors for adverse clinical outcomes in patients with COVID-19: A systematic review and meta-analysis", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100495", + "rel_abs": "ImportanceCOVID-19 is a clinically heterogeneous disease of varying severity and prognosis. Clinical characteristics that impact disease course could offer guidance for clinical decision making and future research endeavors and unveil disease pathways.\n\nObjectiveTo examine risk factors associated with adverse clinical outcomes in patients with COVID-19.\n\nData sourcesWe performed a systematic review in PubMed from January 1 until April 19, 2020.\n\nStudy selectionObservational studies that examined the association of any clinical characteristic with an adverse clinical outcome were considered eligible. We scrutinized studies for potential overlap.\n\nData extraction and synthesisInformation on the effect of clinical factors on clinical endpoints of patients with COVID-19 was independently extracted by two researchers. When an effect size was not reported, crude odds ratios were calculated based on the available information from the eligible articles. Study-specific effect sizes from non-overlapping studies were synthesized applying the random-effects model.\n\nMain outcome and measureThe examined outcomes were severity and progression of disease, admission to ICU, need for mechanical ventilation, mortality, or a composite outcome.\n\nResultsWe identified 88 eligible articles, and we performed a total of 256 meta-analyses on the association of 98 unique risk factors with five clinical outcomes. Seven meta-analyses presented the strongest epidemiological evidence in terms of statistical significance (P-value <0.005), between-study heterogeneity (I2 <50%), sample size (more than 1000 COVID-19 patients), 95% prediction interval excluded the null value, and absence of small-study effects. Elevated C-reactive protein (OR, 6.46; 95% CI, 4.85 - 8.60), decreased lymphocyte count (OR, 4.16; 95% CI, 3.17 - 5.45), cerebrovascular disease (OR, 2.84; 95% CI, 1.55 - 5.20), chronic obstructive pulmonary disease (OR, 4.44; 95% CI, 2.46 - 8.02), diabetes mellitus (OR, 2.04; 95% CI, 1.54 - 2.70), hemoptysis (OR, 7.03; 95% CI, 4.57 - 10.81), and male sex (OR, 1.51; 95% CI, 1.30 - 1.75) were associated with risk of severe COVID-19.\n\nConclusions and relevanceOur results highlight factors that could be useful for prognostic model building, help guide patients selection for randomized clinical trials, as well as provide alternative treatment targets by shedding light to disease pathophysiology.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vanesa Bellou", + "author_inst": "University of Ioannina Medical School" + }, + { + "author_name": "Ioanna Tzoulaki", + "author_inst": "University of Ioannina Medical School" + }, + { + "author_name": "Evangelos Evangelou", + "author_inst": "University of Ioannina Medical School" + }, + { + "author_name": "Lazaros Belbasis", + "author_inst": "University of Ioannina Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.13.20100404", "rel_title": "Clinical characteristics and early outcomes in patients with COVID-19 treated with tocilizumab at a United States academic center", @@ -1450793,61 +1451269,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.14.20101584", - "rel_title": "Risk factors for hospital admission related to COVID-19 in inflammatory rheumatic diseases", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101584", - "rel_abs": "OBJECTIVESTo describe patients with inflammatory rheumatic diseases (IRD) who had COVID-19; to compare patients who need hospital admission versus those that did not and assess risk factors of hospital admission related to COVID-19.\n\nMETHODSWe performed a prospective observational study, from 1st March 2020until the 24th of April. All patients being attended at the rheumatology outpatient clinic of a tertiary hospital of Madrid, with medical diagnosis of inflammatory rheumatic disease, and with symptomatic COVID-19 disease were included. Main variable was the hospital admission related to COVID-19. Covariates: sociodemographic, clinical and treatments. We performed a multivariate logistic regression model to assess risk factors of hospital admission.\n\nRESULTS123 patients with IRD and COVID-19 disease were identified and included. We found\n\n54 patients that need hospital admission, 59.2% were women, with a mean age at hospital admission of 69.7 (15.7) years, and a median lag time from symptoms onset to hospital admission of 5 (3-10) days. The median length of stay was 9 (6-14) days. A total of 12 patients died (22%) during their hospital admission. Factors independently associated with hospital admission were being older (OR 1.08; p = 0.00), and type of diagnosis (OR 3.55; p = 0.01), compared to those who were ambulatory. DMARDs dropped from the model. Male sex, associated comorbidities and glucocorticoids use showed a tendency risk (p<0.2)\n\nCONCLUSIONOur results suggests that age, comorbidities and having an autoimmune systemic condition increased the risk of hospital admission, whereas disease modifying agents were not associated with hospital admission.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Dalifer Freites", - "author_inst": "Hospital Clinico San Carlos, IdISSC, Madrid, Spain" - }, - { - "author_name": "Leticia Leon", - "author_inst": "IdISSC Hospital Clinico San Carlos" - }, - { - "author_name": "Arkaitz Mucientes", - "author_inst": "Hospital Clinico San Carlos, IdISSC, Madrid, Spain" - }, - { - "author_name": "Luis Rodriguez-Rodriguez", - "author_inst": "Hospital Clinico San Carlos, IdISCC, Madrid, Spain" - }, - { - "author_name": "Judit Font", - "author_inst": "Hospital Clinico San Carlos, IdISSC, Madrid, Spain" - }, - { - "author_name": "Alfredo Madrid", - "author_inst": "Hospital Clinico San Carlos, IdISSC, Madrid, Spain" - }, - { - "author_name": "Jose Ignacio Colomer", - "author_inst": "Hospital Clinico San Carlos, IdISSC, Madrid, Spain" - }, - { - "author_name": "Juan Angel Jover", - "author_inst": "Universidad Complutense de Madrid, Spain" - }, - { - "author_name": "Benjamin Fernandez-Gutierrez", - "author_inst": "Hospital Clinico San Carlos, Madrid, Spain" - }, - { - "author_name": "Lydia Abasolo", - "author_inst": "Hospital Clinico San Carlos, IdISSC, Madrid, Spain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.13.20101329", "rel_title": "Empiric model for short-time prediction of COVID-19spreading", @@ -1451015,6 +1451436,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.14.20101824", + "rel_title": "Changing travel patterns in China during the early stages of the COVID-19 pandemic", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101824", + "rel_abs": "Understanding changes in human mobility in the early stages of the COVID-19 pandemic is crucial for assessing the impacts of travel restrictions designed to reduce disease spread. Here, relying on data from mainland China, we investigated the spatio-temporal characteristics of human mobility between 1st January and 1st March 2020 and discussed their public health implications. An outbound travel surge from Wuhan before travel restrictions were implemented was also observed across China due to the Lunar New Year, indicating that holiday travel may have played a larger role in mobility changes compared to impending travel restrictions. Holiday travel also shifted healthcare pressure related to COVID-19 towards locations with lower access to care. Network analyses showed no sign of major changes in the transportation network after Lunar New Year. Changes observed were temporary and have not yet led to structural reorganisation of the transportation network at the time of this study.\n\nOne sentence summaryUnderstanding travel before, during, and after the introduction of travel restrictions in China in response to the COVID-19 Pandemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Hamish Gibbs", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Yang Liu", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Carl AB Pearson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Christopher I Jarvis", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Chris Grundy", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Billy J Quilty", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Charlie Diamond", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.14.20101873", "rel_title": "COVID Faster R-CNN: A Novel Framework to Diagnose Novel Coronavirus Disease (COVID-19) in X-Ray Images", @@ -1452267,97 +1452735,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.15.20084293", - "rel_title": "Clinical evaluation of IFN beta1b in COVID-19 pneumonia: a retrospective study", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20084293", - "rel_abs": "BackgroundCOVID-19 pneumonia is associated with significant mortality and has no approved antiviral therapy. Interferon beta1 has shown in vitro studies a potent inhibition of SARS-CoV and MERS-CoV. In an in vitro study, SARS-CoV-2 had more sensitivity to IFN-I pretreatment that SARS-CoV. A combination of IFN beta1b administered subcutaneously with other antiviral treatments has been recommended in several guidelines. However, clinical trial results for the treatment of COVID-19 are pending. We aimed to assess the efficiency of IFN beta1b in COVID19 comparing the in-hospital mortality between patients who received IFN beta1b and patients did not receive.\n\nMethodsIn this retrospective cohort study, we included hospitalized adults with COVID-19 between February 23th and April 4th, 2020, at the Central Defense Hospital (Madrid, Spain). Subcutaneous interferon beta-1b was recommended in moderate-severe pneumonia. The primary endpoint was in-hospital mortality. Univariate and multivariate analysis was performed to identify variables associated with in-hospital mortality.\n\nFindingsWe analyzed 256 patients (106 patients in interferon group and 150 patients in control group). At admission, patients who did not receive interferon beta1b presented a greater number of comorbidities. The overall mortality rate was 24.6% (63/256). Twenty-two patients (20.8%) in the interferon group died and 41 (27.3%) in the control group (p=0.229). In the multivariate analysis, the predictors of in-hospital mortality were age, severity of clinical picture at admission and hydroxychloroquine treatment.\n\nInterpretationIn hospitalized patients with COVID-19, interferon beta1b treatment was not associated to decrease in-hospital mortality. Further assessment of the earlier administration of this drug in randomized trials is recommended.\n\nFundingnone.\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSWe searched Pubmed on April 27th, 2020, for articles evaluating the efficacy of interferon beta in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), using the terms: \"interferon beta and (COVID-19 or SARS-CoV-2)\". We only found 5 articles. Of them, there was only one original article in English, which was a descriptive study of a case series with solid organ transplant from Spain.\n\nAdded value of this studyThis is the first article that reports the efficacy of interferon beta1b in the treatment of patients with COVID-19. We compared the in-hospital mortality between patients who received interferon beta1b and patients who did not. Patients in both groups received other drugs with a potential antiviral and immunomodulatory effect. There was no significant difference in in-hospital mortality between both groups.\n\nImplications of all the available evidenceIn our retrospective cohort, treatment with interferon beta1b had not impact on in-hospital survival, however it would be of clinical interest to evaluate the effect of early administration of this drug in the control of SARS-CoV-2 infection in larger randomized clinical trials.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Miriam Estebanez", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "German Ramirez-Olivencia", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Tatiana Mata", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "David Marti", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Carlos Gutierrez", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Begona De Dios", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Maria Dolores Herrero", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Ana Roel", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Yolanda Martinez", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Alejandro Aguirre", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Francisco Alcantara Nicolas", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Pablo Fernandez Gonzalez", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Elena Lopez", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Lucia E Ballester", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Maria Mateo-Maestre", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Sergio Campos", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Maria J Sanchez-Carrillo", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Antonio Fe", - "author_inst": "Gomez Ulla Hospital" - }, - { - "author_name": "Francisco J Membrillo de Novales", - "author_inst": "Gomez Ulla Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.17.20105049", "rel_title": "Risk interactions of coronavirus infection across age groups after the peak of COVID-19 epidemic", @@ -1452693,6 +1453070,97 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.18.101493", + "rel_title": "SARS-CoV2 infection in farmed mink, Netherlands, April 2020", + "rel_date": "2020-05-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.18.101493", + "rel_abs": "In April 2020, respiratory disease and increased mortality were observed in farmed mink on two farms in the Netherlands. In both farms, at least one worker had been found positive for SARS-CoV-2. Necropsies of the mink revealed interstitial pneumonia, and organ and swab samples tested positive for SARS-CoV-2 RNA by qPCR. Variations in viral genomes point at between-mink transmission on the farms and lack of infection link between the farms. Inhalable dust in the mink houses contained viral RNA, indicating possible exposure of workers.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Nadia Oreshkova", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Robert-Jan Molenaar", + "author_inst": "GD Animal Health, Deventer, The Netherlands" + }, + { + "author_name": "Sandra Vreman", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Frank Harders", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands WBVR" + }, + { + "author_name": "Bas B. Oude Munnink", + "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Renate W. Hakze-vd Honing", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Nora Gerhards", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Paulien Tolsma", + "author_inst": "Regional Public Health Service Brabant-Zuid-Oost, Eindhoven, The Netherlands" + }, + { + "author_name": "Ruth Bouwstra", + "author_inst": "GD Animal Health, Deventer, The Netherlands" + }, + { + "author_name": "Reina Sikkema", + "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Mirriam Tacken", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Myrna M.T. de Rooij", + "author_inst": "Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands" + }, + { + "author_name": "Eefke Weesendorp", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Marc Engelsma", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "Christianne Bruschke", + "author_inst": "Ministry of Agriculture, Nature and Food Quality, The Hague, The Netherlands" + }, + { + "author_name": "Lidwien A.M. Smit", + "author_inst": "Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands" + }, + { + "author_name": "Marion Koopmans", + "author_inst": "Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands" + }, + { + "author_name": "Wim H.M. van der Poel", + "author_inst": "Wageningen Bioveterinary Research, Wageningen University and Research, Lelystad, The Netherlands" + }, + { + "author_name": "JA Stegeman", + "author_inst": "Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, The Netherlands" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.18.102038", "rel_title": "Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2.", @@ -1454193,37 +1454661,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.12.20095562", - "rel_title": "The impact of testing and infection prevention and control strategies on within-hospital transmission dynamics of COVID-19 in English hospitals", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20095562", - "rel_abs": "Nosocomial transmission of SARS-CoV-2 is a key concern and evaluating the effect of testing and infection prevention control strategies is essential for guiding policy in this area. Using a within-hospital SEIR transition model of SARS-CoV-2 in a typical UK hospital, we predict that approximately 20% of infections in inpatients, and 89% of infections in HCWs were due to nosocomial transmission. Placing suspected COVID-19 patients in single rooms or bays has the potential to reduce hospital-acquired infections in patients by up to 80%. Periodic testing of HCWs has a smaller effect on the patient-burden of COVID-19 but would considerably reduce infection in HCWs by as much as 64% and result in only a small proportion of staff absences (approximately 1% per day). This is considerably fewer than currently observed due to suspected COVID-19 and self-isolation.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Stephanie Evans", - "author_inst": "Public Health England" - }, - { - "author_name": "Emily Agnew", - "author_inst": "Public Health England" - }, - { - "author_name": "Emilia Vynnycky", - "author_inst": "Public Health England" - }, - { - "author_name": "Julie V Robotham", - "author_inst": "Public Health England" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.09.20096701", "rel_title": "Report 21: Estimating COVID-19 cases and reproduction number in Brazil", @@ -1454643,6 +1455080,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.14.20096602", + "rel_title": "Decline in Emergent and Urgent Care during the COVID-19 Pandemic", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20096602", + "rel_abs": "Due to the ongoing coronavirus disease (COVID-19) pandemic, there are concerns that patients may be avoiding care for emergent and urgent health conditions due to fear of contagion or as an unintentional consequence of government orders to postpone \"non-essential\" services. We therefore sought to evaluate the effect of the COVID-19 pandemic on the number of patient encounters for select emergent or urgent diagnoses at a large tertiary-care academic medical center in Boston. Inpatient diagnoses included acute myocardial infarction (MI) and stroke, and outpatient but urgent diagnoses included new referrals for breast and hematologic malignancies. For each condition, we used a \"difference-in-differences\" approach to estimate the proportional change in number of encounters during the pandemic (March - April 2020) compared with earlier in the same year (January - February 2020), using equivalent periods in 2019 as a control. After the onset of the pandemic, we observed significant reductions in hospitalizations for MI (difference-in-differences estimate, 0.67; 95%CI, 0.46-0.96; P=0.04) and stroke (difference-in-differences estimate, 0.42; 95%CI, 0.28-0.65; P<0.001) (Table). In the ambulatory setting, there was a reduction in referrals for breast cancer and hematologic cancers, but this did not reach statistical significance until the month after the onset of the pandemic. Our findings suggest an urgent need for public health messaging to ensure that patients continue to seek care for acute emergencies. In addition, decisions by health systems regarding when to reinitiate non-emergent care should carefully factor in the harms of delayed diagnosis and treatment occurring during the COVID-19 pandemic.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Dhruv S Kazi", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Rishi K Wadhera", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Changyu Shen", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Kalon K.L. Ho", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Rushad Patell", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Magdy H. Selim", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "John H. Urwin", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Mark L. Zeidel", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Peter Zimetbaum", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + }, + { + "author_name": "Kevin Tabb", + "author_inst": "Beth Israel Lahey Health, Cambridge, MA" + }, + { + "author_name": "Robert W. Yeh", + "author_inst": "Beth Israel Deaconess Medical Center, Boston, MA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.05.11.20098053", "rel_title": "Parasites and their protection against COVID-19- Ecology or Immunology?", @@ -1455635,29 +1456131,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.15.20102764", - "rel_title": "Impact of relaxing Covid-19 social distancing measures on rural North Wales: a simulation analysis", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20102764", - "rel_abs": "BackgroundSocial distancing policies aimed to limit Covid-19 are gradually being relaxed as nationally reported peaks in incident cases are passed. Population density is an important driver of national incidence rates; however peak incidences in rural regions may lag national figures by several weeks. We aimed to forecast the impact of relaxed social distancing rules on rural North Wales.\n\nMethodsDaily data on the deaths of people with a positive test for Covid-19 were obtained from Public Health Wales and the UK Government. Sigmoidal growth functions were fitted by non-linear least squares and model averaging used to extrapolate mortality over time. The dates of peak mortality incidences for North Wales, Wales and the UK; and the percentage predicted maximum mortality (as of 7th May 2020) were estimated.\n\nResultsThe peak daily death rates in Wales and the UK were estimated to have occurred on the 14/04/2020 and 15/04/2020, respectively. For North Wales, this occurred on the 07/05/2020, corresponding to the date of analysis. The number of deaths reported in North Wales represents 31% of the predicted total cumulative number, compared with 71% and 60% for Wales and the UK, respectively.\n\nConclusionPolicies governing the movement of people in the gradual release from lockdown are likely to impact significantly on areas -principally rural in nature- where cases of Covid-19, deaths and immunity are likely to be much lower than in populated areas. This is particularly difficult to manage across jurisdictions, such as between England and Wales, and in popular holiday destinations.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rhodri P Hughes", - "author_inst": "Ysgol Glan Clwyd" - }, - { - "author_name": "Dyfrig A Hughes", - "author_inst": "Bangor University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.14.20102343", "rel_title": "Is it Just About Physical Health? An Internet-Based Cross-Sectional Study Exploring the Psychological Impacts of COVID-19 Pandemic on University Students in Jordan Using Kessler Psychological Distress Scale", @@ -1455845,6 +1456318,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2020.05.11.20098392", + "rel_title": "Forecasting Covid-19 dynamics in Brazil: a data driven approach", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098392", + "rel_abs": "This paper has a twofold contribution. The first is a data driven approach for predicting the Covid-19 pandemic dynamics, based on data from more advanced countries. The second is to report and discuss the results obtained with this approach for Brazilian states, as of May 4th, 2020. We start by presenting preliminary results obtained by training an LSTM-SAE network, which are somewhat disappointing. Then, our main approach consists in an initial clustering of the world regions for which data is available and where the pandemic is at an advanced stage, based on a set of manually engineered features representing a countrys response to the early spread of the pandemic. A Modified Auto-Encoder network is then trained from these clusters and learns to predict future data for Brazilian states. These predictions are used to estimate important statistics about the disease, such as peaks. Finally, curve fitting is carried out on the predictions in order to find the distribution that best fits the outputs of the MAE, and to refine the estimates of the peaks of the pandemic. Results indicate that the pandemic is still growing in Brazil, with most states peaks of infection estimated between the 25th of April and the 19th of May 2020. Predicted numbers reach a total of 240 thousand infected Brazilians, distributed among the different states, with Sao Paulo leading with almost 65 thousand estimated, confirmed cases. The estimated end of the pandemics (with 97% of cases reaching an outcome) starts as of May 28th for some states and rests through August 14th, 2020.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Igor Gadelha Pereira", + "author_inst": "Universidade Federal do Rio Grande do Norte" + }, + { + "author_name": "Joris M Guerin", + "author_inst": "Universidade Federal do Rio Grande do Norte" + }, + { + "author_name": "Andouglas Goncalves Silva Jr.", + "author_inst": "Instituto Federal do Rio Grande do Norte" + }, + { + "author_name": "Cosimo Distante", + "author_inst": "CNR" + }, + { + "author_name": "Gabriel Santos Garcia", + "author_inst": "Universidade de Brasilia" + }, + { + "author_name": "Luiz M.G. Goncalves", + "author_inst": "Universidade Federal do Rio Grande do Norte" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.11.20098459", "rel_title": "Distinct systems serology features in children, elderly and COVID patients", @@ -1456901,29 +1457413,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.11.20098780", - "rel_title": "Estimating the Global Infection Fatality Rate of COVID-19", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098780", - "rel_abs": "COVID-19 has become a global pandemic, resulting in nearly three hundred thousand deaths distributed heterogeneously across countries. Estimating the infection fatality rate (IFR) has been elusive due to the presence of asymptomatic or mildly symptomatic infections and lack of testing capacity. We analyze global data to derive the IFR of COVID-19. Estimates of COVID-19 IFR in each country or locality differ due to variable sampling regimes, demographics, and healthcare resources. We present a novel statistical approach based on sampling effort and the reported case fatality rate of each country. The asymptote of this function gives the global IFR. Applying this asymptotic estimator to cumulative COVID-19 data from 139 countries reveals a global IFR of 1.04% (CI: 0.77%,1.38%). Deviation of countries reported CFR from the estimator does not correlate with demography or per capita GDP, suggesting variation is due to differing testing regimes or reporting guidelines by country. Estimates of IFR through seroprevalence studies and point estimates from case studies or sub-sampled populations are limited by sample coverage and cannot inform a global IFR, as mortality is known to vary dramatically by age and treatment availability. Our estimated IFR aligns with many previous estimates and is the first attempt at a global estimate of COVID-19 IFR.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Richard Grewelle", - "author_inst": "Stanford University" - }, - { - "author_name": "Giulio De Leo", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.14.20102079", "rel_title": "Retrospective Pooled Screening for SARS-CoV-2 RNA in late 2019", @@ -1457143,6 +1457632,121 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.05.18.099507", + "rel_title": "Afucosylated immunoglobulin G responses are a hallmark of enveloped virus infections and show an exacerbated phenotype in COVID-19", + "rel_date": "2020-05-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.18.099507", + "rel_abs": "IgG antibodies are crucial for protection against invading pathogens. A highly conserved N-linked glycan within the IgG-Fc-tail, essential for IgG function, shows variable composition in humans. Afucosylated IgG variants are already used in anti-cancer therapeutic antibodies for their elevated binding and killing activity through Fc receptors (Fc{gamma}RIIIa). Here, we report that afucosylated IgG which are of minor abundance in humans ([~]6% of total IgG) are specifically formed against surface epitopes of enveloped viruses after natural infections or immunization with attenuated viruses, while protein subunit immunization does not elicit this low fucose response. This can give beneficial strong responses, but can also go awry, resulting in a cytokine-storm and immune-mediated pathologies. In the case of COVID-19, the critically ill show aggravated afucosylated-IgG responses against the viral spike protein. In contrast, those clearing the infection unaided show higher fucosylation levels of the anti-spike protein IgG. Our findings indicate antibody glycosylation as a potential factor in inflammation and protection in enveloped virus infections including COVID-19.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Mads D. Larsen", + "author_inst": "Sanquin Reseach" + }, + { + "author_name": "Erik L de Graaf", + "author_inst": "Sanquin Reseach" + }, + { + "author_name": "Myrthe E. Sonneveld", + "author_inst": "Sanquin Research" + }, + { + "author_name": "H. Rosina Plomp", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Federica Linty", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Remco Visser", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Maximilian Brinkhaus", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Tonci Sustic", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Steven W. deTaeye", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Arthur E.H. Bentlage", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Jan Nouta", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Suvi Natunen", + "author_inst": "Finnish Red Cross Blood Service" + }, + { + "author_name": "Carolien A.M. Koeleman", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Susanna Sainio", + "author_inst": "Finnish Red Cross Blood Service" + }, + { + "author_name": "Neeltje A. Kootstra", + "author_inst": "University of Amsterdam" + }, + { + "author_name": "Philip J.M. Brouwer", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Rogier W. Sanders", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Marit J. van Gils", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Sanne de Bruin", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Alexander P.J. Vlaar", + "author_inst": "Amsterdam University Medical Centers" + }, + { + "author_name": "Amsterdam UMC COVID-19 biobank study group", + "author_inst": "" + }, + { + "author_name": "Hans L. Zaaijer", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Manfred Wuhrer", + "author_inst": "Leiden University Medical Center," + }, + { + "author_name": "C. Ellen van der Schoot", + "author_inst": "Sanquin Research" + }, + { + "author_name": "Gestur Vidarsson", + "author_inst": "Sanquin Research" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.05.12.20099085", "rel_title": "Understanding the indoor pre-symptomatic transmission mechanism of COVID-19", @@ -1458163,37 +1458767,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.12.20100040", - "rel_title": "A municipality-based approach using commuting census data to characterise the vulnerability to influenza-like epidemic: the COVID-19 application in Italy.", - "rel_date": "2020-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20100040", - "rel_abs": "In February 2020, Italy became the epicentre for COVID-19 in Europe and at the beginning of March, in response to the growing epidemic, the Italian Government put in place emergency measures to restrict the movement of the population. Human mobility represents a crucial element to be considered in modelling human infectious diseases.\n\nIn this paper, we examined the mechanisms underlying COVID-19 propagation using a Susceptible-Infected stochastic model (SI) driven mainly by commuting network in Italy. We modelled a municipality-specific contact rate to capture the disease permeability of each municipality, considering the population at different times of the day and describing the characteristic of the municipalities as attractors of commuters or places that make their workforce available elsewhere.\n\nThe purpose of our analysis is to provide a better understanding of the epidemiological context of COVID-19 in Italy and to characterize the territory in terms of vulnerability at local or national level. The use of data at such a high spatial resolution allows highlighting particular situations on which the health authorities can promptly intervene to control the disease spread.\n\nOur approach provides decision-makers with useful geographically detailed metrics to evaluate those areas at major risk for infection spreading and for which restrictions of human mobility would give the greatest benefits, not only in the beginning of the epidemic but also in the last phase, when the risks deriving from the gradual lockdown exit strategies must be carefully evaluated.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Lara Savini", - "author_inst": "Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise \u201cG. Caporale\u201d, Teramo, Italy" - }, - { - "author_name": "Luca Candeloro", - "author_inst": "Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise \u201cG. Caporale\u201d, Teramo, Italy" - }, - { - "author_name": "Paolo Calistri", - "author_inst": "Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise \u201cG. Caporale\u201d, Teramo, Italy" - }, - { - "author_name": "Annamaria Conte", - "author_inst": "Istituto Zooprofilattico Sperimentale dell'Abruzzo e Molise \"\u201cG. Caporale\u201d, Teramo, Italy" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.13.20100545", "rel_title": "Forecasting undetected COVID-19 cases in Small Island Developing States using Bayesian approach", @@ -1458337,6 +1458910,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.14.20102483", + "rel_title": "Early and massive testing saves lives: COVID-19 related infections and deaths in the United States during March of 2020", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102483", + "rel_abs": "To optimize epidemiologic interventions, predictors of mortality should be identified. The US COVID-19 epidemic data -reported up to 3-31-2020- were analyzed using kernel regularized least squares regression. Six potential predictors of mortality were investigated: (i) the number of diagnostic tests performed in testing week I; (ii) the proportion of all tests conducted during week I of testing; (iii) the cumulative number of (test-positive) cases through 3-31-2020, (iv) the number of tests performed/million citizens; (v) the cumulative number of citizens tested; and (vi) the apparent prevalence rate, defined as the number of cases/million citizens. Two metrics estimated mortality: the number of deaths and the number of deaths/million citizens. While both expressions of mortality were predicted by the case count and the apparent prevalence rate, the number of deaths/million citizens was {approx}3.5 times better predicted by the apparent prevalence rate than the number of cases. In eighteen states, early testing/million citizens/population density was inversely associated with the cumulative mortality reported by 31 March, 2020. Findings support the hypothesis that early and massive testing saves lives. Other factors -e.g., population density-may also influence outcomes. To optimize national and local policies, the creation and dissemination of high-resolution geo-referenced, epidemic data is recommended.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "James B. Hittner", + "author_inst": "Department of Psychology, College of Charleston, Charleston, South Carolina, United States of America" + }, + { + "author_name": "Folorunso O. Fasina", + "author_inst": "Food and Agriculture Organization, Dar es Salam, Tanzania" + }, + { + "author_name": "Almira L. Hoogesteijn", + "author_inst": "Human Ecology, Centro de Investigacion y de Estudios Avanzados (CINVESTAV), Merida, Mexico" + }, + { + "author_name": "Renata Piccinini", + "author_inst": "Department of Veterinary Medicine, University of Milan, Milan, Italy" + }, + { + "author_name": "Prakasha Kempaiah", + "author_inst": "Loyola University Chicaco Stritch School of Medicine, Chicago, USA" + }, + { + "author_name": "Stephen D. Smith", + "author_inst": "Institute for Resource Information Science, College of Agriculture, Cornell University, Ithaca, United States of America" + }, + { + "author_name": "Ariel L. Rivas", + "author_inst": "Center for Global Health, Department of Internal Medicine, Medical School, University of New Mexico, Albuquerque, New Mexico, United States of America" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.13.20099614", "rel_title": "Dynamic liver function indexes monitoring and clinical characteristics in three types of COVID-19 patients", @@ -1459373,45 +1459989,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.12.20099416", - "rel_title": "DERIVATION OF A SCORE TO PREDICT ADMISSION TO INTENSIVE CARE UNIT IN PATIENTS WITH COVID-19: THE ABC-GOALS SCORE", - "rel_date": "2020-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099416", - "rel_abs": "ObjectivesCOVID-19 pandemic poses a burden on hospital resources and intensive care unit (ICU) occupation. This study aimed to provide a scoring system that, assessed upon first-contact evaluation at the emergency department, predicts the need for ICU admission.\n\nMethodsWe prospectively assessed patients admitted to a COVID-19 reference center in Mexico City between March 16th and May 21st, and split them into development and validation cohorts. Patients were segregated into a group that required admission to ICU, and a group that never required ICU admission and was discharged from hospitalization. By logistic regression, we constructed predictive models for ICU admission, including clinical, laboratory, and imaging findings from the emergency department evaluation. The ABC-GOALS score was created by assigning values to the weighted odd ratios. The score was compared to other COVID-19 and pneumonia scores through the area under the curve (AUC).\n\nResultsWe included 569 patients divided into development (n=329) and validation (n=240) cohorts. One-hundred-fifteen patients from each cohort required admission to ICU. The clinical model (ABC-GOALSc) included sex, obesity, the Charlson comorbidity index, dyspnea, arterial pressure, and respiratory rate at triage evaluation. The clinical plus laboratory model (ABC-GOALScl) added serum albumin, glucose, lactate dehydrogenase, and S/F ratio to the clinical model. The model that included imaging (ABC-GOALSclx) added the CT scan finding of >50% lung involvement. The model AUC were 0.79 (95%CI 0.74-0.83) and 0.77 (95%CI 0.71-0.83), 0.86 (95%CI 0.82-0.90) and 0.87 (95%CI 0.83-0.92), 0.88 (95%CI 0.84-0.92) and 0.86 (95%CI 0.81-0.90) for the clinical, laboratory and imaging models in the development and validation cohorts, respectively. The ABC-GOALScl and ABC-GOALSclx scores outperformed other COVID-19 and pneumonia-specific scores.\n\nConclusionThe ABC-GOALS score is a tool to evaluate patients with COVID-19 at admission to the emergency department, which allows to timely predict their risk of admission to an ICU.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Juan M. Mejia-Vilet", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - }, - { - "author_name": "Bertha M. Cordova-Sanchez", - "author_inst": "Instituto Nacional de Cancerologia" - }, - { - "author_name": "Dheni Fernandez-Camargo", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - }, - { - "author_name": "R. Angelica Mendez-Perez", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - }, - { - "author_name": "Luis Eduardo Morales-Buenrostro", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - }, - { - "author_name": "Thierry Hernandez-Gilsoul", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.13.20100198", "rel_title": "Olfactory and Gustatory Dysfunction as An Early Identifier of COVID-19 in Adults and Children: An International Multicenter Study", @@ -1459735,6 +1460312,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.13.20100370", + "rel_title": "Derivation and validation of a prognostic model for predicting in-hospital mortality in patients admitted with COVID-19 in Wuhan, China: the PLANS (Platelet Lymphocyte Age Neutrophil Sex) model", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100370", + "rel_abs": "OBJECTIVETo develop and validate a prognostic model for in-hospital mortality in COVID-19 patients using routinely collected demographic and clinical characteristics.\n\nDESIGNMulticenter, retrospective cohort study.\n\nSETTINGJinyintan Hospital, Union Hospital, and Tongji Hosptial in Wuhan, China.\n\nPARTICIPANTSA pooled derivation cohort of 1008 COVID-19 patients from Jinyintan Hospital, Union Hospital in Wuhan and an external validation cohort of 1031 patients from Tongji Hospital in Wuhan, China.\n\nMAIN OUTCOME MEASURESOutcome of interest was in-hospital mortality, treating discharged alive from hospital as the competing event. Fine-Gray models, using backward elimination for inclusion of predictor variables and allowing non-linear effects of continuous variables, were used to derive a prognostic model for predicting in-hospital mortality among COVID-19 patients. Internal validation was implemented to check model overfitting using bootstrap approach. External validation to a separate hospital was implemented to evaluate the generalizability of the model.\n\nRESULTSThe derivation cohort was a case-mix of mild-to-severe hospitalized COVID-19 patients (n=1008, 43.6% females, median age 55). The final model (PLANS), including five predictor variables of platelet count, lymphocyte count, age, neutrophil count, and sex, had an excellent predictive performance (optimism-adjusted C-index: 0.85, 95% CI: 0.83 to 0.87; averaged calibration slope: 0.95, 95% CI: 0.82 to 1.08). Internal validation showed little overfitting. External validation using an independent cohort (n=1031, 47.8% female, median age 63) demonstrated excellent predictive performance (C-index: 0.87, 95% CI: 0.85 to 0.89; calibration slope: 1.02, 95% CI: 0.92 to 1.12). The averaged predicted survival curves were close to the observed survival curves across patients with different risk profiles.\n\nCONCLUSIONSThe PLANS model based on the five routinely collected demographic and clinical characteristics (platelet count, lymphocyte count, age, neutrophil count, and sex) showed excellent discriminative and calibration accuracy in predicting in-hospital mortality in COVID-19 patients. This prognostic model would assist clinicians in better triaging patients and allocating healthcare resources to reduce COVID-19 fatality.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jiong Li", + "author_inst": "Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine" + }, + { + "author_name": "Yuntao Chen", + "author_inst": "Department of Epidemiology, University Medical Center Groningen, Groningen, The Netherlands" + }, + { + "author_name": "Shujing Chen", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China" + }, + { + "author_name": "Sihua Wang", + "author_inst": "Department of Thoracic Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" + }, + { + "author_name": "Dingyu Zhang", + "author_inst": "Department of Tuberculosis and Respiratory Disease, Jinyintan Hospital, Wuhan, China" + }, + { + "author_name": "Junfeng Wang", + "author_inst": "Julius Center for Health Science and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands" + }, + { + "author_name": "Douwe Postmus", + "author_inst": "Department of Epidemiology, University Medical Center Groningen, Groningen, The Netherlands" + }, + { + "author_name": "Hesong Zeng", + "author_inst": "Department of Cardiology, Tongji Hospital, School of Medicine, Huazhong University of Science and Technology, Wuhan, China." + }, + { + "author_name": "Guoyou Qin", + "author_inst": "Department of Biostatistics, School of Public Health, and The Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China" + }, + { + "author_name": "Yin Shen", + "author_inst": "Eye Center, Medical Research Institute, Wuhan University Renmin Hospital, Wuhan University, Wuhan, China" + }, + { + "author_name": "Jinjun Jiang", + "author_inst": "Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, China" + }, + { + "author_name": "Yongfu Yu", + "author_inst": "Department of Biostatistics, School of Public Health, and The Key Laboratory of Public Health Safety of Ministry of Education, Fudan University, Shanghai, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.13.20101006", "rel_title": "Loss of Taste and Smell as Distinguishing Symptoms of COVID-19", @@ -1461011,49 +1461651,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.05.09.20096388", - "rel_title": "Behaviors and attitudes in response to the COVID-19 pandemic: Insights from a cross-national Facebook survey", - "rel_date": "2020-05-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096388", - "rel_abs": "In the absence of medical treatment and vaccination, individual behaviours are key to controlling the spread of COVID-19. We developed a rapid response monitoring system through an online survey (the \"COVID-19 Health Behavior Survey\"). Participant recruitment takes places continuously via Facebook in eight countries (Belgium, France, Germany, Italy, the Netherlands, Spain, the United Kingdom, the United States). The survey collects key information on peoples health, attitudes, behaviours, and social contacts. In this paper, we present results based on a total of 71,612 completed questionnaires, collected between March 13-April 19, 2020. We find sex-specific patterns, as women show higher threat perceptions, lower confidence in the healthcare system, and a higher likelihood of adopting preventive behaviours. Our findings also show higher awareness and concern among older respondents. Finally, we find spatio-temporal heterogeneity in threat perception, confidence in organisations, and adoption of preventive behaviours.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Daniela Perrotta", - "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" - }, - { - "author_name": "Andr\u00e9 Grow", - "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" - }, - { - "author_name": "Francesco Rampazzo", - "author_inst": "Centre for Population Change, University of Southampton, United Kingdom" - }, - { - "author_name": "Jorge Cimentada", - "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" - }, - { - "author_name": "Emanuele Del Fava", - "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" - }, - { - "author_name": "Sofia Gil-Clavel", - "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" - }, - { - "author_name": "Emilio Zagheni", - "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.10.20095844", "rel_title": "Anxiety, depression, attitudes, and internet addiction during the initial phase of the 2019 coronavirus disease (COVID-19) epidemic: A cross-sectional study in Mexico.", @@ -1461481,6 +1462078,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.11.20095158", + "rel_title": "SARS-CoV-2 antibody seroprevalence in industry workers in Split-Dalmatia and Sibenik-Knin County, Croatia", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20095158", + "rel_abs": "BACKGROUNDAs a result of global spread, COVID-19 has also affected the Republic of Croatia in the last week of February. Although official data show that the number of newly infected is declining, it is still unknown what proportion of the population has been affected by the disease.\n\nAIMTo examine seroprevalence of SARS-CoV-2 antibodies in industry workers population sample.\n\nMETHODSFrom 23 to 28 April 2020, we conducted serological testing for antibodies (IgG and IgM) on 1494 factory employees living in the Split-Dalmatia and [S]ibenik-Knin County (Croatia). We analysed antibody seroprevalence on the level of the company, county, and separately for employees living at the factory premises with limited mobility during the lockdown measures.\n\nRESULTSIn a total sample of tested company employees, we detected antibodies in 1.27% of participants (95% CI 0.77-1.98%). In Split facility 13/1316 (0.99%, 95% CI 0.53-1.68%) of participants were tested positive, of which 13/1079 (1.20%, 95% CI 0.64-2.05%) of those living outside the facility and 0/237 (0%, 95% CI 0-1.26%) of those living inside the facility. In Knin facility, 6/178 (3.37%, 95% CI 1.25-7.19%) participants were tested positive for antibodies. The difference between Split (no mobility restrictions) and Knin, was not statistically significant ({chi}2 = 3.47, P = 0.062).\n\nCONCLUSIONSThe study showed relatively small SARS-CoV-2 antibody seroprevalence in the DIV Group population sample. When the study findings are interpreted on the county levels, they could indicate that most of the counties population was not exposed to the virus.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ivan Jerkovic", + "author_inst": "University Department of Forensic Sciences University of Split" + }, + { + "author_name": "Toni Ljubic", + "author_inst": "University Department of Forensic Sciences University of Split" + }, + { + "author_name": "Zeljana Basic", + "author_inst": "University Department of Forensic Sciences" + }, + { + "author_name": "Ivana Kruzic", + "author_inst": "University Deparment ofForensic Sciences" + }, + { + "author_name": "Nenad Kunac", + "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Center Split" + }, + { + "author_name": "Josko Bezic", + "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Center Split" + }, + { + "author_name": "Arijana Vuko", + "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Center Split" + }, + { + "author_name": "Alemka Markotic", + "author_inst": "Dr. Fran Mihaljevic University Hospital for Infectious Diseases, Zagreb, Croatia; Catholic University of Croatia, Zagreb, Croatia; University of Rijeka School o" + }, + { + "author_name": "Simun Andjelinovic", + "author_inst": "Clinical Department for Pathology, Forensic Medicine and Cytology, University Hospital Center Split, Split, Croatia; University of Split, School of Medicine, Sp" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.10.20097543", "rel_title": "Estimating the extent of true asymptomatic COVID-19 and its potential for community transmission: systematic review and meta-analysis", @@ -1462656,85 +1463304,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.11.20096727", - "rel_title": "A one-year hospital-based prospective CVOID-19 open-cohort in the Eastern Mediterranean region: The Khorshid COVID Cohort (KCC) study", - "rel_date": "2020-05-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20096727", - "rel_abs": "The COVID-19 is rapidly scattering worldwide, and the number of cases in the Eastern Mediterranean Region is rising, there is a need for immediate targeted actions. We designed a longitudinal study in a hot outbreak zone to analyze the serial findings between infected patients for detecting temporal changes from February 2020. In a hospital-based open-cohort study, patients are followed from admission until one year from their discharge (the 1st, 4th, 12th weeks, and the first year). The measurements included demographic, socio-economics, symptoms, health service diagnosis and treatment, contact history, and psychological variables. The signs improvement, death, length of stay in hospital were considered as primary, and impaired pulmonary function and psychotic disorders were considered as main secondary outcomes. Notably, In the last two follow-ups, each patient attends the hospital to complete the Patient Health Questionnaire-9 (PHQ-9) and the Depression Anxiety Stress Scales (DASS-21). Moreover, clinical symptoms and respiratory functions are being determined in such follow-ups. Among the first 600 COVID-19 cases, a total of 490 patients with complete information (39% female; the average age of 57{+/-}15 years) were analyzed. Seven percent of these patients died. The three main leading causes of admission were: fever (77%), dry cough (73%), and fatigue (69%). The most prevalent comorbidities between COVID-19 patients were hypertension (35%), diabetes (28%), and ischemic heart disease (14%). The percentage of primary composite endpoints (PCEP), defined as death, the use of mechanical ventilation, or admission to an intensive care unit was 18%. The following comorbidities were significantly different in the positive and negative PCEP groups: acute kidney disease (p=0.008) and diabetes (p=0.026). For signs and symptoms, fatigue (p=0.020) and sore throat (p=0.001) were significantly different. This long-term prospective Cohort may support healthcare professionals in the management of resources following this pandemic.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Ramin Sami", - "author_inst": "Department of Internal Medicine, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Forogh Soltaninejad", - "author_inst": "The respiratory research center, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Babak Amra", - "author_inst": "Bamdad Respiratory research center, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Zohreh Naderi", - "author_inst": "Department of Pulmonology, University of Medical Science, Isfahan University, Isfahan, Iran" - }, - { - "author_name": "Shaghayegh Haghjooy Javanmard", - "author_inst": "Department of Physiology, School of Medicine, Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isf" - }, - { - "author_name": "Bijan Iraj", - "author_inst": "Isfahan Endocrine and Metabolism Research Center, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Somayeh Haji Ahmadi", - "author_inst": "Department of Radiology, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Azin Shayganfar", - "author_inst": "Department of Radiology, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Mehrnegar Dehghan", - "author_inst": "School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Nilufar Khademi", - "author_inst": "School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Nastaran Sadat Hosseini", - "author_inst": "School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Mojgan Mortazavi", - "author_inst": "Isfahan kidney diseases research center, Isfahan University of Medical Sciences, Isfahan, Iran" - }, - { - "author_name": "Marjan Mansourian", - "author_inst": "Universitat Politecnica de Catalunya-Barcelona Tech (UPC)" - }, - { - "author_name": "Miquel Angel Mananas", - "author_inst": "Biomedical Engineering Research Centre (CREB), Automatic Control Department (ESAII) Universitat Politecnica de Catalunya-Barcelona Tech (UPC), Barcelona, Spain" - }, - { - "author_name": "Hamid Reza Marateb", - "author_inst": "Biomedical Engineering Research Centre (CREB), Automatic Control Department (ESAII) Universitat Politecnica de Catalunya-Barcelona Tech (UPC), Barcelona, Spain" - }, - { - "author_name": "Peyman Adibi", - "author_inst": "Digestive Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.10.20096909", "rel_title": "EXCESS MORTALITY FROM COVID-19. WEEKLY EXCESS DEATH RATES BY AGE AND SEX FOR SWEDEN.", @@ -1463078,6 +1463647,45 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.05.14.097204", + "rel_title": "Expression of ACE2 and TMPRSS2 proteins in the upper and lower aerodigestive tracts of rats", + "rel_date": "2020-05-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.097204", + "rel_abs": "Objective Patients with coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), exhibit not only respiratory symptoms but also symptoms of chemo-sensitive disorders and kidney failure. Cellular entry of SARS-CoV-2 depends on the binding of its spike protein to a cellular receptor named angiotensin-converting enzyme 2 (ACE2), and the subsequent spike protein-priming by host cell proteases, including transmembrane protease serine 2 (TMPRSS2). Thus, high expression of ACE2 and TMPRSS2 are considered to enhance the invading capacity of SARS-CoV-2.Methods To elucidate the underlying histological mechanisms of the aerodigestive disorders caused by SARS-CoV-2, we investigated the expression of ACE2 and TMPRSS2 proteins in the aerodigestive tracts of the tongue, hard palate with partial nasal tissue, larynx with hypopharynx, trachea, esophagus, lung, and kidney of rats through immunohistochemistry.Results Strong co-expression of ACE2 and TMPRSS2 proteins was observed in the nasal respiratory epithelium, trachea, bronchioles, alveoli, kidney, and taste buds of the tongue. Remarkably, TMPRSS2 expression was much stronger in the peripheral alveoli than in the central alveoli. These results coincide with the reported clinical symptoms of COVID-19, such as the loss of taste, loss of olfaction, respiratory dysfunction, and acute nephropathy.Conclusions A wide range of organs have been speculated to be affected by SARS-CoV-2 depending on the expression levels of ACE2 and TMPRSS2. Differential distribution of TMPRSS2 in the lung indicated the COVID-19 symptoms to possibly be exacerbated by TMPRSS2 expression. This study might provide potential clues for further investigation of the pathogenesis of COVID-19.Level of Evidence NACompeting Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rumi Ueha", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Taku Sato", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + }, + { + "author_name": "Takao Goto", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + }, + { + "author_name": "Akihito Yamauchi", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + }, + { + "author_name": "Kenji Kondo", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + }, + { + "author_name": "Tatsuya Yamasoba", + "author_inst": "Department of Otolaryngology and Head and Neck Surgery, the University of Tokyo" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.05.15.097501", "rel_title": "Traffic-derived particulate matter and angiotensin-converting enzyme 2 expression in human airway epithelial cells", @@ -1464666,89 +1465274,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.05.13.093088", - "rel_title": "Potent neutralization of SARS-CoV-2 in vitro and in an animal model by a human monoclonal antibody", - "rel_date": "2020-05-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.13.093088", - "rel_abs": "Effective therapies are urgently needed for the SARS-CoV-2/COVID19 pandemic. We identified panels of fully human monoclonal antibodies (mAbs) from eight large phage-displayed Fab, scFv and VH libraries by panning against the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) glycoprotein. One high affinity mAb, IgG1 ab1, specifically neutralized replication competent SARS-CoV-2 with exceptional potency as measured by two different assays. There was no enhancement of pseudovirus infection in cells expressing Fc{gamma} receptors at any concentration. It competed with human angiotensin-converting enzyme 2 (hACE2) for binding to RBD suggesting a competitive mechanism of virus neutralization. IgG1 ab1 potently neutralized mouse ACE2 adapted SARS-CoV-2 in wild type BALB/c mice and native virus in hACE2 expressing transgenic mice. The ab1 sequence has relatively low number of somatic mutations indicating that ab1-like antibodies could be quickly elicited during natural SARS-CoV-2 infection or by RBD-based vaccines. IgG1 ab1 does not have developability liabilities, and thus has potential for therapy and prophylaxis of SARS-CoV-2 infections. The rapid identification (within 6 days) of potent mAbs shows the value of large antibody libraries for response to public health threats from emerging microbes.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Wei Li", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Aleksandra Drelich", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "David R Martinez", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Lisa E Gralinski", - "author_inst": "Universitty of North Carolina" - }, - { - "author_name": "Chuan Chen", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Zehua Sun", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Alexandra Sch\u00e4fer", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Sarah R Leist", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Xianglei Liu", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Doncho V Zhelev", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Liyong Zhang", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Eric L Peterson", - "author_inst": "Abound Bio" - }, - { - "author_name": "Alex Conard", - "author_inst": "Abound Bio" - }, - { - "author_name": "John W Mellors", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Chien-Te Tseng", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Ralph S Baric", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Dimiter S Dimitrov", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.13.092536", "rel_title": "Network Analysis and Transcriptome Profiling Identify Autophagic and Mitochondrial Dysfunctions in SARS-CoV-2 Infection", @@ -1465056,6 +1465581,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.14.096081", + "rel_title": "Crystal structures of SARS-CoV-2 ADP-ribose phosphatase (ADRP): from the apo form to ligand complexes", + "rel_date": "2020-05-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.096081", + "rel_abs": "Among 15 nonstructural proteins (Nsps), the newly emerging SARS-CoV-2 encodes a large, multidomain Nsp3. One of its units is ADP-ribose phosphatase domain (ADRP, also known as macrodomain) which is believed to interfere with the host immune response. Such a function appears to be linked to the proteins ability to remove ADP-ribose from ADP-ribosylated proteins and RNA, yet the precise role and molecular targets of the enzyme remains unknown. Here, we have determined five, high resolution (1.07 - 2.01 [A]) crystal structures corresponding to the apo form of the protein and complexes with 2-(N-morpholino)ethanesulfonic acid (MES), AMP and ADPr. We show that the protein undergoes conformational changes to adapt to the ligand in a manner previously observed before for in close homologs from other viruses. We also identify a conserved water molecule that may participate in hydrolysis. This work builds foundations for future structure-based research of the ADRP, including search for potential antiviral therapeutics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Karolina Michalska", + "author_inst": "Argonne National Laboratory/University of Chicago" + }, + { + "author_name": "Youngchang Kim", + "author_inst": "Argonne National Laboratory/University of Chicago" + }, + { + "author_name": "Robert Jedrzejczak", + "author_inst": "Argonne National Laboratory/University of Chicago" + }, + { + "author_name": "Natalia I. Maltseva", + "author_inst": "Argonne National Laboratory/University of Chicago" + }, + { + "author_name": "Lucy Stols", + "author_inst": "University of Chicago" + }, + { + "author_name": "Michael Endres", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Andrzej Joachimiak", + "author_inst": "Argonne National Laboratory" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.05.14.092767", "rel_title": "ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study", @@ -1466248,29 +1466816,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.10.20097550", - "rel_title": "A dynamic model for Covid-19 in Brazil.", - "rel_date": "2020-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20097550", - "rel_abs": "1A dynamic model for the current coronavirus outbreak is presented. The most important parameters are identified which determine the number of cases progression. Results of a numerical simulation are compared with existing data of the number of COVID-19 cases and deaths in Sao Paulo and Brazil. On the basis of these results measures are proposed to control the epidemics and to flat the infection curve. A simple three steps procedure is proposed to predict the time evolution of the epidemics and a criteria to start resuming normal activities after quarantine is suggested.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rubens Lichtenthaler Filho V", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Daniel Gomes Lichtenthaler Sr.", - "author_inst": "Hospital da Clinicas da Universidade de Sao Paulo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.10.20097691", "rel_title": "Spread of COVID-19 in India: A Simple Algebraic Study", @@ -1466434,6 +1466979,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.05.10.20097154", + "rel_title": "The Estimated Time-Varying Reproduction Numbers during the Ongoing Pandemic of the Coronavirus Disease 2019 (COVID-19) in 12 Selected Countries outside China", + "rel_date": "2020-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20097154", + "rel_abs": "BackgroundHow can we anticipate the progression of the ongoing pandemic of the coronavirus disease 2019 (COVID-19)? As a measure of transmissibility, we aimed to estimate concurrently the time-varying reproduction number, R0(t), over time during the COVID-19 pandemic for each of the following 12 heavily-attacked countries: Singapore, South Korea, Japan, Iran, Italy, Spain, Germany, France, Belgium, United Kingdom, the United States of America, and South Africa.\n\nMethodsWe downloaded the publicly available COVID-19 pandemic data from the WHO COVID-19 Dashboard website (https://covid19.who.int/) for the duration of January 11, 2020 and May 1, 2020. Then, we specified two plausible distributions of serial interval to apply the novel estimation method implemented in the incidence and EpiEstim packages to the data of daily new confirmed cases for robustly estimating R0(t) in the R software.\n\nResultsWe plotted the epidemic curves of daily new confirmed cases for the 12 selected countries. A clear peak of the epidemic curve appeared in 10 of the 12 selected countries at various time points, and then the epidemic curve declined gradually. However, the United States of America and South Africa happened to have two or more peaks and their epidemic curves either reached a plateau or still climbed up. Almost all curves of the estimated R0(t) monotonically went down to be less than or close to 1.0 up to April 30, 2020 except Singapore, South Korea, Japan, Iran, and South Africa, of which the curves surprisingly went up and down at various time periods during the COVID-19 pandemic. Finally, the United States of America and South Africa were the two countries with the approximate R0(t) [≥] 1.0 at the end of April, and thus they were now facing the harshest battles against the coronavirus among the 12 selected countries. By contrast, Spain, Germany, and France with smaller values of the estimated R0(t) were relatively better than the other 9 countries.\n\nConclusionSeeing the estimated R0(t) going downhill speedily is more informative than looking for the drops in the daily number of new confirmed cases during an ongoing epidemic of infectious disease. We urge public health authorities and scientists to estimate R0(t) routinely during an epidemic of infectious disease and to report R0(t) daily to the public until the end of the epidemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Fu-Chang Hu", + "author_inst": "National Taiwan University, College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.12.091314", "rel_title": "Meta-analysis of transcriptomes of SARS-Cov2 infected human lung epithelial cells identifies transmembrane serine proteases co-expressed with ACE2 and biological processes related to viral entry, immunity, inflammation and cellular stress.", @@ -1467702,25 +1468266,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.05.09.20096768", - "rel_title": "Monitoring the propagation of COVID-19-pandemic first waves", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096768", - "rel_abs": "A phenomenological approach is proposed to monitor the propagation of the COVID-19-pandemic first waves. A large set of data collected at a worldwide scale during the first months of 2020 is compiled into series of semi-logarithmic plots, for a selection of thirty-two countries from the five continents. Three regimes are identified in the propagation of an epidemic wave: a pre-epidemic regime 1, an exponential-growth regime 2, and a resorption regime 3. A two-parameters scaling of the first-wave death variation reported in China is used to fit those reported in other countries. Comparison is made between the propagation of the pandemic in different countries, which are classified in four groups, from group A where the pandemic first waves were contained efficiently, to group D where the pandemic first waves widely spread. Group A is mainly composed of Asian countries, where fast and efficient measures have been applied. Group D is composed of Western-Europe countries and the United States of America, where late decisions and confused political communication (pandemic seriousness, protection masks, herd immunity etc.) led to significant death tolls. The threat of large resurging epidemic waves after a hasty lockdown lift is discussed, in particular for the countries from group D, where the number of contagious people remained high in the beginning of May 2020. The situation is opposite in Asian countries from group A, where the number of contagious people was successfully maintained to a low level. In particular, the results obtained by Hong Kong and South Korea are highlighted, and the measures taken there are presented as virtuous examples that other countries may follow.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "William Knafo", - "author_inst": "CNRS/LNCMI" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.09.20096149", "rel_title": "Three pictures of COVID-19 behavior in Italy: similar growth and different degrowth", @@ -1467872,6 +1468417,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.09.20096420", + "rel_title": "Timing of non-pharmaceutical interventions to mitigate COVID-19 transmission and their effects on mobility: A cross-country analysis", + "rel_date": "2020-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096420", + "rel_abs": "Non-pharmaceutical interventions (NPIs) that encourage physical distancing can decrease and delay the transmission of COVID-19. They have been implemented globally during the pandemic, however, the specific NPIs implemented and the timing of interventions has varied widely. We validated two published datasets on the implementation of NPIs globally. The health and socioeconomic factors associated with delay in implementation of NPIs was analyzed using fractional logit and probit models, and beta regression models. The probability of timely NPI implementation by a country was analyzed using a probit model. The effects of these interventions on mobility changes using Google social mobility reports, were analyzed with propensity score matching methods. Three NPIs were analyzed: national school closure, national lockdown, and global travel ban. Countries with higher incomes, larger populations, and better health preparedness measures had greater delays in implementation. Countries with greater population density, more democratic political systems, lower case detection capacity, and later arrival of first cases were more likely to implement NPIs. Implementation of lockdowns significantly reduced physical mobility. Mobility was further reduced when lockdowns were enforced with curfews or fines, or were more strictly defined. National school closures did not significantly change mobility. The implementation of NPIs is a global public good during pandemics, and the international community needs to address constraints and design incentives so countries implement NPIs in a timely manner. Further analysis is needed on the effect of NPI variations on mobility and transmission, and their associated costs.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Amit Summan", + "author_inst": "Center for Disease Dynamics, Economics, and Policy" + }, + { + "author_name": "Arindam Nandi", + "author_inst": "The Center for Disease Dynamics, Economics & Policy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.09.20096099", "rel_title": "Healthcare workers preparedness for COVID-19 pandemic in the occupied Palestinian territory: a cross-sectional survey", @@ -1469036,137 +1469604,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.05.12.091462", - "rel_title": "Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein", - "rel_date": "2020-05-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.091462", - "rel_abs": "Antibodies are a principal determinant of immunity for most RNA viruses and have promise to reduce infection or disease during major epidemics. The novel coronavirus SARS-CoV-2 has caused a global pandemic with millions of infections and hundreds of thousands of deaths to date1,2. In response, we used a rapid antibody discovery platform to isolate hundreds of human monoclonal antibodies (mAbs) against the SARS-CoV-2 spike (S) protein. We stratify these mAbs into five major classes based on their reactivity to subdomains of S protein as well as their cross-reactivity to SARS-CoV. Many of these mAbs inhibit infection of authentic SARS-CoV-2 virus, with most neutralizing mAbs recognizing the receptor-binding domain (RBD) of S. This work defines sites of vulnerability on SARS-CoV-2 S and demonstrates the speed and robustness of new antibody discovery methodologies.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Seth J Zost", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Pavlo Gilchuk", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Rita Chen", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "James Brett Case", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Joseph X Reidy", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Andrew Trivette", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Rachel S Nargi", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Rachel E Sutton", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Naveen Suryadevara", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Elaine C Chen", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Elad Binshtein", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Swathi Shrihari", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Mario A Ostrowski", - "author_inst": "University of Toronto" - }, - { - "author_name": "Helen Y Chu", - "author_inst": "University of Washington" - }, - { - "author_name": "Jonathan E Didier", - "author_inst": "Berkeley Lights" - }, - { - "author_name": "Keith W MacRenaris", - "author_inst": "Berkeley Lights" - }, - { - "author_name": "Taylor Jones", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Samuel Day", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Luke Myers", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "F. Eun-Hyung Lee", - "author_inst": "Emory University" - }, - { - "author_name": "Doan C Nguyen", - "author_inst": "Emory University" - }, - { - "author_name": "Ignacio Sanz", - "author_inst": "Emory University" - }, - { - "author_name": "David R Martinez", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Lisa Gralinski", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Ralph S Baric", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Larissa Thackray", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Michael S Diamond", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Robert H Carnahan Jr.", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "James E Crowe", - "author_inst": "Vanderbilt University Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.12.091918", "rel_title": "Antibody repertoire induced by SARS-CoV-2 spike protein immunogens", @@ -1469490,6 +1469927,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.12.092163", + "rel_title": "A Computational Toolset for Rapid Identification of SARS-CoV-2, other Viruses, and Microorganisms from Sequencing Data", + "rel_date": "2020-05-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.092163", + "rel_abs": "In this paper, we present a toolset and related resources for rapid identification of viruses and microorganisms from short-read or long-read sequencing data. We present fastv as an ultra-fast tool to detect microbial sequences present in sequencing data, identify target microorganisms, and visualize coverage of microbial genomes. This tool is based on the k-mer mapping and extension method. K-mer sets are generated by UniqueKMER, another tool provided in this toolset. UniqueKMER can generate complete sets of unique k-mers for each genome within a large set of viral or microbial genomes. For convenience, unique k-mers for microorganisms and common viruses that afflict humans have been generated and are provided with the tools. As a lightweight tool, fastv accepts FASTQ data as input, and directly outputs the results in both HTML and JSON formats. Prior to the k-mer analysis, fastv automatically performs adapter trimming, quality pruning, base correction, and other pre-processing to ensure the accuracy of k-mer analysis. Specifically, fastv provides built-in support for rapid SARS-CoV-2 identification and typing. Experimental results showed that fastv achieved 100% sensitivity and 100% specificity for detecting SARS-CoV-2 from sequencing data; and can distinguish SARS-CoV-2 from SARS, MERS, and other coronaviruses. This toolset is available at: https://github.com/OpenGene/fastv.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Shifu Chen", + "author_inst": "HaploX Biotechnology" + }, + { + "author_name": "Changshou He", + "author_inst": "HaploX Biotechnology" + }, + { + "author_name": "Yingqiang Li", + "author_inst": "HaploX Biotechnology" + }, + { + "author_name": "Zhicheng Li", + "author_inst": "Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Charles E Melancon III", + "author_inst": "HaploX Biotechnology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.13.092577", "rel_title": "Lung Disease Network Reveals the Impact of Comorbidity on SARS-CoV-2 infection", @@ -1470458,29 +1470930,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.08.20095083", - "rel_title": "COVID-19 transmission risk factors", - "rel_date": "2020-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095083", - "rel_abs": "We analyze risk factors correlated with the initial transmission growth rate of the recent COVID-19 pandemic in different countries. The number of cases follows in its early stages an almost exponential expansion; we chose as a starting point in each country the first day di with 30 cases and we fitted for 12 days, capturing thus the early exponential growth. We looked then for linear correlations of the exponents with other variables, for a sample of 126 countries. We find a positive correlation, i.e. faster spread of COVID-19, with high confidence level with the following variables, with respective p-value: low Temperature (4 {middle dot} 10-7), high ratio of old vs. working-age people (3 {middle dot} 10-6), life expectancy (8 {middle dot} 10-6), number of international tourists (1{middle dot} 10-5), earlier epidemic starting date di (2{middle dot} 10-5), high level of physical contact in greeting habits (6 {middle dot} 10-5), lung cancer prevalence (6 {middle dot} 10-5), obesity in males (1{middle dot} 10-4), share of population in urban areas (2{middle dot} 10-4), cancer prevalence (3{middle dot} 10-4), alcohol consumption (0.0019), daily smoking prevalence (0.0036), UV index (0.004, 73 countries). We also find a correlation with low Vitamin D serum levels (0.002-- 0.006), but on a smaller sample, 50 countries, to be confirmed on a larger sample. There is highly significant correlation also with blood types: positive correlation with types RH-(3{middle dot} 10-5) and A+ (3 {middle dot}10-3), negative correlation with B+ (2 {middle dot}10-4). We also find positive correlation with moderate confidence level (p-value of 0.02[~] 0.03) with: CO2/SO emissions, type-1 diabetes in children, low vaccination coverage for Tuberculosis (BCG). Several of the above variables are correlated with each other and so they are likely to have common interpretations. We thus performed a Principal Component Analysis, in order to find the significant independent linear combinations of such variables. We also analyzed the possible existence of a bias: countries with low GDP-per capita might have less intense testing and we discuss correlation with the above variables.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Alessio Notari", - "author_inst": "Universitat de Barcelona" - }, - { - "author_name": "Giorgio Torrieri", - "author_inst": "Unicamp, Campinas, SP, Brazil" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.08.20095356", "rel_title": "Global analysis of daily new COVID-19 cases reveals many static-phase countries including US and UK potentially with unstoppable epidemics", @@ -1470784,6 +1471233,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2020.05.08.20095463", + "rel_title": "Using epidemic simulators for monitoring an ongoing epidemic", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095463", + "rel_abs": "Prediction of infection trends, estimating the efficacy of contact tracing, testing or impact of influx of infected are of vital importance for administration during an ongoing epidemic. Most effective methods currently are empirical in nature and their relation to parameters of interest to administrators are not evident. We thus propose a modified SEIRD model that is capable of modeling effect of interventions and in migrations on the progress of an epidemic. The tunable parameters of this model bear relevance to monitoring of an epidemic. This model was used to show that some of the commonly seen features of cumulative infections in real data can be explained by piece wise constant changes in interventions and population influx. We also show that the data of cumulative infections from twelve Indian states between mid March and mid April 2020 can be generated from the model by applying interventions according to a set of heuristic rules. Prediction for the next ten days based on this model, reproduced real data very well. In addition, our model also reproduced the time series of recoveries and deaths. Our work constitutes an important first step towards an effective dashboard for the monitoring of epidemic by the administration, especially in an Indian context.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mohan Raghavan", + "author_inst": "Indian Institute of Technology Hyderabad" + }, + { + "author_name": "Kousik Sarathy Sridharan", + "author_inst": "Indian Institute of Technology Hyderabad" + }, + { + "author_name": "Yashaswini M R", + "author_inst": "Indian Institute of Technology Hyderabad" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.08.20093229", "rel_title": "Placental pathology in COVID-19", @@ -1472119,49 +1472595,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.07.20092965", - "rel_title": "Predicted success of prophylactic antiviral therapy to block or delay SARS-CoV-2 infection depends on the targeted mechanism", - "rel_date": "2020-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20092965", - "rel_abs": "Repurposed drugs that are immediately available and safe to use constitute a first line of defense against new viral infections. Despite limited antiviral activity against SARS-CoV-2, several drugs are being tested as medication or as prophylaxis to prevent infection. Using a stochastic model of early phase infection, we find that a critical efficacy above 87% is needed to block viral establishment. This can be improved by combination therapy. Below the critical efficacy, establishment of infection can sometimes be prevented, most effectively with drugs blocking viral entry into cells or enhancing viral clearance. Even when a viral infection cannot be prevented, antivirals delay the time to detectable viral loads. This delay flattens the within-host viral dynamic curve, possibly reducing transmission and symptom severity. Thus, antiviral prophylaxis, even with reduced efficacy, could be efficiently used to prevent or alleviate infection in people at high risk.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Peter Czuppon", - "author_inst": "Sorbonne Universit\u00e9" - }, - { - "author_name": "Florence D\u00e9barre", - "author_inst": "Sorbonne Universit\u00e9" - }, - { - "author_name": "Antonio Gon\u00e7alves", - "author_inst": "Universit\u00e9 de Paris, INSERM" - }, - { - "author_name": "Olivier Tenaillon", - "author_inst": "Universit\u00e9 de Paris, INSERM" - }, - { - "author_name": "Alan S Perelson", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "J\u00e9r\u00e9mie Guedj", - "author_inst": "Universit\u00e9 de Paris, INSERM" - }, - { - "author_name": "Fran\u00e7ois Blanquart", - "author_inst": "Coll\u00e8ge de France" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.07.20094912", "rel_title": "Facemasks prevent influenza-like illness: implications for COVID-19", @@ -1472373,6 +1472806,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.06.20093419", + "rel_title": "Evidence of Protective Role of Ultraviolet-B (UVB) Radiation in Reducing COVID-19 Deaths", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093419", + "rel_abs": "BackgroundResearch is ongoing to identify an effective way to prevent or treat COVID-19, but thus far these efforts have not yet identified a possible solution. Prior studies indicate the protective role of Ultraviolet-B (UVB) radiation in human health, mediated by vitamin D synthesis. In this study, we empirically outline a negative association of UVB radiation as measured by ultraviolet index (UVI) with the number of deaths attributed to COVID-19 (COVID- 19 deaths).\n\nMethodsWe carry out an observational study, applying a fixed-effect log-linear regression model to a panel dataset of 152 countries over a period of 108 days (n=6524). We use the cumulative number of COVID-19 deaths and case-fatality rate (CFR) as the main dependent variables to test our hypothesis and isolate UVI effect from potential confounding factors such as underlying time trends, country-specific time-constant and time-varying factors such as weather.\n\nFindingsAfter controlling for time-constant and time-varying factors, we find that a permanent unit increase in UVI is associated with a 1.2 percentage points decline in daily growth rates of cumulative COVID-19 deaths [p < 0.01] as well as a 1.0 percentage points decline in the daily growth rates of CFR [p < 0.05]. These results represent a significant percentage reduction in terms of the daily growth rates of cumulative COVID-19 deaths (-11.88%) and CFR (-38.46%). Our results are consistent across different model specifications.\n\nInterpretationWe find a significant negative association between UVI and COVID-19 deaths, indicating evidence of the protective role of UVB in mitigating COVID-19 deaths. If confirmed via clinical studies, then the possibility of mitigating COVID-19 deaths via sensible sunlight exposure or vitamin D intervention will be very attractive because it is cost-effective and widely available.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Rahul Kalippurayil Moozhipurath", + "author_inst": "Goethe University Frankfurt am Main" + }, + { + "author_name": "Lennart Kraft", + "author_inst": "Goethe University Frankfurt am Main" + }, + { + "author_name": "Bernd Skiera", + "author_inst": "Goethe University Frankfurt am Main" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.07.20094888", "rel_title": "SARS-CoV-2 Infection Associated Hemophagocytic Lymphohistiocytosis: An autopsy series with clinical and laboratory correlation.", @@ -1473641,29 +1474101,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.06.20093195", - "rel_title": "Health and Demographic Impact on COVID-19 Infection and Mortality in US Counties", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093195", - "rel_abs": "IntroductionWith the pandemic of COVID-19, the number of confirmed cases and related deaths are increasing in the US. We aimed to understand the potential impact of health and demographic factors on the infection and mortality rates of COVID-19 at the population level.\n\nMethodsWe collected total number of confirmed cases and deaths related to COVID-19 at the county level in the US from January 21, 2020 to April 23, 2020. We extracted health and demographic measures for each US county. Multivariable linear mixed effects models were used to investigate potential correlations of health and demographic characteristics with the infection and mortality rates of COVID-19 in US counties.\n\nResultsOur models showed that several health and demographic factors were positively correlated with the infection rate of COVID-19, such as low education level and percentage of Black. In contrast, several factors, including percentage of smokers and percentage of food insecure, were negatively correlated with the infection rate of COVID-19. While the number of days since first confirmed case and the infection rate of COVID-19 were negatively correlated with the mortality rate of COVID-19, percentage of elders (65 and above) and percentage of rural were positively correlated with the mortality rate of COVID-19.\n\nConclusionsAt the population level, health and demographic factors could impact the infection and mortality rates of COVID-19 in US counties.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Zidian Xie", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Dongmei Li", - "author_inst": "University of Rochester Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.06.20093021", "rel_title": "Selection of homemade mask materials for preventing transmission of COVID-19: a laboratory study", @@ -1474047,6 +1474484,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.05.20092445", + "rel_title": "Smoking and the risk of COVID-19 infection in the UK Biobank Prospective Study", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092445", + "rel_abs": "Several studies suggest a lower prevalence of smoking than expected among adults with coronavirus disease (COVID-19). We conducted logistic regression analyses of the UK Biobank prospective study of 0.5 million adults followed for an average of 11 years. Compared to women, men were more likely to be tested and to test positive. In sex-stratified analyses, current smokers had higher adjusted Odds Ratios (OR) for being tested (male OR 1.60, 95%CI 1.32-1.95 and female OR 1.50,1.21-.1.86). Current smokers were more slightly more likely than never smokers to test positive for COVID-19. Further examination of smoking as a risk factor for COVID-19 is required. These must take into account reverse causality, where smokers quit to avoid disease as well as prior diseases.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Eo Rin Cho", + "author_inst": "Centre for Global Health Research, St. Michael's Hospital, University of Toronto" + }, + { + "author_name": "Arthur S Slutsky", + "author_inst": "Centre for Global Health Research, St. Michael's Hospital, University of Toronto" + }, + { + "author_name": "Prabhat Jha", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.06.20092957", "rel_title": "Associations with covid-19 hospitalisation amongst 406,793 adults: the UK Biobank prospective cohort study", @@ -1475463,49 +1475927,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, - { - "rel_doi": "10.1101/2020.05.07.20094409", - "rel_title": "APOE E4 GENOTYPE PREDICTS SEVERE COVID-19 IN THE UK BIOBANK COMMUNITY COHORT", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094409", - "rel_abs": "The novel respiratory disease COVID-19 produces varying symptoms, with fever, cough, and shortness of breath being common. In older adults, we found that pre-existing dementia is a major risk factor (OR = 3.07, 95% CI: 1.71 to 5.50) for COVID-19 severity in the UK Biobank (UKB). In another UK study of 16,749 patients hospitalized for COVID-19, dementia was among the common comorbidities and was associated with higher mortality. Additionally, impaired consciousness, including delirium, is common in severe cases. The ApoE e4 genotype is associated with both dementia and delirium, with the e4e4 (homozygous) genotype associated with a 14-fold increase in risk of Alzheimer's disease compared to the common e3e3 genotype, in populations with European ancestries. We therefore aimed to test associations between ApoE e4 alleles and COVID-19 severity, using the UKB data.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Chia-Ling Kuo", - "author_inst": "University of Connecticut Health" - }, - { - "author_name": "Luke C Pilling", - "author_inst": "University of Exeter" - }, - { - "author_name": "Janice L Atkins", - "author_inst": "University of Exeter" - }, - { - "author_name": "Jane AH Masoli", - "author_inst": "University of Exeter" - }, - { - "author_name": "Joao Delgado", - "author_inst": "University of Exeter" - }, - { - "author_name": "George A Kuchel", - "author_inst": "University of Connecticut Health" - }, - { - "author_name": "David Melzer", - "author_inst": "University of Exeter" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.05.08.20094664", "rel_title": "Deep learning models for COVID-19 infected area segmentation in CT images", @@ -1475677,6 +1476098,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.07.20094177", + "rel_title": "Clinical and behavioural characteristics of self-isolating healthcare workers during the COVID-19 pandemic: a single-centre observational study", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094177", + "rel_abs": "ObjectivesTo describe a cohort of self-isolating healthcare workers (HCWs) with presumed COVID-19.\n\nDesignA cross-sectional, single-centre study.\n\nSettingA large, teaching hospital based in Central London with tertiary infection services.\n\nParticipants236 HCWs completed a survey distributed by internal staff email bulletin. 167 were female and 65\n\nMeasuresInformation on symptomatology, exposures and health-seeking behaviour were collected from participants by self-report.\n\nResultsThe 236 respondents reported illness compatible with COVID-19 and there was an increase in illness reporting during March 2020. Diagnostic swabs were not routinely performed.. Cough (n=179, 75.8%), fever (n=138, 58.5%), breathlessness (n=84, 35.6%) were reported. Anosmia was reported in 42.2%. Fever generally settled within 1 week (n=110, 88%). Several respondents remained at home and did not seek formal medical attention despite reporting severe breathlessness and measuring hypoxia (n=5/9, 55.6%). 2 patients required hospital admission but recovered following oxygen therapy. 84 respondents (41.2%) required greater than the obligated 7 days off work and 9 required greater than 3 weeks off.\n\nConclusionThere was a significant increase in staff reporting illness compatible with possible COVID-19 during March 2020. Conclusions cannot be drawn about exact numbers of confirmed cases due to lack of diagnostic swabbing. There were significant numbers of respondents reporting anosmia; as well as early non-specific illness prior to onset of cough and fever. This may represent pre-symptomatic HCWs who are likely to be infectious and thus criteria for isolation and swabbing should be broadened. The study also revealed concerning lack of healthcare seeking in respondents with significant red flag symptoms (severe breathlessness, hypoxia). This should be addressed urgently to reduce risk of severe disease being detected late. Finally, this study should inform trusts that HCWs may require longer than 7 days off work to recover from illness.\n\nO_LSTStrengths and limitations of this studyC_LSTO_LITo the authors knowledge, this study presents one of the first descriptive data analysis of self-reported healthcare worker (HCW) COVID-19 exposures and symptomatology in the UK.\nC_LIO_LIStudy respondents represented a broad range of job roles, including both frontline clinical and non-patient facing staff.\nC_LIO_LIThe inclusion of questions focusing on health-seeking behaviour allows results to be used to inform human resource management in the developing pandemic, and provides concerning but important data around late healthcare seeking in HCWs\nC_LIO_LIData were self-reported, cross-sectional and retrospective, which may be subject to recall bias, and the lack of diagnostic swabbing in the majority of respondents limits interpretation of the data\nC_LIO_LIFull demographic data were not collected on participants and certain staff groups may have been over-represented in the sample, which may introduce sampling bias.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Angus de Wilton", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Eliz Kilich", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Zain Chaudhry", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Lucy CK Bell", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Joshua Gahir", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust; Hospital of Tropical Diseases, London" + }, + { + "author_name": "Jane Cadman", + "author_inst": "COVID-19 Response Team, University College London Hospitals NHS Foundation Trust" + }, + { + "author_name": "Robert A Lever", + "author_inst": "Hospital of Tropical Diseases, London; University College London" + }, + { + "author_name": "Sarah Logan", + "author_inst": "Hospital of Tropical Diseases, London; COVID-19 Response Team, University College London Hospitals NHS Foundation Trust;" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.07.20094276", "rel_title": "Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy", @@ -1476937,33 +1477405,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.06.20093336", - "rel_title": "The disease-induced herd immunity level for Covid-19 is substantially lower than the classical herd immunity level", - "rel_date": "2020-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093336", - "rel_abs": "Most countries are suffering severely from the ongoing covid-19 pandemic despite various levels of preventive measures. A common question is if and when a country or region will reach herd immunity h. The classical herd immunity level hC is defined as hC =1-1/R0, where R0 is the basic reproduction number, for covid-19 estimated to lie somewhere in the range 2.2-3.5 depending on country and region. It is shown here that the disease-induced herd immunity level hD, after an outbreak has taken place in a country/region with a set of preventive measures put in place, is actually substantially smaller than hC. As an illustration we show that if R0 =2.5 in an age-structured community with mixing rates fitted to social activity studies, and also categorizing individuals into three categories: low active, average active and high active, and where preventive measures affect all mixing rates proportionally, then the disease-induced herd immunity level is hD = 43% rather than hC =1-1/2.5 = 60%. Consequently, a lower fraction infected is required for herd immunity to appear. The underlying reason is that when immunity is induced by disease spreading, the proportion infected in groups with high contact rates is greater than that in groups with low contact rates. Consequently, disease-induced immunity is stronger than when immunity is uniformly distributed in the community as in the classical herd immunity level.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Tom Britton", - "author_inst": "Stockholm University" - }, - { - "author_name": "Pieter Trapman", - "author_inst": "Stockholm University" - }, - { - "author_name": "Frank G Ball", - "author_inst": "University of Nottingham" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.06.20093062", "rel_title": "A simple model to fit the time evolution of the daily death rate of Covid-19 in European Union countries", @@ -1477103,6 +1477544,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.06.20093492", + "rel_title": "Metapopulation modeling of COVID-19 advancing into the countryside: an analysis of mitigation strategies for Brazil", + "rel_date": "2020-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093492", + "rel_abs": "Since the first case of COVID-19 was confirmed in Brazil on 19 February 2020, this epidemic has spread throughout all states and at least 2142 of 5570 municipalities up to 30 April 2020. In order to understand this spreading, we investigate a stochastic epidemic model using a metapopulation approach. Simulations are supplied with real data for mobility, demography, and confirmed cases of COVID-19 extracted from public sources. Contagion follows a compartmental epidemic model for each municipality; the latter, in turn, interact with each other through recurrent mobility. Considering the number of municipalities with confirmed COVID-19 cases, simulations can infer the level of mitigation (strong, moderate, or none) that each state is effectively adopting. Properties of the epidemic curves such as time and value of epidemic peak and outbreak duration have very broad distributions across different geographical locations. This outbreak variability is observed on several scales from state, passing through intermediate, immediate down to municipality levels. The epidemic waves start from several foci concentrated in highly populated regions and propagate towards the countryside. Correlations between delay of the epidemic outbreak and distance from the respective capital cities are strong in several states, showing propagation towards the countryside, and weak in others, signaling strong influences of multiple centers, not necessarily within the same state. Our take home message is that the responses of different regions to the same mitigation protocol can vary enormously such that the policies of combating COVID-19, such as quarantine or lockdown, must be engineered according to the region specificity but integrated with the overall situation. Even though we restricted our study to Brazil, we believe that these ideas can be generalized to other countries with continental scales and heterogeneous demographic distributions.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Guilherme S Costa", + "author_inst": "Departamento de Fisica, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil" + }, + { + "author_name": "Wesley Cota", + "author_inst": "Departamento de Fisica, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil" + }, + { + "author_name": "Silvio C Ferreira", + "author_inst": "Departamento de Fisica, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil and National Institute of Science and Technology for Complex Systems, Rio d" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.06.20093476", "rel_title": "Sensitivity and specificity of a rapid test for assessment of exposure to SARS-CoV-2 in a community-based setting in Brazil", @@ -1478339,33 +1478807,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.08.084806", - "rel_title": "A single-cell RNA expression map of human coronavirus entry factors", - "rel_date": "2020-05-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.08.084806", - "rel_abs": "To predict the tropism of human coronaviruses, we profile 28 SARS-CoV-2 and coronavirus-associated receptors and factors (SCARFs) using single-cell RNA-sequencing data from a wide range of healthy human tissues. SCARFs include cellular factors both facilitating and restricting viral entry. Among adult organs, enterocytes and goblet cells of the small intestine and colon, kidney proximal tubule cells, and gallbladder basal cells appear most permissive to SARS-CoV-2, consistent with clinical data. Our analysis also suggests alternate entry paths for SARS-CoV-2 infection of the lung, central nervous system, and heart. We predict spermatogonial cells and prostate endocrine cells, but not ovarian cells, to be highly permissive to SARS-CoV-2, suggesting male-specific vulnerabilities. Early stages of embryonic and placental development show a moderate risk of infection. The nasal epithelium looks like another battleground, characterized by high expression of both promoting and restricting factors and a potential age-dependent shift in SCARF expression. Lastly, SCARF expression appears broadly conserved across human, chimpanzee and macaque organs examined. Our study establishes an important resource for investigations of coronavirus biology and pathology.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Manvendra Singh", - "author_inst": "Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA" - }, - { - "author_name": "Vikas Bansal", - "author_inst": "Biomedical Data Science and Machine Learning Group, DZNE, Tuebingen, Germany" - }, - { - "author_name": "Cedric Feschotte", - "author_inst": "Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.05.05.20091785", "rel_title": "The race to find a SARS-CoV-2 drug can only be won by a few chosen drugs: a systematic review of registers of clinical trials of drugs aimed at preventing or treating COVID-19", @@ -1478889,6 +1479330,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.05.20092122", + "rel_title": "Indian communitys Knowledge, Attitude & Practice towards COVID-19", + "rel_date": "2020-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092122", + "rel_abs": "As COVID-19 pandemic has caused unprecedented human health consequences. Knowledge, attitude, perception of general population of India towards the transmission and prevention plays vital role for effective control measures. The study was conducted to assess the knowledge, attitude and practice of the general public of India on COVID-19. In this study, a web-based cross-sectional survey was conducted between 10th March to 18th April 2020. A 19-item questionnaire was generated, Cronbachs alpha was used to measure the internal consistency of the questionnaire & randomly distributed among the public using Google forms through social media networks. The chi-square test or Fischer exact test was used to compare categorical data and multiple linear regression was used to identify factor influencing KAP. Among 7978 participants, the overall knowledge, attitude and practice score was 80.64%, 97.33% and 93.8% consecutively. Majority of Indian population demonstrated preceded good knowledge, positive attitude and good practice regarding COVID-19 pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Balvir Singh Tomar", + "author_inst": "Institute of Gastroenterology Hepatology & Transplant" + }, + { + "author_name": "Pratima Singh", + "author_inst": "Department of Pharmacy Practice, Nims University Rajasthan, Jaipur India" + }, + { + "author_name": "Deepak Nathiya", + "author_inst": "Department of Pharmacy Practice, Nims University Rajasthan Jaipur India" + }, + { + "author_name": "Supriya Suman", + "author_inst": "Department of Pharmacy Practice, Nims University Rajasthan, Jaipur India" + }, + { + "author_name": "Preeti Raj", + "author_inst": "Department of Pharmacy Practice, Nims University Rajasthan, Jaipur, India" + }, + { + "author_name": "Sandeep Tripathi", + "author_inst": "National Institute of Medical Sciences & Research, Nims University Rajasthan, Jaipur, India" + }, + { + "author_name": "Dushyant Singh Chauhan", + "author_inst": "Institute of Advance Sciences, Nims University Rajasthan, Jaipur, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.05.20092254", "rel_title": "County-level factors influence the trajectory of Covid-19 incidence", @@ -1479917,45 +1480401,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.05.20092262", - "rel_title": "Impact of essential workers in the context of social distancing for epidemic control", - "rel_date": "2020-05-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092262", - "rel_abs": "Many governments have responded to the ongoing COVID-19 pandemic by imposing social policies that restrict interactions outside of the home, resulting in a large fraction of the workforce either working from home or not working. However, to maintain essential services, a substantial number of workers are not subject to these limitations, and maintain many of their pre-intervention interactions. To explore how interactions among such \"essential\" workers, and between essential workers and the rest of the population, impact disease risk and the effectiveness of pandemic control, we evaluated several models of essential worker interactions within a standard epidemiology framework. The models were designed to correspond to key characteristics of, respectively, cashiers, factory employees, and healthcare workers. We find in all three models that essential workers are at substantially elevated risk of infection compared to the rest of the population, and that increasing the numbers of essential workers necessitates the imposition of more stringent interaction controls on the rest of the population in order to manage the pandemic. However, different archetypes of essential workers differ in both their individual probability of infection and impact on the broader pandemic, highlighting the need to understand and target for intervention the specific risks faced by different groups of essential workers.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "William R Milligan", - "author_inst": "Columbia University" - }, - { - "author_name": "Zachary L Fuller", - "author_inst": "Columbia University" - }, - { - "author_name": "Ipsita Agarwal", - "author_inst": "Columbia University" - }, - { - "author_name": "Michael B Eisen", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Molly Przeworski", - "author_inst": "Columbia University" - }, - { - "author_name": "Guy Sella", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.05.20092304", "rel_title": "On the impact of early non-pharmaceutical interventions as containment strategies against the COVID-19 pandemic", @@ -1480371,6 +1480816,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.05.20091637", + "rel_title": "Application-oriented mathematical algorithms for group testing", + "rel_date": "2020-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091637", + "rel_abs": "Group testing is a widely used protocol which aims to test a small group of people to identify whether at least one of them is infected. It is particularly efficient if the infection rate is low, because it only requires a single test if everybody in the group is negative. The most efficient use of group testing is a complex mathematical question. However, the answer highly depends on practical parameters and restrictions, which are partially ignored by the mathematical literature. This paper aims to offer practically efficient group testing algorithms, focusing on the current COVID-19 epidemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Endre Csoka", + "author_inst": "Alfred Renyi Institute of Mathematics" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.08.083816", "rel_title": "Intra-genome variability in the dinucleotide composition of SARS-CoV-2", @@ -1481647,81 +1482111,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.03.20089151", - "rel_title": "Occurrence and Timing of Subsequent SARS-CoV-2 RT-PCR Positivity Among Initially Negative Patients", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089151", - "rel_abs": "BackgroundSARS-CoV-2 reverse transcriptase polymerase chain reaction (RT-PCR) testing remains the cornerstone of laboratory-based identification of patients with COVID-19. As the availability and speed of SARS-CoV-2 testing platforms improve, results are increasingly relied upon to inform critical decisions related to therapy, use of personal protective equipment, and workforce readiness. However, early reports of RT-PCR test performance have left clinicians and the public with concerns regarding the reliability of this predominant testing modality and the interpretation of negative results. In this work, two independent research teams report the frequency of discordant SARS-CoV-2 test results among initially negative, repeatedly tested patients in regions of the United States with early community transmission and access to testing.\n\nMethodsAll patients at the University of Washington (UW) and Stanford Health Care undergoing initial testing by nasopharyngeal (NP) swab between March 2nd and April 7th, 2020 were included. SARS-CoV-2 RT-PCR was performed targeting the N, RdRp, S, and E genes and ORF1ab, using a combination of Emergency Use Authorization laboratory-developed tests and commercial assays. Results through April 14th were extracted to allow for a complete 7-day observation period and an additional day for reporting.\n\nResultsA total of 23,126 SARS-CoV-2 RT-PCR tests (10,583 UW, 12,543 Stanford) were performed in 20,912 eligible patients (8,977 UW, 11,935 Stanford) undergoing initial testing by NP swab; 626 initially test-negative patients were re-tested within 7 days. Among this group, repeat testing within 7 days yielded a positive result in 3.5% (4.3% UW, 2.8% Stanford) of cases, suggesting an initial false negative RT-PCR result; the majority (96.5%) of patients with an initial negative result who warranted reevaluation for any reason remained negative on all subsequent tests performed within this window.\n\nConclusionsTwo independent research teams report the similar finding that, among initially negative patients subjected to repeat SARS-CoV-2 RT-PCR testing, the occurrence of a newly positive result within 7 days is uncommon. These observations suggest that false negative results at the time of initial presentation do occur, but potentially at a lower frequency than is currently believed. Although it is not possible to infer the clinical sensitivity of NP SARS-CoV-2 RT-PCR testing using these data, they may be used in combination with other reports to guide the use and interpretation of this common testing modality.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Dustin R Long", - "author_inst": "University of Washington" - }, - { - "author_name": "Saurabh Gombar", - "author_inst": "Stanford University" - }, - { - "author_name": "Catherine A Hogan", - "author_inst": "Stanford" - }, - { - "author_name": "Alex L Greninger", - "author_inst": "University of Washington" - }, - { - "author_name": "Vikas OReilly Shah", - "author_inst": "University of Washington" - }, - { - "author_name": "Chloe Bryson-Cahn", - "author_inst": "University of Washington" - }, - { - "author_name": "Bryan Stevens", - "author_inst": "Center for Biomedical Informatics Research, Stanford University" - }, - { - "author_name": "Arjun Rustagi", - "author_inst": "Stanford University" - }, - { - "author_name": "Keith R Jerome", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Christina S Kong", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "James Zehnder", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Nigam H Shah", - "author_inst": "Stanford University" - }, - { - "author_name": "Noel S Weiss", - "author_inst": "University of Washington School of Public Health" - }, - { - "author_name": "Benjamin A Pinsky", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Jacob Sunshine", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.05.20091561", "rel_title": "AI based Chest X-Ray (CXR) Scan Texture Analysis Algorithm for Digital Test of COVID-19 Patients", @@ -1482093,6 +1482482,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2020.05.04.20090316", + "rel_title": "Early postmortem brain MRI findings in COVID-19 non-survivors", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090316", + "rel_abs": "ImportanceThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is considered to have potential neuro-invasiveness that might lead to acute brain disorders or contribute to respiratory distress in patients with coronavirus disease 2019 (COVID-19). Brain magnetic resonance imaging (MRI) data in COVID-19 patients are scarce due to difficulties to obtain such examination in infected unstable patients during the COVID-19 outbreak.\n\nObjectiveTo investigate the occurrence of structural brain abnormalities in non-survivors of COVID-19 in a virtopsy framework.\n\nDesignProspective, case series study with postmortem brain MRI obtained early (<24h) after death.\n\nSettingMonocentric study.\n\nParticipantsFrom 31/03/2020 to 24/04/2020, consecutive decedents who fulfilled the following inclusion criteria were included: death <24 hours, SARS-CoV-2 detection on nasopharyngeal swab specimen, chest computerized tomographic (CT) scan suggestive of COVID-19, absence of known focal brain lesion, and MRI compatibility.\n\nMain Outcome(s) andMeasure(s)Signs of acute brain injury and MRI signal abnormalities along the olfactory tract and brainstem were searched independently by 3 neuroradiologists, then reviewed with neurologists and clinicians.\n\nResultsAmong the 62 patients who died from COVID-19 during the inclusion period, 19 decedents fulfilled inclusion criteria. Subcortical micro- and macro-bleeds (2 decedents), cortico-subcortical edematous changes evocative of posterior reversible encephalopathy syndrome (PRES, one decedent), and nonspecific deep white matter changes (one decedent) were observed. Asymmetric olfactory bulbs were found in 4 other decedents without downstream olfactory tract abnormalities. No brainstem MRI signal abnormality.\n\nConclusions and RelevancePostmortem brain MRI demonstrates hemorrhagic and PRES-related brain lesions in non-survivors of COVID-19 that might be triggered by the virus-induced endothelial disturbances. SARS-CoV-2-related olfactory impairment seems to be limited to olfactory bulbs. The absence of brainstem MRI abnormalities does not support a brain-related contribution to respiratory distress in COVID-19.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSIs there common brain MRI abnormalities patterns in non-survivors of coronavirus disease 2019 ?\n\nFindingsIn a case series of 19 non-survivors of severe COVID-19 disease, early postmortem brain MRI demonstrated patterns evocative of intracranial vasculopathy in 4 decedents: subcortical micro- and macro-bleeds (2 decedents), cortico-subcortical edematous changes evocative of posterior reversible encephalopathy syndrome (PRES, one decedent), and nonspecific deep white matter changes (one decedent). Asymmetric olfactory bulbs were found in 4 other decedents but without downstream olfactory tract abnormalities.\n\nMeaningPostmortem brain MRI demonstrates hemorrhagic and PRES-related brain lesions in non-survivors of COVID-19 that might be triggered by virus-induced endothelial disturbances.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tim Coolen", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Valentina Lolli", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Niloufar Sadeghi", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Antonin Rovai", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Nicola Trotta", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Fabio S Taccone", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Jacques Creteur", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Sophie Henrard", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Jean-Christophe Goffard", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Olivier Dewitte", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Gilles Naeije", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Serge Goldman", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + }, + { + "author_name": "Xavier De Tiege", + "author_inst": "CUB Hopital Erasme, Universite libre de Bruxelles, Brussels, Belgium" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.05.04.20091041", "rel_title": "The Social and Economic Factors Underlying the Impact of COVID-19 Cases and Deaths in US Counties", @@ -1483513,45 +1483969,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.02.20080036", - "rel_title": "Hydroxychloroquine and azithromycin plus zinc vs hydroxychloroquine and azithromycin alone: outcomes in hospitalized COVID-19 patients", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20080036", - "rel_abs": "BackgroundCOVID-19 has rapidly emerged as a pandemic infection that has caused significant mortality and economic losses. Potential therapies and means of prophylaxis against COVID-19 are urgently needed to combat this novel infection. As a result of in vitro evidence suggesting zinc sulfate may be efficacious against COVID-19, our hospitals began using zinc sulfate as add-on therapy to hydroxychloroquine and azithromycin. We performed a retrospective observational study to compare hospital outcomes among patients who received hydroxychloroquine and azithromycin plus zinc versus hydroxychloroquine and azithromycin alone.\n\nMethodsData was collected from electronic medical records for all patients being treated with admission dates ranging from March 2, 2020 through April 5, 2020. Initial clinical characteristics on presentation, medications given during the hospitalization, and hospital outcomes were recorded. Patients in the study were excluded if they were treated with other investigational medications.\n\nResultsThe addition of zinc sulfate did not impact the length of hospitalization, duration of ventilation, or ICU duration. In univariate analyses, zinc sulfate increased the frequency of patients being discharged home, and decreased the need for ventilation, admission to the ICU, and mortality or transfer to hospice for patients who were never admitted to the ICU. After adjusting for the time at which zinc sulfate was added to our protocol, an increased frequency of being discharged home (OR 1.53, 95% CI 1.12-2.09) reduction in mortality or transfer to hospice remained significant (OR 0.449, 95% CI 0.271-0.744).\n\nConclusionThis study provides the first in vivo evidence that zinc sulfate in combination with hydroxychloroquine may play a role in therapeutic management for COVID-19.\n\n40-word summary: Zinc sulfate added to hydroxychloroquine and azithromycin may improve outcomes among hospitalized patients.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Philip Carlucci", - "author_inst": "New York University Grossman School of Medicine, Department of Medicine, New York, NY" - }, - { - "author_name": "Tania Ahuja", - "author_inst": "New York University Langone Health, Department of Pharmacy, New York, NY" - }, - { - "author_name": "Christopher M Petrilli", - "author_inst": "New York University Grossman School of Medicine, Department of Medicine, New York, NY" - }, - { - "author_name": "Harish Rajagopalan", - "author_inst": "NYU Langone Health, New York, NY" - }, - { - "author_name": "Simon Jones", - "author_inst": "Division of Healthcare Delivery Science, Department of Population Health, NYU Grossman School of Medicine, New York, NY" - }, - { - "author_name": "Joseph Rahimian", - "author_inst": "NYU Langone" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.03.20087056", "rel_title": "Covid-19 Pandemic in relation to levels of Pollution with PM2.5 and Ambient Salinity. An Environmental Wake-up Call", @@ -1483951,6 +1484368,61 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.05.08.084061", + "rel_title": "Comparison of SARS-CoV-2 spike protein binding to human, pet, farm animals, and putative intermediate hosts ACE2 and ACE2 receptors", + "rel_date": "2020-05-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.08.084061", + "rel_abs": "The emergence of a novel coronavirus, SARS-CoV-2, resulted in a pandemic. Here, we used recently released X-ray structures of human ACE2 bound to the receptor-binding domain (RBD) of the spike protein (S) from SARS-CoV-2 to predict its binding to ACE2 proteins from different animals, including pets, farm animals, and putative intermediate hosts of SARS-CoV-2. Comparing the interaction sites of ACE2 proteins known to serve or not serve as receptor allows to define residues important for binding. From the 20 amino acids in ACE2 that contact S up to seven can be replaced and ACE2 can still function as the SARS-CoV-2 receptor. These variable amino acids are clustered at certain positions, mostly at the periphery of the binding site, while changes of the invariable residues prevent S-binding or infection of the respective animal. Some ACE2 proteins even tolerate the loss or the acquisition of N-glycosylation sites located near the S-interface. Of note, pigs and dogs which are not or not effectively infected, respectively, have only a few changes in the binding site have relatively low levels of ACE2 in the respiratory tract. Comparison of the RBD of S of SARS-CoV-2 with viruses from bat and pangolin revealed that the latter contains only one substitution, whereas the bat virus exhibits five. However, ACE2 of pangolin exhibit seven changes relative to human ACE2, a similar number of substitutions is present in ACE2 of bats, raccoon, and civet suggesting that SARS-CoV-2 may not especially adapted to ACE2 of any of its putative intermediate hosts. These analyses provide new insight into the receptor usage and animal source/origin of SARS-COV-2.\n\nIMPORTANCESARS-CoV-2 is threatening people worldwide and there are no drugs or vaccines available to mitigate its spread. The origin of the virus is still unclear and whether pets and livestock can be infected and transmit SARS-CoV-2 are important and unknown scientific questions. Effective binding to the host receptor ACE2 is the first prerequisite for infection of cells and determines the host range. Our analysis provides a framework for the prediction of potential hosts of SARS-CoV-2. We found that ACE2 from species known to support SARS-CoV-2 infection tolerate many amino acid changes indicating that the species barrier might be low. However, the lower expression of ACE2 in the upper respiratory tract of some pets and livestock means more research and monitoring should be done to explore the animal source of infection and the risk of potential cross-species transmission. Finally, the analysis also showed that SARS-CoV-2 may not specifically adapted to any of its putative intermediate hosts.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Xiaofeng Zhai", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Jiumeng Sun", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Ziqing Yan", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Jie Zhang", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Jin Zhao", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Zongzheng Zhao", + "author_inst": "Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, China." + }, + { + "author_name": "Qi Gao", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Wan-Ting He", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + }, + { + "author_name": "Michael Veit", + "author_inst": "Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin, Germany." + }, + { + "author_name": "Shuo Su", + "author_inst": "MOE Joint International Research Laboratory of Animal Health and Food Safety, Engineering Laboratory of Animal Immunity of Jiangsu Province, College of Veterina" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.08.084384", "rel_title": "ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity", @@ -1485195,37 +1485667,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, - { - "rel_doi": "10.1101/2020.05.04.20090779", - "rel_title": "MantisCOVID: Rapid X-Ray Chest Radiograph and Mortality Rate Evaluation With Artificial Intelligence For COVID-19", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090779", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe novel coronavirus pandemic has negative impacts over the health, economy and well-being of the global population. This negative effect is growing with the high spreading rate of the virus. The most critical step to prevent the spreading of the virus is pre-screening and early diagnosis of the individuals. This results in quaranteeing the patients not to effect the healthy population. COVID-19 is the name of the disease caused by the novel coronavirus. It has a high infection rate and it is urgent to diagnose many patients as we can to prevent the spread of the virus at the early stage. Rapid diagnostic tools development is urgent to save lives. MantisCOVID is a cloud-based pre-diagnosis tool to be accessed from the internet. This tool delivers a rapid screening test by analyzing the X-ray Chest Radiograph scans via Artificial Intelligence (AI) and it also evaluates the mortality rate of patients with the synthesis of the patients history with the machine learning methods. This study reveals the methods used over the platform and evaluation of the algorithms via open datasets.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Yagmur Yasar", - "author_inst": "School of Medicine, Health Sciences University" - }, - { - "author_name": "Berat Tuna Karli", - "author_inst": "Graduate School of Informatics, Middle East Technical University" - }, - { - "author_name": "Cem Coteli", - "author_inst": "Department of Cardiology, Ankara City Hospital" - }, - { - "author_name": "Mert Burkay Coteli", - "author_inst": "Graduate School of Informatics, Middle East Technical University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.06.20092734", "rel_title": "The impact of Coronavirus disease 2019 (COVID-19) on health systems and household resources in Africa and South Asia", @@ -1485425,6 +1485866,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2020.05.04.20090076", + "rel_title": "Infection fatality rate of SARS-CoV-2 infection in a German community with a super-spreading event", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090076", + "rel_abs": "The world faces an unprecedented SARS-CoV2 pandemic where many critical factors still remain unknown. The case fatality rates (CFR) reported in the context of the SARS-CoV-2 pandemic substantially differ between countries. For SARS-CoV-2 infection with its broad clinical spectrum from asymptomatic to severe disease courses, the infection fatality rate (IFR) is the more reliable parameter to predict the consequences of the pandemic. Here we combined virus RT-PCR testing and assessment for SARS-CoV2 antibodies to determine the total number of individuals with SARS-CoV-2 infections in a given population.\n\nMethodsA sero-epidemiological GCP- and GEP-compliant study was performed in a small German town which was exposed to a super-spreading event (carnival festivities) followed by strict social distancing measures causing a transient wave of infections. Questionnaire-based information and biomaterials were collected from a random, household-based study population within a seven-day period, six weeks after the outbreak. The number of present and past infections was determined by integrating results from anti-SARS-CoV-2 IgG analyses in blood, PCR testing for viral RNA in pharyngeal swabs and reported previous positive PCR tests.\n\nResultsOf the 919 individuals with evaluable infection status (out of 1,007; 405 households) 15.5% (95% CI: [12.3%; 19.0%]) were infected. This is 5-fold higher than the number of officially reported cases for this community (3.1%). Infection was associated with characteristic symptoms such as loss of smell and taste. 22.2% of all infected individuals were asymptomatic. With the seven SARS-CoV-2-associated reported deaths the estimated IFR was 0.36% [0.29%; 0.45%]. Age and sex were not found to be associated with the infection rate. Participation in carnival festivities increased both the infection rate (21.3% vs. 9.5%, p<0.001) and the number of symptoms in the infected (estimated relative mean increase 1.6, p=0.007). The risk of a person being infected was not found to be associated with the number of study participants in the household this person lived in. The secondary infection risk for study participants living in the same household increased from 15.5% to 43.6%, to 35.5% and to 18.3% for households with two, three or four people respectively (p<0.001).\n\nConclusionsWhile the number of infections in this high prevalence community is not representative for other parts of the world, the IFR calculated on the basis of the infection rate in this community can be utilized to estimate the percentage of infected based on the number of reported fatalities in other places with similar population characteristics. Whether the specific circumstances of a super-spreading event not only have an impact on the infection rate and number of symptoms but also on the IFR requires further investigation. The unexpectedly low secondary infection risk among persons living in the same household has important implications for measures installed to contain the SARS-CoV-2 virus pandemic.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Hendrik Streeck", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Bianca Schulte", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Beate Kuemmerer", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Enrico Richter", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Tobias Hoeller", + "author_inst": "Clinical Study Core Unit, Study Centre Bonn (SZB), University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Christine Fuhrmann", + "author_inst": "Clinical Study Core Unit, Study Centre Bonn (SZB), University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Eva Bartok", + "author_inst": "Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Ramona Dolscheid", + "author_inst": "Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Moritz Berger", + "author_inst": "Institute for Medical Biometry, Informatics and Epidemiology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Lukas Wessendorf", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Monika Eschbach-Bludau", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Angelika Kellings", + "author_inst": "Clinical Study Core Unit, Study Centre Bonn (SZB), University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Astrid Schwaiger", + "author_inst": "Biobank Core Unit, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Martin Coenen", + "author_inst": "Clinical Study Core Unit, Study Centre Bonn (SZB), University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Per Hoffmann", + "author_inst": "Institute of Human Genetics, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Markus Noethen", + "author_inst": "Institute of Human Genetics, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Anna-Maria Eis-Huebinger", + "author_inst": "Institute of Virology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Martin Exner", + "author_inst": "Institute for Hygiene and Public Health, University Hospital, University of Bonn" + }, + { + "author_name": "Ricarda Schmithausen", + "author_inst": "Institute for Hygiene and Public Health, University Hospital, University of Bonn" + }, + { + "author_name": "Matthias Schmid", + "author_inst": "Institute for Medical Biometry, Informatics and Epidemiology, University Hospital, University of Bonn, Germany" + }, + { + "author_name": "Gunther Hartmann", + "author_inst": "Institute of Clinical Chemistry and Clinical Pharmacology, University Hospital, University of Bonn, Germany; German Center for Infection Research (DZIF), partne" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.04.20090555", "rel_title": "Laboratory findings associated with mechanical ventilation requirement and mortality among hospitalized individuals with Covid-19 in Eastern Massachusetts", @@ -1486945,49 +1487485,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.05.20092627", - "rel_title": "Weather Conditions and COVID-19 Transmission: Estimates and Projections", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092627", - "rel_abs": "BackgroundUnderstanding and projecting the spread of COVID-19 requires reliable estimates of the impact of weather on the transmission of the virus. Prior research on this topic has been inconclusive. We estimate the impact of weather on transmission by assembling one of the largest datasets integrating COVID-19 infections and weather, and use the results to project weather impact on transmission in the coming months.\n\nMethodsWe assemble a dataset that includes virus transmission and weather data across 3,739 locations from December 12, 2019 to April 22, 2020. Using simulation, we identify key challenges to reliable estimation of weather impacts on transmission, design a statistical method to overcome these challenges, and validate it in a blinded simulation study. Controlling for location-specific response trends we then estimate how different weather variables are associated with the reproduction number for COVID-19. We then use the estimates to project the relative weather-related risk of COVID-19 transmission across the world and in large cities.\n\nResultsWe show that the delay between exposure and detection of infection complicates the estimation of weather impact on COVID-19 transmission, potentially explaining significant variability in results to date. Correcting for that distributed delay and offering conservative estimates, we find a negative relationship between temperatures above 25 degrees Celsius and estimated reproduction number ([Formula]), with each degree Celsius associated with a 3.1% (95% CI: 1.5-4.8%) reduction in [Formula]. Higher levels of relative humidity strengthen the negative effect of temperature above 25 degrees. Moreover, one millibar of additional pressure increases [Formula] by approximately 0.8 percent (0.6-1%) at the median pressure (1016 millibars) in our sample. We also find significant positive effects for wind speed, precipitation, and diurnal temperature on [Formula]. Sensitivity analysis and simulations show that results are robust to multiple assumptions. Despite conservative estimates, weather effects are associated with a 43% change in [Formula] between the 5th and 95th percentile of weather conditions in our sample.\n\nConclusionsThe results provide evidence for the relationship between several weather variables and the spread of COVID-19, finding a negative association between temperature and humidity and transmission. However, the (conservatively) estimated effects of summer weather are not strong enough to seasonally control the epidemic in most locations.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ran Xu", - "author_inst": "University of Connecticut" - }, - { - "author_name": "Hazhir Rahmandad", - "author_inst": "MIT Sloan School of Management" - }, - { - "author_name": "Marichi Gupta", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Catherine DiGennaro", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Navid Ghaffarzadegan", - "author_inst": "Virginia Tech" - }, - { - "author_name": "Heresh Amini", - "author_inst": "Section of Environmental Health, Department of Public Health, University of Copenhagen; Department of Environmental Health, Harvard T.H. Chan School of Public H" - }, - { - "author_name": "Mohammad S. Jalali", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.04.20079301", "rel_title": "COVID-19 and homelessness in England: a modelling study of theCOVID-19 pandemic among people experiencing homelessness, and theimpact of a residential intervention to isolate vulnerable people andcare for people with symptoms", @@ -1487175,6 +1487672,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.05.06.20092858", + "rel_title": "Spatial Network based model forecasting transmission and control of COVID-19", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20092858", + "rel_abs": "The SARS-CoV-2 driven infectious novel coronavirus disease (COVID-19) has been declared a pandemic by virtue of its brutal impact on the world in terms of loss on human life, health, economy, and other crucial resources. With the aim to explore more about its aspects, we adopted the SEIQRD (Susceptible-Exposed-Infected-Quarantine-Recovered-Death) pandemic spread with a time delay on the heterogeneous population and geography in this work. Focusing on the spatial heterogeneity, the entire population of interest in a region is divided into small distinct geographical sub regions, which interact by means of migration networks across boundaries. Utilizing the estimations of the time delay differential equations based model, we analyzed the spread dynamics of disease in a region and its sub regions. The model based numerical outcomes are validated from real time available data for India. We computed the approximate peak infection in forward time and relative timespan when disease outspread halts. To further evaluate the influence of the delay on the long term system dynamics, the sensitivity analysis is performed on time delay. The most crucial parameter, basic reproduction number R0 and its time-dependent generalization, has been estimated at both regional and sub regional levels. The impact of the most significant lockdown measure that has been implemented in India to contain the pandemic spread has been extensively studied by considering no lockdown scenario. A suggestion based on outcomes, for a bit relaxed lockdown, followed by an extended period of strict social distancing as one of the most effective control measures to manage COVID-19 spread is provided for India.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Arvind Kumar Gupta", + "author_inst": "Indian Institute of Technology Ropar" + }, + { + "author_name": "Natasha Sharma", + "author_inst": "Kanya Maha Vidyalaya, Jalandhar" + }, + { + "author_name": "Atul Kumar Verma", + "author_inst": "Indian Institute of Technology, Ropar" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.03.20089938", "rel_title": "Protocol for a systematic review of qualitative and quantitative effects of cardiovascular disease risk communication using heart age concepts", @@ -1488291,77 +1488815,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.01.20087239", - "rel_title": "Immune alterations during SARS-CoV-2-related acute respiratory distress syndrome", - "rel_date": "2020-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087239", - "rel_abs": "We report a longitudinal analysis of the immune response associated with a fatal case of COVID-19. This patient exhibited a rapid evolution towards multiorgan failure. SARS-CoV-2 was detected in multiple nasopharyngeal, blood, and pleural samples, despite antiviral and immunomodulator treatment. Clinical evolution in the blood was marked by an increase (2-3 fold) in differentiated effector T cells expressing exhaustion (PD-1) and senescence (CD57) markers, an expansion of antibody-secreting cells, a 15-fold increase in {gamma}{delta} T-cell and proliferating NK-cell populations, and the total disappearance of monocytes, suggesting lung trafficking. In the serum, waves of a proinflammatory cytokine storm, Th1 and Th2 activation, and markers of T-cell exhaustion, apoptosis, cell cytotoxicity, and endothelial activation were observed until the fatal outcome. This case underscores the need for well-designed studies to investigate complementary approaches to control viral replication, the source of the hyperinflammatory status, and immunomodulation to target the pathophysiological response.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Lila Bouadma", - "author_inst": "APHP-Hopital Bichat" - }, - { - "author_name": "Aurelie Wiedemann", - "author_inst": "Vaccine research Institute" - }, - { - "author_name": "Juliette Patrier", - "author_inst": "APHP-Hopital Bichat" - }, - { - "author_name": "Mathieu Surenaud", - "author_inst": "Vaccine Research Institute" - }, - { - "author_name": "Paul-Henri Wicky", - "author_inst": "APHP-Hopital Bichat" - }, - { - "author_name": "Emile Foucat", - "author_inst": "VAccine Research Institute" - }, - { - "author_name": "Jean-Luc Diehl", - "author_inst": "APHP-Hopital Georges Pompidou" - }, - { - "author_name": "Boris P Hejblum", - "author_inst": "Univ Bordeaux" - }, - { - "author_name": "Fabrice Sinnah", - "author_inst": "APHP-Hopital Bichat" - }, - { - "author_name": "Etienne de Montmollin", - "author_inst": "APHP-Hopital Bichat" - }, - { - "author_name": "Christine Lacabaratz", - "author_inst": "Vaccine Research Insitute" - }, - { - "author_name": "Rodolphe Thiebaut", - "author_inst": "Univ Bordeaux" - }, - { - "author_name": "Jean-Francois Timsit", - "author_inst": "APHP-Hopital Bichat" - }, - { - "author_name": "Yves Levy", - "author_inst": "VAccine Research Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.01.20088054", "rel_title": "The landscape of host genetic factors involved in infection to common viruses and SARS-CoV-2", @@ -1488648,6 +1489101,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.06.074039", + "rel_title": "The heterogeneous landscape and early evolution of pathogen-associated CpG and UpA dinucleotides in SARS CoV-2", + "rel_date": "2020-05-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.06.074039", + "rel_abs": "COVID-19 can lead to acute respiratory syndrome, which can be due to dysregulated immune signaling. We analyze the distribution of CpG dinucleotides, a pathogen-associated molecular pattern, in the SARS-CoV-2 genome. We find that the CpG content, which we characterize by a force parameter that accounts for statistical constraints acting on the genome at the nucleotidic and amino-acid levels, is, on average, low compared to other pathogenic betacoronaviruses. However, the CpG force widely fluctuates along the genome, with a particularly low value, comparable to the circulating seasonal HKU1, in the spike coding region and a greater value, comparable to SARS and MERS, in the highly expressed nucleocapside coding region (N ORF), whose transcripts are relatively abundant in the cytoplasm of infected cells and present in the 3UTRs of all subgenomic RNA. This dual nature of CpG content could confer to SARS-CoV-2 the ability to avoid triggering pattern recognition receptors upon entry, while eliciting a stronger response during replication. We then investigate the evolution of synonymous mutations since the outbreak of the COVID-19 pandemic, finding a signature of CpG loss in regions with a greater CpG force. Sequence motifs preceding the CpG-loss-associated loci in the N ORF match recently identified binding patterns of the Zinc finger Anti-viral Protein. Using a model of the viral gene evolution under human host pressure, we find that synonymous mutations seem driven in the SARS-CoV-2 genome, and particularly in the N ORF, by the viral codon bias, the transition-transversion bias and the pressure to lower CpG content.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Andrea Di Gioacchino", + "author_inst": "Ecole Normale Superieure, PSL and CNRS" + }, + { + "author_name": "Petr Sulc", + "author_inst": "Arizona State University" + }, + { + "author_name": "Anastassia V Komarova", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Benjamin D Greenbaum", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Remi Monasson", + "author_inst": "Ecole Normale Superieure, PSL and CNRS" + }, + { + "author_name": "Simona Cocco", + "author_inst": "Ecole Normale Superieure, PSL and CNRS" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.05.07.082487", "rel_title": "COVID-19: Viral-host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection.", @@ -1489772,61 +1490264,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.04.20088146", - "rel_title": "Pooling RT-PCR test of SARS-CoV-2 for large cohort of 'healthy' and infection-suspected patients: A prospective and consecutive study on 1,000 individuals", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20088146", - "rel_abs": "BackgroundSARS-CoV-2 testing reagents are expected to become in short supply worldwide. However, little is unknown whether the pooling strategy detects SARS-CoV-2 with accuracy.\n\nMethodTo validate the feasibility of pooling samples, serial dilution analysis and spike-in experiment were conducted using synthetic DNA and nucleic acids extracted from SARS-CoV-2 positive and negative patients. Furthermore, we studied a total of 1,000 individuals, who were 667 \"healthy\" (195 healthcare workers and 472 hospitalized patients with other disorders than COVID-19 infection) individuals and 333 infection-suspected patients with cough and fever, were tested.\n\nResultsSerial dilution analysis showed the limit of detection of around 10-100 copies according to National Institute of Infectious Diseases, Japan. Spike-in experiment demonstrated RT-qPCR detect positive signal in pooling samples of SARS-CoV-2 negative and positive patient at the 5-, 10-, 20-fold dilution. By screening with pooling strategy by the end of April, 2020, there are 12 COVID-19 patients in 333 infection suspected patients (3.6%) and zero in 667 \"healthy\". We obtained these results with total running 538 times (instead of 1,000 times) by pooling strategy.\n\nConclusionPooling samples is feasible for saving test reagents and detecting SARS-CoV-2 in clinical setting to prevent the spread of the virus and nosocomial transmission.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Yosuke Hirotsu", - "author_inst": "Yamanashi Central Hospital" - }, - { - "author_name": "Makoto Maejima", - "author_inst": "Yamanashi Central Hospital" - }, - { - "author_name": "Masahiro Shibusawa", - "author_inst": "Yamanashi Central Hospital" - }, - { - "author_name": "Yuki Nagakubo", - "author_inst": "Yamanashi Central Hospital" - }, - { - "author_name": "Kazuhiro Hosaka", - "author_inst": "Yamanashi Central Hospital" - }, - { - "author_name": "Kenji Amemiya", - "author_inst": "Yamanashi Central Hospital" - }, - { - "author_name": "Hitomi Sueki", - "author_inst": "Yamanashi Central Hospital" - }, - { - "author_name": "Miyoko Hayakawa", - "author_inst": "Yamanashi Central Hospital" - }, - { - "author_name": "Hitoshi Mochizuki", - "author_inst": "Yamanashi Central Hospital" - }, - { - "author_name": "Masao Omata", - "author_inst": "Yamanashi Central Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.01.20088047", "rel_title": "The reproduction number of COVID-19 and its correlation with public health interventions", @@ -1490018,6 +1490455,109 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.06.080119", + "rel_title": "Multiple SARS-CoV-2 introductions shaped the early outbreak in Central Eastern Europe: comparing Hungarian data to a worldwide sequence data-matrix", + "rel_date": "2020-05-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.06.080119", + "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 is the third highly pathogenic human coronavirus in history. Since the emergence in Hubei province, China, during late 2019 the situation evolved to pandemic level. Following China, Europe was the second epicenter of the pandemic. To better comprehend the detailed founder mechanisms of the epidemic evolution in Central-Eastern Europe, particularly in Hungary, we determined the full-length SARS-CoV-2 genomes from 32 clinical samples collected from laboratory confirmed COVID-19 patients over the first month of disease in Hungary. We applied a haplotype network analysis on all available complete genomic sequences of SARS-CoV-2 from GISAID database as of the 21th of April, 2020. We performed additional phylogenetic and phylogeographic analyses to achieve the recognition of multiple and parallel introductory events into our region. Here we present a publicly available network imaging of the worldwide haplotype relations of SARS-CoV-2 sequences and conclude the founder mechanisms of the outbreak in Central-Eastern Europe.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Gabor Kemenesi", + "author_inst": "University of Pecs" + }, + { + "author_name": "Safia Zeghbib", + "author_inst": "University of Pecs" + }, + { + "author_name": "Balazs Somogyi", + "author_inst": "University of Pecs" + }, + { + "author_name": "Gabor E Toth", + "author_inst": "University of Pecs" + }, + { + "author_name": "Krisztian Banyai", + "author_inst": "Centre for Agricultural Research, Hungary" + }, + { + "author_name": "Norbert Solymosi", + "author_inst": "University of Veterinary Medicine Budapest" + }, + { + "author_name": "Peter M Szabo", + "author_inst": "Stromal Biology, Bristol-Myers Squibb, Princeton" + }, + { + "author_name": "Istvan Szabo", + "author_inst": "National Food Safety Office, Budapest" + }, + { + "author_name": "Adam Balint", + "author_inst": "National Food Safety Office, Budapest" + }, + { + "author_name": "Peter Urban", + "author_inst": "Szentagothai Research Centre, Bioinformatics Research Group" + }, + { + "author_name": "Robert Herczeg", + "author_inst": "Szentagothai Research Centre, Bioinformatics Research Group" + }, + { + "author_name": "Attila Gyenesei", + "author_inst": "Szentagothai Research Centre, Bioinformatics Research Group" + }, + { + "author_name": "Agnes Nagy", + "author_inst": "Hungarian Defense Forces, Military Medical Centre" + }, + { + "author_name": "Csaba I Pereszlenyi", + "author_inst": "Hungarian Defense Forces, Military Medical Centre" + }, + { + "author_name": "Gergely Babinszky", + "author_inst": "Hungarian Defense Forces, Military Medical Centre" + }, + { + "author_name": "Gabor Dudas", + "author_inst": "Hungarian Defense Forces, Military Medical Centre" + }, + { + "author_name": "Gabriella Terhes", + "author_inst": "Institute of Clinical Microbiology, University of Szeged" + }, + { + "author_name": "Viktor Zoldi", + "author_inst": "Independent researcher, Vantaa, Finland" + }, + { + "author_name": "Robert Lovas", + "author_inst": "Institute for Computer Science and Control, Hungarian Academy of Sciences" + }, + { + "author_name": "Szabolcs Tenczer", + "author_inst": "Institute for Computer Science and Control, Hungarian Academy of Sciences" + }, + { + "author_name": "Laszlo Kornya", + "author_inst": "Central Hospital of Southern Pest, Budapest" + }, + { + "author_name": "Ferenc Jakab", + "author_inst": "University of Pecs" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.05.079202", "rel_title": "Neutralization of SARS-CoV-2 by destruction of the prefusion Spike", @@ -1491102,97 +1491642,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.02.20080879", - "rel_title": "Validation of a commercially available SARS-CoV-2 serological Immunoassay", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20080879", - "rel_abs": "ObjectivesTo validate the diagnostic accuracy of a Euroimmun SARS-CoV-2 IgG and IgA immunoassay for COVID-19.\n\nMethodsIn this unmatched (1:1) case-control validation study, we used sera of 181 laboratory-confirmed SARS-CoV-2 cases and 176 controls collected before SARS-CoV-2 emergence. Diagnostic accuracy of the immunoassay was assessed against a whole spike protein-based recombinant immunofluorescence assay (rIFA) by receiver operating characteristic (ROC) analyses. Discrepant cases between ELISA and rIFA were further tested by pseudo-neutralization assay.\n\nResultsCOVID-19 patients were more likely to be male and older than controls, and 50.3% were hospitalized. ROC curve analyses indicated that IgG and IgA had high diagnostic accuracies with AUCs of 0.992 (95% Confidence Interval [95%CI]: 0.986-0.996) and 0.977 (95%CI: 0.963-0.990), respectively. IgG assays outperformed IgA assays (p=0.008). Taking an assessed 15% inter-assay imprecision into account, an optimized IgG ratio cut-off > 1.5 displayed a 100% specificity (95%CI: 98-100) and a 100% positive predictive value (95%CI: 97-100). A 0.5 cut-off displayed a 97% sensitivity (95%CI: 93-99) and a 97% negative predictive value (95%CI: 93-99). Substituting these thresholds for the manufacturers, improved assay performance, leaving 12% of IgG ratios indeterminate between 0.5-1.5.\n\nConclusionsThe Euroimmun assay displays a nearly optimal diagnostic accuracy using IgG against SARS-CoV-2 in patient samples, with no obvious gains from IgA serology. The optimized cut-offs are fit for rule-in and rule-out purposes, allowing determination of whether individuals in our study population have been exposed to SARS-CoV-2 or not. IgG serology should however not be considered as a surrogate of protection at this stage.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Benjamin Meyer", - "author_inst": "University of Geneva" - }, - { - "author_name": "Giulia Torriani", - "author_inst": "University of Geneva" - }, - { - "author_name": "Sabine Yerly", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Lena Mazza", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Adrien Calame", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Isabelle Arm-Vernez", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Gert Zimmer", - "author_inst": "University of Bern" - }, - { - "author_name": "Thomas Agoritsas", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Jerome Stirnemann", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Herve Spechbach", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Idris Guessous", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Silvia Stringhini", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Jerome Pugin", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Pascale Roux-Lombard", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Lionel Fontao", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Claire-Anne Siegrist", - "author_inst": "University of Geneva" - }, - { - "author_name": "Isabella Eckerle", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Nicolas Vuilleumier", - "author_inst": "Geneva University Hospitals" - }, - { - "author_name": "Laurent Kaiser", - "author_inst": "Geneva University Hospitals" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.02.20088484", "rel_title": "Effects of Coronavirus Disease 2019 (COVID-19) on Maternal, Perinatal and Neonatal Outcomes: a Systematic Review of 266 Pregnancies", @@ -1491588,6 +1492037,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.05.01.20086801", + "rel_title": "Efficient prevalence estimation and infected sample identification with group testing for SARS-CoV-2", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20086801", + "rel_abs": "Extensive virological testing is central to SARS-CoV-2 containment, but many settings face severe limitations on testing. Group testing offers a way to increase throughput by testing pools of combined samples; however, most proposed designs have not yet addressed key concerns over sensitivity loss and implementation feasibility. Here, we combine a mathematical model of epidemic spread and empirically derived viral kinetics for SARS-CoV-2 infections to identify pooling designs that are robust to changes in prevalence, and to ratify losses in sensitivity against the time course of individual infections. Using this framework, we show that prevalence can be accurately estimated across four orders of magnitude using only a few dozen pooled tests without the need for individual identification. We then exhaustively evaluate the ability of different pooling designs to maximize the number of detected infections under various resource constraints, finding that simple pooling designs can identify up to 20 times as many positives compared to individual testing with a given budget. We illustrate how pooling affects sensitivity and overall detection capacity during an epidemic and on each day post infection, finding that sensitivity loss is mainly attributed to individuals sampled at the end of infection when detection for public health containment has minimal benefit. Crucially, we confirm that our theoretical results can be accurately translated into practice using pooled human nasopharyngeal specimens. Our results show that accounting for variation in sampled viral loads provides a nuanced picture of how pooling affects sensitivity to detect epidemiologically relevant infections. Using simple, practical group testing designs can vastly increase surveillance capabilities in resource-limited settings.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Brian Cleary", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "James A Hay", + "author_inst": "Harvard T H Chan School of Public Health" + }, + { + "author_name": "Brendan Blumenstiel", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Maegan Harden", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Michelle Cipicchio", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Jon Bezney", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Brooke Simonton", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "David Hong", + "author_inst": "Wharton Statistics, University of Pennsylvania" + }, + { + "author_name": "Madikay Senghore", + "author_inst": "Harvard School of Public Health" + }, + { + "author_name": "Abdul K Sesay", + "author_inst": "MRC Unit The Gambia at London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Stacey Gabriel", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Aviv Regev", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Michael J Mina", + "author_inst": "Harvard School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.02.20084947", "rel_title": "Voluntary Cyclical Distancing: A potential alternative to constant level mandatory social distancing, relying on an 'infection weather report'", @@ -1492604,65 +1493120,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.01.20087437", - "rel_title": "Does BCG protect against SARS-CoV-2 infection ?: elements of proof.", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087437", - "rel_abs": "BackgroundThere are several factors explaining the difference in the spread of SARS-CoV-2 infection including the BCG vaccination. This fact is supported by the concept of beneficial non specific effect of this live vaccine associated to its interaction with the immune system.\n\nOur study aims to identify the correlation between the universal BCG vaccination policy and the mortality attributed to COVID-19.\n\nMethodsWe conducted an epidemiological study in which we collected COVID-19 pandemic data of April 11th, 2020 from the web site worldometers.info. The exclusion criteria for our study were a number of inhabitants less than one million, low-income countries according to the World Bank classification, a total number of infection cases less than 500 and countries that have performed less than one hundred tests per million inhabitants.\n\nResultsCountries that never had universal BCG vaccination policy have a higher mortality (correlated to performed diagnostic tests) attributed to SARS-CoV-2 infection (p<0.001).\n\nWe found that the year of introduction of vaccination influenced significantly the mortality. Countries that started immunization policy before 1960 had more favorable results (p=0.049).\n\nFor countries that started the BCG vaccination after 1960, countries with current policies have lower mortality attributed to SARS-CoV-2 infection than countries that have stopped immunization (p=0.047).\n\nConclusionsCountries that have a BCG vaccination policy have a lower mortality attributed to SARS-CoV-2 infection. The populations of countries that applied this immunization before 1960 are more protected even if this universal policy has been interrupted.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Yassine Ouanes", - "author_inst": "University of Tunis El Manar, Faculty of Medicine of Tunis" - }, - { - "author_name": "Mokhtar Bibi", - "author_inst": "University of Tunis El Manar, Faculty of Medicine of Tunis, Tunisia" - }, - { - "author_name": "Nesrine Baradai", - "author_inst": "University of Tunis El Manar, Faculty of Medicine of Tunis, Tunisia" - }, - { - "author_name": "Marouane Boukhris", - "author_inst": "University of Tunis El Manar, Faculty of Medicine of Tunis, Tunisia" - }, - { - "author_name": "Kays Chaker", - "author_inst": "University of Tunis El Manar, Faculty of Medicine of Tunis, Tunisia" - }, - { - "author_name": "Aziz Kacem", - "author_inst": "University of Tunis El Manar, Faculty of Medicine of Tunis, Tunisia" - }, - { - "author_name": "Houcem Hedhli", - "author_inst": "University of Tunis El Manar, Faculty of Medicine of Tunis, Tunisia" - }, - { - "author_name": "Kheireddine Mrad Deli", - "author_inst": "University of Tunis El Manar, Faculty of Medicine of Tunis, Tunisia" - }, - { - "author_name": "Ahmed Sellami", - "author_inst": "University of Tunis El Manar, Faculty of Medicine of Tunis, Tunisia" - }, - { - "author_name": "Sami Ben Rhouma", - "author_inst": "University of Tunis El Manar, Faculty of Medicine of Tunis, Tunisia" - }, - { - "author_name": "Yassine Nouira", - "author_inst": "University of Tunis El Manar, Faculty of Medicine of Tunis, Tunisia" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.01.20087429", "rel_title": "Statistical Properties of Stepped Wedge Cluster-Randomized Trials in Infectious Disease Outbreaks", @@ -1492790,6 +1493247,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.01.20087833", + "rel_title": "Early Evidence of Disparities in COVID-19 Testing in US Cities", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087833", + "rel_abs": "BackgroundPreliminary evidence has shown inequities in COVID-19 related cases and deaths in the US.\n\nObjectiveWe explored the emergence of spatial inequities in COVID-19 testing, positivity, confirmed cases, and mortality in New York City, Philadelphia, and Chicago during the first six months of the pandemic.\n\nDesignEcological, observational study at the zip code tabulation area (ZCTA) level from March to September 2020.\n\nSettingChicago, New York City and Philadelphia.\n\nParticipantsAll populated ZCTAs in the three cities.\n\nMeasuresOutcomes were ZCTA-level COVID-19 testing, positivity, confirmed cases, and mortality cumulatively through the end of September. Predictors were the CDC social vulnerability index and its four domains, obtained from the 2014-2018 American Community Survey. We examined the spatial autocorrelation of COVID-19 outcomes using global and local Morans I and estimated associations using spatial conditional autoregressive negative binomial models.\n\nResultsWe found spatial clusters of high and low positivity, confirmed cases and mortality, co-located with clusters of low and high social vulnerability. We also found evidence for the existence of spatial inequities in testing, positivity, confirmed cases and mortality for the three cities. Specifically, neighborhoods with higher social vulnerability had lower testing rates, higher positivity ratios, confirmed case rates and mortality rates.\n\nLimitationsZCTAs are imperfect and heterogeneous geographical units of analysis. We rely on surveillance data, which may be incomplete.\n\nConclusionWe found spatial inequities in COVID-19 testing, positivity, confirmed cases, and mortality in three large cities of the US.\n\nRegistrationN/A\n\nFunding sourceNIH (DP5OD26429) and RWJF (77644)", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Usama Bilal", + "author_inst": "Drexel University" + }, + { + "author_name": "Loni P Tabb", + "author_inst": "Drexel University" + }, + { + "author_name": "Sharrelle Barber", + "author_inst": "Drexel University" + }, + { + "author_name": "Ana V Diez-Roux", + "author_inst": "Drexel University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.01.20087460", "rel_title": "Prediction of Spreads of COVID-19 in India from Current Trend", @@ -1494130,57 +1494618,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.29.20084277", - "rel_title": "Vitamin D status, body mass index, ethnicity and COVID-19: Initial analysis of the first-reported UK Biobank COVID-19 positive cases (n 580) compared with negative controls (n 723)", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084277", - "rel_abs": "In this short report we present a preliminary assessment of the serum 25-hydroxyvitamin D status (25(OH)D), body mass index (BMI), ethnicity and other lifestyle factors in the first-reported UK Biobank COVID-19 positive cases (n 580) compared with negative controls (n 723). The COVID-19 cases include those who have been treated as a hospital inpatient as well as those who have not, and are from England only. Mean (SD) for age was 57.5 (8.7) in positive cases and 57.9 (8.7) in negative controls.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Andrea L Darling", - "author_inst": "University of Surrey" - }, - { - "author_name": "Kourosh R Ahmadi", - "author_inst": "University of Surrey" - }, - { - "author_name": "Kate A Ward", - "author_inst": "University of Southampton" - }, - { - "author_name": "Nicholas C Harvey", - "author_inst": "University of Southampton" - }, - { - "author_name": "Alexessander Couto Alves", - "author_inst": "University of Surrey" - }, - { - "author_name": "Deborah K Dunn-Waters", - "author_inst": "University of Surrey" - }, - { - "author_name": "Susan Alexandra Lanham-New", - "author_inst": "University of Surrey" - }, - { - "author_name": "Cyrus Cooper", - "author_inst": "University of Southampton/University of Oxford" - }, - { - "author_name": "David J Blackbourn", - "author_inst": "University of Surrey" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.29.20084699", "rel_title": "Agent-Level Pandemic Simulation (ALPS) for Analyzing Effects of Lockdown Measures", @@ -1494332,6 +1494769,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.29.20084376", + "rel_title": "A novel deterministic forecast model for COVID-19 epidemic based on a single ordinary integro-differential equation", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084376", + "rel_abs": "In this paper we present a new approach to deterministic modelling of COVID-19 epidemic. Our model dynamics is expressed by a single prognostic variable which satisfies an integro-differential equation. All unknown parameters are described with a single, time-dependent variable R(t). We show that our model has similarities to classic compartmental models, such as SIR, and that the variable R(t) can be interpreted as a generalized effective reproduction number. The advantages of our approach are the simplicity of having only one equation, the numerical stability due to an integral formulation and the reliability since the model is formulated in terms of the most trustable statistical data variable: the number of cumulative diagnosed positive cases of COVID-19. Once this dynamic variable is calculated, other non-dynamic variables, such as the number of heavy cases (hospital beds), the number of intensive-care cases (ICUs) and the fatalities, can be derived from it using a similarly stable, integral approach. The formulation with a single equation allows us to calculate from real data the values of the sample effective reproduction number, which can then be fitted. Extrapolated values of R(t) can be used in the model to make reliable forecasts, though under the assumption that measures for reducing infections are maintained. We have applied our model to more than 15 countries and the ongoing results are available on a web-based platform [1]. In this paper, we focus on the data for two exemplary countries, Italy and Germany, and show that the model is capable of reproducing the course of the epidemic in the past and forecasting its course for a period of four to five weeks with a reasonable numerical stability.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Felix Koehler-Rieper", + "author_inst": "Goethe-Universtitaet Frankfurt, Germany" + }, + { + "author_name": "Claudius H. F. Roehl", + "author_inst": "Universitaet Leipzig, Germany" + }, + { + "author_name": "Enrico De Micheli", + "author_inst": "IBF - Consiglio Nazionale Delle Ricerche, Genova, Italy" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.01.20084384", "rel_title": "A Susceptible-Infected-Removed (SIR) model of COVID-19 epidemic trend in Malaysia under Movement Control Order (MCO) using a data fitting approach", @@ -1495564,45 +1496028,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.30.20085662", - "rel_title": "Hindsight is 2020 vision: Characterisation of the global response to the COVID-19 pandemic", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20085662", - "rel_abs": "BackgroundThe global impact of COVID-19 and the country-specific responses to the pandemic provide an unparalleled opportunity to learn about different patterns of the outbreak and interventions. We model the global pattern of trajectories of reported COVID-19 cases during the primary response period, with the aim of learning from the past to prepare for the future.\n\nMethodsUsing Bayesian methods, we analyse the response to the COVID-19 outbreak for 158 countries for the period 22 January to 9 June 2020. This encompasses the period in which many countries imposed a variety of response measures and initial relaxation strategies. Instead of modelling specific intervention types and timings for each country explicitly, we adopt a stochastic epidemiological model including a feedback mechanism on virus transmission to capture complex nonlinear dynamics arising from continuous changes in community behaviour in response to rising case numbers. We analyse the overall effect of interventions and community responses across diverse regions. This approach mitigates explicit consideration of issues such as period of infectivity and public adherence to government restrictions.\n\nResultsCountries with the largest cumulative case tallies are characterised by a delayed response, whereas countries that avoid substantial community transmission during the period of study responded quickly. Countries that recovered rapidly also have a higher case identification rate and small numbers of undocumented community transmission at the early stages of the outbreak. We also demonstrate that uncertainty in numbers of undocumented infections dramatically impacts the risk of second waves. Our approach is also effective at pre-empting potential second waves and flare-ups.\n\nConclusionsWe demonstrate the utility of modelling to interpret community behaviour in the early epidemic stages. Two lessons learnt that are important for the future are: i) countries that imposed strict containment measures early in the epidemic fared better with respect to numbers of reported cases; and ii) broader testing is required early in the epidemic to understand the magnitude of undocumented infections and recover rapidly. We conclude that clear patterns of containment are essential prior to relaxation of restrictions and show that modelling can provide insights to this end.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "David J. Warne", - "author_inst": "Queensland University of Technology" - }, - { - "author_name": "Anthony Ebert", - "author_inst": "Universita dell\u00e0 Svizzera italiana" - }, - { - "author_name": "Christopher Drovandi", - "author_inst": "Queensland University of Technology" - }, - { - "author_name": "Wenbiao Hu", - "author_inst": "Queensland Univeristy of Technology" - }, - { - "author_name": "Antonietta Mira", - "author_inst": "Universit\u00e0 della Svizzera italiana" - }, - { - "author_name": "Kerrie Mengersen", - "author_inst": "Queensland University of Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.30.20086223", "rel_title": "The impact of believing you have had COVID-19 on behaviour: Cross-sectional survey", @@ -1495890,6 +1496315,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, + { + "rel_doi": "10.1101/2020.04.30.20086462", + "rel_title": "Kidney Allograft Recipients Diagnosed with Coronavirus Disease-2019: A Single Center Report", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086462", + "rel_abs": "BackgroundOrgan graft recipients receiving immunosuppressive therapy are likely to be at heightened risk for the Coronavirus Disease 2019 (Covid-19) and adverse outcomes including death. It is therefore important to characterize the clinical course and outcome of Covid-19 in this vulnerable population and identify therapeutic strategies that are safe.\n\nMethodsWe performed a retrospective chart review of 54 adult kidney transplant patients diagnosed with Covid-19 and all managed in New York State, the epicenter of Covid-19 pandemic. All 54 patients were evaluated by video visits, or phone interviews, and referred to our Fever Clinic or Emergency Room for respiratory illness symptoms consistent with Covid-19 and admitted if deemed necessary from March 13, 2020 to April 20, 2020. Characteristics of the patients were stratified by hospitalization status and disease severity. Clinical course including alterations in immunosuppressive therapy were retrieved from their electronic medical records. Primary outcomes included recovery from Covid-19 symptoms, acute kidney injury, graft failure, and case fatality rate.\n\nResultsOf the 54 SARS-Cov-2 positive kidney transplant recipients, 39 with moderate to severe symptoms were admitted and 15 with mild symptoms were managed at home. Hospitalized patients compared to non-hospitalized patients were more likely to be male, of Hispanic ethnicity, and to have cardiovascular disease. At baseline, all but 2 were receiving tacrolimus, mycophenolate mofetil (MMF) and 32 were on a steroid free immunosuppression regimen. Tacrolimus dosage was reduced in 46% of hospitalized patients and maintained at baseline level in the non-hospitalized cohort. Mycophenolate mofetil (MMF) dosage was maintained at the baseline dosage in 11% of hospitalized patients and 64% of non-hospitalized patients and was stopped in 61% hospitalized patients and 0% in the non-hospitalized cohort. Azithromycin or doxycycline were prescribed at a similar rate among hospitalized and non-hospitalized patients (38% vs. 40%). In addition, 50% of hospitalized patients were treated for concurrent bacterial infections including pneumonia, urinary tract infections and sepsis. Hydroxychloroquine was prescribed in 79% of hospitalized patients and only one of 15 non-hospitalized patients. Acute kidney injury occurred in 51% of hospitalized patients. Patients with severe disease were more likely to have elevations in inflammatory biomarkers at presentation. At a median of 21 days follow up, 67% of patients have had their symptoms resolved or improved and 33% have persistent symptoms. Graft failure requiring hemodialysis occurred in 3 of 39 hospitalized patients (8%). Three of 39 (8%) hospitalized patients expired and none of the 15 non-hospitalized patients expired.\n\nConclusionsClinical presentation of Covid-19 in kidney transplant recipients was similar to what has been described in the general population. The case fatality rate in our entire cohort of 54 kidney transplant recipients was reassuringly low and patients with mild symptomology could be successfully managed at home. Data from the our study suggest that a strategy of systematic screening and triage to outpatient or inpatient care, close monitoring, early management of concurrent bacterial infections and judicious use of immunosuppressive drugs rather than cessation is beneficial.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Michelle Lubetzky", + "author_inst": "New York Presbyterian, Weill Cornell" + }, + { + "author_name": "Meredith Aull", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Rebecca Craig-Shapiro", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Jun Lee", + "author_inst": "New York Presbyterian" + }, + { + "author_name": "John Lee", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Samuel Sultan", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Jehon Marku-Podvorica", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Laura Gingras", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Rosy Priya Kodiyanplakkal", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Choli Hartono", + "author_inst": "New York Presbyterian" + }, + { + "author_name": "Stuart Saal", + "author_inst": "New York Presbyterian" + }, + { + "author_name": "Thangamani Muthukumar", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Sandip Kapur", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Manikkam Suthanthiran", + "author_inst": "New York Presbyterian-Weill Cornell" + }, + { + "author_name": "Darshana Dadhania", + "author_inst": "New York Presbyterian-Weill Cornell" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2020.04.30.20086447", "rel_title": "Evaluation of effects of public health interventions on COVID-19 transmission for Pakistan: A mathematical simulation study", @@ -1496822,41 +1497322,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.03.075549", - "rel_title": "COVIDier: A Deep-learning Tool For Coronaviruses Genome And Virulence Proteins Classification", - "rel_date": "2020-05-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.03.075549", - "rel_abs": "COVID-19, caused by SARS-CoV-2 infection, has already reached pandemic proportions in a matter of a few weeks. At the time of writing this manuscript, the unprecedented public health crisis caused more than 2.5 million cases with a mortality range of 5-7%. The SARS-CoV-2, also called novel Coronavirus, is related to both SARS-CoV and bat SARS. Great efforts have been spent to control the pandemic that has become a significant burden on the health systems in a short time. Since the emergence of the crisis, a great number of researchers started to use the AI tools to identify drugs, diagnosing using CT scan images, scanning body temperature, and classifying the severity of the disease. The emergence of variants of the SARS-CoV-2 genome is a challenging problem with expected serious consequences on the management of the disease. Here, we introduce COVIDier, a deep learning-based software that is enabled to classify the different genomes of Alpha coronavirus, Beta coronavirus, MERS, SARS-CoV-1, SARS-CoV-2, and bronchitis-CoV. COVIDier was trained on 1925 genomes, belonging to the three families of SARS retrieved from NCBI Database to propose a new method to train deep learning model trained on genome data using Multi-layer Perceptron Classifier (MLPClassifier), a deep learning algorithm, that could blindly predict the virus family name from the genome of by predicting the statistically similar genome from training data to the given genome. COVIDier able to predict how close the emerging novel genomes of SARS to the known genomes with accuracy 99%. COVIDier can replace tools like BLAST that consume higher CPU and time.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Peter Habib", - "author_inst": "Department of Biodiversity and Crop Improvement, International Center for Agriculture Research in the Dry Areas (ICARDA), Giza, Egypt." - }, - { - "author_name": "Alsamman M Alsamman", - "author_inst": "Molecular Genetics and genome Mapping" - }, - { - "author_name": "Maha Saber-Ayad", - "author_inst": "College of Medicine, University of Sharjah" - }, - { - "author_name": "Sameh E. Hassanein", - "author_inst": "Department of Bioinformatics & Computer Networks, AGERI, Agricultural Research Center (ARC), Giza, Egypt." - }, - { - "author_name": "Aladdin Hamwieh", - "author_inst": "Department of Biodiversity and Crop Improvement, International Center for Agriculture Research in the Dry Areas (ICARDA), Giza, Egypt." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.05.01.20078360", "rel_title": "Profiling COVID-19 pneumonia progressing into the cytokine storm syndrome: results from a single Italian Centre study on tocilizumab versus standard of care.", @@ -1497072,6 +1497537,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.30.20081828", + "rel_title": "Modeling COVID-19 on a network: super-spreaders, testing and containment", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20081828", + "rel_abs": "To model COVID-19 spread, we use an SEIR agent-based model on a graph, which takes into account several important real-life attributes of COVID-19: super-spreaders, realistic epidemiological parameters of the disease, testing and quarantine policies. We find that mass-testing is much less effective than testing the symptomatic and contact tracing, and some blend of these with social distancing is required to achieve suppression. We also find that the fat tail of the degree distribution matters a lot for epidemic growth, and many standard models do not account for this. Additionally, the average reproduction number for individuals, equivalent in many models to R0, is not an upper bound for the effective reproduction number, R. Even with an expectation of less than one new case per person, our model shows that exponential spread is possible. The parameter which closely predicts growth rate is the ratio between 2nd to 1st moments of the degree distribution. We provide mathematical arguments to argue that certain results of our simulations hold in more general settings.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ofir Reich", + "author_inst": "Google" + }, + { + "author_name": "Guy Shalev", + "author_inst": "Google" + }, + { + "author_name": "Tom Kalvari", + "author_inst": "Tel Aviv University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.30.20077594", "rel_title": "Early transmission dynamics and control of COVID-19 in a southern hemisphere setting: Lima-Peru, February 29th-March 30th, 2020 .", @@ -1498432,65 +1498924,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.30.20081257", - "rel_title": "Single-cell Transcriptome Analysis Indicates New Potential Regulation Mechanism of ACE2 and NPs signaling among heart failure patients infected with SARS-CoV-2", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20081257", - "rel_abs": "BackgroundCOVID-19 patients with comorbidities such as hypertension or heart failure (HF) are associated with poor clinical outcomes. Angiotensin-converting enzyme 2 (ACE2), the critical enzyme for SARS-CoV-2 infection, is broadly expressed in many organs including heart. However, the cellular distribution of ACE2 in the human heart, particularly the failing heart is unknown.\n\nMethodsWe analyzed single-cell RNA sequencing (scRNA-seq) data in both normal and failing hearts, and characterized the ACE2 gene expression profile in various cell subsets, especially in cardiomyocyte subsets, as well as its interaction with gene networks relating to various defense and immune responses at the single cell level.\n\nResultsThe results demonstrated that ACE2 is present in cardiomyocytes (CMs), endothelial cells, fibroblasts and smooth muscle cells in the heart, while the number of ACE2-postive (ACE2+) CMs and ACE2 gene expression in these CMs are significantly increased in the failing hearts. Interestingly, both brain natriuretic peptides (BNP) and atrial natriuretic peptide (ANP) are significantly up-regulated in the ACE2+ CMs. Further analysis shows that ANP, BNP and ACE2 may form a negative feedback loop with a group of genes associated with the development of heart failure. To our surprise, we found that genes related to virus entry, virus replication and suppression of interferon-gamma (IFN-{gamma}) signaling are all up-regulated in CMs in failing hearts, and the increases were significantly higher in ACE2+ CMs as compared with ACE2 negative (ACE2-) CMs, suggesting that these ACE2+ CMs may be more vulnerable to virus infection. Since ACE2 expression is correlated with BNP expression, we further performed retrospective analysis of the plasma BNP levels and clinic outcome of 91 COVID-19 patients from a single-center. Patients with higher plasma BNP were associated with significantly higher mortality rate and expression levels of inflammatory and infective markers such as procalcitonin and C-reactive protein.\n\nConclusionIn the failing heart, the upregulation of ACE2 and virus infection associated genes, as well as the increased expression of ANP and BNP could facilitate SARS-CoV-2 virus entry and replication in these vulnerable cardiomyocyte subsets. These findings may advance our understanding of the underlying molecular mechanisms of myocarditis associated with COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Xiaojiang Xu", - "author_inst": "NIEHS, NIH" - }, - { - "author_name": "Dachun Xu", - "author_inst": "Tongji University School of Medicine,PR. China" - }, - { - "author_name": "Hong Li", - "author_inst": "NIEHS, NIH" - }, - { - "author_name": "Mengqiu Ma", - "author_inst": "Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine" - }, - { - "author_name": "Yanhua Xu", - "author_inst": "Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine" - }, - { - "author_name": "Yang Su", - "author_inst": "Department of Cardiology, Shanghai Tenth People's Hospital, Tongji University School of Medicine" - }, - { - "author_name": "Sang-Bing Ong", - "author_inst": "Department of Medicine and Therapeutics, Chinese University of Hong Kong, Hongkong, China" - }, - { - "author_name": "Xindong Hu", - "author_inst": "Department of Critical Care Medicine, The Third people's Hospital of Guizhou Province, Guiyang, China" - }, - { - "author_name": "Min Cai", - "author_inst": "Department of Critical Care Medicine, Ezhou Central Hospital, Ezhou, China" - }, - { - "author_name": "Maojun Zhao", - "author_inst": "Emergency department, The First People Hospital of Guiyang Guiyang, Guizhou, China" - }, - { - "author_name": "Yingjie Chen", - "author_inst": "Department of Physiology & Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.28.20083758", "rel_title": "Estimation of the basic reproduction number, average incubation time, asymptomatic infection rate, and case fatality rate forCOVID-19: Meta-analysis and sensitivity analysis", @@ -1498734,6 +1499167,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.29.20084244", + "rel_title": "Are COVID-19 infected children with gastrointestinal symptoms different from those without symptoms? A comparative study of the clinical characteristics and epidemiological trend of 244 pediatric cases from Wuhan", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084244", + "rel_abs": "ObjectiveCOVID-19 patients presenting with gastrointestinal (GI) symptoms occur in both adults and children. To date, however, no large sample size study focusing on gastrointestinal symptoms in pediatric cases has been published. We analyzed COVID-19 infected children in Wuhan who presented with initial GI symptoms to determine the GI characteristics and epidemiological trend of the disease.\n\nDesignWe retrospectively analyzed 244 children patients confirmed with COVID-19 at Wuhan Childrens Hospital from 21 Jan to 20 Mar 2020. Symptomatic cases were divided into two groups according to whether the patients presented with or without GI symptoms on admission. Demographic, epidemiological, symptoms, and laboratory data were compared. We also analyzed the respective trends of case number changes of GI cases and asymptomatic cases.\n\nResults34 out of 193 symptomatic children had GI symptoms. They had lower median age and weight, a higher rate of fever, a longer length of stay and more hematological and biochemical abnormalities than patients without GI symptoms. There was no significant difference in chest CT findings or stool SARS-CoV-2 test positive percentages between the two groups. The number of patients admitted with GI symptoms showed an overall downward trend with time. At the time of writing, 242 patients were discharged, one died, and one critically ill patient was still in the intensive care unit.\n\nConclusionCOVID-19 infected children with GI symptoms are prone to presenting with more clinical and laboratory abnormalities than patients without GI symptoms. More attention and timely hospital admission are needed for these patients.\n\nSignificance of this studyO_LSTWhat is already known on this subject?C_LSTO_LICOVID-19 is now a pandemic with more than 1.6 million people infected worldwide\nC_LIO_LIAlthough attacking the respiratory tract mostly, both adult and children infected with COVID-19 can present with GI symptoms\nC_LI\n\nO_LSTWhat are the new findings?C_LSTO_LIInfants younger than two years old and presence of fever are the two risk factors of presenting with GI symptoms\nC_LIO_LIA high proportion of patients without GI symptoms and asymptomatic patients will have positive RT-PCR for the virus in stool\nC_LIO_LIEarlier testing through contact screening of family members means more COVID-19 infected children are diagnosed when completely asymptomatic\nC_LI\n\nO_LSTHow might it impact on clinical practice in the foreseeable future?C_LSTO_LIThe presence of COVID-19 in stool in infected children will have a major implication for parents and carers of young infants\nC_LIO_LIIncreasing number of asymptomatic COVID-19 patients who are detected through screening could provide a useful lesson for other countries still experiencing the rise and peak of the pandemic\nC_LI", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Xiaoli Xiong", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Kenenth Kak-Yuen Wong", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Shuiqing Chi", + "author_inst": "Union Hospital, Wuhan" + }, + { + "author_name": "Aifen Zhou", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Jianqiao Tang", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Lishan Zhou", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Patrick Ho-yu Chung", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Gilbert Chua", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Keith TS Tung", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ian CK Wong", + "author_inst": "The Univeristy of Hong Kong" + }, + { + "author_name": "Celine SL Chui", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Xue Li", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Mike Yat-wah Kwan", + "author_inst": "Princess Margaret Hospital, Hong Kong" + }, + { + "author_name": "Wilfred HS Wong", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Marco Hok-kung Ho", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Godfrey CF Chan", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Guoqing Cao", + "author_inst": "Union Hospital, Wuhan" + }, + { + "author_name": "Kang Li", + "author_inst": "Union Hospital, Wuhan" + }, + { + "author_name": "Patrick Ip", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Peng Chen", + "author_inst": "Wuhan Children's Hospital" + }, + { + "author_name": "Shaotao Tang", + "author_inst": "Union Hospital, Wuhan" + }, + { + "author_name": "Paul KH Tam", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.04.30.20083881", "rel_title": "Associations between psychiatric disorders, COVID-19 testing probability and COVID-19 testing results: Findings from a population-based study", @@ -1499962,165 +1500498,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.26.20081059", - "rel_title": "Preliminary evidence from a multicenter prospective observational study of the safety and efficacy of chloroquine for the treatment of COVID-19", - "rel_date": "2020-05-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20081059", - "rel_abs": "BackgroundEffective therapies are urgently needed for the SARS-CoV-2 pandemic. Chloroquine has been proved to have antiviral effect against coronavirus in vitro. In this study, we aimed to assess the efficacy and safety of chloroquine with different doses in COVID-19.\n\nMethodIn this multicenter prospective observational study, we enrolled patients older than 18 years old with confirmed SARS-CoV-2 infection excluding critical cases from 12 hospitals in Guangdong and Hubei Provinces. Eligible patients received chloroquine phosphate 500mg, orally, once (half dose) or twice (full dose) daily. Patients treated with non-chloroquine therapy were included as historical controls. The primary endpoint is the time to undetectable viral RNA. Secondary outcomes include the proportion of patients with undetectable viral RNA by day 10 and 14, hospitalization time, duration of fever, and adverse events.\n\nResultsA total of 197 patients completed chloroquine treatment, and 176 patients were included as historical controls. The median time to achieve an undetectable viral RNA was shorter in chloroquine than in non-chloroquine (absolute difference in medians -6.0 days; 95% CI -6.0 to -4.0). The duration of fever is shorter in chloroquine (geometric mean ratio 0.6; 95% CI 0.5 to 0.8). No serious adverse events were observed in the chloroquine group. Patients treated with half dose experienced lower rate of adverse events than with full dose.\n\nConclusionsAlthough randomised trials are needed for further evaluation, this study provides evidence for safety and efficacy of chloroquine in COVID-19 and suggests that chloroquine can be a cost-effective therapy for combating 102 the COVID-19 pandemic.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Mingxing Huang", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Man Li", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-Sen University" - }, - { - "author_name": "Fei Xiao", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Jiabi Liang", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Pengfei Pang", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Tiantian Tang", - "author_inst": "Sun Yat-sen Memorial Hospital, Sun Yat-sen University" - }, - { - "author_name": "Shaoxuan Liu", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Binghui Chen", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Jingxian Shu", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Yingying You", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Yang Li", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Meiwen Tang", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Jianhui Zhou", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Guanmin Jiang", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-Sen University." - }, - { - "author_name": "Jingfen Xiang", - "author_inst": "Wuhan East West Lake Mobile Cabin Hospitals" - }, - { - "author_name": "Wenxin Hong", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Songmei He", - "author_inst": "Dongguan Ninth People's Hospital" - }, - { - "author_name": "Zhaoqin Wang", - "author_inst": "Shenzhen Third People's Hospital" - }, - { - "author_name": "Jianhua Feng", - "author_inst": "Zhongshan Second People's Hospital" - }, - { - "author_name": "Changqing Lin", - "author_inst": "Huizhou Central People's Hospital" - }, - { - "author_name": "Yinong Ye", - "author_inst": "Foshan First people's Hospital" - }, - { - "author_name": "Zhilong Wu", - "author_inst": "Foshan Fourth People's Hospital" - }, - { - "author_name": "Yaocai Li", - "author_inst": "Maoming People's Hospital" - }, - { - "author_name": "Bei Zhong", - "author_inst": "Qingyuan People's Hospital" - }, - { - "author_name": "Ruilin Sun", - "author_inst": "Guangdong Second People's Hospital" - }, - { - "author_name": "Zhongsi Hong", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Jing Liu", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Huili Chen", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Xiaohua Wang", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Zhonghe Li", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Duanqing Pei", - "author_inst": "Guangzhou Regenerative Medicine and Health Guangdong Laboratory" - }, - { - "author_name": "Lin Tian", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Jinyu Xia", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - }, - { - "author_name": "Shanping Jiang", - "author_inst": "Sun Yat-sen Memorial Hospital, Sun Yat-sen University" - }, - { - "author_name": "Nanshan Zhong", - "author_inst": "The First Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Hong Shan", - "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.27.20078436", "rel_title": "Full-spectrum dynamics of the coronavirus disease outbreak in Wuhan, China: a modeling study of 32,583 laboratory-confirmed cases", @@ -1500480,6 +1500857,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.05.03.073080", + "rel_title": "Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication", + "rel_date": "2020-05-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.03.073080", + "rel_abs": "The COVID-19 pandemic, attributed to the SARS-CoV-2 coronavirus infection, resulted in millions infected worldwide and an immediate need for antiviral treatments. The main protease (Mpro) in SARS-CoV-2 is a viable drug target because of its essential role in the cleavage of the virus polypeptide and subsequent viral replication. Feline infectious peritonitis, a fatal infection in cats caused by a coronavirus, was successfully treated previously with a dipeptide-based protease inhibitor. Here we show this drug, GC376, and its analog GC373, are effective inhibitors of the Mpro from both SARS-CoV and SARS-CoV-2 with IC50 values in the nanomolar range. Crystal structures of the SARS-CoV and SARS-CoV-2 Mpro with these inhibitors have a covalent modification of the nucleophilic Cys145. NMR analysis reveals that inhibition proceeds via reversible formation of a hemithioacetal. GC373 and GC376 are potent inhibitors of SARS-CoV-2 in cell culture, with EC50 values near one micromolar and little to no toxicity. These protease inhibitors are soluble, non-toxic, and bind reversibly. They are strong drug candidates for the treatment of human coronavirus infections because they have already been successful in animals (cats). The work here lays the framework for their use in human trials for the treatment of COVID-19.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Wayne Vuong", + "author_inst": "University of Alberta" + }, + { + "author_name": "Muhammad Bashir Khan", + "author_inst": "University of Alberta" + }, + { + "author_name": "Conrad Fischer", + "author_inst": "University of Alberta" + }, + { + "author_name": "Elena Arutyunova", + "author_inst": "University of Alberta" + }, + { + "author_name": "Tess Lamer", + "author_inst": "University of Alberta" + }, + { + "author_name": "Justin Shields", + "author_inst": "University of Alberta" + }, + { + "author_name": "Holly A Saffran", + "author_inst": "University of Alberta" + }, + { + "author_name": "Ryan T McKay", + "author_inst": "University of Alberta" + }, + { + "author_name": "Marco J van Belkum", + "author_inst": "University of Alberta" + }, + { + "author_name": "Michael Joyce", + "author_inst": "University of Alberta" + }, + { + "author_name": "Howard S Young", + "author_inst": "University of Alberta" + }, + { + "author_name": "D. Lorne Tyrrell", + "author_inst": "University of Alberta" + }, + { + "author_name": "John C Vederas", + "author_inst": "University of Alberta" + }, + { + "author_name": "M Joanne Lemieux", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.05.02.043554", "rel_title": "Catalytic cleavage of HEAT and subsequent covalent binding of the tetralone moiety by the SARS-CoV-2 main protease", @@ -1501736,61 +1502184,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.05.03.074914", - "rel_title": "Isolating multiple formats of human monoclonal neutralizing antibodies against SARS-CoV-2 by in vitro site-directed antibody screening", - "rel_date": "2020-05-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.03.074914", - "rel_abs": "Neutralizing antibody is one of the most effective interventions for acute pathogenic infection. Currently, over three million people have been identified for SARS-CoV-2 infection but SARS-CoV-2-specific vaccines and neutralizing antibodies are still lacking. SARS-CoV-2 infects host cells by interacting with angiotensin converting enzyme-2 (ACE2) via the S1 receptor-binding domain (RBD) of its surface spike glycoprotein. Therefore, blocking the interaction of SARS-CoV-2-RBD and ACE2 by antibody would cause a directly neutralizing effect against virus. In the current study, we selected the ACE2 interface of SARS-CoV-2-RBD as the targeting epitope for neutralizing antibody screening. We performed site-directed screening by phage display and finally obtained one IgG antibody (4A3) and several domain antibodies. Among them, 4A3 and three domain antibodies (4A12, 4D5, and 4A10) were identified to act as neutralizing antibodies due to their capabilities to block the interaction between SARS-CoV-2-RBD and ACE2-positive cells. The domain antibody 4A12 was predicted to have the best accessibility to all three ACE2-interfaces on the spike homotrimer. Pseudovirus and authentic SARS-CoV-2 neutralization assays showed that all four antibodies could potently protect host cells from virus infection. Overall, we isolated multiple formats of SARS-CoV-2-neutralizing antibodies via site-directed antibody screening, which could be promising candidate drugs for the prevention and treatment of COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Xiaoyu Liu", - "author_inst": "Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Scien" - }, - { - "author_name": "Fang Gao", - "author_inst": "Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Scien" - }, - { - "author_name": "Liming Gou", - "author_inst": "Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Scien" - }, - { - "author_name": "Yin Chen", - "author_inst": "Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health Institute of Pathogenic Microbiology, Jiangsu Province Center for Disease Control and Prev" - }, - { - "author_name": "Yayun Gu", - "author_inst": "Department of Epidemiology and Biostatistics, International Joint Research Center on Environment and Human Health, School of Public Health, State Key Laboratory" - }, - { - "author_name": "Lei Ao", - "author_inst": "Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Scien" - }, - { - "author_name": "Hongbing Shen", - "author_inst": "Department of Epidemiology and Biostatistics, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public He" - }, - { - "author_name": "Zhibin Hu", - "author_inst": "Department of Epidemiology and Biostatistics, International Joint Research Center on Environment and Human Health, School of Public Health, State Key Laboratory" - }, - { - "author_name": "Xiling Guo", - "author_inst": "Key Laboratory of Enteric Pathogenic Microbiology, Ministry of Health Institute of Pathogenic Microbiology, Jiangsu Province Center for Disease Control and Prev" - }, - { - "author_name": "Wei Gao", - "author_inst": "Key Laboratory of Human Functional Genomics of Jiangsu Province, National Health Commission Key Laboratory of Antibody Techniques, School of Basic Medical Scien" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.04.27.20081505", "rel_title": "Simulating a community mental health service during the COVID-19 pandemic: effects of clinician-clinician encounters, clinician-patient-family encounters, symptom-triggered protective behaviour, and household clustering", @@ -1502194,6 +1502587,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2020.04.27.20081794", + "rel_title": "Predicting community mortality risk due to CoVID-19 using machine learning and development of a prediction tool", + "rel_date": "2020-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081794", + "rel_abs": "BackgroundThe recent pandemic of CoVID-19 has emerged as a threat to global health security. There are a very few prognostic models on CoVID-19 using machine learning.\n\nObjectivesTo predict mortality among confirmed CoVID-19 patients in South Korea using machine learning and deploy the best performing algorithm as an open-source online prediction tool for decision-making.\n\nMaterials and methodsMortality for confirmed CoVID-19 patients (n=3,299) between January 20, 2020 and April 30, 2020 was predicted using five machine learning algorithms (logistic regression, support vector machine, K nearest neighbor, random forest and gradient boosting). Performance of the algorithms was compared, and the best performing algorithm was deployed as an online prediction tool.\n\nResultsThe random forest algorithm was the best performer in terms of predictive ability (accuracy=0.981), discrimination (area under ROC curve=0.886), calibration (Matthews Correlation Coefficient=0.459; Brier Score=0.063) and. The best performer algorithm (random forest) was deployed as the online CoVID-19 Community Mortality Risk Prediction tool named CoCoMoRP (https://ashis-das.shinyapps.io/CoCoMoRP/).\n\nConclusionsWe describe the development and deployment of an open-source machine learning tool to predict mortality risk among CoVID-19 confirmed patients using publicly available surveillance data. This tool can be utilized by potential stakeholders such as health providers and policy makers to triage patients at the community level in addition to other approaches.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "ASHIS DAS", + "author_inst": "The World Bank" + }, + { + "author_name": "Shiba Mishra", + "author_inst": "Credit Suisse Private Limited" + }, + { + "author_name": "Saji Saraswathy Gopalan", + "author_inst": "The World Bank Group" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.27.20081539", "rel_title": "An ARIMA Model to Forecast the Spread and the Final Size of COVID-2019 Epidemic in Italy", @@ -1503850,33 +1504270,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.27.20082206", - "rel_title": "SARS-CoV-2 receptor mutation in Egyptian population", - "rel_date": "2020-05-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20082206", - "rel_abs": "The Coronavirus disease 2019 (COVID-19) is a respiratory tract infectious disease caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 triggers severe pneumonia leading to acute respiratory distress syndrome and death in severe cases. According to WHO reported, Egypt is among the countries with low confirmed SARS CoV2 infected symptomatic cases and death. We postulate that one of the reasons for this may be due mutations in the viral receptor. Therefore this study was conducted to confirm or reject this postulation.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Mohamed Abouelhoda", - "author_inst": "Cairo University" - }, - { - "author_name": "Abdel-Rahman N. Zekri", - "author_inst": "Cairo University" - }, - { - "author_name": "Mohammed M Hafez", - "author_inst": "Cairo University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.27.20082362", "rel_title": "Performance Characteristics of the Abbott Architect SARS-CoV-2 IgG Assay and Seroprevalence Testing in Idaho", @@ -1504068,6 +1504461,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.27.20081893", + "rel_title": "Individual variation in susceptibility or exposure to SARS-CoV-2 lowers the herd immunity threshold", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081893", + "rel_abs": "Individual variation in susceptibility and exposure is subject to selection by natural infection, accelerating the acquisition of immunity, and reducing herd immunity thresholds and epidemic final sizes. This is a manifestation of a wider population phenomenon known as \"frailty variation\". Despite theoretical understanding, public health policies continue to be guided by mathematical models that leave out considerable variation and as a result inflate projected disease burdens and overestimate the impact of interventions. Here we focus on trajectories of the coronavirus disease (COVID-19) pandemic in England and Scotland until November 2021. We fit models to series of daily deaths and infer relevant epidemiological parameters, including coefficients of variation and effects of non-pharmaceutical interventions which we find in agreement with independent empirical estimates based on contact surveys. Our estimates are robust to whether the analysed data series encompass one or two pandemic waves and enable projections compatible with subsequent dynamics. We conclude that vaccination programmes may have contributed modestly to the acquisition of herd immunity in populations with high levels of pre-existing naturally acquired immunity, while being critical to protect vulnerable individuals from severe outcomes as the virus becomes endemic.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC=\"FIGDIR/small/20081893v5_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (19K):\norg.highwire.dtl.DTLVardef@aeb87forg.highwire.dtl.DTLVardef@d2c441org.highwire.dtl.DTLVardef@152aeceorg.highwire.dtl.DTLVardef@1526779_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIVariation in susceptibility/exposure responds to selection by natural infection\nC_LIO_LISelection on susceptibility/exposure flattens epidemic curves\nC_LIO_LIModels with incomplete heterogeneity overestimate intervention impacts\nC_LIO_LIIndividual variation lowered the natural herd immunity threshold for SARS-CoV-2\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "M. Gabriela M. Gomes", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Marcelo U. Ferreira", + "author_inst": "Universidade de Sao Paulo, Brazil" + }, + { + "author_name": "Rodrigo M. Corder", + "author_inst": "Universidade de Sao Paulo, Brazil" + }, + { + "author_name": "Jessica G. King", + "author_inst": "University of Edinburgh, UK" + }, + { + "author_name": "Caetano Souto-Maior", + "author_inst": "National Institutes of Health, USA" + }, + { + "author_name": "Carlos Penha-Goncalves", + "author_inst": "Instituto Gulbenkian de Ciencia, Portugal" + }, + { + "author_name": "Guilherme Goncalves", + "author_inst": "Universidade do Porto, Portugal" + }, + { + "author_name": "Maria Chikina", + "author_inst": "University of Pittsburgh, USA" + }, + { + "author_name": "Wesley Pegden", + "author_inst": "Carnegie Mellon University, USA" + }, + { + "author_name": "Ricardo Aguas", + "author_inst": "University of Oxford, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.27.20074849", "rel_title": "Performance verification of detecting COVID-19 specific antibody by using four chemiluminescence immunoassay systems", @@ -1505268,77 +1505716,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.28.20082743", - "rel_title": "Protocol of a population-based prospective COVID-19 cohort study Munich, Germany (KoCo19)", - "rel_date": "2020-05-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20082743", - "rel_abs": "BackgroundThe SARS-CoV-2 pandemic is leading to the global introduction of public health interventions to prevent the spread of the virus and avoid the overload of health care systems, especially for the most severely affected patients. Scientific studies to date have focused primarily on describing the clinical course of patients, identifying treatment options and developing vaccines. In Germany, as in many other regions, current tests for SARS-CoV2 are not being conducted on a representative basis and in a longitudinal design. Furthermore, knowledge about the immune status of the population is lacking. Yet these data are needed to understand the dynamics of the pandemic and to thus appropriately design and evaluate interventions. For this purpose, we recently started a prospective population-based cohort in Munich, Germany, with the aim to better understand the state and dynamics of the pandemic.\n\nMethodsIn 100, randomly selected constituencies out of 755, 3,000 Munich households are identified via random route and offered enrollment into the study. All household members are asked to complete a baseline questionnaire and subjects [≥]14 years of age are asked to provide a venous blood sample of [≤]3 ml for the determination of SARS-CoV-2 IgG/IgA status. The residual plasma and the blood pellet are preserved for later genetic and molecular biological investigations. For twelve months, each household member is asked to keep a diary of daily symptoms, whereabouts and contacts via WebApp. If symptoms suggestive for COVID-19 are reported, family members, including children <14 years, are offered a pharyngeal swab taken at the Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, for molecular testing for SARS-CoV-2. In case of severe symptoms, participants will be transferred to a Munich hospital. For one year, the study teams re-visits the households for blood sampling every six weeks.\n\nDiscussionWith the planned study we will establish a reliable epidemiological tool to improve the understanding of the spread of SARS-CoV-2 and to better assess the effectiveness of public health measures as well as their socio-economic effects. This will support policy makers in managing the epidemic based on scientific evidence.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Katja Radon", - "author_inst": "Center for International Health and Institute for Occupational, Social and Environmental Medicine, LMU University Hospital Munich" - }, - { - "author_name": "Elmar Saathoff", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany and German Center for Infection Research (DZIF), partner site Mun" - }, - { - "author_name": "Michael Pritsch", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany" - }, - { - "author_name": "Jessica Michelle Guggenbuehl Noller", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany" - }, - { - "author_name": "Inge Kroidl", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany and German Center for Infection Research (DZIF), partner site Mun" - }, - { - "author_name": "Laura Olbrich", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany" - }, - { - "author_name": "Verena Thiel", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany" - }, - { - "author_name": "Maximilian Diefenbach", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany" - }, - { - "author_name": "Friedrich Riess", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany" - }, - { - "author_name": "Felix Forster", - "author_inst": "Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig Maximilian University (LMU) University Hospital Munich" - }, - { - "author_name": "Fabian J Theis", - "author_inst": "Helmholtz Center Munich and Departments of Mathematics and Life Sciences, Technical University of Munich" - }, - { - "author_name": "Andreas Wieser", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich, Germany and Max von Pettenkofer Institute, Faculty of Medicine, LMU of Mu" - }, - { - "author_name": "Michael Hoelscher", - "author_inst": "Division of Infectious Diseases and Tropical Medicine, LMU University Hospital Munich; Center for International Health, LMU of Munich and German Center for Infe" - }, - { - "author_name": "KoCo19 collaboration group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.28.20083139", "rel_title": "Early viral clearance and antibody kinetics of COVID-19 among asymptomatic carriers", @@ -1505646,6 +1506023,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.04.28.20083089", + "rel_title": "A possible role of immunopathogenesis in COVID-19 progression", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083089", + "rel_abs": "BackgroundThe role of cellular immunity in pathogenesis of COVID-19 is unclear and conflicting data points to insufficient or pathogenic immunity as drivers of COVID-19 progression. Here we aimed to delineate the phenotype and function of the immune system in patients with moderate, severe, and critical COVID-19.\n\nMethodsIn this prospective study, we included 53 patients with moderate (n=21), severe (n=18), and critical (n=14) COVID-19 manifestations. Using multiparametric flow cytometry we compared quantitative, phenotypic, and functional characteristics of circulating immune cells, SARS-CoV-2 antigen-reactive T-cells, and humoral immunity.\n\nResultsDeep phenotypic profiling revealed a depletion of circulating bulk CD8+ T-cells, CD4+ and CD8+ T-cell subsets with activated memory/effector T-cells expressing CD57+, HLA-DR+, and the key activation and migration molecule CD11a++ in critical COVID-19. Importantly, survival from acute respiratory distress syndrome was accompanied by a recovery of the depleted CD11++ T-cell subsets including T-cells expressing CD28, CD57, HLA-DR activation/effector molecules. We further observed a stronger response of S-protein specific T-cells producing inflammatory cytokines in critical COVID-19 cases. This seemingly contradictory observation is in fact confirmation of the underlying immunopathogenesis in patients with critical COVID-19.\n\nConclusionOur findings suggest a CD11a-based immune signature as a possible prognostic marker for disease development. Our data further reveal that increased rather than decreased SARS-CoV-2 specific T cell immunity is associated with adverse outcome in COVID-19. Tissue migration of activated effectors T-cells may constitute a crucial cornerstone in the immunopathogenesis of SARS-CoV-2 associated tissue injury.\n\nTrial registrationThis is a prospective observational study without a trial registration number.\n\nFundingThis work was supported by grants from Mercator Foundation, the BMBF e:KID (01ZX1612A), and BMBF NoChro (FKZ 13GW0338B).\n\n25 Word summaryStronger S-protein reactivity and decreased frequency of activated memory/effector T-cells expressing CD11a++ suggests immunopathogenesis in critical COVID-19 mediated by tissue migration of activated effector T-cells.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Moritz Anft", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Krystallenia Paniskaki", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Arturo Blazquez-Navarro", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Adrian Atila Nicolas Doevelaar", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Felix Seibert", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Bodo Hoelzer", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Sarah Skrzypczyk", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Eva Kohut", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Julia Kurek", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Jan Zapka", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Patrizia Wehler", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Sviatlana Kaliszczyk", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Sharon Bajda", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Constantin Thieme", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Toralf Roch", + "author_inst": "Charite Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute of Health, Berlin-Bran" + }, + { + "author_name": "Margarethe Justine Konik", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Thorsten Brenner", + "author_inst": "Department of Anesthesiology, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Clemens Tempfer", + "author_inst": "Department of Gynecology and Obstetrics, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Hoelkeskampring 40, 44625 Herne, Germany" + }, + { + "author_name": "Carsten Watzl", + "author_inst": "Department of Immunology, Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund (IfADo), Ardeystrasse 67, 44139" + }, + { + "author_name": "Sebastian Dolff", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Ulf Dittmer", + "author_inst": "Germany Institute for Virology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" + }, + { + "author_name": "Timm Westhoff", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Oliver Witzke", + "author_inst": "Department of Infectious Diseases, West German Centre of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Germany" + }, + { + "author_name": "Ulrik Stervbo", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + }, + { + "author_name": "Nina Babel", + "author_inst": "Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Boc" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.04.26.20080341", "rel_title": "How the COVID-19 pandemic is favoring the adoption of digital technologies in healthcare: a rapid literature review", @@ -1506942,29 +1507434,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.27.20082503", - "rel_title": "Latent Blowout of COVID-19 Globally: An Effort to Healthcare Alertness via Medical GIS Approach", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20082503", - "rel_abs": "Since January 2020, the COVID-19 pandemic has been escalating from North America to Asia. Various studies projected the spread of pandemic globally, using air passenger data from an infected area. But there could be various parameters that can be the basis for the forecasting of the pandemic. Current research adopts the Medical GIS approach and incorporates critical parameters from various domains to create a global alertness scale to combat the pandemic. The finding of the study ranks the countries on a 1 to 9 scale based on the spatial alertness In this context, the study focuses on the role of GIS techniques as an enabler to fight against the global pandemic and could be beneficial for the authorities to adopt timely preventive actions.\n\nOne Sentence SummaryGlobal Alertness Ranking to combat COVID-19", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "LAXMIKANT SHARMA", - "author_inst": "CENTRAL UNIVERSITY OF RAJASTHAN" - }, - { - "author_name": "RAJANIKANT VERMA", - "author_inst": "CENTRAL UNIVERSITY OF RAJASTHAN" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.04.26.20080580", "rel_title": "Liver Chemistries in COVID-19 Patients with Survival or Death: A Meta-Analysis", @@ -1507216,6 +1507685,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.26.20080770", + "rel_title": "A first study on the impact of containment measure on COVID-19 spread in Morocco", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20080770", + "rel_abs": "BackgroundSince the appearance of the first case of COVID-19 in Morocco, the cumulative number of reported infectious cases continues to increase and, consequently, the government imposed the containment measure within the country. Our aim is to predict the impact of the compulsory containment on COVID-19 spread. Earlier knowledge of the epidemic characteristics of COVID-19 transmission related to Morocco will be of great interest to establish an optimal plan-of-action to control the epidemic.\n\nMethodUsing a Susceptible-Asymptomatic-Infectious model and the data of reported cumulative confirmed cases in Morocco from March 2nd to April 9, 2020, we determined the basic and control reproduction numbers and we estimated the model parameter values. Furthermore, simulations of different scenarios of containment are performed.\n\nResultsEpidemic characteristics are predicted according to different rates of containment. The basic reproduction number is estimated to be 2.9949, with CI(2.6729-3.1485). Furthermore, a threshold value of containment rate, below which the epidemic duration is postponed, is determined.\n\nConclusionOur findings show that the basic reproduction number reflects a high speed of spread of the epidemic. Furthermore, the compulsory containment can be efficient if more than 73% of population are confined. However, even with 90% of containment, the end-time is estimated to happen on July 4th which can be harmful and lead to consequent social-economic damages. Thus, containment need to be accompanied by other measures such as mass testing to reduce the size of asymptomatic population. Indeed, our sensitivity analysis investigation shows that the COVID-19 dynamics depends strongly on the asymptomatic duration as well as the contact and containment rates. Our results can help the Moroccan government to anticipate the spread of COVID-19 and avoid human loses and consequent social-economic damages as well.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Aayah Hammoumi", + "author_inst": "Cadi Ayyad University" + }, + { + "author_name": "Redouane Qesmi", + "author_inst": "USMBA University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.27.20076000", "rel_title": "The effect of a national lockdown in response to COVID-19 pandemic on the prevalence of clinical symptoms in the population", @@ -1508264,41 +1508756,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.26.20081125", - "rel_title": "Compositional Cyber-Physical Epidemiology of COVID-19", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20081125", - "rel_abs": "COVID-19 pandemic has posed significant challenges globally. Countries have adopted different strategies with varying degrees of success. Epidemiologists are studying the impact of government actions using scenario analysis. However, the interactions between the government policy and the disease dynamics are not formally captured.\n\nWe, for the first time, formally study the interaction between the disease dynamics, which is modelled as a physical process, and the government policy, which is modelled as the adjoining controller. Our approach enables compositionality, where either the plant or the controller could be replaced by an alternative model. Our work is inspired by the engineering approach for the design of Cyber-Physical Systems (CPSs). Consequently, we term the new framework Compositional Cyber-Physical Epidemiology (CCPE). We created different classes of controllers and applied these to control the disease in New Zealand and Italy. Our controllers closely follow government decisions based on their published data. We not only reproduce the pandemic progression faithfully in New Zealand and Italy but also show the tradeoffs produced by differing control actions.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jin Woo Ro", - "author_inst": "Department of Electrical, Computer and Software Engineering, University of Auckland, New Zealand" - }, - { - "author_name": "Nathan Allen", - "author_inst": "Department of Electrical, Computer and Software Engineering, University of Auckland, New Zealand" - }, - { - "author_name": "Weiwei Ai", - "author_inst": "Department of Electrical, Computer and Software Engineering, University of Auckland, New Zealand" - }, - { - "author_name": "Debi Prasad", - "author_inst": "Faculty of Medical and Health Sciences, University of Auckland, New Zealand" - }, - { - "author_name": "Partha S. Roop", - "author_inst": "Department of Electrical, Computer and Software Engineering, University of Auckland, New Zealand" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.26.20081315", "rel_title": "First peak of COVID-19 outbreak in Japan might pass as of April 26, 2020", @@ -1508462,6 +1508919,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.30.069922", + "rel_title": "Broad-spectrum antiviral activity of naproxen: from Influenza A to SARS-CoV-2 Coronavirus", + "rel_date": "2020-05-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.30.069922", + "rel_abs": "There is an urgent need for specific antiviral drugs directed against SARS-CoV-2 both to prevent the most severe forms of COVID-19 and to reduce viral excretion and subsequent virus dissemination; in the present pandemic context, drug repurposing is a priority. Targeting the nucleoprotein N of the SARS-CoV-2 coronavirus in order to inhibit its association with viral RNA could be a strategy to impeding viral replication and possibly other essential functions associated with viral N. The antiviral properties of naproxen, belonging to the NSAID family, previously demonstrated against Influenza A virus, were evaluated against SARS-CoV-2. Naproxen binding to the nucleoprotein of SARS-CoV2 was shown by molecular modeling. In VeroE6 cells and reconstituted human primary respiratory epithelium models of SARS-CoV-2 infection, naproxen inhibited viral replication and protected the bronchial epithelia against SARS-CoV-2 induced-damage. The benefit of naproxen addition to the standard of care is tested in an on-going clinical study.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Olivier Terrier", + "author_inst": "Centre International de Recherche en Infectiologie" + }, + { + "author_name": "Sebastien Dilly", + "author_inst": "INSERM and Sorbonne University, CRSA UMR S_938" + }, + { + "author_name": "Mario-Andres Pizzorno", + "author_inst": "Lyon I University, CIRI, INSERM 1111, CNRS UMR 5308, Ens de Lyon" + }, + { + "author_name": "Julien Henri", + "author_inst": "Institut de Biologie Physico-Chimique CNRS UMR 8226" + }, + { + "author_name": "Francis Berenbaum", + "author_inst": "Sorbonne University, INSERM, CRSA UMR S_938, AP-HP" + }, + { + "author_name": "Bruno Lina", + "author_inst": "Lyon I University, CIRI, INSERM U 1111, CNRS UMR 5308, Ens de Lyon" + }, + { + "author_name": "Bruno Feve", + "author_inst": "INSERM and Sorbonne Universitu CRSA UMR S_938, AP-HP, ICAN" + }, + { + "author_name": "Frederic Adnet", + "author_inst": "AP-HP, SAMU, Avicenne Hospital" + }, + { + "author_name": "Michele Sabbah", + "author_inst": "INSERM and Sorbonne University, CRSA UMR S_938" + }, + { + "author_name": "Manuel Rosa-Calavatra", + "author_inst": "University Lyon I, CIRI, INSERM U1111, CNRS UMR 5308, Ens de Lyon" + }, + { + "author_name": "Vincent Marechal", + "author_inst": "INSERM and Sorbonne University, CRSA UMR S_938" + }, + { + "author_name": "Anny Slama-Schwok", + "author_inst": "INSERM and Sorbonne University, CRSA UMR S_938" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.30.071175", "rel_title": "Electrostatic Characteristics of SARS-CoV-2 Spike and Human ACE2 Protein Variations Predict Mutable Binding Efficacy", @@ -1509726,45 +1510246,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2020.04.24.20073924", - "rel_title": "Factors Associated with Access and Use of PPE during COVID-19: A Cross-sectional Study of Italian Physicians", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20073924", - "rel_abs": "ObjectivesDuring the course of the Novel Coronavirus (SARS-CoV-2) pandemic, Italy has reported one of the highest number of infections. Nearly ten percent of reported coronavirus infections in Italy occurred in healthcare workers. This study aimed to understand physicians access to personal protective equipment (PPE) and to information about their use, risk perception and strategies adopted to prevent contracting the infection.\n\nMethodsWe undertook a cross-sectional, online self-reported survey implemented between March 31 and April 5 2020 of Italian physicians.\n\nResultsResponses were received from 529 physicians, only 13% of which reported to have access to PPE every time they need them. Approximately half of the physicians reported that the information received about the use of PPE was either clear (47%) or complete (54%). Risk perception about contracting the infection was influenced by receiving adequate information on the use of PPE. Access to adequate information on the use of PPE was associated with better ability to perform donning and doffing procedures [OR=2.2 95% C.I. 1.7-2.8] and reduced perception of risk [OR=0.5, 95% C.I. 0.4-0.6].\n\nConclusionsResults from this rapid survey indicate that while ramping up supplies on PPE for healthcare workers is certainly of mandatory importance, adequate training and clear instructions are just as important.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Elena Savoia", - "author_inst": "Emergency Preparedness Research, Evaluation, & Practice (EPREP) program, Division of Policy Translation & Leadership Development, Harvard T.H. Chan School of Pu" - }, - { - "author_name": "Giorgia Argentini", - "author_inst": "IRCCS Burlo Garofolo" - }, - { - "author_name": "Davide Gori", - "author_inst": "Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna" - }, - { - "author_name": "Elena Neri", - "author_inst": "Azienda Sanitaria Giuliano Isontina" - }, - { - "author_name": "Rachael Piltch-Loeb", - "author_inst": "Emergency Preparedness Research, Evaluation, & Practice (EPREP) program, Division of Policy Translation & Leadership Development, Harvard T.H. Chan School of Pu" - }, - { - "author_name": "Maria Pia Fantini", - "author_inst": "Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.26.20076265", "rel_title": "Optimal Pool Size for COVID-19 Group Testing", @@ -1509960,6 +1510441,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.27.20078329", + "rel_title": "Population-scale testing can suppress the spread of COVID-19", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20078329", + "rel_abs": "We propose an additional intervention that would contribute to the control of the COVID-19 pandemic, offer more protection for people working in essential jobs, and help guide an eventual reopening of society. The intervention is based on: (1) testing every individual (2) repeatedly, and (3) self-quarantine of infected individuals. Using a standard epidemiological model (SIR), we show here that by identification and isolation of the majority of infectious individuals, including those who may be asymptomatic, the reproduction number R0 of SARS-CoV-2 would be reduced well below 1.0, and the epidemic would collapse. We replicate these observations in a more complex stochastic dynamic model on a social network graph. We also find that the testing regime would be additive to other interventions, and be effective at any level of prevalence. If adopted as a policy, any industrial society could sustain the regime for as long as it takes to find a safe and effective cure or vaccine. Our model also indicates that unlike sampling-based tests, population-scale testing does not need to be very accurate: false negative rates up to 15% could be tolerated if 80% comply with testing every ten days, and false positives can be almost arbitrarily high when a high fraction of the population is already effectively quarantined. Testing at the required scale would be feasible if existing qPCR-based methods are scaled up and multiplexed. A mass produced, low throughput field test kit could also be carried out at home. Economic analysis also supports the feasibility of the approach: current reagent costs for tests are in the range of a dollar or less, and the estimated benefits for population-scale testing are so large that the policy would be cost-effective even if the costs were larger by more than two orders of magnitude. To identify both active and previous infections, both viral RNA and antibodies could be tested. All technologies to build such test kits, and to produce them in the scale required to test the entire worlds population exist already. Integrating them, scaling up production, and implementing the testing regime will require resources and planning, but at a scale that is very small compared to the effort that every nation would devote to defending itself against a more traditional foe.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jussi Taipale", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Paul Romer", + "author_inst": "New York University" + }, + { + "author_name": "Sten Linnarsson", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.24.20078717", "rel_title": "Full lockdown policies in Western Europe countries have no evident impacts on the COVID-19 epidemic.", @@ -1510928,73 +1511436,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2020.04.25.20080127", - "rel_title": "Early analysis of the Australian COVID-19 epidemic", - "rel_date": "2020-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20080127", - "rel_abs": "As of 18 April 2020, there had been 6,533 confirmed cases of COVID-19 in Australia [1]. Of these, 67 had died from the disease. The daily count of new confirmed cases was declining. This suggests that the collective actions of the Australian public and government authorities in response to COVID-19 were sufficiently early and assiduous to avert a public health crisis -- for now. Analysing factors, such as the intensity and timing public health interventions, that contribute to individual country experiences of COVID-19 will assist in the next stage of response planning globally. Using data from the Australian national COVID-19 database, we describe how the epidemic and public health response unfolded in Australia up to 13 April 2020. We estimate that the effective reproduction number was likely below 1 (the threshold value for control) in each Australian state since mid-March and forecast that hospital ward and intensive care unit occupancy will remain below capacity thresholds over the next two weeks.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "David J Price", - "author_inst": "Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Freya M Shearer", - "author_inst": "Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Michael T Meehan", - "author_inst": "Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia" - }, - { - "author_name": "Emma McBryde", - "author_inst": "Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia" - }, - { - "author_name": "Robert Moss", - "author_inst": "Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia" - }, - { - "author_name": "Nick Golding", - "author_inst": "Telethon Kids Institute and Curtin University, Perth, Australia" - }, - { - "author_name": "Eamon J Conway", - "author_inst": "Victorian Infectious Diseases Reference Laboratory Epidemiology Unit at The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and " - }, - { - "author_name": "Peter Dawson", - "author_inst": "Defence Science and Technology, Department of Defence, Australia" - }, - { - "author_name": "Deborah Cromer", - "author_inst": "Kirby Institute for Infection and Immunity, University of New South Wales, Sydney, Australia" - }, - { - "author_name": "James Wood", - "author_inst": "School of Public Health and Community Medicine, University of New South Wales, Sydney, Australia" - }, - { - "author_name": "Sam Abbott", - "author_inst": "Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Lon" - }, - { - "author_name": "Jodie McVernon", - "author_inst": "The Peter Doherty Institute for Infection and Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Australia" - }, - { - "author_name": "James M McCaw", - "author_inst": "School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.24.20077800", "rel_title": "Epidemiological characteristics of novel coronavirus infection: A statistical analysis of publicly available case data", @@ -1511162,6 +1511603,85 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.04.29.069054", + "rel_title": "Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2", + "rel_date": "2020-04-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.29.069054", + "rel_abs": "We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified thirteen mutations in Spike that are accumulating. Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer selective advantages in transmission or resistance to interventions. Each one is evaluated for evidence of positive selection, and the implications of the mutation are explored through structural modeling. The mutation Spike D614G is of urgent concern; it began spreading in Europe in early February, and when introduced to new regions it rapidly becomes the dominant form. Also, we present evidence of recombination between locally circulating strains, indicative of multiple strain infections. These finding have important implications for SARS-CoV-2 transmission, pathogenesis and immune interventions.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Bette Korber", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Will Fischer", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "S. Gnana Gnanakaran", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Heyjin Yoon", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "James Theiler", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Werner Abfalterer", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Brian Foley", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Elena E Giorgi", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Tanmoy Bhattacharya", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Matthew D Parker", + "author_inst": "The University of Sheffield" + }, + { + "author_name": "David G Partridge", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Cariad M Evans", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust" + }, + { + "author_name": "Thushan de Silva", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Celia C LaBranche", + "author_inst": "Duke Univerisity" + }, + { + "author_name": "David C Montefiori", + "author_inst": "Duke University" + }, + { + "author_name": "- Sheffield COVID-19 Genomics Group", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.04.30.029736", "rel_title": "Susceptibility of tree shrew to SARS-CoV-2 infection", @@ -1512318,37 +1512838,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.24.20078345", - "rel_title": "No Detectable Surge in SARS-CoV-2 Transmission due to the April 7, 2020 Wisconsin Election", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078345", - "rel_abs": "We analyze confirmed cases and new hospitalizations in Wisconsin in the weeks surrounding the April 7, 2020 election, and find no evidence of a surge in SARS-CoV-2 transmission.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Kathy Leung", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Joseph T Wu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Kuang Xu", - "author_inst": "Stanford University" - }, - { - "author_name": "Lawrence M Wein", - "author_inst": "Stanford Unversity" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.24.20078402", "rel_title": "A Statistical Analysis Of CoV-19 Positive Test Frequency Data Indicates A Need For Greater Attention To CoV-19 Test Quality And Pre-Wuhan Cov-19 Prevalence", @@ -1512504,6 +1512993,29 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.04.24.20078824", + "rel_title": "Estimating COVID-19 Antibody Seroprevalence in Santa Clara County, California. A re-analysis of Bendavid et al.", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078824", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWA recent study by Bendavid et al. claimed that the rate of infection of COVID-19 in Santa Clara county was between 2.49% and 4.16%, 50-85 times higher than the number of officially confirmed cases. The statistical methodology used in that study overestimates of rate of infection given the available data. We jointly estimate the sensitivity and specificity of the test kit along with rate of infection with a simple Bayesian model, arriving at lower estimates of the rate of COVID-19 in Santa Clara county. Re-analyzing their data, we find that the rate of infection was likely between 0.27% and 3.21%.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Stephen T Bennett", + "author_inst": "University of California, Irvine" + }, + { + "author_name": "Mark Steyvers", + "author_inst": "University of California, Irvine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.24.20078808", "rel_title": "Reacting to outbreaks at neighboring localities", @@ -1513408,177 +1513920,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.04.24.20078907", - "rel_title": "Pneumask: Modified Full-Face Snorkel Masks as Reusable Personal Protective Equipment for Hospital Personnel", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078907", - "rel_abs": "Here we adapt and evaluate a full-face snorkel mask for use as personal protective equipment (PPE) for health care workers, who lack appropriate alternatives during the COVID-19 crisis in the spring of 2020. The design (referred to as Pneumask) consists of a custom snorkel-specific adapter that couples the snorkel-port of the mask to a rated filter (either a medical-grade ventilator inline filter or an industrial filter). This design has been tested for the sealing capability of the mask, filter performance, CO2 buildup and clinical usability. These tests found the Pneumask capable of forming a seal that exceeds the standards required for half-face respirators or N95 respirators. Filter testing indicates a range of options with varying performance depending on the quality of filter selected, but with typical filter performance exceeding or comparable to the N95 standard. CO2 buildup was found to be roughly equivalent to levels found in half-face elastomeric respirators in literature. Clinical usability tests indicate sufficient visibility and, while speaking is somewhat muffled, this can be addressed via amplification (Bluetooth voice relay to cell phone speakers through an app) in noisy environments. We present guidance on the assembly, usage (donning and doffing) and decontamination protocols. The benefit of the Pneumask as PPE is that it is reusable for longer periods than typical disposable N95 respirators, as the snorkel mask can withstand rigorous decontamination protocols (that are standard to regular elastomeric respirators). With the dire worldwide shortage of PPE for medical personnel, our conclusions on the performance and efficacy of Pneumask as an N95-alternative technology are cautiously optimistic.\n\nKey pointsFull-face snorkel masks are adapted for use as Personal Protective Equipment during the COVID-19 crisis, using a custom adapter that facilitates the attachment of inline medical-grade respiratory filters or NIOSH industrial respirator filters. This solution was designed as a reusable stopgap solution for healthcare workers to help address the short-term global N95 respirator shortage.", - "rel_num_authors": 39, - "rel_authors": [ - { - "author_name": "Laurel Kroo", - "author_inst": "Stanford University" - }, - { - "author_name": "Anesta Kothari", - "author_inst": "Stanford University" - }, - { - "author_name": "Melanie Hannebelle", - "author_inst": "EPFL" - }, - { - "author_name": "George Herring", - "author_inst": "Stanford University" - }, - { - "author_name": "Thibaut Pollina", - "author_inst": "Stanford University" - }, - { - "author_name": "Ray Chang MD", - "author_inst": "Stanford University" - }, - { - "author_name": "Samhita P. Banavar", - "author_inst": "Stanford University" - }, - { - "author_name": "Elliot Flaum", - "author_inst": "Stanford University" - }, - { - "author_name": "Hazel Soto-Montoya", - "author_inst": "Stanford University" - }, - { - "author_name": "Hongquan Li", - "author_inst": "Stanford University" - }, - { - "author_name": "Kyle Combes", - "author_inst": "Olin College" - }, - { - "author_name": "Emma Pan", - "author_inst": "Olin College" - }, - { - "author_name": "Khang Vu", - "author_inst": "Olin College" - }, - { - "author_name": "Kelly Yen", - "author_inst": "Olin College" - }, - { - "author_name": "James Dale", - "author_inst": "Melbourne, Australia" - }, - { - "author_name": "Patrick Kolbay", - "author_inst": "University of Utah" - }, - { - "author_name": "Simon Ellgas", - "author_inst": "Waymo" - }, - { - "author_name": "Rebecca Konte", - "author_inst": "Stanford University" - }, - { - "author_name": "Rozhin Hajian", - "author_inst": "Harvard University" - }, - { - "author_name": "Grace Zhong", - "author_inst": "Stanford University" - }, - { - "author_name": "Noah Jacobs", - "author_inst": "Mountain View, CA" - }, - { - "author_name": "Amit Jain", - "author_inst": "Mountain View, CA" - }, - { - "author_name": "Filip Kober", - "author_inst": "Poznan, Poland" - }, - { - "author_name": "Gerry Ayala", - "author_inst": "WildHorn Outfitters, Utah" - }, - { - "author_name": "Quentin Allinne", - "author_inst": "Decathlon" - }, - { - "author_name": "Nicholas Cucinelli", - "author_inst": "University of Michigan" - }, - { - "author_name": "Dave Kasper", - "author_inst": "iSnorkel" - }, - { - "author_name": "Luca Borroni", - "author_inst": "Italy" - }, - { - "author_name": "Patrick Gerber", - "author_inst": "EPFL" - }, - { - "author_name": "Ross Venook", - "author_inst": "Stanford University" - }, - { - "author_name": "Peter Baek MD", - "author_inst": "US. Anesthesia Partners Texas, Dallas, USA" - }, - { - "author_name": "Nitin Arora M.D.", - "author_inst": "University of Alabama at Birmingham, Birmingham USA" - }, - { - "author_name": "Philip Wagner MD", - "author_inst": "Hospital for Special Surgery, New York City, USA" - }, - { - "author_name": "Roberto Miki MD", - "author_inst": "Miki & Alfonso Hand & Upper Extremity Center, Miami, USA" - }, - { - "author_name": "Jocelyne Kohn MD", - "author_inst": "Instituto de Oftalmologia, Ophthalmologist, Santiago, Chile" - }, - { - "author_name": "David Kohn Bitran MD", - "author_inst": "Instituto de Oftalmologia, Ophthalmologist, Santiago, Chile" - }, - { - "author_name": "John Pearson MD", - "author_inst": "University of Utah" - }, - { - "author_name": "Cristian Muniz Herrera MD", - "author_inst": "Santiago, Chile" - }, - { - "author_name": "Manu Prakash", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.04.26.20081182", "rel_title": "Integrated analysis of bulk multi omic and single-cell sequencing data confirms the molecular origin of hemodynamic changes in Covid-19 infection explaining coagulopathy and higher geriatric mortality", @@ -1513942,6 +1514283,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.24.20078774", + "rel_title": "State-by-State prediction of likely COVID-19 scenarios in the United States and assessment of the role of testing and control measures", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078774", + "rel_abs": "Due to the heterogeneity among the States in the US, predicting COVID-19 trends and quantitatively assessing the effects of government testing capability and control measures need to be done via a State-by-State approach. We develop a comprehensive model for COVID-19 incorporating time delays and population movements. With key parameter values determined by empirical data, the model enables the most likely epidemic scenarios to be predicted for each State, which are indicative of whether testing services and control measures are vigorous enough to contain the disease. We find that government control measures play a more important role than testing in suppressing the epidemic. The vast disparities in the epidemic trends among the States imply the need for long-term placement of control measures to fully contain COVID-19.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Zheng-Meng Zhai", + "author_inst": "East China Normal University" + }, + { + "author_name": "Yong-Shang Long", + "author_inst": "East China Normal University" + }, + { + "author_name": "Jie Kang", + "author_inst": "East China Normal University" + }, + { + "author_name": "Yi-Lin Li", + "author_inst": "East China Normal University" + }, + { + "author_name": "Lang Zeng", + "author_inst": "East China Normal University" + }, + { + "author_name": "Li-Lei Han", + "author_inst": "East China Normal University" + }, + { + "author_name": "Zhao-Hua Lin", + "author_inst": "East China Normal University" + }, + { + "author_name": "Yin-Qi Zeng", + "author_inst": "East China Normal University" + }, + { + "author_name": "Da-Yu Wu", + "author_inst": "East China Normal University" + }, + { + "author_name": "Ming Tang", + "author_inst": "East China Normal University" + }, + { + "author_name": "Di Xu", + "author_inst": "Fudan University" + }, + { + "author_name": "Zonghua Liu", + "author_inst": "East China Normal University" + }, + { + "author_name": "Ying-Cheng Lai", + "author_inst": "Arizona State University - Tempe Campus" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.28.066977", "rel_title": "Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world", @@ -1514946,173 +1515354,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.25.20077396", - "rel_title": "Epidemiological and clinical characteristics of the early phase of the COVID-19 epidemic in Brazil", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20077396", - "rel_abs": "BackgroundThe first case of COVID-19 was detected in Brazil on February 25, 2020. We report the epidemiological, demographic, and clinical findings for confirmed COVID-19 cases during the first month of the epidemic in Brazil.\n\nMethodsIndividual-level and aggregated COVID-19 data were analysed to investigate demographic profiles, socioeconomic drivers and age-sex structure of COVID-19 tested cases. Basic reproduction numbers (R0) were investigated for Sao Paulo and Rio de Janeiro. Multivariate logistic regression analyses were used to identify symptoms associated with confirmed cases and risk factors associated with hospitalization. Laboratory diagnosis for eight respiratory viruses were obtained for 2,429 cases.\n\nFindingsBy March 25, 1,468 confirmed cases were notified in Brazil, of whom 10% (147 of 1,468) were hospitalised. Of the cases acquired locally (77{middle dot}8%), two thirds (66{middle dot}9% of 5,746) were confirmed in private laboratories. Overall, positive association between higher per capita income and COVID-19 diagnosis was identified. The median age of detected cases was 39 years (IQR 30-53). The median R0 was 2{middle dot}9 for Sao Paulo and Rio de Janeiro. Cardiovascular disease/hypertension were associated with hospitalization. Co-circulation of six respiratory viruses, including influenza A and B and human rhinovirus was detected in low levels.\n\nInterpretationSocioeconomic disparity determines access to SARS-CoV-2 testing in Brazil. The lower median age of infection and hospitalization compared to other countries is expected due to a younger population structure. Enhanced surveillance of respiratory pathogens across socioeconomic statuses is essential to better understand and halt SARS-CoV-2 transmission.\n\nFundingSao Paulo Research Foundation, Medical Research Council, Wellcome Trust and Royal Society.", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "William Marciel de Souza", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Lewis Fletcher Buss", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Darlan da Silva Candido", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jean Paul Carrera", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sabrina Li", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alexander Zarebski", - "author_inst": "University of Oxford" - }, - { - "author_name": "Maria Vincenti-Gonzalez", - "author_inst": "Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Janey Messina", - "author_inst": "University of Oxford" - }, - { - "author_name": "Flavia Cristina da Silva Sales", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Pamela dos Santos Andrade", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Carlos A Prete Jr.", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Vitor Heloiz Nascimento", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Fabio Ghilardi", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Rafael Henrique Moraes Pereira", - "author_inst": "Institute for Applied Economic Research" - }, - { - "author_name": "Andreza Aruska de Souza Santos", - "author_inst": "University of Oxford" - }, - { - "author_name": "Leandro Abade", - "author_inst": "University of Oxford" - }, - { - "author_name": "Bernardo Gutierrez", - "author_inst": "University of Oxford" - }, - { - "author_name": "Moritz U. G. Kraemer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Renato Santana Aguiar", - "author_inst": "Universidade Federal de Minas Gerais" - }, - { - "author_name": "Neal Alexander", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Philippe Mayaud", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Oliver J Brady", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Izabel Oliva Marcilio de Souza", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Nelson Gouveia", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Guangdi Li", - "author_inst": "Central South University Xiangya School of Medicine" - }, - { - "author_name": "Adriana Tami", - "author_inst": "Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Silvano Barbosa Oliveira", - "author_inst": "Ministerio da Saude do Brasil" - }, - { - "author_name": "Victor Bertollo Gomes Porto", - "author_inst": "Ministerio da Saude do Brasil" - }, - { - "author_name": "Fabiana Ganem", - "author_inst": "Ministerio da Saude do Brasil" - }, - { - "author_name": "Walquiria Ferreira Almeida", - "author_inst": "Ministerio da Saude do Brasil" - }, - { - "author_name": "Francieli Fontana Sutile Tardetti Fantinato", - "author_inst": "Ministerio da Saude do Brasil" - }, - { - "author_name": "Eduardo Marques Macario", - "author_inst": "Ministerio da Saude do Brasil" - }, - { - "author_name": "Wanderson Kleber Oliveira", - "author_inst": "Ministerio da Saude do Brasil" - }, - { - "author_name": "Oliver Pybus", - "author_inst": "University of Oxford" - }, - { - "author_name": "Chieh-Hsi Wu", - "author_inst": "University of Southampton" - }, - { - "author_name": "Julio Croda", - "author_inst": "Oswaldo Cruz Foundation" - }, - { - "author_name": "Ester Cerdeira Sabino", - "author_inst": "University of Sao Paulo" - }, - { - "author_name": "Nuno R. Faria", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.23.20076984", "rel_title": "Real-time estimation of R_0 for supporting public-health policies against COVID-19", @@ -1515400,6 +1515641,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.23.20077230", + "rel_title": "Analysis of national and international guidelines on respiratory protection equipment for COVID-19 in healthcare settings.", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077230", + "rel_abs": "BackgroundConsistent guidelines on respiratory protection for healthcare professionals combined with improved global supply chains are critical to prevent COVID-19. We analysed the guidelines published by national and international societies/organizations on facemasks and respirators to prevent COVID-19 in healthcare settings.\n\nMethodsFrom the 1st January to the 2nd April 2020, guidelines published in four countries (France, Germany, United States, United Kingdom), and two international organizations (US and European Centre for Diseases Control, and World Health Organization) were reviewed to analyse the mask and respirators recommended for healthcare settings during the COVID-19 outbreak. The aerosol generating procedures (AGP) definitions and the strategy recommended for optimizing supplies and overcoming shortages were collected.\n\nFindingsThe recommendation of respirator was universally recommended for AGP across countries, although the type of respirators and what constituted an AGP was variable. Some guidance maintained the use of N95/99 for all contact with confirmed COVID-19 cases (i.e. Germany) whereas others, recommended a surgical mask (i.e. WHO, UK, France). Most guidelines were published in March with either downgraded (US and European CDC), relatively stable (WHO, Germany, and UK), or a mixing of high and low level equipment (France). The strategies to overcome shortage of respiratory protection equipment were based on minimizing the need and rationalizing the use, but also prolonging their use, reusing them after cleaning/sterilization, or using cloth masks.\n\nInterpretationsIn a crisis context, stable and consistent guidelines clearly detailing the respiratory protection type, and their indications, may prevent the confusion and anxiety among frontline staff, and avoid shortage.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Gabriel Birgand", + "author_inst": "Imperial College London" + }, + { + "author_name": "Nico T. Mutters", + "author_inst": "Heidelberg University Hospital" + }, + { + "author_name": "Jonathan Otter", + "author_inst": "Imperial College London" + }, + { + "author_name": "Vanessa M. Eichel", + "author_inst": "Heidelberg University Hospital" + }, + { + "author_name": "Didier Lepelletier", + "author_inst": "CHU de Nantes" + }, + { + "author_name": "Daniel J. Morgan", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Jean Christophe Lucet", + "author_inst": "AP-HP, Hopital Bichat Claude Bernard" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.25.20074856", "rel_title": "Test performance evaluation of SARS-CoV-2 serological assays", @@ -1516496,49 +1516780,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.24.20077818", - "rel_title": "A prototype for decision support tool to help decision-makers with the strategy of handling the COVID-19 UK epidemic", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20077818", - "rel_abs": "The primary objective of this work is to model and compare different exit scenarios from the lock-down for the COVID-19 UK epidemic. In doing so we provide an additional modelling basis for laying out the strategy options for the decision-makers. The main results are illustrated and discussed in Part I. In Part II, we describe the stochastic model that we have developed for modelling this epidemic. As argued in Part II, the developed model is more flexible than the SEIR/SEIRS models and can be used for modelling the scenarios which may be difficult or impossible to model with the SEIR/SEIRS models. To compare different scenarios for exiting from the lock-down, in Part III we provide our previous report on the same topic where similar (although not as detailed) scenarios were considered. As the possible exit dates, we have chosen May 4, May 11, May 18 and May 25.\n\nWe model differently the regions with high initial reproductive number chosen to be R0 = 2.5, medium R0 = 2.3 and low R0 = 2. The numbers for the whole of the UK can be obtained by appropriate averaging of the numbers given in the report. Typical figures are given in Section 4. For each scenario considered, we plot the expected proportion of infected at time t and the expected number of deaths at time t. To compute the expected numbers of deaths we used the total mortality rate 0.66%. Many recent studies suggest lower values and therefore the numbers in our projections should be considered as rather pessimistic. Our analysis suggests a value around 0.5% for the mortality rate.\n\nIn the model, we assume that the isolation of older and vulnerable people continues and the public carries on certain level of isolation until the end of 2020; also we assume that immunity is kept for at least a year and there is no international travel influence. Our main conclusions are:\n\nO_LIIn regions with higher initial reproductive number 2.5 the proportion of susceptible at the start of the lock-down should be not smaller than 0.95, the epidemic curve in such regions is in the fast monotonic decline irrespectively of the date of the lock-down lift;\nC_LIO_LIIn regions with lower initial reproductive number 2.0 the second mild wave can be expected, the difference between the expected mortality rates is very small for all May 2020 lifting lock-down dates;\nC_LIO_LIIn regions with initial reproductive number 2.3, a mild second wave can be expected in the case of large proportion of susceptible at the start of the lock-down, but its severity and resulting mortality depend very little on the date of lifting the lock-down;\nC_LIO_LIFor the overall UK epidemic, even for rather pessimistic scenarios considered, the second wave is much less pronounced (in terms of the expected mortality rate) than the first one, and the total numbers of expected deaths are within 2% for all May 2020 dates of lifting the lock-down. Moreover, by keeping R0-value after lifting the lock-down below 1.75 is likely to lead to the avoidance of a UK-wide second wave, see Section 4.\nC_LI\n\nWe believe that the model build in this work can be considered as an important decision support tool to help decision-makers with the strategy of handling the epidemic. We invite other scholars to participate in an open discussion of the strategy options. We feel that this kind of models should be used in the short and long term management of the disease. We recommend the development of a permanent and modularised modelling suite for COVID-19 management to which additional modules can be added as anti-viral drugs and vaccination are introduced, extending the options. We trust that this work makes a start in that direction and demonstrates the advantages of a heterogeneous demographic refinement, which can only improve targeting role out of treatments.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Anatoly Zhigljavsky", - "author_inst": "Cardiff University" - }, - { - "author_name": "Ivan Fesenko", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Henry Wynn", - "author_inst": "Alan Turing Institute" - }, - { - "author_name": "Kobi Kremnitzer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jack Noonan", - "author_inst": "Cardiff University" - }, - { - "author_name": "Jonathan Gillard", - "author_inst": "Cardiff University" - }, - { - "author_name": "Roger Whitaker", - "author_inst": "Cardiff University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.24.20077792", "rel_title": "COVID-19 in India: State-wise Analysis and Prediction", @@ -1516766,6 +1517007,217 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.26.20073411", + "rel_title": "Machine Learning to Predict Mortality and Critical Events in COVID-19 Positive New York City Patients", + "rel_date": "2020-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20073411", + "rel_abs": "Coronavirus 2019 (COVID-19), caused by the SARS-CoV-2 virus, has become the deadliest pandemic in modern history, reaching nearly every country worldwide and overwhelming healthcare institutions. As of April 20, there have been more than 2.4 million confirmed cases with over 160,000 deaths. Extreme case surges coupled with challenges in forecasting the clinical course of affected patients have necessitated thoughtful resource allocation and early identification of high-risk patients. However, effective methods for achieving this are lacking. In this paper, we use electronic health records from over 3,055 New York City confirmed COVID-19 positive patients across five hospitals in the Mount Sinai Health System and present a decision tree-based machine learning model for predicting in-hospital mortality and critical events. This model is first trained on patients from a single hospital and then externally validated on patients from four other hospitals. We achieve strong performance, notably predicting mortality at 1 week with an AUC-ROC of 0.84. Finally, we establish model interpretability by calculating SHAP scores to identify decisive features, including age, inflammatory markers (procalcitonin and LDH), and coagulation parameters (PT, PTT, D-Dimer). To our knowledge, this is one of the first models with external validation to both predict outcomes in COVID-19 patients with strong validation performance and identify key contributors in outcome prediction that may assist clinicians in making effective patient management decisions.\n\nOne-Sentence SummaryWe identify clinical features that robustly predict mortality and critical events in a large cohort of COVID-19 positive patients in New York City.", + "rel_num_authors": 49, + "rel_authors": [ + { + "author_name": "Akhil Vaid", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sulaiman Somani", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adam J Russak", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jessica K De Freitas", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Fayzan F Chaudhry", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ishan Paranjpe", + "author_inst": "Ican School of Medicine at Mount Sinai" + }, + { + "author_name": "Kipp W Johnson", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Samuel J Lee", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Riccardo Miotto", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Shan Zhao", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Noam Beckmann", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Nidhi Naik", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kodi Arfer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Arash Kia", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Prem Timsina", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Anuradha Lala", + "author_inst": "Icahn School of Medicine Mount Sinai" + }, + { + "author_name": "Manish Paranjpe", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Patricia Glowe", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Eddye Golden", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Matteo Danieletto", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Manbir Singh", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Dara Meyer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Paul F O'Reilly", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Laura H Huckins", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Patricia Kovatch", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Joseph Finkelstein", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Robert M Freeman", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Edgar Argulian", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Andrew Kasarskis", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Bethany Percha", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Judith A Aberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Emilia Bagiella", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Carol R Horowitz", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Barbara Murphy", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Eric J Nestler", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Eric E Schadt", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Judy H Cho", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Carlos Cordon-Cardo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Valentin Fuster", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Dennis S Charney", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "David L Reich", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Erwin P Bottinger", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Matthew A Levin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jagat Narula", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Zahi A Fayad", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Allan Just", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alexander W Charney", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Girish N Nadkarni", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Benjamin S Glicksberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.22.20074351", "rel_title": "Resilient SARS-CoV-2 diagnostics workflows including viral heat inactivation", @@ -1518142,81 +1518594,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.23.20076976", - "rel_title": "Performing risk stratification for COVID-19 when individual level data is not available, the experience of a large healthcare organization", - "rel_date": "2020-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076976", - "rel_abs": "With the global coronavirus disease 2019 (COVID-19) pandemic, there is an urgent need for risk stratification tools to support prevention and treatment decisions. The Centers for Disease Control and Prevention (CDC) listed several criteria that define high-risk individuals, but multivariable prediction models may allow for a more accurate and granular risk evaluation. In the early days of the pandemic, when individual level data required for training prediction models was not available, a large healthcare organization developed a prediction model for supporting its COVID-19 policy using a hybrid strategy. The model was constructed on a baseline predictor to rank patients according to their risk for severe respiratory infection or sepsis (trained using over one-million patient records) and was then post-processed to calibrate the predictions to reported COVID-19 case fatality rates. Since its deployment in mid-March, this predictor was integrated into many decision-processes in the organization that involved allocating limited resources. With the accumulation of enough COVID-19 patients, the predictor was validated for its accuracy in predicting COVID-19 mortality among all COVID-19 cases in the organization (3,176, 3.1% death rate). The predictor was found to have good discrimination, with an area under the receiver-operating characteristics curve of 0.942. Calibration was also good, with a marked improvement compared to the calibration of the baseline model when evaluated for the COVID-19 mortality outcome. While the CDC criteria identify 41% of the population as high-risk with a resulting sensitivity of 97%, a 5% absolute risk cutoff by the model tags only 14% to be at high-risk while still achieving a sensitivity of 90%. To summarize, we found that even in the midst of a pandemic, shrouded in epidemiologic \"fog of war\" and with no individual level data, it was possible to provide a useful predictor with good discrimination and calibration.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Noam Barda", - "author_inst": "Clalit Research Institute, Innovation Division, Clalit Health Services, Tel Aviv, Israel" - }, - { - "author_name": "Dan Riesel", - "author_inst": "Clalit Research Institute, Innovation Division, Clalit Health Services, Tel Aviv, Israel" - }, - { - "author_name": "Amichay Akriv", - "author_inst": "Clalit Research Institute, Innovation Division, Clalit Health Services, Tel Aviv, Israel" - }, - { - "author_name": "Joseph Levi", - "author_inst": "Clalit Research Institute, Innovation Division, Clalit Health Services, Tel Aviv, Israel" - }, - { - "author_name": "Uriah Finkel", - "author_inst": "Clalit Research Institute, Innovation Division, Clalit Health Services, Tel Aviv, Israel" - }, - { - "author_name": "Gal Yona", - "author_inst": "Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Israel" - }, - { - "author_name": "Daniel Greenfeld", - "author_inst": "Faculty of Industrial Engineering and Management, Technion University, Haifa, Israel" - }, - { - "author_name": "Shimon Sheiba", - "author_inst": "Faculty of Industrial Engineering and Management, Technion University, Haifa, Israel" - }, - { - "author_name": "Jonathan Somer", - "author_inst": "Faculty of Industrial Engineering and Management, Technion University, Haifa, Israel" - }, - { - "author_name": "Eitan Bachmat", - "author_inst": "Department of Computer Science, Ben Gurion University of the Negev, Be'er Sheva, Israel" - }, - { - "author_name": "Guy N Rothblum", - "author_inst": "Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Israel" - }, - { - "author_name": "Uri Shalit", - "author_inst": "Faculty of Industrial Engineering and Management, Technion University, Haifa, Israel" - }, - { - "author_name": "Doron Netzer", - "author_inst": "Community Medical Services Division, Clalit Health Services, Tel Aviv, Israel" - }, - { - "author_name": "Ran Balicer", - "author_inst": "Clalit Research Institute, Innovation Division, Clalit Health Services, Tel Aviv, Israel" - }, - { - "author_name": "Noa Dagan", - "author_inst": "Clalit Research Institute, Innovation Division, Clalit Health Services, Tel Aviv, Israel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.23.20076919", "rel_title": "A simple mathematical model for Coronavirus (COVID-19)", @@ -1518396,6 +1518773,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.28.066761", + "rel_title": "Heparin inhibits cellular invasion by SARS-CoV-2: structural dependence of the interaction of the surface protein (spike) S1 receptor binding domain with heparin.", + "rel_date": "2020-04-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.28.066761", + "rel_abs": "The dependence of the host on the interaction of hundreds of extracellular proteins with the cell surface glycosaminoglycan heparan sulphate (HS) for the regulation of homeostasis is exploited by many microbial pathogens as a means of adherence and invasion. The closely related polysaccharide heparin, the widely used anticoagulant drug, which is structurally similar to HS and is a common experimental proxy, can be expected to mimic the properties of HS. Heparin prevents infection by a range of viruses if added exogenously, including S-associated coronavirus strain HSR1. Heparin prevents infection by a range of viruses if added exogenously, including S-associated coronavirus strain HSR1. Here, we show that the addition of heparin to Vero cells between 6.25 - 200 g.ml-1, which spans the concentration of heparin in therapeutic use, and inhibits invasion by SARS-CoV-2 at between 44 and 80%. We also demonstrate that heparin binds to the Spike (S1) protein receptor binding domain and induces a conformational change, illustrated by surface plasmon resonance and circular dichroism spectroscopy studies. The structural features of heparin on which this interaction depends were investigated using a library of heparin derivatives and size-defined fragments. Binding is more strongly dependent on the presence of 2-O or 6-O sulphation, and the consequent conformational consequences in the heparin structure, than on N-sulphation. A hexasaccharide is required for conformational changes to be induced in the secondary structure that are comparable to those that arise from heparin binding. Enoxaparin, a low molecular weight clinical anticoagulant, also binds the S1 RBD protein and induces conformational change. These findings have implications for the rapid development of a first-line therapeutic by repurposing heparin as well as for next-generation, tailor-made, GAG-based antiviral agents against SARS-CoV-2 and other members of the Coronaviridae.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Courtney Mycroft-West", + "author_inst": "Keele University" + }, + { + "author_name": "Dunhao Su", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Isabel Pagani", + "author_inst": "IRCCS San Raffaele Scientific Institute" + }, + { + "author_name": "Timothy Rudd", + "author_inst": "National Institute for Biological Standards and Control" + }, + { + "author_name": "Stefano Elli", + "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" + }, + { + "author_name": "Scott Guimond", + "author_inst": "Keele University" + }, + { + "author_name": "Gavin Miller", + "author_inst": "Keele University" + }, + { + "author_name": "Maria Meneghetti", + "author_inst": "Universidade Federal de Sao Paulo" + }, + { + "author_name": "Helena Nader", + "author_inst": "Universidade Federal de Sao Paulo" + }, + { + "author_name": "Yong Li", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Quentin Nunes", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Patricia Procter", + "author_inst": "Keele University" + }, + { + "author_name": "Nicasio Mancini", + "author_inst": "Universita Vita-Salute San Raffaele" + }, + { + "author_name": "Massimo Clementi", + "author_inst": "Universita Vita-Salute San Raffaele" + }, + { + "author_name": "Antonella Bisio", + "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" + }, + { + "author_name": "Nicholas Forsyth", + "author_inst": "Keele University" + }, + { + "author_name": "Jeremy Turnbull", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Marco Guerrini", + "author_inst": "Istituto di Ricerche Chimiche e Biochimiche G. Ronzoni" + }, + { + "author_name": "David Fernig", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Elisa Vicenzi", + "author_inst": "San Raffaele Scientific Institute" + }, + { + "author_name": "Edwin Yates", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Marcelo Lima", + "author_inst": "Keele University" + }, + { + "author_name": "Mark A Skidmore", + "author_inst": "Keele University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.27.064139", "rel_title": "A Modular Framework for Multiscale Spatial Modeling of Viral Infection and Immune Response in Epithelial Tissue", @@ -1519532,53 +1520016,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.04.22.20071050", - "rel_title": "Eosinopenia Phenotype in Patients with Coronavirus Disease 2019: A Multi-center Retrospective Study from Anhui, China", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20071050", - "rel_abs": "BackgroundCoronavirus disease 19 (COVID-19) has become a global unprecedented pandemic infecting more than one millon people, which is declared by WHO as a international public health emergency. Eosinopenia may predict a poor prognosis of COVID-19. However, to date, there is no detailed analysis of the clinical characteristics of COVID-19 patients with eosinopenia.\n\nResearch questionThe aim of this study was to describe clinical characteristics of COVID-19 patients with eosinopenia.\n\nStudy Design and MethodsThis was a multi-center retrospective study conducted in three tertiary hospitals. A total of 59 patients with COVID-19 were reviewed from January 23, 2020 to March 10, 2020. We described clincial characteristics of patients with COIVD-19 and eosinopenia phenotype.\n\nResultsThe median age of patients with COVID-19 was 39 years old, and 32 (54,2%) were male. Patients with severe type had higher proportions of dyspnea (50%) and gastrointestinal symptoms (50%) compared with mild or moderate patients. Laboratory findings indicated that lower counts of lymphocyte and eosnophils were observed in patients with severe type. Cough, sputum, and fatigue were more common symptoms in eosinopenia patients compared with non-eosinopenia patients. High proportion of comorbidities was observed in eosinopenia patients. Laboratory findings indicated that lymphocyte counts (median: 101 cells/l) in eosinopenia patients were significantly less than those of non-eosinopenia patients (median: 167 cells/l, p<0.001). The use of corticosteroids therapy in COVID-19 patients with eosinopenia were notably higher than those in patients with non-eosinopenia (50% vs 13.8%, respectively, p=0.005). Compared with parameters in non-eosinopenia patients, eosinopenia patients were more inclined to have less lymphocyte counts (OR value 6.566, 95%CI[1.101-39.173], p=0.039).\n\nInterpretationEosinopenia are very common in COVID-19 patient, particularly in severe patients. Common symptoms included fever, cough, sputum, and fatigue are frequent in eosinopenia patients. Eosinopenia may represent a novel phenotype in COVID-19, which needs further investigation.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yusheng Cheng", - "author_inst": "Yijishan Hospital of Wannan Medical College" - }, - { - "author_name": "Yun Zhou", - "author_inst": "Second People Hospital of Wuhu" - }, - { - "author_name": "Mengde Zhu", - "author_inst": "First People Hospital of Hefei" - }, - { - "author_name": "Lei Zha", - "author_inst": "Infection and Global Health" - }, - { - "author_name": "Zhiwei Lu", - "author_inst": "Yijishan Hospital of Wannan Medical College" - }, - { - "author_name": "Zhen Ding", - "author_inst": "First People Hospital of Hefei" - }, - { - "author_name": "Jianghua Yang", - "author_inst": "Yijishan Hospital of Wannan Medical College" - }, - { - "author_name": "Gang Yang", - "author_inst": "Second People Hospital of Wuhu" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.04.22.20075416", "rel_title": "Estimating Survival of Hospitalized COVID-19 Patients from Admission Information", @@ -1519810,6 +1520247,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.21.20074450", + "rel_title": "The dynamics of Covid-19: weather, demographics and infection timeline", + "rel_date": "2020-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20074450", + "rel_abs": "We study the effects of temperature, absolute humidity, population density and when country/U.S. state reached 100 cases on early pace of Covid-19 expansion, for all 50 U.S. states and 110 countries with enough data. For U.S. states, weather variables show opposite effects when compared to the case of countries: higher temperature or absolute humidity imply faster early outbreak. The higher the population density or the earlier the date when state reached 100th case, the faster the pace of outbreak. When all variables are considered, only population density and the timeline variable show statistical significance. Discounting the effect of the timeline variable, we obtain an estimate for the initial growth rate of Covid-19, which can be also used to estimate the basic reproduction number for a region, in terms of population density. This has policy implications regarding how to control the pace of Covid-10 outbreak in a particular area, and we discuss some of them. In the case of countries, for which we did not have demographic information, weather variables lose statistical significance once the timeline variable is added. Relaxing CI requirements, absolute humidity contributes mildly to the reduction of growth rate of cases for the countries studied. Our results suggest that population density should be employed as a control variable and that analysis should have a local character, for subregions and countries separately, in studies involving the dynamics of Covid-19 and similar infectious diseases.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Renato H.L. Pedrosa", + "author_inst": "Unicamp" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.22.20075762", "rel_title": "Proactive social distancing mitigates COVID-19 outbreaks within a month across 58 mainland China cities", @@ -1520630,29 +1521086,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.21.20074070", - "rel_title": "The proportion testing positive for SARS-COV-2 among the tested population in the U.S.: Benefits of the positive test ratio under scaled testing scenarios", - "rel_date": "2020-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20074070", - "rel_abs": "The ratios offer simple ways to account for variations in testing and reporting. Tracking the ratios in addition to cases offer a more precise view of the pandemic. Our observations underscore the need to scale mass testing with accurate and reliable tests, to implement testing systematically and report results consistently.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "George Ng", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Constance Wang", - "author_inst": "University of California, Berkeley" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.22.20074286", "rel_title": "Taking Account of Asymptomatic Infections in Modeling the Transmission Potential of the COVID-19 Outbreak on the Diamond Princess Cruise Ship", @@ -1520828,6 +1521261,53 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.04.26.062406", + "rel_title": "How did SARS-CoV-19 spread in India from Italy, Iran and China? Genetic surveillance of early cases and virus demography", + "rel_date": "2020-04-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.26.062406", + "rel_abs": "SARS-CoV-19 after emerging from Wuhan, drastically devastated all sectors of human life by crushing down the global economy and increased psychological burden on public, government, and healthcare professionals. We manifested by analyzing 35 early coronavirus cases of India, that virus introduction in India, occurred from Italy, Iran and China and population demography apparently revealed a rapid population expansion after the outbreak with a present steady growth. We depicted nucleotide substitutions in structural genes, drove for the adaptive selection and plead for sequencing more genomes to facilitate identification of new emerged mutants, genetic evolution and disease transmission caused by coronavirus.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mukesh Thakur", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Abhishek Singh", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Bheem Dutt Joshi", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Avijit Ghosh", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Sujeet Kumar Singh", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Neha Singh", + "author_inst": "University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Lalit Kumar Sharma", + "author_inst": "Zoological Survey of India, Kolkata" + }, + { + "author_name": "Kailash Chandra", + "author_inst": "Zoological Survey of India, Kolkata" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.04.23.20076612", "rel_title": "A systematic review of Anakinra, Tocilizumab, Sarilumab and Siltuximab for coronavirus-related infections", @@ -1522004,53 +1522484,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.04.22.20076117", - "rel_title": "Microwave-Generated Steam Decontamination of N95 Respirators Utilizing Universally Accessible Materials", - "rel_date": "2020-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20076117", - "rel_abs": "The SARS-CoV-2 pandemic has caused a severe, international shortage of N95 respirators, which are essential to protect healthcare providers from infection. Given the contemporary limitations of the supply chain, it is imperative to identify effective means of decontaminating, reusing, and thereby conserving N95 respirator stockpiles. To be effective, decontamination must result in sterilization of the N95 respirator without impairment of respirator filtration or user fit. Although numerous methods of N95 decontamination exist, none are universally accessible. In this work we describe a microwave-generated steam decontamination protocol for N95 respirators for use in healthcare systems of all sizes, geographies, and means. Using widely available glass containers, mesh from commercial produce bags, a rubber band, and a 1100W commercially available microwave, we constructed an effective, standardized, and reproducible means of decontaminating N95 respirators. Employing this methodology against MS2 phage, a highly conservative surrogate for SARS-CoV-2 contamination, we report an average 6-log10 plaque forming unit (PFU) (99.9999%) and a minimum 5-log10 PFU (99.999%) reduction after a single three-minute microwave treatment. Notably, quantified respirator fit and function were preserved, even after 20 sequential cycles of microwave steam decontamination. This method provides a valuable means of effective decontamination and reuse of N95 respirators by frontline providers facing urgent need.\n\nIMPORTANCEDue to the rapid spread of COVID-19 there is an increasing shortage of protective gear necessary to keep health care providers safe from infection. The CDC reports 9,282 cases of COVID-19 among U.S. healthcare workers to date (1). N95 respirators are recommended by the CDC as the ideal method of protection from COVID-19. Although N95 respirators are traditionally single-use, the shortages have necessitated the need for re-use. Effective methods of N95 decontamination that do not affect the fit or filtration ability of N95 respirators are essential. Numerous methods of N95 decontamination exist; however, none are universally accessible. In this study we describe an effective, standardized, and reproducible means of decontaminating N95 respirators using widely available materials. The N95 decontamination method described in this work will provide a valuable resource for hospitals, healthcare centers, and outpatients practices that are experiencing increasing shortages of N95 respirators due to the COVID-19 pandemic.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Kate E Zulauf", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Alex B Green", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Alex N. Nguyen Ba", - "author_inst": "Harvard University" - }, - { - "author_name": "Tanush Jagdish", - "author_inst": "Harvard University" - }, - { - "author_name": "Dvir Reif", - "author_inst": "Harvard University" - }, - { - "author_name": "Robert Seeley", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Alana Dale", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "James E Kirby", - "author_inst": "Beth Israel Deaconess Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.04.22.20074963", "rel_title": "Lack of association between genetic variants at ACE2 and TMPRSS2 genes involved in SARS-CoV-2 infection and human quantitative phenotypes", @@ -1522514,6 +1522947,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.21.20074641", + "rel_title": "Association between rRT-PCR test results upon admission and outcome in hospitalized chest CT-Positive COVID-19 patients; a provincial retrospective cohort with active follow-up", + "rel_date": "2020-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20074641", + "rel_abs": "BackgroundThe Covid-19 pandemic imposed the most devastating challenge on healthcare systems worldwide. Iran was among the first countries that had to confront serious shortages in RT-PCR testing for SARS-CoV-2 and ventilators availabilities throughout the COVID-19 outbreak. This study aimed to investigate the clinical course of hospitalized COVID-19 patients with different rRT-PCR test results during the first 3 weeks of the outbreak in Qazvin province, Iran.\n\nMethodsFor this retrospective cohort study, data of hospitalized patients primarily diagnosed as having COVID-19 in all 12 centers across the whole Qazvin province during Feb 20-Mar 11, 2020 was analyzed. A multivariate logistic regression model was applied to assess the independent associates of death among COVID-19 patients.\n\nResults998 patients (57% male, median age 54 years) with positive chest CT-scan changes were included in this study. Among them, 558 patients were examined with rRT-PCR test and 73{middle dot}8% tested positive. Case fatality rate was 20{middle dot}68% and 7{middle dot}53% among test-positive and test negative hospitalized patients, respectively. While only 5{middle dot}2% of patients were ICU admitted, case fatality rates outside ICU were 17{middle dot}70% and 4{middle dot}65% in test-positive and test-negative non-ICU admitted patients, correspondingly. The independent associates of death were age [≥] 70 years, testing positive with rRT-PCR test, having immunodeficiency disorders and ICU admission.\n\nConclusionsHospitalized COVID-19 patients with mild symptoms despite positive chest CT changes and major comorbidities were more probable to have negative rRT-PCR test result, hence lower case fatality rate and a more favorable outcome.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Saeed Nemati", + "author_inst": "Cancer Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Hamid Reza Najari", + "author_inst": "1. Department of Internal Medicine, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran; 2. Deputy of health, Qazvin University of Medical S" + }, + { + "author_name": "Anita Eftekharzadeh", + "author_inst": "Obesity Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti Universiy School of Medicine, Tehran, Iran" + }, + { + "author_name": "Amir Mohammad Kazemifar", + "author_inst": "Department of Internal Medicine, School of Medicine, Qazvin University of Medical Sciences, Qazvin, Iran" + }, + { + "author_name": "Ali Qandian", + "author_inst": "Office of Communicable Disease, Deputy of health, Qazvin University of Medical Sciences, Qazvin, Iran" + }, + { + "author_name": "Pedram Fattahi", + "author_inst": "Cancer Research Center, Cancer Research Institute, Tehran University of Medical Sciences, Tehran, Iran" + }, + { + "author_name": "Maedeh Zokaei Nikoo", + "author_inst": "Student Research Committee, Qazvin University of Medical Sciences, Qazvin, Iran" + }, + { + "author_name": "Shiva Leghaei", + "author_inst": "Office of Communicable Disease, Deputy of health, Qazvin University of Medical Sciences, Qazvin, Iran" + }, + { + "author_name": "Mohammad Reza Rouhollahi", + "author_inst": "1. Cancer Research Center, Cancer Research Institute, Tehran University of Medical Sciences, Tehran, Iran; 2. Clinical Cancer Research Center (CCRC), Milad Hosp" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.21.20074757", "rel_title": "Knowledge, attitude, practice and perception regarding COVID-19 among students in Bangladesh: Survey in Rajshahi University", @@ -1523402,45 +1523886,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.24.060376", - "rel_title": "The anti-HIV Drug Nelfinavir Mesylate (Viracept) is a Potent Inhibitor of Cell Fusion Caused by the SARS-CoV-2 Spike (S) Glycoprotein Warranting further Evaluation as an Antiviral against COVID-19 infections", - "rel_date": "2020-04-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.24.060376", - "rel_abs": "Coronaviruses belong to a group of enveloped, positive-single stranded RNA viruses that are known to cause severe respiratory distress in animals and humans. The current SARS coronavirus-2 (SARS CoV-2) pandemic has caused more than 2,000,000 infections globally and nearly 200,000 deaths. Coronaviruses enter susceptible cells via fusion of the viral envelope with the plasma membrane and/or via fusion of the viral envelope with endosomal membranes after endocytosis of the virus into endosomes. Previous results with SARS and MERS CoV have shown that the Spike (S) glycoprotein is a major determinant of virus infectivity and immunogenicity. Herein, we show that expression of SARS CoV-2 S (S-n) glycoprotein after transient transfection of African green monkey kidney (Vero) cells caused extensive cell fusion in comparison to limited cell fusion caused by the SARS S (S-o) glycoprotein. S-n expression was detected intracellularly and on transfected Vero cell surfaces and caused the formation of very large multinucleated cells (syncytia) by 48 hours post transfection. These results are in agreement with published pathology observations of extensive syncytial formation in lung tissues of COVID-19 patients. This differential S-n versus S-o-mediated cell fusion suggests that SARS-CoV-2 is able to spread from cell-to-cell much more efficiently than SARS effectively avoiding extracellular spaces and neutralizing antibodies. A systematic screening of several drugs for ability to inhibit S-n and S-o cell fusion revealed that the FDA approved HIV-protease inhibitor, nelfinavir mesylate (Viracept) drastically inhibited S-n and S-o-mediated cell fusion in a dose-dependent manner. Complete inhibition of cell fusion was observed at a 10 micromolar concentration. Computational modeling and in silico docking experiments suggested the possibility that nelfinavir may bind inside the S trimer structure, proximal to the S2 amino terminus directly inhibiting S-n and S-o-mediated membrane fusion. Also, it is possible that nelfinavir mesylate acts on cellular processes to inhibit S proteolytic processing. These results warrant further investigations of the potential of nelfinavir mesylate as an antiviral drug, especially at early times after SARS-CoV-2 symptoms appear.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Farhana Musarrat", - "author_inst": "Louisiana State University" - }, - { - "author_name": "Vladimir Chouljenko", - "author_inst": "Louisiana State University" - }, - { - "author_name": "Rafiq Nabi", - "author_inst": "Louisiana State University" - }, - { - "author_name": "Achyut Dahai", - "author_inst": "University of Louisiana Monroe" - }, - { - "author_name": "Seetharama Jois", - "author_inst": "University of Louisiana Monroe" - }, - { - "author_name": "Konstantin Kousoulas", - "author_inst": "Louisiana State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.21.20068858", "rel_title": "SARS-CoV-2 serological analysis of COVID-19 hospitalized patients, pauci-symptomatic individuals and blood donors.", @@ -1523912,6 +1524357,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.24.059576", + "rel_title": "Introductions and early spread of SARS-CoV-2 in France", + "rel_date": "2020-04-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.24.059576", + "rel_abs": "Following the emergence of coronavirus disease (COVID-19) in Wuhan, China in December 2019, specific COVID-19 surveillance was launched in France on January 10, 2020. Two weeks later, the first three imported cases of COVID-19 into Europe were diagnosed in France. We sequenced 97 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from samples collected between January 24 and March 24, 2020 from infected patients in France. Phylogenetic analysis identified several early independent SARS-CoV-2 introductions without local transmission, highlighting the efficacy of the measures taken to prevent virus spread from symptomatic cases. In parallel, our genomic data reveals the later predominant circulation of a major clade in many French regions, and implies local circulation of the virus in undocumented infections prior to the wave of COVID-19 cases. This study emphasizes the importance of continuous and geographically broad genomic sequencing and calls for further efforts with inclusion of asymptomatic infections.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Fabiana Gambaro", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Artem Baidaliuk", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Sylvie Behillil", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Flora Donati", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Melanie Albert", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Andreea Alexandru", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Maud Vanpeene", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Meline Bizard", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Angela Brisebarre", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Marion Barbet", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Fawzi Derrar", + "author_inst": "Institut Pasteur of Algiers" + }, + { + "author_name": "Sylvie van der Werf", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Vincent Enouf", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Etienne Simon-Loriere", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.04.20.20064899", "rel_title": "Epidemiological characteristics of COVID-19 in medical staff members of neurosurgery departments in Hubei province: A multicentre descriptive study", @@ -1525556,61 +1526072,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.20.20071423", - "rel_title": "Detection of Nucleocapsid Antibody to SARS-CoV-2 is More Sensitive than Antibody to Spike Protein in COVID-19 Patients", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20071423", - "rel_abs": "BackgroundSARS-CoV-2, the cause of coronavirus disease 2019 (COVID-19), is associated with respiratory-related morbidity and mortality. Assays to detect virus-specific antibodies are important to understand the prevalence of infection and the course of the immune response.\n\nMethodologyQuantitative measurements of plasma or serum antibodies by luciferase immunoprecipitation assay systems (LIPS) to the nucleocapsid and spike proteins were analyzed in 100 cross-sectional or longitudinal samples from SARS-CoV-2-infected patients. A subset of samples was tested with and without heat inactivation.\n\nResultsFifteen or more days after symptom onset, antibodies against SARS-CoV-2 nucleocapsid protein showed 100% sensitivity and 100% specificity, while antibodies to spike protein were detected with 91% sensitivity and 100% specificity. Neither antibody levels nor the rate of seropositivity were significantly reduced by heat inactivation of samples. Analysis of daily samples from six patients with COVID-19 showed anti-nucleocapsid and spike antibodies appearing between day 8 to day 14 after initial symptoms. Immunocompromised patients generally had a delayed antibody response to SARS-CoV-2 compared to immunocompetent patients.\n\nConclusionsAntibody to the nucleocapsid protein of SARS-CoV-2 is more sensitive than spike protein antibody for detecting early infection. Analyzing heat-inactivated samples by LIPS is a safe and sensitive method for detecting SARS-CoV-2 antibodies.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Peter D Burbelo", - "author_inst": "NIH" - }, - { - "author_name": "Francis X Riedo", - "author_inst": "EvergreenHealth, Kirkland, WA" - }, - { - "author_name": "Chihiro Morishima", - "author_inst": "University of Washington, Seattle" - }, - { - "author_name": "Stephen Rawlings", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Davey Smith", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Sanchita Das", - "author_inst": "NIH" - }, - { - "author_name": "Jeffrey R Strich", - "author_inst": "NIH" - }, - { - "author_name": "Daniel S Chertow", - "author_inst": "NIH" - }, - { - "author_name": "Richard T Davey Jr.", - "author_inst": "NIH" - }, - { - "author_name": "Jeffrey I Cohen", - "author_inst": "National Institutes of Health" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.21.20073668", "rel_title": "Nonlinear Markov Chain Modelling of the Novel Coronavirus (Covid-19) Pandemic", @@ -1525830,6 +1526291,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.20.20072157", + "rel_title": "Multiple drivers of the COVID-19 spread: role of climate, international mobility, and region-specific conditions", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20072157", + "rel_abs": "The novel Coronavirus Disease 2019 (COVID-19) has spread quickly across the globe. Here, we evaluated the role of climate (temperature and precipitation), region-specific susceptibility (BCG vaccination, malaria infection, and elderly population) and international traveller population (human mobility) in shaping the geographical patterns of COVID-19 cases across 1,055 countries/regions, and examined the sequential shift of multiple drivers of the accumulated cases from December, 2019 to April 12, 2020. The accumulated numbers of COVID-19 cases (per 1 million population) were well explained by a simple regression model. The explanatory power (R2) of the model increased up to > 70% in April 2020 as the COVID-19 spread progressed. Climate, host mobility, and host susceptibility largely explained the variance of the COVID-19 cases (per 1 million population), and their explanatory power improved as the pandemic progressed; the relative importance of host mobility and host susceptibility have been greater than that of climate. The number of days from outbreak onset showed greater explanatory power in the earlier stages of COVID-19 spread but rapidly lost its influence. Our findings demonstrate that the COVID-19 pandemic is deterministically driven by climate suitability, cross-border human mobility, and region-specific susceptibility. The present distribution of COVID-19 cases has not reached an equilibrium and is changing daily, especially in the Southern Hemisphere. Nevertheless, the present results, based on mapping the spread of COVID-19 and identifying multiple drivers of this outbreak trajectory, may contribute to a better understanding of the COVID-19 disease transmission risk and the measures against long-term epidemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Yasuhiro Kubota", + "author_inst": "University of the Ryukyus" + }, + { + "author_name": "Takayuki Shiono", + "author_inst": "University of the Ryukyus" + }, + { + "author_name": "Buntarou Kusumoto", + "author_inst": "University of the Ryukyus" + }, + { + "author_name": "Junichi Fujinuma", + "author_inst": "University of the Ryukyus" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.22.20076141", "rel_title": "COVID-19: Public Compliance with and Public Support for Stay-at-Home Mitigation Strategies", @@ -1526950,33 +1527442,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.21.20073932", - "rel_title": "Optimal strategies for quarantine stopping in France. General expected patterns of strategies focusing on contact between age groups", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20073932", - "rel_abs": "Due to the COVID-19 pandemic, many countries have implemented a complete lockdown of their population that may not be sustainable for long. To identify the best strategy to replace this full lockdown, sophisticated models that rely on mobility data have been developed. In this study, using the example of France as a case-study, we develop a simple model considering contacts between age classes to derive the general impact of partial lockdown strategies targeted at specific age groups. We found that epidemic suppression can only be achieved by targeting isolation of young and middle age groups with high efficiency. All other strategies tested result in a flatter epidemic curve, with outcomes in (e.g. mortality and health system over-capacity) dependent of the age groups targeted and the isolation efficiency. Targeting only the elderly can decrease the expected mortality burden, but in proportions lower than more integrative strategies involving several age groups. While not aiming to provide quantitative forecasts, our study shows the benefits and constraints of different partial lockdown strategies, which could help guide decision-making.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Benjamin ROCHE", - "author_inst": "IRD" - }, - { - "author_name": "Andres Garchitorena", - "author_inst": "Institut de Recherche pour le Developpement" - }, - { - "author_name": "David Roiz", - "author_inst": "Institut de Recherche pour le Developpement" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.20.20072793", "rel_title": "Prediction of the Peak, Effect of Intervention and Total Infected by the CoronavirusDisease in India", @@ -1527132,6 +1527597,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.20.20072892", + "rel_title": "Estimation of Undetected Covid-19 Infections in India", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20072892", + "rel_abs": "Background and ObjectivesWhile the number of detected COVID-19 infections are widely available, an understanding of the extent of undetected COVID-19 cases is urgently needed for an effective tackling of the pandemic and as a guide to lifting the lockdown. The aim of this work is to estimate and predict the true number of COVID-19 (detected and undetected) infections in India for short to medium forecast horizons. In particular, using publicly available COVID-19 infection data upto 16th April 2020, we predict the true number of infections in India during and upto the end of the formal lockdown period (21st April 2020).\n\nMethodsThe high death rate observed in most COVID-19 hit countries is suspected to be a function of the undetected infections existing in the population. An estimate of the age weighted infection fatality rate (IFR) of the disease of 0.41%, specifically calculated by taking into account the age structure of Indian population, is already available in the literature. In addition, the recorded case fatality rate (CFR= 0.70%) of Kerala, the only state in India to report single digit new infections over the second week of April, is used as a second estimate of the IFR. These estimates are used to formulate a relationship between deaths recorded and the true number of infections. The estimated undetected and detected cases time series based on these two IFR estimates are then used to fit a discrete time multivariate infection model to predict the total infections at the end of the formal lockdown period.\n\nResultsIn two consecutive fortnights during the lockdown, it was noted that the rise in detected infections has decreased by 2.7 times. For an IFR of 0.41%, the rise in undetected infections decreased by 3.2 times and the predicted number of total infections in India is 3.14 lakhs. While for an IFR of 0.70%, the rise in undetected cases decreased by 3.3 times and the total number of infections predicted on 21st April is 1.75 lakhs.\n\nInterpretation and ConclusionsThe behaviour of the undetected cases over time effectively illustrates the effects of lockdown and increased testing. From our estimates, it is found that the lockdown has brought down the undetected to detected cases ratio, and has consequently dampened the increase in the number of total cases. However, even though the rate of rise in total infections has fallen, the lifting of the lockdown should be done keeping in mind that 1.75 to 3 lakhs undetected cases will already exist in the population on 21st April.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Siuli Mukhopadhyay", + "author_inst": "Department of Mathematics, Indian Institute of Technology Bombay" + }, + { + "author_name": "Debraj Chakraborty", + "author_inst": "Indian Institute of Technology Bombay" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.20.20072462", "rel_title": "ESTIMATING R0 OF SARS-COV-2 IN HEALTHCARE SETTINGS", @@ -1528284,77 +1528772,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.22.054981", - "rel_title": "The anticoagulant nafamostat potently inhibits SARS-CoV-2 infection in vitro: an existing drug with multiple possible therapeutic effects", - "rel_date": "2020-04-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.22.054981", - "rel_abs": "Although infection by SARS-CoV-2, the causative agent of COVID-19, is spreading rapidly worldwide, no drug has been shown to be sufficiently effective for treating COVID-19. We previously found that nafamostat mesylate, an existing drug used for disseminated intravascular coagulation (DIC), effectively blocked MERS-CoV S protein-initiated cell fusion by targeting TMPRSS2, and inhibited MERS-CoV infection of human lung epithelium-derived Calu-3 cells. Here we established a quantitative fusion assay dependent on SARS-CoV-2 S protein, ACE2 and TMPRSS2, and found that nafamostat mesylate potently inhibited the fusion while camostat mesylate was about 10-fold less active. Furthermore, nafamostat mesylate blocked SARS-CoV-2 infection of Calu-3 cells with an EC50 around 10 nM, which is below its average blood concentration after intravenous administration through continuous infusion. These findings, together with accumulated clinical data regarding its safety, make nafamostat a likely candidate drug to treat COVID-19.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Mizuki Yamamoto", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Maki Kiso", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Yuko Sakai-Tagawa", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Kiyoko Iwatsuki-Horimoto", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Masaki Imai", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Makoto Takeda", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Noriko Kinoshita", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Norio Ohmagari", - "author_inst": "National Center for Global Health and Medicine" - }, - { - "author_name": "Jin Gohda", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Kentaro Semba", - "author_inst": "Waseda University" - }, - { - "author_name": "Zene Matsuda", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Yasushi Kawaguchi", - "author_inst": "Institute of Medical Science, University of Tokyo" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Jun-ichiro Inoue", - "author_inst": "University of Tokyo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.21.054122", "rel_title": "Population genomics insights into the recent evolution of SARS-CoV-2", @@ -1528702,6 +1529119,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.23.057810", + "rel_title": "TARGETED PROTEOMICS FOR THE DETECTION OF SARS-COV-2 PROTEINS.", + "rel_date": "2020-04-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.23.057810", + "rel_abs": "The rapid, sensitive and specific detection of SARS-CoV-2 is critical in responding to the current COVID-19 outbreak. In this proof-of-concept study, we explored the potential of targeted mass spectrometry based (MS) proteomics for the detection of SARS-CoV-2 proteins in both research samples and clinical specimens. First, we assessed the limit of detection for several SARS-CoV-2 proteins by parallel reaction monitoring (PRM) MS in infected Vero E6 cells. For tryptic peptides of Nucleocapsid protein, the limit of detection was in the mid-attomole range (9E-13 g). Next, this PRM methodology was applied to the detection of viral proteins in various COVID-19 patient clinical specimens, such as sputum and nasopharyngeal swabs. SARS-CoV-2 proteins were detected in these samples with high sensitivity in all specimens with PCR Ct values <24 and in several samples with higher CT values. A clear relationship was observed between summed MS peak intensities for SARS-CoV-2 proteins and Ct values reflecting the abundance of viral RNA. Taken together, these results suggest that targeted MS based proteomics may have the potential to be used as an additional tool in COVID-19 diagnostics.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Karel Bezstarosti", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Mart M Lamers", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Wouter AS Doff", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Peter C Wever", + "author_inst": "Jeroen Bosch Hospital" + }, + { + "author_name": "Khoa TD Thai", + "author_inst": "Star-shl diagnostic laboratories" + }, + { + "author_name": "Jeroen JA van Kampen", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Bart L Haagmans", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Jeroen AA Demmers", + "author_inst": "Erasmus University Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.22.046565", "rel_title": "Functional and Genetic Analysis of Viral Receptor ACE2 Orthologs Reveals Broad Potential Host Range of SARS-CoV-2", @@ -1530066,85 +1530530,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.04.19.20069997", - "rel_title": "Analysis of SteraMist ionized hydrogen peroxide technology as a method for sterilizing N95 respirators and other personal protective equipment", - "rel_date": "2020-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20069997", - "rel_abs": "ObjectiveThe COVID-19 pandemic has led to widespread shortages of personal protective equipment (PPE) for healthcare workers, including filtering facepiece respirators (FFRs) such as N95 masks. These masks are normally intended for single use, but their sterilization and subsequent reuse could substantially mitigate a world-wide shortage.\n\nDesignQuality assurance.\n\nSettingA sealed environment chamber installed in the animal facility of an academic medical center.\n\nInterventionsOne to five sterilization cycles using ionized hydrogen peroxide (iHP), generated by SteraMist(R) equipment (TOMI; Frederick, MD).\n\nMain outcome measuresPersonal protective equipment, including five N95 mask models from three manufacturers, were evaluated for efficacy of sterilization following iHP treatment (measured with bacterial spores in standard biological indicator assemblies). Additionally, N95 masks were assessed for their ability to efficiently filter particles down to 0.3{micro}m and for their ability to form an airtight seal using a quantitative fit test. Filtration efficiency was measured using ambient particulate matter at a university lab and an aerosolized NaCl challenge at a National Institute for Occupational Safety and Health (NIOSH) pre-certification laboratory.\n\nResultsThe data demonstrate that N95 masks sterilized using SteraMist iHP technology retain function up to five cycles, the maximum number tested to date. Some but not all PPE could also be sterilized using an iHP environmental chamber, but pre-treatment with a handheld iHP generator was required for semi-enclosed surfaces such as respirator hoses.\n\nConclusionsA typical iHP environment chamber with a volume of ~80 m3 can treat ~7000 masks per day, as well as other items of PPE, making this an effective approach for a busy medical center.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Avilash Cramer", - "author_inst": "Harvard-MIT Division of Health Sciences & Technology" - }, - { - "author_name": "Deborah Plana", - "author_inst": "Harvard-MIT Division of Health Sciences & Technology; Harvard Ludwig Cancer Research Center and Department of Systems Biology" - }, - { - "author_name": "Helen L Yang", - "author_inst": "Harvard-MIT Center for Regulatory Science, Harvard Medical School" - }, - { - "author_name": "Mary Carmack", - "author_inst": "Harvard-MIT Center for Regulatory Science; Computational Health Informatics Program, Boston Children's Hospital" - }, - { - "author_name": "Enze Tian", - "author_inst": "Department of Building Science, Tsinghua University; Department of Nuclear Science and Engineering and Department of Materials Science and Engineering, MIT" - }, - { - "author_name": "Michael S Sinha", - "author_inst": "Harvard-MIT Center for Regulatory Science, Harvard Medical School" - }, - { - "author_name": "David Krikorian", - "author_inst": "Dana-Farber Cancer Institute" - }, - { - "author_name": "David Turner", - "author_inst": "Dana-Farber Cancer Institute" - }, - { - "author_name": "Jinhan Mo", - "author_inst": "Department of Building Science, Tsinghua University" - }, - { - "author_name": "Ju Li", - "author_inst": "Department of Nuclear Science and Engineering and Department of Materials Science and Engineering, MIT" - }, - { - "author_name": "Rajiv Gupta", - "author_inst": "Harvard Medical School; Department of Radiology, Massachusetts General Hospital" - }, - { - "author_name": "Heather Manning", - "author_inst": "Dana-Farber Cancer Institute" - }, - { - "author_name": "Florence T. Bourgeois", - "author_inst": "Harvard-MIT Center for Regulatory Science, Harvard Medical School; Computational Health Informatics Program, Boston Children's Hospital" - }, - { - "author_name": "Sherry H Yu", - "author_inst": "Harvard Combined Dermatology Residency Training Program" - }, - { - "author_name": "Peter Sorger", - "author_inst": "Harvard Ludwig Cancer Research Center, Department of Systems Biology, and Harvard-MIT Center for Regulatory Science; Harvard Medical School" - }, - { - "author_name": "Nicole R. LeBoeuf", - "author_inst": "Brigham and Women's Hospital Department of Dermatology" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.04.19.20071704", "rel_title": "COVID-19 OUTBREAK IN POST-SOVIET STATES: MODELING THE BEST AND WORST POSSIBLE SCENARIOS", @@ -1530592,6 +1530977,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.19.20071654", + "rel_title": "A study on control of novel corona-virus (2019-nCoV) disease process by using PID controller", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071654", + "rel_abs": "BackgroundIn this paper, the SEIR dynamic model will be used to model the epidemic of coronvirus (2019-nCoV)disease. The SEIR model has been used to model infectious diseases in Malaysia.Then, the spread and control of the disease is simulated applying a PID controller. The results of this study show that the implementation of strict restrictions such as quarantine, social distancing and closure of gathering centers is effective in controlling the disease. Using the results and analyzing them, it was found that early and strict implementation of strict restrictions such as quarantine, social distance and closure of centers with a high percentage of community is very important to control this disease and prevent irreparable economic losses and depreciation of medical staff.\n\nObjectiveModeling the prevalence and control of corona-virus (2019-nCoV)and the impact of government actions using control engineering methods.\n\nMethodIn this study, the SEIR dynamic model was used and the common data on the prevalence of the virus in Wuhan, China and Malaysia were used. As an example, the use of control target schemes is simulated in this paper.\n\nResultsThe findings of this study use control methods and forecasting in control engineering to provide a clear picture of macro-decisions for different governments in the field of infectious diseases.\n\nConclusionManagement and control schemes such as travel restrictions, quarantine, social distance and closure of offices, higher education institutions must be implemented immediately to prevent major economic and social losses. The implementation of these restrictions should not be delayed during the outbreak of corona-virus(2019-nCoV) infectious diseases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "habibollah arasteh rad", + "author_inst": "Institute of applied Inteligent Systems Of University of Tehran" + }, + { + "author_name": "arshia badi", + "author_inst": "Institute of applied Inteligent Systems Of University of Tehran" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.18.20070821", "rel_title": "Estimating the Prevalence of COVID-19 in the United States: Three Complementary Approaches", @@ -1532048,77 +1532456,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.18.20070367", - "rel_title": "Utah-Stanford Ventilator (Vent4US): Developing a rapidlyscalable ventilator for COVID-19 patients with ARDS", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.18.20070367", - "rel_abs": "We describe a minimum, rapidly scalable ventilator designed for COVID-19 patients with ARDS. Our design philosophy is not only to try to address potential ventilator shortages, but also to account for uncertainties in the supply chains of parts commonly used in traditional ventilators. To do so we employ a modular design approach and broadly explore taking advantage of parts from non-traditional supply chains. In our current prototype, we demonstrate volume control with assist control on a test lung and present a linear actuator-driven pinch valve-based implementation for both pressure control and volume control with decelerating inspiratory flow. We estimate the component cost of the system to be around $500. We publish our draft design documents and current implementation which is open and accessible in the hope that broadening the community globally will accelerate arriving at a solution and that peer review will improve the final design.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Hongquan Li", - "author_inst": "Stanford University" - }, - { - "author_name": "Ethan Li", - "author_inst": "Stanford University" - }, - { - "author_name": "Deepak Krishnamurthy", - "author_inst": "Stanford University" - }, - { - "author_name": "Patrick Kolbay", - "author_inst": "University of Utah" - }, - { - "author_name": "Beca Chacin", - "author_inst": "University of Utah" - }, - { - "author_name": "Soeren Hoehne", - "author_inst": "University of Utah" - }, - { - "author_name": "Jim Cybulski", - "author_inst": "Foldscope Instruments" - }, - { - "author_name": "Lara Brewer", - "author_inst": "University of Utah" - }, - { - "author_name": "Tomasz Petelenz", - "author_inst": "University of Utah" - }, - { - "author_name": "Joseph Orr", - "author_inst": "University of Utah" - }, - { - "author_name": "Derek Sakata", - "author_inst": "University of Utah" - }, - { - "author_name": "Thomas Clardy", - "author_inst": "CKC Medical, Utah" - }, - { - "author_name": "Kai Kuck", - "author_inst": "University of Utah" - }, - { - "author_name": "Manu Prakash", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.04.16.20067991", "rel_title": "The Contribution of Age Structure to the Number of Deaths from Covid-19 in the UK by Geographical Units", @@ -1532370,6 +1532707,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.04.17.20068601", + "rel_title": "The effect of BCG vaccination on COVID-19 examined by a statistical approach: no positive results from the Diamond Princess and cross-national differences previously reported by world-wide comparisons are flawed in several ways", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20068601", + "rel_abs": "Recently, the controversial hypothesis that past BCG (Bacillus Calmette-Guerin) vaccination reduces infection or severity of COVID-19 has been proposed. The present study examined this hypothesis using statistical approaches based on the public data. Three approaches were utilized: 1) comparing the infection and mortality ratio of people on the cruise ship Diamond Princess, 2) comparing the number of mortalities among nations, and 3) comparing the maximum daily increase rate of total mortalities among nations. The result of 1) showed that there is no significant difference in infection per person onboard or mortality-infection between Japanese citizens vs. US citizens and BCG obligatory nations vs. non-BCG obligatory nations on the Diamond Princess. The result of 2) showed that the number of mortalities among nations is similar to the previous studies, but this analysis also considered the timing of COVID-19 arrival in each nation. After correcting for arrival time, previously reported effect of BCG vaccination on decreasing total mortality disappeared. This is because nations that lack BCG vaccination are concentrated in Western Europe, which is near an epicenter of COVID-19. Therefore some previous reports are now considered to be affected by this artifact; the result may have been flawed by dispersal from an epicenter. However, some results showed weakly significant differences in the number of deaths at a particular time among BCG obligatory and non-BCG nations (especially the use of Japanese BCG strain Tokyo 172). However, these results are affected by the results of three countries and the effect of BCG vaccination remains inconclusive. The result of 3) showed that the maximum daily increasing rate in death among nations showed no significant difference among BCG vaccination policies. In the present study, although some results showed statistically significant differences among BCG vaccination policies, they may be affected by the impact of various other factors, such as national infection-control policies, social distancing, behavioral changes of people, possible previous local epidemics of closely related viruses, or inter-population differences in ACE2 or other genetic polymorphism. Further research is needed to better understand the underlying cause of the observed differences in infection and mortality of the disease among nations. Nevertheless, our results show that the effect of past BCG vaccination, if any, can be masked by many other factors. Therefore, the possible effect might be relatively small. In fact, in Japan, where almost all citizens have been vaccinated, COVID-19 cases are constantly increasing. Given the importance of peoples behavior in preventing viral propagation, the spread of optimism triggered by this hypothesis would be harmful to BCG vaccination nations.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Masakazu Asahara", + "author_inst": "Aichi Gakuin University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.17.20069716", "rel_title": "Years of life lost due to the psychosocial consequences of COVID19 mitigation strategies based on Swiss data", @@ -1533462,65 +1533818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.17.20069708", - "rel_title": "Multivariate Analysis of Factors Affecting COVID-19 Case and Death Rate in U.S. Counties: The Significant Effects of Black Race and Temperature", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20069708", - "rel_abs": "ObjectivesCoronavirus disease-19 (COVID-19) has spread rapidly around the world, and many risk factors including patient demographics, social determinants of health, environmental variables, underlying health conditions, and adherence to social distancing have been hypothesized to affect case and death rates. However, little has been done to account for the potential confounding effects of these factors. Using a large multivariate analysis, this study illuminates modulators of COVID-19 incidence and mortality in U.S. counties while controlling for risk factors across multiple domains.\n\nMethodsData on COVID-19 and various risk factors in all U.S. counties was collected from publicly available data sources through April 14, 2020. Counties with at least 50 COVID-19 cases were included in case analyses and those with at least 10 deaths were included in mortality models. The 661 counties meeting inclusion criteria for number of cases were grouped into quartiles and comparisons of risk factors were made using t-tests between the highest and lowest quartiles. Similar comparisons for 217 counties were made for above average and below average deaths/100,000. Adjusted linear and logistic regression analyses were performed to evaluate the independent effects of factors that significantly impacted cases and deaths.\n\nResultsUnivariate analyses demonstrated numerous significant differences between cohorts for both cases and deaths. Risk factors associated with increased cases and/or deaths per 100,000 included increased GDP per capita, decreased social distancing, increased age, increased percent Black, decreased percent Hispanic, decreased percent Asian, decreased health, increased poverty, increased diabetes, increased coronary heart disease, increased physical inactivity, increased alcohol consumption, increased tobacco use, and decreased access to primary care. Multivariate regression analyses demonstrated Black race is a risk factor for worse COVID-19 outcome independent of comorbidities, poverty, access to health care, and other mitigating factors. Lower daily temperatures was also an independent risk factor in case load but not deaths.\n\nConclusionsU.S. counties with a higher proportion of Black residents are associated with increased COVID-19 cases and deaths. However, the various suggested mechanisms, such as socioeconomic and healthcare predispositions, did not appear to drive the effect of race in our model. Counties with higher average daily temperatures are also associated with decreased COVID-19 cases but not deaths. Several theories are posited to explain these findings, including prevalence of vitamin D deficiency. Additional studies are needed to further understand these effects.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Adam Y Li", - "author_inst": "Mount Sinai" - }, - { - "author_name": "Theodore C Hannah", - "author_inst": "Mount Sinai" - }, - { - "author_name": "John Durbin", - "author_inst": "Mount Sinai" - }, - { - "author_name": "Nickolas Dreher", - "author_inst": "Mount Sinai" - }, - { - "author_name": "Fiona M McAuley", - "author_inst": "Mount Sinai" - }, - { - "author_name": "Naoum Fares Marayati", - "author_inst": "Mount Sinai" - }, - { - "author_name": "Zachary Spiera", - "author_inst": "Mount Sinai" - }, - { - "author_name": "Muhammad Ali", - "author_inst": "Mount Sinai" - }, - { - "author_name": "Alex Gometz", - "author_inst": "Concussion Management of New York" - }, - { - "author_name": "JT Kostman", - "author_inst": "ProtectedBy.AI" - }, - { - "author_name": "Tanvir F Choudhri", - "author_inst": "Mount Sinai" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.21.053967", "rel_title": "protein-sol pKa: prediction of electrostatic frustration, with application to coronaviruses", @@ -1533740,6 +1534037,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.20.052290", + "rel_title": "Dynamical asymmetry exposes 2019-nCoV prefusion spike", + "rel_date": "2020-04-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.20.052290", + "rel_abs": "The novel coronavirus (2019-nCoV) spike protein is a smart molecular machine that instigates the entry of coronavirus to the host cell causing the COVID-19 pandemic. In this study, a structural-topology based model Hamiltonian of C3 symmetric trimeric spike is developed to explore its complete conformational energy landscape using molecular dynamic simulations. The study finds 2019-nCoV to adopt a unique strategy by undertaking a dynamic conformational asymmetry induced by a few unique inter-chain interactions. This results in two prevalent asymmetric structures of spike where one or two spike heads lifted up undergoing a dynamic transition likely to enhance rapid recognition of the host-cell receptor turning on its high-infectivity. The crucial interactions identified in this study are anticipated to potentially affect the efficacy of therapeutic targets.\n\nOne Sentence SummaryInter-chain-interaction driven rapid symmetry breaking strategy adopted by the prefusion trimeric spike protein likely to make 2019-nCoV highly infective.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Susmita Roy", + "author_inst": "Indian Institute of Science Education and Research Kolkata" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.04.16.20068163", "rel_title": "Projections for first-wave COVID-19 deaths across the US using social-distancing measures derived from mobile phones", @@ -1534904,37 +1535220,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.16.20068387", - "rel_title": "Predicting the impact of asymptomatic transmission,non-pharmaceutical intervention and testing on the spread of COVID19COVID19", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20068387", - "rel_abs": "We introduce a novel mathematical model to analyze the effect of removing non-pharmaceutical interventions on the spread of COVID19 as a function of disease testing rate. We find that relaxing interventions has a strong impact on the size of the epidemic peak as a function of intervention removal time. We show that it is essential for predictive models to explicitly capture transmission from asymptomatic carriers and important to obtain precise information on asymptomatic transmission by testing. The asymptomatic reservoir, reported to account for as much as 85% of transmission, will contribute to resurgence of the epidemic if public health interventions are removed too soon. Use of more basic models that fail to capture asymptomatic transmission can result in large errors in predicted clinical caseload or in fitted epidemiological parameters and, therefore, may be unreliable in estimating the risk of a second wave based on the timing of terminated interventions.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ira B Schwartz", - "author_inst": "US Naval Research Laboratory" - }, - { - "author_name": "James H Kaufman", - "author_inst": "IBM Almaden Research Center" - }, - { - "author_name": "Kun Hu", - "author_inst": "IBM Almaden Research Center" - }, - { - "author_name": "Simone Bianco", - "author_inst": "IBM Almaden Research Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.19.20071399", "rel_title": "Identification of super-transmitters of SARS-CoV-2", @@ -1535190,6 +1535475,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.19.20071605", + "rel_title": "Spatial analysis of COVID-19 spread in Iran: Insights into geographical and structural transmission determinants at a province level", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071605", + "rel_abs": "The Islamic Republic of Iran reported its first COVID-19 cases by 19th February 2020, since then it has become one of the most affected countries, with more than 73,000 cases and 4,585 deaths at the date. Spatial modeling could be used to approach an understanding of structural and sociodemographic factors that have impacted COVID-19 spread at a province-level in Iran. In the present paper, we developed a spatial statistical approach to describe how COVID-19 cases are spatially distributed and to identify significant spatial clusters of cases and how the socioeconomic features of Iranian provinces might predict the number of cases. We identified a cluster of provinces with significantly higher rates of COVID-19 cases around Tehran, which indicated that the spread of COVID-19 within Iran was spatially correlated. Urbanized, highly connected provinces with older population structures and higher average temperatures were the most susceptible to present a higher number of COVID-19 cases. Interestingly, literacy is a protective factor that might be directly related to health literacy and compliance with public health measures. These features indicate that policies related to social distancing, protecting older adults, and vulnerable populations, as well as promoting health literacy, might be targeted to reduce SARS-CoV2 spread in Iran. Our approach could be applied to model COVID-19 outbreaks in other countries with similar characteristics or in case of an upturn in COVID-19 within Iran.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ricardo Ram\u00edrez-Aldana", + "author_inst": "Research Division, Instituto Nacional de Geriatr\u00eda (INGER), Anillo Perif. 2767, San Jeronimo Lidice, La Magdalena Contreras, 10200, Mexico City, Mexico." + }, + { + "author_name": "Juan Carlos Gomez-Verjan", + "author_inst": "Instituto Nacional de Geriatria" + }, + { + "author_name": "Omar Yaxmehen Bello-Chavolla", + "author_inst": "Instituto Nacional de Geriatria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.19.20071712", "rel_title": "Potential magnitude of COVID-19-induced healthcare resource depletion in Ontario, Canada", @@ -1536290,61 +1536602,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.21.053058", - "rel_title": "Inhibition of PIKfyve kinase prevents infection by EBOV and SARS-CoV-2", - "rel_date": "2020-04-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.21.053058", - "rel_abs": "Virus entry is a multistep process. It initiates when the virus attaches to the host cell and ends when the viral contents reach the cytosol. Genetically unrelated viruses can subvert analogous subcellular mechanisms and use similar trafficking pathways for successful entry. Antiviral strategies targeting early steps of infection are therefore appealing, particularly when the probability for successful interference through a common step is highest. We describe here potent inhibitory effects on content release and infection by chimeric VSV containing the envelope proteins of Zaire ebolavirus (VSV-ZEBOV) or SARS-CoV-2 (VSV-SARS-CoV-2) elicited by Apilimod and Vacuolin-1, small molecule inhibitors of the main endosomal Phosphatidylinositol-3-Phosphate/Phosphatidylinositol 5-Kinase, PIKfyve. We also describe potent inhibition of SARS-CoV-2 strain 2019-nCoV/USA-WA1/2020 by Apilimod. These results define new tools for studying the intracellular trafficking of pathogens elicited by inhibition of PIKfyve kinase and suggest the potential for targeting this kinase in developing small-molecule antivirals against SARS-CoV-2.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Yuan-Lin Kang", - "author_inst": "Harvard University" - }, - { - "author_name": "Yi-Ying Chou", - "author_inst": "Biogen, Inc" - }, - { - "author_name": "Paul W Rothlauf", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Zhuoming Liu", - "author_inst": "Washington University in Saint Louis" - }, - { - "author_name": "Timothy K Soh", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "David Cureton", - "author_inst": "Boehringer Ingelheim Animal Health, Inc" - }, - { - "author_name": "James Brett Case", - "author_inst": "Washington University in Saint Louis" - }, - { - "author_name": "Rita E Chen", - "author_inst": "Washington University in Saint Louis" - }, - { - "author_name": "Michael S Diamond", - "author_inst": "Washington University in Saint Louis" - }, - { - "author_name": "Sean P.J. Whelan", - "author_inst": "Washington University in Saint Louis" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.04.21.053199", "rel_title": "Bioinformatics Study on Structural Protein of Severe Acute Respiratory Syndrome Coronavirus 2 (Sars-Cov-2) For Better Understanding the Vaccine Development", @@ -1536512,6 +1536769,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.17.20064691", + "rel_title": "Development and validation of an early warning score (EWAS) for predicting clinical deterioration in patients with coronavirus disease 2019", + "rel_date": "2020-04-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20064691", + "rel_abs": "BackgroundSince the pandemic outbreak of coronavirus disease 2019 (COVID-19), the health system capacity in highly endemic areas has been overwhelmed. Approaches to efficient management are urgently needed. We aimed to develop and validate a score for early prediction of clinical deterioration of COVID-19 patients.\n\nMethodsIn this retrospective multicenter cohort study, we included 1138 mild to moderate COVID-19 patients admitted to 33 hospitals in Guangdong Province from December 27, 2019 to March 4, 2020 (N =818; training cohort), as well as two hospitals in Hubei Province from January 21 to February 22, 2020 (N =320; validation cohort) in the analysis.\n\nResultsThe 14-day cumulative incidences of clinical deterioration were 7.9% and 12.1% in the training and validation cohorts, respectively. An Early WArning Score (EWAS) (ranging from 0 to 4.5), comprising of age, underlying chronic disease, neutrophil to lymphocyte ratio, C-reactive protein, and D-dimer levels, was developed (AUROC: 0.857). By applying the EWAS, patients were categorized into low-, medium-, and high risk groups (cut-off values: two and three). The 14-day cumulative incidence of clinical deterioration in the low-risk group was 1.8%, which was significantly lower than the incidence rates in the medium-(14.4%) and high-risk (40.9%) groups (P <.001). The predictability of EWAS was similar in the validation cohort (AUROC =0.781), patients in the low-, medium-, and high-risk groups had 14-day cumulative incidences of 2.6%, 10.0%, and 25.7%, respectively (P <.001).\n\nConclusionThe EWAS, which is based on five common parameters, can predict COVID-19-related clinical deterioration and may be a useful tool for a rapid triage and establishing a COVID-19 hierarchical management system that will greatly focus clinical management and medical resources to reduce mortality in highly endemic areas.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Yabing Guo", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Yingxia Liu", + "author_inst": "National Clinical Research Centre for Infectious Disease, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Tec" + }, + { + "author_name": "Jiatao Lu", + "author_inst": "Wuhan Hankou Hospital" + }, + { + "author_name": "Rong Fan", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Fuchun Zhang", + "author_inst": "Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Xueru Yin", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Zhihong Liu", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Qinglang Zeng", + "author_inst": "Honghu People's Hospital" + }, + { + "author_name": "Jing Yuan", + "author_inst": "National Clinical Research Centre for Infectious Disease, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Tec" + }, + { + "author_name": "Shufang Hu", + "author_inst": "Wuhan Hankou Hospital" + }, + { + "author_name": "Qiongya Wang", + "author_inst": "Wuhan Hankou Hospital" + }, + { + "author_name": "Baolin Liao", + "author_inst": "Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Mingxing Huang", + "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Sichun Yin", + "author_inst": "The Ninth Dongguan People's Hospital" + }, + { + "author_name": "Xilin Zhang", + "author_inst": "The Fourth Foshan People's Hospital" + }, + { + "author_name": "Rui Xin", + "author_inst": "Guangdong Second Provincial General Hospital" + }, + { + "author_name": "Zhanzhou Lin", + "author_inst": "Huizhou Central People's Hospital" + }, + { + "author_name": "Changzheng Hu", + "author_inst": "Jiangmen Central Hospital" + }, + { + "author_name": "Boliang Zhao", + "author_inst": "The First Zhaoqing People's Hospital" + }, + { + "author_name": "Ridong He", + "author_inst": "Zhanjiang Central People's Hospital" + }, + { + "author_name": "Minfeng Liang", + "author_inst": "The First Foshan People's Hospital" + }, + { + "author_name": "Zheng Zhang", + "author_inst": "National Clinical Research Centre for Infectious Disease, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Tec" + }, + { + "author_name": "Li Liu", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Jian Sun", + "author_inst": "Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Lu Tang", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Lisi Deng", + "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Jinyu Xia", + "author_inst": "The Fifth Affiliated Hospital, Sun Yat-sen University" + }, + { + "author_name": "Xiaoping Tang", + "author_inst": "Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Lei Liu", + "author_inst": "National Clinical Research Centre for Infectious Disease, Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Tec" + }, + { + "author_name": "Jinlin Hou", + "author_inst": "Nanfang Hospital, Southern Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.15.20064931", "rel_title": "Sequencing analysis of the spread of SARS-CoV2 in the Greater New York City region", @@ -1538352,69 +1538744,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.20.049924", - "rel_title": "SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology", - "rel_date": "2020-04-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.20.049924", - "rel_abs": "The sudden emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the end of 2019 from the Chinese province of Hubei and its subsequent pandemic spread highlight the importance of understanding the full molecular details of coronavirus infection and pathogenesis. Here, we compared a variety of replication features of SARS-CoV-2 and SARS-CoV and analysed the cytopathology caused by the two closely related viruses in the commonly used Vero E6 cell line. Compared to SARS-CoV, SARS-CoV-2 generated higher levels of intracellular viral RNA, but strikingly about 50-fold less infectious viral progeny was recovered from the culture medium. Immunofluorescence microscopy of SARS-CoV-2-infected cells established extensive cross-reactivity of antisera previously raised against a variety of nonstructural proteins, membrane and nucleocapsid protein of SARS-CoV. Electron microscopy revealed that the ultrastructural changes induced by the two SARS viruses are very similar and occur within comparable time frames after infection. Furthermore, we determined that the sensitivity of the two viruses to three established inhibitors of coronavirus replication (Remdesivir, Alisporivir and chloroquine) is very similar, but that SARS-CoV-2 infection was substantially more sensitive to pre-treatment of cells with pegylated interferon alpha. An important difference between the two viruses is the fact that - upon passaging in Vero E6 cells - SARS-CoV-2 apparently is under strong selection pressure to acquire adaptive mutations in its spike protein gene. These mutations change or delete a putative furin-like cleavage site in the region connecting the S1 and S2 domains and result in a very prominent phenotypic change in plaque assays.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Natacha Ogando", - "author_inst": "Leiden University Medical Center, Leiden" - }, - { - "author_name": "Timmothy Dalebout", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Jessika C. Zevenhoven-Dobbe", - "author_inst": "Leids Universitair Medisch Centrum" - }, - { - "author_name": "Ronald W.A.L. Limpens", - "author_inst": "Leids Universitair Medisch Centrum" - }, - { - "author_name": "Yvonne van der Meer", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Leon Caly", - "author_inst": "Doherty Institute" - }, - { - "author_name": "Julian Druce", - "author_inst": "Doherty Institute" - }, - { - "author_name": "Jutte de Vries", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Marjolein Kikkert", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Montse Barcena", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Igor Sidorov", - "author_inst": "Leiden University Medical Center" - }, - { - "author_name": "Eric J Snijder", - "author_inst": "Leiden University Medical Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.19.049643", "rel_title": "Blocking antibodies against SARS-CoV-2 RBD isolated from a phage display antibody library using a competitive biopanning strategy", @@ -1538662,6 +1538991,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.04.20.051219", + "rel_title": "Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays", + "rel_date": "2020-04-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.20.051219", + "rel_abs": "SARS-CoV-2 enters cells using its Spike protein, which is also the main target of neutralizing antibodies. Therefore, assays to measure how antibodies and sera affect Spike-mediated viral infection are important for studying immunity. Because SARS-CoV-2 is a biosafety-level-3 virus, one way to simplify such assays is to pseudotype biosafety-level-2 viral particles with Spike. Such pseudotyping has now been described for single-cycle lentiviral, retroviral and VSV particles, but the reagents and protocols are not widely available. Here we detail how to effectively pseudotype lentiviral particles with SARS-CoV-2 Spike and infect 293T cells engineered to express the SARS-CoV-2 receptor, ACE2. We also make all the key experimental reagents available in the BEI Resources repository of ATCC and the NIH. Furthermore, we demonstrate how these pseudotyped lentiviral particles can be used to measure the neutralizing activity of human sera or plasma against SARS-CoV-2 in convenient luciferase-based assays, thereby providing a valuable complement to ELISA-based methods that measure antibody binding rather than neutralization.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kate H.D. Crawford", + "author_inst": "University of Washington" + }, + { + "author_name": "Rachel Eguia", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Adam S Dingens", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Andrea N Loes", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Keara D Malone", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Caitlin R Wolf", + "author_inst": "University of Washington" + }, + { + "author_name": "Helen Y Chu", + "author_inst": "University of Washington" + }, + { + "author_name": "M. Alejandra Tortorici", + "author_inst": "University of Washington" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + }, + { + "author_name": "Michael Murphy", + "author_inst": "University of Washington" + }, + { + "author_name": "Deleah Pettie", + "author_inst": "University of Washington" + }, + { + "author_name": "Neil P King", + "author_inst": "University of Washington" + }, + { + "author_name": "Alejandro B Balazs", + "author_inst": "Ragon Institute" + }, + { + "author_name": "Jesse D Bloom", + "author_inst": "Fred Hutchinson Cancer Research Center" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.20.051581", "rel_title": "Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease", @@ -1539978,49 +1540378,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.04.15.20066860", - "rel_title": "TOWARD A COVID-19 SCORE-RISK ASSESSMENTS AND REGISTRY", - "rel_date": "2020-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20066860", - "rel_abs": "ImportanceCritical care resources like ventilators, used to manage the current COVID-19 pandemic, are potentially inadequate. Established triage standards and guidelines may not contain the most appropriate severity assessment and outcome prediction models.\n\nObjectivesDevelop a draft pandemic specific triage assessment score for the current COVID-19 pandemic. Design a website where initial Toward a COVID-19 Scores (TACS) can be quickly calculated and used to compare various treatment strategies. Create a TACS Registry where data and outcomes for suspected and confirmed COVID-19 patients can be recorded. Use the TACS Registry to develop an influenza epidemic specific database and score for use in future respiratory based epidemics.\n\nDesign, Setting, ParticipantsRetrospective analysis of 3,301 ICU admissions with respiratory failure admitted to 41 U.S. Intensive Care Units from 2015-19. Independent external validation on 1,175 similar ICU Admissions using identical entry criteria from Barnes Jewish Hospital (BJH), Washington University from 2016-2019.\n\nMain OutcomesTACS was created with 16 readily available predictive variables for risk assessment of hospital mortality 24 hours after ICU Admission and the need for prolonged assisted mechanical ventilation (PAMV) (> 96 hours) at 24- and 48-hours post ICU admission.\n\nResultsTACS achieved an Area Under the Curve (AUC) for hospital mortality after 24 hours of 0.80 in the development dataset; 0.81 in the internal validation dataset. At a probability of 50% hospital mortality, positive predictive value (PPV) was 0.55, negative predictive value (NPV) 0.89; sensitivity 22%, specificity 97%.\n\nFor PAMV after 24 hours, the AUC was 0.84 in the development dataset, 0.81 in the validation dataset. For PAMV after 48 hours, the AUC was 0.82 in the development dataset, 0.78 in the validation dataset.\n\nIn the external validation the AUC for TACS was 0.76 +/- 0.024. We launched a website that is scaled for mobile device use (https://covid19score.azurewebsites.net/) that provides open access to a user-friendly TACS Calculator for all predictions. We also designed a voluntary TACS Registry for collection of data and outcomes on ICU Admissions with COVID-19.\n\nConclusions and RelevanceToward a COVID-19 score is a starting point for an epidemic specific triage assessment that could be used to evaluate various approaches to treatment. The TACS Registry provides the ability to establish a respiratory specific outcomes database that can be used to create a triage approach for future such pandemics.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSCan a rapid epidemic specific risk assessment severity score and data and outcome repository be constructed in the midst of a pandemic.\n\nFindingsUsing development and validation datasets with ICU admissions similar to those developing COVID-19, developed an initial Toward a COVID-19 Score that could be used to compare various treatment approaches. Also launched an online facilitated data collection and outcome assessment registry for collection of a pandemic specific database so a new triage score could be created for use in the next pandemic.\n\nMeaningIn the midst of a pandemic rapid development of an epidemic specific triage score and a data registry for the creation of a new score for use in future pandemics appears feasible.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Cristina Vazquez Guillamet", - "author_inst": "Wasington University School of Medicine" - }, - { - "author_name": "Rodrigo Vazquez Guillamet", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Andrew A. Kramer", - "author_inst": "Prescient-Healthcare Consulting" - }, - { - "author_name": "Paula M. Maurer", - "author_inst": "Medical Decision Network" - }, - { - "author_name": "Greg A. Menke", - "author_inst": "Medical Decision Network" - }, - { - "author_name": "Cherie L. Hill", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "William A. Knaus", - "author_inst": "University of Virginia School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.04.18.047878", "rel_title": "Mass Spectrometric Identification of SARS-CoV-2 Proteins from Gargle Solution Samples of COVID-19 Patients", @@ -1540256,6 +1540613,157 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.04.17.046375", + "rel_title": "Rapid development of an inactivated vaccine for SARS-CoV-2", + "rel_date": "2020-04-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.17.046375", + "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 has brought about an unprecedented crisis, taking a heavy toll on human health, lives as well as the global economy. There are no SARS-CoV-2-specific treatments or vaccines available due to the novelty of this virus. Hence, rapid development of effective vaccines against SARS-CoV-2 is urgently needed. Here we developed a pilot-scale production of a purified inactivated SARS-CoV-2 virus vaccine candidate (PiCoVacc), which induced SARS-CoV-2-specific neutralizing antibodies in mice, rats and non-human primates. These antibodies potently neutralized 10 representative SARS-CoV-2 strains, indicative of a possible broader neutralizing ability against SARS-CoV-2 strains circulating worldwide. Immunization with two different doses (3g or 6 g per dose) provided partial or complete protection in macaques against SARS-CoV-2 challenge, respectively, without any antibody-dependent enhancement of infection. Systematic evaluation of PiCoVacc via monitoring clinical signs, hematological and biochemical index, and histophathological analysis in macaques suggests that it is safe. These data support the rapid clinical development of SARS-CoV-2 vaccines for humans.\n\nOne Sentence SummaryA purified inactivated SARS-CoV-2 virus vaccine candidate (PiCoVacc) confers complete protection in non-human primates against SARS-CoV-2 strains circulating worldwide by eliciting potent humoral responses devoid of immunopathology", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Qiang Gao", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Linlin Bao", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Haiyan Mao", + "author_inst": "Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Lin Wang", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Kangwei Xu", + "author_inst": "Division of Respiratory Virus Vaccines, National Institute for Food and Drug Control" + }, + { + "author_name": "minnan Yang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Yajing Li", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Ling Zhu", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Nan Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Zhe Lv", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Hong Gao", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Xiaoqin Ge", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Biao Kan", + "author_inst": "National Institute for Communicable Disease Control and Prevention, China CDC" + }, + { + "author_name": "Yaling Hu", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Jiangning Liu", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Fang Cai", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Deyu Jiang", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Yanhui Yin", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Chengfeng Qin", + "author_inst": "Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences" + }, + { + "author_name": "Jing Li", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Xuejie Gong", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Xiuyu Lou", + "author_inst": "Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Wen Shi", + "author_inst": "Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Dongdong Wu", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Hengming Zhang", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Lang Zhu", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Wei Deng", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College" + }, + { + "author_name": "Yurong Li", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Jinxing Lu", + "author_inst": "National Institute for Communicable Diseases" + }, + { + "author_name": "Changgui Li", + "author_inst": "Division of Respiratory Virus Vaccines, National Institute for Food and Drug Control" + }, + { + "author_name": "Xiangxi Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Weidong Yin", + "author_inst": "Sinovac Biotech Ltd" + }, + { + "author_name": "Yanjun Zhang", + "author_inst": "Zhejiang Center for Disease Control and Prevention" + }, + { + "author_name": "Chuan Qin", + "author_inst": "Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.14.20060160", "rel_title": "Patient-derived mutations impact pathogenicity of SARS-CoV-2", @@ -1541512,41 +1542020,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.14.20063958", - "rel_title": "A Rapidly Deployable Negative Pressure Enclosure for Aerosol-Generating Medical Procedures", - "rel_date": "2020-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20063958", - "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) pandemic presents significant safety challenges to healthcare professionals. In some jurisdictions, over 10% of confirmed cases of COVID-19 have been found among healthcare workers. Aerosol-generating medical procedures (AGMPs) may increase the risk of nosocomial transmission, exacerbated by present global shortages of personal protective equipment (PPE). Improved methods for mitigating risk during AGMPs are therefore urgently needed.\n\nMethodsThe Aerosol Containment Enclosure (ACE) was constructed from acrylic with silicone gaskets for arm port seals and completed with a thin plastic sheet. Hospital wall suction generated negative pressure within the ACE. To evaluate protective capability, differential pressures were recorded under static conditions and during simulated AGMPs. Smoke flow patterns, fluorescence aerosolization, and sodium saccharin aerosolization tests were also conducted.\n\nResultsNegative pressures of up to -47.7 mmH2O were obtained using the enclosure with two wall suction units (combined outflow of 70 L min-1), with inflow of O2 of 15 L min-1. Negative pressures between -10 and - 35 mmH2O were maintained during simulated AGMPs, including oxygen delivery by mask, airway suctioning, bag-mask manual ventilation and endotracheal intubation of a potential COVID-19 patient. The ACE effectively contained smoke, fluorescein aerosol, and sodium saccharin aerosol within the enclosure during use.\n\nConclusionsThe ACE is capable of maintaining negative pressure during simulated AGMPs. In all cases, containment was improved relative to an identical enclosure with non-occluded ports at ambient pressure. During the current COVID-19 pandemic, the use of such a device may assist in reducing nosocomial infections among healthcare providers.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Anthony M. Chahal", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Kenneth Van Dewark", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Robert Gooch", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Erin Fukushima", - "author_inst": "The University of British Columbia" - }, - { - "author_name": "Zachary M. Hudson", - "author_inst": "The University of British Columbia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.04.14.20063750", "rel_title": "Modeling Exit Strategies from COVID-19 Lockdown with a Focus on Antibody Tests", @@ -1542230,6 +1542703,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.14.20065466", + "rel_title": "Modelling strategies to predict hospital demand during the COVID-19 outbreak in Bogota, Colombia", + "rel_date": "2020-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065466", + "rel_abs": "Colombia, like many developing nations, does not have a strong health system able to respond to a pandemic of the magnitude of Covid-19. There is an increasing need to create a model that allows particular clinics and hospitals to estimate the number of patients that require Intensive Care Units-ICU care (critical), and the number of patients that require hospital care (severe), but not ICU care, in order to manage their limited resources.\n\nThis paper presents a prediction of the total number of ICU and regular beds that will be needed during the pandemic COVID-19 for Bogota-Colombia. We use a SEIR model that includes three different compartments of infection: those who can stay at home, those in regular hospital beds and those in need of ICU treatment. The model allows for a time varying transmission rate which we use to incorporate the measures introduced by the government over the period of one semester. The model predicts that by mid October 2020, the city will need 4 524 prevalent ICUs needed and 16 738 regular hospital beds needed. By the third week of July 2020, the number of patients that need ICUs will overpass the capacity set at 1 200 beds for ICU hospital beds in the city. The model predicts that the death toll by the same date will reach 1 752 people and the number of cases will be 30 216 inhabitants by then. We provide a Shiny app available in https://claudia-rivera-rodriguez.shinyapps.io/shinyappcovidclinic/. The original values in the app reproduce the results of this paper, but the parameters and starting values can be changed according to the users needs. COVID-19 has posed too many challenges to health systems around the globe, this model is an useful tool for cities, hospitals and clinics in Colombia that need to prepare for the excess demand of services that a pandemic like this one generates. Unfortunately, the model predicts that by the third week of July the projected capacity of the system in Bogota will not be enough. We expect the lockdown rules strength in the future days, so the death toll is not as bad as predicted by this model.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Claudia Rivera-Rodriguez", + "author_inst": "The University of Auckland" + }, + { + "author_name": "Beatriz Piedad Urdinola", + "author_inst": "National University of Colombia" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.14.20065706", "rel_title": "Has mortality due to other causes increased during the Covid-19 pandemic? Early evidence from England and Wales", @@ -1543202,129 +1543698,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.15.043364", - "rel_title": "Analysis of SARS-CoV-2 Antibodies in COVID-19 Convalescent Plasma using a Coronavirus Antigen Microarray", - "rel_date": "2020-04-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.15.043364", - "rel_abs": "The current practice for diagnosis of COVID-19, based on SARS-CoV-2 PCR testing of pharyngeal or respiratory specimens in a symptomatic patient at high epidemiologic risk, likely underestimates the true prevalence of infection. Serologic methods can more accurately estimate the disease burden by detecting infections missed by the limited testing performed to date. Here, we describe the validation of a coronavirus antigen microarray containing immunologically significant antigens from SARS-CoV-2, in addition to SARS-CoV, MERS-CoV, common human coronavirus strains, and other common respiratory viruses. A comparison of antibody profiles detected on the array from control sera collected prior to the SARS-CoV-2 pandemic versus convalescent blood specimens from virologically confirmed COVID-19 cases demonstrates near complete discrimination of these two groups, with improved performance from use of antigen combinations that include both spike protein and nucleoprotein. This array can be used as a diagnostic tool, as an epidemiologic tool to more accurately estimate the disease burden of COVID-19, and as a research tool to correlate antibody responses with clinical outcomes.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Rafael R de Assis", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Aarti Jain", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Rie Nakajima", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Algis Jasinskas", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Jiin Felgner", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Joshua Miago Obiero", - "author_inst": "University of California, Irvine" - }, - { - "author_name": "Oluwasanmi Oladapo Adenaiye", - "author_inst": "University of Maryland" - }, - { - "author_name": "Sheldon Tai", - "author_inst": "University of Maryland" - }, - { - "author_name": "Filbert H Hong", - "author_inst": "University of Maryland" - }, - { - "author_name": "Philip Norris", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Mars Stone", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Graham Simmons", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Anil Bagri", - "author_inst": "Cerus Corporation" - }, - { - "author_name": "Martin Schreiber", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Andreas Buser", - "author_inst": "University of Basel" - }, - { - "author_name": "Andreas Holbro", - "author_inst": "University of Basel" - }, - { - "author_name": "Manuel Battegay", - "author_inst": "University of Basel" - }, - { - "author_name": "Philip Hosimer", - "author_inst": "Ortho Clinical Diagnostics" - }, - { - "author_name": "Charles Noesen", - "author_inst": "Ortho Clinical Diagnostics" - }, - { - "author_name": "Donald K Milton", - "author_inst": "University of Maryland School of Public Health" - }, - { - "author_name": "- Prometheus Study Group", - "author_inst": "-" - }, - { - "author_name": "Huw Davies", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Paul Contestable", - "author_inst": "Ortho Clinical Diagnostics" - }, - { - "author_name": "Laurence M Corash", - "author_inst": "Cerus Corporation" - }, - { - "author_name": "Michael P Busch", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Philip L Felgner", - "author_inst": "University of California Irvine" - }, - { - "author_name": "Saahir Khan", - "author_inst": "University of California Irvine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.04.13.20064519", "rel_title": "Estimating the number of SARS-CoV-2 infections in the United States", @@ -1543588,6 +1543961,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.16.044503", + "rel_title": "SARS-CoV-2 is transmitted via contact and via the air between ferrets.", + "rel_date": "2020-04-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.16.044503", + "rel_abs": "SARS-CoV-2, a coronavirus that newly emerged in China in late 2019 1,2 and spread rapidly worldwide, caused the first witnessed pandemic sparked by a coronavirus. As the pandemic progresses, information about the modes of transmission of SARS-CoV-2 among humans is critical to apply appropriate infection control measures and to slow its spread. Here we show that SARS-CoV-2 is transmitted efficiently via direct contact and via the air (via respiratory droplets and/or aerosols) between ferrets. Intranasal inoculation of donor ferrets resulted in a productive upper respiratory tract infection and long-term shedding, up to 11 to 19 days post-inoculation. SARS-CoV-2 transmitted to four out of four direct contact ferrets between 1 and 3 days after exposure and via the air to three out of four independent indirect recipient ferrets between 3 and 7 days after exposure. The pattern of virus shedding in the direct contact and indirect recipient ferrets was similar to that of the inoculated ferrets and infectious virus was isolated from all positive animals, showing that ferrets were productively infected via either route. This study provides experimental evidence of robust transmission of SARS-CoV-2 via the air, supporting the implementation of community-level social distancing measures currently applied in many countries in the world and informing decisions on infection control measures in healthcare settings 3.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Mathilde Richard", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Adinda Kok", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Dennis de Meulder", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Theo M. Bestebroer", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Mart M. Lamers", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Nisreen M.A. Okba", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Martje Fentener van Vlissingen", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Barry Rockx", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Bart L. Haagmans", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Marion P.G. Koopmans", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Ron A.M. Fouchier", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Sander Herfst", + "author_inst": "ErasmusMC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.14.20064733", "rel_title": "Chest Computed Tomography for the Diagnosis of Patients with Coronavirus Disease 2019 (COVID-19): A Rapid Review and Meta-Analysis", @@ -1544940,81 +1545376,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.14.20065771", - "rel_title": "A systematic review of antibody mediated immunity to coronaviruses: antibody kinetics, correlates of protection, and association of antibody responses with severity of disease", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065771", - "rel_abs": "The duration and nature of immunity generated in response to SARS-CoV-2 infection is unknown. Many public health responses and modeled scenarios for COVID-19 outbreaks caused by SARS-CoV-2 assume that infection results in an immune response that protects individuals from future infections or illness for some amount of time. The timescale of protection is a critical determinant of the future impact of the pathogen. The presence or absence of protective immunity due to infection or vaccination (when available) will affect future transmission and illness severity. The dynamics of immunity and nature of protection are relevant to discussions surrounding therapeutic use of convalescent sera as well as efforts to identify individuals with protective immunity. Here, we review the scientific literature on antibody immunity to coronaviruses, including SARS-CoV-2 as well as the related SARS-CoV-1, MERS-CoV and human endemic coronaviruses (HCoVs). We reviewed 1281 abstracts and identified 322 manuscripts relevant to 5 areas of focus: 1) antibody kinetics, 2) correlates of protection, 3) immunopathogenesis, 4) antigenic diversity and cross-reactivity, and 5) population seroprevalence. While studies of SARS-CoV-2 are necessary to determine immune responses to it, evidence from other coronaviruses can provide clues and guide future research.\n\nKey QuestionsO_TEXTBOXKey Questions for SARS-CoV-2\n\nO_LIWhat are the kinetics of immune responses to infection?\nC_LIO_LIDo people who have more severe disease mount stronger antibody responses after infection?\nC_LIO_LIHow do antibody responses vary between different types of antibodies or as measured by different assays?\nC_LIO_LIHow does the presence of antibodies impact the clinical course and severity of the disease?\nC_LIO_LIIs there cross-reactivity with different coronaviruses?\nC_LIO_LIDoes cross-reactivity lead to cross-protection?\nC_LIO_LIWill infection protect you from future infection?\nC_LIO_LIHow long will immunity last?\nC_LIO_LIWhat are correlates of protection?\nC_LI\n\nC_TEXTBOX", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Angkana T. Huang", - "author_inst": "University of Florida" - }, - { - "author_name": "Bernardo Garcia-Carreras", - "author_inst": "University of Florida" - }, - { - "author_name": "Matt D.T. Hitchings", - "author_inst": "University of Florida" - }, - { - "author_name": "Bingyi Yang", - "author_inst": "University of Florida" - }, - { - "author_name": "Leah Katzelnick", - "author_inst": "University of Florida" - }, - { - "author_name": "Susan M Rattigan", - "author_inst": "University of Florida" - }, - { - "author_name": "Brooke Borgert", - "author_inst": "University of Florida" - }, - { - "author_name": "Carlos Moreno", - "author_inst": "University of Florida" - }, - { - "author_name": "Benjamin D. Solomon", - "author_inst": "US National Institutes of Health" - }, - { - "author_name": "Isabel Rodriguez-Barraquer", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Justin Lessler", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Henrik Salje", - "author_inst": "Cambridge University" - }, - { - "author_name": "Donald S. Burke", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Amy Wesolowski", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Derek A.T. Cummings", - "author_inst": "University of Florida" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.14.20065680", "rel_title": "Association of inflammatory markers with the severity of COVID-19", @@ -1545230,6 +1545591,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.17.20067348", + "rel_title": "Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-qPCR", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20067348", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The most widely used method of COVID-19 diagnostics is a reverse transcription polymerase chain reaction (RT-PCR) assay, to detect the presence of SARS-CoV-2 RNA in patient samples, typically from nasopharyngeal swabs. RNA extraction is a major bottleneck in current COVID-19 testing, in terms of turn-around, logistics, component availability and cost, which delays or completely precludes COVID-19 diagnostics in many settings. Efforts to simplify the current methods are critical, as increased diagnostic availability and efficiency would benefit patient care and infection control. Here, we describe methods to circumvent RNA extraction in COVID-19 testing by performing RT-PCR directly on heat-inactivated subject samples as well as samples lysed with readily available detergents. Our data, including benchmarking with 597 clinically diagnosed patient samples against a standardised and sensitive diagnostic system, show that direct RT-PCR is a viable option to extraction-based COVID-19 diagnostics. Furthermore, using controlled amounts of active SARS-CoV-2, we evaluated performance of generic buffers as sample medium for the direct RT-PCR assay, identifying several suitable formulations. We also confirmed the effectiveness of heat inactivation of SARS-CoV-2 by plaque assay. Significant savings in terms of time and cost can be achieved by embracing RNA-extraction-free protocols, that feed directly into the established PCR-based testing pipeline. This could aid the expansion of COVID-19 testing.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Ioanna Smyrlaki", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Martin Ekman", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Antonio Lentini", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Nuno Rufino de Sousa", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Natali Papanicoloau", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Martin Vondracek", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Johan Aarum", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Hamzah Safari", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Shaman Muradrasoli", + "author_inst": "Public Health Agency of Sweden" + }, + { + "author_name": "Antonio Gigliotti Rothfuchs", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Jan Albert", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Bj\u00f6rn H\u00f6gberg", + "author_inst": "Karolinska Institute" + }, + { + "author_name": "Bj\u00f6rn Reinius", + "author_inst": "Karolinska Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.14.20064501", "rel_title": "What influences COVID-19 infection rates: A statistical approach to identify promising factors applied to infection data from Germany", @@ -1546126,37 +1546554,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.11.20060749", - "rel_title": "Survival After In-Hospital Cardiac Arrest In Critically Ill Patients: Implications For The Covid-19 Pandemic?", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20060749", - "rel_abs": "The coronavirus disease 2019 (COVID-19) outbreak is placing a considerable strain on U.S. healthcare systems. Due to presumptions of poor outcomes in such critically ill patients, many hospitals have started considering a universal do-not-resuscitate order in patients with confirmed Covid-19 given a limited supply of intensive care unit (ICU) beds and the potential risk of transmission of infection to healthcare workers during resuscitation. However, empirical data on survival of cardiac arrest in Covid-19 patients are unavailable at this time.\n\nTo inform this debate, we report survival outcomes following cardiopulmonary resuscitation in a cohort of similar critically ill patients with pneumonia or sepsis who were receiving mechanical ventilation in an ICU at the time of arrest. The probability of survival without severe neurological disability (CPC of 1 or 2) ranged from less than 3% to over 22% across key patient subgroups, For patients with an initial rhythm of asystole or PEA, who were also receiving vasopressors at the time of arrest, fewer than 10% were discharged without severe neurological disability (CPC of 1 or 2), and this number dropped to less than 3% in patients over 80 years old. In contrast, survival rates were much higher in younger patients, patients with an initial rhythm of VF or pulseless VT, and in patients receiving ventilatory support without vasopressors.\n\nOur findings suggest caution in universal resuscitation policies. Even in a cohort of critically ill patients on mechanical ventilation, survival outcomes following in-hospital resuscitation were not uniformly poor and varied markedly depending on age, co-morbidities and illness severity. We believe that these data can help inform discussions among patients, providers and hospital leaders regarding resuscitation policies and goals of care in the context of the COVID-19 pandemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Saket Girotra", - "author_inst": "University of Iowa Carver College of Medicine" - }, - { - "author_name": "Yuanyuan Tang", - "author_inst": "St. Luke's Mid America Heart Institute" - }, - { - "author_name": "Paul Chan", - "author_inst": "University of Missouri - Kansas City and St. Luke's Mid America Heart Institute, Kansas City, MO" - }, - { - "author_name": "Brahmajee K Nallamothu", - "author_inst": "University of Michigan, Ann Arbor, MI" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.04.11.20061366", "rel_title": "A Fractal kinetics SI model can explain the dynamics of COVID-19 epidemics", @@ -1546320,6 +1546717,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.16.20061044", + "rel_title": "EFFECTIVENESS OF BASELINE AND POST-PROCESSED CHEST X-RAY IN NONEARLY COVID-19 PATIENTS", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20061044", + "rel_abs": "BackgroundCT is a very sensitive technique to detect pneumonia in COVID-19 patients. However, it is impaired by high costs, logistic issues and high risk of exposure.\n\nChest x-ray (CXR) is a low-cost, low-risk, not time consuming technique and is emerging as the recommended imaging modality to use in COVID-19 pandemic.\n\nThis technique, although less sensitive than CT-scan, can provide useful information about pulmonary involvement.\n\nPurposeTo describe chest x-ray features of COVID-19 pneumonia and to evaluate the sensitivity of this technique in detecting pneumonia. A further scope is to assess the effectiveness of a post-processing algorithm in improving lung lesions detectability.\n\nMaterials and Methods72 patients with laboratory-confirmed COVID-19 underwent bedside chest X-ray.\n\nTwo radiologists were asked to express their opinion about: (i) presence of pneumonia (negative or positive); (ii) localization (unilateral or bilateral); (iii) topography (according to pulmonary fields); (iv) density (non consolidative ground-glass or inhomogeneous opacities; consolidative nodular-type or triangular; mixed consolidative e non-consolidative); and (v) presence of pleural effusion. The point (i) was evaluated separately, while the other points in consensus.\n\nA quality assessment of post-processed x-ray images was performed by two different readers.\n\nResultsThe agreement about presence of pneumonia was almost perfect with K value of 0.933 and p < 0.001.\n\nSensitivity was 69%.\n\nThe following findings were seen: unilateral lung involvement in 50%; lower lung lesions in 54%; peripheral distribution in 48%; and non-consolidative pattern in 44%.\n\nPost-processed images improved the detection of lesions in 7 out 72 patients ({cong}10%)\n\nConclusionCXR owns a good sensitivity in detecting COVID-19 lung involvement. Use of post-processing algorithm can improve detection of lesions. Our data support recommendations of the Radiological Society of North America (RSNA) to consider chest x-ray as first step imaging examination in Covid-19 patients.\n\nSUMMARYBedside CXR has a good sensitivity in evaluating COVID-19 lung involvement in hospitalized patients and should be considered as the first step imaging technique according to RSNA recommendations.\n\nKEY RESULTSO_LIBedside CXR has a good sensitivity in evaluating COVID-19 lung involvement in non-early clinical cases.\nC_LIO_LIThe most common findings of lung involvement were slight different from the well-described CT-ones, with less common patterns of bilateral and peripheral distribution.\nC_LIO_LIPost-processing algorithm enhances detection of pulmonary lesions.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Michele Gaeta", + "author_inst": "University of Messina" + }, + { + "author_name": "Giuseppe Cicero", + "author_inst": "University of Messina" + }, + { + "author_name": "Maria Adele Marino", + "author_inst": "University of Messina" + }, + { + "author_name": "Tommaso D'Angelo", + "author_inst": "University of Messina" + }, + { + "author_name": "Enrico Maria Mormina", + "author_inst": "University of Messina" + }, + { + "author_name": "Silvio Mazziotti", + "author_inst": "University of Messina" + }, + { + "author_name": "Alfredo Blandino", + "author_inst": "University of Messina" + }, + { + "author_name": "Giulio Siracusano", + "author_inst": "University of Catania" + }, + { + "author_name": "Aurelio La Corte", + "author_inst": "University of Catania" + }, + { + "author_name": "Massimo Chiappini", + "author_inst": "Instituto Nazionale di Geofisica e Vulcanologia" + }, + { + "author_name": "Giovanni Finocchio", + "author_inst": "University of Messina" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.04.12.20062695", "rel_title": "Shut it down: a cross country panel analysis on the efficacy of lockdown measures", @@ -1547224,25 +1547680,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.12.20062794", - "rel_title": "Modelling and analysis of COVID-19 epidemic in India.", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.12.20062794", - "rel_abs": "COVID-19 epidemic is declared as the public health emergency of international concern by the World Health Organisation in the second week of March 2020. This disease originated from China in December 2019 has already caused havoc around the world, including India. The first case in India was reported on 30th January 2020, with the cases crossing 6000 on the day paper was written. Complete lockdown of the nation for 21 days and immediate isolation of infected cases are the proactive steps taken by the authorities. For a better understanding of the evolution of COVID-19 in the country, Susceptible-Infectious-Quarantined-Recovered (SIQR) model is used in this paper. It is predicted that actual infectious population is ten times the reported positive case (quarantined) in the country. Also, a single case can infect 1.55 more individuals of the population. Epidemic doubling time is estimated to be around 4.1 days. All indicators are compared with Brazil and Italy as well. SIQR model has also predicted that India will see the peak with 22,000 active cases during the last week of April followed by reduction in active cases. It may take complete July for India to get over with COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "ALOK TIWARI", - "author_inst": "IIT BOMBAY" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.15.20063107", "rel_title": "Association between ABO blood groups and clinical outcome of coronavirus disease 2019: Evidence from two cohorts", @@ -1547550,6 +1547987,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.13.20063644", + "rel_title": "Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063644", + "rel_abs": "BackgroundAs governments across Europe have issued non-pharmaceutical interventions (NPIs) such as social distancing and school closing, the mobility patterns in these countries have changed. It is likely different countries and populations respond differently to the same NPIs and that these differences are reflected in the epidemic development.\n\nMethodsWe build a Bayesian model that estimates the number of deaths on a given day dependent on changes in the basic reproductive number, R0, due to changes in mobility patterns. We utilize mobility data from Google mobility reports using five different categories: retail and recreation, grocery and pharmacy, transit stations, workplace and residential. The importance of each mobility category for predicting changes in R0 is estimated through the model.\n\nFindingsThe changes in mobility have a large overlap with the introduction of governmental NPIs, highlighting the importance of government action for population behavioural change. The grocery and pharmacy sector is estimated to account for 97 % of the reduction in R0 (95% confidence interval [0{middle dot}79,0{middle dot}99]).\n\nInterpretationOur model predicts three-week epidemic forecasts, using real-time observations of changes in mobility patterns, which can provide governments with direct feedback on the effects of their NPIs. The model predicts the changes in a majority of the countries accurately but overestimates the impact of NPIs in Sweden and Denmark and underestimates them in France and Belgium.\n\nFundingFinancial support: Swedish Research Council for Natural Science, grant No. VR-2016-06301 and Swedish E-science Research Center. Computational resources: Swedish National Infrastructure for Computing, grant No. SNIC-2019/3-319.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Patrick Bryant", + "author_inst": "Stockholm University/Science for Life Laboratory" + }, + { + "author_name": "Arne Elofsson", + "author_inst": "Stockholm University/Science for Life Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.13.20063610", "rel_title": "The December 2019 New Corona Virus Disease (SARS-CoV-2) Outbreak: A Behavioral Infectious Disease Policy Model", @@ -1548358,41 +1548818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.13.20064048", - "rel_title": "The Prediction for the Outbreak of COVID-19 for 15 States in USA by Using Turning Phase Concepts as of April 10, 2020", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20064048", - "rel_abs": "Based on a new concept called \"Turning Period\", the goal of this report is to show how we can conduct the prediction for the outlook in the different stages for the battle with outbreak of COVID-19 currently in US, in particular, to identify when each of top 15 states in USA (basically on their populations) is going to enter into the stage that the outbreak of COVID-19 is under the control by the criteria such as daily change of new patients is less than 10% smoothly. Indeed, based on the data of April 10, 2020 with the numerical analysis, we are able to classify 15 states of US into the following four different categories for the Prevention and Control of Infectious Diseases Today and the main conclusion are:\n\nFirst, staring around April 14, 20202, three states which are Washington State, Louisiana and Indiana are entering the stage that the outbreak of COVID-19 is under the control, which means daily change of new patients is less than 10% and the gamma is less than zero in general.\n\nSecond, staring around April 15, 20202, two states which are New Jersey, and New York are entering the stage that the outbreak of COVID-19 is under the control, which means daily change of new patients is less than 10% and the gamma is less than zero in general.\n\nThird, staring around April 16, 20202, seven states which are California, Florida, Georgia (GA), Illinois, Maryland, Indiana, Michigan, and Pennsylvania are entering the stage that the outbreak of COVID-19 is under the control, which means daily change of new patients is less than 10% and the gamma is less than zero in general.\n\nFourth, staring around April 17, 20202, three states which are Texas, Massachusetts, and Connecticut are entering the stage that the outbreak of COVID-19 is under the control, which means daily change of new patients is less than 10% and the gamma is less than zero in general.\n\nFinally, we want to reinforce that emergency risk management is always associated with the implementation of an emergency plan. The identification of the Turning Time Period is key to emergency planning as it provides a timeline for effective actions and solutions to combat a pandemic by reducing as much unexpected risk as soon as possible.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "George X Yuan", - "author_inst": "Soochow University" - }, - { - "author_name": "Lan Di", - "author_inst": "Jiangnan University" - }, - { - "author_name": "Yudi Gu", - "author_inst": "Jiangnan University" - }, - { - "author_name": "Guoqi Qian", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Xiaosong Qian", - "author_inst": "Soochow University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.13.20063933", "rel_title": "Expected impact of lockdown in Ile-de-France and possible exit strategies", @@ -1548568,6 +1548993,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.11.20061721", + "rel_title": "COVID-19-related mortality by age groups in Europe: A meta-analysis", + "rel_date": "2020-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20061721", + "rel_abs": "Background and ObjectivesTo date, more than 1,000,000 confirmed cases and 65,000 deaths due to coronavirus disease 2019 (COVID-19) have been reported globally. Early data have indicated that older patients are at higher risk of dying from COVID-19 than younger ones, but precise international estimates of the age-breakdown of COVID-19-related deaths are lacking.\n\nMaterials and MethodsWe evaluated the distribution of COVID-19-related fatalities by age groups in Europe. On April 6, 2020, we systematically reviewed COVID-19-related mortality data from 32 European countries (European Union/European Economic Area and the United Kingdom). We collated official reports provided by local Public Health or Ministry of Health websites. We included countries if they provided data regarding more than 10 COVID-19-related deaths stratified by age according to pre-specified groups (i.e., < 40, 40-69, [≥] 70 years). We used random-effects meta-analysis to estimate the proportion of age groups among all COVID-19-related fatalities.\n\nResultsThirteen European countries were included in the review, for a total of 31,864 COVID-19-related deaths (range: 27-14,381 per country). In the main meta-analysis (including data from Germany, Hungary, Italy, Netherlands, Portugal, Spain, Switzerland; 21,522 COVID-19-related fatalities), the summary proportions of persons < 40, 40-69, and [≥] 70 years of age among all COVID-19-related deaths were 0.1% (0.0-0.2%; I2 24%), 12.8% (10.3-15.6%; I2 94%), and 84.8% (81.3-88.1%; I2 96%), respectively.\n\nConclusionsPeople under 40 years of age represent a small fraction of the total number of COVID-19-related deaths in Europe. These results may help health authorities respond to public concerns and guide future physical distancing and mitigation strategies.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "J\u00e9r\u00e9mie F. Cohen", + "author_inst": "Inserm UMR 1153, Universite de Paris" + }, + { + "author_name": "Dani\u00ebl A. Korevaar", + "author_inst": "Department of Respiratory Medicine, Amsterdam University Medical Center, University of Amsterdam, PO Box 22700, 1100 DE, Amsterdam, The Netherlands" + }, + { + "author_name": "Soraya Matczak", + "author_inst": "Department of General Pediatrics and Pediatric Infectious Diseases, AP-HP, Necker Hospital for Sick Children, Universite de Paris, 75015, Paris, France" + }, + { + "author_name": "Jos\u00e9phine Brice", + "author_inst": "Department of General Pediatrics and Pediatric Infectious Diseases, AP-HP, Necker Hospital for Sick Children, Universite de Paris, 75015, Paris, France" + }, + { + "author_name": "Martin Chalumeau", + "author_inst": "Department of General Pediatrics and Pediatric Infectious Diseases, AP-HP, Necker Hospital for Sick Children, Universite de Paris, 75015, Paris, France" + }, + { + "author_name": "Julie Toubiana", + "author_inst": "Department of General Pediatrics and Pediatric Infectious Diseases, AP-HP, Necker Hospital for Sick Children, Universite de Paris, 75015, Paris, France" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.12.20062869", "rel_title": "Cardiovascular Diseases and COVID-19 Mortality and Intensive Care Unit Admission: A Systematic Review and Meta-analysis", @@ -1549591,37 +1550055,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.12.20059618", - "rel_title": "COVID-19 outbreak at a large homeless shelter in Boston: Implications for universal testing", - "rel_date": "2020-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.12.20059618", - "rel_abs": "The circumstances of homelessness create the potential for rapid transmission of SARS-CoV-2 in this vulnerable population. Upon observing a cluster of COVID-19 cases from a single large homeless shelter in Boston, Boston Health Care for the Homeless Program conducted symptom assessments and polymerase chain reaction (PCR) testing for SARS-CoV-2 among all guests residing at the shelter over a 2-day period. Of 408 participants, 147 (36.0%) were PCR-positive for SARS-CoV-2. COVID-positive individuals were more likely to be male (p<0.001) but did not differ significantly from COVID-negative individuals with respect to other demographic and clinical characteristics. Cough (7.5%), shortness of breath (1.4%), and fever (0.7%) were all uncommon among COVID-positive individuals. Our findings illustrate the rapidity with which COVID-19 can be widely transmitted in a homeless shelter setting and suggest that universal PCR testing, rather than a symptom triggered approach, may be a better strategy for identifying and mitigating COVID-19 among people experiencing homelessness.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Travis P. Baggett", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Harrison Keyes", - "author_inst": "Boston Health Care for the Homeless Program" - }, - { - "author_name": "Nora Sporn", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Jessie M. Gaeta", - "author_inst": "Boston Health Care for the Homeless Program" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.11.20062356", "rel_title": "Pregnancy outcomes, Newborn complications and Maternal-Fetal Transmission of SARS-CoV-2 in women with COVID-19: A systematic review", @@ -1549841,6 +1550274,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.10.20060905", + "rel_title": "COVID-19: A model correlating BCG vaccination to protection from mortality implicates trained immunity", + "rel_date": "2020-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060905", + "rel_abs": "O_LIWe use a data quality model to demonstrate that BCG vaccination is correlated with protection from death from COVID19\nC_LIO_LIFrom a mechanistic perspective, BCG is well described to elicit its protective non-specific effects through the process of trained immunity.\nC_LIO_LITherapeutically enhancing trained immunity may therefore be an important mechanism in protection from the lethal effects of COVID19\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Cameron M. Green", + "author_inst": "Fresh Software A.G." + }, + { + "author_name": "Stephanie Fanucchi", + "author_inst": "Division of Chemical, Systems & Synthetic Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town" + }, + { + "author_name": "Ezio T. Fok", + "author_inst": "Epigenomics & Single Cell Biophysics Group, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, The Netherlands" + }, + { + "author_name": "Simone J.C.F.M. Moorlag", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands" + }, + { + "author_name": "Jorge Dominguez-Andres", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands" + }, + { + "author_name": "Yutaka Negishi", + "author_inst": "Epigenomics & Single Cell Biophysics Group, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, The Netherlands" + }, + { + "author_name": "Leo A.B. Joosten", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands" + }, + { + "author_name": "Mihai G. Netea", + "author_inst": "Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands" + }, + { + "author_name": "Musa M. Mhlanga", + "author_inst": "Radboud University, Radboud Institute for Molecular Life Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.11.20062372", "rel_title": "Self-Collected Oral Fluid and Nasal Swabs Demonstrate Comparable Sensitivity to Clinician Collected Nasopharyngeal Swabs for Covid-19 Detection", @@ -1550997,109 +1551481,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.15.043166", - "rel_title": "Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2", - "rel_date": "2020-04-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.15.043166", - "rel_abs": "BackgroundEffective therapeutics to treat COVID-19 are urgently needed. Remdesivir is a nucleotide prodrug with in vitro and in vivo efficacy against coronaviruses. Here, we tested the efficacy of remdesivir treatment in a rhesus macaque model of SARS-CoV-2 infection.\n\nMethodsTo evaluate the effect of remdesivir treatment on SARS-CoV-2 disease outcome, we used the recently established rhesus macaque model of SARS-CoV-2 infection that results in transient lower respiratory tract disease. Two groups of six rhesus macaques were infected with SARS-CoV-2 and treated with intravenous remdesivir or an equal volume of vehicle solution once daily. Clinical, virological and histological parameters were assessed regularly during the study and at necropsy to determine treatment efficacy.\n\nResultsIn contrast to vehicle-treated animals, animals treated with remdesivir did not show signs of respiratory disease and had reduced pulmonary infiltrates on radiographs. Virus titers in bronchoalveolar lavages were significantly reduced as early as 12hrs after the first treatment was administered. At necropsy on day 7 after inoculation, lung viral loads of remdesivir-treated animals were significantly lower and there was a clear reduction in damage to the lung tissue.\n\nConclusionsTherapeutic remdesivir treatment initiated early during infection has a clear clinical benefit in SARS-CoV-2-infected rhesus macaques. These data support early remdesivir treatment initiation in COVID-19 patients to prevent progression to severe pneumonia.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Brandi Williamson", - "author_inst": "NIAID" - }, - { - "author_name": "Friederike Feldmann", - "author_inst": "NIAID" - }, - { - "author_name": "Benjamin Schwarz", - "author_inst": "NIAID" - }, - { - "author_name": "Kimberly Meade-White", - "author_inst": "NIAID" - }, - { - "author_name": "Danielle Porter", - "author_inst": "Gilead" - }, - { - "author_name": "Jonathan Schulz", - "author_inst": "NIAID" - }, - { - "author_name": "Neeltje van Doremalen", - "author_inst": "NIH" - }, - { - "author_name": "Ian Leighton", - "author_inst": "NIAID" - }, - { - "author_name": "Claude Kwe Yinda", - "author_inst": "NIAID" - }, - { - "author_name": "Lizzette Perez-Perez", - "author_inst": "NIAID" - }, - { - "author_name": "Atsushi Okumura", - "author_inst": "NIAID" - }, - { - "author_name": "Jamie Lovaglio", - "author_inst": "NIAID" - }, - { - "author_name": "Patrick Hanley", - "author_inst": "NIAID" - }, - { - "author_name": "Greg Saturday", - "author_inst": "NIAID" - }, - { - "author_name": "Catharine Bosio", - "author_inst": "NIAID" - }, - { - "author_name": "Sarah Anzick", - "author_inst": "NIAID" - }, - { - "author_name": "Kent Barbian", - "author_inst": "NIAID" - }, - { - "author_name": "Tomas Chilar", - "author_inst": "Gilead" - }, - { - "author_name": "Craig Martens", - "author_inst": "NIAID" - }, - { - "author_name": "Dana Scott", - "author_inst": "NIAID" - }, - { - "author_name": "Vincent Munster", - "author_inst": "NIAID" - }, - { - "author_name": "Emmie de Wit", - "author_inst": "NIAID, NIH" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.14.041459", "rel_title": "Glycosaminoglycan binding motif at S1/S2 proteolytic cleavage site on spike glycoprotein may facilitate novel coronavirus (SARS-CoV-2) host cell entry", @@ -1551391,6 +1551772,57 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.04.14.041962", + "rel_title": "De novo 3D models of SARS-CoV-2 RNA elements and small-molecule-binding RNAs to guide drug discovery", + "rel_date": "2020-04-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.14.041962", + "rel_abs": "The rapid spread of COVID-19 is motivating development of antivirals targeting conserved SARS-CoV-2 molecular machinery. The SARS-CoV-2 genome includes conserved RNA elements that offer potential small-molecule drug targets, but most of their 3D structures have not been experimentally characterized. Here, we provide a compilation of chemical mapping data from our and other labs, secondary structure models, and 3D model ensembles based on Rosettas FARFAR2 algorithm for SARS-CoV-2 RNA regions including the individual stems SL1-8 in the extended 5 UTR; the reverse complement of the 5 UTR SL1-4; the frameshift stimulating element (FSE); and the extended pseudoknot, hypervariable region, and s2m of the 3 UTR. For eleven of these elements (the stems in SL1-8, reverse complement of SL1-4, FSE, s2m, and 3 UTR pseudoknot), modeling convergence supports the accuracy of predicted low energy states; subsequent cryo-EM characterization of the FSE confirms modeling accuracy. To aid efforts to discover small molecule RNA binders guided by computational models, we provide a second set of similarly prepared models for RNA riboswitches that bind small molecules. Both datasets ( FARFAR2-SARS-CoV-2, https://github.com/DasLab/FARFAR2-SARS-CoV-2; and FARFAR2-Apo-Riboswitch, at https://github.com/DasLab/FARFAR2-Apo-Riboswitch) include up to 400 models for each RNA element, which may facilitate drug discovery approaches targeting dynamic ensembles of RNA molecules.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ramya Rangan", + "author_inst": "Stanford University" + }, + { + "author_name": "Andrew M. Watkins", + "author_inst": "Stanford University" + }, + { + "author_name": "Jose Chacon", + "author_inst": "Stanford University" + }, + { + "author_name": "Wipapat Kladwang", + "author_inst": "Stanford University" + }, + { + "author_name": "Ivan N. Zheludev", + "author_inst": "Stanford University" + }, + { + "author_name": "Jill Townley", + "author_inst": "Eterna Massive Open Laboratory" + }, + { + "author_name": "Mats Rynge", + "author_inst": "University of Southern California" + }, + { + "author_name": "Gregory Thain", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Rhiju Das", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.08.20058180", "rel_title": "Impact of COVID-19 pandemic on severity of illness and resources required during intensive care in the greater New York City area", @@ -1552211,41 +1552643,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.10.20060954", - "rel_title": "Global convergence of COVID-19 basic reproduction number and estimation from early-time SIR dynamics", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060954", - "rel_abs": "The SIR ( susceptible-infectious-recovered) formulation is used to uncover the generic spread mechanisms observed by COVID-19 dynamics globally, especially in the early phases of infectious spread. During this early period, potential controls were not effectively put in place or enforced in many countries. Hence, the early phases of COVID-19 spread in countries where controls were weak offer a unique perspective on the ensemble-behavior of COVID-19 basic reproduction number Ro. The work here shows that there is global convergence (i.e. across many nations) to an uncontrolled Ro = 4.5 that describes the early time spread of COVID-19. This value is in agreement with independent estimates from other sources reviewed here and adds to the growing consensus that the early estimate of Ro = 2.2 adopted by the World Health Organization is low. A reconciliation between power-law and exponential growth predictions is also featured within the confines of the SIR formulation. Implications for evaluating potential control strategies from this uncontrolled Ro are briefly discussed in the context of the maximum possible infected fraction of the population (needed for assessing health care capacity) and mortality (especially in the USA given diverging projections). Model results indicate that if intervention measures still result in Ro > 2.7 within 49 days after first infection, intervention is unlikely to be effective in general for COVID-19. Current optimistic projections place mortality figures in the USA in the range of 100,000 fatalities. For fatalities to be confined to 100,000 requires a reduction in Ro from 4.5 to 2.7 within 17 days of first infection assuming a mortality rate of 3.4%.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Gabriel G. Katul", - "author_inst": "Duke University" - }, - { - "author_name": "Assaad Mrad", - "author_inst": "Duke University" - }, - { - "author_name": "Sara Bonetti", - "author_inst": "ETH Zurich" - }, - { - "author_name": "Gabriele Manoli", - "author_inst": "University College London" - }, - { - "author_name": "Anthony J. Parolari", - "author_inst": "Marquette University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.10.20060962", "rel_title": "Impact of Social Vulnerability on COVID-19 Incidence and Outcomes in the United States", @@ -1552521,6 +1552918,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.10.20060616", + "rel_title": "Chaos, Percolation and the Coronavirus Spread: the Italian case", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060616", + "rel_abs": "A model based on chaotic maps and turbulent flows is applied to the spread of Coronavirus for each Italian region in order to obtain useful information and help to contrast it. We divide the regions into different risk categories and discuss anomalies. The worst cases are confined between the Appenine and the Alps mountain ranges but the situation seem to improve closer to the sea. The Veneto region gave the most efficient response so far and some of their resources could be diverted to other regions, in particular more tests to the Lombardia, Liguria, Piemonte, Marche and V. Aosta regions, which seem to be worst affected. We noticed worrying anomalies in the Lazio, Campania and Sicilia regions to be monitored. We stress that the number of fatalities we predicted on March 12 has been confirmed daily by the bulletins. This suggests a change of strategy in order to reduce such number maybe moving the weaker population (and negative to the virus test) to beach resorts, which should be empty presently. The ratio deceased/positives on April 4, 2020 is 5.4% worldwide, 12.3% in Italy, 1.4% in Germany, 2.7% in the USA, 10.3% in the UK and 4.1% in China. These large fluctuations should be investigated starting from the Italian regions, which show similar large fluctuations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Aldo Bonasera", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Giacomo Bonasera", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Suylatu Zhang", + "author_inst": "Inner Mongolia University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.10.20060673", "rel_title": "COVID-19 lockdowns cause global air pollution declines with implications for public health risk", @@ -1553677,81 +1554101,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.09.20058651", - "rel_title": "Scaling diagnostics in times of COVID-19: Rapid prototyping of 3D-printed water circulators for Loop-mediated Isothermal Amplification (LAMP) and detection of SARS-CoV-2 virus", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20058651", - "rel_abs": "By the third week of June 2020, more than 8,500,000 positive cases of COVID-19 and more than 450,000 deaths had been officially reported worldwide. The COVID-19 pandemic arrived in Latin America, India, and Africa--territories in which the mounted infrastructure for diagnosis is greatly underdeveloped. Here, we demonstrate the combined use of a three-dimensional (3D)-printed incubation chamber for commercial Eppendorf PCR tubes, and a colorimetric embodiment of a loop-mediated isothermal amplification (LAMP) reaction scheme for the detection of SARS-CoV-2 nucleic acids. We used this strategy to detect and amplify SARS-CoV-2 genetic sequences using a set of in-house designed initiators that target regions encoding the N protein. We were able to detect and amplify SARS-CoV-2 nucleic acids in the range of 62 to 2 x 105 DNA copies by this straightforward method. Using synthetic SARS-CoV-2 samples and a limited number of RNA extracts from patients, we also demonstrate that colorimetric LAMP is a quantitative method comparable in diagnostic performance to RT-qPCR. We envision that LAMP may greatly enhance the capabilities for COVID-19 testing in situations where RT-qPCR is not feasible or is unavailable. Moreover, the portability, ease of use, and reproducibility of this strategy make it a reliable alternative for deployment of point-of-care SARS-CoV-2 detection efforts during the pandemics.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Everardo Gonzalez-Gonzalez", - "author_inst": "Tecnologico de Monterrey" - }, - { - "author_name": "Itzel Montserrat Lara-Mayorga", - "author_inst": "Tecnologico de Monterrey" - }, - { - "author_name": "Iram Pablo Rodriguez-Sanchez", - "author_inst": "Universidad Autonoma de Nuevo Leon" - }, - { - "author_name": "Felipe Yee-de Leon", - "author_inst": "Delee, Corp." - }, - { - "author_name": "Andres Garcia-Rubio", - "author_inst": "Tecnologico de Monterrey" - }, - { - "author_name": "Carlos Ezio Garciamendez-Mijares", - "author_inst": "Division of Engineering in Medicine, Harvard Medical School" - }, - { - "author_name": "Gilberto Emilio Guerra-Alvarez", - "author_inst": "Tecnologico de Monterrey" - }, - { - "author_name": "German Garcia-Martinez", - "author_inst": "Division of Engineering in Medicine, Harvard Medical School" - }, - { - "author_name": "Juan Andres Aguayo-Hernandez", - "author_inst": "Tecnologico de Monterrey" - }, - { - "author_name": "Eduardo Marquez-Garcia", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas" - }, - { - "author_name": "Yu-Shrike Zhang", - "author_inst": "Division of Engineering in Medicine, Harvard Medical School" - }, - { - "author_name": "Sergio Omar Martinez-Chapa", - "author_inst": "Tecnologico de Monterrey" - }, - { - "author_name": "Joaquin Zu\u00f1iga", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas" - }, - { - "author_name": "Grissel Trujillo-de Santiago", - "author_inst": "Tecnologico de Monterrey" - }, - { - "author_name": "Mario Moises Alvarez", - "author_inst": "Tecnologico de Monterrey" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.13.039198", "rel_title": "Identification of potential vaccine candidates against SARS-CoV-2, A step forward to fight novel coronavirus 2019-nCoV: A Reverse Vaccinology Approach", @@ -1553935,6 +1554284,25 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.04.11.20061432", + "rel_title": "Application of COVID-19 pneumonia diffusion data to predict epidemic situation", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20061432", + "rel_abs": "ObjectiveTo evaluate novel coronavirus pneumonia cases by establishing the mathematical model of the number of confirmed cases daily, and to assess the current situation and development of the epidemic situation, so as to provide a digital basis for decision-making.\n\nMethodsThe number of newly confirmed covid-19 cases per day was taken as the research object, and the seven-day average value (M) and the sequential value (R) of M were calculated to study the occurrence and development of covid-19 epidemic through the analysis of charts and data.\n\nResultsM reflected the current situation of epidemic development; R reflected the current level of infection and the trend of epidemic development.\n\nConclusionThe current data can be used to evaluate the number of people who have been infected, and when R < 1, the peak of epidemic can be predicted.\n\nPrefaceIn December 2019, a number of cases of pneumonia with unknown causes were found in some hospitals in Wuhan, Hubei province, China. On 11 March 2020, the director-general of the world health organization (WHO), Tedros Adhanom Ghebreyesus, announced that based on the assessment, WHO believes that the current outbreak of COVID-19 can be called a global pandemic. By early April 2020, there were more than one million confirmed cases worldwide.\n\nCOVID-19 has developed from sporadic cases to pandemic in a short period of 3 months. The analysis and research of its infectious data will help to prevent and control the next stage of epidemic prevention and other infectious diseases in the future.\n\nIn this paper, COVID-19 rounded average of seven days (M), and Ms ring ratio (R) are used to predict the current potential patients data, and the relative state of epidemic prevention and control is judged through the graphic features and characteristic data, so as to provide evidence for the prevention and control decisions.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Zhenguo Wu", + "author_inst": "Xi'an Jioatong University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.12.037580", "rel_title": "Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection", @@ -1555203,73 +1555571,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.09.20058875", - "rel_title": "Stability of the COVID-19 virus under wet, dry and acidic conditions", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20058875", - "rel_abs": "COVID-19 has become a pandemic and is spreading fast worldwide. The COVID-19 virus is transmitted mainly through respiratory droplets and close contact. However, the fecal-oral transmission of the virus has not been ruled out and it is important to ascertain how acidic condition in the stomach affects the infectivity of the virus. Besides, it is unclear how stable the COVID-19 virus is under dry and wet conditions. In the present study, we have shown that the COVID-19 virus is extremely infectious as manifested by the infection of Vero-E6 cells by one PFU (Plaque Forming Unit) of the virus. We then investigated the stability of the COVID-19 virus in wet, dry and acidic (pH2.2) environments at room temperature. Results showed that the COVID-19 virus could survive for three days in wet and dry environments, but the dry condition is less favorable for the survival of the virus. Our study also demonstrated that the COVID-19 virus at a relative high titer (1.2 x 103 PFU) exhibits a certain degree of tolerance to acidic environment at least for 60 minutes. When the virus titer was [≤]1.0 x 103 PFU, acid treatment (pH2.2) for 30 or 60 minute resulted in virus inactivation. It suggests that the virus at a high concentration may survive in the acidic environment of the stomach. The finding of the present study will contribute to the control of the spread of the COVID-19 virus.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Zhi-ping Sun", - "author_inst": "BSL-3 laboratory of Fudan University, School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - }, - { - "author_name": "Xia Cai", - "author_inst": "BSL-3 laboratory of Fudan University, School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - }, - { - "author_name": "Chen-jian Gu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Rong Zhang", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Wen-dong Han", - "author_inst": "BSL-3 laboratory of Fudan University, School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - }, - { - "author_name": "Yun Qian", - "author_inst": "BSL-3 laboratory of Fudan University, School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - }, - { - "author_name": "Yu-yan Wang", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Wei Xu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Yang Wu", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Xun-jia Cheng", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Zheng-hong Yuan", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "You-hua Xie", - "author_inst": "Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Shanghai Med" - }, - { - "author_name": "Di Qu", - "author_inst": "BSL-3 laboratory of Fudan University, School of Basic Medical Sciences, Shanghai Medical College, Fudan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.11.20055483", "rel_title": "Anosmia and dysgeusia in patients with mild SARS-CoV-2 infection", @@ -1555405,6 +1555706,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.10.036533", + "rel_title": "Structural interactions between pandemic SARS-CoV-2 spike glycoprotein and human Furin protease", + "rel_date": "2020-04-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.10.036533", + "rel_abs": "The SARS-CoV-2 pandemic is an urgent global public health emergency and warrants investigating molecular and structural studies addressing the dynamics of viral proteins involved in host cell adhesion. The recent comparative genomic studies highlight the insertion of Furin protease site in the SARS-CoV-2 spike glycoprotein alerting possible modification in the viral spike protein and its eventual entry to host cell and presence of Furin site implicated to virulence. Here we structurally show how Furin interacts with the SARS-CoV-2 spike glycoprotein homotrimer at S1/S2 region, which underlined the mechanism and mode of action, which is a key for host cell entry. Unravelling the structural features of biding site opens the arena in rising bonafide antibodies targeting to block the Furin cleavage and have great implications in the development of Furin inhibitors or therapeutics.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Naveen Vankadari", + "author_inst": "Monash University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.04.10.036020", "rel_title": "Analysis of Ten Microsecond simulation data of SARS-CoV-2 dimeric main protease", @@ -1556581,29 +1556901,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.07.20056481", - "rel_title": "A pragmatic model to forecast the COVID-19 epidemic in different countries and allowing for daily updates", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056481", - "rel_abs": "Due to high infections rates and a high death toll of the COVID-19 pandemic, it is important to have daily updated forecasted estimates for the next weeks in order to allocate the scare resources as good as possible. We propose a pragmatic model to forecast the COVID-19 epidemic by applying a mixture normal distribution to open accessible WHO data. We specified a simple joint model on data from 20 countries with number of confirmed COVID-19 infections and number of COVID-19 deaths. We found that the duration of an epidemic wave (99% of total size) was usually between 45 - 48 days. Using data up to April 6, 2020, we found in six of 20 counties two waves, spaced between 21 and 47 days. In China and Korea the first wave was bigger, and in Denmark, Iran, Japan, and Sweden the second wave was stronger. Lag time between time trends in confirmed infections and time trends in deaths varied between 3.1 and 9.5 days. We obtained a good fit between observed and modelled data in almost all countries. In about halve of the countries the highest peak of the COVID-19 epidemic had been reached until April 6, 2020. Among the 20 countries, it is predicted that the USA will reach the highest numbers of confirmed infections (653 683 - 802 205) and number of deaths (36 591 - 53 286). Taken together, for many countries reasonable and up-to-date forecasting seems to be feasible. This method therefore bears a high potential for assisting decision makers to adjust the measures aiming at reducing the spread of the virus appropriately.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Carlos Nordt", - "author_inst": "Psychiatric Hospital, University of Zurich" - }, - { - "author_name": "Marcus Herdener", - "author_inst": "Psychiatric Hospital, University of Zurich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.06.20056119", "rel_title": "INFEKTA: A General Agent-based Model for Transmission of Infectious Diseases: Studying the COVID-19 Propagation in Bogota - Colombia", @@ -1556811,6 +1557108,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.04.08.20054023", + "rel_title": "There are asymptomatic and pre-symptomatic patients infected with COVID-19. So what? Pandemic response implications", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20054023", + "rel_abs": "Asymptomatic but infectious people have been reported in many infectious diseases. Asymptomatic and pre-symptomatic carriers would be a hidden reservoir of COVID-19.\n\nAimThis review identifies primary empirical evidence about the ability of asymptomatic carriers to infect others with COVID-19 pandemic and reflects on the implications for control measures.\n\nMethodsA systematic review is followed by a narrative report and commentary inclusion criteria were: studies reporting primary data on asymptomatic or pre-symptomatic patients, who were considered to have passed on COVID-19 infection; and published in indexed journals or in peer review between January 1 and March 31, 2020.\n\nResultsNine articles reported on 83 asymptomatic or pre-symptomatic persons.\n\nConclusionsThe evidence confirms COVID-19 transmission from people who were asymptomatic at the time. A series of implications for health service response are laid out.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Nelson Aguirre-Duarte", + "author_inst": "The University of Auckland" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.09.20059014", "rel_title": "How much India detecting SARS-CoV-2 Infections? A model-based estimation", @@ -1557875,25 +1558191,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.06.20055616", - "rel_title": "Association Between BCG Policy is Significantly Confounded by Age and is Unlikely to Alter Infection or Mortality Rates", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20055616", - "rel_abs": "Recently a number of publications looked at the association between COVID-19 morbidity and mortality on one hand and countries policies with respect to BCG vaccination on the other. This connection arises from differences in the rates of infection in countries where BCG vaccination is mandatory compared to countries where mandatory vaccination no longer exists or was never implemented in the first place. In at least 2 preprint publications the authors expressed the view that the \"known immunological benefits\" of BCG vaccination may be behind the biological mechanism of such observation.\n\nOne study accounted for different income levels in different groups. Another study did not attempted to do so, instead exploring the differences between countries where a booster shot is given vs others where no such practice exists (finding no connection).\n\nBoth of these studies did not explore other potential confounding factors. Meanwhile the press has focused on these headlines and pushed the narrative that BCG vaccination is causally linked to infection and mortality rates. This poses a serious challenge, demonstrated by the recently initiated clinical trials on BCG vaccination within the COVID19 context.\n\nThis study shows that population age is a very significant confounding factor that explains the rates of infections much better and has a solid biology mechanism which explains this correlation. It suggests that BCG vaccination may have little or no causal link to infection rates and advises that any follow up studies should control for several confounding factors, such as population age, ethnicity, rates of certain chronic diseases, time from community spread start date, major public policy decisions and income levels.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "STEFAN Kirov", - "author_inst": "Bristol Myers Squibb" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.06.20055830", "rel_title": "Covid-19 predictions using a Gauss model, based on data from April 2", @@ -1558081,6 +1558378,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.08.20057851", + "rel_title": "Age-stratified Infection Probabilities Combined with Quarantine-Modified SEIR Model in the Needs Assessments for COVID-19", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057851", + "rel_abs": "We use the age-stratified COVID-19 infection and death distributions from China (more than 44,672 infectious as of February 11, 2020) as an estimate for a study areas infection and morbidity probabilities at each age group. We then apply these probabilities into the actual age-stratified population to predict infectious individuals and deaths at peak. Testing with different countries shows the predicted infectious skewing with the countrys median age and age stratification, as expected. We added a Q parameter to the classic SEIR compartmental model to include the effect of quarantine (Q-SEIR). The projections from the age-stratified probabilities give much lower predicted incidences of infection than the Q-SEIR model. As expected, quarantine tends to delay the peaks for both Exposed and Infectious, and to flatten the curve or lower the predicted values for each compartment. These two estimates were used as a range to inform planning and response to the COVID-19 threat.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vena Pearl Bongolan", + "author_inst": "Department of Computer Science, UP Diliman, Philippines" + }, + { + "author_name": "Jose Marie Antonio Minoza", + "author_inst": "Department of Computer Science, UP Diliman, Philippines" + }, + { + "author_name": "Romulo de Castro", + "author_inst": "Center for Informatics, University of San Agustin, Iloilo City, Philippines" + }, + { + "author_name": "Jesus Emmanuel Sevilleja", + "author_inst": "National Center for Mental Health, Mandaluyong City, Philippines" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.08.20058040", "rel_title": "Blood glucose is a representative of the clustered indicators of multi-organ injury for predicting mortality of COVID-19 in Wuhan, China", @@ -1559044,37 +1559372,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.10.20058222", - "rel_title": "Understanding Economic and Health Factors Impacting the Spread of COVID-19 Disease", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20058222", - "rel_abs": "BackgroundThe rapid spread of the Coronavirus 2019 disease (COVID-19) had drastically impacted life all over the world. While some economies are actively recovering from this pestilence, others are experiencing fast and consistent disease spread, compelling governments to impose social distancing measures that have put a halt on routines, especially in densely populated areas.\n\nObjectiveAiming at bringing more light on key economic and population health factors affecting the disease spread, this initial study utilizes a quantitative statistical analysis based on the most recent publicly available COVID-19 datasets.\n\nMethodsWe have applied Pearson Correlation Analysis and Clustering Analysis (X-Means Clustering) techniques on the data obtained by combining multiple datasets related to country economics, medical system & health, and COVID-19 - related statistics. The resulting dataset consisted of COVID-19 Case and Mortality Rates, Economic Statistics, and Population Public Health Statistics for 165 countries reported between 22 January 2020 and 28 March 2020. The correlation analysis was conducted with the significance level of 0.05. The clustering analysis was guided by the value of Bayesian Information Criterion (BIC) with the bin value b = 1.0 and the cutoff factor c = 0.5, and have provided a stable split into four country-level clusters.\n\nResultsThe study showed and explained multiple significant relationships between the COVID-19 data and other country-level statistics. We also identified and statistically profiled four major country-level clusters with relation to different aspects of COVID-19 development and country-level economic and health indicators. Specifically, this study identified potential COVID-19 under-reporting traits, as well as various economic factors that impact COVID-19 Diagnosis, Reporting, and Treatment. Based on the country clusters, we also described the four disease development scenarios, which are tightly knit to country-level economic and population health factors. Finally, we highlighted the potential limitation of reporting and measuring COVID-19 and provided recommendations on further in-depth quantitative research.\n\nConclusionsIn this study, we first identified possible COVID-19 reporting issues and biases across different countries and regions. Second, we identified crucial factors affecting the speed of COVID-19 disease spread and provided recommendations on choosing and operating economic and health system factors when analyzing COVID-19 progression. Particularly, we discovered that the political system and compliance with international disease control norms are crucial for effective COVID-19 pandemic cessation. However, the role of some widely-adopted measures, such as GHS Health Index, might have been overestimated in lieu of multiple biases and underreporting challenges. Third, we benchmarked our findings against the widely-adopted Global Health Security (GHS) model and found that the latter might be redundant when measuring and forecasting COVID-19 spread, while its individual components could potentially serve as stronger COVID-19 indicators. Fourth, we discovered four clusters of countries characterized by different COVID-19 development scenarios, highlighting the differences of the disease reporting and progression in different economic and health system settings. Finally, we provided recommendations on sophisticated measures and research approaches to be implemented for effective outbreak measurements, evaluation and forecasting. We have supported the latter recommendations by a preliminary regression analysis based on the our-collected dataset. We believe that our work would encourage further in-depth quantitative research along the direction as well as would be of support to public policy development when addressing the COVID-19 crisis worldwide.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Aleksandr Farseev", - "author_inst": "ITMO University" - }, - { - "author_name": "Yu-Yi Chu-Farseeva", - "author_inst": "SoMin.ai Research" - }, - { - "author_name": "Yang Qi", - "author_inst": "ITMO University" - }, - { - "author_name": "Daron Benjamin Loo", - "author_inst": "National University of Singapore" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.10.023358", "rel_title": "SARS-CoV-2 detection with CRISPR diagnostics", @@ -1559290,6 +1559587,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2020.04.08.20057679", + "rel_title": "COVID-19 Epidemic Analysis using Machine Learning and Deep Learning Algorithms", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057679", + "rel_abs": "The catastrophic outbreak of Severe Acute Respiratory Syndrome - Coronavirus (SARS-CoV-2) also known as COVID-2019 has brought the worldwide threat to the living society. The whole world is putting incredible efforts to fight against the spread of this deadly disease in terms of infrastructure, finance, data sources, protective gears, life-risk treatments and several other resources. The artificial intelligence researchers are focusing their expertise knowledge to develop mathematical models for analyzing this epidemic situation using nationwide shared data. To contribute towards the well-being of living society, this article proposes to utilize the machine learning and deep learning models with the aim for understanding its everyday exponential behaviour along with the prediction of future reachability of the COVID-2019 across the nations by utilizing the real-time information from the Johns Hopkins dashboard.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Narinder Singh Punn", + "author_inst": "Indian Institute of Information Technology Allahabad" + }, + { + "author_name": "Sanjay Kumar Sonbhadra", + "author_inst": "Indian Institute of Information Technology Allahabad" + }, + { + "author_name": "Sonali Agarwal", + "author_inst": "Indian Institute of Information Technology Allahabad" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.07.20057224", "rel_title": "UV light dosage distribution over irregular respirator surfaces. Methods and implications for safety", @@ -1560226,41 +1560550,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.07.20056762", - "rel_title": "Chest CT Scan of Hospitalized Patients with COVID-19: A Case-Control Study", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056762", - "rel_abs": "IntroductionThis paper sought to investigate the clinical characteristic differences between suspected and confirmed patients with COVID-19 from CT scan to prevent and treat this infectious disease, since the coronavirus outbreak in the world has seriously affected the quality of life.\n\nMethodsWe proposed to use a retrospective case-control study to give a comparison between suspected patients and confirmed patients in the clinical characteristics.\n\nResults(56%) patients were confirmed for COVID-19 from suspected 167 patients. We find that elder people were more likely to be infected by COVID-19. Among the confirmed 94 patients, 2 (2%) patients were admitted to an intensive care unit, and 0 (0%) patients died during the study period. We find that images of CT scan of patients with a COVID-19 are significantly different from patients without a COVID-19.\n\nConclusionsTo our best knowledge, it is the first time to use the case-control design to study the coronavirus disease, since it is particularly appropriate for investigating infectious disease outbreaks. The clinical treatment experience in this study can supply a guideline for treating COVID-19 as the number of the infected patients is increasing in the world. Compared with other studies, we find that the mortality rate and the intensive care unit rate can be reduced if patients can be treated timely in the right identification and detection with nucleic acid testing and chest CT scan. Therefore, we recommend nucleic acid testing and chest CT scan for the clinical treatment practice from this successful clinical treatment study.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jianghu Dong", - "author_inst": "College of Public Health" - }, - { - "author_name": "Lianpin Wu", - "author_inst": "Wenzhou Medical University" - }, - { - "author_name": "QIKE Jin", - "author_inst": "Wenzhou Medical University" - }, - { - "author_name": "Jie Chen", - "author_inst": "Wenzhou Medical University" - }, - { - "author_name": "Jiawei He", - "author_inst": "Wenzhou Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.04.07.20053744", "rel_title": "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection During Pregnancy In China: A Retrospective Cohort Study", @@ -1560472,6 +1560761,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.09.20056291", + "rel_title": "Risk factors for mortality of adult inpatients with Coronavirus disease 2019 (COVID-19): a systematic review and meta-analysis of retrospective studies", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20056291", + "rel_abs": "PurposeCoronavirus disease 2019 (COVID-19) is an emerging disease that was first reported in Wuhan city, the capital of Hubei province in China, and has subsequently spread worldwide. Risk factors for mortality have not been well summarized. Current meta-analysis of retrospective cohort studies was done to summarize available findings on the association between age, gender, comorbidities and risk of death from COVID-19 infection.\n\nMethodsOnline databases including Web of Science, PubMed, Scopus, Cochrane Library and Google scholar were searched to detect relevant publications up to 1 May 2020, using relevant keywords. To pool data, random-effects model was used. Furthermore, sensitivity analysis and publication bias test were also done.\n\nResultsIn total, 14 studies with 29,909 COVID-19 infected patients and 1,445 cases of death were included in the current meta-analysis. Significant associations were found between older age ([≥]65 vs <65 years old) (pooled ORs=4.59, 95% CIs=2.61-8.04, p<0.001), gender (male vs female) (pooled ORs=1.50, 95% CIs=1.06-2.12, p=0.021) and risk of death from COVID-19 infection. In addition, hypertension (pooled ORs=2.70, 95% CIs= 1.40-5.24, p=0.003), cardiovascular diseases (CVDs) (pooled ORs=3.72, 95% CIs=1.77-7.83, p=0.001), diabetes (pooled ORs=2.41, 95% CIs=1.05-5.51, p=0.037), chronic obstructive pulmonary disease (COPD) (pooled ORs=3.53, 95% CIs=1.79-6.96, p<0.001) and cancer (pooled ORs=3.04, 95% CIs=1.80-5.14, p<0.001), were associated with higher risk of mortality.\n\nConclusionOlder age ([≥]65 years old), male gender, hypertension, CVDs, diabetes, COPD and malignancies were associated with greater risk of death from COVID-19 infection. These findings could help clinicians to identify patients with poor prognosis at an early stage.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Mohammad Parohan", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Sajad Yaghoubi", + "author_inst": "Iranshahr University of Medical Sciences" + }, + { + "author_name": "Asal Seraji", + "author_inst": "Islamic Azad University, Damavand Branch" + }, + { + "author_name": "Mohammad Hassan Javanbakht", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Payam Sarraf", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Mahmoud Djalali", + "author_inst": "Tehran University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.07.20055723", "rel_title": "SARS-CoV-2 infection in Health Care Workers in a large public hospital in Madrid, Spain, during March 2020", @@ -1561572,29 +1561900,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.07.20057133", - "rel_title": "On Data-Driven Management of the COVID-19 Outbreak in South Africa", - "rel_date": "2020-04-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20057133", - "rel_abs": "The rapid spread of the novel coronavirus (SARS-CoV-2) has highlighted the need for the development of rapid mitigating responses under conditions of extreme uncertainty. While numerous works have provided projections of the progression of the pandemic, very little work has been focused on its progression in Africa and South Africa, in particular. In this work, we calibrate the susceptible-infected-recovered (SIR) compartmental model to South African data using initial conditions inferred from progression in Hubei, China and Lombardy, Italy. The results suggest two plausible hypotheses - either the COVID-19 pandemic is still at very early stages of progression in South Africa or a combination of prompt mitigating measures, demographics and social factors have resulted in a slowdown in its spread and severity. We further propose pandemic monitoring and health system capacity metrics for assisting decision-makers in evaluating which of the two hypotheses is most probable.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rendani Mbuvha", - "author_inst": "University of Witwatersrand" - }, - { - "author_name": "Tshilidzi Marwala", - "author_inst": "University of Johannesburg" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.08.20057471", "rel_title": "Protocol for a multicentre study of nosocomial SARS-CoV2 transmission The NOSO-COR Project", @@ -1561766,6 +1562071,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.09.033522", + "rel_title": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) envelope (E) protein harbors a conserved BH3-like motif", + "rel_date": "2020-04-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.09.033522", + "rel_abs": "Disclaimer textThe authors have withdrawn their manuscript whilst they perform additional experiments to test some of their conclusions further. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vincent Navratil", + "author_inst": "PRABI, Rhone Alpes Bioinformatics Center, UCBL, Lyon1, Universite de Lyon, Lyon, France" + }, + { + "author_name": "Sonia Longhi", + "author_inst": "AFMB lab, CNRS & Aix-Marseille University" + }, + { + "author_name": "Marie Hardwick", + "author_inst": "W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, U" + }, + { + "author_name": "Christophe Combet", + "author_inst": "Centre de Recherche en Cancerologie de Lyon, UMR Inserm U1052, CNRS 5286, Universite Claude Bernard Lyon 1, Centre Leon Berard, Lyon, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.07.20057315", "rel_title": "Clinical analysis and early differential diagnosis of suspected pediatric patients with 2019 novel coronavirus infection", @@ -1562794,37 +1563130,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.04.07.20056945", - "rel_title": "A model to predict COVID-19 epidemics withapplications to South Korea, Italy, and Spain", - "rel_date": "2020-04-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056945", - "rel_abs": "1In this work, our team develops a differential equations model of COVID-19 epidemics. Our goal is to predict forward in time the future number of cases from early reported case data in regions throughout the world. Our model incorporates the following important elements of COVID-19 epidemics: (1) the number of asymptomatic infectious individuals (with very mild or no symptoms), (2) the number of symptomatic reported infectious individuals (with severe symptoms) and (3) the number of symptomatic unreported infectious individuals (with less severe symptoms). We apply our model to COVID-!9 epidemics in South Korea, Italy and Spain.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Glenn F Webb", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Pierre Magal", - "author_inst": "University of Bordeaux" - }, - { - "author_name": "Zhihua Liu", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Ousmane Seydi", - "author_inst": "Ecole Polytechnique de Thies, Senegal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.09.034454", "rel_title": "Type 2 and interferon inflammation strongly regulate SARS-CoV-2 related gene expression in the airway epithelium", @@ -1563396,6 +1563701,121 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.04.07.023903", + "rel_title": "Structural and functional analysis of a potent sarbecovirus neutralizing antibody", + "rel_date": "2020-04-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.07.023903", + "rel_abs": "SARS-CoV-2 is a newly emerged coronavirus responsible for the current COVID-19 pandemic that has resulted in more than one million infections and 73,000 deaths1,2. Vaccine and therapeutic discovery efforts are paramount to curb the pandemic spread of this zoonotic virus. The SARS-CoV-2 spike (S) glycoprotein promotes entry into host cells and is the main target of neutralizing antibodies. Here we describe multiple monoclonal antibodies targeting SARS-CoV-2 S identified from memory B cells of a SARS survivor infected in 2003. One antibody, named S309, potently neutralizes SARS-CoV-2 and SARS-CoV pseudoviruses as well as authentic SARS-CoV-2 by engaging the S receptor-binding domain. Using cryo-electron microscopy and binding assays, we show that S309 recognizes a glycan-containing epitope that is conserved within the sarbecovirus subgenus, without competing with receptor attachment. Antibody cocktails including S309 along with other antibodies identified here further enhanced SARS-CoV-2 neutralization and may limit the emergence of neutralization-escape mutants. These results pave the way for using S309 and S309-containing antibody cocktails for prophylaxis in individuals at high risk of exposure or as a post-exposure therapy to limit or treat severe disease.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Dora Pinto", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Young-Jun Park", + "author_inst": "University of Washington" + }, + { + "author_name": "Martina Beltramello", + "author_inst": "Humabs BioMed SA" + }, + { + "author_name": "Alexandra C. Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "M. Alejandra Tortorici", + "author_inst": "University of Washington" + }, + { + "author_name": "Siro Bianchi", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Stefano Jaconi", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Katja Culap", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Fabrizia Zatta", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Anna De Marco", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Alessia Peter", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Barbara Guarino", + "author_inst": "Humabs Biomed SA" + }, + { + "author_name": "Roberto Spreafico", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Elisabetta Cameroni", + "author_inst": "Humabs Biomed" + }, + { + "author_name": "James Brett Case", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Rita E. Chen", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Colin Havenar-Daughton", + "author_inst": "Vir Biotehcnology" + }, + { + "author_name": "Gyorgy Snell", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Amalio Telenti", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Herbert W. Virgin", + "author_inst": "Vir Biotechnology" + }, + { + "author_name": "Antonio Lanzavecchia", + "author_inst": "Institute for Research in Biomedicine" + }, + { + "author_name": "Michael S. Diamond", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Katja Fink", + "author_inst": "Humabs Biomed" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + }, + { + "author_name": "Davide Corti", + "author_inst": "Humabs Biomed SA, subsidiary of Vir Biotechnology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.04.07.028589", "rel_title": "The IMPDH inhibitor merimepodib suppresses SARS-CoV-2 replication in vitro.", @@ -1564784,45 +1565204,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.05.20047944", - "rel_title": "A model to predict SARS-CoV-2 infection based on the first three-month surveillance data in Brazil.", - "rel_date": "2020-04-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.05.20047944", - "rel_abs": "BackgroundCOVID-19 diagnosis is a critical problem, mainly due to the lack or delay in the test results. We aimed to obtain a model to predict SARS-CoV-2 infection in suspected patients reported to the Brazilian surveillance system.\n\nMethodsWe analyzed suspected patients reported to the National Surveillance System that corresponded to the following case definition: patients with respiratory symptoms and fever, who traveled to regions with local or community transmission or who had close contact with a suspected or confirmed case. Based on variables routinely collected, we obtained a multiple model using logistic regression. The area under the receiver operating characteristic curve (AUC) and accuracy indicators were used for validation.\n\nResultsWe described 1468 COVID-19 cases (confirmed by RT-PCR) and 4271 patients with other illnesses. With a data subset, including 80% of patients from Sao Paulo (SP) and Rio Janeiro (RJ), we obtained a function which reached an AUC of 95.54% (95% CI: 94.41% - 96.67%) for the diagnosis of COVID-19 and accuracy of 90.1% (sensitivity 87.62% and specificity 92.02%). In a validation dataset including the other 20% of patients from SP and RJ, this model exhibited an AUC of 95.01% (92.51% - 97.5%) and accuracy of 89.47% (sensitivity 87.32% and specificity 91.36%).\n\nConclusionWe obtained a model suitable for the clinical diagnosis of COVID-19 based on routinely collected surveillance data. Applications of this tool include early identification for specific treatment and isolation, rational use of laboratory tests, and input for modeling epidemiological trends.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Fredi A Diaz-Quijano", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Jose Mario Nunes da Silva", - "author_inst": "University of Sao Paulo, School of Public Health, Postgraduate Student in Epidemiology." - }, - { - "author_name": "Fabiana Ganem", - "author_inst": "Secretariat of Health Surveillance, Department of Immunization and Communicable Diseases, Ministry of Health, Brasilia, DF, Brazil." - }, - { - "author_name": "Silvano Oliveira", - "author_inst": "Secretariat of Health Surveillance, Department of Immunization and Communicable Diseases, Ministry of Health, Brasilia, DF, Brazil." - }, - { - "author_name": "Andrea Liliana Vesga-Varela", - "author_inst": "University of Sao Paulo, School of Public Health, Postgraduate Student in Public Heath." - }, - { - "author_name": "Julio Croda", - "author_inst": "Oswaldo Cruz Foundation, Mato Grosso do Sul, Campo Grande, MS, Brazil." - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.05.20054494", "rel_title": "Physician Deaths from Corona Virus Disease (COVID-19)", @@ -1564989,6 +1565370,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.04.20052308", + "rel_title": "The basic reproduction number and prediction of the epidemic size of the novel coronavirus (COVID-19) in Shahroud, Iran", + "rel_date": "2020-04-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20052308", + "rel_abs": "ObjectivesTo estimate the basic reproduction number (R0) of COVID-19 in the early stage of the epidemic and predict the expected number of new cases in Shahroud, Northeast of Iran.\n\nMethodsThe R0 of COVID-19 was estimated using the serial interval distribution and the number of incidence cases. The serial interval was fit with a gamma distribution. The probable incidence and cumulative incidence in the next 30 days were predicted using the assumption that daily incidence follows a Poisson distribution determined by daily infectiousness. Data analysis was done using \"earlyR\" and \"projections\" packages in R software.\n\nResultsThe maximum-likelihood value of R0 was 2.7 (95% confidence interval (CI): 2.1 to 3.4) for the COVID-19 epidemic in the early 14 days and decreased to 1.13 (95% CI: 1.03 to 1.25) by the end of the day 41. The expected average number of new cases in Shahroud is 9.0{+/-}3.8 case/day, which means an estimated total of 271 (95% CI: 178-383) new cases in the next 30 days.\n\nConclusionsIt is essential to reduce the R0 to values below one. Therefore, we strongly recommend enforcing and continuing the current preventive measures, restricting travel, and providing screening tests for a larger proportion of the population.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ahmad Khosravi", + "author_inst": "Ophthalmic Epidemiology Research Center, Shahroud University of Medical Sciences, Shahroud, Iran" + }, + { + "author_name": "Reza Chaman", + "author_inst": "Department of Epidemiology, School of Public Health, Shahroud University of Medical Sciences, Shahroud, Iran" + }, + { + "author_name": "Marzieh Rohani-Rasaf", + "author_inst": "Department of Epidemiology, School of Public Health, Shahroud University of Medical Sciences, Shahroud, Iran" + }, + { + "author_name": "Fariba Zare", + "author_inst": "Center for Health Related Social and Behavioral Sciences Research, Shahroud University of Medical Sciences, Shahroud, Iran." + }, + { + "author_name": "Shiva Mehravaran", + "author_inst": "ASCEND Center for Biomedical Research, Morgan State University, Baltimore, USA" + }, + { + "author_name": "Mohammad Hassan Emamian", + "author_inst": "Ophthalmic Epidemiology Research Center, Shahroud University of Medical Sciences, Shahroud, Iran" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.03.20052845", "rel_title": "Use Crow-AMSAA Method to predict the cases of the Coronavirus 19 in Michigan and U.S.A", @@ -1566169,33 +1566589,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.04.20053173", - "rel_title": "Control Strategies to Curtail Transmission of COVID-19", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20053173", - "rel_abs": "Recently the World Health Organization has declared the outbreak of a severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) as a pandemic, and declared it as Public Health Emergency of International Concern. More than 683,536 positive cases and 32,139 deaths caused by novel corona virus 2019 (COVID-19) has affected 199 countries and territories. This pandemic can transform into an extremely destructive form if we still do not take it seriously. In the present study, we propose a generalized SEIR model of COVID-19 to study the behaviour of its transmission under different control strategies. In the model, all possible cases of human to human transmission are taken care and its reproduction number is formulated to analyse accurate transmission dynamics of the coronavirus outbreak. Optimal control theory is applied in the model to pretend the impact of various intervention strategies, including voluntary quarantine, isolation of infected individuals, improving an individuals immunity and hospitalisation. Also, effect of the control strategies on model is analysed graphically by simulating the model numerically.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Nita H Shah", - "author_inst": "Gujarat University" - }, - { - "author_name": "Ankush H Suthar", - "author_inst": "Gujarat University" - }, - { - "author_name": "Ekta N Jayswal", - "author_inst": "Gujarat University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.04.20053462", "rel_title": "Generic probabilistic modelling and non-homogeneity issues for the UK epidemic of COVID-19", @@ -1566339,6 +1566732,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.04.04.20052696", + "rel_title": "Face mask use in the general population and optimal resource allocation during the COVID-19 pandemic", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20052696", + "rel_abs": "The ongoing novel coronavirus disease (COVID-19) pandemic has rapidly spread in early 2020, causing tens of thousands of deaths, over a million cases and widespread socioeconomic disruption. With no vaccine available and numerous national healthcare systems reaching or exceeding capacity, interventions to limit transmission are urgently needed. While there is broad agreement that travel restrictions and closure of non-essential businesses and schools are beneficial in limiting local and regional spread, recommendations around the use of face masks for the general population are less consistent internationally. In this study, we examined the role of face masks in mitigating the spread of COVID-19 in the general population, using epidemic models to estimate the total reduction of infections and deaths under various scenarios. In particular, we examined the optimal deployment of face masks when resources are limited, and explored a range of supply and demand dynamics. We found that face masks, even with a limited protective effect, can reduce infections and deaths, and can delay the peak time of the epidemic. We consistently found that a random distribution of masks in the population was a suboptimal strategy when resources were limited. Prioritizing coverage among the elderly was more beneficial, while allocating a proportion of available resources for diagnosed infected cases provided further mitigation under a range of scenarios. In summary, face mask use, particularly for a pathogen with relatively common asymptomatic carriage, can effectively provide some mitigation of transmission, while balancing provision between vulnerable healthy persons and symptomatic persons can optimize mitigation efforts when resources are limited.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Colin J Worby", + "author_inst": "Broad Institute" + }, + { + "author_name": "Hsiao-Han Chang", + "author_inst": "National Tsing Hua University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.03.20052720", "rel_title": "Mitigating COVID-19 outbreak via high testing capacity and strong transmission-intervention in the United States", @@ -1567327,25 +1567743,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.04.20050328", - "rel_title": "COVID-19 pandemic: Impact of lockdown, contact and non-contact transmissions on infection dynamics", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.04.20050328", - "rel_abs": "COVID-19 coronavirus pandemic has virtually locked down the entire world of human population, and through its rapid and unstoppable spread COVID-19 has essentially compartmentalised the population merely into susceptible, exposed, infected and recovered classes. Adapting the classical epidemic modelling framework, two distinct routes of COVID-19 transmission are incorporated into a model: (a) direct person-to-person contact transmission, and (b) indirect airborne and fomites-driven transmission. The indirect non-contact transmission route needs to explored in models of COVID-19 spread, because evidences show that this route of transmission is entirely viable with hugely uncertain level of relative contribution. This theoretical study based on model simulations demonstrates the following: (1) Not incorporating indirect transmission route in the model leads to underestimation of the basic reproduction number, and hence will impact on the COVID-19 mitigation decisions; (2) Lockdown measures can suppress the primary infection peak, but will lead to a secondary peak whose relative strength and time of occurrence depend on the success and duration of the lockdown measures; (3) To make lockdown effective, a considerable level of reduction in both contact and non-contact transmission rates over a long period is required; (4) To bring down the infection cases below any hypothetical health-care capacity, reduction of non-contact transmission rate is key, and hence active measures should be taken to reduce non-contact transmission (e.g., extensive uses of areal and aerosol disinfectant in public spaces to improve contaminated surfaces and air); (5) Any premature withdrawal of lockdown following the sign of a brief retracement in the infection cases can backfire, and can lead to a quicker, sharper and higher secondary peak, due to reactivation of the two transmission routes. Based on these results, this study recommends that any exit policy from lockdown, should take into account the level of transmission reduction in both routes, the absolute scale of which will vary among countries depending on their health-service capacity, but should be computed using accurate time-series data on infection cases and transmission rates.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Shovonlal Roy", - "author_inst": "University of Reading" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.04.20050427", "rel_title": "Fast spread of COVID-19 in Europe and the US and its implications: even modest public health goals require comprehensive intervention", @@ -1567505,6 +1567902,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.06.20053918", + "rel_title": "Thoughts on Higher Medical Education Under Major Public Health Emergencies: Thinking Ahead After COVID-19 Outbreak", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20053918", + "rel_abs": "ImportanceThe spread of coronavirus disease 2019 (COVID-19) has posed great threat to peoples health and several medical schools in the world suspended classes as a precaution against the virus. China has also adopted precautionary measures to keep medical schools running without suspending classes. Thinking ahead after COVID-19 Outbreak is important.\n\nObjectiveTo explore the most suitable teaching and learning pattern in medical school during COVID-19 Outbreak.\n\nDesignThis study is a case-control study. We had tried to apply a new blended teaching model based on 5G network that combined team-based learning (TBL) and online interaction to the students before the outbreak and then universities responded to the COVID-19 outbreak by closing campuses and shifting to other forms of distance learning. In other word, the courses started using blended teaching model before COVID-19 outbreak and might last using other forms of distance learning throughout the pandemic. Five Point Likert Scale Questionnaires which contains 20 items were used, and the effect of the two kinds of teaching patterns was compared by evaluating the indicators of core competencies of students including professionalism, attitude towards learning, knowledge and learning skills, teamwork skills, motivation in learning, adaptability and acceptance of the courses and network environment.\n\nSettingOur study based on a single center.\n\nParticipantsFifty fourth-year medical students receiving the \"5+3\" pattern courses regarding internal medicine were enrolled in the study.\n\nExposure(s) (for observational studies)The teaching and learning patter started using blended teaching model before COVID-19 outbreak and might last using other forms of distance learning throughout the pandemic.\n\nMain Outcome(s)According to the descriptive statistical analysis of the first part of the questionnaire (question 1-16), the average score of adaptability and acceptance of the courses is 2.60 lower than 3, indicating that students are more adapted to other forms of distance learning during COVID-19 outbreak; the average score of the rest of the questions is higher than 3, indicating that blended teaching model based on 5G network is superior to other forms of distance learning. The number of male students who are inclined to the blended teaching model based on 5G network is 0.13 times as much as that of female students (95%CI:0.028[~]0.602, p=0.009).\n\nResultsOnline forms of distance learning were accepted by the students. Female students had higher expectations on the course and were more likely to adapt well to the change during the COVID-19 outbreak. However, all students preferred the blended teaching model based on 5G network that combined team-based learning (TBL) and online interaction before the pandemic.\n\nConclusionIt indicates that medical education based on 5G network that combined team-based learning (TBL) and online interaction is a more suitable option to teach medical students online. Chinas experience in online higher medical education may serve as a reference to other countries during the pandemic.\n\nKey pointO_ST_ABSQuestionsC_ST_ABSWhat are the reflections on approaches to teaching and learning during COVID-19 Outbreak?\n\nFindingsFifty fourth-year medical students receiving the \"5+3\" pattern courses regarding internal medicine were enrolled. Five Point Likert Scale Questionnaires which contains 20 items were used. This study indicates that medical education based on 5G network that combined team-based learning (TBL) and online interaction is a more suitable option to teach medical students online during COVID-19 outbreak.\n\nMeaningChinas experience in online higher medical education may serve as a reference to other countries during the pandemic.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Wei Lin", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Yan Chen", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Songchang Shi", + "author_inst": "Fujian Provincial Hospital South Branch" + }, + { + "author_name": "Jixing Liang", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Huibin Huang", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Liantao Li", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Liangchun Cai", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Liyao Zong", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Nengying Wang", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Junping Wen", + "author_inst": "Fujian Provincial Hospital" + }, + { + "author_name": "Gang Chen", + "author_inst": "Fujian Provincial Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical education" + }, { "rel_doi": "10.1101/2020.04.03.20052936", "rel_title": "An \"Infodemic\": Leveraging High-Volume Twitter Data to Understand Public Sentiment for the COVID-19 Outbreak", @@ -1568513,49 +1568969,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.02.20051557", - "rel_title": "Modelling fatality curves of COVID-19 and the effectiveness of intervention strategies", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051557", - "rel_abs": "The main objective of the present paper is twofold: first, to model the fatality curves of the COVID-19 disease, as represented by the cumulative number of deaths as a function of time; and second, to use the corresponding mathematical model to study the effectiveness of possible intervention strategies. We applied the Richards growth model (RGM) to the COVID-19 fatality curves from several countries, where we used the data from the Johns Hopkins University database up to May 8, 2020. Countries selected for analysis with the RGM were China, France, Germany, Iran, Italy, South Korea, and Spain. The RGM was shown to describe very well the fatality curves of China, which is in a late stage of the COVID-19 outbreak, as well as of the other above countries, which supposedly are in the middle or towards the end of the outbreak at the time of this writing. We also analysed the case of Brazil, which is in an initial sub-exponential growth regime, and so we used the generalised growth model which is more appropriate for such cases. An analytic formula for the efficiency of intervention strategies within the context of the RGM is derived. Our findings show that there is only a narrow window of opportunity, after the onset of the epidemic, during which effective countermeasures can be taken. We applied our intervention model to the COVID-19 fatality curve of Italy of the outbreak to illustrate the effect of several possible interventions.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Giovani L. Vasconcelos", - "author_inst": "Universidade Federal do Paran\u00e1" - }, - { - "author_name": "Ant\u00f4nio M. S. Mac\u00eado", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Raydonal Ospina", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "Francisco A. G. Almeida", - "author_inst": "Universidade Federal de Sergipe" - }, - { - "author_name": "Gerson C. Duarte-Filho", - "author_inst": "Universidade Federal de Sergipe" - }, - { - "author_name": "Arthur Ara\u00fajo Brum", - "author_inst": "Universidade Federal de Pernambuco" - }, - { - "author_name": "In\u00eas C. L. Souza", - "author_inst": "3Hippos" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.03.20051706", "rel_title": "Reliability of self-sampling for accurate assessment of respiratory virus viral and immunologic kinetics", @@ -1568859,6 +1569272,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.03.31.20048652", + "rel_title": "Widespread use of face masks in public may slow the spread of SARS CoV-2: an ecological study", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20048652", + "rel_abs": "BackgroundThe reasons for the large differences between countries in the sizes of their SARS CoV-2 epidemics is unknown. Individual level studies have found that the use of face masks was protective for the acquisition and transmission of a range of respiratory viruses including SARS CoV-1. We hypothesized that population level usage of face masks may be negatively associated SARS CoV-2 spread.\n\nMethodsAt a country level, linear regression was used to assess the association between COVID-19 diagnoses per inhabitant and the national promotion of face masks in public (coded as a binary variable), controlling for the age of the COVID-19 epidemic and testing intensity.\n\nResultsEight of the 49 countries with available data advocated wearing face masks in public - China, Czechia, Hong Kong, Japan, Singapore, South Korea, Thailand and Malaysia. In multivariate analysis face mask use was negatively associated with number of COVID-19 cases/inhabitant (coef. -326, 95% CI -601- -51, P=0.021). Testing intensity was positively associated with COVID-19 cases (coef. 0.07, 95% CI 0.05-0.08, P<0.001).\n\nConclusionWhilst these results are susceptible to residual confounding, they do provide ecological level support to the individual level studies that found face mask usage to reduce the transmission and acquisition of respiratory viral infections.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Chris Kenyon", + "author_inst": "Institute of Tropical Medicine, Antwerp" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.30.20048165", "rel_title": "Association of BCG vaccination policy with prevalence and mortality of COVID-19", @@ -1570031,41 +1570463,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.01.20049528", - "rel_title": "Facemasks and similar barriers to prevent respiratory illness such asCOVID-19: A rapid systematic review", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20049528", - "rel_abs": "The current pandemic of COVID-19 has lead to conflicting opinions on whether wearing facemasks outside of health care facilities protects against the infection. To better understand the value of wearing facemasks we undertook a rapid systematic review of existing scientific evidence about development of respiratory illness, linked to use of facemasks in community settings.\n\nMethodsWe included all study designs. There were 31 eligible studies (including 12 RCTs). Narrative synthesis and random-effects meta-analysis of attack rates for primary and secondary prevention in 28 studies were performed. Results were reported by design, setting and type of face barrier in primary prevention, and by who wore the facemask (index patient or well contacts) in secondary prevention trials. The preferred outcome was influenza-like illness (ILI) but similar outcomes were pooled with ILI when ILI was unavailable. GRADE quality assessment was based on RCTs with support from observational studies.\n\nResultsWhere specific information was available, most studies reported about use of medical grade (surgical paper masks). In 3 RCTs, wearing a facemask may very slightly reduce the odds of developing ILI/respiratory symptoms, by around 6% (OR 0.94, 95% CI 0.75 to 1.19, I 29%, low-certainty evidence). Greater effectiveness was suggested by observational studies. When both house-mates and an infected household member wore facemasks the odds of further household members becoming ill may be modestly reduced by around 19% (OR 0.81, 95%CI 0.48 to 1.37, I 45%, 5 RCTs, low certainty evidence). The protective effect was very small if only the well person (OR 0.93, 95% CI 0.68 to 1.28, I 11%, 2 RCTs, low uncertainty evidence) or the infected person wore the facemask (very low certainty evidence).\n\nDiscussionBased on the RCTs we would conclude that wearing facemasks can be very slightly protective against primary infection from casual community contact, and modestly protective against household infections when both infected and uninfected members wear facemasks. However, the RCTs often suffered from poor compliance and controls using facemasks. Across observational studies the evidence in favour of wearing facemasks was stronger. We expect RCTs to under-estimate the protective effect and observational studies to exaggerate it. The evidence is not sufficiently strong to support widespread use of facemasks as a protective measure against COVID-19. However, there is enough evidence to support the use of facemasks for short periods of time by particularly vulnerable individuals when in transient higher risk situations. Further high quality trials are needed to assess when wearing a facemask in the community is most likely to be protective.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Julii Suzanne Brainard", - "author_inst": "Norwich Medical School, University of East Anglia" - }, - { - "author_name": "Natalia Jones", - "author_inst": "School of Environmental Sciences, University of East Anglia" - }, - { - "author_name": "Iain Lake", - "author_inst": "School of Environmental Science, University of East Anglia" - }, - { - "author_name": "Lee Hooper", - "author_inst": "Norwich Medical School, University of East Anglia" - }, - { - "author_name": "Paul Hunter", - "author_inst": "Norwich Medical School, University of East Anglia" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.02.20049189", "rel_title": "Optimal COVID-19 epidemic control until vaccine deployment", @@ -1570229,6 +1570626,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.31.20049387", + "rel_title": "The impacts of diagnostic capability and prevention measures on transmission dynamics of COVID-19 in Wuhan", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20049387", + "rel_abs": "BackgroundAlthough by late February 2020 the COVID-19 epidemic was effectively controlled in Wuhan, China, the virus has since spread around the world and been declared a pandemic on March 11. Estimating the effects of interventions, such as transportation restrictions and quarantine measures, on the early COVID-19 transmission dynamics in Wuhan is critical for guiding future virus containment strategies. Since the exact number of COVID-19 infected cases is unknown, the number of documented cases was used by many disease transmission models to infer epidemiological parameters. However, this means that it would not be possible to adequately estimate epidemiological parameters and the effects of intervention measures, because the percentage of all infected cases that were documented changed during the first 2 months of the epidemic as a consequence of a gradually increasing diagnostic capability.\n\nMethodsTo overcome the limitations, we constructed a stochastic susceptible-exposed-infected-quarantined-recovered (SEIQR) model, accounting for intervention measures and temporal changes in the proportion of new documented infections out of total new infections, to characterize the transmission dynamics of COVID-19 in Wuhan across different stages of the outbreak. Pre-symptomatic transmission was taken into account in our model, and all epidemiological parameters were estimated using Particle Markov-chain Monte Carlo (PMCMC) method.\n\nResultsOur model captured the local Wuhan epidemic pattern as a two-peak transmission dynamics, with one peak on February 4 and the other on February 12, 2020. The impact of intervention measures determined the timing of the first peak, leading to an 86% drop in the Re from 3.23 (95% CI, 2.22 to 4.20) to 0.45 (95% CI, 0.20 to 0.69). An improved diagnostic capability led to the second peak and a higher proportion of documented infections. Our estimated proportion of new documented infections out of the total new infections increased from 11% (95% CI 1% - 43%) to 28% (95% CI 4% - 62%) after January 26 when more detection kits were released. After the introduction of a new diagnostic criterion (case definition) on February 12, a higher proportion of daily infected cases were documented (49% (95% CI 7% - 79%)).", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jingbo LIANG", + "author_inst": "Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Hsiang-Yu Yuan", + "author_inst": "Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Lindsey Wu", + "author_inst": "Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, United Kingdom" + }, + { + "author_name": "Dirk Udo Pfeiffer", + "author_inst": "Centre for Applied One Health Research and Policy Advice, City University of Hong Kong, Hong Kong, China" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.31.20049452", "rel_title": "A Covid-19 case mortality rate without time delay systematics", @@ -1571089,45 +1571517,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.02.20050781", - "rel_title": "Synchronized travel restrictions across cities can be effective in COVID-19 control", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20050781", - "rel_abs": "The COVID-19 outbreak is under control in China. Mobility interventions, including both the Wuhan lockdown and travel restrictions in other cities, have been undertaken in China to mitigate the epidemic. However, the impact of mobility restrictions in cites outside Wuhan has not been systematically analyzed. Here we ascertain the relationships between all mobility patterns and the epidemic trajectory in Chinese cities outside Hubei Province, and we estimate the impact of local travel restrictions. We estimate local inter-city travel bans averted 22.4% (95% PI: 16.8-27.9%) more infections in the two weeks after the Wuhan lockdown, while local intra-city travel prevented 32.5% (95% PI: 18.9-46.1%) more infections in the third and fourth weeks. More synchronized implementation of mobility interventions would further decrease the number of confirmed cases in the first two weeks by 15.7% (95% PI:15.4-16.0%). This study shows synchronized travel restrictions across cities can be effective in COVID-19 control.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Haiyan Liu", - "author_inst": "wuhan university" - }, - { - "author_name": "Xuemei Bai", - "author_inst": "Australian National University" - }, - { - "author_name": "Huanfeng Shen", - "author_inst": "Wuhan University" - }, - { - "author_name": "Xiaoping Pang", - "author_inst": "Wuhan University" - }, - { - "author_name": "Zeyu Liang", - "author_inst": "Wuhan University" - }, - { - "author_name": "Yue Liu", - "author_inst": "Wuhan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.01.20049957", "rel_title": "Pre-outbreak determinants of perceived risks of corona infection and preventive measures taken. A prospective population-based study", @@ -1571323,6 +1571712,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.04.02.20050773", + "rel_title": "Exponential phase of covid19 expansion is not driven by climate at global scale", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20050773", + "rel_abs": "The pandemic state of COVID-19 caused by the SARS CoV-2 put the world in quarantine, led to hundreds of thousands of deaths and is causing an unprecedented economic crisis. However, COVID-19 is spreading in different rates at different countries. Here, we tested the effect of three classes of predictors, i.e., socioeconomic, climatic and transport, on the rate of daily increase of COVID-19. We found that global connections, represented by countries importance in the global air transportation network, is the main explanation for the growth rate of COVID-19 in different countries. Climate, geographic distance and socioeconomics had a milder effect in this big picture analysis. Geographic distance and climate were significant barriers in the past but were surpassed by the human engine that allowed us to colonize most of our planet land surface. Our results indicate that the current claims that the growth rate of COVID-19 may be lower in warmer and humid tropical countries should be taken very carefully, at risk to disturb well-established and effective policy of social isolation that may help to avoid higher mortality rates due to the collapse of national health systems.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Marco Tulio Pacheco Coelho", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Joao Fabricio Mota Rodrigues", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Anderson Matos Medina", + "author_inst": "Universidade Federal da Bahia" + }, + { + "author_name": "Paulo Scalco", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Levi Carina Terribile", + "author_inst": "Universidade Federal de Jatai" + }, + { + "author_name": "Bruno Vilela", + "author_inst": "Universidade Federal da Bahia" + }, + { + "author_name": "Jose Alexandre Felizola Diniz-Filho", + "author_inst": "Universidade Federal de Goias" + }, + { + "author_name": "Ricardo Dobrovolski", + "author_inst": "Universidade Federal da Bahia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.02.20050922", "rel_title": "Inferring COVID-19 spreading rates and potential change points for case number forecasts", @@ -1572367,25 +1572803,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.04.03.023887", - "rel_title": "Topological Analysis of SARS CoV-2 Main Protease", - "rel_date": "2020-04-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.03.023887", - "rel_abs": "There is an urgent necessity of effective medication against SARS CoV-2, which is producing the COVID-19 pandemic across the world. Its main protease (Mpro) represents an attractive pharmacological target due to its involvement in essential viral functions. The crystal structure of free Mpro shows a large structural resemblance with the main protease of SARS CoV (nowadays known as SARS CoV-1). Here we report that as average SARS CoV-2 Mpro is 1900% more sensitive than SARS CoV-1 Mpro in transmitting tiny structural changes across the whole protein through long-range interactions. The largest sensitivity of Mpro to structural perturbations is located exactly around the catalytic site Cys-145, and coincides with the binding site of strong inhibitors. These findings, based on a simplified representation of the protein as a residue network, may help in designing potent inhibitors of SARS CoV-2 Mpro.\n\nThe main protease of the new coronavirus SARS CoV-2 represents one of the most important targets for the antiviral pharmacological actions againsts COVID-19. This enzyme is essential for the virus due to its proteolytic processing of polyproteins. Here we discover that the main protease of SARS CoV-2 is topologically very similar to that of the SARS CoV-1. This is not surprising taking into account that both proteases differ only in 12 amino acids. However, we remarkable found a topological property of SARS CoV-2 that has increased in more than 1900% repect to its SARS CoV-1 analogue. This property reflects the capacity of the new protease of transmitting perturbations across its domains using long-range interactions. Also remarkable is the fact that the amino acids displaying such increased sensitivity to perturbations are around the binding site of the new protease, and close to its catalytic site. We also show that this sensititivy to perturbations is related to the effects of powerful protease inhibitors. In fact, the strongest inhibitors of the SARS CoV-2 main protease are those that produce the least change of this capacity of transmitting perturbations across the protein. We think that these findings may help in the design of new potent anti-SARS CoV-2 inhibitors.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ernesto Estrada", - "author_inst": "Institute of Mathematics and Applications, University of Zaragoza" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.04.03.022939", "rel_title": "Triphosphates of the Two Components in DESCOVY and TRUVADA are Inhibitors of the SARS-CoV-2 Polymerase", @@ -1572589,6 +1573006,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.02.022384", + "rel_title": "One-step RNA extraction for RT-qPCR detection of 2019-nCoV", + "rel_date": "2020-04-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.02.022384", + "rel_abs": "The global outbreak of coronavirus disease 2019 (COVID-19) has placed an unprecedented burden on healthcare systems as the virus spread from the initial 27 reported cases in the city of Wuhan, China to a global pandemic in under three month[1]. Resources essential to monitoring virus transmission have been challenged with a demand for expanded surveillance. The CDC 2019-nCoV Real-Time Diagnostic Panel uses a real-time reverse transcription polymerase chain reaction (RT-PCR) consisting of two TaqMan probe and primer sets specific for the 2019-nCoV N gene, which codes for the nucleocapsid structural protein that encapsulates viral RNA, for the qualitative detection of 2019-nCoV viral RNA in respiratory samples. To isolate RNA from respiratory samples, the CDC lists RNA extraction kits from four manufacturers. In anticipation of a limited supply chain of RNA extraction kits and the need for test scalability, we sought to identify alternative RNA extraction methods. Here we show that direct lysis of respiratory samples can be used in place of RNA extraction kits to run the CDC 2019-nCoV Real-Time Diagnostic assay with the additional benefits of higher throughput, lower cost, faster turnaround and possibly higher sensitivity and improved safety.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Monica Sentmanat", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Evguenia Kouranova", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Xiaoxia Cui", + "author_inst": "Washington University in St. Louis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.04.02.019075", "rel_title": "Rapid community-driven development of a SARS-CoV-2 tissue simulator", @@ -1573849,41 +1574293,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.04.01.20050492", - "rel_title": "Evaluation of the Anticipated Burden of COVID-19 on Hospital-Based Healthcare Services Across the United States", - "rel_date": "2020-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20050492", - "rel_abs": "BackgroundCoronavirus disease-19 (COVID-19) is a global pandemic, with the potential to infect nearly 60% of the population. The anticipated spread of the virus requires an urgent appraisal of the capacity of US healthcare services and the identification of states most vulnerable to exceeding their capacity\n\nMethodsIn the American Hospital Association survey for 2018, a database of US community hospitals, we identified total inpatient beds, adult intensive care unit (ICU) beds, and airborne isolation rooms across all hospitals in each state of continental US. The burden of COVID-19 hospitalizations was estimated based on a median hospitalization duration of 12 days and was evaluated for a 30-day reporting period.\n\nResultsAt 5155 US community hospitals across 48 states in the contiguous US and Washington DC, there were a total of 788,032 inpatient beds, 68,280 adult ICU beds, and 44,222 isolation rooms. The median daily bed occupancy was 62.8% (IQR 58.1%, 66.6%) across states. Nationally, for every 10,000 individuals, there are 24.2 inpatient beds, 2.8 adult ICU beds, and 1.4 isolation beds. There is a 3-fold variation in the number of inpatient beds available across the US, ranging from 16.4 per 10,000 in Oregon to 47 per 10,000 in South Dakota. There was also a similar 3-fold variation in available or non-occupied beds, ranging from 4.7 per 10,000 in Connecticut through 18.3 per 10,000 in North Dakota. The availability of ICU beds is low nationally, ranging from 1.4 per 10,000 in Nevada to 4.7 per 10000 in Washington DC.\n\nHospitalizations for COVID-19 in a median 0.2% (IQR 0.2 %, 0.3%) of state population, or 1.4% of states older adults (1.0%, 1.9%) will require all non-occupied beds. Further, a median 0.6% (0.5%, 0.8%) of state population, or 3.9% (3.1%, 4.6%) of older individuals would require 100% of inpatient beds.\n\nConclusionThe COVID-19 pandemic is likely to overwhelm the limited number of inpatient and ICU beds for the US population. Hospitals in half of US states would exceed capacity if less than 0.2% of the state population requires hospitalization in any given month.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Rohan Khera", - "author_inst": "UT Southwestern Medical Center" - }, - { - "author_name": "Snigdha Jain", - "author_inst": "UT Southwestern Medical Center" - }, - { - "author_name": "Zhenqiu Lin", - "author_inst": "Yale University" - }, - { - "author_name": "Joseph S. Ross", - "author_inst": "Yale University" - }, - { - "author_name": "Harlan Krumholz", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.01.20049833", "rel_title": "Clinical Manifestations of Children with COVID-19: a Systematic Review", @@ -1574075,6 +1574484,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.01.20049668", + "rel_title": "Spatial variability in the risk of death from COVID-19 in Italy, 2020", + "rel_date": "2020-04-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20049668", + "rel_abs": "ObjectivesItaly has been disproportionately affected by the COVID-19 pandemic, becoming the nation with the third highest death toll in the world as of May 10th, 2020. We analyzed the severity of COVID-19 pandemic across 20 Italian regions.\n\nMethodWe manually retrieved the daily cumulative numbers of laboratory-confirmed cases and deaths attributed to COVID-19 across 20 Italian regions. For each region, we estimated the crude case fatality ratio and time-delay adjusted case fatality ratio (aCFR). We then assessed the association between aCFR and sociodemographic, health care and transmission factors using multivariate regression analysis.\n\nResultsThe overall aCFR in Italy was estimated at 17.4%. Lombardia exhibited the highest aCFR (24.7%) followed by Marche (19.3%), Emilia Romagna (17.7%) and Liguria (17.6%). Our aCFR estimate was greater than 10% for 12 regions. Our aCFR estimates were statistically associated with population density and cumulative morbidity rate in a multivariate analysis.\n\nConclusionOur aCFR estimates for overall Italy and for 7 out of 20 regions exceeded those reported for the most affected region in China. Our findings highlight the importance of social distancing to suppress incidence and reduce the death risk by preventing saturating the health care system.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kenji Mizumoto", + "author_inst": "Kyoto University" + }, + { + "author_name": "Sushma Dahal", + "author_inst": "Georgia State University School of Public Health" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.31.20049007", "rel_title": "Harmonizing heterogeneous endpoints in COVID-19 trials without loss of information - an essential step to facilitate decision making", @@ -1575015,29 +1575451,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.31.20048942", - "rel_title": "A Gaussian model for the time development of the Sars-Cov-2 corona pandemic disease. Predictions for Germany made on March 30, 2020", - "rel_date": "2020-04-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20048942", - "rel_abs": "For Germany it is predicted that the first wave of the corona pandemic disease reaches its maximum of new infections on April 11th, 2020 [Formula] days with 90 percent confidence. With a delay of about 7 days the maximum demand on breathing machines in hospitals occurs on April 18th, 2020 [Formula] days. The first pandemic wave ends in Germany end of May 2020. The predictions are based on the assumption of a Gaussian time evolution well justified by the central limit theorem of statistics. The width and the maximum time and thus the duration of this Gaussian distribution are determined from a statistical{chi} 2-fit to the observed doubling times before March 28, 2020.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Reinhard Schlickeiser", - "author_inst": "Ruhr-University-Bochum, institut for theoretical physics" - }, - { - "author_name": "Frank Schlickeiser", - "author_inst": "Private Person" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.31.20048835", "rel_title": "Importance of suppression and mitigation measures in managing COVID-19 outbreaks", @@ -1575165,6 +1575578,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.03.31.20048439", + "rel_title": "Research on the Influence of Information Diffusion on the Transmission of the Novel Coronavirus (COVID-19)", + "rel_date": "2020-04-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20048439", + "rel_abs": "With the rapid development of mobile Internet in China, the information of the epidemic is full-time and holographic, and the role of information diffusion in epidemic control is increasingly prominent. At the same time, the publicity of all kinds of big data also provides the possibility to explore the impact of media information diffusion on disease transmission. This paper explores the mechanism of the influence of information diffusion on the spread of the novel coronavirus, develops a model of the interaction between information diffusion and disease transmission based on the SIR model, and empirically tests the role and mechanism of information diffusion in the spread of COCID-19 by using econometric method. The result shows that there was a significant negative correlation between the information diffusion and the spread of the novel coronavirus; The result of robust test shows that the spread of both epidemic information and protection information hindered the further spread of the epidemic.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lin Shanlang", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Ma Chao", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Lin Ruofei", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Huang Junpei", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Xu Ruohan", + "author_inst": "School of Economics and Management, Tongji University, China" + }, + { + "author_name": "Yuan Aini", + "author_inst": "School of Economics and Management, Tongji University, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.03.31.20047142", "rel_title": "Clinical features and outcomes of 2019 novel coronavirus-infected patients with high plasma BNP levels", @@ -1576145,201 +1576597,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.30.20048108", - "rel_title": "Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR assays", - "rel_date": "2020-04-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20048108", - "rel_abs": "The recent spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exemplifies the critical need for accurate and rapid diagnostic assays to prompt clinical and public health interventions. Currently, several quantitative reverse-transcription polymerase chain reaction (qRT-PCR) assays are being used by clinical, research, and public health laboratories. However, it is currently unclear if results from different tests are comparable. Our goal was to evaluate the primer-probe sets used in four common diagnostic assays available on the World Health Organization (WHO) website. To facilitate this effort, we generated RNA transcripts to be used as assay standards and distributed them to other laboratories for internal validation. We then used (1) RNA transcript standards, (2) full-length SARS-CoV-2 RNA, (3) pre-COVID-19 nasopharyngeal swabs, and (4) clinical samples from COVID-19 patients to determine analytical efficiency and sensitivity of the qRT-PCR primer-probe sets. We show that all primer-probe sets can be used to detect SARS-CoV-2 at 500 virus copies per reaction, except for the RdRp-SARSr (Charite) confirmatory primer-probe set which has low sensitivity. Our findings characterize the limitations of currently used primer-probe sets and can assist other laboratories in selecting appropriate assays for the detection of SARS-CoV-2.", - "rel_num_authors": 45, - "rel_authors": [ - { - "author_name": "Chantal B.F. Vogels", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Anderson F. Brito", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Anne Louise Wyllie", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Joseph R Fauver", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Isabel M. Ott", - "author_inst": "Yale University" - }, - { - "author_name": "Chaney C. Kalinich", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Mary E. Petrone", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Arnau Casanovas-Massana", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "M. Catherine Muenker", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Adam J. Moore", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Jonathan Klein", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Peiwen Lu", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Alice Lu-Culligan", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Xiaodong Jiang", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Daniel J. Kim", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Eriko Kudo", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Tianyang Mao", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Miyu Moriyama", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Ji Eun Oh", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Annsea Park", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Julio Silva", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Eric Song", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Takehiro Takehashi", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Manabu Taura", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Maria Tokuyama", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Arvind Venkataraman", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Orr-El Weizman", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Patrick Wong", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Yexin Yang", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Nagarjuna R. Cheemarla", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Elizabeth White", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Sarah Lapidus", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Rebecca Earnest", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Bertie Geng", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Pavithra Vijayakumar", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Camila Odio", - "author_inst": "Yale-New Haven Health" - }, - { - "author_name": "John Fournier", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Santos Bermejo", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Shelli Farhadian", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Charles Dela Cruz", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Akiko Iwasaki", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Albert I. Ko", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Marie-Louise Landry", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Ellen F. Foxman", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Nathan D. Grubaugh", - "author_inst": "Yale School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.29.20046789", "rel_title": "Perception of emergent epidemic of COVID-2019 / SARS CoV-2 on the Polish Internet", @@ -1576471,6 +1576728,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.30.20047589", + "rel_title": "The Institutional and Cultural Context of Cross-National Variation in COVID-19 Outbreaks", + "rel_date": "2020-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20047589", + "rel_abs": "BackgroundThe COVID-19 pandemic poses an unprecedented and cascading threat to the health and economic prosperity of the worlds population.\n\nObjectivesTo understand whether the institutional and cultural context influences the COVID-19 outbreak.\n\nMethodsAt the ecological level, regression coefficients are examined to figure out contextual variables influencing the pandemics exponential growth rate across 96 countries.\n\nResultsWhile a strong institutional context is negatively associated with the outbreak (B = -0.55 ... -0.64, p < 0.001), the pandemics growth rate is steeper in countries with a quality education system (B = 0.33, p < 0.001). Countries with an older population are more affected (B = 0.46, p < 0.001). Societies with individualistic (rather than collectivistic) values experience a flatter rate of pathogen proliferation (B = -0.31, p < 0.001), similarly for higher levels of power distance (B = -0.32, p < 0.001). Hedonistic values, that is seeking indulgence and not enduring restraints, are positively related to the outbreak (B = 0.23, p = 0.001).\n\nConclusionsThe results emphasize the need for public policy makers to pay close attention to the institutional and cultural context in their respective countries when instigating measures aimed at constricting the pandemics growth.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Wolfgang Messner", + "author_inst": "University of South Carolina" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.30.20047894", "rel_title": "Forecasting the CoViD19 Diffusion in Italy and the Related Occupancy of Intensive Care Units", @@ -1577319,77 +1577595,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.30.20043513", - "rel_title": "Ad hoc laboratory-based surveillance of SARS-CoV-2 by real-time RT-PCR using minipools of RNA prepared from routine respiratory samples", - "rel_date": "2020-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20043513", - "rel_abs": "We report a laboratory-based surveillance for SARS-CoV-2 using minipools of respiratory samples submitted for routine diagnostics. We tested a total of 70 minipools resembling 700 samples shortly before the upsurge of cases in Germany. We identified one SARS-CoV-2 positive patient. Our approach proved its concept, is easily adaptable and resource-saving.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Anna Maria Eis-Huebinger", - "author_inst": "Institute of Virology, University of Bonn, Faculty of Medicine, Bonn, Germany" - }, - { - "author_name": "Mario Hoenemann", - "author_inst": "Institute of Virology, University of Leipzig, Leipzig, Germany" - }, - { - "author_name": "Juergen J. Wenzel", - "author_inst": "Institute of Clinical Microbiology and Hygiene, Regensburg University Hospital, Regensburg, Germany" - }, - { - "author_name": "Annemarie Berger", - "author_inst": "Institute of Medical Virology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany" - }, - { - "author_name": "Marek Widera", - "author_inst": "Institute of Medical Virology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany" - }, - { - "author_name": "Barbara Schmidt", - "author_inst": "Institute of Clinical Microbiology and Hygiene, Regensburg University Hospital, Regensburg, Germany" - }, - { - "author_name": "Souhaib Aldabbagh", - "author_inst": "Institute of Virology, University of Bonn, Faculty of Medicine, Bonn, Germany" - }, - { - "author_name": "Benjamin Marx", - "author_inst": "Institute of Virology, University of Bonn, Faculty of Medicine, Bonn, Germany" - }, - { - "author_name": "Hendrik Streeck", - "author_inst": "Institute of Virology, University of Bonn, Faculty of Medicine, Bonn, Germany" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Institute of Medical Virology, University Hospital, Goethe University Frankfurt am Main, Frankfurt, Germany" - }, - { - "author_name": "Uwe G. Liebert", - "author_inst": "Institute of Virology, University of Leipzig, Leipzig, Germany" - }, - { - "author_name": "Daniela Huzly", - "author_inst": "Institute of Virology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Hartmut Hengel", - "author_inst": "Institute of Virology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany" - }, - { - "author_name": "Marcus Panning", - "author_inst": "Institute of Virology, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.28.20046235", "rel_title": "Current State and Predicting Future Scenario of Highly Infected Nations for COVID-19 Pandemic", @@ -1577541,6 +1577746,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.29.20043547", + "rel_title": "Health Communication Through News Media During the Early Stage of the COVID-19 Outbreak in China: A Digital Topic Modeling Approach", + "rel_date": "2020-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20043547", + "rel_abs": "BackgroundIn December 2019, some COVID-19 cases were first reported and soon the disease broke out. As this dreadful disease spreads rapidly, the mass media has been active in community education on COVID-19 by delivering health information about this novel coronavirus.\n\nMethodsWe adopted the Huike database to extract news articles about coronavirus from major press media, between January 1st, 2020, to February 20th, 2020. The data were sorted and analyzed by Python software and Python package Jieba. We sought a suitable topic number using the coherence number. We operated Latent Dirichlet Allocation (LDA) topic modeling with the suitable topic number and generated corresponding keywords and topic names. We divided these topics into different themes by plotting them into two-dimensional plane via multidimensional scaling.\n\nFindingsAfter removing duplicates, 7791 relevant news reports were identified. We listed the number of articles published per day. According to the coherence value, we chose 20 as our number of topics and obtained their names and keywords. These topics were categorized into nine primary themes based on the topic visualization figure. The top three popular themes were prevention and control procedures, medical treatment and research, global/local social/economic influences, accounting for 32{middle dot}6%, 16{middle dot}6%, 11{middle dot}8% of the collected reports respectively.\n\nInterpretationThe Chinese mass media news reports lag behind the COVID-19 outbreak development. The major themes accounted for around half the content and tended to focus on the larger society than on individuals. The COVID-19 crisis has become a global issue, and society has also become concerned about donation and support as well as mental health. We recommend that future work should address the mass medias actual impact on readers during the COVID-19 crisis through sentiment analysis of news data.\n\nFundingNational Social Science Foundation of China (18CXW021)\n\nEvidence before this studyThe novel coronavirus related news reports have engaged public attention in China during the COVID-19 crisis. Topic modeling of these news articles can produce useful information about the significance of mass media for early health communication. We searched the Huike database, the most professional Chinese media content database, using the search term \"coronavirus\" for related news articles published from January 1st, 2020, to February 20th, 2020. We found that these articles can be classified into different themes according to their emphasis, however, we found no other studies apply topic modeling method to study them.\n\nAdded value of this studyTo our knowledge, this study is the first to investigate the patterns of health communications through media and the role the media have played and are still playing in the light of the current COVID-19 crisis in China with topic modeling method. We compared the number of articles each day with the outbreak development and identified theres a delay in reporting COVID-19 outbreak progression for Chinese mass media. We identify nine main themes for 7791 collected news reports and detail their emphasis respectively.\n\nImplications of all the available evidenceOur results show that the mass media news reports play a significant role in health communication during the COVID-19 crisis, government can strengthen the report dynamics and enlarge the news coverage next time another disease strikes. Sentiment analysis of news data are needed to assess the actual effect of the news reports.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Qian Liu", + "author_inst": "School of Journalism and Communication, National Media Experimental Teaching Demonstration Center, Jinan University, Guangzhou, China; Department of Communicati" + }, + { + "author_name": "Zequan Zheng", + "author_inst": "International School, Jinan University, China; Faculty of Medicine, Jinan University, China" + }, + { + "author_name": "Jiabin Zheng", + "author_inst": "International School, Jinan University, China; Faculty of Medicine, Jinan University, China" + }, + { + "author_name": "Qiuyi Chen", + "author_inst": "School of Journalism and Communication, National Media Experimental Teaching Demonstration Center, Jinan University, Guangzhou, China" + }, + { + "author_name": "Guan Liu", + "author_inst": "Faculty of Computer Centre, Jinan University, China" + }, + { + "author_name": "Sihan Chen", + "author_inst": "International School, Jinan University, China" + }, + { + "author_name": "Bojia Chu", + "author_inst": "International School, Jinan University, China" + }, + { + "author_name": "Hongyu Zhu", + "author_inst": "International School, Jinan University, China" + }, + { + "author_name": "Babatunde Akinwunmi", + "author_inst": "Pulmonary and Critical Care Medicine Unit, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Harvard University, Boston, Massachuset" + }, + { + "author_name": "Jian Huang", + "author_inst": "MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, St Mary's Campus, Imperial College London, Norfolk" + }, + { + "author_name": "Casper J. P. Zhang", + "author_inst": "School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China" + }, + { + "author_name": "Wai-kit Ming", + "author_inst": "Department of Public Health and Preventive Medicine, School of Medicine, Jinan University, Guangzhou, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.03.29.20046565", "rel_title": "Eco-epidemiological assessment of the COVID-19 epidemic in China, January-February 2020", @@ -1578676,29 +1578944,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.03.30.015891", - "rel_title": "Biophysical characterization of the SARS-CoV2 spike protein binding with the ACE2 receptor explains increased COVID-19 pathogenesis", - "rel_date": "2020-03-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.30.015891", - "rel_abs": "SARS-CoV-2 is a novel highly virulent pathogen which gains entry to human cells by binding with the cell surface receptor - angiotensin converting enzyme (ACE2). We computationally contrasted the binding interactions between human ACE2 and coronavirus spike protein receptor binding domain (RBD) of the 2002 epidemic-causing SARS-CoV-1, SARS-CoV-2, and bat coronavirus RaTG13 using the Rosetta energy function. We find that the RBD of the spike protein of SARS-CoV-2 is highly optimized to achieve very strong binding with human ACE2 (hACE2) which is consistent with its enhanced infectivity. SARS-CoV-2 forms the most stable complex with hACE2 compared to SARS-CoV-1 (23% less stable) or RaTG13 (11% less stable) while occupying the greatest number of residues in the ATR1 binding site. Notably, the SARS-CoV-2 RBD out-competes the angiotensin 2 receptor type I (ATR1) which is the native binding partner of ACE2 by 35% in terms of the calculated binding affinity. Strong binding is mediated through strong electrostatic attachments with every fourth residue on the N-terminus alpha-helix (starting from Ser19 to Asn53) as the turn of the helix makes these residues solvent accessible. By contrasting the spike protein SARS-CoV-2 Rosetta binding energy with ACE2 of different livestock and pet species we find strongest binding with bat ACE2 followed by human, feline, equine, canine and finally chicken. This is consistent with the hypothesis that bats are the viral origin and reservoir species. These results offer a computational explanation for the increased infectivity of SARS-CoV-2 and allude to therapeutic modalities by identifying and rank-ordering the ACE2 residues involved in binding with the virus.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ratul Chowdhury", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Costas D Maranas", - "author_inst": "The Pennsylvania State University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.03.29.014407", "rel_title": "Combined prophylactic and therapeutic use maximizes hydroxychloroquine anti-SARS-CoV-2 effects in vitro", @@ -1579062,6 +1579307,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.27.20043299", + "rel_title": "Failed detection of the full-length genome of SARS-CoV-2 by ultra-deep sequencing from the recovered and discharged patients retested viral PCR positive", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20043299", + "rel_abs": "Over 10 percent of recovered and discharged patients retested positive for SARS-CoV-2, raising a public health concern whether they could be potential origins of infection. In this study, we found that detectable viral genome in discharged patients might only mean the presence of viral fragments, and could hardly form an infection origin for its extremely low concentration.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Fengyu Hu", + "author_inst": "Guangzhou Eighth People Hospital" + }, + { + "author_name": "Fengjuan Chen", + "author_inst": "Guangzhou Eighth People Hospital" + }, + { + "author_name": "Yaping Wang", + "author_inst": "Guangzhou Eighth People Hospital" + }, + { + "author_name": "Teng Xu", + "author_inst": "Vision Medicals" + }, + { + "author_name": "Xiaoping Tang", + "author_inst": "Guangzhou Eighth People Hospital" + }, + { + "author_name": "Feng Li", + "author_inst": "Guangzhou Eighth People Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.25.20043505", "rel_title": "Machine Learning Approach for Confirmation of COVID-19 Cases: Positive, Negative, Death and Release", @@ -1580214,45 +1580498,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.27.20045500", - "rel_title": "COVID-19: Projecting the impact in Rohingya refugee camps and beyond", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045500", - "rel_abs": "BackgroundCOVID-19 could have even more dire consequences in refugees camps than in general populations. Bangladesh has confirmed COVID-19 cases and hosts almost 1 million Rohingya refugees from Myanmar with 600,000 concentrated in Kutupalong-Balukhali Expansion Site (age mean: 21 years, sd: 18 years, 52% female). Projections of the potential COVID-19 burden, epidemic speed, and healthcare needs in such settings are critical for preparedness planning.\n\nMethods and FindingsTo explore the potential impact of the introduction of SARS-CoV-2 in Kutupalong-Balukhali Expansion Site, we used a stochastic SEIR transmission model with parameters derived from emerging literature and age as the primary determinant of infection severity. We considered three scenarios with different assumptions about the transmission potential of SARS-CoV-2. From the simulated infections, we estimated hospitalizations, deaths, and healthcare needs expected, age-adjusted for the Kutupalong-Balukhali Expansion Site age distribution.\n\nOur findings suggest that a large-scale outbreak is likely after a single introduction of the virus into the camp with 61-92% of simulations leading to at least 1,000 people infected across scenarios. On average, in the first 30 days of the outbreak, we expect 18 (95% prediction interval (PI), 2-65), 54 (95% PI, 3-223), and 370 (95% PI, 4-1,850) people infected in the low, moderate, and high transmission scenarios, respectively. These reach 421,500 (95% PI, 376,300-463,500), 546,800 (95% PI, 499,300-567,000) and 589,800 (95% PI, 578,800-595,600) people infected in 12 months, respectively. Hospitalization needs exceeded the existing hospitalization capacity of 340 beds after 55-136 days between the low and high transmission scenarios. We estimate 2,040 (95% PI, 1,660-2,500), 2,650 (95% PI, 2,030-3,380), and 2,880 (95% PI, 2,090-3,830) deaths in the low, moderate and high transmission scenarios, respectively.\n\nDue to limited data at the time of analyses, we assumed that age was the primary determinant of infection severity and hospitalization. We expect that comorbidities and limited hospitalization and intensive care capacity may increase this risk, thus we may be underestimating the potential burden.\n\nConclusionsOur findings suggest that a COVID-19 epidemic in a refugee settlement may have profound consequences, requiring large increases in healthcare capacity and infrastructure that may exceed what is currently feasible in these settings. Detailed and realistic planning for the worst-case in Kutupalong-Balukhali and all refugee camps worldwide must begin now. Plans should consider novel and radical strategies to reduce infectious contacts and fill health worker gaps while recognizing that refugees may not have access to national health systems.\n\nAUTHORS SUMMARYO_LSTWhy was this study done?C_LSTO_LIForcibly displaced populations, especially those who reside in settlements with high density, poor access to water and sanitation, and limited health services, are especially vulnerable to COVID-19.\nC_LIO_LIBangladesh, which has confirmed COVID-19 cases, hosts almost 900,000 Rohingya refugees from Myanmar in the Coxs Bazar district, approximately 600,000 of whom are concentrated in the Kutupalong-Balukhali Expansion Site.\nC_LIO_LIThe capacity to meet the existing health needs of this population is limited; an outbreak of COVID-19 within this population threatens to severely disrupt an already fragile situation.\nC_LIO_LIWe conducted this study to estimate the number of people infected, hospitalizations, and deaths that might occur in the Kutupalong-Balukhali Expansion Site to inform ongoing preparedness and response activities by the Bangladesh government, the United Nations agencies, and other national and international actors.\nC_LI\n\nO_LSTWhat did the researchers do and find?C_LSTO_LIUsing a dynamic model of SARS-CoV-2 transmission, we simulated how a COVID-19 outbreak could spread within the Expansion Site according to three possible transmission scenarios (high, moderate, and low).\nC_LIO_LIOur results suggest that a large-scale outbreak is very likely in this setting after a single infectious person enters the camp, with 0.5-91% of the population expected to be infected within the first three months and over 70-98% during the first year depending on the transmission scenario, should no effective interventions be put into place.\nC_LIO_LIHospitalization needs may exceed the existing hospitalization capacity of 340 beds after 55-136 days of introduction.\nC_LI\n\nO_LSTWhat do these findings mean?C_LSTO_LIA COVID-19 epidemic in a high population density refugee settlement may have profound consequences, requiring increases in healthcare capacity and infrastructure that exceed what is feasible in this setting.\nC_LIO_LIAs many of the approaches used to prevent and respond to COVID-19 in the most affected areas so far will not be practical in humanitarian settings, novel and untested strategies to protect the most vulnerable population groups should be considered, as well as innovative solutions to fill health workforce gaps.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Shaun A Truelove", - "author_inst": "Johns Hopksin Bloomberg School of Public Health" - }, - { - "author_name": "Orit Abrahim", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Chiara Altare", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Stephen A Lauer", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Andrew Azman", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Paul B Spiegel", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.27.20045328", "rel_title": "Elementary time-delay dynamics of COVID-19 disease", @@ -1580388,6 +1580633,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.27.20045252", + "rel_title": "Estimation of protection for COVID-19 in children from epidemiological information and estimate effect of policy in Japan", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045252", + "rel_abs": "BackgroundIncidence in children was much less than in adults during the COVID-19 outbreak. Sports and entertainment events were canceled (VEC) in Japan for two weeks during 26 February - 13 March. Most schools were closed (SC).\n\nObjectWe construct a susceptible-infected-recovered model using three age classes and estimate the basic reproduction number (R0) and protection level among children simultaneously. Then we simulate SC and VEC effects.\n\nMethodWe used data of patients with symptoms in Japan during 14 January to assess SC and VEC introduction. Effects of SC and VEC were incorporated into the model through change in the contact pattern or frequencies among age classes.\n\nResultsResults suggest R0 as 2.86 [95%CI of 2.73, 2.97]. The protection level was estimated as 0.4 [0.2, 0.7]. SC and VEC can reduce the total number of patients significantly, by 6-7%.\n\nDiscussion and ConclusionThe estimated R0 was similar to that found from other studies in China and Japan. We found a significant protection level among children, and by effects of SC and VEC. Introduction", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Junko Kurita", + "author_inst": "Center for Medical Sciences, Ibaraki Prefectural University of Health Sciences, Ibaraki, Japan" + }, + { + "author_name": "Yoshiyuki Sugishita", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Tamie Sugawara", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + }, + { + "author_name": "Yasushi Ohkusa", + "author_inst": "National Institute of Infectious Diseases, Tokyo, Japan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.03.27.20044958", "rel_title": "Research on the Influence of Effective Distance Between Cities on the Cross-regional Transmission of COVID-19", @@ -1581500,61 +1581776,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.24.20043075", - "rel_title": "Prevalence and Factors Associated with Depression and Anxiety of Hospitalized Patients with COVID-19", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20043075", - "rel_abs": "ObjectiveThe 2019 coronavirus disease (COVID-19) epidemic has raised international concern. Mental health is becoming an issue that cannot be ignored in our fight against it. This study aimed to explore the prevalence and factors linked to anxiety and depression in hospitalized patients with COVID-19.\n\nMethodsA total of 144 patients diagnosed with COVID-19 were included in this study. We assessed depression and anxiety symptoms using the Hospital Anxiety and Depression Scale (HADS), and social support using the Perceived Social Support Scale (PSSS) among patients at admission. Multivariate linear regression analyses were performed to identify factors associated with symptoms of anxiety and depression.\n\nResultsOf the 144 participants, 34.72% and 28.47% patients with COVID-19 had symptoms of anxiety or depression, respectively. The bivariate correlations showed that less social support was correlated with more anxious (r=-0.196, p<0.05) and depressive (r=-0.360,p<0.05) symptoms among patients with COVID-19. The multiple linear regression analysis showed that gender ({beta}=1.446, p=0.034), age ({beta}=0.074, p=0.003), oxygen saturation ({beta} =-2.140, p=0.049), and social support ({beta} =-1.545, p=0.017) were associated with anxiety for COVID-19 patients. Moreover, age ({beta}=0.084, p=0.001), family infection with SARS-CoV-2 ({beta} =1.515, p=0.027) and social support ({beta} =-2.236, p<0.001) were the factors associated with depression.\n\nConclusionHospitalized patients with COVID-19 presented features of anxiety and depression. Mental concern and appropriate intervention are essential parts of clinical care for those who are at risk.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Xiangyu Kong", - "author_inst": "Huoshenshan Hospital" - }, - { - "author_name": "Kailian Zheng", - "author_inst": "Huoshenshan Hospital" - }, - { - "author_name": "Min Tang", - "author_inst": "Huoshenshan Hospital" - }, - { - "author_name": "Fanyang Kong", - "author_inst": "Department of Gastroenterology, Shanghai Changhai Hospital, Shanghai, China" - }, - { - "author_name": "Jiahuan Zhou", - "author_inst": "Shanghai Zhangjiang Institue of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd." - }, - { - "author_name": "Le Diao", - "author_inst": "Shanghai Zhangjiang Institue of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd." - }, - { - "author_name": "Shouxin Wu", - "author_inst": "Shanghai Zhangjiang Institue of Medical Innovation, Shanghai Biotecan Pharmaceuticals Co., Ltd." - }, - { - "author_name": "Piqi Jiao", - "author_inst": "Huoshenshan Hospital" - }, - { - "author_name": "Tong Su", - "author_inst": "College of Psychology, Navy Medical University, Shanghai, China" - }, - { - "author_name": "Yuchao Dong", - "author_inst": "Huoshenshan Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.03.27.20042820", "rel_title": "Evaluating COVID-19 Public Health Messaging in Italy: Self-Reported Compliance and Growing Mental Health Concerns", @@ -1581806,6 +1582027,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.03.26.20044388", + "rel_title": "The more I fear about COVID-19, the more I wear medical masks: A survey on risk perception and medical masks uses", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044388", + "rel_abs": "The legal behaviors in using medical masks in public have been finally promulgated by the Vietnamese Government after 47 days since the WHO declared the Public Health Emergency of International Concern (PHEIC) due to the COVID-19 pandemic. From a sample of 345 Vietnamese respondents aged from 15 to 47 years, this brief note found that the risk perception of COVID-19 danger significantly increases the likelihood of wearing the medical masks. In addition, there is a weak evidence about the differences in age under the COVID-19 outbreaks. More noticeably, those who use masks before COVID-19 pandemic tend to maintain their behaviors. Our results offer the insightful into Vietnamese citizens responses in terms of using medical masks; even the uses of this method are still controversial. Our results are robust by performing Exploratory Factor Analysis for five features and further regressions.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Toan D Huynh", + "author_inst": "University of Economics HCMC" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.03.28.20046110", "rel_title": "Which Measures are Effective in Containing COVID-19?Empirical Research Based on Prevention and Control Cases in China", @@ -1582770,37 +1583010,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.29.20044461", - "rel_title": "Effects of temperature on COVID-19 transmission", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20044461", - "rel_abs": "Coronavirus disease 2019 (COVID-19) is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), it was first identified in 2019 in Wuhan, China and has resulted in the 2019-20 coronavirus pandemic. As of March 1, 2020, 79,968 patients in China and 7169 outside of China had tested positive for COVID-19 and a mortality rate of 3.6% has been observed amongst Chinese patients. Its primary mode of transmission is via respiratory droplets from coughs and sneezes. The virus can remain viable for up to three days on plastic and stainless steel or in aerosols for upto 3 hours and is relatively more stable than the known human coronaviruses. It is stable in faeces at room temperature for at least 1-2 days and can be stable in infected patients for up to 4 days. Heat at 56{degrees}C kills the SARS coronavirus at around 10000 units per 15 minutes. Thus, temperature is an important factor in survival of COVID-19 virus and this article focuses on understanding the relationship between temperature and COVID-19 transmission from the data available between January-March 2020.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "shrikant pawar", - "author_inst": "Yale University" - }, - { - "author_name": "Aditya Stanam", - "author_inst": "University of Iowa" - }, - { - "author_name": "Mamata Chaudhari", - "author_inst": "Western Kentucky University" - }, - { - "author_name": "Durga Rayudu", - "author_inst": "NTR University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.25.20043109", "rel_title": "Mitigation and herd immunity strategy for COVID-19 is likely to fail", @@ -1583132,6 +1583341,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.26.20044651", + "rel_title": "A deductive approach to modeling the spread of COVID-19", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044651", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-COV-2), previously known as 2019-nCoV, is responsible for the atypical pneumonia pandemic designated as Coronavirus Disease 2019 (COVID-19). The number of cases continues to grow exponentially reaching 492,000 people in 175 countries as of March 25, 2020. 22,169 people ([~]4.5%) infected with SARS-COV-2 virus have died. We have developed an exponential regression model using the COVID-19 case data (Jan 22 - Mar 22, 2020). Our primary model uses designated Phase 1 countries, who exceed 2500 cases on Mar 22. The model is then applied to Phase 2 countries: those that escaped the initial Phase 1 global expansion of COVID-19. With the exception of stabilizing countries (South Korea, Japan, and Iran) all Phase 1 countries are growing exponentially, as per I2500(t) = 120.4 x e0.238t, with a rate, r = 0.238 {+/-} 0.068. Excluding China, the BRICS developing nations and Australia are in Phase 2. Case data from Phase 2 countries are following the model derived from Phase 1 countries. In the absence of measures employed to flatten the curve including social distancing, quarantine, and healthcare expansion, our model projects over 274,000 cases and 12,300 deaths in the US by Mar 31. India can expect 123,000 cases by April 16. By flattening the curve to the growth rate of stabilizing countries (r = 0.044 {+/-} 0.062), the US would prevent 8,500 deaths by Mar 31, and India would prevent 5,500 deaths by April 16.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Pranav Kumar Mishra", + "author_inst": "Kasturba Medical College, Manipal; Manipal Academy of Higher Education" + }, + { + "author_name": "Shekhar Mishra", + "author_inst": "Discovery Science and Innovation Management" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.25.20043927", "rel_title": "Dangers of ACE inhibitor and ARB usage in COVID-19: evaluating the evidence", @@ -1584088,41 +1584320,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.03.27.012013", - "rel_title": "SARS-CoV-2 and ORF3a: Non-Synonymous Mutations and Polyproline Regions", - "rel_date": "2020-03-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.27.012013", - "rel_abs": "The effect of the rapid accumulation of non-synonymous mutations on the pathogenesis of SARS-CoV-2 is not yet known. To predict the impact of non-synonymous mutations and polyproline regions identified in ORF3a on the formation of B-cell epitopes and their role in evading the immune response, nucleotide and protein sequences of 537 available SARS-CoV-2 genomes were analyzed for the presence of non-synonymous mutations and polyproline regions. Mutations were correlated with changes in epitope formation. A total of 19 different non-synonymous amino acids substitutions were detected in ORF3a among 537 SARS-CoV-2 strains. G251V was the most common and identified in 9.9% (n=53) of the strains and was predicted to lead to the loss of a B-cell like epitope in ORF3a. Polyproline regions were detected in two strains (EPI_ISL_410486, France and EPI_ISL_407079, Finland) and affected epitopes formation. The accumulation of non-synonymous mutations and detected polyproline regions in ORF3a of SARS-CoV-2 could be driving the evasion of the host immune response thus favoring viral spread. Rapid mutations accumulating in ORF3a should be closely monitored throughout the COVID-19 pandemic.\n\nImportanceAt the surge of the COVID-19 pandemic and after three months of the identification of SARS-CoV-2 as the disease-causing pathogen, nucleic acid changes due to host-pathogen interactions are insightful into the evolution of this virus. In this paper, we have identified a set of non-synonymous mutations in ORF3a and predicted their impact on B-cell like epitope formation. The accumulation of non-synonymous mutations in ORF3a could be driving protein changes that mediate immune evasion and favoring viral spread.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Elio Issa", - "author_inst": "Lebanese American University" - }, - { - "author_name": "Georgi Merhi", - "author_inst": "Lebanese American University" - }, - { - "author_name": "Balig Panossian", - "author_inst": "Lebanese American University" - }, - { - "author_name": "Tamara Salloum", - "author_inst": "Lebanese American University" - }, - { - "author_name": "Sima T Tokajian", - "author_inst": "Lebanese American University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.03.26.010322", "rel_title": "Site-specific analysis of the SARS-CoV-2 glycan shield", @@ -1584470,6 +1584667,29 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.03.26.009605", + "rel_title": "Re-analysis of SARS-CoV-2 infected host cell proteomics time-course data by impact pathway analysis and network analysis. A potential link with inflammatory response.", + "rel_date": "2020-03-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.26.009605", + "rel_abs": "The disease known as coronavirus disease 19 (COVID-19), potentially caused by an outbreak of the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) in Wuhan, China, has hit the world hard, and has led to an unprecedent health and economic crisis. In order to develop treatment options able to stop or ameliorate SARS-CoV-2 effects, we need to understand the biology of the virus inside cells, but this kind of studies are still scarce. A recent study investigated translatome and proteome host cell changes induced in vitro by SARS-CoV-2. In the present study, we use the publicly available proteomics data from this study to re-analyze the mechanisms altered by the virus infection by impact pathways analysis and network analysis. Proteins linked to inflammatory response, but also proteins related to chromosome segregation during mitosis, were found to be regulated. The up-regulation of the inflammatory-related proteins observed could be linked to the propagation of inflammatory reaction and lung injury that is observed in advanced stages of COVID-19 patients.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ignacio Ortea", + "author_inst": "Instituto de Investigacion e Innovacion Biomedica de Cadiz (INiBICA)" + }, + { + "author_name": "Jens-Ole Bock", + "author_inst": "Cobo Technologies Aps" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.03.27.012906", "rel_title": "RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses", @@ -1585626,33 +1585846,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.22.20041004", - "rel_title": "COVID-19 attack rate increases with city size", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20041004", - "rel_abs": "The current outbreak of novel coronavirus disease 2019 (COVID-19) poses an unprecedented global health and economic threat to interconnected human societies. Until a vaccine is developed, strategies for controlling the outbreak rely on aggressive social distancing. These measures largely disconnect the social network fabric of human societies, especially in urban areas. Here, we estimate the growth rates and reproductive numbers of COVID-19 in US cities from March 14th through March 19th to reveal a power-law scaling relationship to city population size. This means that COVID-19 is spreading faster on average in larger cities with the additional implication that, in an uncontrolled outbreak, larger fractions of the population are expected to become infected in more populous urban areas. We discuss the implications of these observations for controlling the COVID-19 outbreak, emphasizing the need to implement more aggressive distancing policies in larger cities while also preserving socioeconomic activity.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Andrew J. Stier", - "author_inst": "University of Chicago" - }, - { - "author_name": "Marc G. Berman", - "author_inst": "University of Chicago" - }, - { - "author_name": "Luis M. A. Bettencourt", - "author_inst": "University of Chicago" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.23.20041590", "rel_title": "Modeling COVID-19 epidemics in an Excel spreadsheet: Democratizing the access to first-hand accurate predictions of epidemic outbreaks", @@ -1585968,6 +1586161,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.24.20042234", + "rel_title": "Mechanical Ventilator Milano (MVM):A Novel Mechanical Ventilator Designed for Mass Scale Production in response to the COVID-19 Pandemics", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042234", + "rel_abs": "We present here the design of the Mechanical Ventilator Milano (MVM), a novel mechanical ventilator designed for mass scale production in response to the COVID-19 pandemics, to compensate for the dramatic shortage of such ventilators in many countries. This ventilator is an electro-mechanical equivalent of the old, reliable Manley Ventilator. Our design is optimized to permit large sale production in short time and at a limited cost, relying on off-the-shelf components, readily available worldwide from hardware suppliers. Operation of the MVM requires only a source of compressed oxygen (or compressed medical air) and electrical power. The MVM control and monitoring unit can be connected and networked via WiFi so that no additional electrical connections are necessary other than the connection to the electrical power.\n\nAt this stage the MVM is not a certified medical device. Construction of the first prototypes is starting with a team of engineers, scientists and computing experts. The purpose of this paper is to disseminate the conceptual design of the MVM broadly and to solicit feed-back from the scientific and medical community to speed the process of review, improvement and possible implementation.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Galbiati Cristiano", + "author_inst": "Physics Department, Princeton University, Princeton, NJ 08544, USA" + }, + { + "author_name": "Walter Bonivento", + "author_inst": "INFN Cagliari, Cagliari 09042, Italy" + }, + { + "author_name": "Mauro Caravati", + "author_inst": "INFN Cagliari, Cagliari 09042, Italy" + }, + { + "author_name": "Marco Razeti", + "author_inst": "INFN Cagliari, Cagliari 09042, Italy" + }, + { + "author_name": "Sandro DeCecco", + "author_inst": "Physics Department, Sapienza Universit`a di Roma, Roma 00185, Italy and INFN Sezione di Roma, Roma 00185, Italy" + }, + { + "author_name": "Giuliana Fiorillo", + "author_inst": "Physics Department, Universita degli Studi Federico II di Napoli, Napoli 80126, Italy and INFN Napoli, Napoli 80126, Italy" + }, + { + "author_name": "Federico Gabriele", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Roberto Tartaglia", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Alessandro Razeto", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Davide Sablone", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Eugenio Scapparone", + "author_inst": "INFN Bologna, Bologna 40126, Italy" + }, + { + "author_name": "Gemma Testera", + "author_inst": "INFN Genova, Genova 16146, Italy" + }, + { + "author_name": "Marco Rescigno", + "author_inst": "INFN Sezione di Roma, Roma 00185, Italy" + }, + { + "author_name": "Davide Franco", + "author_inst": "APC, Universite Paris Diderot, CNRS/IN2P3, CEA/Irfu, Obs de Paris, USPC, Paris 75205, France" + }, + { + "author_name": "Iza Kochanek", + "author_inst": "INFN Laboratori Nazionali del Gran Sasso, Assergi (AQ) 67100, Italy" + }, + { + "author_name": "Cary Kendziora", + "author_inst": "Fermi National Accelerator Laboratory, Batavia, IL 60510, USA" + }, + { + "author_name": "Stephen H. Pordes", + "author_inst": "Fermi National Accelerator Laboratory, Batavia, IL 60510, USA" + }, + { + "author_name": "Hanguo Wang", + "author_inst": "Physics and Astronomy Department, University of California, Los Angeles, CA 90095, USA" + }, + { + "author_name": "Andrea Ianni", + "author_inst": "Physics Department, Princeton University, Princeton, NJ 08544, USA" + }, + { + "author_name": "Art McDonald", + "author_inst": "Department of Physics, Engineering Physics and Astronomy, Queen s University, Kingston, ON K7L 3N6, Canada" + }, + { + "author_name": "L. Molinari Tosatti", + "author_inst": "CNR STIIMA, Milano 20133, Italy" + }, + { + "author_name": "T. Dinon", + "author_inst": "CNR STIIMA, Milano 20133, Italy" + }, + { + "author_name": "M. Malosio", + "author_inst": "CNR STIIMA, Milano 20133, Italy" + }, + { + "author_name": "D. Minuzzo", + "author_inst": "AZ Pneumatica S.r.l., Misinto (MB) 20826, Italy" + }, + { + "author_name": "A. Zardoni", + "author_inst": "AZ Pneumatica S.r.l., Misinto (MB) 20826, Italy" + }, + { + "author_name": "A. Prini", + "author_inst": "CNR STIIMA, Milano 20133, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.03.23.004176", "rel_title": "Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 antigens", @@ -1587084,29 +1587396,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.25.20043679", - "rel_title": "Epidemiological Tools that Predict Partial Herd Immunity to SARS Coronavirus 2", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.25.20043679", - "rel_abs": "The outbreak of SARS coronavirus 2 (SARS-CoV-2), which occurred in Wuhan, China in December 2019, has caused a worldwide pandemic of coronavirus disease 2019 (COVID-19). However, there is a lack of epidemiological tools to guide effective public policy development. Here we present epidemiological evidence that SARS-CoV-2 S type exited Wuhan or other epicenters in China earlier than L type and conferred partial resistance to the virus on infected populations. Analysis of regional disparities in incidence has revealed that a sharp decline in influenza epidemics is a useful surrogate indicator for the undocumented spread of SARS-CoV-2. The biggest concern in the world is knowing when herd immunity has been achieved and scheduling a time to regain the living activities of each country. This study provides a useful tool to guide the development of local policies to contain the virus.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Yasuhiko Kamikubo", - "author_inst": "Graduate School of Medicine, Kyoto University" - }, - { - "author_name": "Atsushi Takahashi", - "author_inst": "Kibi International University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.25.20043364", "rel_title": "Questionnaire assessment helps the self-management of patients with inflammatory bowel disease during the outbreak of Coronavirus Disease 2019", @@ -1587318,6 +1587607,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.03.23.20041889", + "rel_title": "Coincidence of COVID-19 epidemic and olfactory dysfunction outbreak", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20041889", + "rel_abs": "BackgroundRecent surge of olfactory dysfunction in patients who were referred to ENT clinics and concurrent COVID-19epidemic in Iran motivated us to evaluate anosmic/hyposmic patients to find any relation between these two events.\n\nMethodsThis is a cross-sectional study with an online checklist on voluntary cases in all provinces of Iran between the 12th and 17th March, 2020. Cases was defined as self-reported anosmia/hyposmia in responders fewer than 4 weeks later (from start the of COVID-19 epidemic in Iran). Variables consist of clinical presentations, related past medical history, family history of recent respiratory tract infection and hospitalization.\n\nResultsIn this study 10069 participants aged 32.5{+/-}8.6 (7-78) years, 71.13% female and 81.68% non-smoker completed online checklist. They reported 10.55% a history of a trip out of home town and 1.1% hospitalization due to respiratory problems recently. From family members 12.17% had a history of severe respiratory disease in recent days and 48.23% had anosmia/hyposmia.\n\nCorrelation between the number of olfactory disorder and reported COVID-19 patients in all 31 provinces till 16th March 2020 was highly significant (Spearman correlation coefficient=0.87, p-Value<0.001). The onset of anosmia was sudden in 76.24% and till the time of filling the questionnaire in 60.90% of patients decreased sense of smell was constant. Also 83.38 of this patients had decreased taste sensation in association with anosmia.\n\nConclusionsIt seems that we have a surge in outbreak of olfactory dysfunction happened in Iran during the COVID-19 epidemic. The exact mechanism of anosmia/hyposmia in COVID-19 patients needs further investigations.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Seyed Hamid Reza Bagheri", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences" + }, + { + "author_name": "Ali Mohammad Asghari", + "author_inst": "Skull base research center, The five senses institute, Iran University of Medical Sciences" + }, + { + "author_name": "Mohammad Farhadi", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences" + }, + { + "author_name": "Ahmad Reza Shamshiri", + "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences" + }, + { + "author_name": "Ali Kabir", + "author_inst": "Minimally Invasive Surgery Research Center, Iran University of Medical Sciences" + }, + { + "author_name": "Seyed Kamran Kamrava", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences" + }, + { + "author_name": "Maryam Jalessi", + "author_inst": "Skull base research center, The five senses institute, Iran University of Medical Sciences" + }, + { + "author_name": "Alireza Mohebbi", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences" + }, + { + "author_name": "Rafieh Alizadeh", + "author_inst": "ENT and Head & Neck Research center and department, The five senses Institute, Iran University of Medical Sciences, Tehran" + }, + { + "author_name": "Ali Asghar Honarmand", + "author_inst": "Electronic learning Committee, Iran Medical Council" + }, + { + "author_name": "Babak Ghalehbaghi", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Alireza Salimi", + "author_inst": "Department of anesthesiology, Shahid Beheshti University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "otolaryngology" + }, { "rel_doi": "10.1101/2020.03.24.20042796", "rel_title": "Reproducibility and reporting practices in COVID-19 preprint manuscripts", @@ -1588582,73 +1588934,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.03.23.20039446", - "rel_title": "Transmission Potential of SARS-CoV-2 in Viral Shedding Observed at the University of Nebraska Medical Center", - "rel_date": "2020-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20039446", - "rel_abs": "Summary ParagraphThe novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan, China4 in late 2019, and its resulting coronavirus disease, COVID-19, was declared a pandemic by the World Health Organization on March 11, 2020. The rapid global spread of COVID-19 represents perhaps the most significant public health emergency in a century. As the pandemic progressed, a continued paucity of evidence on routes of SARS-CoV-2 transmission has resulted in shifting infection prevention and control guidelines between clasically-defined airborne and droplet precautions. During the initial isolation of 13 individuals with COVID-19 at the University of Nebraska Medical Center, we collected air and surface samples to examine viral shedding from isolated individuals. We detected viral contamination among all samples, indicating that SARS-CoV-2 may spread through both direct (droplet and person-to-person) as well as indirect mechanisms (contaminated objects and airborne transmission). Taken together, these finding support the use of airborne isolation precautions when caring for COVID-19 patients.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Joshua L Santarpia", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Danielle N Rivera", - "author_inst": "National Strategic Research Institute" - }, - { - "author_name": "Vicki Herrera", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "M. Jane Morwitzer", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Hannah Creager", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "George W. Santarpia", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Kevin K Crown", - "author_inst": "National Strategic Research Institute" - }, - { - "author_name": "David Brett-Major", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Elizabeth Schnaubelt", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "M. Jana Broadhurst", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "James V. Lawler", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "St. Patrick Reid", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "John J. Lowe", - "author_inst": "University of Nebraska Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.24.20042283", "rel_title": "Metabolic disturbances and inflammatory dysfunction predict severity of coronavirus disease 2019 (COVID-19): a retrospective study", @@ -1588892,6 +1589177,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.24.20042291", + "rel_title": "Fundamental principles of epidemic spread highlight the immediate need forlarge-scale serological surveys to assess the stage of the SARS-CoV-2 epidemic", + "rel_date": "2020-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042291", + "rel_abs": "The spread of a novel pathogenic infectious agent eliciting protective immunity is typically characterised by three distinct phases: (I) an initial phase of slow accumulation of new infections (often undetectable), (II) a second phase of rapid growth in cases of infection, disease and death, and (III) an eventual slow down of transmission due to the depletion of susceptible individuals, typically leading to the termination of the (first) epidemic wave. Before the implementation of control measures (e.g. social distancing, travel bans, etc) and under the assumption that infection elicits protective immunity, epidemiological theory indicates that the ongoing epidemic of SARS-CoV-2 will conform to this pattern.\n\nHere, we calibrate a susceptible-infected-recovered (SIR) model to data on cumulative reported SARS-CoV-2 associated deaths from the United Kingdom (UK) and Italy under the assumption that such deaths are well reported events that occur only in a vulnerable fraction of the population. We focus on model solutions which take into consideration previous estimates of critical epidemiological parameters such as the basic reproduction number (R0), probability of death in the vulnerable fraction of the population, infectious period and time from infection to death, with the intention of exploring the sensitivity of the system to the actual fraction of the population vulnerable to severe disease and death.\n\nOur simulations are in agreement with other studies that the current epidemic wave in the UK and Italy in the absence of interventions should have an approximate duration of 2-3 months, with numbers of deaths lagging behind in time relative to overall infections. Importantly, the results we present here suggest the ongoing epidemics in the UK and Italy started at least a month before the first reported death and have already led to the accumulation of significant levels of herd immunity in both countries. There is an inverse relationship between the proportion currently immune and the fraction of the population vulnerable to severe disease.\n\nThis relationship can be used to determine how many people will require hospitalisation (and possibly die) in the coming weeks if we are able to accurately determine current levels of herd immunity. There is thus an urgent need for investment in technologies such as virus (or viral pseudotype) neutralization assays and other robust assays which provide reliable read-outs of protective immunity, and for the provision of open access to valuable data sources such as blood banks and paired samples of acute and convalescent sera from confirmed cases of SARS-CoV-2 to validate these. Urgent development and assessment of such tests should be followed by rapid implementation at scale to provide real-time data. These data will be critical to the proper assessment of the effects of social distancing and other measures currently being adopted to slow down the case incidence and for informing future policy direction.\n\nDisclaimer(a) This material is not final and is subject to be updated any time. (b) Code used will be made available as soon as possible. (c) Contact for press enquiries: Cairbre Sugrue, cairbre@sugruecomms.com, +44 (0)7502 203 769.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Jose Lourenco", + "author_inst": "University of Oxford" + }, + { + "author_name": "Robert Paton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Craig Thompson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Paul Klenerman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sunetra Gupta", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.24.20042705", "rel_title": "Mathematical modeling of COVID-19 transmission and mitigation strategies in the population of Ontario, Canada", @@ -1590332,29 +1590652,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.20.20040048", - "rel_title": "Window of Opportunity for Mitigation to Prevent Overflow of ICU capacity in Chicago by COVID-19", - "rel_date": "2020-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.20.20040048", - "rel_abs": "Executive SummaryWe estimate the growth in demand for ICU beds in Chicago during the emerging COVID-19 epidemic, using state-of-the-art computer simulations calibrated for the SARS-CoV-2 virus. The questions we address are these:\n\nO_LIWill the ICU capacity in Chicago be exceeded, and if so by how much?\nC_LIO_LICan strong mitigation strategies, such as lockdown or shelter in place order, prevent the overflow of capacity?\nC_LIO_LIWhen should such strategies be implemented?\nC_LI\n\nOur answers are as follows:\n\nO_LIThe ICU capacity may be exceeded by a large amount, probably by a factor of ten.\nC_LIO_LIStrong mitigation can avert this emergency situation potentially, but even that will not work if implemented too late.\nC_LIO_LIIf the strong mitigation precedes April 1st, then the growth of COVID-19 can be controlled and the ICU capacity could be adequate. The earlier the strong mitigation is implemented, the greater the probability that it will be successful. After around April 1 2020, any strong mitigation will not avert the emergency situation. In Italy, the lockdown occurred too late and the number of deaths is still doubling every 2.3 days. It is difficult to be sure about the precise dates for this window of opportunity, due to the inherent uncertainties in computer simulation. But there is high confidence in the main conclusion that it exists and will soon be closed.\nC_LI\n\nOur conclusion is that, being fully cognizant of the societal trade-offs, there is a rapidly closing window of opportunity to avert a worst-case scenario in Chicago, but only with strong mitigation/lockdown implemented in the next week at the latest. If this window is missed, the epidemic will get worse and then strong mitigation/lockdown will be required after all, but it will be too late.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Sergei Maslov", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Nigel Goldenfeld", - "author_inst": "University of Illinois at Urbana-Champaign" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.22.20041079", "rel_title": "Social distancing strategies for curbing the COVID-19 epidemic", @@ -1590574,6 +1590871,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.21.20040139", + "rel_title": "Tracking and forecasting milepost moments of the epidemic in the early-outbreak: framework and applications to the COVID-19", + "rel_date": "2020-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20040139", + "rel_abs": "BackgroundThe outbreak of the 2019 novel coronavirus (COVID-19) has attracted global attention. In the early stage of the outbreak, the most important question concerns some meaningful milepost moments, including (1) the time when the number of daily confirmed cases decreases, (2) the time when the number of daily confirmed cases becomes smaller than that of the daily removed (recovered and death), (3) the time when the number of daily confirmed cases becomes zero, and (4) the time when the number of patients treated in hospital is zero, which indicates the end of the epidemic. Intuitively, the former two can be regarded as two important turning points which indicate the alleviation of epidemic to some extent, while the latter two as two \"zero\" points, respectively. Unfortunately, it is extremely difficult to make right and precise prediction due to the limited amount of available data at a early stage of the outbreak.\n\nMethodTo address it, in this paper, we propose a flexible framework incorporating the effectiveness of the government control to forecast the whole process of a new unknown infectious disease in its early-outbreak. Specially, we first establish the iconic indicators to characterize the extent of epidemic spread, yielding four periods of the whole process corresponding to the four meaningful milepost moments: two turning points and two \"zero\" points. Then we develop the tracking and forecasting procedure with mild and reasonable assumption. Finally we apply it to analyze and evaluate the COVID-19 using the public available data for mainland China beyond Hubei Province from the China Centers for Disease Control (CDC) during the period of Jan 29th, 2020, to Feb 29th, 2020, which shows the effectiveness of the proposed procedure.\n\nResultsResults show that our model can clearly outline the development of the epidemic at a very early stage. The first prediction results on Jan 29th reveal that the first and second milepost moments for mainland China beyond Hubei Province would appear on Jan 31st and Feb 14th respectively, which are only one day and three days behind the real world situations. Forecasting results indicate that the number of newly confirmed cases will become zero in the mid-late March, and the number of patients treated in the hospital will become zero between mid-March and mid-April in mainland China beyond Hubei Province. The framework proposed in this paper can help people get a general understanding of the epidemic trends in counties where COVID-19 are raging as well as any other outbreaks of new and unknown infectious diseases in the future.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Huiwen Wang", + "author_inst": "School of Economics and Management, Beihang University, Beijing, China" + }, + { + "author_name": "Yanwen Zhang", + "author_inst": "School of Economics and Management, Beihang University, Beijing, China" + }, + { + "author_name": "Shan Lu", + "author_inst": "School of Statistics and Mathematics, Central University of Finance and Economics, Beijing, China" + }, + { + "author_name": "Shanshan Wang", + "author_inst": "School of Economics and Management, Beihang University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.22.20034504", "rel_title": "High risk of infection caused posttraumatic stress symptoms in individuals with poor sleep quality: A study on influence of coronavirus disease (COVID-19) in China", @@ -1592058,29 +1592386,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.20.20038406", - "rel_title": "High COVID-19 incidence among Norwegian travellers returned from Lombardy: implications for travel restrictions", - "rel_date": "2020-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.20.20038406", - "rel_abs": "On February 27th, three cases of COVID-19 were reported among Norwegians that had recently returned from Lombardy, Italy. Travellers from the region rapidly became the most common source of imported infections in the earliest stage of the Norwegian COVID-19 epidemic. The situation was exacerbated by the unfortunate temporal overlap between the Norwegian winter holidays and intense epidemic spread of COVID-19 in Northern Italy, resulting in a large number of infected travellers. Here we combined flight data on travels between Norway and Lombardy with patient-level data to determine the fraction of travellers returning to Norway that had been infected with SARS-CoV-2.\n\nTravellers returning to Norway from Lombardy contracted COVID-19 at incidence rates up to 0.02 per person-day in the period spanning February 21st and March 1st, with a clear uptick in transmission in the middle of the period.\n\nThis shows an example of the infection risk in tourist destinations being several fold higher than elsewhere in the region. In Norway, this is also supported by high rates of infections among tourists returning from Austria in February and March, despite a low number of reported cases in the country at the time.\n\nThe massive COVID-19 prevalence among travellers suggest that mandatory quarantine of returning travellers or suspension of non-essential international flights is essential if the aim is to control or suppress the COVID-19 pandemic.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ola Brynildsrud", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Vegard Eldholm", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.19.20039131", "rel_title": "Assessing the potential impacts of COVID-19 in Brasil: Mobility, Morbidity and Impact to the Health System", @@ -1592232,6 +1592537,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.19.20032532", + "rel_title": "Geo temporal distribution of 1,688 Chinese healthcare workers infected with COVID-19 in severe conditions, a secondary data analysis", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20032532", + "rel_abs": "IntroductionThe COVID-19 outbreak is posing an unprecedented challenge to healthcare workers. This study analyzes the geo-temporal effects on disease severity for the 1,688 Chinese healthcare workers infected with COVID-19.\n\nMethodUsing the descriptive results recently reported by the Chinese CDC, we compare the percentage of infected healthcare workers in severe conditions over time and across three areas in China, and the fatality rate of infected healthcare workers with all the infected individuals in China aged 22-59 years.\n\nResultsAmong the infected Chinese healthcare workers whose symptoms onset appeared during the same ten-day period, the percentage of those in severe conditions decreased statistical significantly from 19.7% (Jan 11 - 20) to 14.4% (Jan 21 - 31) to 8.7% (Feb 1 - 11). Across the country, there was also a significant difference in the disease severity among patients symptoms onset during the same period, with Wuhan being the most severe (17%), followed by Hubei Province (10.4%), and the rest of China (7.0%). The case fatality rate for the 1,688 infected Chinese healthcare workers was significantly lower than that for the 29,798 infected patients aged 20-59 years--0.3% (5/1,688) vs. 0.65% (193/29,798), respectively.\n\nConclusionThe disease severity improved considerably over a short period of time in China. The more severe conditions in Wuhan compared to the rest of the country may be attributable to the draconian lockdown. The clinical outcomes of infected Chinese healthcare workers may represent a more accurate estimation of the severity of COVID-19 for those who have access to quality healthcare.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Wayne Gao", + "author_inst": "Taipei Medical University" + }, + { + "author_name": "Mattia Sanna", + "author_inst": "Taipei Medical University" + }, + { + "author_name": "Chi Pang Wen", + "author_inst": "National Health Research Institute; China Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.19.20039404", "rel_title": "Healthcare worker absenteeism, child care costs, and COVID-19 school closures: a simulation analysis", @@ -1593248,53 +1593580,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.21.20040022", - "rel_title": "A mathematical model for the spatiotemporal epidemic spreading of COVID19", - "rel_date": "2020-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.21.20040022", - "rel_abs": "An outbreak of a novel coronavirus, named SARS-CoV-2, that provokes the COVID-19 disease, was first reported in Hubei, mainland China on 31 December 2019. As of 20 March 2020, cases have been reported in 166 countries/regions, including cases of human-to-human transmission around the world. The proportions of this epidemics is probably one of the largest challenges faced by our interconnected modern societies. According to the current epidemiological reports, the large basic reproduction number, R0 [~] 2.3, number of secondary cases produced by an infected individual in a population of susceptible individuals, as well as an asymptomatic period (up to 14 days) in which infectious individuals are undetectable without further analysis, pave the way for a major crisis of the national health capacity systems. Recent scientific reports have pointed out that the detected cases of COVID19 at young ages is strikingly short and that lethality is concentrated at large ages. Here we adapt a Microscopic Markov Chain Approach (MMCA) metapopulation mobility model to capture the spread of COVID-19. We propose a model that stratifies the population by ages, and account for the different incidences of the disease at each strata. The model is used to predict the incidence of the epidemics in a spatial population through time, permitting investigation of control measures. The model is applied to the current epidemic in Spain, using the estimates of the epidemiological parameters and the mobility and demographic census data of the national institute of statistics (INE). The results indicate that the peak of incidence will happen in the first half of April 2020 in absence of mobility restrictions. These results can be refined with improved estimates of epidemiological parameters, and can be adapted to precise mobility restrictions at the level of municipalities. The current estimates largely compromises the Spanish health capacity system, in particular that for intensive care units, from the end of March. However, the model allows for the scrutiny of containment measures that can be used for health authorities to forecast with accuracy their impact in prevalence of COVID-19. Here we show by testing different epidemic containment scenarios that we urge to enforce total lockdown to avoid a massive collapse of the Spanish national health system.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Alex Arenas", - "author_inst": "Universitat Rovira i Virgili" - }, - { - "author_name": "Wesley Cota", - "author_inst": "Universidade Federal de Vicosa" - }, - { - "author_name": "Jesus Gomez-Gardenes", - "author_inst": "Universidad de Zaragoza" - }, - { - "author_name": "Sergio G\u00f3mez", - "author_inst": "Universitat Rovira i Virgili" - }, - { - "author_name": "Clara Granell", - "author_inst": "Universidad de Zaragoza" - }, - { - "author_name": "Joan T. Matamalas", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "David Soriano-Panos", - "author_inst": "Universidad de Zaragoza" - }, - { - "author_name": "Benjamin Steinegger", - "author_inst": "Universitat Rovira i Virgili" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.20.20039644", "rel_title": "Effectiveness and cost-effectiveness of public health measures to control COVID-19: a modelling study", @@ -1593654,6 +1593939,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.20.20039818", + "rel_title": "Potential Factors for Prediction of Disease Severity of COVID-19 Patients", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.20.20039818", + "rel_abs": "ObjectiveCoronavirus disease 2019 (COVID-19) is an escalating global epidemic caused by SARS-CoV-2, with a high mortality in critical patients. Effective indicators for predicting disease severity in SARS-CoV-2 infected patients are urgently needed.\n\nMethodsIn this study, 43 COVID-19 patients admitted in Chongqing Public Health Medical Center were involved. Demographic data, clinical features, and laboratory examinations were obtained through electronic medical records. Peripheral blood specimens were collected from COVID-19 patients and examined for lymphocyte subsets and cytokine profiles by flow cytometry. Potential contributing factors for prediction of disease severity were further analyzed.\n\nResultsA total of 43 COVID-19 patients were included in this study, including 29 mild patients and 14 sever patients. Severe patients were significantly older (61.9{+/-}9.4 vs 44.4{+/-}15.9) and had higher incidence in co-infection with bacteria compared to mild group (85.7%vs27.6%). Significantly more severe patients had the clinical symptoms of anhelation (78.6%) and asthma (71.4%). For laboratory examination, 57.1% severe cases showed significant reduction in lymphocyte count. The levels of Interluekin-6 (IL6), IL10, erythrocyte sedimentation rate (ESR) and D-Dimer (D-D) were significantly higher in severe patients than mild patients, while the level of albumin (ALB) was remarkably lower in severe patients. Further analysis demonstrated that ESR, D-D, age, ALB and IL6 were the major contributing factors for distinguishing severe patients from mild patients. Moreover, ESR was identified as the most powerful factor to predict disease progression of COVID-19 patients.\n\nConclusionAge and the levels of ESR, D-D, ALB and IL6 are closely related to the disease severity of COVID-19 patients. ESR can be used as a valuable indicator for distinguishing severe COVID-19 patients in early stage, so as to increase the survival of severe patients.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "huizheng zhang", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "xiaoying wang", + "author_inst": "Chongqing Medical and Pharmaceutical College" + }, + { + "author_name": "zongqiang fu", + "author_inst": "Henan Province hospital of traditional chinese" + }, + { + "author_name": "ming luo", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "zhen zhang", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "ke zhang", + "author_inst": "Chongqing emergency center" + }, + { + "author_name": "ying he", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "dongyong wan", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "liwen zhang", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "jing wang", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "xiaofeng yan", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "mei han", + "author_inst": "Chongqing Public Health Medical Center" + }, + { + "author_name": "yaokai chen", + "author_inst": "Chongqing Public Health Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.21.001933", "rel_title": "SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability", @@ -1595218,57 +1595570,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.16.20037168", - "rel_title": "Roles of meteorological conditions in COVID-19 transmission on a worldwide scale", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20037168", - "rel_abs": "The novel coronavirus (SARS-CoV-2/2019-nCoV) identified in Wuhan, China, in December 2019 has caused great damage to public health and economy worldwide with over 140,000 infected cases up to date. Previous research has suggested an involvement of meteorological conditions in the spread of droplet-mediated viral diseases, such as influenza. However, as for the recent novel coronavirus, few studies have discussed systematically about the role of daily weather in the epidemic transmission of the virus. Here, we examine the relationships of meteorological variables with the severity of the outbreak on a worldwide scale. The confirmed case counts, which indicates the severity of COVID-19 spread, and four meteorological variables, i.e., air temperature, relative humidity, wind speed, and visibility, were collected daily between January 20 and March 11 (52 days) for 430 cities and districts all over China, 21 cities/provinces in Italy, 21 cities/provinces in Japan, and 51 other countries around the world. Four different time delays of weather (on the day, 3 days ago, 7 days ago, and 14 days ago) as to the epidemic situation were taken for modeling and we finally chose the weather two weeks ago to model against the daily epidemic situation as its correlated with the outbreak best. Taken Chinese cities as a discovery dataset, it was suggested that temperature, wind speed, and relative humidity combined together could best predict the epidemic situation. The meteorological model could well predict the outbreak around the world with a high correlation (r2>0.6) with the real data. Using this model, we further predicted the possible epidemic situation in the future 12 days in several high-latitude cities with potential outbreak. This model could provide more information for governments future decisions on COVID-19 outbreak control.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Biqing Chen", - "author_inst": "Research Center of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, the Affiliated Hospital of Nanjing University of Chinese Medicine" - }, - { - "author_name": "Hao Liang", - "author_inst": "Department of Hematology, Jiangsu Province Hospital of Chinese Medicine, the Affiliated Hospital of Nanjing University of Chinese Medicine" - }, - { - "author_name": "Xiaomin Yuan", - "author_inst": "Research Center of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, the Affiliated Hospital of Nanjing University of Chinese Medicine" - }, - { - "author_name": "Yingying Hu", - "author_inst": "Department of Hematology, Jiangsu Province Hospital of Chinese Medicine, the Affiliated Hospital of Nanjing University of Chinese Medicine" - }, - { - "author_name": "Miao Xu", - "author_inst": "Department of Hematology, Jiangsu Province Hospital of Chinese Medicine, the Affiliated Hospital of Nanjing University of Chinese Medicine" - }, - { - "author_name": "Yating Zhao", - "author_inst": "School of Atmospheric Sciences, Nanjing University" - }, - { - "author_name": "Binfen Zhang", - "author_inst": "Department of Hematology, Jiangsu Province Hospital of Chinese Medicine, the Affiliated Hospital of Nanjing University of Chinese Medicine" - }, - { - "author_name": "Fang Tian", - "author_inst": "Research Center of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, the Affiliated Hospital of Nanjing University of Chinese Medicine" - }, - { - "author_name": "Xuejun Zhu", - "author_inst": "Department of Hematology, Research Center of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, the Affiliated Hospital of Nanjing University of C" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.17.20036954", "rel_title": "Evaluation of recombinant nucleocapsid and spike proteins for serological diagnosis of novel coronavirus disease 2019 (COVID-19)", @@ -1595572,6 +1595873,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.16.20036939", + "rel_title": "COVID-19: Forecasting short term hospital needs in France", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20036939", + "rel_abs": "1Europe is now considered as the epicenter of the SARS-CoV-2 pandemic, France being among the most impacted country. In France, there is an increasing concern regarding the capacity of the healthcare system to sustain the outbreak, especially regarding intensive care units (ICU). The aim of this study was to estimate the dynamics of the epidemic in France, and to assess its impact on healthcare resources for each French metropolitan Region. We developed a deterministic, age-structured, Susceptible-Exposed-Infectious-Removed (SEIR) model based on catchment areas of each COVID-19 referral hospitals. We performed one month ahead predictions (up to April 14, 2020) for three different scenarios (R0 = 1.5, R0 = 2.25, R0 = 3), where we estimated the daily number of COVID-19 cases, hospitalizations and deaths, the needs in ICU beds per Region and the reaching date of ICU capacity limits. At the national level, the total number of infected cases is expected to range from 22,872 in the best case (R0 = 1.5) to 161,832 in the worst case (R0 = 3), while the total number of deaths would vary from 1,021 to 11,032, respectively. At the regional level, all ICU capacities may be overrun in the worst scenario. Only seven Regions may lack ICU beds in the mild scenario (R0 = 2.25) and only one in the best case. In the three scenarios, Corse may be the first Region to see its ICU capacities overrun. The two other Regions, whose capacity will be overrun shortly after are Grand-Est and Bourgogne-Franche-Comte. Our analysis shows that, even in the best case scenario, the French healthcare system will very soon be overwhelmed. While drastic social distancing measures may temper our results, a massive reorganization leading to an expansion of French ICU capacities seems to be necessary to manage the coming wave of critically affected COVID-19 patients.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Cl\u00e9ment Massonnaud", + "author_inst": "Univ Rennes, EHESP, REPERES - EA 7449; Rouen University Hospital, Department of Biostatistics" + }, + { + "author_name": "Jonathan Roux", + "author_inst": "Univ Rennes, EHESP, REPERES - EA 7449" + }, + { + "author_name": "Pascal Cr\u00e9pey", + "author_inst": "Univ Rennes, EHESP, REPERES - EA 7449" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.14.20035659", "rel_title": "Maximum entropy method for estimating the reproduction number: An investigation for COVID-19 in China", @@ -1596588,57 +1596916,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.18.20038067", - "rel_title": "Estimating the Risks from COVID-19 Infection in Adult Chemotherapy Patients", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.18.20038067", - "rel_abs": "BackgroundDuring the coronavirus disease 2019 (COVID) pandemic, various organisations have produced management guidance for cancer patients and the delivery of cytotoxic chemotherapy, but none offer estimates of risk, or the potential impact across populations.\n\nMethodsWe combine data from four countries to produce pooled age-banded Case Fatality Rates (CFRs), calculate the sex-difference in survival and use data from four recent studies to convert CFRs into age-sex stratified Infection Fatality Rates (IFRs). We estimate the additional risk of death in cancer patients, and in those receiving chemotherapy. We illustrate the impact of these by considering the impact on a national incident cancer cohort and present some clinical scenarios.\n\nResultsWe obtained data based on 412,985 cases and 41,854 deaths. The pooled estimate for IFR was 0.92%. Age-related IFRs for patients with cancer range from 0.01% to 29%, and higher in patients receiving chemotherapy. The risk is significantly higher in men than women. 40% of all male and 32% of all female patients with a new diagnosis of cancer this year have an IFR of [≥] 5%.\n\nConclusionsOlder male patients are at a higher risk of death with COVID infection. Patients with cancer are also at higher risk, as are those who have recently received chemotherapy. We provide well-founded estimates to allow patients and clinicians to better balance these risks, and illustrate the wider impact in a national incident cohort.\n\nFUNDING & DISCLOSURESMW receives funding from the Imperial/ NIHR BRC; SD receives funding from the IC/ICR CRUK Major Centre; LPS receives funding from Brain Tumour Research and the Brain Tumour Research Campaign. JC is supported by the Guangdong International Young Research Talents Training Programme for Postdoctoral Researchers. The funders had no role in study design, data collection, data analysis, data interpretation, or writing of the report. The corresponding author had full access to all the data in the study and had final responsibility for the decision to submit for publication. Code, data and appendicies are available at: https://gitlab.com/computational.oncology/covidcancerrisk\n\nHIGHLIGHTSO_LIWe report case and infection fatality rates based on a large multi-national cohort\nC_LIO_LIWe provide sex and age-specific estimates of risk\nC_LIO_LIWe provide estimates of additional risk for patients with cancer to allow patients and clinicians to balance risk and benefit\nC_LI", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Matt Williams", - "author_inst": "Computational Oncology Group, Imperial College London" - }, - { - "author_name": "Ella Mi", - "author_inst": "Department of Radiotherapy, Imperial College Healthcare Trust" - }, - { - "author_name": "Kerlann Le Calvez", - "author_inst": "Computational Oncology Group, Imperial College London" - }, - { - "author_name": "Jiarong Chen", - "author_inst": "Computational Oncology Group, Imperial College London" - }, - { - "author_name": "Lillie Pakzad-Shahabi", - "author_inst": "John Fulcher Neuro-oncology Lab, Imperial College London" - }, - { - "author_name": "Seema Dadhania", - "author_inst": "Computational Oncology Group, Imperial College London" - }, - { - "author_name": "James Wang", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Andrew LK Ho", - "author_inst": "Addenbrooke Hospital Cambridge" - }, - { - "author_name": "Simon Rabinowicz", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.03.18.20038026", "rel_title": "Chinese Public Attention to COVID-19 Epidemic: Based on Social Media", @@ -1596834,6 +1597111,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.16.20037135", + "rel_title": "Hydroxychloroquine and Azithromycin as a treatment of COVID-19: preliminary results of an open-label non-randomized clinical trial", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20037135", + "rel_abs": "BackgroundChloroquine and hydroxychloroquine have been found to be efficient on SARS-CoV-2, and reported to be efficient in Chinese COV-19 patients. We evaluate the role of hydroxychloroquine on respiratory viral loads.\n\nPatients and methodsPatients were included in a single arm protocol to receive 600mg of hydroxychloroquine daily and their viral load in nasal swabs was tested daily. Depending on their clinical presentation, azithromycin was added to the treatment. Untreated patients from another center and cases refusing the protocol were included as negative controls. Presence and absence of virus at Day6-post inclusion was considered the end point.\n\nResultsTwenty cases were treated in this study and showed a significant reduction of the viral carriage at D6-post inclusion compared to controls, and much lower average carrying duration than reported of untreated patients in the literature. Azithromycin added to hydroxychloroquine was significantly more efficient for virus elimination.\n\nConclusionHydroxychloroquine is significantly associated with viral load reduction/disappearance in COVID-19 patients and its effect is reinforced by azithromycin.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Philippe GAUTRET", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Jean Christophe LAGIER", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Philippe PAROLA", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Van Thuan HOANG", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Line MEDDED", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Morgan MAILHE", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Barbara DOUDIER", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Johan COURJON", + "author_inst": "Centre Hospitalier Universitaire de Nice" + }, + { + "author_name": "Valerie GIORDANENGO", + "author_inst": "Centre Hospitalier Universitaire de Nice" + }, + { + "author_name": "Vera ESTEVES VIEIRA", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Herve TISSOT DUPONT", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Stephane HONORE", + "author_inst": "Aix Marseille University" + }, + { + "author_name": "Philippe COLSON", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Eric CHABRIERE", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Bernard LA SCOLA", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Jean Marc ROLAIN", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Philippe BROUQUI", + "author_inst": "Aix Marseille University IHU Mediterranee Infection" + }, + { + "author_name": "Didier RAOULT Sr.", + "author_inst": "IHU Mediterrane Infection, Aix Marseille University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.19.20038844", "rel_title": "A framework for identifying regional outbreak and spread of COVID-19 from one-minute population-wide surveys", @@ -1598014,45 +1598378,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.03.15.20036582", - "rel_title": "Estimating unobserved SARS-CoV-2 infections in the United States", - "rel_date": "2020-03-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20036582", - "rel_abs": "By March 2020, COVID-19 led to thousands of deaths and disrupted economic activity worldwide. As a result of narrow case definitions and limited capacity for testing, the number of unobserved SARS-CoV-2 infections during its initial invasion of the US remains unknown. We developed an approach for estimating the number of unobserved infections based on data that are commonly available shortly after the emergence of a new infectious disease. The logic of our approach is, in essence, that there are bounds on the amount of exponential growth of new infections that can occur during the first few weeks after imported cases start appearing. Applying that logic to data on imported cases and local deaths in the US through March 12, we estimated that 22,876 (95% posterior predictive interval: 7,451 - 53,044) infections occurred in the US by this date. By comparing the models predictions of symptomatic infections to local cases reported over time, we obtained daily estimates of the proportion of symptomatic infections detected by surveillance. This revealed that detection of symptomatic infections decreased throughout February as exponential growth of infections outpaced increases in testing. Between February 21 and March 12, we estimated an increase in detection of symptomatic infections, which was strongly correlated (median: 0.97, 95% PPI: 0.85 - 0.98) with increases in testing. These results suggest that testing was a major limiting factor in assessing the extent of SARS-CoV-2 transmission during its initial invasion of the US.\n\nSignificance StatementCountries across the world observed dramatic rises in COVID-19 cases and deaths in March 2020. In the United States, delays in the availability of diagnostic testing prompted questions about the extent of unobserved community transmission. Using a simulation model informed by reported cases and deaths, we estimated that tens of thousands of people were infected by the time a national emergency was declared on March 13. Our results indicate that fewer than 20% of locally acquired, symptomatic infections in the US were detected over a period of a month. The existence of a large, unobserved reservoir of infection argues for the necessity of large-scale social distancing that went into effect to mitigate the impacts of SARS-CoV-2 on the US.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alex Perkins", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Sean M. Cavany", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Sean M Moore", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Rachel J Oidtman", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Anita Lerch", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Marya Poterek", - "author_inst": "University of Notre Dame" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.15.20036624", "rel_title": "Effect of large-scale testing platform in prevention and control of the COVID-19 pandemic: an empirical study with a novel numerical model", @@ -1598472,6 +1598797,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.15.20036368", + "rel_title": "Coronavirus disease-19: The First 7,755 Cases in the Republic of Korea", + "rel_date": "2020-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20036368", + "rel_abs": "We report the first 7,755 patients with confirmed COVID-19 in Korea as of March 13, 2020. A total of 66 deaths were identified, resulting case fatality proportion of 0.9%. Older people, and those with coexisting medical conditions were at risk for fatal outcomes. The highest number of cases were from Daegu, followed by Gyeongbuk, with elevated age-stratified case fatality. This summary may help to understand the disease dynamics in the early phase of COVID-19 outbreak, therefore, to guide future public health measures.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "- COVID-19 National Emergency Response Center Korea Centers for Disease Control and Prevention", + "author_inst": "-" + }, + { + "author_name": "Young June Choe", + "author_inst": "Hallym University College of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.15.20036350", "rel_title": "Coronavirus disease-19: Summary of 2,370 Contact Investigations of the First 30 Cases in the Republic of Korea", @@ -1599624,49 +1599972,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.03.13.20035261", - "rel_title": "The effects of border control and quarantine measures on global spread of COVID-19", - "rel_date": "2020-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.13.20035261", - "rel_abs": "The rapid expansion of coronavirus (COVID-19) has been observed in many parts of the world. Many newly reported cases of this new coronavirus during early outbreak phases have been associated with travel history from an epidemic region (identified as imported cases). For those cases without travel history, the risk of wider spreads through community contact is even higher. However, most population models assume a homogeneous infected population without considering that the imported and secondary cases contracted by the imported cases can pose a different risk to community spread.\n\nWe have developed an \"easy-to-use\" mathematical framework extending from a meta-population model embedding city-to-city connections to stratify the dynamics of transmission waves caused by imported, secondary, and others from an outbreak source region when control measures are considered. Using the dynamics of the secondary cases, we are able to determine the probability of community spread.\n\nUsing the top 10 visiting cities from Wuhan in China as an example, we first demonstrated that the arrival time and the dynamics of the outbreaks at these cities can be successfully predicted under the reproductive number R0 = 2.92 and latent period{tau} = 5.2 days. Next, we showed that although control measures can gain extra 32.5 and 44.0 days in arrival time through a high intensive border control measure and a shorter time to quarantine under a low R0 (1.4), if the R0 is higher (2.92), only 10 extra days can be gained for each of the same measures. This suggests the importance of lowering the incidence at source regions together with infectious disease control measures in susceptible regions. The study allows us to assess the effects of border control and quarantine measures on the emergence and the global spread in a fully connected world using the dynamics of the secondary cases.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "M. Pear Hossain", - "author_inst": "Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong" - }, - { - "author_name": "Alvin Junus", - "author_inst": "Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong" - }, - { - "author_name": "Xiaolin Zhu", - "author_inst": "Department of Land Surveying and Geo-Informatics , The Hong Kong Polytechnic University, Hong Kong" - }, - { - "author_name": "Pengfei Jia", - "author_inst": "Academic Information Center, China Academy of Urban Planning and Design, Beijing, China" - }, - { - "author_name": "Tzai-Hung Wen", - "author_inst": "Department of Geography, National Taiwan University, Taiwan" - }, - { - "author_name": "Dirk Pfeiffer", - "author_inst": "Centre for Applied One Health Research and Policy Advice, City University of Hong Kong, Hong Kong" - }, - { - "author_name": "Hsiang-Yu Yuan", - "author_inst": "Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.03.15.992925", "rel_title": "Master Regulator Analysis of the SARS-CoV-2/Human interactome", @@ -1600046,6 +1600351,57 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.03.15.20035204", + "rel_title": "International expansion of a novel SARS-CoV-2 mutant", + "rel_date": "2020-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20035204", + "rel_abs": "Letter to the editor. There is no abstract. The summary was showed: SARS-CoV-2 has inevitably mutated during its pandemic spread to cause unpredictable effects on COVID-19 and complicate epidemic control efforts. Here we report that a novel SARS-CoV-2 mutation (ORF3a) appears to be spreading worldwide, which deserves close attention.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Minjin Wang", + "author_inst": "Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China" + }, + { + "author_name": "Mengjiao Li", + "author_inst": "Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China" + }, + { + "author_name": "Ruotong Ren", + "author_inst": "1. Genskey Biotechnology Co., Ltd. 2. Department of Hematology, The First Hospital of Lanzhou University" + }, + { + "author_name": "Andreas Brave", + "author_inst": "Department of microbiology,Public Health Agency of Sweden" + }, + { + "author_name": "Sylvie van der Werf", + "author_inst": "Department of Virology,Molecular Genetics of RNA Viruses unit,CNRS UMR-3569, University of Paris, National Reference Center for Respiratory Viruses Institut Pas" + }, + { + "author_name": "En-Qiang Chen", + "author_inst": "Center of Infectious Diseases, West China Hospital of Sichuan University" + }, + { + "author_name": "Zhiyong Zong", + "author_inst": "Department of Infection Control and Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu, China" + }, + { + "author_name": "Weimin Li", + "author_inst": "Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, Chengdu, China" + }, + { + "author_name": "Binwu Ying", + "author_inst": "Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.10.986711", "rel_title": "Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols", @@ -1601182,65 +1601538,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.10.20033795", - "rel_title": "Active or latent tuberculosis increases susceptibility to COVID-19 and disease severity", - "rel_date": "2020-03-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.10.20033795", - "rel_abs": "ImportanceRisk factors associated with COVID-19, the viral pneumonia originating in Wuhan, China, in Dec 2019, require clarification so that medical resources can be prioritized for those at highest risk of severe COVID-19 complications. Infection with M. tuberculosis (MTB), the pathogen that causes TB and latently infects [~]25% of the global population, may be a risk factor for SARS-CoV-2 infection and severe COVID-19 pneumonia.\n\nObjectiveTo determine if latent or active TB increase susceptibility to SARS-COV-19 infection and disease severity, and lead to more rapid development of COVID-19 pneumonia.\n\nDesignAn observational case-control study of 36 confirmed COVID-19 cases from Shenyang, China, conducted in Feb 2020. Final date of follow-up: Feb 29, 2020. Cases were grouped according to COVID-19 pneumonia severity (mild/moderate, severe/critical), and MTB infection status compared. Comparisons were made with MTB infection data from another case-control study on bacterial/viral pneumonia at Shenyang Chest Hospital.\n\nSettingMulti-center study involving three primary care hospitals in Shenyang, China.\n\nParticipants86 suspected COVID-19 cases from participating primary-care hospitals in Shenyang. All 36 SARS-CoV-2 +ve cases (based on RT-PCR assay) were included. Disease severity was assessed using the Diagnostic and Treatment Guidelines of the National Health Commission of China (v6). Mean age, 47 years (range: 25-79), gender ratio, 1:1.\n\nExposuresConfirmed COVID-19 pneumonia. Interferon-gamma Release Assays (IGRA) were performed using peripheral blood to determine MTB infection.\n\nMain Outcome and MeasuresEpidemiological, demographic, clinical, radiological, and laboratory data were collected. Comparison of MTB infection status between patients with mild/moderate and severe/critical COVID-19 pneumonia.\n\nResultsMean age of 36 COVID-19 patients: 47 (range: 25-79); M/F: 18/18; Wuhan/Hubei connection: 42%. Mild/moderate cases: 27 (75%); severe/critical: 9 (25%). MTB infection (IGRA+ve): 13 cases (36.11%), including 7 of 9 severe/critical cases. MTB infection rate: higher in COVID-19 (36.11%) than bacterial pneumonia (20%; p=0.0047) and viral pneumonia patients (16.13%; p=0.024). MTB infection more common than other co-morbidities (36.11% vs diabetes: 25%; hypertension: 22.2%; coronary heart disease: 8.33%; COPD: 5.56%). MTB co-infection linked with disease severity (severe/critical 78% vs mild/moderate cases 22%; p=0.0049), and rate of disease progression: infection to development of symptoms (MTB+SARS-CoV-2: 6.5{+/-}4.2 days vs SARS-COV-2: 8.9{+/-}5.2 days; p=0.073); from symptom development to diagnosed as severe (MTB+SARS-CoV-2: 3.4{+/-}2.0 days vs SARS-COV-2: 7.5{+/-}0.5 days; p=0.075).\n\nConclusions and RelevanceMTB infection likely increases susceptibility to SARS-CoV-2, and increases COVID-19 severity, but this requires validation in a larger study. MTB infection status of COVID-19 patients should be checked routinely at hospital admission.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSIs latent or active tuberculosis (TB) a risk factor for SARS-CoV-19 infection and progression to severe COVID-19 pneumonia?\n\nFindingsIn this observational case-control study of 36 COVID-19 cases from Shenyang, China, we found tuberculosis history (both of active TB and latent TB) to be an important risk factor for SARS-CoV-2 infection. Patients with active or latent TB were more susceptible to SARS-CoV-2, and COVID-19 symptom development and progression were more rapid and severe.\n\nMeaningTuberculosis status should be assessed carefully at patient admission and management and therapeutic strategies adjusted accordingly to prevent rapid development of severe COVID-19 complications.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Yongyu Liu", - "author_inst": "Shenyang Chest Hospital, Shenyang, Liaoning Province, 110044, P.R. China" - }, - { - "author_name": "Lijun Bi", - "author_inst": "Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Aca" - }, - { - "author_name": "Yu Chen", - "author_inst": "Shenyang Chest Hospital, Shenyang, Liaoning Province, 110044, P.R. China" - }, - { - "author_name": "Yaguo Wang", - "author_inst": "Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Aca" - }, - { - "author_name": "Joy Fleming", - "author_inst": "Key Laboratory of RNA Biology and National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Aca" - }, - { - "author_name": "Yanhong Yu", - "author_inst": "Shenyang Chest Hospital, Shenyang, Liaoning Province, 110044, P.R. China" - }, - { - "author_name": "Ye Gu", - "author_inst": "Shenyang Sixth People Hospital, Shenyang, Liaoning Province, 110044, P.R. China" - }, - { - "author_name": "Chang Liu", - "author_inst": "Shenyang Chest Hospital, Shenyang, Liaoning Province, 110044, P.R. China" - }, - { - "author_name": "Lichao Fan", - "author_inst": "Shenyang Chest Hospital, Shenyang, Liaoning Province, 110044, P.R. China" - }, - { - "author_name": "Xiaodan Wang", - "author_inst": "Shenyang Chest Hospital, Shenyang, Liaoning Province, 110044, P.R. China" - }, - { - "author_name": "Moxin Cheng", - "author_inst": "Shenyang Chest Hospital, Shenyang, Liaoning Province, 110044, P.R. China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.11.20033688", "rel_title": "Social distance and SARS memory: impact on the public awareness of 2019 novel coronavirus (COVID-19) outbreak", @@ -1601496,6 +1601793,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.11.20034512", + "rel_title": "A Method to Model Outbreaks of New Infectious Diseases with Pandemic Potential such as COVID-19", + "rel_date": "2020-03-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.11.20034512", + "rel_abs": "The emergence of the novel coronavirus (a.k.a. COVID-19, SARS-CoV-2) out of Wuhan, Hubei Province, China caught the world by surprise. As the outbreak began to spread outside of China, too little was known about the virus to model its transmission with any acceptable accuracy. World governments responded to rampant misinformation about the virus leading to collateral disasters, such as plunging financial markets, that could have been avoided if better models of the outbreak had been available. This is an engineering approach to model the spread of a new infectious disease from sparse data when little is known about the infectious agent itself. The paper is not so much about the model itself - because there are many good scientific approaches to model an epidemic - as it is about crunching numbers when there are barely any numbers to crunch. The coronavirus outbreak in USA is used to illustrate the implementation of this modeling approach. A Monte Carlo approach is implemented by using incubation period and testing efficiency as variables. Among others it is demonstrated that imposing early travel restrictions from infected countries slowed down the outbreak in the USA by about 26 days.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Willem G Odendaal", + "author_inst": "Virginia Tech" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.11.20031096", "rel_title": "Relationship between the ABO Blood Group and the COVID-19 Susceptibility", @@ -1603034,37 +1603350,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.11.20034314", - "rel_title": "Predicting the cumulative number of cases for the COVID-19 epidemic in China from early data", - "rel_date": "2020-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.11.20034314", - "rel_abs": "We model the COVID-19 coronavirus epidemic in China. We use early reported case data to predict the cumulative number of reported cases to a final size. The key features of our model are the timing of implementation of major public policies restricting social movement, the identification and isolation of unreported cases, and the impact of asymptomatic infectious cases.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Zhihua Liu", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "pierre magal", - "author_inst": "University of Bordeaux" - }, - { - "author_name": "Ousmane Seydi", - "author_inst": "Ecole polytichnique de Thies" - }, - { - "author_name": "Glenn Webb", - "author_inst": "Vanderbilt University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.09.20033357", "rel_title": "Estimates of the severity of COVID-19 disease", @@ -1603379,6 +1603664,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.09.20033126", + "rel_title": "Clinical features of imported cases of coronavirus disease 2019 in Tibetan patients in the Plateau area", + "rel_date": "2020-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.09.20033126", + "rel_abs": "Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, has rapidly spread throughout China, but the clinical characteristics of Tibetan patients living in the Qinghai-Tibetan plateau are unknown. We aimed to investigate the epidemiological, clinical, laboratory and radiological characteristics of these patients. We included 67 Tibetan patients with confirmed SARS-CoV-2 infection. The patients were divided into two groups based on the presence of clinical symptoms at admission, with 31 and 36 patients in the symptomatic and asymptomatic groups, respectively. The epidemiological, clinical, laboratory and radiological characteristics were extracted and analysed. No patient had a history of exposure to COVID-19 patients from Wuhan or had travelled to Wuhan. The mean age of Tibetan patients was 39.3 years and 59% of the patients were male. Seven patients presented with fever on admission and lymphocytopenia was present in 20 patients. 47 patients had abnormal chest CTs at admission instead of stating that 20 were unchanged. Lactate dehydrogenase levels were increased in 31 patients. Seven patients progressed to severe COVID-19; however, after treatment, their condition was stable. No patients died. Of the 36 asymptomatic patients, the mean age was younger than the symptomatic group (34.4{+/-}17.3vs 44.9{+/-}18.1 years, P=0.02). Lymphocyte count and prealbumin levels were higher in the asymptomatic group than the group with clinical symptoms (1.6{+/-}0.5 vs 1.3{+/-}0.6 and 241.8{+/-}68.2 vs 191.9{+/-}60.3, respectively; P<0.05). Imported cases of COVID-19 in Tibetan patients were generally mild in this high-altitude area. Absence of fever or radiologic abnormalities on initial presentation were common.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Yu Lei", + "author_inst": "sichuan academy of medical sciences&sichuan provincial people's hospital" + }, + { + "author_name": "yunping lan", + "author_inst": "sichuan academy of medical sciences&sichuan provincial people's hospital" + }, + { + "author_name": "jianli lu", + "author_inst": "363 hospital of chengdu" + }, + { + "author_name": "xiaobo huang", + "author_inst": "sichuan academy of medical sciences&sichuan provincial people's hospital" + }, + { + "author_name": "bamu silang", + "author_inst": "daofu people's hospital" + }, + { + "author_name": "fan zeng", + "author_inst": "sichuan academy of medical sciences&sichuan provincial people's hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.11.20033159", "rel_title": "Prolonged presence of SARS-CoV-2 in feces of pediatric patients during the convalescent phase", @@ -1604631,57 +1604955,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.08.20032946", - "rel_title": "Quantifying dynamics of SARS-CoV-2 transmission suggests that epidemic control and avoidance is feasible through instantaneous digital contact tracing", - "rel_date": "2020-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.08.20032946", - "rel_abs": "The newly emergent human virus SARS-CoV-2 is resulting in high fatality rates and incapacitated health systems. Preventing further transmission is a priority. We analysed key parameters of epidemic spread to estimate the contribution of different transmission routes and determine requirements for case isolation and contact-tracing needed to stop the epidemic. We conclude that viral spread is too fast to be contained by manual contact tracing, but could be controlled if this process was faster, more efficient and happened at scale. A contact-tracing App which builds a memory of proximity contacts and immediately notifies contacts of positive cases can achieve epidemic control if used by enough people. By targeting recommendations to only those at risk, epidemics could be contained without need for mass quarantines ( lock-downs) that are harmful to society. We discuss the ethical requirements for an intervention of this kind.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Luca Ferretti", - "author_inst": "University of Oxford" - }, - { - "author_name": "Chris Wymant", - "author_inst": "University of Oxford" - }, - { - "author_name": "Michelle Kendall", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lele Zhao", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anel Nurtay", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lucie Abeler-Dorner", - "author_inst": "University of Oxford" - }, - { - "author_name": "Michael Parker", - "author_inst": "University of Oxford" - }, - { - "author_name": "David G Bonsall", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christophe Fraser", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.10.20032755", "rel_title": "Effects of Chinese strategies for controlling the diffusion and deterioration of novel coronavirus-infected pneumonia in China", @@ -1605612,6 +1605885,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.03.08.980383", + "rel_title": "In silico approach to accelerate the development of mass spectrometry-based proteomics methods for detection of viral proteins: Application to COVID-19", + "rel_date": "2020-03-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.08.980383", + "rel_abs": "We describe a method for rapid in silico selection of diagnostic peptides from newly described viral pathogens and applied this approach to SARS-CoV-2/COVID-19. This approach is multi-tiered, beginning with compiling the theoretical protein sequences from genomic derived data. In the case of SARS-CoV-2 we begin with 496 peptides that would be produced by proteolytic digestion of the viral proteins. To eliminate peptides that would cause cross-reactivity and false positives we remove peptides from consideration that have sequence homology or similar chemical characteristics using a progressively larger database of background peptides. Using this pipeline, we can remove 47 peptides from consideration as diagnostic due to the presence of peptides derived from the human proteome. To address the complexity of the human microbiome, we describe a method to create a database of all proteins of relevant abundance in the saliva microbiome. By utilizing a protein-based approach to the microbiome we can more accurately identify peptides that will be problematic in COVID-19 studies which removes 12 peptides from consideration. To identify diagnostic peptides, another 7 peptides are flagged for removal following comparison to the proteome backgrounds of viral and bacterial pathogens of similar clinical presentation. By aligning the protein sequences of SARS-CoV-2 field isolates deposited to date we can identify peptides for removal due to their presence in highly variable regions that may lead to false negatives as the pathogen evolves. We provide maps of these regions and highlight 3 peptides that should be avoided as potential diagnostic or vaccine targets. Finally, we leverage publicly deposited proteomics data from human cells infected with SARS-CoV-2, as well as a second study with the closely related MERS-CoV to identify the two proteins of highest abundance in human infections. The resulting final list contains the 24 peptides most unique and diagnostic of SARS-CoV-2 infections. These peptides represent the best targets for the development of antibodies are clinical diagnostics. To demonstrate one application of this we model peptide fragmentation using a deep learning tool to rapidly generate targeted LCMS assays and data processing method for detecting CoVID-19 infected patient samples.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=156 HEIGHT=200 SRC=\"FIGDIR/small/980383v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (37K):\norg.highwire.dtl.DTLVardef@1d7fd4borg.highwire.dtl.DTLVardef@136563borg.highwire.dtl.DTLVardef@57641dorg.highwire.dtl.DTLVardef@16de9a4_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ben Orsburn", + "author_inst": "UVA School of Medicine" + }, + { + "author_name": "Conor Jenkins", + "author_inst": "Hood College Biology Department" + }, + { + "author_name": "Sierra D Miller", + "author_inst": "Millersville University" + }, + { + "author_name": "Benjamin A Neely", + "author_inst": "Proteomic und Genomic Sciences" + }, + { + "author_name": "Namandje M Bumpus", + "author_inst": "Johns Hopkins University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.03.10.985150", "rel_title": "A proposal of an alternative primer for the ARTIC Network's multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing", @@ -1606748,53 +1607056,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.07.982264", - "rel_title": "SARS-CoV-2 sensitive to type I interferon pretreatment.", - "rel_date": "2020-03-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.07.982264", - "rel_abs": "SARS-CoV-2, a novel coronavirus (CoV) that causes COVID-19, has recently emerged causing an ongoing outbreak of viral pneumonia around the world. While distinct from SARS-CoV, both group 2B CoVs share similar genome organization, origins to bat CoVs, and an arsenal of immune antagonists. In this report, we evaluate type-I interferon (IFN-I) sensitivity of SARS-CoV-2 relative to the original SARS-CoV. Our results indicate that while SARS-CoV-2 maintains similar viral replication to SARS-CoV, the novel CoV is much more sensitive to IFN-I. In Vero and in Calu3 cells, SARS-CoV-2 is substantially attenuated in the context of IFN-I pretreatment, while SARS-CoV is not. In line with these findings, SARS-CoV-2 fails to counteract phosphorylation of STAT1 and expression of ISG proteins, while SARS-CoV is able to suppress both. Comparing SARS-CoV-2 and influenza A virus in human airway epithelial cultures (HAEC), we observe the absence of IFN-I stimulation by SARS-CoV-2 alone, but detect failure to counteract STAT1 phosphorylation upon IFN-I pretreatment resulting in near ablation of SARS-CoV-2 infection. Next, we evaluated IFN-I treatment post infection and found SARS-CoV-2 was sensitive even after establishing infection. Finally, we examined homology between SARS-CoV and SARS-CoV-2 in viral proteins shown to be interferon antagonists. The absence of an equivalent open reading frame (ORF) 3b and changes to ORF6 suggest the two key IFN-I antagonists may not maintain equivalent function in SARS-CoV-2. Together, the results identify key differences in susceptibility to IFN-I responses between SARS-CoV and SARS-CoV-2 that may help inform disease progression, treatment options, and animal model development.\n\nImportanceWith the ongoing outbreak of COVID-19, differences between SARS-CoV-2 and the original SARS-CoV could be leveraged to inform disease progression and eventual treatment options. In addition, these findings could have key implications for animal model development as well as further research into how SARS-CoV-2 modulates the type I IFN response early during infection.\n\nArticle SummarySARS-CoV-2 has similar replication kinetics to SARS-CoV, but demonstrates significant sensitivity to type I interferon treatment.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Kumari G Lokugamage", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Adam Hage", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Maren Devries", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Ana M Vallero-Jimenez", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Craig Schindewolf", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Meike Dittmann", - "author_inst": "New York University School of Medicine" - }, - { - "author_name": "Ricardo Rajsbaum", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Vineet D Menachery", - "author_inst": "University of Texas Medical Branch" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.04.20030965", "rel_title": "Comparison of severe and non-severe COVID-19 pneumonia: review and meta-analysis", @@ -1607102,6 +1607363,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.05.20031906", + "rel_title": "COVID-19 early warning score: a multi-parameter screening tool to identify highly suspected patients", + "rel_date": "2020-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.05.20031906", + "rel_abs": "BACKGROUNDCorona Virus Disease 2019 (COVID-19) is spreading worldwide. Effective screening for patients is important to limit the epidemic. However, some defects make the currently applied diagnosis methods are still not very ideal for early warning of patients. We aimed to develop a diagnostic model that allows for the quick screening of highly suspected patients using easy-to-get variables.\n\nMETHODSA total of 1,311 patients receiving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleicacid detection were included, whom with a positive result were classified into COVID-19 group. Multivariate logistic regression analyses were performed to construct the diagnostic model. Receiver operating characteristic (ROC) curve analysis were used for model validation.\n\nRESULTSAfter analysis, signs of pneumonia on CT, history of close contact, fever, neutrophil-to-lymphocyte ratio (NLR), Tmax and sex were included in the diagnostic model. Age and meaningful respiratory symptoms were enrolled into COVID-19 early warning score (COVID-19 EWS). The areas under the ROC curve (AUROC) indicated that both of the diagnostic model (training dataset 0.956 [95%CI 0.935-0.977, P < 0.001]; validation dataset 0.960 [95%CI 0.919-1.0, P < 0.001]) and COVID-19 EWS (training dataset 0.956 [95%CI 0.934-0.978, P < 0.001]; validate dataset 0.966 [95%CI 0.929-1, P < 0.001]) had good discrimination capacity. In addition, we also obtained the cut-off values of disease severity predictors, such as CT score, CD8+ T cell count, CD4+ T cell count, and so on.\n\nCONCLUSIONSThe new developed COVID-19 EWS was a considerable tool for early and relatively accurately warning of SARS-CoV-2 infected patients.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Cong-Ying Song", + "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" + }, + { + "author_name": "Jia Xu", + "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" + }, + { + "author_name": "Jian-Qin He", + "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" + }, + { + "author_name": "Yuan-Qiang Lu", + "author_inst": "The First Affiliated Hospital, School of Medicine, Zhejiang University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.06.20031955", "rel_title": "Transmission of corona virus disease 2019 during the incubation period may lead to a quarantine loophole", @@ -1608329,41 +1608621,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.03.04.977736", - "rel_title": "Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis Mechanisms of SARS-Related Coronaviruses", - "rel_date": "2020-03-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.04.977736", - "rel_abs": "A novel coronavirus (SARS-CoV-2) is the causative agent of an emergent severe respiratory disease (COVID-19) in humans that is threatening to result in a global health crisis. By using genomic, sequence, structural and evolutionary analysis, we show that Alpha- and Beta-CoVs possess several novel families of immunoglobulin (Ig) domain proteins, including ORF8 and ORF7a from SARS-related coronaviruses and two protein groups from certain Alpha-CoVs. Among them, ORF8 is distinguished in being rapidly evolving, possessing a unique insert and a hypervariable position among SARS-CoV-2 genomes in its predicted ligand-binding groove. We also uncover many Ig proteins from several metazoan viruses which are distinct in sequence and structure but share an architecture comparable to that of CoV Ig domain proteins. Hence, we propose that deployment of Ig domain proteins is a widely-used strategy by viruses, and SARS-CoV-2 ORF8 is a potential pathogenicity factor which evolves rapidly to counter the immune response and facilitate the transmission between hosts.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yongjun Tan", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Theresa Schneider", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Matthew Leong", - "author_inst": "Saint Louis University" - }, - { - "author_name": "L Aravind", - "author_inst": "NCBI, NLM, NIH" - }, - { - "author_name": "Dapeng Zhang", - "author_inst": "Saint Louis University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.05.979260", "rel_title": "LY6E impairs coronavirus fusion and confers immune control of viral disease", @@ -1608707,6 +1608964,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.02.20030148", + "rel_title": "Validity of Wrist and Forehead Temperature in Temperature Screening in the General Population During the Outbreak of 2019 Novel Coronavirus: a prospective real-world study", + "rel_date": "2020-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20030148", + "rel_abs": "AimsTemperature screening is important in the population during the outbreak of 2019 Novel Coronavirus (COVID-19). This study aimed to compare the accuracy and precision of wrist and forehead temperature with tympanic temperature under different circumstances.\n\nMethodsWe performed a prospective observational study in a real-life population. We consecutively collected wrist and forehead temperatures in Celsius ({degrees}C) using a non-contact infrared thermometer (NCIT). We also measured the tympanic temperature using a tympanic thermometers (IRTT) and defined fever as a tympanic temperature [≥]37.3{degrees}C.\n\nResultsWe enrolled a total of 528 participants including 261 indoor and 267 outdoor participants. We divided outdoor participants into four types according to their means of transportation to the hospital as walk, bicycle, electric vehicle, car, and inside the car. Under different circumstance, the mean difference ranged from -1.72 to -0.56{degrees}C in different groups for the forehead measurements, and -0.96 to -0.61{degrees}C for the wrist measurements. Both measurements had high fever screening abilities in inpatients (wrist: AUC 0.790; 95% CI: 0.725-0.854, P <0.001; forehead: AUC 0.816; 95% CI: 0.757-0.876, P <0.001). The cut-off value of wrist measurement for detecting tympanic temperature [≥]37.3{degrees}C was 36.2{degrees}C with a 86.4% sensitivity and a 67.0% specificity, and the best threshold of forehead measurement was also 36.2{degrees}C with a 93.2% sensitivity and a 60.0% specificity.\n\nConclusionsWrist measurement is more stable than forehead measurement under different circumstance. Both measurements have great fever screening abilities for indoor patients. The cut-off value of both measurements was 36.2{degrees}C. (ClinicalTrials.gov number: NCT04274621)", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ge Chen", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Jiarong Xie", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Guangli Dai", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Peijun Zheng", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Xiaqing Hu", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Hongpeng Lu", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Lei Xu", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Xueqin Chen", + "author_inst": "Ningbo First Hospital" + }, + { + "author_name": "Xiaomin Chen", + "author_inst": "Ningbo First Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.03.04.20031005", "rel_title": "Case fatality risk of novel coronavirus diseases 2019 in China", @@ -1609943,109 +1610251,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.02.20029975", - "rel_title": "Exuberant elevation of IP-10, MCP-3 and IL-1ra during SARS-CoV-2 infection is associated with disease severity and fatal outcome", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20029975", - "rel_abs": "The outbreak of Coronavirus Disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in Wuhan, December 2019, and continuously poses a serious threat to public health. Our previous study has shown that cytokine storm occurred during SARS-CoV-2 infection, while the detailed role of cytokines in the disease severity and progression remained unclear due to the limited case number. In this study, we examined 48 cytokines in the plasma samples from 53 COVID-19 cases, among whom 34 were severe cases, and the others moderate. Results showed that 14 cytokines were significantly elevated upon admission in COVID-19 cases. Moreover, IP-10, MCP-3, and IL-1ra were significantly higher in severe cases, and highly associated with the PaO2/FaO2 and Murray score. Furthermore, the three cytokines were independent predictors for the progression of COVID-19, and the combination of IP-10, MCP-3 and IL-1ra showed the biggest area under the curve (AUC) of the receiver-operating characteristics (ROC) calculations. Serial detection of IP-10, MCP-3 and IL-1ra in 14 severe cases showed that the continuous high levels of these cytokines were associated with disease deterioration and fatal outcome. In conclusion, we report biomarkers that closely associated with disease severity and outcome of COVID-19. These findings add to our understanding of the immunopathologic mechanisms of SARS-CoV-2 infection, providing novel therapeutic targets and strategy.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Yang Yang", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Chenguang Shen", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Jinxiu Li", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Jing Yuan", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Minghui Yang", - "author_inst": "Shenzhen Third People's Hospital" - }, - { - "author_name": "Fuxiang Wang", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Guobao Li", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Yanjie Li", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Li Xing", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Ling Peng", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Jinli Wei", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Mengli Cao", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Haixia Zheng", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Weibo Wu", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Rongrong Zou", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Delin Li", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Zhixiang Xu", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Haiyan Wang", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Mingxia Zhang", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Zheng Zhang", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Lei Liu", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - }, - { - "author_name": "Yingxia Liu", - "author_inst": "Shenzhen Third People's Hospital, Second Affiliated Hospital of Southern University of Science and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.03.20030437", "rel_title": "Restoration of leukomonocyte counts is associated with viral clearance in COVID-19 hospitalized patients", @@ -1610321,6 +1610526,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.03.20030627", + "rel_title": "SOCRATES: An online tool leveraging a social contact data sharing initiative to assess mitigation strategies for COVID-19", + "rel_date": "2020-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.03.20030627", + "rel_abs": "ObjectiveEstablishing a social contact data sharing initiative and an interactive tool to assess mitigation strategies for COVID-19.\n\nResultsWe organized data sharing of published social contact surveys via online repositories and formatting guidelines. We analyzed this social contact data in terms of weighted social contact matrices, next generation matrices, relative incidence and R0. We incorporated location-specific isolation measures (e.g. school closure or telework) and capture their effect on transmission dynamics. All methods have been implemented in an online application based on R Shiny and applied to COVID-19 with age-specific susceptibility and infectiousness. Using our online tool with the available social contact data, we illustrate that social distancing could have a considerable impact on reducing transmission for COVID-19. The effect itself depends on assumptions made about disease-specific characteristics and the choice of intervention(s).", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Lander Willem", + "author_inst": "Centre for Health Economic Research and Modelling Infectious Diseases,University of Antwerp, Antwerp, Belgium" + }, + { + "author_name": "Thang Van Hoang", + "author_inst": "Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute, Hasselt University, Hasselt, Belgium" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "Centre for the Mathematical Modelling of Infectious Diseases,London School of Hygiene & Tropical Medicine, London, United Kingdom" + }, + { + "author_name": "Pietro Coletti", + "author_inst": "Interuniversity Institute of Biostatistics and statistical Bioinformatics, Data Science Institute,Hasselt University, Hasselt, Belgium" + }, + { + "author_name": "Philippe Beutels", + "author_inst": "(1) Centre for Health Economic Research and Modelling Infectious Diseases,University of Antwerp, Antwerp, Belgium; (2) School of Public health and Community Med" + }, + { + "author_name": "Niel Hens", + "author_inst": "(1) Centre for Health Economic Research and Modelling Infectious Diseases,University of Antwerp, Antwerp, Belgium; (2) Interuniversity Institute of Biostatistic" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.03.20030593", "rel_title": "Evolving Epidemiology and Impact of Non-pharmaceutical Interventions on the Outbreak of Coronavirus Disease 2019 in Wuhan, China", @@ -1611728,29 +1611972,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.02.29.20029561", - "rel_title": "A simple model to assess Wuhan lock-down effect and region efforts during COVID-19 epidemic in China Mainland", - "rel_date": "2020-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.29.20029561", - "rel_abs": "Since COVID-19 emerged in early December, 2019 in Wuhan and swept across China Mainland, a series of large-scale public health interventions, especially Wuhan lock-down combined with nationwide traffic restrictions and Stay At Home Movement, have been taken by the government to control the epidemic. Based on Baidu Migration data and the confirmed cases data, we identified two key factors affecting the later (e.g February 27, 2020) cumulative confirmed cases in non-Wuhan region (y). One is the sum travelers from Wuhan during January 20 to January 26 (x1), which had higher infected probability but lower transmission ability because the human-to-human transmission risk of COVID-19 was confirmed and announced on January 20. The other is the \"seed cases\" from Wuhan before January 19, which had higher transmission ability and could be represented with the confirmed cases before January 29 (x2) due to a mean 10-day delay between infection and detection. A simple yet effective regression model then was established as follow: y= 70.0916+0.0054xx1+2.3455xx2 (n = 44, R2 = 0.9330, P<10-7). Even the lock-down date only delay or in advance 3 days, the estimated confirmed cases by February 27 in non-Wuhan region will increase 35.21% or reduce 30.74% - 48.59%. Although the above interventions greatly reduced the human mobility, Wuhan lock-down combined with nationwide traffic restrictions and Stay At Home Movement do have a determining effect on the ongoing spread of COVID-19 across China Mainland. The strategy adopted by China has changed the fast-rising curve of newly diagnosed cases, the international community should learn from lessons of Wuhan and experience from China. Efforts of 29 Provinces and 44 prefecture-level cities against COVID-19 were also assessed preliminarily according to the interpretive model. Big data has played and will continue playing an important role in public health.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Yuan zheming", - "author_inst": "Hunan Agricultural University" - }, - { - "author_name": "Chen Yuan", - "author_inst": "Hunan Agricultural University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.02.28.20029181", "rel_title": "Highly ACE2 Expression in Pancreas May Cause Pancreas Damage After SARS-CoV-2 Infection", @@ -1612018,6 +1612239,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.02.973255", + "rel_title": "Evidence for RNA editing in the transcriptome of 2019 Novel Coronavirus", + "rel_date": "2020-03-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.02.973255", + "rel_abs": "The COVID-19 outbreak has become a global health risk and understanding the response of the host to the SARS-CoV-2 virus will help to contrast the disease. Editing by host deaminases is an innate restriction process to counter viruses, and it is not yet known whether it operates against Coronaviruses. Here we analyze RNA sequences from bronchoalveolar lavage fluids derived from infected patients. We identify nucleotide changes that may be signatures of RNA editing: Adenosine-to-Inosine changes from ADAR deaminases and Cytosine-to-Uracil changes from APOBEC ones. A mutational analysis of genomes from different strains of human-hosted Coronaviridae reveals mutational patterns compatible to those observed in the transcriptomic data. Our results thus suggest that both APOBECs and ADARs are involved in Coronavirus genome editing, a process that may shape the fate of both virus and patient.\n\nFor the casual ReaderJust to make a few things clear: - RNA editing and DNA editing are PHYSIOLOGICAL processes. Organisms uses them to (a) try to fight viruses, (b) increase heterogeneity inside cells (on many levels), (c) recognise their own RNA.\n- our work suggests that: (a) cells use RNA editing in trying to deal with Coronaviruses. We don't know to what extent they succeed (and it would be nice if we could help them). (b) Whatever happens, mutations inserted by RNA editing fuel viral evolution. We don't know whether viruses actively exploit this.\n- If you (scientist or not) think our work suggests ANYTHING ELSE, contact us. It can be a first step to help fight these !@#$ coronavirus, or towards a Nobel prize - but we need to discuss it thoroughly.\n- If you think these cellular processes are fascinating, join the club and contact us. We can have a nice cup of tea while chatting how wondrous nature is at coming up with extraordinary solutions...", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Salvatore Di Giorgio", + "author_inst": "Core Research Laboratory, ISPRO, Firenze, 50139, Italy; Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy" + }, + { + "author_name": "Filippo Martignano", + "author_inst": "Core Research Laboratory, ISPRO, Firenze, 50139, Italy; Department of Medical Biotechnologies, University of Siena, Siena, 53100, Italy" + }, + { + "author_name": "Maria Gabriella Torcia", + "author_inst": "Department of Experimental and Clinical Medicine, University of Florence, Firenze 50139, Italy" + }, + { + "author_name": "Giorgio Mattiuz", + "author_inst": "Core Research L 5 aboratory, ISPRO, Firenze, 50139, Italy; Department of Experimental and Clinical Medicine, University of Florence, Firenze 50139, Italy" + }, + { + "author_name": "Silvestro G Conticello", + "author_inst": "Institute for Cancer Research, Prevention and Clinical Network (ISPRO); Institute of Clinical Physiology, National Research Council, 56124, Pisa, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.02.28.20029025", "rel_title": "Clinical significance of IgM and IgG test for diagnosis of highly suspected COVID-19 infection", @@ -1613682,25 +1613938,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.02.29.965418", - "rel_title": "The within-host viral kinetics of SARS-CoV-2", - "rel_date": "2020-03-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.29.965418", - "rel_abs": "In this work, we use a within-host viral dynamic model to describe the SARS-CoV-2 kinetics in host. Chest radiograph score data are used to estimate the parameters of that model. Our result shows that the basic reproductive number of SARS-CoV-2 in host growth is around 3.79. Using the same method we also estimate the basic reproductive number of MERS virus is 8.16 which is higher than SARS-CoV-2. The PRCC method is used to analyze the sensitivities of model parameters and the drug effects on virus growth are also implemented to analyze the model.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jiawei Liu", - "author_inst": "University of Chicago" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.02.26.961938", "rel_title": "Predictions for the binding domain and potential new drug targets of 2019-nCoV", @@ -1613916,6 +1614153,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.02.20030080", + "rel_title": "Estimation of local novel coronavirus (COVID-19) cases in Wuhan, China from off-site reported cases and population flow data from different sources", + "rel_date": "2020-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20030080", + "rel_abs": "BackgroundsIn December 2019, a novel coronavirus (COVID-19) pneumonia hit Wuhan, Hubei Province, China and spread to the rest of China and overseas. The emergence of this virus coincided with the Spring Festival Travel Rush in China. It is possible to estimate total number of cases of COVID-19 in Wuhan, by 23 January 2020, given the cases reported in other cities and population flow data between cities.\n\nMethodsWe built a model to estimate the total number of cases in Wuhan by 23 January 2020, based on the number of cases detected outside Wuhan city in China, with the assumption that if the same screening effort used in other cities applied in Wuhan. We employed population flow data from different sources between Wuhan and other cities/regions by 23 January 2020. The number of total cases was determined by the maximum log likelihood estimation.\n\nFindingsFrom overall cities/regions data, we predicted 1326 (95% CI: 1177, 1484), 1151 (95% CI: 1018, 1292) and 5277 (95% CI: 4732, 5859) as total cases in Wuhan by 23 January 2020, based on different source of data from Changjiang Daily newspaper, Tencent, and Baidu. From separate cities/regions data, we estimated 1059 (95% CI: 918, 1209), 5214 (95% CI: 4659, 5808) as total cases in Wuhan in Wuhan by 23 January 2020, based on different sources of population flow data from Tencent and Baidu.\n\nConclusionSources of population follow data and methods impact the estimates of local cases in Wuhan before city lock down.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Zian Zhuang", + "author_inst": "Hong Kong Polytechnic University" + }, + { + "author_name": "Peihua Cao", + "author_inst": "Southern Medical University" + }, + { + "author_name": "Shi Zhao", + "author_inst": "Chinese University of Hong Kong" + }, + { + "author_name": "Yijun Lou", + "author_inst": "Hong Kong Polytechnic University" + }, + { + "author_name": "Weiming Wang", + "author_inst": "Huaiyin Normal University" + }, + { + "author_name": "Shu Yang", + "author_inst": "Chengdu University of Traditional Chinese Medicine, Chengdu, China" + }, + { + "author_name": "Lin Yang", + "author_inst": "The Hong Kong Polytechnic University" + }, + { + "author_name": "Daihai He", + "author_inst": "Hong Kong Polytechnic University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.28.20029173", "rel_title": "Analysis on the Clinical Characteristics of 36 Cases of Novel Coronavirus Pneumonia in Kunming", @@ -1615087,41 +1615371,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.26.20028308", - "rel_title": "Perceptions of the Adult US Population regarding the Novel Coronavirus Outbreak", - "rel_date": "2020-02-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.26.20028308", - "rel_abs": "BackgroundCOVID-19 outbreak is spreading globally. Although the risk of infection in the US is currently low, it is important to understand the public perception of risk and trust in sources of information to better inform public health messaging. In this study, we surveyed the adult US population to understand their risk perceptions about the COVID-19 outbreak.\n\nMethods and FindingsWe used an online platform to survey 718 adults in the US in early February 2020 using a questionnaire that we developed. Our sample was fairly similar to the general adult US population in terms of age, gender, race, ethnicity and education. We found that 69% of the respondents wanted the scientific/public health leadership (either the CDC Director or NIH Director) to lead the US response to COVID-19 outbreak as compared to 14% who wanted the political leadership (either the president or the Congress) to lead the response. Risk perception was low (median score of 5 out of 10) with the respondents trusting health professionals and health officials for information on COVID-19. Majority of the respondents were in favor of strict infection prevention policies to control the outbreak.\n\nConclusionGiven our results, the public health/scientific leadership should be at the forefront of the COVID-19 response to promote trust.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "SarahAnn M McFadden", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Amyn A Malik", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Obianuju G Aguolu", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Kathryn S Willebrand", - "author_inst": "Yale Institute for Global Health" - }, - { - "author_name": "Saad B Omer", - "author_inst": "Yale Institute for Global Health" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.25.20027672", "rel_title": "Illness and Fatality Risks of COVID-19 of General Public in Hubei Provinces and Other Parts of China", @@ -1615529,6 +1615778,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2020.02.24.20027649", + "rel_title": "Transmission potential of the New Corona (COVID-19) onboard the Princess Cruises Ship, 2020", + "rel_date": "2020-02-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.24.20027649", + "rel_abs": "An outbreak of COVID-19 developed aboard the Princess Cruises Ship during January-February 2020. Using mathematical modeling and time-series incidence data describing the trajectory of the outbreak among passengers and crew members, we characterize how the transmission potential varied over the course of the outbreak. Our estimate of the mean reproduction number in the confined setting reached values as high as [~]11, which is higher than mean estimates reported from community-level transmission dynamics in China and Singapore (approximate range: 1.1-7). Our findings suggest that Rt decreased substantially compared to values during the early phase after the Japanese government implemented an enhanced quarantine control. Most recent estimates of Rt reached values largely below the epidemic threshold, indicating that a secondary outbreak of the novel coronavirus was unlikely to occur aboard the Diamond Princess Ship.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Kenji Mizumoto", + "author_inst": "Kyoto University" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.25.20025643", "rel_title": "Correlation Analysis Between Disease Severity and Inflammation-related Parameters in Patients with COVID-19 Pneumonia", @@ -1616837,49 +1617109,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.23.20024935", - "rel_title": "Conjunctival polymerase chain reaction-tests of 2019 novel coronavirus in patients in Shenyang,China", - "rel_date": "2020-02-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.23.20024935", - "rel_abs": "PurposeThe 2019 novel coronavirus(COVID-19) mainly transmitted by person-to-person through inhalation of respiratory droplets. We report the laboratory results of conjunctival PCR-tests and some clinical features of these patients in shenyang China.\n\nDesignThis is a cross-sectional non-randomized study\n\nSubjectsThe study include 14 confirmly diagnosed cases, 16 suspected cases and some medical observed patients.\n\nMethodsAll patients with diagnosed and suspected COVID-19 were admitted to a designated hospital in Shenyang, China. We collected conjunctival samples of these patients to do the laboratory tests by real time RT-PCR. Medical observed patients were enrolled if they had clinical symptoms. Then we analysed the PCR results and clinical data from eletronic medical records in order to find some relationships.\n\nMain Outcome MeasuresClinical condition and PCR results. of conjunctival swabs compared with other specimens\n\nResultsOne of the identified case coverted from suspected case without typical clinical symptoms. Twenty-two medical observed cases were removed because none of them converted to identified cases. One of the suspected converted to identified case recently. The included cases in our study are imported cases with less underlying diseases and the severity of their infection was relatively moderate. All the conjunctival results of PCR-test were negative. Two cases had typical clinical symptoms but were finally confirmed by repeated pharynxswabtests.\n\nConclusionConjunctiva may be a transmission way of COVID-19. And ocular conjunctival swabs in combination with PCR test could be a non-invasive, convenient and feasible diagnostic method for identifying the infection of COVID-19. Emphasis on the false-negative results is vital.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "li Xu", - "author_inst": "Shenyang Fourth People Hospital" - }, - { - "author_name": "Xinyue Zhang", - "author_inst": "Shengjing Hospital of Chinese Medical University" - }, - { - "author_name": "Wei Song", - "author_inst": "Shenyang Center for Disease Control and Prevention" - }, - { - "author_name": "Baijun Sun", - "author_inst": "Shenyang Center for Disease Control and Prevention" - }, - { - "author_name": "Jinping Mu", - "author_inst": "Shenyang Center for Disease Control and Prevention" - }, - { - "author_name": "Xue Dong", - "author_inst": "Shenyang Center for Disease Control and Prevention" - }, - { - "author_name": "Bing Wang", - "author_inst": "Shenyang Center for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "ophthalmology" - }, { "rel_doi": "10.1101/2020.02.22.20026500", "rel_title": "Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study", @@ -1617155,6 +1617384,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.20.20025999", + "rel_title": "Generation of antibodies against COVID-19 virus for development of diagnostic tools", + "rel_date": "2020-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025999", + "rel_abs": "The COVID-19 China coronavirus started in Dec 2019 was challenged by the lack of accurate serological diagnostic tool for this deadly disease to quickly identify and isolate the infected patients. The generation of COVID-19-specific antibodies is essential for such tasks. Here we report that polyclonal and monoclonal antibodies were generated by immunizing animals with synthetic peptides corresponding to different areas of Nucleoprotein (N) of COVID-19. The specificities of the COVID-19 antibodies were assessed by Western Blot analysis against NPs from COVID-19, MERS and SARS. Antibodies were used for immunohistochemistry staining of the tissue sections from COVID-19 infected patient, as a potential diagnostic tool. A Sandwich ELISA kit was quickly assembled for quantitation of the virus/NP of COVID-19 concentrations in the vaccine preparations. Development of POCT is also aggressively undergoing.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Maohua Li", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Ronghua Jin", + "author_inst": "Beijing You'an Hospital, Capital Medical University" + }, + { + "author_name": "Ya Peng", + "author_inst": "Laboratory of Animal Infectious Diseases, College of Animal Sciences and Veterinary Medicine, Guangxi University" + }, + { + "author_name": "Cuiyan Wang", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Wenlin Ren", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Fudong Lv", + "author_inst": "Beijing You'an Hospital, Capital Medical University" + }, + { + "author_name": "Sitao Gong", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Feng Fang", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Qianyun Wang", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Jianli Li", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Tong Shen", + "author_inst": "AbMax Biotechnology Co., LTD" + }, + { + "author_name": "Hunter Sun", + "author_inst": "AnyGo Technology Co., Ltd" + }, + { + "author_name": "Lei Zhou", + "author_inst": "State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences" + }, + { + "author_name": "Yali Cui", + "author_inst": "College of Life Sciences, Northwest University" + }, + { + "author_name": "Hao Song", + "author_inst": "Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences" + }, + { + "author_name": "Le Sun", + "author_inst": "AbMax Biotechnology Co., LTD" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.23.20026864", "rel_title": "Higher severity and mortality in male patients with COVID-19 independent of age and susceptibility", @@ -1618427,117 +1618735,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.21.20026328", - "rel_title": "Evolving epidemiology of novel coronavirus diseases 2019 and possible interruption of local transmission outside Hubei Province in China: a descriptive and modeling study", - "rel_date": "2020-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.21.20026328", - "rel_abs": "BackgroundThe COVID-19 epidemic originated in Wuhan City of Hubei Province in December 2019 and has spread throughout China. Understanding the fast evolving epidemiology and transmission dynamics of the outbreak beyond Hubei would provide timely information to guide intervention policy.\n\nMethodsWe collected individual information on 8,579 laboratory-confirmed cases from official publically sources reported outside Hubei in mainland China, as of February 17, 2020. We estimated the temporal variation of the demographic characteristics of cases and key time-to-event intervals. We used a Bayesian approach to estimate the dynamics of the net reproduction number (Rt) at the provincial level.\n\nResultsThe median age of the cases was 44 years, with an increasing of cases in younger age groups and the elderly as the epidemic progressed. The delay from symptom onset to hospital admission decreased from 4.4 days (95%CI: 0.0-14.0) until January 27 to 2.6 days (0.0-9.0) from January 28 to February 17. The mean incubation period was estimated at 5.2 days (1.8-12.4) and the mean serial interval at 5.1 days (1.3-11.6). The epidemic dynamics in provinces outside Hubei was highly variable, but consistently included a mix of case importations and local transmission. We estimate that the epidemic was self-sustained for less than three weeks with Rt reaching peaks between 1.40 (1.04-1.85) in Shenzhen City of Guangdong Province and 2.17 (1.69-2.76) in Shandong Province. In all the analyzed locations (n=10) Rt was estimated to be below the epidemic threshold since the end of January.\n\nConclusionOur findings suggest that the strict containment measures and movement restrictions in place may contribute to the interruption of local COVID-19 transmission outside Hubei Province. The shorter serial interval estimated here implies that transmissibility is not as high as initial estimates suggested.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Juanjuan Zhang", - "author_inst": "Fudan University" - }, - { - "author_name": "Maria Litvinova", - "author_inst": "ISI Foundation" - }, - { - "author_name": "Wei Wang", - "author_inst": "Fudan University" - }, - { - "author_name": "Yan Wang", - "author_inst": "Fudan University" - }, - { - "author_name": "Xiaowei Deng", - "author_inst": "Fudan University" - }, - { - "author_name": "Xinghui Chen", - "author_inst": "Fudan University" - }, - { - "author_name": "Mei Li", - "author_inst": "Fudan University" - }, - { - "author_name": "Wen Zheng", - "author_inst": "Fudan University" - }, - { - "author_name": "Lan Yi", - "author_inst": "Fudan University" - }, - { - "author_name": "Xinhua Chen", - "author_inst": "Fudan University" - }, - { - "author_name": "Qianhui Wu", - "author_inst": "Fudan University" - }, - { - "author_name": "Yuxia Liang", - "author_inst": "Fudan University" - }, - { - "author_name": "Xiling Wang", - "author_inst": "Fudan University" - }, - { - "author_name": "Juan Yang", - "author_inst": "Fudan University" - }, - { - "author_name": "Kaiyuan Sun", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Ira M. Longini Jr.", - "author_inst": "University of Florida" - }, - { - "author_name": "M. Elizabeth Halloran", - "author_inst": "Fred Hutchinson Cancer Research Center; University of Washington" - }, - { - "author_name": "Peng Wu", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Benjamin J. Cowling", - "author_inst": "University of Hong Kong" - }, - { - "author_name": "Stefano Merler", - "author_inst": "Bruno Kessler Foundation" - }, - { - "author_name": "Cecile Viboud", - "author_inst": "National Institutes of Health" - }, - { - "author_name": "Alessandro Vespignani", - "author_inst": "Northeastern University" - }, - { - "author_name": "Marco Ajelli", - "author_inst": "Bruno Kessler Foundation" - }, - { - "author_name": "Hongjie Yu", - "author_inst": "Fudan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.19.20025031", "rel_title": "A descriptive study of the impact of diseases control and prevention on the epidemics dynamics and clinical features of SARS-CoV-2 outbreak in Shanghai, lessons learned for metropolis epidemics prevention", @@ -1618873,6 +1619070,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.20.20025866", + "rel_title": "Estimating the Asymptomatic Ratio of 2019 Novel Coronavirus onboard the Princess Cruises Ship, 2020", + "rel_date": "2020-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025866", + "rel_abs": "The potential infectiousness of asymptomatic COVID-19 cases together with a substantial fraction of asymptomatic infections among all infections, have been highlighted in clinical studies. We conducted statistical modeling analysis to derive the delay-adjusted asymptomatic proportion of the positive COVID-19 infections onboard the Princess Cruises ship along with the timeline of infections. We estimated the asymptomatic proportion at 17.9% (95% CrI: 15.5%-20.2%), with most of the infections occurring before the start of the 2-week quarantine.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kenji Mizumoto", + "author_inst": "Kyoto University" + }, + { + "author_name": "Katsushi Kagaya", + "author_inst": "Kyoto University" + }, + { + "author_name": "Alexander Zarebski", + "author_inst": "Oxford University" + }, + { + "author_name": "Gerardo Chowell", + "author_inst": "Georgia State University School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.22.20025460", "rel_title": "Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus", @@ -1620208,25 +1620436,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.02.16.951913", - "rel_title": "Single cell RNA sequencing of 13 human tissues identify cell types and receptors of human coronaviruses", - "rel_date": "2020-02-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.16.951913", - "rel_abs": "The new coronavirus (2019-nCoV) outbreak from December 2019 in Wuhan, Hubei, China, has been declared a global public health emergency. Angiotensin I converting enzyme 2 (ACE2), is the host receptor by 2019-nCov to infect human cells. Although ACE2 is reported to be expressed in lung, liver, stomach, ileum, kidney and colon, its expressing levels are rather low, especially in the lung. 2019-nCoV may use co-receptors/auxiliary proteins as ACE2 partner to facilitate the virus entry. To identify the potential candidates, we explored the single cell gene expression atlas including 119 cell types of 13 human tissues and analyzed the single cell co-expression spectrum of 51 reported RNA virus receptors and 400 other membrane proteins. Consistent with other recent reports, we confirmed that ACE2 was mainly expressed in lung AT2, liver cholangiocyte, colon colonocytes, esophagus keratinocytes, ileum ECs, rectum ECs, stomach epithelial cells, and kidney proximal tubules. Intriguingly, we found that the candidate co-receptors, manifesting the most similar expression patterns with ACE2 across 13 human tissues, are all peptidases, including ANPEP, DPP4 and ENPEP. Among them, ANPEP and DPP4 are the known receptors for human CoVs, suggesting ENPEP as another potential receptor for human CoVs. We also conducted \"CellPhoneDB\" analysis to understand the cell crosstalk between CoV-targets and their surrounding cells across different tissues. We found that macrophages frequently communicate with the CoVs targets through chemokine and phagocytosis signaling, highlighting the importance of tissue macrophages in immune defense and immune pathogenesis.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Shuye Zhang", - "author_inst": "Shanghai Public Health Clinical Center and Institute of Biomedical Sciences, Fudan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.02.17.951939", "rel_title": "Protection of Rhesus Macaque from SARS-Coronavirus challenge by recombinant adenovirus vaccine", @@ -1620418,6 +1620627,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.02.17.952895", + "rel_title": "Functional pangenome analysis provides insights into the origin, function and pathways to therapy of SARS-CoV-2 coronavirus", + "rel_date": "2020-02-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.17.952895", + "rel_abs": "The spread of the novel coronavirus (SARS-CoV-2) has triggered a global emergency, that demands urgent solutions for detection and therapy to prevent escalating health, social and economic impacts. The spike protein (S) of this virus enables binding to the human receptor ACE2, and hence presents a prime target for vaccines preventing viral entry into host cells1. The S proteins from SARS-CoV-1 and SARS-CoV-2 are similar2, but structural differences in the receptor binding domain (RBD) preclude the use of SARS-CoV-1-specific neutralizing antibodies to inhibit SARS-CoV-23. Here we used comparative pangenomic analysis of all sequenced Betacoronaviruses to reveal that, among all core gene clusters present in these viruses, the envelope protein E shows a variant shared by SARS and SARS-Cov2 with two completely-conserved key functional features, an ion-channel and a PDZ-binding Motif (PBM). These features trigger a cytokine storm that activates the inflammasome, leading to increased edema in lungs causing the acute respiratory distress syndrome (ARDS)4-6, the leading cause of death in SARS-CoV-1 and SARS-CoV-2 infection7,8. However, three drugs approved for human use may inhibit SARS-CoV-1 and SARS-CoV-2 Protein E, either acting upon the ion channel (Amantadine and Hexamethylene amiloride9,10) or the PBM (SB2035805), thereby potentially increasing the survival of the host, as already demonstrated for SARS-CoV-1in animal models. Hence, blocking the SARS protein E inhibits development of ARDS in vivo. Given that our results demonstrate that the protein E subcluster for the SARS clade is quasi-identical for the key functional regions of SARS-CoV-1 and SARS-CoV-2, we conclude that use of approved drugs shown to act as SARS E protein inhibitors can help prevent further casualties from COVID-2019 while vaccines and other preventive measures are being developed.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Intikhab Alam", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + }, + { + "author_name": "Allan K Kamau", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + }, + { + "author_name": "Maxat Kulmanov", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Stefan T Arold", + "author_inst": "King Abdullah University of Science and Technology" + }, + { + "author_name": "Arnab T Pain", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + }, + { + "author_name": "Takashi Gojobori", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + }, + { + "author_name": "Carlos M. Duarte", + "author_inst": "King Abdullah University of Science and Technology (KAUST)" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.02.21.959817", "rel_title": "Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform", @@ -1621690,49 +1621942,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.18.20024448", - "rel_title": "Psychological responses, behavioral changes and public perceptions during the early phase of the COVID-19 outbreak in China: a population based cross-sectional survey", - "rel_date": "2020-02-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.18.20024448", - "rel_abs": "ObjectiveTo investigate psychological and behavioral responses to the threat of SARS-CoV-2 infections and their associations with public perceptions in China\n\nDesignCross sectional population-based telephone survey via random digital dialing between 1 and 10 February, 2020\n\nSettingWuhan (the epicentre and quarantined city), and Shanghai (a typical major city with close transportation link with Wuhan)\n\nParticipantsRandom sample of 510 residents in Wuhan and 501 residents in Shanghai aged above 18\n\nMain outcome measuresAnxiety (measured by the 7-item generalized anxiety disorder [GAD-7] scale), recommended and avoidance behaviors (engaged in all six behaviors such as increasing surface cleaning and reducing going out).\n\nResultsThe prevalence rates of moderate or severe anxiety (score [≥]10 on GAD-7) were 32.7% (n=167) among Wuhan participants and 20.4% (n=102) among Shanghai participants. 78.6% (n=401) of Wuhan participants and 63.9% (n=320) of Shanghai participants had carried out all six precautionary behaviors. For both measures, Wuhan participants were more responsive to the outbreak (p<0.001). Controlling for personal characteristics, logistic regression results suggested that risks of moderate or severe anxiety were positively associated with perceived susceptibility (odds ratio 1.6, 95% confidence interval 1.3-1.8) and severity of the disease (1.6, 1.4-1.9) and confusion about information reliability (1.6, 1.5-1.9). Having confidence in taking measures to protect oneself against the disease was associated with a lower risk (0.6, 0.5-0.7). The strongest predictor of behavioral change was perceived severity (1.2, 1.1-1.4), followed by confusion about information reliability (1.1, 1.0-1.3).\n\nConclusionsPsychological and behavioral responses to COVID-19 have been dramatic during the rising phase of the outbreak. Our results support efforts for timely dissemination of accurate and reliable information to address the high anxiety level.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Mengcen Qian", - "author_inst": "School of Public Health, Fudan University" - }, - { - "author_name": "Qianhui Wu", - "author_inst": "School of Public Health, Fudan University" - }, - { - "author_name": "Peng Wu", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Zhiyuan Hou", - "author_inst": "School of Public Health, Fudan University" - }, - { - "author_name": "Yuxia Liang", - "author_inst": "School of Public Health, Fudan University" - }, - { - "author_name": "Benjamin J Cowling", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Hongjie Yu", - "author_inst": "Fudan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.18.20024364", "rel_title": "Reduction and Functional Exhaustion of T Cells in Patients with Coronavirus Disease 2019 (COVID-19)", @@ -1621948,6 +1622157,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.18.955195", + "rel_title": "Structure and immune recognition of the porcine epidemic diarrhea virus spike protein", + "rel_date": "2020-02-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.18.955195", + "rel_abs": "Porcine epidemic diarrhea virus is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism and entry, the PEDV spike protein is a key target for the host antibody response and a good candidate for a protein-based vaccine immunogen. We used electron microscopy to evaluate the PEDV spike structure, as well as pig polyclonal antibody responses to viral infection. The structure of the PEDV spike reveals a configuration similar to that of HuCoV-NL63. Several PEDV protein-protein interfaces are mediated by non-protein components including a glycan at Asn264 and two bound palmitoleic acid molecules. The polyclonal antibody response to PEDV infection shows a dominance of epitopes in the S1 region. This structural and immune characterization provides new insights into coronavirus spike stability determinants and explores the immune landscape of viral spike proteins.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Robert Kirchdoerfer", + "author_inst": "University of Wisconsin-Madison" + }, + { + "author_name": "Mahesh Bhandari", + "author_inst": "Iowa State University" + }, + { + "author_name": "Olnita Martini", + "author_inst": "The Scripps Research Intitute" + }, + { + "author_name": "Leigh M Sewell", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Sandhya Bangaru", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Kyoung-Jin Yoon", + "author_inst": "Iowa State University" + }, + { + "author_name": "Andrew Ward", + "author_inst": "The Scripps Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.02.18.20021881", "rel_title": "Association between 2019-nCoV transmission and N95 respirator use", @@ -1623052,25 +1623304,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.16.20023606", - "rel_title": "Estimation of the final size of the coronavirus epidemic by the logistic model", - "rel_date": "2020-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.16.20023606", - "rel_abs": "In this short paper, the logistic growth model and classic susceptible-infected-recovered dynamic model are used to estimate the final size of the coronavirus epidemic.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "milan batista", - "author_inst": "university of ljubljana" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.13.20022673", "rel_title": "Optimizing diagnostic strategy for novel coronavirus pneumonia, a multi-center study in Eastern China", @@ -1623342,6 +1623575,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.14.20022913", + "rel_title": "Estimating the Efficacy of Traffic Blockage and Quarantine for the Epidemic Caused by 2019-nCoV (COVID-19)", + "rel_date": "2020-02-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.14.20022913", + "rel_abs": "BackgroundSince the 2019-nCoV (COVID-19) outbreaks in Wuhan, China, the cumulative number of confirmed cases is increasing every day, and a large number of populations all over the world are at risk. The quarantine and traffic blockage can alleviate the risk of the epidemic and the infections, henceforth evaluating the efficacy of such actions is essential to inform policy makers and raise the public awareness of the importance of self-isolation and quarantine.\n\nMethodWe collected confirmed case data and the migration data, and introduced the quarantine factor and traffic blockage factor to the Flow-SEIR model. By varying the quarantine factor and traffic blockage factor, we simulated the change of the peak number and arrival time of infections, then the efficacy of these two intervation measures can be analyzed in our simulation. In our study, the self-protection at home is also included in quarantine.\n\nResultsIn the simulated results, the quarantine and traffic blockage are effective for epidemic control. For Hubei province, the current quarantine factor is estimaed to be 0.405, which means around 40.5% of suceptibles who are close contacting with are in quarantine, and the current traffic blockage factor is estimaed to be 0.66, which indicates around 34% of suceptibles who had flowed out from Hubei. For the other provinces outside Hubei, the current quarantine factor is estimated to be 0.285, and the current traffic blockage factor is estimated to be 0.26. With the quarantine and traffic blockage factor increasing, the number of infections decrease dramatically. We also simulated the start dates of quarantine and traffic blockage at four time points, the simulated results show that the early of warning is also effective for epidemic containing. However, provincial level traffic blockage can only alleviate 21.06% - 22.38% of the peak number of infections. In general, the quarantine is much more effective than the traffic blockage control.\n\nConclusionBoth of quarantine and traffic blockage are effective ways to control the spread of COVID-19. However, the eff icacy of quarantine is found to be much stronger than that of traffic blockage. Considering traffic blockage may also cause huge losses of economy, we propose to gradually deregulate the traffic blockage, and improve quarantine instead. Also, there might be a large number of asymptomatic carriers of COVID-19, the quarantine should be continued for a long time until the epidemic is totally under control.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Deqiang Li", + "author_inst": "Southeast University" + }, + { + "author_name": "Zhicheng Liu", + "author_inst": "Southeast University" + }, + { + "author_name": "Qinghe Liu", + "author_inst": "Southeast University" + }, + { + "author_name": "Zefei Gao", + "author_inst": "Southeast University" + }, + { + "author_name": "Junkai Zhu", + "author_inst": "Southeast University" + }, + { + "author_name": "Junyan Yang", + "author_inst": "Southeast University" + }, + { + "author_name": "Qiao Wang", + "author_inst": "Southeast University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.14.20021535", "rel_title": "Clinical Characteristics of 2019 Novel Infected Coronavirus Pneumonia\uff1aA Systemic Review and Meta-analysis", @@ -1624306,41 +1624582,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.11.20022236", - "rel_title": "Lockdown may partially halt the spread of 2019 novel coronavirus in Hubei province, China", - "rel_date": "2020-02-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.11.20022236", - "rel_abs": "We present a timely evaluation of the impact of lockdown on the 2019-nCov epidemic in Hubei province, China. The implementation appears to be effective in reducing about 60% of new infections and deaths, and its effect also appears to be sustainable even after its removal. Delaying its implementation reduces its effectiveness. However, the direct economic cost of such a lockdown remains to be seen and whether the model is replicable in other Chinese regions remains a matter of further investigation.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mingwang Shen", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Zhihang Peng", - "author_inst": "Nanjing Medical University" - }, - { - "author_name": "Yuming Guo", - "author_inst": "Monash University" - }, - { - "author_name": "Yanni Xiao", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Lei Zhang", - "author_inst": "Xi'an Jiaotong University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.11.20020735", "rel_title": "Facemask shortage and the novel coronavirus (2019-nCoV) outbreak: Reflection on public health measures", @@ -1624680,6 +1624921,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.10.20021725", + "rel_title": "Beyond R0: the importance of contact tracing when predicting epidemics", + "rel_date": "2020-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.10.20021725", + "rel_abs": "The basic reproductive number -- R0 -- is one of the most common and most commonly misapplied numbers in public health. Although often used to compare outbreaks and forecast pandemic risk, this single number belies the complexity that two different pathogens can exhibit, even when they have the same R0 [1-3]. Here, we show how to predict outbreak size using estimates of the distribution of secondary infections, leveraging both its average R0 and the underlying heterogeneity. To do so, we reformulate and extend a classic result from random network theory [4] that relies on contact tracing data to simultaneously determine the first moment (R0) and the higher moments (representing the heterogeneity) in the distribution of secondary infections. Further, we show the different ways in which this framework can be implemented in the data-scarce reality of emerging pathogens. Lastly, we demonstrate that without data on the heterogeneity in secondary infections for emerging infectious diseases like COVID-19, the uncertainty in outbreak size ranges dramatically. Taken together, our work highlights the critical need for contact tracing during emerging infectious disease outbreaks and the need to look beyond R0 when predicting epidemic size.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Laurent H\u00e9bert-Dufresne", + "author_inst": "University of Vermont" + }, + { + "author_name": "Benjamin M. Althouse", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Samuel V. Scarpino", + "author_inst": "Northeastern University" + }, + { + "author_name": "Antoine Allard", + "author_inst": "Universit\u00e9 Laval" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.11.20022095", "rel_title": "Primary Care Practitioners' Response to 2019 Novel Coronavirus Outbreak in China", @@ -1625892,81 +1626164,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.02.09.20021261", - "rel_title": "The effect of travel restrictions on the spread of the 2019 novel coronavirus (2019-nCoV) outbreak", - "rel_date": "2020-02-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.09.20021261", - "rel_abs": "Motivated by the rapid spread of a novel coronavirus (2019-nCoV) in Mainland China, we use a global metapopulation disease transmission model to project the impact of both domestic and international travel limitations on the national and international spread of the epidemic. The model is calibrated on the evidence of internationally imported cases before the implementation of the travel quarantine of Wuhan. By assuming a generation time of 7.5 days, the reproduction number is estimated to be 2.4 [90% CI 2.2-2.6]. The median estimate for number of cases before the travel ban implementation on January 23, 2020 is 58,956 [90% CI 40,759 - 87,471] in Wuhan and 3,491 [90% CI 1,924 - 7,360] in other locations in Mainland China. The model shows that as of January 23, most Chinese cities had already received a considerable number of infected cases, and the travel quarantine delays the overall epidemic progression by only 3 to 5 days. The travel quarantine has a more marked effect at the international scale, where we estimate the number of case importations to be reduced by 80% until the end of February. Modeling results also indicate that sustained 90% travel restrictions to and from Mainland China only modestly affect the epidemic trajectory unless combined with a 50% or higher reduction of transmission in the community.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Matteo Chinazzi", - "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA" - }, - { - "author_name": "Jessica T. Davis", - "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA" - }, - { - "author_name": "Marco Ajelli", - "author_inst": "Bruno Kessler Foundation, Trento, Italy" - }, - { - "author_name": "Corrado Gioannini", - "author_inst": "ISI Foundation, Turin, Italy" - }, - { - "author_name": "Maria Litvinova", - "author_inst": "ISI Foundation, Turin, Italy" - }, - { - "author_name": "Stefano Merler", - "author_inst": "Bruno Kessler Foundation, Trento, Italy" - }, - { - "author_name": "Ana Pastore y Piontti", - "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA" - }, - { - "author_name": "Luca Rossi", - "author_inst": "ISI Foundation, Turin, Italy" - }, - { - "author_name": "Kaiyuan Sun", - "author_inst": "Fogarty International Center, NIH, USA" - }, - { - "author_name": "C\u00e9cile Viboud", - "author_inst": "Fogarty International Center, NIH, USA" - }, - { - "author_name": "Xinyue Xiong", - "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA" - }, - { - "author_name": "Hongjie Yu", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "M. Elizabeth Halloran", - "author_inst": "Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA" - }, - { - "author_name": "Ira M. Longini Jr.", - "author_inst": "Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, USA" - }, - { - "author_name": "Alessandro Vespignani", - "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA, USA; ISI Foundation, Turin, Italy" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.04.934232", "rel_title": "Design of multi epitope-based peptide vaccine against E protein of human 2019-nCoV: An immunoinformatics approach", @@ -1626254,6 +1626451,57 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.02.07.20021071", + "rel_title": "Incorporating Human Movement Data to Improve Epidemiological Estimates for 2019-nCoV", + "rel_date": "2020-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.07.20021071", + "rel_abs": "Estimating the key epidemiological features of the novel coronavirus (2019-nCoV) epidemic proves to be challenging, given incompleteness and delays in early data reporting, in particular, the severe under-reporting bias in the epicenter, Wuhan, Hubei Province, China. As a result, the current literature reports widely varying estimates. We developed an alternative geo-stratified debiasing estimation framework by incorporating human mobility with case reporting data in three stratified zones, i.e., Wuhan, Hubei Province excluding Wuhan, and mainland China excluding Hubei. We estimated the latent infection ratio to be around 0.12% (18,556 people) and the basic reproduction number to be 3.24 in Wuhan before the citys lockdown on January 23, 2020. The findings based on this debiasing framework have important implications to prioritization of control and prevention efforts.\n\nOne Sentence SummaryA geo-stratified debiasing approach incorporating human movement data was developed to improve modeling of the 2019-nCoV epidemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Zhidong Cao", + "author_inst": "Institute of Automation, Chinese Academy of Sciences" + }, + { + "author_name": "Qingpeng Zhang", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Xin Lu", + "author_inst": "National University of Defense Technology" + }, + { + "author_name": "Dirk Pfeiffer", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Lei Wang", + "author_inst": "Chinese Academy of Sciences" + }, + { + "author_name": "Hongbing Song", + "author_inst": "Chinese PLA Center for Disease Control and Prevention" + }, + { + "author_name": "Tao Pei", + "author_inst": "Institute of Geographical Sciences and Natural Resources Research, Chinese Academy of Sciences" + }, + { + "author_name": "Zhongwei Jia", + "author_inst": "Peking University" + }, + { + "author_name": "Daniel Dajun Zeng", + "author_inst": "Institute of Automation, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.06.20020941", "rel_title": "Analysis of the epidemic growth of the early 2019-nCoV outbreak using internationally confirmed cases", @@ -1627498,45 +1627746,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.02.03.932350", - "rel_title": "Machine learning-based analysis of genomes suggests associations between Wuhan 2019-nCoV and bat Betacoronaviruses", - "rel_date": "2020-02-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.03.932350", - "rel_abs": "As of February 20, 2020, the 2019 novel coronavirus (renamed to COVID-19) spread to 30 countries with 2130 deaths and more than 75500 confirmed cases. COVID-19 is being compared to the infamous SARS coronavirus, which resulted, between November 2002 and July 2003, in 8098 confirmed cases worldwide with a 9.6% death rate and 774 deaths. Though COVID-19 has a death rate of 2.8% as of 20 February, the 75752 confirmed cases in a few weeks (December 8, 2019 to February 20, 2020) are alarming, with cases likely being under-reported given the comparatively longer incubation period. Such outbreaks demand elucidation of taxonomic classification and origin of the virus genomic sequence, for strategic planning, containment, and treatment. This paper identifies an intrinsic COVID-19 genomic signature and uses it together with a machine learning-based alignment-free approach for an ultra-fast, scalable, and highly accurate classification of whole COVID-19 genomes. The proposed method combines supervised machine learning with digital signal processing for genome analyses, augmented by a decision tree approach to the machine learning component, and a Spearmans rank correlation coefficient analysis for result validation. These tools are used to analyze a large dataset of over 5000 unique viral genomic sequences, totalling 61.8 million bp. Our results support a hypothesis of a bat origin and classify COVID-19 as Sarbecovirus, within Betacoronavirus. Our method achieves high levels of classification accuracy and discovers the most relevant relationships among over 5,000 viral genomes within a few minutes, ab initio, using raw DNA sequence data alone, and without any specialized biological knowledge, training, gene or genome annotations. This suggests that, for novel viral and pathogen genome sequences, this alignment-free whole-genome machine-learning approach can provide a reliable real-time option for taxonomic classification.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Gurjit S Randhawa", - "author_inst": "University of Western Ontario" - }, - { - "author_name": "Maximillian P.M. Soltysiak", - "author_inst": "University of Western Ontario" - }, - { - "author_name": "Hadi El Roz", - "author_inst": "University of Western Ontario" - }, - { - "author_name": "Camila P.E. de Souza", - "author_inst": "University of Western Ontario" - }, - { - "author_name": "Kathleen A. Hill", - "author_inst": "University of Western Ontario" - }, - { - "author_name": "Lila Kari", - "author_inst": "University of Waterloo" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.02.03.933226", "rel_title": "Preliminary identification of potential vaccine targets for 2019-nCoV based on SARS-CoV immunological studies", @@ -1627676,6 +1627885,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.01.31.20019901", + "rel_title": "Early dynamics of transmission and control of 2019-nCoV: a mathematical modelling study", + "rel_date": "2020-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.01.31.20019901", + "rel_abs": "BackgroundAn outbreak of the novel coronavirus SARS-CoV-2 has led to 46,997 confirmed cases as of 13th February 2020. Understanding the early transmission dynamics of the infection and evaluating the effectiveness of control measures is crucial for assessing the potential for sustained transmission to occur in new areas.\n\nMethodsWe combined a stochastic transmission model with data on cases of novel coronavirus disease (COVID-19) in Wuhan and international cases that originated in Wuhan to estimate how transmission had varied over time during January and February 2020. Based on these estimates, we then calculated the probability that newly introduced cases might generate outbreaks in other areas.\n\nFindingsWe estimated that the median daily reproduction number, Rt, declined from 2.35 (95% CI: 1.15-4.77) one week before travel restrictions were introduced on 23rd January to 1.05 (95% CI: 0.413-2.39) one week after. Based on our estimates of Rt,we calculated that in locations with similar transmission potential as Wuhan in early January, once there are at least four independently introduced cases, there is a more than 50% chance the infection will establish within that population.\n\nInterpretationOur results show that COVID-19 transmission likely declined in Wuhan during late January 2020, coinciding with the introduction of control measures. As more cases arrive in international locations with similar transmission potential to Wuhan pre-control, it is likely many chains of transmission will fail to establish initially, but may still cause new outbreaks eventually.\n\nFundingWellcome Trust (206250/Z/17/Z, 210758/Z/18/Z), HDR UK (MR/S003975/1), Gates Foundation (INV-003174), NIHR (16/137/109)", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Adam J Kucharski", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Timothy W Russell", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Charlie Diamond", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Yang Liu", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "CMMID nCoV working group", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "John Edmunds", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene & Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.01.30.20019844", "rel_title": "Early evaluation of the Wuhan City travel restrictions in response to the 2019 novel coronavirus outbreak", @@ -1628672,33 +1628928,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.01.27.921536", - "rel_title": "Protective Population Behavior Change in Outbreaks of Emerging Infectious Disease", - "rel_date": "2020-01-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.27.921536", - "rel_abs": "During outbreaks of emerging infections, the lack of effective drugs and vaccines increases reliance on non-pharmacologic public health interventions and behavior change to limit human-to-human transmission. Interventions that increase the speed with which infected individuals remove themselves from the susceptible population are paramount, particularly isolation and hospitalization. Ebola virus disease (EVD), Severe Acute Respiratory Syndrome (SARS), and Middle East Respiratory Syndrome (MERS) are zoonotic viruses that have caused significant recent outbreaks with sustained human-to-human transmission. This investigation quantified changing mean removal rates (MRR) and days from symptom onset to hospitalization (DSOH) of infected individuals from the population in seven different outbreaks of EVD, SARS, and MERS, to test for statistically significant differences in these metrics between outbreaks. We found that epidemic week and viral serial interval were correlated with the speed with which populations developed and maintained health behaviors in each outbreak.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Evans K Lodge", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Annakate M Schatz", - "author_inst": "University of Georgia" - }, - { - "author_name": "John M Drake", - "author_inst": "University of Georgia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2020.01.27.921627", "rel_title": "Nelfinavir was predicted to be a potential inhibitor of 2019 nCov main protease by an integrative approach combining homology modelling, molecular docking and binding free energy calculation", @@ -1628889,6 +1629118,121 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.01.25.919787", + "rel_title": "Transmission dynamics of 2019 novel coronavirus (2019-nCoV)", + "rel_date": "2020-01-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.25.919787", + "rel_abs": "RationaleSeveral studies have estimated basic production number of novel coronavirus pneumonia (NCP). However, the time-varying transmission dynamics of NCP during the outbreak remain unclear.\n\nObjectivesWe aimed to estimate the basic and time-varying transmission dynamics of NCP across China, and compared them with SARS.\n\nMethodsData on NCP cases by February 7, 2020 were collected from epidemiological investigations or official websites. Data on severe acute respiratory syndrome (SARS) cases in Guangdong Province, Beijing and Hong Kong during 2002-2003 were also obtained. We estimated the doubling time, basic reproduction number (R0) and time-varying reproduction number (Rt) of NCP and SARS.\n\nMeasurements and main resultsAs of February 7, 2020, 34,598 NCP cases were identified in China, and daily confirmed cases decreased after February 4. The doubling time of NCP nationwide was 2.4 days which was shorter than that of SARS in Guangdong (14.3 days), Hong Kong (5.7 days) and Beijing (12.4 days). The R0 of NCP cases nationwide and in Wuhan were 4.5 and 4.4 respectively, which were higher than R0 of SARS in Guangdong (R0=2.3), Hongkong (R0=2.3), and Beijing (R0=2.6). The Rt for NCP continuously decreased especially after January 16 nationwide and in Wuhan. The R0 for secondary NCP cases in Guangdong was 0.6, and the Rt values were less than 1 during the epidemic.\n\nConclusionsNCP may have a higher transmissibility than SARS, and the efforts of containing the outbreak are effective. However, the efforts are needed to persist in for reducing time-varying reproduction number below one.\n\nAt a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSSince December 29, 2019, pneumonia infection with 2019-nCoV, now named as Novel Coronavirus Pneumonia (NCP), occurred in Wuhan, Hubei Province, China. The disease has rapidly spread from Wuhan to other areas. As a novel virus, the time-varying transmission dynamics of NCP remain unclear, and it is also important to compare it with SARS.\n\nWhat This Study Adds to the FieldWe compared the transmission dynamics of NCP with SARS, and found that NCP has a higher transmissibility than SARS. Time-varying production number indicates that rigorous control measures taken by governments are effective across China, and persistent efforts are needed to be taken for reducing instantaneous reproduction number below one.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Tao Liu", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jianxiong Hu", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jianpeng Xiao", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Guanhao He", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Min Kang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Zuhua Rong", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Lifeng Lin", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Haojie Zhong", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Qiong Huang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Aiping Deng", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Weilin Zeng", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Xiaohua Tan", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Siqing Zeng", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Zhihua Zhu", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jiansen Li", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Dexin Gong", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Donghua Wan", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Shaowei Chen", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Lingchuan Guo", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Yan Li", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Limei Sun", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Wenjia Liang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Tie Song", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Jianfeng He", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Wenjun Ma", + "author_inst": "Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.01.25.919688", "rel_title": "Origin time and epidemic dynamics of the 2019 novel coronavirus",