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Merge pull request #908 from ScilifelabDataCentre/develop
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Update W44
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@senthil10
senthil10 authored Nov 3, 2022
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7 changes: 4 additions & 3 deletions Dockerfiles/Dockerfile
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FROM klakegg/hugo:0.91.2-onbuild AS build
FROM klakegg/hugo:0.104.3-ubuntu-onbuild AS build

FROM nginx:alpine
COPY Dockerfiles/default.conf /etc/nginx/conf.d/default.conf
FROM nginxinc/nginx-unprivileged:alpine
COPY --from=build /target /usr/share/nginx/html

EXPOSE 8080
31 changes: 0 additions & 31 deletions Dockerfiles/default.conf
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1 change: 0 additions & 1 deletion content/english/dashboards/_index.md
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Expand Up @@ -122,4 +122,3 @@ CSSS continuously collects data on COVID-19 prevalence, symptoms, and vaccinatio

<script src="https://datagraphics.dckube.scilifelab.se/graphic/e4c6a7b8bff648a5adaabbdd3d994bf9.js?id=serology"></script>
<script src="https://datagraphics.dckube.scilifelab.se/graphic/93bad55e86ad4b0f97d4d27c77862bc9.js?id=stockholm_wastewater"></script>
<script src="https://datagraphics.dckube.scilifelab.se/graphic/530ca62cc6f7449680793a252155fee3.js?id=postcovid_halthcare_contacts"></script>
6 changes: 1 addition & 5 deletions content/english/resources/rapid_type_variants.md
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Expand Up @@ -12,8 +12,4 @@ for_background_table:
lab: Uppsala University Hospital
---

During the recent SARS-CoV-2 pandemic it has been evident that a swift response relies on the capacity to quickly establish methodologies for clinical diagnostics and epidemiologic surveillance.Whereas the first generation of commercial kits were sold as Research Use Only, had low capacity and often characterized by poor performance, robust methodologies were despite tremendous effort from the manufacturers and frequent use of Emergency Use labeling by regulatory agencies not available until the first wave was almost over.

When the virus variants of concern (VOCs) emerged, it was clear that ambitious sequencing programs, although remarkably impressive and invaluable for generation of big data, nevertheless were insufficient in terms of capacity and sensitivity and were inherently too slow for clinical usage. Instead, first line surveillance had to be accomplished by simpler methods that focused on critical sites for defining polymorphism rather than whole genome sequencing.

From spring 2021 to summer 2022, we have typed almost all positive samples and monitored the emergence of different VOCs including B.1.1.7/Alpha, B.617.2/Delta, as well as the Omicron variants BA.1, BA.2 and BA.5. While the resolution is lower, the sensitivity is higher and its focus on relevant mutations mostly provides sufficient information to correctly identify the VOCs. For contact tracing and for clinical decisions regarding type-specific therapy, rapid typing was far superior compared to whole genome sequencing. In this project, we will develop a generalized platform based on focused sequencing techniques combined with serological testing that can be used for rapid detection and characterization of emerging variants of any etiologic agent.
Throughout the recent SARS-CoV-2 pandemic, it has been evident that a swift response relies on the capacity to quickly establish methodologies for clinical diagnostics and epidemiologic surveillance. The first generation of commercial kits were sold as "Research Use Only", had low capacity, and were often characterised by poor performance. Robust methodologies were, despite tremendous effort from the manufacturers and the frequent use of "Emergency Use" labelling by regulatory agencies, not available until the first wave was almost over. When the virus variants of concern (VOCs) emerged, it was clear that ambitious sequencing programs, although remarkably impressive and invaluable for the generation of big data, were nevertheless insufficient in terms of capacity and sensitivity, and were inherently too slow for clinical usage. Instead, first line surveillance had to be accomplished by simpler methods that focused on critical sites for defining polymorphism, rather than whole genome sequencing. From spring 2021 to summer 2022, we have typed almost all positive samples and monitored the emergence of different VOCs, including B.1.1.7/Alpha, B.617.2/Delta, as well as the Omicron variants BA.1, BA.2 and BA.5. Whilst the resolution is lower, the sensitivity is higher and its focus on relevant mutations mostly provides sufficient information to correctly identify the VOCs. For both contact tracing and clinical decisions regarding type-specific therapy, rapid typing was far superior compared to whole genome sequencing. In this project, we will develop a generalised platform based on focused sequencing techniques combined with serological testing that can be used for the rapid detection and characterisation of emerging variants of any etiologic agent.
1 change: 0 additions & 1 deletion content/svenska/dashboards/_index.md
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Expand Up @@ -110,4 +110,3 @@ CSSS samlar kontinuerligt in data om Covid-19 förekomste, symptom, och vaccinat

<script src="https://datagraphics.dckube.scilifelab.se/graphic/e4c6a7b8bff648a5adaabbdd3d994bf9.js?id=serology"></script>
<script src="https://datagraphics.dckube.scilifelab.se/graphic/93bad55e86ad4b0f97d4d27c77862bc9.js?id=stockholm_wastewater"></script>
<script src="https://datagraphics.dckube.scilifelab.se/graphic/530ca62cc6f7449680793a252155fee3.js?id=postcovid_halthcare_contacts"></script>
273 changes: 272 additions & 1 deletion data/available_datasets.json
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{
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"Dang J.",
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"title": "Development and cross-national investigation of a model explaining participation in WHO-recommended and placebo behaviours to prevent COVID-19 infection",
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"Bieniek H.",
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"title": "Family still matters: Human social motivation across 42 countries during a global pandemic",
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"author": [
"Pick C. M.",
"Ko A.",
"Wormley A. S.",
"Wiezel A.",
"Kenrick D. T."
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"title": "Treating intrusive memories after trauma in healthcare workers: a Bayesian adaptive randomised trial developing an imagery-competing task intervention",
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"Ramineni V.",
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"doi": "10.15252/emmm.202215821",
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17 changes: 16 additions & 1 deletion data/funding.json
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{
"last_updated": "2022-09-30",
"last_updated": "2022-11-01",
"calls": [
{
"topic": [
"Infectious diseases",
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],
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"call_title": "Medical Research",
"call_url": "http://www.hedlundsstiftelse.se/ansokan/default_eng.htm",
"call_description": "The overall objective of the call is to support research related to brain diseases (including psychiatry), infectious disease, and chronic inflammatory diseases.",
"submission_deadline": "2023-01-31",
"submission_opendate": "2022-11-01",
"applicant": "A PhD researcher at a Swedish University/college conducting qualified medical research. The funds are paid out to the University/college.",
"funding_period": "Applications are approved one year at a time for a maximum of 3 years.",
"decision_date": "Following board meeting in April/May 2023."
},
{
"topic": [
"COVID-19",
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2 changes: 1 addition & 1 deletion data/publications.json
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