Merge pull request #897 from ScilifelabDataCentre/develop

Updates W41

content/english/dashboards/npc-statistics.md

@@ -11,16 +11,19 @@ aliases:
 ---
 
 <div class="alert alert-info small">
-  <p><i class="bi bi-exclamation-triangle-fill"></i>The National Pandemic Center (NPC) at Karolinska Institute ceased operations of high throughput PCR diagnostics on 2020-12-21.</p>
-  <p><span class="font-weight-bold">The data presented here receives no further updates</span> and only remains for historical reference.</p>
+  <p><i class="bi bi-exclamation-triangle-fill"></i>The National Pandemic Centre (NPC) at Karolinska Institute ceased operations of high throughput PCR diagnostics on 2020-12-21.</p>
+  <p><span class="font-weight-bold">The data presented here is no longer updated</span> but is kept for historical reference.</p>
   <a href="https://nyheter.ki.se/covid-19-tester-ki-atergar-till-ordinarie-laboratorieverksamhet-men-har-fortsatt-beredskap">KI Press Release</a>
 </div>
 
+The dataset visualised in the graphs on this page is available [here](https://datagraphics.dckube.scilifelab.se/dataset/bbbaf64a25a1452287a8630503f07418).  The numbers reported here were compiled automatically and, as such, might not correspond to
+the numbers reported through other sources for different reasons.
+
 #### Total NPC test numbers
 
-The total number of SARS-CoV-2 (COVID-19) tests run at NPC since
-the start, split up into positive, negative and invalid/inconclusive
-results.
+The total number of SARS-CoV-2 (COVID-19) tests conducted at the national Pandemic Centre (NPC) since the start of the pandemic, separated according to whether the results were positive, negative, or invalid/inconclusive.
+
+Source code for the below graph is available [here](https://datagraphics.dckube.scilifelab.se/graphic/ba0b27320fe74ad0aef59a26be6c37f1).
 
 <div class="d-lg-none alert alert-info">
   Scroll the plot sideways to view all data.
@@ -32,8 +35,9 @@ results.
 
 #### NPC test numbers
 
-The number of SARS-CoV-2 (COVID-19) tests run daily or weekly, split up into
-positive, negative and invalid/inconclusive results.
+The number of SARS-CoV-2 (COVID-19) tests ran daily or weekly, divided according to whether results were positive, negative, or invalid/inconclusive.
+
+Source code is available for both the [daily](https://datagraphics.dckube.scilifelab.se/graphic/ddb1119aefce47d58d0b3a49e98b4fcc) and [weekly](https://datagraphics.dckube.scilifelab.se/graphic/1f2322f4301c4773878c956c578e8caf) graphs below.
 
   <div id="dwbuttons"><button class="btn btn-secondary" type="button" data-toggle="collapse" data-target="#daily_stacked_bar_chart" aria-expanded="true" aria-controls="#daily_stacked_bar_chart">
     Daily
@@ -62,8 +66,10 @@ positive, negative and invalid/inconclusive results.
 
 #### NPC tests positive fraction
 
-The fraction of daily or weekly SARS-CoV-2 (COVID-19) tests that are positive,
-as percent of all tests (excluding invalid/inconclusive).
+The fraction of daily or weekly SARS-CoV-2 (COVID-19) tests that were positive,
+as percentage of all tests conducted (excluding invalid/inconclusive).
+
+Source code is available for both the [daily](https://datagraphics.dckube.scilifelab.se/graphic/b31c50be59c84c93986c25b052115a65) and [weekly](https://datagraphics.dckube.scilifelab.se/graphic/7f27ae237b8146a498ab4014aadc35db) graphs below.
 
   <div id="dwbuttons"><button class="btn btn-secondary" type="button" data-toggle="collapse" data-target="#daily_positive_bar_chart" aria-expanded="true" aria-controls="#daily_positive_bar_chart">
     Daily
@@ -91,9 +97,10 @@ as percent of all tests (excluding invalid/inconclusive).
 
 #### Cumulative NPC test numbers
 
-The sum of all SARS-CoV-2 (COVID-19) virus tests run at NPC since the
-start, as a function of date, and split up into positive, negative
-and invalid/inconclusive results.
+The sum of all SARS-CoV-2 (COVID-19) virus tests conducted at NPC since the
+start of the pandemic, as a function of date, and divided according to whether results were positive, negative, or invalid/inconclusive.
+
+Source code for the below graph is available [here](https://datagraphics.dckube.scilifelab.se/graphic/9145856246004419983d39fcf56d9eb6).
 
 <div class="d-lg-none alert alert-info">
   Scroll the plot sideways to view all data.
@@ -103,40 +110,25 @@ and invalid/inconclusive results.
   <div id="cumulative-plot"></div>
 </div>
 
-NPC was a facility for
+The National Pandemic Centre (NPC) was a facility for
 [SARS-CoV-2 (COVID-19) testing](https://ki.se/mtc/ctmr-and-covid-19)
-set up within the
+established within the
 [Centre for Translational Microbiome Research (CTMR)](https://ki.se/en/research/centre-for-translational-microbiome-research-ctmr)
 at
 [Karolinska Institutet (KI)](https://ki.se/en)/[SciLifeLab](https://www.scilifelab.se/).
-At the end of March 2020 the large-scale microbiome research lab was
-quickly converted into a center to assist Sweden in analyzing
-SARS-CoV-2 tests. This was made possible through a donation by the
-[Knut and Alice Wallenberg Foundation (KAW)](https://kaw.wallenberg.org/en)
-in combination with a previously established collaboration with
-[MGI Tech](https://en.mgitech.cn/) in Shenzen, China. Initially providing
-assistance with RNA-extraction capacity to Karolinska
-Universitetslaboratoriet, NPC quickly expanded into providing a
-facility providing increased SARS-CoV-2 testing capacity to all
-regions of Sweden.
-
-The final capacity of the National Pandemic Center at KI/SciLifeLab
-reached approximately 10,000 test per day, with results typically
-returned within 24 hours from the sample arriving to the lab. NPC
+At the end of March 2020, the large-scale microbiome research lab was
+quickly converted into a centre to assist Sweden with analysing
+SARS-CoV-2 tests. This was made possible by a donation from the
+[Knut and Alice Wallenberg Foundation (KAW)](https://kaw.wallenberg.org/en) and a previously established collaboration with
+[MGI Tech](https://en.mgitech.cn/) in Shenzen, China. The NPC initially helped to expand the RNA-extraction capacity at Karolinska
+Universitets laboratoriet. However, it quickly expanded into a facility that increased the testing capacity across all regions of Sweden.
+
+The final capacity of the National Pandemic Centre at KI/SciLifeLab
+was approximately 10,000 tests per day. The results were typically
+returned within 24 hours of the sample arriving to the lab. NPC
 exclusively performed PCR-based analyses, not serological
 (antibody-based) analyses.
 
-These numbers are compiled automatically and might not correspond to
-the numbers reported through other sources for different reasons.
-
-The dataset visualized in the graphs is available
-[here](https://datagraphics.dckube.scilifelab.se/dataset/bbbaf64a25a1452287a8630503f07418).
-The source code for the graphs are
-[here](https://datagraphics.dckube.scilifelab.se/graphic/ba0b27320fe74ad0aef59a26be6c37f1),
-[here](https://datagraphics.dckube.scilifelab.se/graphic/ddb1119aefce47d58d0b3a49e98b4fcc),
-[here](https://datagraphics.dckube.scilifelab.se/graphic/b31c50be59c84c93986c25b052115a65)
-and [here](https://datagraphics.dckube.scilifelab.se/graphic/9145856246004419983d39fcf56d9eb6).
-
 <script src="https://cdn.jsdelivr.net/npm/[email protected]"></script>
 <script src="https://cdn.jsdelivr.net/npm/[email protected]"></script>
 <script src="https://cdn.jsdelivr.net/npm/[email protected]"></script>

content/english/data-management.md

@@ -25,15 +25,16 @@ Here we give an overview of available resources regarding research data manageme
 - [ENA submission guidelines](/support_services/tutorial_ena/tutorial_ena_intro/) - guidance developed to aid submissions to the European Nucleotide Archive (ENA)
 - [SciLifeLab Data Guidelines](https://scilifelab-data-guidelines.readthedocs.io/en/latest/docs/index.html) - data type specific guidelines for good data management practices
 - [SciLifeLab Data Stewardship Wizard, DSW](http://dsw.scilifelab.se/) - a customised tool for creating Data Management Plans (DMPs) with templates conforming to the requirements of the Swedish Research Council and other stakeholders
-- [SciLifeLab Data Management helpdesk](mailto:[email protected]) - data stewards from NBIS and SciLifeLab Data Centre are available to discuss and provide support regarding data management questions
+- [SciLifeLab Data Management Helpdesk](mailto:[email protected]) - data stewards from NBIS and SciLifeLab Data Centre are available to discuss and provide support regarding data management questions
+- [SciLifeLab Research Data Management Guidelines](https://data-guidelines.scilifelab.se) - NBIS and SciLifeLab Data Centre have aggregated resources related to life science reseach data management in Sweden. Guidelines are available for each stage of the data lifecycle
 
 ### ELIXIR Research Data Management Kit (RDMkit)
 
 ![SND logo](/img/logos/rdmkit_logo.png#floatright)
 
 The [ELIXIR Research Data Management Kit (RDMkit)](https://rdmkit.elixir-europe.org/) is an online guide containing good data management practices applicable to research projects from the beginning to the end. Developed and managed by people who work every day with life science data, the RDMkit has guidelines, information, and pointers to help you with problems throughout the data’s life cycle. RDMkit supports FAIR data — Findable, Accessible, Interoperable and Reusable — by-design, from the first steps of data management planning to the final steps of depositing data in public archives.
 
-Information is organised by role (e.g., researcher, data steward), scientific domain (e.g., proteomics, human data, bioimaging data), tasks (e.g., data analysis, data management plan, licensing).
+Information is organised by role (e.g. researcher, data steward), scientific domain (e.g. proteomics, human data, bioimaging data), tasks (e.g. data analysis, data management plan, licensing).
 
 ### Swedish National Data Service (SND)
 

content/english/pathogens/_index.md

@@ -5,7 +5,7 @@ toc: false
 
 Our **Emerging pathogens** section is dedicated to bringing you the latest information on new and emerging pathogens. Each page will be dedicated to the data/tools/publications available for a given pathogen. You are also able to submit announcements, which you can use to alert others of useful resources. Please note that, due to the necessarily fast-paced nature of work related to emerging pathogens, that much of the work detailed on these pages may not have been subject to *peer review*. Further, pages may be subject to frequent change as more information becomes available.
 
-- **[Monkeypox](monkeypox)**, active, maintained starting from May 2022
-- **Severe hepatitis of unknown origin in children** ([WHO](https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON376))
+- **[Acute hepatitis of unknown origin in children](hepatitis_unknown_origin)**
+- **[Monkeypox](monkeypox)**
 - **[SARS-CoV-2 Variants of Concern](voc/):**
-    - [Omicron](voc/omicron/), archived, maintained between December 2021 and February 2022
+    - [Omicron](voc/omicron/) (page no longer actively maintained - last updated February 2022)

content/english/pathogens/hepatitis_unknown_origin.md

@@ -0,0 +1,39 @@
+---
+title: "Children with acute hepatitis of unknown etiology"
+toc: true
+---
+
+## Background
+
+Hepatitis (severe liver inflammation) can result from pathogens, toxins, or autoimmune reactions. Most often, it is caused by the hepatitis A, B, D, or E viruses (hepatitis D is always found together with B). However, other viruses, such as the Epstein-Barr virus or Cytomegalovirus (CMV), may cause hepatitis in children.
+
+Patients often exhibit a yellowish colouration in the skin and whites of the eye, as well as gastrointestinal symptoms, such as vomiting, diarrhea, and light faeces. In severe cases, it can ultimately lead to liver failure that requires dialysis or transplantation to treat. Hepatitis in children (<16 years) is not common, but cases can become acute. Today, between every second and third case of childhood hepatitis is of unknown origin, meaning that the cause is not identified, according to estimates from the Centre for Disease Control (CDC) [(CDC, 2022)](https://www.cdc.gov/ncird/investigation/hepatitis-unknown-cause/overview-what-to-know.html). There has been an unusual increase in the number of cases of acute heptatitis of unknown etiology in children over the last year.
+
+## Outbreak in 2022
+
+In April 2022, a number of cases of severe hepatitis of unknown origin were detected in children in the UK. These cases were subsequently reported to the WHO International Health Regulations system. The children had not tested positive for any of the most common viral hepatitis types A-E, nor any other known causes of hepatitis
+[UK Health Security Agency, 2022](https://www.gov.uk/government/news/hepatitis-liver-inflammation-cases-in-children-latest-updates). Since then, multiple countries, including the US, Japan, Ireland, Netherlands, Denmark, and Sweden, have reported similar increases in the number of pediatric patients with hepatitis of unknown origin ([Folkhälsomyndigheten, 2022](https://www.folkhalsomyndigheten.se/nyheter-och-press/nyhetsarkiv/2022/maj/misstankta-fall-av-hepatit-med-okand-orsak-rapporterade-i-sverige/)). Research into the possible causes and contributing factors, is still ongoing, as are monitoring efforts focussed on identifying cases.
+
+The primary hypothesis, as of October 2022, is that the cases may be caused by human adenovirus (HAdV). In support of this, adenovirus was the most frequently detected potential pathogen in a [matched case control study of 74 cases and 225 controls in the UK](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1094573/acute-hepatitis-technical-briefing-4.pdf). However, not all pediatric patients with acute hepatitis of unknown etiology have tested positive for adenovirus. In the same study, researchers considered the possibility that there may be a connection to COVID-19, but found no evidence for this.
+
+Adenoviruses are common viruses, with >100 types and seven species (A-G), capable of infecting both humans and animals. Usually, adenoviruses cause only mild symptoms in humans, although the types of symptoms differ, with some subtypes causing respiratory illnesses and others causing gastroenteritis, for example. Adenovirus type F41, which is currently under investigation by the CDC, is part of the latter group; typically causing diarrhea, abdominal pain, and vomiting over a relatively short period (1-2 weeks) in otherwise healthy children and adults. [Rafie *et al.* (2021)](https://doi.org/10.1126/sciadv.abe0974) recently identified the structural information about the  HAdVs types F40 and F41. These two HAdVs are common causes of global diarrhea-associated death in young children.
+
+The CDC is currently conducting research and working in close collaboration with health providers across the US to identify children with hepatitis of unknown origin ([CDC, 2022](https://www.cdc.gov/ncird/investigation/hepatitis-unknown-cause/overview-what-to-know.html)). Today, many research groups are investigating possible causes for increased hepatitis of unknown etiology in children. In addition, there are multiple ongoing surveillance efforts including, for example, monitoring focussed on the detection on pathogens, including adenoviruses, in wastewater. A group in Sweden have recently developed new primer sets to detect recent human adenovirus F41 variants in wastewater to this end ([Perez-Zabaleta *et al.*, 2022](https://www.medrxiv.org/content/10.1101/2022.09.16.22280038v1.full)). The Swedish COVID-19 and Pandemic Preparedness Portal hopes to add more content on adenoviruses in the near future.
+
+### Timeline of outbreak
+<br>
+<figure><img width="1000" src="/img/other/hepatitis_timeline.png"></figure>
+
+## Resources
+
+* Swedish Health Agency (Folkhälsomyndigheten): [Suspected cases of hepatitis of unknown cause reported in Sweden](https://www.folkhalsomyndigheten.se/nyheter-och-press/nyhetsarkiv/2022/maj/misstankta-fall-av-hepatit-med-okand-orsak-rapporterade-i-sverige/)
+
+* European Centre for Disease Prevention and Control (ECDC): [Surveillance bulletin](https://www.ecdc.europa.eu/en/hepatitis/joint-hepatitis-unknown-origin-children-surveillance-bulletin)
+
+* World Health Organisation (WHO): [Information about hepatitis outbreaks](https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON400)
+
+* [Technical briefing from the UK government](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1073704/acute-hepatitis-technical-briefing-2.pdf)
+
+* National Health Service (NHS): [Investigating the rise in hepatitis in children, UK](https://www.gosh.nhs.uk/news/investigating-the-rise-in-hepatitis-in-children/)
+
+* Centre for Disease Control (CDC): [Information about Hepatitis of unknown cause, US](https://www.cdc.gov/ncird/investigation/hepatitis-unknown-cause/overview-what-to-know.html) and [General information about adenoviruses](https://www.cdc.gov/adenovirus/index.html)

content/english/pathogens/voc/_index.md

@@ -1,5 +1,5 @@
 ---
-title: SARS-CoV-2 Variants of Concern (VOC)
+title: SARS-CoV-2 variants of concern (VoC)
 toc: true
 aliases:
     - /voc/