Merge pull request #1003 from ScilifelabDataCentre/develop

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content/english/about/partner_organisations.md

@@ -62,3 +62,19 @@ title: Partner organisations
     <p><a href="https://nbis.se">NBIS (National Bioinformatics Infrastructure Sweden)</a> is a distributed national research infrastructure supported by the Swedish Research Council (Vetenskapsrådet), Science for Life Laboratory, all major Swedish universities, and the Knut and Alice Wallenberg Foundation. It provides state-of-the-art bioinformatics to the life science research community in Sweden. NBIS is also the Swedish contact point to the European infrastructure for biological information, <a href="https://www.elixir-europe.org/">ELIXIR Europe</a>.</p>
   </div>
 </div>
+<hr class="faded" />
+
+<div class="row mt-4">
+  <div class="col-sm-12 col-md-12 col-lg-3 mt-3">
+    <figure class="figure">
+      <img height="65" alt="Global Alliance for Genomics & Health logo" src="/img/logos/ga4gh_logo.png">
+    </figure>
+  </div>
+  <div class="col-sm-12 col-md-12 col-lg-9">
+      <h6>GA4GH</h6>
+    <p>The Swedish COVID-19 & Pandemic Preparedness Data Portal is one of the many partners of the <a href="https://www.ga4gh.org/">Global Alliance for Genomics and Health (GA4GH)</a> and part of their <a href="https://www.ga4gh.org/what-we-do/communities-of-interest/">Infectious Disease Community</a>.</p>
+    <p>GA4GH is an international, non-profit organisation focused on advancing the responsible and effective sharing of genomic and health-related data. GA4GH aims to establish harmonised frameworks and standards in order to promote data interoperability and collaboration in genomics research and healthcare. At the same time, the alliance focuses on fully protecting the human rights of people who share their data. GA4GH brings together experts from various sectors, including academia, industry, and government, to address the ethical, legal, and technical challenges associated with genomic data sharing.</p>
+    <p>The Infectious Disease Community, a vital component of the GA4GH, plays a crucial role in bridging the realms of pathogen and host genomics. This community brings together international groups dedicated to standardising the use of genomic data for improved diagnosis and treatment of infectious diseases. International groups within the community collaborate to identify opportunities for sharing datasets, workflows, and processes, enabling them to address complex and previously insurmountable questions. Through these collective activities, the Infectious Disease Community facilitates the advancement of genomic research, ultimately leading to improved diagnostic and treatment approaches for infectious diseases.
+    </p>
+  </div>
+</div>

content/english/dashboards/_index.md

@@ -13,4 +13,4 @@ aliases:
       - /dashboards_topics/
 ---
 
-The *Dashboards* section describes research done on a given subject relevant to pandemic preparedness research by researchers affiliated with a Swedish research institute. Specifically, in our case we write about COVID-19 and SARS-CoV-2, infectious diseases in general, antibiotic resistance, and Mpox. The goal is to highlight and visualise openly shared data that can potentially be used by many other researchers to make further discoveries.
+The *Dashboards* section describes research done on a given subject relevant to pandemic preparedness research by researchers affiliated with a Swedish research institute. Specifically, in our case we write about COVID-19 and SARS-CoV-2, infectious diseases in general, antibiotic resistance, enteric viruses and Mpox. The goal is to highlight and visualise openly shared data that can potentially be used by many other researchers to make further discoveries.

content/english/dashboards/wastewater/_index.md

@@ -5,21 +5,21 @@ banner: /dashboard_thumbs/wastewater.jpg
 inline_toc: true
 type: wastewater
 menu:
-    dashboard_menu:
-        identifier: wastewater
-        name: Wastewater-based epidemiology in Sweden
-    other_data:
-        name: Environment
-        identifier: environment
-        weight: 50
-    wastewater:
-        name: Introduction
-        weight: 10
+  dashboard_menu:
+    identifier: wastewater
+    name: Wastewater-based epidemiology in Sweden
+  other_data:
+    name: Environment
+    identifier: environment
+    weight: 50
+  wastewater:
+    name: Introduction
+    weight: 10
 plotly: true
 aliases:
-    - /data_types/environment/wastewater/
-    - /data_types/environment/
-    - /dashboards/wastewater/introduction/
+  - /data_types/environment/wastewater/
+  - /data_types/environment/
+  - /dashboards/wastewater/introduction/
 dashboards_topics: [COVID-19, Infectious diseases]
 ---
 
@@ -55,9 +55,9 @@ Below is a map showing the wastewater treatment plants (WWTPs) from which wastew
 
 ## Background: Wastewater-based epidemiology
 
-The genomes of many pathogens, including SARS-CoV-2, can be detected in faecal samples collected from infected individuals (e.g. COVID-19 patients) using polymerase chain reaction (PCR) tests (see, for example, [Wu *et al*. (2020)](https://doi.org/10.1016/S2468-1253(20)30083-2)). Monitoring the levels of pathogens (e.g. SARS-CoV-2) in wastewater from communities can therefore provide an indication of the prevalence of that pathogen at a population-wide level, referred to as wastewater-based epidemiology ([Corpuz *et al.*, 2020](https://doi.org/10.1016/j.scitotenv.2020.140910)).
+The genomes of many pathogens, including SARS-CoV-2, can be detected in faecal samples collected from infected individuals (e.g. COVID-19 patients) using polymerase chain reaction (PCR) tests (see, for example, [Wu _et al_. (2020)](<https://doi.org/10.1016/S2468-1253(20)30083-2>)). Monitoring the levels of pathogens (e.g. SARS-CoV-2) in wastewater from communities can therefore provide an indication of the prevalence of that pathogen at a population-wide level, referred to as wastewater-based epidemiology ([Corpuz _et al._, 2020](https://doi.org/10.1016/j.scitotenv.2020.140910)).
 
-Wastewater, also referred to as “sewage” includes water from multiple sources in each household, including kitchen sinks, toilets, and showers. However, it could also include water from multiple other sources (for example, rainwater and water from industrial use). Samples used for wastewater epidemiology studies are collected periodically at wastewater treatment facilities; enabling assessments of viral load over time. Wastewater monitoring has been shown to be an effective early-warning system for outbreaks. For example, [Peccia *et al.* (2020)](https://doi.org/10.1038/s41587-020-0684-z) showed early on in the COVID-19 pandemic that SARS CoV-2 virus content in wastewater predicted increases in infection in the population and followed the epidemic trend, as measured by the number of COVID-19 cases and hospitalisation rates. More recently, [Wang *et al.* (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/) showed that the level of SARS-CoV-2 viral genomes in wastewater increased 1-2 weeks before there was an increase in the number of hospitalised COVID-19 patients. During the COVID-19 pandemic, surveillance of viral RNA levels in wastewater has been increasingly used to monitor and predict the spread of the disease.
+Wastewater, also referred to as “sewage” includes water from multiple sources in each household, including kitchen sinks, toilets, and showers. However, it could also include water from multiple other sources (for example, rainwater and water from industrial use). Samples used for wastewater epidemiology studies are collected periodically at wastewater treatment facilities; enabling assessments of viral load over time. Wastewater monitoring has been shown to be an effective early-warning system for outbreaks. For example, [Peccia _et al._ (2020)](https://doi.org/10.1038/s41587-020-0684-z) showed early on in the COVID-19 pandemic that SARS CoV-2 virus content in wastewater predicted increases in infection in the population and followed the epidemic trend, as measured by the number of COVID-19 cases and hospitalisation rates. More recently, [Wang _et al._ (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/) showed that the level of SARS-CoV-2 viral genomes in wastewater increased 1-2 weeks before there was an increase in the number of hospitalised COVID-19 patients. During the COVID-19 pandemic, surveillance of viral RNA levels in wastewater has been increasingly used to monitor and predict the spread of the disease.
 
 Wastewater monitoring should primarily be seen as a surveillance system. Taken together with data for infection testing, intensive care admissions etc., it may help in understanding the regional dynamics of disease outbreaks.
 

content/english/dashboards/wastewater/covid_quantification/_index.md

@@ -2,19 +2,20 @@
 title: SARS-CoV-2 quantification
 type: wastewater
 menu:
-    wastewater:
-        name: SARS-CoV-2 quantification
-        weight: 20
+  wastewater:
+    name: SARS-CoV-2 quantification
+    weight: 20
 plotly: true
 ---
 
 ## Quantification of SARS-CoV-2 across Sweden
+
 <br>
 
 All three groups involved in this dashboard quantify the levels of SARS-CoV-2 in wastewater. **The groups each measure different regions of Sweden, and some regions are covered by multiple groups**. Below are lists of the areas covered by each group. Click on the name of the group to go to their SARS-CoV-2 quantification data.
 
 - [**Gothenburg university (GU):**](/dashboards/wastewater/covid_quantification/covid_quant_gu/) Quantification of the level of SARS-CoV-2 in wastewater from Gothenburg by the Norder group at GU.
 
-- [**SEEC-KTH node:**](/dashboards/wastewater/covid_quantification/covid_quant_kth/) Quantification of the levels of SARS-CoV-2 in wastewater from Stockholm and Malmö by the SEEC-KTH node.
+- [**SEEC-KTH node:**](/dashboards/wastewater/covid_quantification/covid_quant_kth/) Quantification of the levels of SARS-CoV-2 in wastewater from Stockholm and Malmö by the SEEC-KTH node (no longer updated after June 2023, historic data is available).
 
 - [**SEEC-SLU node:**](/dashboards/wastewater/covid_quantification/covid_quant_slu/) Quantification of the levels of SARS-CoV-2 in wastewater from multiple sites, including Stockholm, Malmö, Gothenburg, Uppsala, Västerås, Örebro, Umeå, and many others, by the SEEC-SLU node.

content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md

@@ -109,6 +109,10 @@ After concentration, filtering, and preparation, the samples are analysed using
 
 - [Historic data for Stockholm; Gene copy number/week (raw wastewater) with bovine + PMMoV factor between April 2020 and August 2021](/dashboards/wastewater/covid_quantification/historic_stockholm).
 
+## Related data
+
+- SARS-CoV-2 variant analysis from wastewater (data available in the European Nucleotide Archive (ENA) under project number [PRJEB60156](https://www.ebi.ac.uk/ena/browser/view/PRJEB60156)): The group at KTH analysed samples from Stockholm and Malmö (2021-2022).
+
 <br>
 <div class="mt-3">
   <a href="/dashboards/wastewater/covid_quantification/"><i class="bi bi-arrow-left-circle-fill"></i> Go back to SARS-CoV-2 quantification within the wastewater epidemiology dashboard</a>

content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md

@@ -21,7 +21,7 @@ The data and visualisation on this page are usually updated weekly, typically on
 SLU-SEEC collect and analyse samples from multiple areas. The below table shows details about each of these sites. The table lists the towns/cities monitored, wastewater treatment plants (WWTP) that samples were collected from, the number of people in the catchment area (Number of people), and the dates that monitoring by SLU-SEEC started and ended monitoring (Start and End date, respectively). A value of 'null' for the end date indicates that collection is ongoing. An asterisk next to the number of people indicates that the figure is preliminary.
 
   <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slusites.json" height="775px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slusites.json" height="850px" >}}</div>
 </div>
 
 <!-- <p>
@@ -96,7 +96,7 @@ Please note that although the same methods are used for all cities shown on this
 </div>
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_slu_regular.json" height="550px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_slu_regular.json" height="600px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/wastewater/combined_slu_regular.py).
@@ -137,6 +137,10 @@ The data in the below graph and datafile represent the ratio of the copy numbers
 
 - [Historic data for Örebro and Umeå; amount of SARS-CoV-2 in Umeå and Örebro wastewater between October 2020 and June 2021](/dashboards/wastewater/covid_quantification/historic_orebro_umea).
 
+## Related data
+
+- SARS-CoV-2 variant analysis from wastewater (data available in the European Nucleotide Archive (ENA) under project number [PRJEB60156](https://www.ebi.ac.uk/ena/browser/view/PRJEB60156)): The group at SLU analysed samples from Uppsala, Örebro, Umeå, and Kalmar (2021-2022).
+
 <br>
 <div class="mt-3">
   <a href="/dashboards/wastewater/covid_quantification/"><i class="bi bi-arrow-left-circle-fill"></i> Go back to SARS-CoV-2 quantification within the wastewater epidemiology dashboard</a>

content/english/highlights/poliovirus_replication.md

@@ -6,7 +6,7 @@ banner: /highlights/banners/segmentation_highReso.jpeg
 banner_large: /highlights/banners/segmentation_highReso_large.jpeg
 banner_caption: A cryo-electron tomogram gives a 3D view of a poliovirus-infected cell six hours after infection. Newly produced virus capsids that have not yet been loaded with the viral genome are shown in white, whereas new particles that are loaded with the viral genome, and thus infectious, are shown in red. Double-membrane structures, that related to the cellular pathway of autophagy, are shown in purple. For scale, the capsids have a diameter of 30 nanometers.
 toc: false
-highlights_topics: [Infectious diseases]
+highlights_topics: [Infectious diseases, Enteric viruses]
 aliases:
     - /news/poliovirus_replication
     - /sv/news/poliovirus_replication

content/english/topics/covid-19.md

@@ -1,6 +1,6 @@
 ---
 title: COVID-19
-description:  COVID-19, caused by SARS-CoV-2, is a global pandemic challenging societies worldwide. Vaccines are crucial, but research is ongoing to address early detection, variant identification, treatment development, and future preparedness.
+description: COVID-19, caused by SARS-CoV-2, is a global pandemic challenging societies worldwide. Vaccines are crucial, but research is ongoing to address early detection, variant identification, treatment development, and future preparedness.
 banner: /topic_thumbs/topic_covid.jpg
 credits:
 toc: false

content/english/topics/enteric-virus.md

@@ -0,0 +1,30 @@
+---
+title: Enteric viruses
+description: Enteric viruses spread primarily through faecal-oral route, causing enteric disease (e.g. nausea, diarrhea, vomiting, abdominal pain). They include calicivirus, adenoviruses, astroviruses, rotaviruses, hepatitis viruses, and enteroviruses.
+banner: /topic_thumbs/topic_enteric.png
+credits:
+toc: false
+topic: Enteric viruses
+menu:
+    topics_menu:
+        name: Enteric viruses
+        identifier: enteric_viruses
+        weight: 50
+---
+
+## Background
+
+Enteric viruses are viruses that are primarily transmitted via the faecal-oral route, and that cause enteric disease (with symptoms e.g. nausea, diarrhea, vomiting, and abdominal pain). Many families of viruses are enteric viruses, including, for example, *calicivirus (including norovirus and sapovirus), adenoviruses, astroviruses, rotaviruses, hepatitis viruses, and enteroviruses*. Most enteric viruses cause only relatively mild symptoms in healthy individuals, some enteric viruses (e.g. poliovirus) can have serious health effect, with symptoms including meningitis and paralysis. Enteric viruses have been known to cause epidemics, for example, outbreaks of hepatitis A and coxsackieviruses have been reported worldwide within the latest decade.
+
+In the below paragraphs, we provide more detail regarding some examples of enteric viruses.
+
+**Noroviruses** belong to the Caliciviruses family. The norovirus GG2 is more commonly known as the "winter vomiting disease virus". Cases are typically seasonal, with peaks in winter. It is often spread between people in environments where individuals come into close contact, such as hospitals, nurseries, schools, and cruise ships. To read more about GG2, see resources by [folkhälsomyndigheten](https://www.folkhalsomyndigheten.se/folkhalsorapportering-statistik/statistik-a-o/sjukdomsstatistik/calicivirus-veckorapporter/sasong-20222023-for-calicivirusrapporter-vinterkraksjuka/), for example.
+
+**Hepatitis A (HAV)** and **hepatitis E (HEV)** are other examples of enteric viruses. The other four human hepatitis viruses are not transmitted via the faecal–oral route. Outbreaks of hepatitits A, caused by transmission in contaminated food or water, occur regularly. Read more about the 2022 outbreak in [our emerging pathogens section](https://www.covid19dataportal.se/pathogens/hepatitis_unknown_origin/).
+
+The **Enteroviruses** comprise of a group of around one hundred viruses of the Picornaviridae family. Examples include Enterovirus A-D (which includes Poliovirus (typ 1-3)) and Coxsackievirus (group A and B). All three Polioviruses can cause poliomyelitis, more commonly known as polio. There was a major polio epidemic in the early 20th century, polio vaccines were created in the 1950s in response, and mass vaccination programs were quickly implemented. In Sweden, the polio vaccine became part of the routine vaccination program for children in the mid-1960s and there have been no reported cases since the late 1970s. More information about the mass vaccination program is available (in Swedish) from [Folkälsomyndigheten](https://www.folkhalsomyndigheten.se/smittskydd-beredskap/vaccinationer/vacciner-som-anvands-i-sverige/polio/#:~:text=Polio%20i%20Sverige&text=I%20Sverige%20inleddes%20massvaccination%20i,sista%20inhemska%20fallet%20rapporterades%201977), along with more [information about ongoing efforts with polio virus globally](https://www.folkhalsomyndigheten.se/nyheter-och-press/nyhetsarkiv/2022/oktober/varlden-ar-nara-att-utrota-polio-men-har-en-bit-kvar/). Most non-polio enteroviruses will only cause a mild illness, with patients reporting symptoms similar to the common cold with a fever, runny nose, a cough, and muscle aches. Most people recover easily without medical intervention, or with only mild ‘over the counter’ remedies. A number of outbreaks of non-polio enteroviruses, such as coxsackieviruses, have been reported within the latest decade. Information about the surveillance for outbreaks of non-polio enteroviruses is available from [American Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov/non-polio-enterovirus/outbreaks-surveillance.html).
+
+**Adenoviruses** are part of the Adenoviridae family. There are seven human adenoviruses (A to G) and >60 (sero)types, some of which are water-borne. These viruses commonly cause gastroenteritis among children younger than 5.
+
+**Astroviruses**, part of the Astroviridae family comprise of eight serotypes (HAst1-8) causing gastrointenstinal symptoms. Most enteric viruses do  not give immunity, but astroviruses are an exception, with healthy individuals generally acquiring immunity after infection, making reinfection rare.
+The [National Respiratory and Enteric Virus Surveillance System (NREVSS)](https://www.cdc.gov/surveillance/nrevss/index.html) is an American surveillance program that monitors many enteric viruses. They monitor respiratory syncytial virus (RSV), human parainfluenza viruses (HPIV), human metapneumovirus (HMPV), respiratory adenoviruses, human coronavirus (excluding SARS-CoV-2), rotavirus, and norovirus.