diff --git a/content/english/about/partner_organisations.md b/content/english/about/partner_organisations.md index 630270b5a..efedb1294 100644 --- a/content/english/about/partner_organisations.md +++ b/content/english/about/partner_organisations.md @@ -62,3 +62,19 @@ title: Partner organisations

NBIS (National Bioinformatics Infrastructure Sweden) 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, ELIXIR Europe.

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GA4GH
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The Swedish COVID-19 & Pandemic Preparedness Data Portal is one of the many partners of the Global Alliance for Genomics and Health (GA4GH) and part of their Infectious Disease Community.

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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.

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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. +

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diff --git a/content/english/dashboards/_index.md b/content/english/dashboards/_index.md index 63ac456d7..fd18d3b1b 100644 --- a/content/english/dashboards/_index.md +++ b/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. diff --git a/content/english/dashboards/wastewater/_index.md b/content/english/dashboards/wastewater/_index.md index e475fe91a..2e9c7748e 100644 --- a/content/english/dashboards/wastewater/_index.md +++ b/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)]()). 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. diff --git a/content/english/dashboards/wastewater/covid_quantification/_index.md b/content/english/dashboards/wastewater/covid_quantification/_index.md index d4cd20dc6..7f27221e3 100644 --- a/content/english/dashboards/wastewater/covid_quantification/_index.md +++ b/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 +
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. diff --git a/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md b/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md index 0d403996b..7efec25d3 100644 --- a/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md +++ b/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). +
Go back to SARS-CoV-2 quantification within the wastewater epidemiology dashboard diff --git a/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md b/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md index 4d7e8fcca..c87b29993 100644 --- a/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md +++ b/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.
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{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slusites.json" height="775px" >}}
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{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_slusites.json" height="850px" >}}
{{ range .Site.Menus.homepage_dashboards }} diff --git a/layouts/partials/dashboards.html b/layouts/partials/dashboards.html index 6f9d15210..8e8f010e1 100644 --- a/layouts/partials/dashboards.html +++ b/layouts/partials/dashboards.html @@ -18,6 +18,7 @@ {{ if eq .LinkTitle "COVID-19"}}topic_badge_covid {{ else if eq .LinkTitle "Infectious diseases"}}topic_badge_infectious_d {{ else if eq .LinkTitle "Antibiotic resistance"}}topic_badge_antib_r + {{ else if eq .LinkTitle "Enteric viruses"}}topic_badge_enteric_v {{ else if eq .LinkTitle "Mpox"}}topic_badge_mpox {{ else }}topic_badge_general {{ end }} ">{{ .LinkTitle }} diff --git a/layouts/partials/highlights.html b/layouts/partials/highlights.html index db166f236..307f4eb1a 100644 --- a/layouts/partials/highlights.html +++ b/layouts/partials/highlights.html @@ -17,6 +17,7 @@ {{ if eq .LinkTitle "COVID-19"}}topic_badge_covid {{ else if eq .LinkTitle "Infectious diseases"}}topic_badge_infectious_d {{ else if eq .LinkTitle "Antibiotic resistance"}}topic_badge_antib_r + {{ else if eq .LinkTitle "Enteric viruses"}}topic_badge_enteric_v {{ else }}topic_badge_general {{ end }} ">{{ .LinkTitle }} {{ end }} diff --git a/layouts/partials/navbar.html b/layouts/partials/navbar.html index f07bf1367..644acd014 100644 --- a/layouts/partials/navbar.html +++ b/layouts/partials/navbar.html @@ -185,6 +185,7 @@ {{ else if eq .Name "Infectious diseases"}}topic_badge_infectious_d {{ else if eq .Name "Mpox"}}topic_badge_mpox {{ else if eq .Name "Antibiotic resistance"}}topic_badge_antib_r + {{ else if eq .Name "Enteric viruses"}}topic_badge_enteric_v {{ else }}topic_badge_general {{ end }} ">{{ .Name }} diff --git a/layouts/partials/topics.html b/layouts/partials/topics.html index e34ef9337..170856e94 100644 --- a/layouts/partials/topics.html +++ b/layouts/partials/topics.html @@ -1,4 +1,4 @@ -{{ $topics := slice "covid_19" "antibiotic_resistance" "infectious_diseases" "mpox" }} +{{ $topics := slice "covid_19" "antibiotic_resistance" "infectious_diseases" "mpox" "enteric_viruses" }}
{{ range .Site.Menus.topics_menu }} {{ if (in $topics .Identifier) }} diff --git a/layouts/shortcodes/funding_table.html b/layouts/shortcodes/funding_table.html index 83ec31685..142c291a1 100644 --- a/layouts/shortcodes/funding_table.html +++ b/layouts/shortcodes/funding_table.html @@ -115,6 +115,7 @@ {{ else if eq . "Infectious diseases"}}topic_badge_infectious_d {{ else if eq . "Mpox"}}topic_badge_mpox {{ else if eq . "Antibiotic resistance"}}topic_badge_antib_r + {{ else if eq . "Enteric viruses"}}topic_badge_enteric_v {{ else }}topic_badge_general {{ end }} ">{{ . }}{{ end }} diff --git a/layouts/shortcodes/research_projects_table.html b/layouts/shortcodes/research_projects_table.html index 5b1a8e781..c81d9f2d5 100644 --- a/layouts/shortcodes/research_projects_table.html +++ b/layouts/shortcodes/research_projects_table.html @@ -115,6 +115,7 @@ {{ if eq . "COVID-19"}}topic_badge_covid {{ else if eq . "Infectious diseases"}}topic_badge_infectious_d {{ else if eq . "Antibiotic resistance"}}topic_badge_antib_r + {{ else if eq . "Enteric viruses"}}topic_badge_enteric_v {{ else }}topic_badge_general {{ end }} ">{{ . }}{{ end }} diff --git a/layouts/topics/single.html b/layouts/topics/single.html index ce0651b48..018bcf261 100644 --- a/layouts/topics/single.html +++ b/layouts/topics/single.html @@ -25,6 +25,7 @@

Data highlights ({{ len $taxonomy. {{ else if eq .LinkTitle "Infectious diseases"}}topic_badge_infectious_d {{ else if eq .LinkTitle "Antibiotic resistance"}}topic_badge_antib_r {{ else if eq .LinkTitle "Mpox"}}topic_badge_mpox + {{ else if eq .LinkTitle "Enteric viruses"}}topic_badge_enteric_v {{ else }}topic_badge_general {{ end }} ">{{ .LinkTitle }} {{ end }} @@ -63,6 +64,7 @@

Dashboards ({{ len $taxonomy.Pages {{ else if eq .LinkTitle "Infectious diseases"}}topic_badge_infectious_d {{ else if eq .LinkTitle "Antibiotic resistance"}}topic_badge_antib_r {{ else if eq .LinkTitle "Mpox"}}topic_badge_mpox + {{ else if eq .LinkTitle "Enteric viruses"}}topic_badge_enteric_v {{ else }}topic_badge_general {{ end }} ">{{ .LinkTitle }} {{ end }} diff --git a/static/css/styles.css b/static/css/styles.css index 871de7c6f..80a4cfda5 100644 --- a/static/css/styles.css +++ b/static/css/styles.css @@ -482,23 +482,27 @@ a.topics_title:active, a.topics_title:focus, a.topics_title:hover { } .topic_badge_general { - background-color: #6c757d; + background-color: #295986; } .topic_badge_mpox { - background-color: #2e68a5; + background-color: #295986; } .topic_badge_covid { - background-color: #de2c6c; + background-color: #295986; } .topic_badge_antib_r { - background-color: #6a60af; + background-color: #295986; } .topic_badge_infectious_d { - background-color: #a34fa4; + background-color: #295986; +} + +.topic_badge_enteric_v { + background-color: #295986; } .dataset_badge_data { diff --git a/static/img/logos/ga4gh_logo.png b/static/img/logos/ga4gh_logo.png new file mode 100644 index 000000000..ba5b6880f Binary files /dev/null and b/static/img/logos/ga4gh_logo.png differ diff --git a/static/topic_thumbs/topic_enteric.png b/static/topic_thumbs/topic_enteric.png new file mode 100644 index 000000000..dfc2d2dec Binary files /dev/null and b/static/topic_thumbs/topic_enteric.png differ