-
#### Introduction
The _Swedish Pathogens Portal_ provides information about available datasets, resources, tools, and services related to pandemic preparedness in Sweden. We offer support to all those involved in pandemic preparedness research that are affiliated with a Swedish research institution or university.
@@ -50,28 +37,28 @@ Many people from SciLifeLab, NBIS, other organisations, and the community have b
The team are happy to help with using the Portal, to take suggestions regarding new and existing sections, and to answer any questions that you may have. Please just get in touch using for [contact](/contact/) form.
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Below are the six editorial committee members for 2023, alongside their affiliation and area of expertise. The editorial committee enable a more direct link between the Portal and the wider research community. They collaborate with the Portal team to create content and advise on resources that would be beneficial to researchers in their area of expertise.
{{< editorial_committee_cards >}}
diff --git a/content/english/about/organisations_and_programs.md b/content/english/about/organisations_and_programs.md
index 95f34f88d..b35fc3dc7 100644
--- a/content/english/about/organisations_and_programs.md
+++ b/content/english/about/organisations_and_programs.md
@@ -1,31 +1,19 @@
---
title: Programs and organisations behind the portal
+menu:
+ navbar_about:
+ name: "Programs & organisations behind the portal"
+ weight: 20
+layout: about_navbar
---
-
SciLifeLab (Science for Life Laboratory) was commissioned by the Swedish govenment to prepare resources and capabilities that can be used to deal with future pandemics. The assignment broadly involved supporting research related to infectious diseases (e.g. in diagnostics, analysis of infection, immunity, and the development of resistance to therapies in pathogens), and building competence and developing technologies related to pandemic research (e.g. in sequencing, genetic analysis, immunology, and big data).
The Pandemic Laboratory Preparedness (PLP) program was established as a result of the commission from the government in December 2020. The services, tools, and resources (termed ‘capabilities’) established through the PLP program are intended to complement those established elsewhere in society (e.g. authorities, municipalities and regions) when tackling future pandemics. As such, the PLP program will work closely with governmental agencies, e.g. Swedish Public Health Agency (FoHM).
@@ -35,12 +23,12 @@ title: Programs and organisations behind the portal
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+
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+
SciLifeLab & Wallenberg National Program for Data-Driven Life Science
Life science research is becoming increasingly data-driven. The amount and complexity of data is also growing exponentially. Data is the most valuable product of research, and it is therefore crucially important that we ensure it is managed appropriately throughout its lifecycle. To this end, SciLifeLab and The Knut and Alice Wallenberg Foundation have established the Data-Driven Life Science (DDLS) program in Sweden. The mission of the DDLS program is to recruit and train the next generation of life scientists, and to create strong data science capabilities for life science in Sweden that are internationally competitive. The DDLS program has been funded by The Knut and Alice Wallenberg foundation for 12 years. SciLifeLab, as a national infrastructure for life science, coordinates this program in close collaboration with ten Swedish universities and the Swedish Museum of Natural History. You can read more about the DDLS program here.
@@ -48,12 +36,13 @@ title: Programs and organisations behind the portal
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+
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Science for Life Laboratory
SciLifeLab (Science for Life Laboratory) is an institution for the advancement of molecular biosciences in Sweden. We are funded as a national research infrastructure by the Swedish government. Our organisation leverages the unique strengths of individual researchers across Sweden into a focused resource for the life science community. Thousands of researchers rely on us to provide access to the cutting-edge instrumentation and deep scientific expertise needed to produce internationally competitive bioscience research. These technologies are supported and developed by our research community, which includes internationally recognised experts in life science and technology. Our facilities and expertise create a unique environment for carrying out health and environmental research at the highest level.
@@ -61,12 +50,13 @@ title: Programs and organisations behind the portal
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+
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Scilifelab Data Centre
Life science research is increasingly becoming data-driven, rather than primarily technology-driven. SciLifeLab coordinates and supports activities throughout the data life cycle, from project planning and data production, right through to data publishing and reuse, where researchers are dependent on advanced data analysis and e-infrastructures.
At SciLifeLab, we see data as one of the most valuable and long-lasting products of our operations. We strive to ensure our data adheres to the principles of FAIR and Open Science. We also put considerable effort into maximising the long-term value of our data to the scientific community.
The Pathogens Portal, maintained by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) and partners, was launched in July 2023. The Pathogens Portal is a resource for e.g. researchers, clinicians, and policymakers. Its aim is to facilitate access to the latest and most comprehensive datasets on pathogens. The COVID-19 pandemic put a spotlight on the importance of data sharing and for focused access to relevant datasets. Therefore, the Pathogens Portal was developed as a centralised platform for data sharing and accessing data on key pathogens. These pathogens include both pathogens affecting humans and animals, and on vectors and hosts. Bringing together data from a number of sources, and linking data contributes to a better understand Pathogen ́s Biology. Funded through five European Union projects funded under the Horizon 2020 and Horizon Europe programmes: RECODID, VEO, EOSC-Life, CONVERGE and BY-COVID. Moving forward, national nodes of the Pathogens Portal will be added, the Swedish Pathogens Portal is the first to launch in Sept 2023.
The European COVID-19 Data Platform aims to facilitate data sharing and analysis in order to accelerate coronavirus research. It enables researchers to upload, access and analyse reference data and specialist datasets related to COVID-19. It is synchronised with COVID-19-related data and scientific literature held in EMBL-EBI's data resources, including ENA, UniProt, PDBe, EMDB, Expression Atlas and Europe PMC. The data continues to grow in diversity and volume, but include sequences, structures, expression data, compound screens, biochemistries and scientific publications.
@@ -47,12 +35,12 @@ title: Partner organisations
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BY-COVID consortium
The Swedish Pathogens Portal is one of the partners in the BY-COVID consortium. BY-COVID is a Horizon project funded by the European Comission and brings together 53 partners from 19 countries. Stakeholders include individuals and organisation from multiple areas, including the biomedical field, hospitals, public health, social sciences and humanities.
The BeYond-COVID (BY-COVID) project aims to make COVID-19 data accessible to anyone that can use it, including medical staff in hospitals, researchers in labs, and government officials. The project will provide a framework for making data from other infectious diseases open and accessible to everyone. The project will integrate established national and European infrastructures with ELIXIR, BBMRI, ECRIN, PHIRI and CESSDA. It will build on existing efforts, such as the COVID-19 Data Platform and the Versatile Emerging infectious disease Observatory project (VEO), in order to maximise efficiency. It will also develop synergies with the European Health Data Space.
@@ -62,7 +50,7 @@ title: Partner organisations
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+
@@ -70,7 +58,7 @@ title: Partner organisations
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NBIS and ELIXIR Sweden
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.
@@ -78,7 +66,7 @@ title: Partner organisations
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diff --git a/content/english/contact/_index.md b/content/english/contact/_index.md
index 7ef1021dd..e4cfceae7 100644
--- a/content/english/contact/_index.md
+++ b/content/english/contact/_index.md
@@ -6,8 +6,8 @@ menu:
weight: 20
identifier: contact
footer_about:
- name: Contact form
- weight: 20
+ name: Support & Feedback
+ weight: 30
aliases:
- /suggestions/
recaptcha: true
diff --git a/content/english/dashboards/RECOVAC.md b/content/english/dashboards/RECOVAC.md
index 3a5aca635..ff09ec972 100644
--- a/content/english/dashboards/RECOVAC.md
+++ b/content/english/dashboards/RECOVAC.md
@@ -89,6 +89,10 @@ When hovering over the plot with the cursor, additional grey icons appear in the
diff --git a/content/english/dashboards/covid_publications.md b/content/english/dashboards/covid_publications.md
index 033566a9a..f07f3acea 100644
--- a/content/english/dashboards/covid_publications.md
+++ b/content/english/dashboards/covid_publications.md
@@ -5,20 +5,25 @@ banner: /dashboard_thumbs/publications.jpg
toc: false
plotly: true
menu:
- dashboard_menu:
- identifier: covid_19_publications_vis
- name: "COVID-19 publication overview"
+ dashboard_menu:
+ identifier: covid_19_publications_vis
+ name: "COVID-19 publication overview"
aliases:
- - /projects/dashboard/
+ - /projects/dashboard/
dashboards_topics: [COVID-19, Infectious diseases]
---
+
The visualisations on this page evaluate the development of COVID-19 and SARS-CoV-2 research across Sweden by assessing publication output. Specifically, we consider multiple aspects of journal publications and preprints where at least one author has an affiliation with a Swedish research institute. The database containing the publications themselves [can be found on this page](/publications/). Note that our database is manually curated and, as such, may not be exhaustive. The full database is available for download and use for other purposes, please see [DOI: 10.17044/scilifelab.14124014](https://doi.org/10.17044/scilifelab.14124014) for details.
The code used to produce the visulations on this page can be found on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations). Specifically, code related to the number of publications can be found in the ['Count_publications' folder of the repository](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Count_publications), and code used to generated the wordclouds can be found in the ['Wordcloud' folder](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Wordcloud).
## Number of new publications
-This graph displays the number of publications (including both journal publications and preprints) published each month, as well as the cumulative daily total of publications contained in the database. The dates reflect either the preprint upload date or the official journal publication date, whichever is the most recent. Where a given day of publication is not specified in the publication/upload date, we assign the date as the first of the month. This causes the appearance of a relatively sharp increase at the start of each month. This chart is updated daily, though the publications database is not.
+This graph displays the number of publications (including both journal publications and preprints) published each month, as well as the cumulative daily total of publications contained in the database. The dates reflect either the preprint upload date or the official journal publication date, whichever is the most recent. Where a given day of publication is not specified in the publication/upload date, we assign the date as the first of the month. This causes the appearance of a relatively sharp increase at the start of each month. This chart is updated weekly, though the publications database is not.
+
+
+ Rotating your phone may improve graph layout
+
{{< publications_per_month >}}
diff --git a/content/english/dashboards/post_covid.md b/content/english/dashboards/post_covid.md
index 65d115e5d..3b155b7bb 100644
--- a/content/english/dashboards/post_covid.md
+++ b/content/english/dashboards/post_covid.md
@@ -5,23 +5,23 @@ banner: /dashboard_thumbs/postcovid.jpg
toc: true
plotly: true
menu:
- dashboard_menu:
- identifier: post_covid
- name: Post COVID-19 condition
+ dashboard_menu:
+ identifier: post_covid
+ name: Post COVID-19 condition
aliases:
- - /data_types/health_data/post_covid/
+ - /data_types/health_data/post_covid/
dashboards_topics: [COVID-19, Infectious diseases]
---
Since the beginning of 2020, the COVID-19 pandemic has challenged healthcare and dramatically changed daily life for people worldwide. The severity of symptoms experienced by patients during the acute infection phase of COVID-19 disease varies between individuals from mild to severe. After this phase, there are usually no indications that the disease will have any long-term effects on their health, regardless of the severity of symptoms experienced during the acute infection phase. However, some patients continue to exhibit symptoms for prolonged periods after the acute phase. The symptoms experienced by such patients are broad, but can include, for example, deep fatigue, joint pain, ‘brain fog’ (difficulty concentrating on certain tasks for longer periods of time), and heart palpitations ([Brodin, 2021](https://doi.org/10.1038/s41591-020-01202-8), [Marx, 2021](https://doi.org/10.1038/s41592-021-01145-z)). These symptoms can have a significant impact on the patients' quality of life.
-Most studies that have explored what causes some patients to experience prolonged symptoms have been descriptive. However, several recent studies have explored potential causes in detail. For example, [Važgėlienė *et al.* (2022)](https://www.mdpi.com/2077-0383/11/21/6278) investigated potential links between prolonged symptoms after COVID-19 infection and other types of chronic disease or daily medication. They found an association between the taking of daily medication and the development of prolonged symptoms after COVID-19 infection. Other studies have found that multiple other factors, including being female, advanced age, and poor general health, are associated with an increased risk of experiencing prolonged symptoms after a COVID-19 infection ([Sudre *et al.*, 2021](https://www.nature.com/articles/s41591-021-01292-y)).
+Most studies that have explored what causes some patients to experience prolonged symptoms have been descriptive. However, several recent studies have explored potential causes in detail. For example, [Važgėlienė _et al._ (2022)](https://www.mdpi.com/2077-0383/11/21/6278) investigated potential links between prolonged symptoms after COVID-19 infection and other types of chronic disease or daily medication. They found an association between the taking of daily medication and the development of prolonged symptoms after COVID-19 infection. Other studies have found that multiple other factors, including being female, advanced age, and poor general health, are associated with an increased risk of experiencing prolonged symptoms after a COVID-19 infection ([Sudre _et al._, 2021](https://www.nature.com/articles/s41591-021-01292-y)).
-This condition (i.e. the presistance of symptoms following the acute phase of COVID-19 infection) has been referred to in multiple ways, including *Post COVID-19 condition*, *Post-COVID*, and *Long COVID*. On this page, we use the term *Post COVID-19 condition* for consistency. See the *[Background Information](#background)* section below for more detail about the nomenclature used and relevant research.
+This condition (i.e. the presistance of symptoms following the acute phase of COVID-19 infection) has been referred to in multiple ways, including _Post COVID-19 condition_, _Post-COVID_, and _Long COVID_. On this page, we use the term _Post COVID-19 condition_ for consistency. See the _[Background Information](#background)_ section below for more detail about the nomenclature used and relevant research.
-On this page, you can find visualisations of data related to *Post COVID-19 condition* in Sweden from The Swedish Board of Health and Welfare ([Socialstyrelsen](https://www.socialstyrelsen.se)), an overview of ongoing *Post COVID-19 condition* research projects in Sweden, and scientific publications regarding *Post COVID-19 condition* by researchers affiliated with Swedish universities or research institutes.
+On this page, you can find visualisations of data related to _Post COVID-19 condition_ in Sweden from The Swedish Board of Health and Welfare ([Socialstyrelsen](https://www.socialstyrelsen.se)), an overview of ongoing _Post COVID-19 condition_ research projects in Sweden, and scientific publications regarding _Post COVID-19 condition_ by researchers affiliated with Swedish universities or research institutes.
-For more information on *Post COVID-19 condition* in Sweden, please see [this section](https://www.socialstyrelsen.se/coronavirus-covid-19/socialstyrelsens-roll-och-uppdrag/postcovid/) of The Swedish Board of Health and Welfare (Socialstyrelsen)’s website and their [report on *Post-COVID condition* (published April 2021)](https://www.socialstyrelsen.se/globalassets/sharepoint-dokument/artikelkatalog/ovrigt/2021-4-7351.pdf). More [general information](https://www.cdc.gov/coronavirus/2019-ncov/long-term-effects/index.html) is also available from the Centers for Disease Control and Prevention (CDC).
+For more information on _Post COVID-19 condition_ in Sweden, please see [this section](https://www.socialstyrelsen.se/coronavirus-covid-19/socialstyrelsens-roll-och-uppdrag/postcovid/) of The Swedish Board of Health and Welfare (Socialstyrelsen)’s website and their [report on _Post-COVID condition_ (published April 2021)](https://www.socialstyrelsen.se/globalassets/sharepoint-dokument/artikelkatalog/ovrigt/2021-4-7351.pdf). More [general information](https://www.cdc.gov/coronavirus/2019-ncov/long-term-effects/index.html) is also available from the Centers for Disease Control and Prevention (CDC).
## Availability of data and code
@@ -37,9 +37,9 @@ All code used to produce the visualisations on this page is available on [GitHub
## Statistics on Post COVID-19 condition in Sweden
-Since Post COVID-19 condition is not clearly defined, over time, it has been assigned multiple diagnosis codes for use by medical professionals/researchers. After the first cases of prolonged disease following COVID-19 infection were detected in spring 2020, The Swedish Board of Health and Welfare initiated the diagnosis *Z86.1A - COVID-19 in own medical history* (Covid-19 i den egna sjukhistorien). This diagnosis code has been used since 1st June 2020. From 1st January 2021, this diagnosis code was replaced by *U08.9 (ICD-10-SE) - COVID-19 in own medical history, unspecified* (Covid-19 i den egna sjukhistorien) in accordance with new [WHO (World Health Organization)](https://www.who.int) guidelines. This diagnosis should be used when an individual is receiving treatment for an illness/physical damage for which the patient’s history of COVID-19 infection is considered relevant (i.e. a contributory factor to the present illness/damage). Importantly, this diagnosis should only be given if the individual is no longer considered to have COVID-19, and if the current health condition is not considered to result from infection with COVID-19. *U08.9* is an additional diagnosis, as such, it should only be assigned alongside a main diagnosis; it cannot be the main diagnosis.
+Since Post COVID-19 condition is not clearly defined, over time, it has been assigned multiple diagnosis codes for use by medical professionals/researchers. After the first cases of prolonged disease following COVID-19 infection were detected in spring 2020, The Swedish Board of Health and Welfare initiated the diagnosis _Z86.1A - COVID-19 in own medical history_ (Covid-19 i den egna sjukhistorien). This diagnosis code has been used since 1st June 2020. From 1st January 2021, this diagnosis code was replaced by _U08.9 (ICD-10-SE) - COVID-19 in own medical history, unspecified_ (Covid-19 i den egna sjukhistorien) in accordance with new [WHO (World Health Organization)](https://www.who.int) guidelines. This diagnosis should be used when an individual is receiving treatment for an illness/physical damage for which the patient’s history of COVID-19 infection is considered relevant (i.e. a contributory factor to the present illness/damage). Importantly, this diagnosis should only be given if the individual is no longer considered to have COVID-19, and if the current health condition is not considered to result from infection with COVID-19. _U08.9_ is an additional diagnosis, as such, it should only be assigned alongside a main diagnosis; it cannot be the main diagnosis.
-From 16th October 2020, the Swedish Board of Health and Welfare initiated a new diagnosis, *U09.9 (ICD-10-SE) - Postinfectious state associated with COVID-19, unspecified* (Postinfektiöst tillstånd efter covid-19, ospecificerat), in accordance with new WHO guidelines. This new diagnosis supplemented and partially replaced the *Z86.1A* diagnosis. As with *U08.9*, the *U09.9* diagnosis should only be given after the person is no longer considered to have COVID-19. This diagnosis code should be used for conditions that persist or begin after the acute infection stage has passed. *U09.9* is also an additional diagnosis, and should only be assigned alongside a separate main diagnosis.
+From 16th October 2020, the Swedish Board of Health and Welfare initiated a new diagnosis, _U09.9 (ICD-10-SE) - Postinfectious state associated with COVID-19, unspecified_ (Postinfektiöst tillstånd efter covid-19, ospecificerat), in accordance with new WHO guidelines. This new diagnosis supplemented and partially replaced the _Z86.1A_ diagnosis. As with _U08.9_, the _U09.9_ diagnosis should only be given after the person is no longer considered to have COVID-19. This diagnosis code should be used for conditions that persist or begin after the acute infection stage has passed. _U09.9_ is also an additional diagnosis, and should only be assigned alongside a separate main diagnosis.
For more information and current guidelines regarding diagnoses used for conditions related to a history of COVID-19, see [this webpage](https://www.socialstyrelsen.se/utveckla-verksamhet/e-halsa/klassificering-och-koder/icd-10/) from The Swedish Board of Health and Welfare.
@@ -113,28 +113,32 @@ The maps below show the number of people that received the diagnoses of interest
#### Diagnosis U09.9
-The below table displays the most common types of diagnosis (diagnosis groups) that have been reported together with the *U09.9 (ICD-10-SE) - Postinfectious state associated with COVID-19, unspecified* diagnosis. In particular, the values in the table represent the amount of individuals that received the *U09.9* diagnosis alongside one of the diagnoses below. The data was recorded between 16th October 2020 and the most recent data update (see above).
+The below table displays the most common types of diagnosis (diagnosis groups) that have been reported together with the _U09.9 (ICD-10-SE) - Postinfectious state associated with COVID-19, unspecified_ diagnosis. In particular, the values in the table represent the amount of individuals that received the _U09.9_ diagnosis alongside one of the diagnoses below. The data was recorded between 16th October 2020 and the most recent data update (see above).
-*Note that an individual may have more than one of the accompanying diagnoses. However, if an individual has the same issue on multiple doctor visits/healthcare contacts, the diagnosis will only be counted once*
+_Note that an individual may have more than one of the accompanying diagnoses. However, if an individual has the same issue on multiple doctor visits/healthcare contacts, the diagnosis will only be counted once_
**Code used to produce table:** [Script to produce table (English)](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses.py), [Script to produce table (Swedish)](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_accomp_diagnoses_swe.py).
### Contacts with healthcare
-The below plot shows the number of times that patients given the diagnoses of interest have sought healthcare. Note that while the weekly data below starts from week 21 of 2020, some diagnosis codes (*U08.9* and *U09.9*) were not used until after this date (see information above). It is important to note that the data is not complete, given that data from some healthcare providers (e.g. general practitioners) are not reported to the Patient Registry due to privacy concerns. Where data is reported to registers, data from the most recent weeks should be considered preliminary, as the registers are not instantaneously updated. A delay in reporting data to registers may be particularly evident during traditional holiday periods, including over the summer months.
+The below plot shows the number of times that patients given the diagnoses of interest have sought healthcare. Note that while the weekly data below starts from week 21 of 2020, some diagnosis codes (_U08.9_ and _U09.9_) were not used until after this date (see information above). It is important to note that the data is not complete, given that data from some healthcare providers (e.g. general practitioners) are not reported to the Patient Registry due to privacy concerns. Where data is reported to registers, data from the most recent weeks should be considered preliminary, as the registers are not instantaneously updated. A delay in reporting data to registers may be particularly evident during traditional holiday periods, including over the summer months.
- Scroll the plot sideways to view all data.
+ Rotating your phone may improve graph layout
+
+
**Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare.py).
### Contacts with healthcare, divided by patient sex
@@ -144,7 +148,7 @@ The below plots show the number of times that patients given one of the diagnose
#### Diagnosis U09.9
- Scroll the plot sideways to view all data.
+ Rotating your phone may improve graph layout
@@ -156,7 +160,7 @@ The below plots show the number of times that patients given one of the diagnose
#### Diagnosis Z86.1A/U08.9
- Scroll the plot sideways to view all data.
+ Rotating your phone may improve graph layout
@@ -167,7 +171,7 @@ The below plots show the number of times that patients given one of the diagnose
## Ongoing research projects
-Below is a manually curated overview of research projects on *Post COVID-19 condition* that are funded by major funding agencies in Sweden. As it is manually curated, the list may not be exhaustive and new projects will be added as soon as possible. If you think that your project should be listed here but isn’t, please [get in touch with us](/contact/). For a list of all research projects funded by major funding agencies in Sweden [see this section of the portal](/projects/ongoing/).
+Below is a manually curated overview of research projects on _Post COVID-19 condition_ that are funded by major funding agencies in Sweden. As it is manually curated, the list may not be exhaustive and new projects will be added as soon as possible. If you think that your project should be listed here but isn’t, please [get in touch with us](/contact/). For a list of all research projects funded by major funding agencies in Sweden [see this section of the portal](/projects/ongoing/).
{{< display_funded_projects filter_variable="post_covid" >}}
@@ -175,7 +179,7 @@ Below is a manually curated overview of research projects on *Post COVID-19 cond
## Publications
-Below is a list of pre-prints and published scientific journal articles on *Post COVID-19 condition* involving at least one author affiliated with a Swedish university or research institute. Note that this list is based on a manually curated database and, as such, may not be exhaustive. If you think that a publication should be listed here but isn’t, or feel that information about a publication needs correction, please [get in touch with us](/contact/). For a list of all publications on COVID-19 and SARS-CoV-2 involving at least one author affiliated with a Swedish univerisity or research institute [see this section of the portal](/publications/).
+Below is a list of pre-prints and published scientific journal articles on _Post COVID-19 condition_ involving at least one author affiliated with a Swedish university or research institute. Note that this list is based on a manually curated database and, as such, may not be exhaustive. If you think that a publication should be listed here but isn’t, or feel that information about a publication needs correction, please [get in touch with us](/contact/). For a list of all publications on COVID-19 and SARS-CoV-2 involving at least one author affiliated with a Swedish univerisity or research institute [see this section of the portal](/publications/).
{{< postcovid_publications >}}
@@ -185,18 +189,18 @@ Below is a list of pre-prints and published scientific journal articles on *Post
### Post COVID-19 condition
-Individuals with *Post COVID-19 condition* exhibit symptoms lasting at least two months after the acute phase of COVID-19 infection ([Brodin, 2021](https://doi.org/10.1038/s41591-020-01202-8)). The particular symptoms exhibited vary between patients, as does the duration and severity of symptoms. In general though, symptoms are usually debilitating and may include persistent fatigue, myalgia (muscle aches and pains), and autonomic dysregulation, among others. Some individuals with *Post COVID-19 condition* exhibit the same symptoms as they did during the acute infection stage of COVID-19, while others with *Post COVID-19 condition* exhibit new symptoms following the acute infection phase ([Brodin 2021](https://www.nature.com/articles/s41591-020-01202-8), [Dennis *et al.*, 2021](http://dx.doi.org/10.1136/bmjopen-2020-048391), [Davido *et al.*, 2020](https://doi.org/10.1016/j.cmi.2020.07.028).
+Individuals with _Post COVID-19 condition_ exhibit symptoms lasting at least two months after the acute phase of COVID-19 infection ([Brodin, 2021](https://doi.org/10.1038/s41591-020-01202-8)). The particular symptoms exhibited vary between patients, as does the duration and severity of symptoms. In general though, symptoms are usually debilitating and may include persistent fatigue, myalgia (muscle aches and pains), and autonomic dysregulation, among others. Some individuals with _Post COVID-19 condition_ exhibit the same symptoms as they did during the acute infection stage of COVID-19, while others with _Post COVID-19 condition_ exhibit new symptoms following the acute infection phase ([Brodin 2021](https://www.nature.com/articles/s41591-020-01202-8), [Dennis _et al._, 2021](http://dx.doi.org/10.1136/bmjopen-2020-048391), [Davido _et al._, 2020](https://doi.org/10.1016/j.cmi.2020.07.028).
### No consensus on definition
-In September 2020, WHO established the [ICD10](https://www.who.int/standards/classifications/classification-of-diseases/emergency-use-icd-codes-for-covid-19-disease-outbreak) code for *Post COVID-19 condition* *U09.9 - Post COVID-19 condition, unspecified*. A [WHO report from April 2021](https://www.who.int/publications/i/item/9789240025035) stated that there is a real need to characterise and formally define *Post COVID-19 condition* in order to increase understanding about the condition and facilitate diagnosis. However, to date, *Post COVID-19 condition* still lacks a universal definition with regard to the symptoms and disease duration necessary for diagnosis. Consequently, governmental agencies and research institutes in different countries use their own definitions and terms. Related diagnoses established by WHO are *U08.9 - Personal history of COVID-19, unspecified* and *U10.9 - Multisystem inflammatory syndrome associated with COVID-19, unspecified*. The *U08.9* diagnosis is used to describe an earlier episode of COVID-19 (either confirmed or probable) that influenced the individual's health status, though they no longer have COVID-19. The code *U10.9* is used to describe a temporal association with COVID-19: cytokine storm, Kawasaki-like syndrome, multisystem inflammatory syndrome in children (MIS-C), and paediatric inflammatory multisystem syndrome (PIMS).
+In September 2020, WHO established the [ICD10](https://www.who.int/standards/classifications/classification-of-diseases/emergency-use-icd-codes-for-covid-19-disease-outbreak) code for _Post COVID-19 condition_ _U09.9 - Post COVID-19 condition, unspecified_. A [WHO report from April 2021](https://www.who.int/publications/i/item/9789240025035) stated that there is a real need to characterise and formally define _Post COVID-19 condition_ in order to increase understanding about the condition and facilitate diagnosis. However, to date, _Post COVID-19 condition_ still lacks a universal definition with regard to the symptoms and disease duration necessary for diagnosis. Consequently, governmental agencies and research institutes in different countries use their own definitions and terms. Related diagnoses established by WHO are _U08.9 - Personal history of COVID-19, unspecified_ and _U10.9 - Multisystem inflammatory syndrome associated with COVID-19, unspecified_. The _U08.9_ diagnosis is used to describe an earlier episode of COVID-19 (either confirmed or probable) that influenced the individual's health status, though they no longer have COVID-19. The code _U10.9_ is used to describe a temporal association with COVID-19: cytokine storm, Kawasaki-like syndrome, multisystem inflammatory syndrome in children (MIS-C), and paediatric inflammatory multisystem syndrome (PIMS).
-In England, the [National Institute for Health and Care Excellence (NICE)](https://www.nice.org.uk) has [defined](https://www.nice.org.uk/guidance/ng188/chapter/context) *Post-COVID-19 syndrome* as "...signs and symptoms that develop during or after an infection consistent with COVID‑19, continue for more than 12 weeks, and are not explained by an alternative diagnosis. It usually presents with clusters of symptoms, often overlapping, which can fluctuate and change over time and can affect any system in the body...". NICE states that *Post‑COVID‑19 syndrome* can be considered as a diagnosis during the first three months after the acute infection phase of COVID-19 while healthcare assessments are completed to determine whether the symptoms could be explained by an alternative disease. Further, NICE [defines](https://www.nice.org.uk/guidance/ng188/chapter/context) the term *Long COVID* as "...signs and symptoms that continue or develop after acute COVID‑19. It includes both ongoing symptomatic COVID‑19 (from 4 to 12 weeks) and post‑COVID‑19 syndrome (12 weeks or more)...”. In December 2020, NICE, in partnership with the Scottish Intercollegiate Guidelines Network and the Royal College of General Practitioners, published a [guideline for health and care practitioners](https://www.nice.org.uk/guidance/NG188) (NG188) on identifying, assessing, and managing the long-term effects of COVID-19.
+In England, the [National Institute for Health and Care Excellence (NICE)](https://www.nice.org.uk) has [defined](https://www.nice.org.uk/guidance/ng188/chapter/context) _Post-COVID-19 syndrome_ as "...signs and symptoms that develop during or after an infection consistent with COVID‑19, continue for more than 12 weeks, and are not explained by an alternative diagnosis. It usually presents with clusters of symptoms, often overlapping, which can fluctuate and change over time and can affect any system in the body...". NICE states that _Post‑COVID‑19 syndrome_ can be considered as a diagnosis during the first three months after the acute infection phase of COVID-19 while healthcare assessments are completed to determine whether the symptoms could be explained by an alternative disease. Further, NICE [defines](https://www.nice.org.uk/guidance/ng188/chapter/context) the term _Long COVID_ as "...signs and symptoms that continue or develop after acute COVID‑19. It includes both ongoing symptomatic COVID‑19 (from 4 to 12 weeks) and post‑COVID‑19 syndrome (12 weeks or more)...”. In December 2020, NICE, in partnership with the Scottish Intercollegiate Guidelines Network and the Royal College of General Practitioners, published a [guideline for health and care practitioners](https://www.nice.org.uk/guidance/NG188) (NG188) on identifying, assessing, and managing the long-term effects of COVID-19.
-In the USA, The [Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov) defines *Post-COVID conditions* as "...a wide range of new, returning, or ongoing health problems people can experience more than four weeks after first being infected with the virus that causes COVID-19...". The CDC distinguishes between *Long COVID*, *Multiorgan Effects of COVID-19*, and *Effects of COVID-19 Treatment or Hospitalisation*. For example, they define *Long COVID* as "a range of symptoms that can last weeks or months after first being infected with the virus that causes COVID-19 or can appear weeks after infection.". For information on *Post-COVID conditions* from the CDC, [see this page](https://www.cdc.gov/coronavirus/2019-ncov/long-term-effects.html). The [National Institutes of Health (NIH)](https://www.nih.gov) in the USA uses the term *Post-Acute Sequelae of SARS-CoV-2 infection* (PASC) to refer to the effects of COVID-19 after the initial stages of infection. In February 2021, The NIH [launched a research initiative](https://www.nih.gov/about-nih/who-we-are/nih-director/statements/nih-launches-new-initiative-study-long-covid) to identify the causes of PASC and, ultimately, to find methods for prevention and treatments for individuals that don’t recover fully over a period of a few weeks following the acute infection phase of COVID-19.
+In the USA, The [Centers for Disease Control and Prevention (CDC)](https://www.cdc.gov) defines _Post-COVID conditions_ as "...a wide range of new, returning, or ongoing health problems people can experience more than four weeks after first being infected with the virus that causes COVID-19...". The CDC distinguishes between _Long COVID_, _Multiorgan Effects of COVID-19_, and _Effects of COVID-19 Treatment or Hospitalisation_. For example, they define _Long COVID_ as "a range of symptoms that can last weeks or months after first being infected with the virus that causes COVID-19 or can appear weeks after infection.". For information on _Post-COVID conditions_ from the CDC, [see this page](https://www.cdc.gov/coronavirus/2019-ncov/long-term-effects.html). The [National Institutes of Health (NIH)](https://www.nih.gov) in the USA uses the term _Post-Acute Sequelae of SARS-CoV-2 infection_ (PASC) to refer to the effects of COVID-19 after the initial stages of infection. In February 2021, The NIH [launched a research initiative](https://www.nih.gov/about-nih/who-we-are/nih-director/statements/nih-launches-new-initiative-study-long-covid) to identify the causes of PASC and, ultimately, to find methods for prevention and treatments for individuals that don’t recover fully over a period of a few weeks following the acute infection phase of COVID-19.
-The [Swedish Board of Health and Welfare (Socialstyrelsen)](https://www.socialstyrelsen.se/) describes patients with *Postcovid* as individuals exhibiting prolonged symptoms, or experiencing new relevant symptoms after the acute phase of COVID-19 infection. While the severity of symptoms will diminish over time for most individuals (such individuals do not need assistance from healthcare during the recovery), some individuals experience symptoms that are debilitating and need treatment, rehabilitation, and other follow-up medical care. In April 2021, Socialstyrelsen [published a report dedicated to Postcovid](https://www.socialstyrelsen.se/globalassets/sharepoint-dokument/artikelkatalog/ovrigt/2021-4-7351.pdf) that defines the condition and provides recommendations.
+The [Swedish Board of Health and Welfare (Socialstyrelsen)](https://www.socialstyrelsen.se/) describes patients with _Postcovid_ as individuals exhibiting prolonged symptoms, or experiencing new relevant symptoms after the acute phase of COVID-19 infection. While the severity of symptoms will diminish over time for most individuals (such individuals do not need assistance from healthcare during the recovery), some individuals experience symptoms that are debilitating and need treatment, rehabilitation, and other follow-up medical care. In April 2021, Socialstyrelsen [published a report dedicated to Postcovid](https://www.socialstyrelsen.se/globalassets/sharepoint-dokument/artikelkatalog/ovrigt/2021-4-7351.pdf) that defines the condition and provides recommendations.
### Research efforts
-A large number of research articles, case reports, and reviews focused on *Post COVID-19 condition* have been published over the last year (e.g. [Dani *et al.* (2020)](https://doi.org/10.7861/clinmed.2020-0896), [Nabavi (2020)](https://doi.org/10.1136/bmj.m3489), [Sudre *et al.* (2021)](https://doi.org/10.1038/s41591-021-01292-y), [Tarybagil *et al.* (2020)](https://doi.org/10.1136/bcr-2020-241485), [Yelin *et al.* (2020)](https://doi.org/10.1016/j.cmi.2020.12.001)). The primary aims of these studies are to identify factors that could be used to predict when *Post COVID-19 condition* is more likely to develop, the underlying causes of the condition, and potential treatments. A recently published study by [Sudre and colleagues](https://doi.org/10.1038/s41591-021-01292-y) proposed a prediction model to identify individuals at risk of *Post COVID-19 condition* using data from the [COVID Symptom Study](/data_types/health_data/symptom_study_sweden/), where participants self-reported their symptoms in an app on their mobile devices. The results indicated that individuals experiencing more than five symptoms during the first week of illness were more likely to develop *Post COVID-19 condition* (odds ratio = 3.53 (2.76–4.50)). In addition, the study showed that the development of *Post COVID-19 condition* was more likely in females, and that the risk also rose with increasing age and body mass index. The researchers behind the study propose that their model could be used to identify individuals at risk of developing *Post COVID-19 condition*. This could inform trials of preventative or treatment methods, and aid in the planning of education and rehabilitation services.
+A large number of research articles, case reports, and reviews focused on _Post COVID-19 condition_ have been published over the last year (e.g. [Dani _et al._ (2020)](https://doi.org/10.7861/clinmed.2020-0896), [Nabavi (2020)](https://doi.org/10.1136/bmj.m3489), [Sudre _et al._ (2021)](https://doi.org/10.1038/s41591-021-01292-y), [Tarybagil _et al._ (2020)](https://doi.org/10.1136/bcr-2020-241485), [Yelin _et al._ (2020)](https://doi.org/10.1016/j.cmi.2020.12.001)). The primary aims of these studies are to identify factors that could be used to predict when _Post COVID-19 condition_ is more likely to develop, the underlying causes of the condition, and potential treatments. A recently published study by [Sudre and colleagues](https://doi.org/10.1038/s41591-021-01292-y) proposed a prediction model to identify individuals at risk of _Post COVID-19 condition_ using data from the [COVID Symptom Study](/data_types/health_data/symptom_study_sweden/), where participants self-reported their symptoms in an app on their mobile devices. The results indicated that individuals experiencing more than five symptoms during the first week of illness were more likely to develop _Post COVID-19 condition_ (odds ratio = 3.53 (2.76–4.50)). In addition, the study showed that the development of _Post COVID-19 condition_ was more likely in females, and that the risk also rose with increasing age and body mass index. The researchers behind the study propose that their model could be used to identify individuals at risk of developing _Post COVID-19 condition_. This could inform trials of preventative or treatment methods, and aid in the planning of education and rehabilitation services.
diff --git a/content/english/dashboards/vaccines.md b/content/english/dashboards/vaccines.md
index 843fffe63..9a7125dfc 100644
--- a/content/english/dashboards/vaccines.md
+++ b/content/english/dashboards/vaccines.md
@@ -5,11 +5,11 @@ banner: /dashboard_thumbs/vaccines.jpg
toc: true
plotly: true
menu:
- dashboard_menu:
- identifier: vaccines
- name: "Vaccine administration: COVID-19"
+ dashboard_menu:
+ identifier: vaccines
+ name: "Vaccine administration: COVID-19"
aliases:
- - /data_types/health_data/vaccines/
+ - /data_types/health_data/vaccines/
dashboards_topics: [COVID-19, Infectious diseases]
---
@@ -77,7 +77,7 @@ Vaccination data is spread between multiple tabs of the [FoHM data file](https:/
**Code used to generate the 'live text' in the summary paragraph below:** ['Live text' script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_livetext.py).
-To summarise, in total, % of the population that are eligible for the first dose have received at least one dose of vaccination against COVID-19, which represents % of the whole population. The values indicate that % of the eligible population were vaccinated last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). By contrast, % of those eligible, and % of the whole population have received at least two doses in total. The values indicate that % of those eligible and % of the whole population received their second dose last week (a change in rate of % and % compared to the previous week, respectively). In total, % of the eligible population received the third dose, representing % of the whole population. This means that % of the eligible population received their third dose last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). To date, % of the whole population has received a fourth dose, and % of those eligible. In the last week, % of the whole population were vaccinated with a fourth dose, a change in rate of % compared to the previous week. By contast, % of the eligible population were vaccinated with a fourth dose, a relative change in rate of % compared to the previous week. A fifth dose was added in September 2022, % of the Swedish population have received that dose to date, which amounts to % of those eligible. A total of % of the whole population were vaccinated with a fifth dose in the last week, a change of % compared to the week before. When considering only the eligible population, % were given a fifth dose last week, which constitutes a relative change in rate of % compared to the previous week.
+To summarise, in total, % of the population that are eligible for the first dose have received at least one dose of vaccination against COVID-19, which represents % of the whole population. The values indicate that % of the eligible population were vaccinated last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). By contrast, % of those eligible, and % of the whole population have received at least two doses in total. The values indicate that % of those eligible and % of the whole population received their second dose last week (a change in rate of % and % compared to the previous week, respectively). In total, % of the eligible population received the third dose, representing % of the whole population. This means that % of the eligible population received their third dose last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). To date, % of the whole population has received a fourth dose, and % of those eligible. In the last week, % of the whole population were vaccinated with a fourth dose, a change in rate of % compared to the previous week. By contast, % of the eligible population were vaccinated with a fourth dose, a relative change in rate of % compared to the previous week. A fifth dose was added in September 2022, % of the Swedish population have received that dose to date, which amounts to % of those eligible. A total of % of the whole population were vaccinated with a fifth dose in the last week, a change of % compared to the week before. When considering only the eligible population, % were given a fifth dose last week, which constitutes a relative change in rate of % compared to the previous week.
### Administration of vaccinations over time
diff --git a/content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md b/content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md
index daa082294..3bab5ba33 100644
--- a/content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md
+++ b/content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md
@@ -2,7 +2,7 @@
title: Amount of SARS-CoV-2 in wastewater (GU)
plotly: true
aliases:
- - /dashboards/wastewater/covid_quant_gu/
+ - /dashboards/wastewater/covid_quant_gu/
---
@@ -18,13 +18,13 @@ The data and visualisation on this page are usually updated weekly.
## Wastewater collection sites
-Influent wastewater samples were collected from Ryaverket wastewater treatment plant (WWTP) in Gothenburg. Wastewater sample collection began on February 10th (week 7) of 2020. Ryaverket WWTP receives wastewater from the households of more than 790,000 residents of Gothenburg, as well as from industry in the area. Wastewater is also received from residents and industry in surrounding municipalities, including Ale, Härryda, Kungälv, Lerum, Mölndal, and Partille, as well as storm and snow-melt water from older parts of Gothenburg. The amount of wastewater from households remains relatively consistent throughout the year. However, the amount of wastewater overall can be affected by the weather (with higher precipitation resulting in greater amounts). More information about the sample location, sample week, volume, and influent wastewater flow, is available in [Wang *et al.* (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/).
+Influent wastewater samples were collected from Ryaverket wastewater treatment plant (WWTP) in Gothenburg. Wastewater sample collection began on February 10th (week 7) of 2020. Ryaverket WWTP receives wastewater from the households of more than 790,000 residents of Gothenburg, as well as from industry in the area. Wastewater is also received from residents and industry in surrounding municipalities, including Ale, Härryda, Kungälv, Lerum, Mölndal, and Partille, as well as storm and snow-melt water from older parts of Gothenburg. The amount of wastewater from households remains relatively consistent throughout the year. However, the amount of wastewater overall can be affected by the weather (with higher precipitation resulting in greater amounts). More information about the sample location, sample week, volume, and influent wastewater flow, is available in [Wang _et al._ (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/).
## Visualisations
Last updated:
-*The blue block on the graph indicates the period where sample collection was not completed (week 45 2022 - week 2 2023).*
+_The blue block on the graph indicates the period where sample collection was not completed (week 45 2022 - week 2 2023)._
+
@@ -72,7 +76,7 @@ Influent wastewater samples were collected from Ryaverket wastewater treatment p
**Download the data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://blobserver.dc.scilifelab.se/blob/wastewater_data_gu_allviruses.xlsx). Results are available for SARS-CoV-2 from week 7 of 2020 (with a small gap over winter 2022-2023), and for enteric viruses from week 2 of 2023. Updated weekly.\
**Contact:**
-**How to cite the dataset:** Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501).
+**How to cite the dataset:** Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501).
**How to cite method:**
Saguti, F., Magnil, E., Enache, L., Churqui, M.P., Johansson, A., Lumley, D., Davidsson, F., Dotevall, L., Mattsson, A., Trybala, E., Lagging, M., Lindh, M., Gisslen, M., Brezicka, T., Nystrom, K. and Norder, H. (2021). Surveillance of wastewater revealed peaks of SARS-CoV-2 preceding those of hospitalized patients with COVID-19. [https://doi.org/10.1016/j.watres.2020.116620](https://doi.org/10.1016/j.watres.2020.116620).
@@ -83,7 +87,7 @@ Wang, H., Churqui, M.P., Tunovic, T., Enache, L., Johansson, A., Karmander, A.,
Samples of wastewater were collected using a fixed-site sampler that collected 30ml per 10,000m3 of the incoming wastewater. For the purposes of analysis, seven samples (each representing a 24 hour period) were pooled to create a weekly sample. The weekly sample, which consisted of 1.5-15l of wastewater (depending on the flow) was sent to the Clinical Microbiology Laboratory at Sahlgrenska University Hospital for analysis. Analyses were conducted on the Monday after the sample was collected.
-At the Clinical Microbiology Laboratory, viruses were concentrated to a final volume of 2.5ml, using a method that was developed in-house. This method uses the NanoCeram electropositive filter (Argonide, Florida, USA) as the primary means of concentration, and then ultracentrifugation as secondary concentration method ([Saguti *et al.*, 2021](https://pubmed.ncbi.nlm.nih.gov/33212338/)). Nucleic acids were extracted from 1ml of the concentrated sample using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). Real-time quantitative PCR (RT-qPCR) was performed to detect the RNA-dependent RNA polymerase (RdRP) region of SARS-CoV-2. In all runs, a 10-fold serial diluted plasmid (Eurofins Genomics, Ebersberg, Germany) that contained the target SARS-CoV-2 region was used as a positive control. Nuclease-free water was used as a negative control. The Ct values from the qPCR were used to quantify the amount of SARS-CoV-2 genome in the sample. Details about the method of calculation are provided in [Saguti *et al.* (2021)](https://pubmed.ncbi.nlm.nih.gov/33212338/). The relative amount of viral genome in the wastewater was calculated by dividing the amount of viral genome in the sample by the amount of SARS-CoV-2 genome in the incoming wastewater during week 11 (mid-March) of 2020. Samples from all subsequent weeks contained detectable SARS-CoV-2 genome.
+At the Clinical Microbiology Laboratory, viruses were concentrated to a final volume of 2.5ml, using a method that was developed in-house. This method uses the NanoCeram electropositive filter (Argonide, Florida, USA) as the primary means of concentration, and then ultracentrifugation as secondary concentration method ([Saguti _et al._, 2021](https://pubmed.ncbi.nlm.nih.gov/33212338/)). Nucleic acids were extracted from 1ml of the concentrated sample using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). Real-time quantitative PCR (RT-qPCR) was performed to detect the RNA-dependent RNA polymerase (RdRP) region of SARS-CoV-2. In all runs, a 10-fold serial diluted plasmid (Eurofins Genomics, Ebersberg, Germany) that contained the target SARS-CoV-2 region was used as a positive control. Nuclease-free water was used as a negative control. The Ct values from the qPCR were used to quantify the amount of SARS-CoV-2 genome in the sample. Details about the method of calculation are provided in [Saguti _et al._ (2021)](https://pubmed.ncbi.nlm.nih.gov/33212338/). The relative amount of viral genome in the wastewater was calculated by dividing the amount of viral genome in the sample by the amount of SARS-CoV-2 genome in the incoming wastewater during week 11 (mid-March) of 2020. Samples from all subsequent weeks contained detectable SARS-CoV-2 genome.
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 7efec25d3..dd9f04558 100644
--- a/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md
+++ b/content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md
@@ -65,6 +65,10 @@ Please also note that although the same methods are used for all cities shown on
@@ -76,7 +80,7 @@ Please also note that although the same methods are used for all cities shown on
Last updated:
- Scroll the plot sideways to view all data.
+ Rotating your phone may improve graph layout
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 2bdc3b4eb..30cb7e79a 100644
--- a/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md
+++ b/content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md
@@ -65,6 +65,10 @@ Please note that although the same methods are used for all cities shown on this
diff --git a/content/english/dashboards/wastewater/enteric_quantification/_index.md b/content/english/dashboards/wastewater/enteric_quantification/_index.md
index 675acff03..bc188685c 100644
--- a/content/english/dashboards/wastewater/enteric_quantification/_index.md
+++ b/content/english/dashboards/wastewater/enteric_quantification/_index.md
@@ -34,6 +34,10 @@ The wastewater samples for virus analysis are collected at Ryaverket's wastewate
Please see [the section with summary information about the viruses](#basic-virus-information) for more information on each of the viruses for which data is being collected.
+
diff --git a/content/english/dashboards/wastewater/influenza_quantification/_index.md b/content/english/dashboards/wastewater/influenza_quantification/_index.md
index 8197bd8ae..7cce7c7c6 100644
--- a/content/english/dashboards/wastewater/influenza_quantification/_index.md
+++ b/content/english/dashboards/wastewater/influenza_quantification/_index.md
@@ -32,6 +32,10 @@ SLU-SEEC collects and analyses samples for influenza A and B viruses from multip
### Influenza A
+
diff --git a/content/english/highlights/COVseq_surveillance_VOCs.md b/content/english/highlights/COVseq_surveillance_VOCs.md
index 0f5bddbce..96f20e40e 100644
--- a/content/english/highlights/COVseq_surveillance_VOCs.md
+++ b/content/english/highlights/COVseq_surveillance_VOCs.md
@@ -7,6 +7,7 @@ banner: /highlights/banners/COVseq_small.png
banner_large: /highlights/banners/COVseq.png
banner_caption: "Source: Figure 1b of Simonetti et al. 2021"
highlights_topics: [COVID-19, Infectious diseases]
+tags: [COVID-19, Variant of concern, Large scale, Genomic surveillance, WGS, COVseq]
aliases:
- /news/covseq_surveillance_vocs
- /sv/news/covseq_surveillance_vocs
diff --git a/content/english/highlights/G3BP_antivirual_target.md b/content/english/highlights/G3BP_antivirual_target.md
index a427a6b59..d77104a6c 100644
--- a/content/english/highlights/G3BP_antivirual_target.md
+++ b/content/english/highlights/G3BP_antivirual_target.md
@@ -6,6 +6,7 @@ banner: /highlights/banners/G3BP_thumbnail.png
banner_large: /highlights/banners/G3BP_figure1.png
banner_caption: "Source: Figure 1 Kruse et al. 2021"
highlights_topics: [COVID-19, Infectious diseases]
+tags: [SARS-CoV-2, Phage display library, Discovery, Proteomics data, Antiviral intervention]
---
The current COVID-19 pandemic has challenged societies world-wide over the last two years. Although vaccines have been developed in record time, and therapeutic drugs have been developed and repurposed, the pandemic is still challenging healthcare. More treatment options (e.g. novel antivirals) are warranted in preparation for future pandemic outbreaks.
diff --git a/content/english/highlights/Interferon_signatures_Liver.md b/content/english/highlights/Interferon_signatures_Liver.md
index 99471ae15..0ed126822 100644
--- a/content/english/highlights/Interferon_signatures_Liver.md
+++ b/content/english/highlights/Interferon_signatures_Liver.md
@@ -6,6 +6,7 @@ banner: /highlights/banners/Interferon_liver_small.png
banner_large: /highlights/banners/Interferon_liver.png
banner_caption: "Source: Figure 2B from Chen and Saccon et al. 2021"
highlights_topics: [COVID-19, Infectious diseases]
+tags: [COVID-19, SARS-CoV-2, Interferon, Type-1 interferon signalling]
aliases:
- /news/interferon_signatures_liver
- /sv/news/interferon_signatures_liver
diff --git a/content/english/highlights/Metabolic_perturbation_therapeutic_target.md b/content/english/highlights/Metabolic_perturbation_therapeutic_target.md
index b60b82690..5f6ac41e0 100644
--- a/content/english/highlights/Metabolic_perturbation_therapeutic_target.md
+++ b/content/english/highlights/Metabolic_perturbation_therapeutic_target.md
@@ -6,6 +6,7 @@ banner: /highlights/banners/Krishnan_abstract_thumbnail.png
banner_large: /highlights/banners/Krishnan_graphical_abstract.png
banner_caption: Graphical abstract from Krishnan et al. (2021).
highlights_topics: [COVID-19, Infectious diseases]
+tags: [SARS-CoV-2, Therapeutic target, Multiomics data, Metabolic pathways, Viral reproduction]
aliases:
- /news/metabolic_perturbation_therapeutic_target
- /sv/news/metabolic_perturbation_therapeutic_target
diff --git a/content/english/highlights/Phenomics_method_drug_discovery.md b/content/english/highlights/Phenomics_method_drug_discovery.md
index 255568450..a7c822f48 100644
--- a/content/english/highlights/Phenomics_method_drug_discovery.md
+++ b/content/english/highlights/Phenomics_method_drug_discovery.md
@@ -6,6 +6,7 @@ banner: /highlights/banners/Rietdijk_abstract_small.png
banner_large: /highlights/banners/Rietdijk_abstract_big.png
banner_caption: "Source: Graphical abstract from Rietdijk et al. 2021"
highlights_topics: [COVID-19, Infectious diseases]
+tags: [Phenomics, Pertubations, Antiviralm, Drug discovery]
aliases:
- /news/phenomics_method_drug_discovery
- /sv/news/phenomics_method_drug_discovery
diff --git a/content/english/highlights/adenovirus.md b/content/english/highlights/adenovirus.md
index aa8b780e4..0153ecb35 100644
--- a/content/english/highlights/adenovirus.md
+++ b/content/english/highlights/adenovirus.md
@@ -6,6 +6,7 @@ banner: /highlights/banners/adenovirus.png
banner_large: /highlights/banners/adenovirus.png
banner_caption: "Source: Figure 3 of Persson et al. 2021"
highlights_topics: [COVID-19, Infectious diseases]
+tags: [COVID-19, Adenovirus, Vaccine, Vector]
aliases:
- /news/adenovirus/
- /sv/news/adenovirus/
diff --git a/content/english/highlights/alpaca-nanobody.md b/content/english/highlights/alpaca-nanobody.md
index 3355cc6f2..8210e613e 100644
--- a/content/english/highlights/alpaca-nanobody.md
+++ b/content/english/highlights/alpaca-nanobody.md
@@ -6,6 +6,7 @@ summary: Leo Hanke and colleagues identified a SARS-CoV-2 RBD-specific single do
banner: /highlights/banners/tyson.jpg
banner_caption: "Tyson the alpaca. Photo courtesy of Leo Hanke."
highlights_topics: [COVID-19, Infectious diseases]
+tags: [COVID-19 SARS-CoV-2, Nanobody, Ty1, Neutralization, Antiviral therapy]
aliases:
- /news/alpaca-nanobody
- /sv/news/alpaca-nanobody
diff --git a/content/english/highlights/antibiotic_resistance_development.md b/content/english/highlights/antibiotic_resistance_development.md
index 37c65c560..6213a7346 100644
--- a/content/english/highlights/antibiotic_resistance_development.md
+++ b/content/english/highlights/antibiotic_resistance_development.md
@@ -6,6 +6,7 @@ banner: /highlights/banners/antibiotic_resistance_development_small.jpg
banner_large: /highlights/banners/antibiotic_resistance_development.jpg
banner_caption: Artistic illustration of perseverance courtesy Elf lab / Johan Elf, Irmeli Barkefors
highlights_topics: [Antibiotic resistance]
+tags: [Antibiotic resistance, Bacteria, Escherichia coli, Perseverance, Time-lapse microscopy]
announcement: "This data highlight was also [published on the SciLifeLab Data Platform](https://data.scilifelab.se/highlights/antibiotic_resistance_development/), as the work described in this highlight constitutes data-driven life science. The Platform is a hub for data-driven life science in Sweden, containing multiple relevant resources, tools, and services. It includes information on multiple subjects, including infectious diseases, please check out the [Data Platform](https://data.scilifelab.se/) for more."
---
diff --git a/content/english/highlights/antivirals.md b/content/english/highlights/antivirals.md
index d7f601da7..6494661ff 100644
--- a/content/english/highlights/antivirals.md
+++ b/content/english/highlights/antivirals.md
@@ -6,6 +6,7 @@ banner: /highlights/banners/antivirals.png
banner_large: /highlights/banners/antivirals_large.png
banner_caption: "Source: Courtesy of Marjo-Riitta Puumalainen"
highlights_topics: [COVID-19, Infectious diseases]
+tags: [COVID-19, Host-targeted, Small molecule inhibitors, Antiviral screening , Cellular pathways, Broad spectrum antivirals]
aliases:
- /news/antivirals
- /sv/news/antivirals
diff --git a/content/english/highlights/bacterial_replication.md b/content/english/highlights/bacterial_replication.md
index 9a6862519..c4b079b3e 100644
--- a/content/english/highlights/bacterial_replication.md
+++ b/content/english/highlights/bacterial_replication.md
@@ -6,6 +6,7 @@ banner: /highlights/banners/ELF_banner.png
banner_large: /highlights/banners/ELF_large.png
banner_caption: Image courtesy Johan Elf lab
highlights_topics: [Infectious Diseases]
+tags: [Infectious diseasese, Replication, Escherichia coli]
announcement: "This data highlight was also [published on the SciLifeLab Data Platform](https://data.scilifelab.se/highlights/bacterial_replication/), as the work described in this highlight constitutes data-driven life science. The Platform is a hub for data-driven life science in Sweden, containing multiple relevant resources, tools, and services. It includes information on multiple subjects, including infectious diseases, please check out the [Data Platform](https://data.scilifelab.se/) for more."
---
diff --git a/content/english/highlights/bevacizumab_treatment.md b/content/english/highlights/bevacizumab_treatment.md
index cf4b97d22..8145c3d91 100644
--- a/content/english/highlights/bevacizumab_treatment.md
+++ b/content/english/highlights/bevacizumab_treatment.md
@@ -6,6 +6,7 @@ banner: /highlights/banners/bevacizumab_small.png
banner_large: /highlights/banners/bevacizumab_large.png
banner_caption: "Source: Figure 4 of Pang et al. (2021)."
highlights_topics: [COVID-19, Infectious diseases]
+tags: [COVID-19, Drug repurposing, Bevacizumab, Severe COVID]
aliases:
- /news/bevacizumab_treatment
- /sv/news/bevacizumab_treatment
diff --git a/content/english/highlights/bispecific_monomeric_nanobody.md b/content/english/highlights/bispecific_monomeric_nanobody.md
index 4b650f8ec..b24284b04 100644
--- a/content/english/highlights/bispecific_monomeric_nanobody.md
+++ b/content/english/highlights/bispecific_monomeric_nanobody.md
@@ -6,6 +6,7 @@ banner: /highlights/banners/bispecific_monomeric_nanobody.png
banner_large: /highlights/banners/bispecific_monomeric_nanobody_large.png
banner_caption: Fig 2-f Modelling of simultaneous spike-Fu2-ACE2 binding shows that Fu2 blocks the binding of ACE2, from Hanke, L., Das, H., Sheward, D.J. et al (2022)
highlights_topics: [COVID-19, Infectious diseases]
+tags: [COVID-19, SARS-CoV-2, Variant of concern, Nanobody, Neutralization, Antiviral]
---
The COVID-19 pandemic, which is going into its third year, has had major societal and economic consequences worldwide. Despite lockdowns and non-pharmaceutical interventions (NPIs), such as restrictions on gatherings, social distancing requirements, and face mask mandates, the pandemic is still ongoing. The vaccine roll-out is progressing, and several treatment options and drugs are now registered for use. However, the continuous emergence of new [*Variants of Concern* (VoC)](/voc/) has delayed the re-opening of society. It is unfortunately likely to continue to do so, as research has confirmed that new variants are less effectively neutralised by antibodies elicited by the first-generation vaccines (*cf* [Cele et al. 2021](https://www.nature.com/articles/s41586-021-03471-w)). The development of novel treatments and vaccines that protects against SARS-CoV-2 variants, particularly VoCs, is therefore urgently needed.
diff --git a/content/english/highlights/cellular_response.md b/content/english/highlights/cellular_response.md
index 6804481e3..a1c85b9cb 100644
--- a/content/english/highlights/cellular_response.md
+++ b/content/english/highlights/cellular_response.md
@@ -6,6 +6,7 @@ banner: /highlights/banners/cellular_response.png
banner_large: /highlights/banners/cellular_response_large.png
banner_caption: "Source: Graphical Abstract of Saccon, Chen and Mikaeloff et al 2021"
highlights_topics: [COVID-19, Infectious diseases]
+tags: [COVID-19, Proteomics, Signaling pathway, Stype-I interferon regulation]
aliases:
- /news/cellular_response
- /sv/news/cellular_response
diff --git a/content/english/highlights/covidtest_spatiotemp_uppsala.md b/content/english/highlights/covidtest_spatiotemp_uppsala.md
index 8a58fe57f..09f546a41 100644
--- a/content/english/highlights/covidtest_spatiotemp_uppsala.md
+++ b/content/english/highlights/covidtest_spatiotemp_uppsala.md
@@ -6,6 +6,7 @@ banner: /highlights/banners/COV_spatiopredict_fig7.png
banner_large: /highlights/banners/COV_spatiopredict_fig7.png
banner_caption: "Source: Figure 7 of van Zoest et al. (2022)"
highlights_topics: [COVID-19, Infectious diseases]
+tags: [COVID-19, Spatio-temportal prediction, Pandemic preparedness]
---
diff --git a/content/svenska/dashboards/vaccines.md b/content/svenska/dashboards/vaccines.md
index b1ade3c1d..2d73ed204 100644
--- a/content/svenska/dashboards/vaccines.md
+++ b/content/svenska/dashboards/vaccines.md
@@ -5,12 +5,13 @@ banner: /dashboard_thumbs/vaccines.jpg
toc: true
plotly: true
menu:
- dashboard_menu:
- identifier: vaccines
- name: Administrering av covid-19 vaccin
+ dashboard_menu:
+ identifier: vaccines
+ name: Administrering av covid-19 vaccin
aliases:
- - /sv/data_types/health_data/vaccines/
+ - /sv/data_types/health_data/vaccines/
---
+
Uppgifterna på den här sidan uppdateras inte längre vid datakällan. Vi utvärderar för närvarande användningen av andra datakällor för vaccindata. Se vår RECOVAC dashboard för mer information om vaccin effektivitet och säkerhet (denna dashboard är endast tillgänglig på engelska).
@@ -75,7 +76,7 @@ Vaccination data is spread between multiple tabs of the [FoHM data file](https:/
**Code used to generate the 'live text' in the summary paragraph below:** ['Live text' script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_livetext.py).
-To summarise, in total, % of the population that are eligible for the first dose have received at least one dose of vaccination against COVID-19, which represents % of the whole population. The values indicate that % of the eligible population were vaccinated last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). By contrast, % of those eligible, and % of the whole population have received at least two doses in total. The values indicate that % of those eligible and % of the whole population received their second dose last week (a change in rate of % and % compared to the previous week, respectively). In total, % of the eligible population received the third dose, representing % of the whole population. This means that % of the eligible population received their third dose last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). To date, % of the whole population has received a fourth dose, and % of those eligible. In the last week, % of the whole population were vaccinated with a fourth dose, a change in rate of % compared to the previous week. By contast, % of the eligible population were vaccinated with a fourth dose, a relative change in rate of % compared to the previous week. A fifth dose was added in September 2022, % of the Swedish population have received that dose to date, which amounts to % of those eligible. A total of % of the whole population were vaccinated with a fifth dose in the last week, a change of % compared to the week before. When considering only the eligible population, % were given a fifth dose last week, which constitutes a relative change in rate of % compared to the previous week.
+To summarise, in total, % of the population that are eligible for the first dose have received at least one dose of vaccination against COVID-19, which represents % of the whole population. The values indicate that % of the eligible population were vaccinated last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). By contrast, % of those eligible, and % of the whole population have received at least two doses in total. The values indicate that % of those eligible and % of the whole population received their second dose last week (a change in rate of % and % compared to the previous week, respectively). In total, % of the eligible population received the third dose, representing % of the whole population. This means that % of the eligible population received their third dose last week (a change in rate of % compared to the previous week), or % of the whole population (a change of % compared to the previous week). To date, % of the whole population has received a fourth dose, and % of those eligible. In the last week, % of the whole population were vaccinated with a fourth dose, a change in rate of % compared to the previous week. By contast, % of the eligible population were vaccinated with a fourth dose, a relative change in rate of % compared to the previous week. A fifth dose was added in September 2022, % of the Swedish population have received that dose to date, which amounts to % of those eligible. A total of % of the whole population were vaccinated with a fifth dose in the last week, a change of % compared to the week before. When considering only the eligible population, % were given a fifth dose last week, which constitutes a relative change in rate of % compared to the previous week.
### Administration of vaccinations over time
diff --git a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md
index 4e21a5951..9eb83ba55 100644
--- a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md
+++ b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_GU.md
@@ -2,7 +2,7 @@
title: Mängd SARS-COV-2 i avloppsvatten (GU)
plotly: true
aliases:
- - /sv/dashboards/wastewater/covid_quant_gu/
+ - /sv/dashboards/wastewater/covid_quant_gu/
---
@@ -12,13 +12,13 @@ aliases:
## Introduktion
-Detta projekt leds av professor Helene Norder (Göteborgs universitet, GU), i samarbete med anställda vid Göteborgs universitet och Sahlgrenska Universitetssjukhuset (Hao Wang, Marianela Patzi Churqui, Timur Tunovic, Fredy Saguti och Kristina Nyström). Avloppsvattenprover insamlas av Lucica Enache vid Ryaverkets avloppsreningsverk, Gryaab AB, Göteborg.
+Detta projekt leds av professor Helene Norder (Göteborgs universitet, GU), i samarbete med anställda vid Göteborgs universitet och Sahlgrenska Universitetssjukhuset (Hao Wang, Marianela Patzi Churqui, Timur Tunovic, Fredy Saguti och Kristina Nyström). Avloppsvattenprover insamlas av Lucica Enache vid Ryaverkets avloppsreningsverk, Gryaab AB, Göteborg.
Data och visualiseringar på denna sida uppdateras veckovis.
## Insamlingsplatser för avloppsvatten
-Ingående avloppsvattenprover insamlas från Ryaverkets avloppsreningsverk (eng. waste water plant WWTP) i Göteborg. Insamling av avloppsvattenprov startade 10 februari 2020 (vecka 7). Ryaverkets avloppsreningsverk samlar in avloppsvatten från mer än 790,000 invånare samt även från närliggande industrier. Avloppsvatten samlas även in från invånare och industrier inom närliggande områden som exempelvis Ale, Härryda, Kungälv, Lerum, Mölndal och Partille, samt från smältvatten från äldre delar av Göteborg. Mängd avloppsvatten från hushåll ligger på samma nivå över året, men den totala mängden avloppsvatten kan variera över året beroende på väderlek (högre luftfuktighet ger större mängd avloppsvatten). För mer information om uppsamling av avloppsvatten, veckor, volym avloppsvatten och flöde se [Wang *et al.* (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/).
+Ingående avloppsvattenprover insamlas från Ryaverkets avloppsreningsverk (eng. waste water plant WWTP) i Göteborg. Insamling av avloppsvattenprov startade 10 februari 2020 (vecka 7). Ryaverkets avloppsreningsverk samlar in avloppsvatten från mer än 790,000 invånare samt även från närliggande industrier. Avloppsvatten samlas även in från invånare och industrier inom närliggande områden som exempelvis Ale, Härryda, Kungälv, Lerum, Mölndal och Partille, samt från smältvatten från äldre delar av Göteborg. Mängd avloppsvatten från hushåll ligger på samma nivå över året, men den totala mängden avloppsvatten kan variera över året beroende på väderlek (högre luftfuktighet ger större mängd avloppsvatten). För mer information om uppsamling av avloppsvatten, veckor, volym avloppsvatten och flöde se [Wang _et al._ (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/).
## Visualiseringar
@@ -53,6 +53,10 @@ Ingående avloppsvattenprover insamlas från Ryaverkets avloppsreningsverk (eng.
-->
+
+ Att rotera mobiltelefonen kan förbättra grafens layout
+
@@ -69,9 +73,9 @@ Ingående avloppsvattenprover insamlas från Ryaverkets avloppsreningsverk (eng.
**Kontakt:**
-**Nedladdning av data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://blobserver.dc.scilifelab.se/blob/wastewater_data_gu_allviruses.xlsx). Resultat finns tillgängliga för mängd SARS-CoV-2 från vecka 7 2020 (ett mindre uppehåll under vintern 2022-2023) , och för enterovirus från vecka 2 2023. Data uppdateras veckovis.\
+**Nedladdning av data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://blobserver.dc.scilifelab.se/blob/wastewater_data_gu_allviruses.xlsx). Resultat finns tillgängliga för mängd SARS-CoV-2 från vecka 7 2020 (ett mindre uppehåll under vintern 2022-2023) , och för enterovirus från vecka 2 2023. Data uppdateras veckovis.\
-**För att citera datasetet:** Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501).
+**För att citera datasetet:** Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501).
**För att citera metoden som används:**
Saguti, F., Magnil, E., Enache, L., Churqui, M.P., Johansson, A., Lumley, D., Davidsson, F., Dotevall, L., Mattsson, A., Trybala, E., Lagging, M., Lindh, M., Gisslen, M., Brezicka, T., Nystrom, K. and Norder, H. (2021). Surveillance of wastewater revealed peaks of SARS-CoV-2 preceding those of hospitalized patients with COVID-19. [https://doi.org/10.1016/j.watres.2020.116620](https://doi.org/10.1016/j.watres.2020.116620).
@@ -80,9 +84,9 @@ Wang, H., Churqui, M.P., Tunovic, T., Enache, L., Johansson, A., Karmander, A.,
## Metoder
-Insamling av avloppsvatten sker genom en fast insamlare som samlar in 30ml avlopps vatten per 10,000m3 av inkommande avloppsvatten. För analys veckovis poolas sju prover (varje avloppsvatten prov representerar insamling under ett dygn). Veckoprovet består av 1.5-15l avloppsvatten (beroende av flödet) som skickas till Klinisk Mikrobiologi vid Sahlgrenska Universitetssjukhuset för analys. Analys sker på måndagen i veckan efter provinsamling.
+Insamling av avloppsvatten sker genom en fast insamlare som samlar in 30ml avlopps vatten per 10,000m3 av inkommande avloppsvatten. För analys veckovis poolas sju prover (varje avloppsvatten prov representerar insamling under ett dygn). Veckoprovet består av 1.5-15l avloppsvatten (beroende av flödet) som skickas till Klinisk Mikrobiologi vid Sahlgrenska Universitetssjukhuset för analys. Analys sker på måndagen i veckan efter provinsamling.
-På Klinisk Mikrobiologi, koncentreras virusmängd genom en metod utvecklad på laboratoriet till en volym av 2.5ml. Denna metod använder NanoCeram electropositive filter (Argonide, Florida, USA) för att koncentrera prover, följt av ultracentrifugering som sekundär metod för att koncentrera prover ([Saguti *et al.*, 2021](https://pubmed.ncbi.nlm.nih.gov/33212338/)). Nukleinsyror extraherades därefter från ett 1ml koncentrerat prov med hjälp av QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). Realtids-PCR (RT-qPCR) användes för att detektera den RNA-beroende RNA polymerase (RdRP) regionen på SARS-CoV-2. Alla körningar innehöll en positiv kontroll bestående av en seriellt utspädd plasmid (Eurofins Genomics, Ebersberg, Germany). Nukleasfritt vatten används som negativ kontroll. Ct-värden från qPCR användes för att kvantifiera mängd SARS-CoV-2 genom i provet. En detaljerad beskrivning av hur mängd SARS-CoV-2 beräknas finns i [Saguti *et al.* (2021)](https://pubmed.ncbi.nlm.nih.gov/33212338/). Den relativa virusmängden i avloppsvatten beräknades genom att dela mängd viralt genom i prover med mängd SARS-CoV-2 genom i ingående mängd avloppsvatten vecka 11 (mitten av mars) 2020. Prover från alla följande veckor har innehållit detekterbara SARS-CoV-2 genom.
+På Klinisk Mikrobiologi, koncentreras virusmängd genom en metod utvecklad på laboratoriet till en volym av 2.5ml. Denna metod använder NanoCeram electropositive filter (Argonide, Florida, USA) för att koncentrera prover, följt av ultracentrifugering som sekundär metod för att koncentrera prover ([Saguti _et al._, 2021](https://pubmed.ncbi.nlm.nih.gov/33212338/)). Nukleinsyror extraherades därefter från ett 1ml koncentrerat prov med hjälp av QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). Realtids-PCR (RT-qPCR) användes för att detektera den RNA-beroende RNA polymerase (RdRP) regionen på SARS-CoV-2. Alla körningar innehöll en positiv kontroll bestående av en seriellt utspädd plasmid (Eurofins Genomics, Ebersberg, Germany). Nukleasfritt vatten används som negativ kontroll. Ct-värden från qPCR användes för att kvantifiera mängd SARS-CoV-2 genom i provet. En detaljerad beskrivning av hur mängd SARS-CoV-2 beräknas finns i [Saguti _et al._ (2021)](https://pubmed.ncbi.nlm.nih.gov/33212338/). Den relativa virusmängden i avloppsvatten beräknades genom att dela mängd viralt genom i prover med mängd SARS-CoV-2 genom i ingående mängd avloppsvatten vecka 11 (mitten av mars) 2020. Prover från alla följande veckor har innehållit detekterbara SARS-CoV-2 genom.
diff --git a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md
index 9dcd6f2aa..c20872a57 100644
--- a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md
+++ b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_KTH.md
@@ -64,6 +64,10 @@ Notera också att även om samma metoder används för alla städer som visas p
+
+ Att rotera mobiltelefonen kan förbättra grafens layout
+
@@ -75,7 +79,7 @@ Notera också att även om samma metoder används för alla städer som visas p
Senast uppdaterad:
- Skrolla grafen horisontellt för att se alla data.
+ Att rotera mobiltelefonen kan förbättra grafens layout
diff --git a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md
index b6ef33c51..a086e7c1b 100644
--- a/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md
+++ b/content/svenska/dashboards/wastewater/covid_quantification/covid_quant_SLU.md
@@ -64,6 +64,10 @@ Notera också att även om samma metoder används för alla städer som visas p
+
+ Att rotera mobiltelefonen kan förbättra grafens layout
+
diff --git a/content/svenska/dashboards/wastewater/enteric_quantification/_index.md b/content/svenska/dashboards/wastewater/enteric_quantification/_index.md
index 8994099f1..192e8c617 100644
--- a/content/svenska/dashboards/wastewater/enteric_quantification/_index.md
+++ b/content/svenska/dashboards/wastewater/enteric_quantification/_index.md
@@ -32,6 +32,10 @@ Avloppsvattenprover för virusanalys samlas in vid Ryaverkets avloppsreningsverk
Vänligen se [avsnittet med sammanfattande information om virusen](#grundläggande-virusinformation) för mer information om vart och ett av de virus som data samlas in för.
+
+ Att rotera mobiltelefonen kan förbättra grafens layout
+
diff --git a/content/svenska/dashboards/wastewater/influenza_quantification/_index.md b/content/svenska/dashboards/wastewater/influenza_quantification/_index.md
index b8dcd00a3..419c52b7a 100644
--- a/content/svenska/dashboards/wastewater/influenza_quantification/_index.md
+++ b/content/svenska/dashboards/wastewater/influenza_quantification/_index.md
@@ -32,6 +32,10 @@ SLU-SEEC samlar in och analyserar prover för kvantifiering av nivåerna av infl
### Influensa A
+
+ Att rotera mobiltelefonen kan förbättra grafens layout
+
diff --git a/content/svenska/partners.md b/content/svenska/partners.md
index 853424a95..dbec80833 100644
--- a/content/svenska/partners.md
+++ b/content/svenska/partners.md
@@ -4,7 +4,7 @@ toc: false
menu:
footer_about:
name: Andra nationella dataportaler
- weight: 30
+ weight: 20
---
Patogens Portal Sverige lanserades ursprungligen som den 'svenska Covid-19 dataportalen. Portalen var den första nationella noden av den [Europeiska COVID-19 dataportalen](https://covid19dataportal.org/); en europeisk plattform som möjliggör för forskare att dela, får åtkomst till och analysera Covid-19-relaterade data. [Europeiska COVID-19 dataportalen](https://covid19dataportal.org/) finansieras av den Europeiska kommissionen och drivs av European Biobinformatics Institute (EBI) som är en del av Europeiska molekylärbiologiska laboratoriet (EMBL).
diff --git a/content/svenska/privacy.md b/content/svenska/privacy.md
index 26df63b51..71419f6d4 100644
--- a/content/svenska/privacy.md
+++ b/content/svenska/privacy.md
@@ -1,6 +1,10 @@
---
title: Integritetspolicy / Dataskyddspolicy
toc: false
+menu:
+ footer_about:
+ name: Integritetspolicy
+ weight: 40
---
SciLifeLab driver webbplatsen [pathogens.se](https://www.pathogens.se/sv/) och covid19dataportal webbplatser (inkluderande subdomäner som exempelvis [biobanks.covid19dataportal.se](https://biobanks.covid19dataportal.se/)), som tillhandahåller **tjänsten**.
@@ -17,7 +21,7 @@ Vi vill informera dig om att varje gång du besöker vår **tjänst** samlar vi
You can opt out of your Log Data being collected below:
-
+
## Formulär
diff --git a/layouts/about/about_navbar.html b/layouts/about/about_navbar.html
new file mode 100644
index 000000000..f2a2a54e3
--- /dev/null
+++ b/layouts/about/about_navbar.html
@@ -0,0 +1,32 @@
+{{ define "main" }}
+
+
+
+
+{{ .Content }}
+
+{{ end }}
\ No newline at end of file
diff --git a/layouts/highlights/single.html b/layouts/highlights/single.html
index 7119107a5..44c316d09 100644
--- a/layouts/highlights/single.html
+++ b/layouts/highlights/single.html
@@ -13,35 +13,23 @@
{{ if .Params.title_full }}{{ .Params.title_full }}{{ else }}{{ .Title}}{{ end }}
{{ end }}
diff --git a/layouts/index.html b/layouts/index.html
index 0ee279538..f985c8b8a 100644
--- a/layouts/index.html
+++ b/layouts/index.html
@@ -207,9 +207,9 @@
Om dataportalen
{{ end }}
-
-
-
{{ if eq $.Site.Language.LanguageName "Svenska" }}Dela nya data{{ else }}Share new data{{ end }}
+
+
+
{{ if eq $.Site.Language.LanguageName "Svenska" }}Dela nya data{{ else }}Share new data{{ end }}
{{ if eq $.Site.Language.LanguageName "Svenska" }}Teamet som arbetar med dataportalen hjälper dig
gärna dela dina forskningsdata i öppna databaser och svarar på frågor om datahantering.{{ else }}The portal
team is happy to assist you with submitting your data to open repositories or answer any questions about data
diff --git a/layouts/partials/footer.html b/layouts/partials/footer.html
index c6a4dd73a..f19823712 100644
--- a/layouts/partials/footer.html
+++ b/layouts/partials/footer.html
@@ -1,32 +1,21 @@
- 
- 
- 
- 
-
diff --git a/content/english/dashboards/covid_publications.md b/content/english/dashboards/covid_publications.md
index 033566a9a..f07f3acea 100644
--- a/content/english/dashboards/covid_publications.md
+++ b/content/english/dashboards/covid_publications.md
@@ -5,20 +5,25 @@ banner: /dashboard_thumbs/publications.jpg
toc: false
plotly: true
menu:
- dashboard_menu:
- identifier: covid_19_publications_vis
- name: "COVID-19 publication overview"
+ dashboard_menu:
+ identifier: covid_19_publications_vis
+ name: "COVID-19 publication overview"
aliases:
- - /projects/dashboard/
+ - /projects/dashboard/
dashboards_topics: [COVID-19, Infectious diseases]
---
+
The visualisations on this page evaluate the development of COVID-19 and SARS-CoV-2 research across Sweden by assessing publication output. Specifically, we consider multiple aspects of journal publications and preprints where at least one author has an affiliation with a Swedish research institute. The database containing the publications themselves [can be found on this page](/publications/). Note that our database is manually curated and, as such, may not be exhaustive. The full database is available for download and use for other purposes, please see [DOI: 10.17044/scilifelab.14124014](https://doi.org/10.17044/scilifelab.14124014) for details.
The code used to produce the visulations on this page can be found on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations). Specifically, code related to the number of publications can be found in the ['Count_publications' folder of the repository](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Count_publications), and code used to generated the wordclouds can be found in the ['Wordcloud' folder](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Wordcloud).
## Number of new publications
-This graph displays the number of publications (including both journal publications and preprints) published each month, as well as the cumulative daily total of publications contained in the database. The dates reflect either the preprint upload date or the official journal publication date, whichever is the most recent. Where a given day of publication is not specified in the publication/upload date, we assign the date as the first of the month. This causes the appearance of a relatively sharp increase at the start of each month. This chart is updated daily, though the publications database is not.
+This graph displays the number of publications (including both journal publications and preprints) published each month, as well as the cumulative daily total of publications contained in the database. The dates reflect either the preprint upload date or the official journal publication date, whichever is the most recent. Where a given day of publication is not specified in the publication/upload date, we assign the date as the first of the month. This causes the appearance of a relatively sharp increase at the start of each month. This chart is updated weekly, though the publications database is not.
+
+
+