diff --git a/content/english/about/_index.md b/content/english/about/_index.md index b7f4e00e3..6d0bc65e0 100644 --- a/content/english/about/_index.md +++ b/content/english/about/_index.md @@ -39,27 +39,27 @@ The team are happy to help with using the Portal, to take suggestions regarding
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Picute of Liane H
Liane Hughes
Project leader
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Picute of Katarina ÖS
Katarina Öjefors Stark
Data steward
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Picute of Senthilkumar P
Senthilkumar Panneerselvam
Systems developer
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Picute of Hanna K
Hanna Kultima
Vice head of SciLifeLab Data Centre
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Picute of Johan R
Johan Rung
Head of SciLifeLab Data Centre
diff --git a/content/english/about/organisations_and_programs.md b/content/english/about/organisations_and_programs.md index b35fc3dc7..24fb0a599 100644 --- a/content/english/about/organisations_and_programs.md +++ b/content/english/about/organisations_and_programs.md @@ -25,7 +25,7 @@ layout: about_navbar
- + KAW logo
@@ -38,7 +38,7 @@ layout: about_navbar
- + Scilifelab logo
diff --git a/content/english/about/partner_organisations.md b/content/english/about/partner_organisations.md index a47f7d704..dbe20c62e 100644 --- a/content/english/about/partner_organisations.md +++ b/content/english/about/partner_organisations.md @@ -10,7 +10,7 @@ layout: about_navbar
- The European COVID-19 Data Platform logo + The European pathogens portal logo
diff --git a/content/english/data-management.md b/content/english/data-management.md index 7edffd8a2..ba56613f7 100644 --- a/content/english/data-management.md +++ b/content/english/data-management.md @@ -14,11 +14,11 @@ On this page, you will find information about where to access direct, one-on-one ### Swedish Pathogens Portal -Whilst the portal contains many general guidelines for RDM e.g. how to [share data](/share-data/), we also offer direct support for individual projects. To access this, please send an email to pathogens@scilifelab.se or send a messsage via the [contact form](/contact/). You can typically expect a response within one working day. +Whilst the portal contains many general guidelines for RDM e.g. how to [share data](/share-data/), we also offer direct support for individual projects. To access this, please send an email to [pathogens@scilifelab.se](mailto:pathogens@scilifelab.se) or send a messsage via the [contact form](/contact/). You can typically expect a response within one working day. ### SciLifeLab Data Management Helpdesk -The SciLifeLab Data Management Helpdesk is operated by experts in RDM from the SciLifeLab Data Centre and National Bioinformatics Infrastructure Sweden (NBIS). The purpose of the helpdesk is to provide direct, customised RDM support for those working in life science research in Sweden. To get in touch, send an email to data-management@scilifelab.se. Alternatively, you can go to the [SciLifeLab Research Data Management Guidelines](https://data-guidelines.scilifelab.se) and submit questions via the contact form. +The SciLifeLab Data Management Helpdesk is operated by experts in RDM from the SciLifeLab Data Centre and National Bioinformatics Infrastructure Sweden (NBIS). The purpose of the helpdesk is to provide direct, customised RDM support for those working in life science research in Sweden. To get in touch, send an email to [data-management@scilifelab.se](mailto:data-management@scilifelab.se). Alternatively, you can go to the [SciLifeLab Research Data Management Guidelines](https://data-guidelines.scilifelab.se) and submit questions via the contact form. ## Resources for infectious disease data diff --git a/content/english/highlights/antibiotic_resistance_development.md b/content/english/highlights/antibiotic_resistance_development.md index 84b53b228..189de2a3d 100644 --- a/content/english/highlights/antibiotic_resistance_development.md +++ b/content/english/highlights/antibiotic_resistance_development.md @@ -7,7 +7,7 @@ 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." +announcement: "This data highlight was also published on the SciLifeLab Data Platform, 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 for more." images: [/highlights/banners/antibiotic_resistance_development_small.jpg] --- diff --git a/content/english/highlights/bacterial_replication.md b/content/english/highlights/bacterial_replication.md index 036f38526..e8b83c094 100644 --- a/content/english/highlights/bacterial_replication.md +++ b/content/english/highlights/bacterial_replication.md @@ -7,7 +7,7 @@ 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." +announcement: "This data highlight was also published on the SciLifeLab Data Platform, 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 for more." images: [/highlights/banners/ELF_banner.png] --- diff --git a/content/english/highlights/covimapp.md b/content/english/highlights/covimapp.md index 25517bb2f..d9a7b873f 100644 --- a/content/english/highlights/covimapp.md +++ b/content/english/highlights/covimapp.md @@ -21,7 +21,7 @@ tags: SARS-CoV-2, ] authors: [Katarina Öjefors Stark] -announcement: "This data highlight was also published on the SciLifeLab Data Platform, 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 for more." +announcement: "This data highlight was also published on the SciLifeLab Data Platform, 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 for more." images: [/highlights/banners/covimapp_logo.png"] --- diff --git a/content/english/highlights/igh_antibody_genes.md b/content/english/highlights/igh_antibody_genes.md index 10d459364..985736b12 100644 --- a/content/english/highlights/igh_antibody_genes.md +++ b/content/english/highlights/igh_antibody_genes.md @@ -7,7 +7,7 @@ banner_large: /highlights/banners/igh_antibody_genes.jpg banner_caption: Graphical abstract (Image courtesy Pushparaj et al. 2023) highlights_topics: [COVID-19, Infectious Diseases] tags: [SARS-CoV-2, Genotyping, Haplotype analysis, Cryo-EM, IGHV1-69, Variability, Individual response, Infection] -announcement: "This data highlight was also [published on the SciLifeLab Data Platform](https://data.scilifelab.se/highlights/igh_antibody_genes/), 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." +announcement: "This data highlight was also published on the SciLifeLab Data Platform, 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 for more." images: [/highlights/banners/igh_antibody_genes_small.jpg] --- diff --git a/content/english/highlights/mettl3_localisation.md b/content/english/highlights/mettl3_localisation.md index 3e834fda9..c8e16a859 100644 --- a/content/english/highlights/mettl3_localisation.md +++ b/content/english/highlights/mettl3_localisation.md @@ -7,7 +7,7 @@ banner_large: /highlights/banners/mettl3_localisation.png banner_caption: Graphical abstract (Image courtesy Vaid and Mendez et al. (2023)). highlights_topics: [COVID-19, Infectious Diseases] tags: [Infectious diseases, COVID-19, gene expression, Antivirual strategy, METTL3, Antiviral, Pandemic Preparedness] -announcement: "This data highlight was also [published on the SciLifeLab Data Platform](https://data.scilifelab.se/highlights/mettl3_localisation/), 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." +announcement: "This data highlight was also published on the SciLifeLab Data Platform, 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 for more." images: [/highlights/banners/mettl3_localisation_small.png] --- diff --git a/content/english/highlights/poliovirus_replication.md b/content/english/highlights/poliovirus_replication.md index 62a127815..436bf27e5 100644 --- a/content/english/highlights/poliovirus_replication.md +++ b/content/english/highlights/poliovirus_replication.md @@ -12,7 +12,7 @@ aliases: - /news/poliovirus_replication - /sv/news/poliovirus_replication images: ["/highlights/banners/segmentation_highReso.jpeg"] -announcement: "This data highlight was also [published on the SciLifeLab Data Platform](https://data.scilifelab.se/highlights/poliovirus_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." +announcement: "This data highlight was also published on the SciLifeLab Data Platform, 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 for more." images: [/highlights/banners/segmentation_highReso.jpeg] --- diff --git a/content/english/highlights/sars-cov2_T-cell_response.md b/content/english/highlights/sars-cov2_T-cell_response.md index c6fd0aa52..621dc2229 100644 --- a/content/english/highlights/sars-cov2_T-cell_response.md +++ b/content/english/highlights/sars-cov2_T-cell_response.md @@ -22,7 +22,7 @@ In summary, the sensitivity and specificity of a FluoroSpot SARS-CoV-2 T-cell as
SciLifeLab/KAW National COVID-19 Research Program
- The aim of the SciLifeLab/KAW National COVID-19 research program is to provide useful knowledge about the current situation during the corona pandemic and also to provide knowledge for future pandemics. In addition, the program aims to improve preventions, diagnostics and treatments of viral disease, a clearer real-time overview of the pandemic, integrate data across technologies, and research domains, and create better predictive models. This research program is made possible by funding from Knut and Alice Wallenberg Foundation (KAW). More about the COVID-19 efforts funded by KAW here. + The aim of the SciLifeLab/KAW National COVID-19 research program is to provide useful knowledge about the current situation during the corona pandemic and also to provide knowledge for future pandemics. In addition, the program aims to improve preventions, diagnostics and treatments of viral disease, a clearer real-time overview of the pandemic, integrate data across technologies, and research domains, and create better predictive models. This research program is made possible by funding from Knut and Alice Wallenberg Foundation (KAW). More about the COVID-19 efforts funded by KAW here. #### Data diff --git a/content/english/highlights/symptom-study-sweden.md b/content/english/highlights/symptom-study-sweden.md index 5854aa899..a8c7577dd 100644 --- a/content/english/highlights/symptom-study-sweden.md +++ b/content/english/highlights/symptom-study-sweden.md @@ -18,7 +18,7 @@ The global COVID-19 pandemic has increased challenges to healthcare, society and COVID Symptom Study Sweden is run by Lund University and Uppsala University in collaboration with King’s College London and Zoe Global Ltd (Swedish PIs: prof. Tove Fall, Uppsala University, and prof. Maria Gomez and prof. Paul Franks, Lund University). The project aims to map the spread of COVID-19 in Sweden as well as to increase knowledge about the effect of SARS-CoV-2 on human body. The first aim includes investigation of temporal and geographical trends in SARS-CoV-2 spread and investigations of how changes in national strategies affect the spread.
- + Symptoms case map image
Estimated prevalence of symptomatic cases of COVID-19 in various counties in Sweden, as % of population. Estimates based on data reported by COVID Symptom Study App users, 29.03.2021.
diff --git a/content/english/pathogens/hepatitis_unknown_origin.md b/content/english/pathogens/hepatitis_unknown_origin.md index da05aa83e..27a51b155 100644 --- a/content/english/pathogens/hepatitis_unknown_origin.md +++ b/content/english/pathogens/hepatitis_unknown_origin.md @@ -22,7 +22,7 @@ The CDC is currently conducting research and working in close collaboration with ### Timeline of outbreak
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+
Image of Hepatitis outbreak timeline
## Resources diff --git a/content/english/pathogens/mpox.md b/content/english/pathogens/mpox.md index 4eb6770e4..17902d55b 100644 --- a/content/english/pathogens/mpox.md +++ b/content/english/pathogens/mpox.md @@ -92,3 +92,21 @@ These tools have been adapted/developed for use with the mpox virus. They could - [Information from the Centers for Disease Control (CDC) in the USA](https://www.cdc.gov/poxvirus/monkeypox/index.html) - [ONA Mpox Outbreak Dashboard](https://onaghi.akuko.io/post/84cd71fb-9ce0-480a-8571-0e608a287849) - [Global map and case count](https://www.cdc.gov/poxvirus/monkeypox/response/2022/world-map.html) and [U.S. map and case count](https://www.cdc.gov/poxvirus/monkeypox/response/2022/us-map.html) for mpox in 2022 from the Centers for Disease Control (CDC) + + diff --git a/content/english/resources/_index.md b/content/english/resources/_index.md index 6d661ecd1..8027fdb1d 100644 --- a/content/english/resources/_index.md +++ b/content/english/resources/_index.md @@ -11,5 +11,5 @@ This section of the Swedish Pathogens Portal is dedicted to capabilities related The pages for each capability are regularly updated with new information as it becomes available.
- To add or update information about pandemic preparedness capabilities, email us at pathogens@scilifelab.se or use our contact form to get in touch. + To add or update information about pandemic preparedness capabilities, email us at pathogens@scilifelab.se or use our contact form to get in touch.
diff --git a/content/english/topics/mpox.md b/content/english/topics/mpox.md index efddc7462..cb3762e8b 100644 --- a/content/english/topics/mpox.md +++ b/content/english/topics/mpox.md @@ -15,7 +15,7 @@ aliases:
  -  This page is under development, with more resources being added shortly. In the meantime, check out the mpox page in our 'emerging pathogens' section. That page contains more extensive information and useful links to other related resources. +  This page is under development, with more resources being added shortly. In the meantime, check out the mpox page in our 'emerging pathogens' section. That page contains more extensive information and useful links to other related resources.
## Background diff --git a/content/english/updates/first_year.md b/content/english/updates/first_year.md index 2b3e97ee9..db7b60d6a 100644 --- a/content/english/updates/first_year.md +++ b/content/english/updates/first_year.md @@ -17,7 +17,7 @@ In the spring of 2020, the European Commission [took the initiative to develop a The Swedish COVID-19 Data Portal provides guidance, tools, and services for finding and sharing research data made available by Swedish and international researchers. Since its launch, [the Swedish COVID-19 Data Portal](https://covid19dataportal.se/) has had >22,000 visitors and >100,000 pageviews and [the portal team](/about) has provided support for a wide range of research projects.
- + Image of portal stat
The Swedish COVID-19 Data Portal in numbers. The number of visitors and pageviews and the geographical distribution of visitors is displayed on the right pane, the content of different sections of the Portal on the middle pane, and the number of projects receiving direct support on the left pane.
@@ -26,7 +26,7 @@ The Swedish COVID-19 Data Portal provides guidance, tools, and services for find The Portal website comprises a number of services launched over the last year. For example, anyone looking for data and/or code can make use of discipline-specific, [manually curated lists of openly shared data and/or code](/data_types/all/data/) that have been made available by researchers affiliated with a Swedish research institute. Those wishing to make use of biomaterials and data accumulated in biobanks across Sweden will find the [the Swedish COVID-19 Sample Collection Database](/biobanks/) useful. This database, developed in collaboration with [Biobank Sweden](https://biobanksverige.se), allows researchers to look for biomaterial collections matching their criteria (it is possible to perform searches based on materials, diagnosis, sample collection types). The database contains biobanks and sample collections from both healthcare and academia. To date, it contains information about 29 sample collections from 16 different biobanks. Another service within the Portal is [a manually curated database of publications on COVID-19 and SARS-CoV-2](/publications/) that lists all published articles and preprints involving at least one author affiliated with a Swedish research institute. To date, the publication database contains information on over 1300 publications.
- + Image of portal time line
Timeline of the events during the last year of the Swedish COVID-19 Data Portal; illustrating the timings of the launches of various services and key milestones.
diff --git a/content/english/updates/wastewater-data.md b/content/english/updates/wastewater-data.md index 5eb5edb13..149f7fbf5 100644 --- a/content/english/updates/wastewater-data.md +++ b/content/english/updates/wastewater-data.md @@ -19,7 +19,7 @@ Coronavirus genome can be detected in faecal samples from COVID-19 patients usin During the COVID-19 pandemic surveillance of SARS-CoV-2 RNA levels in wastewater has become increasingly used to monitor and predict the spread of the disease. Early during the pandemic international studies (see for example [this article by Peccia and colleagues](https://www.nature.com/articles/s41587-020-0684-z)) proposed wastewater surveillance as an important source of day-to-day data. Presence of SARS-CoV-2 in municipal wastewater was reported early in the COVID-19 pandemic in [studies from the Netherlands](https://www.rivm.nl/en/news/novel-coronavirus-found-in-wastewater). However, wastewater surveillance has long been used to track spread of other diseases such as for example [polio](https://stm.sciencemag.org/content/9/383/eaaf6786).
- + Wastewater cycle image
Wastewater Epidemiology during the COVID-19 pandemic. (1) Towns and cities generate wastewater e.g. from sewage, that accumulates at wastewater plants. (2) Wastewater samples are collected from wastewater plants (3) Samples are processed in laboratories where the levels of SARS CoV-2 RNA are tested using qPCR (4) If SARS-CoV-2 RNA is not detected, people are advised to adopt some non-pharmaceutical interventions (NPIs), like handwashing (5) If SARS CoV-2 RNA is detected, people are advised to also adopt additional NPIs, like social distancing and wearing face masks. Source: SciLifeLab Data Centre.
@@ -29,7 +29,7 @@ In Stockholm, associate professor Zeynep Cetecioglu Gurol, KTH Royal Institute o In addition, the researchers in Stockholm have shown, in preliminary yet unpublished data, that increased SARS-CoV-2 levels in Stockholm correspond to both increased ICU admission levels and positive case numbers (see figure below). Zeynep Cetecioglu Gurol explains: "These results are important to show the significant correlation between gene copy number of SARS-CoV-2 in wastewater and positive case numbers. In addition of the reflection of transmission in the population, wastewater data provides us an early information of upcoming waves." -
The amount of SARS-CoV-2 virus in wastewater and the number of COVID-19 cases in Stockholm. Source: research group of Zeynep Cetecioglu Gurol.
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Wastewater Stockholm image
The amount of SARS-CoV-2 virus in wastewater and the number of COVID-19 cases in Stockholm. Source: research group of Zeynep Cetecioglu Gurol.
Associate professor Maja Malmberg, SLU, is collaborating with [Mette Myrmel](https://www.nmbu.no/emp/mette.myrmel) at the Norwegian University of Life Sciences to measure SARS CoV-2 levels in Umeå and Örebro. "By sharing our SARS CoV-2 wastewater data openly on the COVID-19 Data Portal we can in an easy and quick way make the results available to the general public, relevant authorities and researchers. I hope this can be useful as an early warning system for new waves of COVID-19 and contribute to preparedness for future pandemics," says Maja Malmberg. diff --git a/data/mpox_page_announcements.json b/data/mpox_page_announcements.json index 00012ffe9..4c0d74667 100644 --- a/data/mpox_page_announcements.json +++ b/data/mpox_page_announcements.json @@ -2,18 +2,18 @@ { "date_time": "2022-06-03", "title": "Workflows for sequence variant analysis", - "text": "Two Galaxy workflows for mpox sequence variant analysis have been made available. One workflow (Illumina metatranscriptomic PE) deals with variant analysis from metatranscriptomic data. The other workflow (Report generation) can be used to generate the final variant analysis reports/plots. The workflows, and instructions on how to use them, [are found here](https://galaxyproject.org/projects/mpxv/). More workflows will be added here over time" + "text": "Two Galaxy workflows for mpox sequence variant analysis have been made available. One workflow (Illumina metatranscriptomic PE) deals with variant analysis from metatranscriptomic data. The other workflow (Report generation) can be used to generate the final variant analysis reports/plots. The workflows, and instructions on how to use them, are found here. More workflows will be added here over time" }, { "date_time": "2022-05-25", "name": "European COVID-19 Data Portal/BY-COVID", "contact_info": "virus-dataflow@ebi.ac.uk", "title": "Mpox viral data submission", - "text": "Since 13 May 2022, 92 laboratory confirmed cases of mpox have been reported to the WHO from Member States that are not endemic for mpox virus. With epidemiological investigations ongoing we are repurposing the pipelines built during the COVID-19 pandemic to demonstrate preparedness for other infectious disease outbreaks. Therefore we are seeking your help in connecting us to laboratories or individuals who are active in sequencing mpox virus. We have created [a document outlining the data submission into our open databases](https://www.covid19dataportal.org/news/monkeypox-viral-data-submissions?nid=2038) with a particular focus on attribution for data producers and can provide technical support to streamline the data submission process. If you are aware of ongoing sequencing efforts of mpox virus or would like to suggest any other data resources that should be connected please contact virus-dataflow@ebi.ac.uk." + "text": "Since 13 May 2022, 92 laboratory confirmed cases of mpox have been reported to the WHO from Member States that are not endemic for mpox virus. With epidemiological investigations ongoing we are repurposing the pipelines built during the COVID-19 pandemic to demonstrate preparedness for other infectious disease outbreaks. Therefore we are seeking your help in connecting us to laboratories or individuals who are active in sequencing mpox virus. We have created a document outlining the data submission into our open databases with a particular focus on attribution for data producers and can provide technical support to streamline the data submission process. If you are aware of ongoing sequencing efforts of mpox virus or would like to suggest any other data resources that should be connected please contact virus-dataflow@ebi.ac.uk." }, { "date_time": "2022-05-25", "title": "Nextstrain build", - "text": "Nextstrain have updated their *mpox build* with additional available genomes from Portugal and a genome from Germany associated with the current multi-country outbreak. The latest Nextstrain build [can found here](https://nextstrain.org/monkeypox?c=country&p=grid)." + "text": "Nextstrain have updated their *mpox build* with additional available genomes from Portugal and a genome from Germany associated with the current multi-country outbreak. The latest Nextstrain build can found here." } ] diff --git a/data/omicron_page_announcements.json b/data/omicron_page_announcements.json index 09ae48964..b6d82a5f5 100644 --- a/data/omicron_page_announcements.json +++ b/data/omicron_page_announcements.json @@ -3,27 +3,27 @@ "name": "Anna Székely", "contact_info": "anna.szekely@slu.se", "title": "Omicron overcame delta in a couple weeks in analysed Swedish wastewaters", - "text": "By quantifying K417N and wild-type K417 mutations we estimated the ratio of omicron and delta in major cities. In all places up till Christmas delta was the dominant variant but during the holiday weeks omicron took-over. By the 10th of January delta fall below the detection limit of the assay, indicating outcompeting by omicron. For more, check out our latest press-release: [https://www.slu.se/ew-nyheter/2022/1/omikron-dominerar-nu-nastan-helt-i-avloppsvattnet/](https://www.slu.se/ew-nyheter/2022/1/omikron-dominerar-nu-nastan-helt-i-avloppsvattnet/)" + "text": "By quantifying K417N and wild-type K417 mutations we estimated the ratio of omicron and delta in major cities. In all places up till Christmas delta was the dominant variant but during the holiday weeks omicron took-over. By the 10th of January delta fall below the detection limit of the assay, indicating outcompeting by omicron. For more, check out our latest press-release:
https://www.slu.se/ew-nyheter/2022/1/omikron-dominerar-nu-nastan-helt-i-avloppsvattnet/" }, { "date_time": "2022-01-13 14:40", "name": "Arnold Kochari", "contact_info": "arnold.kochari@scilifelab.se", "title": "Omicron VoC detected in Uppsala wastewater", - "text": "Anna Szekely [shared first results](https://mobile.twitter.com/mikromara/status/1479728491377696769) in work attempting to detect Omicron VoC in Uppsala wastewater samples. Here they are: 'On w51 delta dominated, omicron mutations were barely detectable. On w52 delta continued to increase but omicron also showed a strong signal (probably similar ratio of the 2 variants). On w1 delta started to decrease and omicron more than doubled.' See [Anna Szekely's twitter account](https://mobile.twitter.com/mikromara) for future updates." + "text": "Anna Szekely shared first results in work attempting to detect Omicron VoC in Uppsala wastewater samples. Here they are: 'On w51 delta dominated, omicron mutations were barely detectable. On w52 delta continued to increase but omicron also showed a strong signal (probably similar ratio of the 2 variants). On w1 delta started to decrease and omicron more than doubled.' See Anna Szekely's twitter account for future updates." }, { "date_time": "2021-12-22 16:50", "name": "Arnold Kochari", "contact_info": "arnold.kochari@scilifelab.se", "title": "Proportion of Omicron VoC in Region Skåne", - "text": "Region Skåne is publishing the proportion of variants in the samples sequenced every week, [it can be followed on this page](https://www.skane.se/digitala-rapporter/lagesbild-covid-19-i-skane/sekvensering/). During week 49, 21.8% of samples were of the Omicron VoC (out of 565 sequenced samples in total that week)." + "text": "Region Skåne is publishing the proportion of variants in the samples sequenced every week, it can be followed on this page. During week 49, 21.8% of samples were of the Omicron VoC (out of 565 sequenced samples in total that week)." }, { "date_time": "2021-12-20 12:55", "name": "Arnold Kochari", "contact_info": "arnold.kochari@scilifelab.se", "title": "Preliminary results on neutralization resistance of the Omicron VoC from the Murrell lab", - "text": "On December 7 the Murrell lab has made public two sets of prelimiary results on neutralization resistance of the Omicron VoC: [Neutralization resistance of the Omicron SARS-CoV-2 Variant of Concern against monoclonal antibodies](https://drive.google.com/file/d/10rLK4oBxZbLbx0fIau4AFGimWr2VoVRR/view) and [Quantification of the neutralization resistance of the Omicron Variant of Concern](https://drive.google.com/file/d/1CuxmNYj5cpIuxWXhjjVmuDqntxXwlfXQ/view). Both are prelimiary reports, subject to modification. I recommend following [Ben Murrell's Twitter account](https://twitter.com/BenjMurrell) for updates." + "text": "On December 7 the Murrell lab has made public two sets of prelimiary results on neutralization resistance of the Omicron VoC: Neutralization resistance of the Omicron SARS-CoV-2 Variant of Concern against monoclonal antibodies and Quantification of the neutralization resistance of the Omicron Variant of Concern. Both are prelimiary reports, subject to modification. I recommend following Ben Murrell's Twitter account for updates." } ] diff --git a/layouts/highlights/list.html b/layouts/highlights/list.html index 4bdb7aa43..3850d13bf 100644 --- a/layouts/highlights/list.html +++ b/layouts/highlights/list.html @@ -79,8 +79,8 @@ data highlight myself.
- - + +
@@ -118,6 +118,11 @@ alert("Please tick 'I'm not a robot' above the 'Submit the form' button."); } }); + + // Function to fill ARIA text for recaptcha button + window.addEventListener("load", function () { + $('textarea#g-recaptcha-response').attr('aria-label', "The recaptcha response will appear here"); + }); // Function to filter the service based on search text $("input[type=text]").on("input", function(){ diff --git a/layouts/highlights/single.html b/layouts/highlights/single.html index 81ae77c68..c3c82e57a 100644 --- a/layouts/highlights/single.html +++ b/layouts/highlights/single.html @@ -26,9 +26,12 @@

{{ if .Params.title_full }}{{ .Params.title_full }}{{ else }}{{ .Title}}{{ e

Share this: - - - + + +
diff --git a/layouts/partials/resources_display.html b/layouts/partials/resources_display.html index 3044240e1..ddfa6c90f 100644 --- a/layouts/partials/resources_display.html +++ b/layouts/partials/resources_display.html @@ -1,12 +1,12 @@
-
\ No newline at end of file diff --git a/layouts/partials/topics.html b/layouts/partials/topics.html index d0ce69d2a..9ddad95bd 100644 --- a/layouts/partials/topics.html +++ b/layouts/partials/topics.html @@ -2,9 +2,10 @@ {{ range where .Site.Menus.topics_menu "Identifier" "ne" "all_topics"}}
-
- -
{{ .Page.Params.credits }}
+
{{ .Name }}

{{ .Page.Description }}

diff --git a/layouts/shortcodes/editorial_committee_cards.html b/layouts/shortcodes/editorial_committee_cards.html index 43ea03782..0e73a6929 100644 --- a/layouts/shortcodes/editorial_committee_cards.html +++ b/layouts/shortcodes/editorial_committee_cards.html @@ -4,18 +4,18 @@
- + Picture of {{ .name }}
{{ .name }}
- {{ .affiliation }} + {{ .affiliation }}
Expertise:
-

{{ .expertise | safeHTML }}

+

{{ .expertise | safeHTML }}

diff --git a/layouts/shortcodes/omicron_page_form_scripts.html b/layouts/shortcodes/omicron_page_form_scripts.html index f574c1ed6..c6797131c 100644 --- a/layouts/shortcodes/omicron_page_form_scripts.html +++ b/layouts/shortcodes/omicron_page_form_scripts.html @@ -26,4 +26,10 @@ document.getElementById('originUrl_ann').value = location.href; document.getElementById('originUrl_av_data').value = location.href; + // Add ARIA label for recaptcha + window.addEventListener("load", function () { + $('textarea#g-recaptcha-response').attr('aria-label', "The recaptcha response will appear here"); + $('textarea#g-recaptcha-response-1').attr('aria-label', "The recaptcha response will appear here"); + }); + diff --git a/layouts/shortcodes/pathogens_add_announcement.html b/layouts/shortcodes/pathogens_add_announcement.html index cfd273854..f031cd9d3 100644 --- a/layouts/shortcodes/pathogens_add_announcement.html +++ b/layouts/shortcodes/pathogens_add_announcement.html @@ -36,8 +36,8 @@
- - + +
diff --git a/layouts/shortcodes/pathogens_list_announcements.html b/layouts/shortcodes/pathogens_list_announcements.html index 94c496794..7e75bf093 100644 --- a/layouts/shortcodes/pathogens_list_announcements.html +++ b/layouts/shortcodes/pathogens_list_announcements.html @@ -6,7 +6,7 @@ {{ range $announcement_list_data }}
{{ .title }}
-

{{ .date_time }}

+

{{ .date_time }}

{{ .text | markdownify }}

{{ if or .name .contact_info }}

Contact: {{ .name }}, {{ .contact_info }}{{ end }}

diff --git a/layouts/shortcodes/pathogens_suggest_available_data.html b/layouts/shortcodes/pathogens_suggest_available_data.html index 76fb8fcd3..d8a993e73 100644 --- a/layouts/shortcodes/pathogens_suggest_available_data.html +++ b/layouts/shortcodes/pathogens_suggest_available_data.html @@ -35,8 +35,8 @@ If data is not available openly, please provide a clear description of access conditions - who will be granted access, what is the procedure, and what are expections.
- - + +
diff --git a/layouts/shortcodes/voc_data_highlights.html b/layouts/shortcodes/voc_data_highlights.html index 924800426..aceb54f03 100644 --- a/layouts/shortcodes/voc_data_highlights.html +++ b/layouts/shortcodes/voc_data_highlights.html @@ -6,7 +6,7 @@
{{ .Title }}
{{ .Title }}
-

{{.Date.Format "2006-01-02"}}

+

{{.Date.Format "2006-01-02"}}

{{ .Summary }}

{{ end }} diff --git a/layouts/topics/single.html b/layouts/topics/single.html index 4819346ff..9c4f54f71 100644 --- a/layouts/topics/single.html +++ b/layouts/topics/single.html @@ -160,7 +160,7 @@
{{ if .url }}{{ end }}{{ .project_title }}{{ if .url }}
- + diff --git a/layouts/updates/list.html b/layouts/updates/list.html index 1e1bb2dda..5370850c7 100644 --- a/layouts/updates/list.html +++ b/layouts/updates/list.html @@ -10,7 +10,7 @@
{{ .Title }}
-

{{.Date.Format "2006-01-02"}}

+

{{.Date.Format "2006-01-02"}}

{{ .Summary }}

Read more

diff --git a/static/css/styles.css b/static/css/styles.css index 679ce0c53..e0985fbaa 100644 --- a/static/css/styles.css +++ b/static/css/styles.css @@ -534,8 +534,8 @@ for rows with images to fix that. .btn_details_primary { color: #fff; - background-color: #308acf; - border-color: #308acf; + background-color: #4770b1; + border-color: #4770b1; } .btn-blue {