Skip to main content
Swedish Pathogens Portal SciLifeLab

News & Updates

In this section, we report major pieces of news related to the Portal. This can include, for example, new pages, new/improved features, or important progress in the field of pandemic preparedness in Sweden.

New data highlight on investigating growth interactions in the human gut microbiome
New data highlight on investigating growth interactions in the human gut microbiome
Systematic profiling of human gut bacteria reveals predominantly inhibitory growth interactions, although some factors did promote growth.
Connecting Sweden’s microbiology data for research and preparedness
Connecting Sweden’s microbiology data for research and preparedness
CRITICAL MICROBES aims to develop a national research infrastructure that brings together clinical microbiology results and links them with patient characteristics and health outcomes.
Outbreak of measles in Sweden
Outbreak of measles in Sweden
Cases have been reported from nine Swedish regions, indicating secondary spread following exposure at the festival.
New Pathogens Portal Node launched by Chile
New Pathogens Portal Node launched by Chile
The Chilean Pathogens Portal, built using the PPN Toolbox, marks another important milestone in the growing international ecosystem related to infectious disease research.
Outbreak of Campylobacter in Sweden
Outbreak of Campylobacter in Sweden
FoHM notes that elevated case numbers are expected to continue during August.
New data highlight on a new MLST scheme for tracking Giardia duodenalis assemblage B outbreaks
New data highlight on a new MLST scheme for tracking Giardia duodenalis assemblage B outbreaks
A novel seven-marker MLST scheme enhances molecular typing of Giardia duodenalis assemblage B, improving outbreak detection and epidemiological surveillance.
Outbreak of Salmonella Stanley in Sweden
Outbreak of Salmonella Stanley in Sweden
Salmonella Stanley outbreak in Sweden declared over.
New data highlight on a new digital approach for identifying rare antibiotic-resistant bacterial subpopulations
New data highlight on a new digital approach for identifying rare antibiotic-resistant bacterial subpopulations
A droplet microfluidics platform combined with image texture analysis enables rapid detection of rare antibiotic-resistant bacterial subpopulations that are often missed by standard diagnostic methods.
PLP engaged in preparedness activities related to the Hanta-/Andesvirus outbreak
PLP engaged in preparedness activities related to the Hanta-/Andesvirus outbreak
The PLP program at SciLifeLab is actively engagaed in national and international efforts related to the recent Hanta-/Andesvirus outbreak.
Ebola outbreak in Africa
Ebola outbreak in Africa
In May 2026, an outbreak of ebola virus disease, caused by the rare Bundibugyo virus, was reported in the Ituri Province of the Democratic Republic of the Congo (DRC).
New data highlight on exploring vaccine effectiveness against influenza in European children
New data highlight on exploring vaccine effectiveness against influenza in European children
Influenza vaccination provided strong protection against infection in European children across two recent seasons, supporting its role in reducing pediatric disease burden.
BSL3 Network: hantavirus research readiness
BSL3 Network: hantavirus research readiness
Biosafety Level 3 (BSL3) facilities within the Swedish BSL3 Network are prepared to support research on hantaviruses.
Information about the Hantavirus outbreak
Information about the Hantavirus outbreak
The recent hantavirus outbreak in South America has led to localised clusters of severe illness. The Andes virus is of particular concern due to its rare ability to spread between people.
From bottlenecks to breakthroughs - decoding malaria transmission biology
From bottlenecks to breakthroughs - decoding malaria transmission biology
High-resolution omics approaches are uncovering critical bottlenecks in malaria transmission, providing new insights into host–parasite interactions and opportunities for next-generation interventions.
New data highlight on expanding the genomic landscape of Pseudomonas aeruginosa clone C
New data highlight on expanding the genomic landscape of Pseudomonas aeruginosa clone C
A recent study delivers whole genome sequences of three Pseudomonas aeruginosa clone C strains isolated from distinct sources.
New data highlight on multidrug‑resistant Enterobacterales in Swedish wastewater effluent
New data highlight on multidrug‑resistant Enterobacterales in Swedish wastewater effluent
The recent appearance of Carbapenem‑resistant Enterobacterales (CRE) at a wastewater treatment plant indicates a need for integrated surveillance of resistance genes across discipline.
New capabilities from the Pandemic Laboratory Preparedness (PLP) program
New capabilities from the Pandemic Laboratory Preparedness (PLP) program
Check out the latest capabilities developed from SciLifeLab's Pandemic Laboratory Preparedness (PLP) program.
Uppsala Antibiotic Center’s approach to research and education
Uppsala Antibiotic Center’s approach to research and education
This editorial discusses Uppsala Antibiotic Center's ethos and activities.
“Seasonal flu” is not predictable or stable
“Seasonal flu” is not predictable or stable
This editorial focuses on how we can strategically approach the influenza drift, steering the discussion between scientists and stakeholders.
Beta version of the Swedish Pathogens Portal released
Beta version of the Swedish Pathogens Portal released
A new, beta version of the Swedish Pathogens Portal has been made available for community feedback.
New data highlight on host range expansion in Giardia duodenalis linked to Muller's Ratchet
New data highlight on host range expansion in Giardia duodenalis linked to Muller's Ratchet
A recently derived asexual lineage of Giardia reveals how mutation accumulation and loss of host-specific adaptations can reshape parasite ecology, offering new insight into the evolutionary forces governing host-range expansion.
Study on Mpox vaccination strategies in Sweden highlights the need for booster doses
Study on Mpox vaccination strategies in Sweden highlights the need for booster doses
A cohort study aimed to find insights into vaccine-induced immunity over time for mpox (clade 2b) infection. Neutralising antibodies declined noticeably by 9 months, highlighting the potential need for booster doses.
New layout for information on outbreaks
New layout for information on outbreaks
We have updated the layout of pages to improve the readability, navigation, and presentation of information related to outbreaks impacting Sweden.
New Pathogens Portal Nodes launched by Hungary and Mexico
New Pathogens Portal Nodes launched by Hungary and Mexico
New nodes have been launched in Hungary and Mexico. Both made use of the PPN Toolbox.
Outbreak of Hepatitis A in Sweden
Outbreak of Hepatitis A in Sweden
A total of 5 confirmed cases of hepatitis A have been identified across three different regions in Sweden.
Generating Guidelines for Community-Driven Portals for Infectious Disease Research
Generating Guidelines for Community-Driven Portals for Infectious Disease Research
The global research community came together to discuss what types of information should be included on community-driven infectious disease research portals.
The survey results are in!
The survey results are in!
We recently conducted a user survey to understand the priorities of our audience and to identify opportunities for improvement.
Accessing more Swedish research
Accessing more Swedish research
The portal is currently undergoing a transition to be able to show more Swedish data and research.
Outbreak of Listeria in Sweden
Outbreak of Listeria in Sweden
A total of 15 confirmed cases of listeria have been identified in Stockholm, Sweden.
Latest from the PLP program
Latest from the PLP program
Check out the latest updates from SciLifeLab's Pandemic Laboratory Preparedness (PLP) program.
Survey to improve the Swedish Pathogens Portal
Survey to improve the Swedish Pathogens Portal
The Swedish Pathogens Portal is seeking feedback from users to identify how it can be improved to better meet their needs. Please complete the survey to share your thoughts!
Two new Pathogens Portal Nodes launched
Two new Pathogens Portal Nodes launched
New nodes have been launched in Costa Rica and Spain. Both made use of the PPN Toolbox.
DEADLINE EXTENDED: Call for Portal Resource Proposals
DEADLINE EXTENDED: Call for Portal Resource Proposals
The Swedish Pathogens Portal aims to identify four large-scale use cases that will result in new resources on the portal that are beneficial to the community. The deadline for submitting proposals for this call has now been extended.
New data highlight on GUI-based workflows for SARS-CoV-2 Nanopore sequencing analysis
New data highlight on GUI-based workflows for SARS-CoV-2 Nanopore sequencing analysis
Researchers from Uppsala University Hospital, developed and validated two automated workflows within the GUI-based software Geneious Prime 2022.1.1. Validation data and tools are openly available via GitHub, and the Sequence Read Archive.
Toolbox for creating Pathogen Portal Nodes
Toolbox for creating Pathogen Portal Nodes
The Pathogen Portal Node (PPN) Toolbox comprises a minimal code for a PPN. A roadmap outlining future work is now available for the PPN Toolbox.
Call for Portal Resource Proposals
Call for Portal Resource Proposals
The Swedish Pathogens Portal aims to identify four large-scale use cases that will result in new resources on the portal that are beneficial to the community.
New national Pathogens Portal node launched
New national Pathogens Portal node launched
The Netherlands Pathogens Portal is the latest national node to be launched.
Swedish Pathogens Portal as part of the Pathogen Data Network
Swedish Pathogens Portal as part of the Pathogen Data Network
The Swedish Pathogens Portal is leading work to support the establishment of similar portals around the world.
New editorial discussing the environmental surveillance of antimicrobial resistance.
New editorial discussing the environmental surveillance of antimicrobial resistance.
A thought-piece on how environmental tracking of antimicrobial resistance should be done. It aims to provoke discussion between scientists and stakeholders, particularly in light of upcoming EU legislation.
Suggest national data services in the Epidemiology and Biology of Infection research area
Suggest national data services in the Epidemiology and Biology of Infection research area
The Swedish Pathogens Portal is a service in which the Epidemiology and Biology of Infection data science node, hosted at Umeå University, is heavily involved.
New dashboard on predicting the next dominant strain of SARS-CoV-2
New dashboard on predicting the next dominant strain of SARS-CoV-2
"The latest dashboard: “SARS-CoV-2 variant competition” on the Portal features the results of a model capable of predicting the variant of SARS-CoV-2 that's likely to become dominant based on geographical statistics."
Information about mpox in Sweden
Information about mpox in Sweden
A case of clade 1 mpox has recently been detected in Sweden. See here to see the resources currently available on the Swedish Pathogens Portal.
New data sources and repositories section
New data sources and repositories section
A section showing sources and repositories for data related to infectious disease and pandemic preparedness has been added. This will contribute to making data more Open and FAIR.
New data highlight on the incompatablility of receptors in influenza A transmission
New data highlight on the incompatablility of receptors in influenza A transmission
Nilsson et al. showed that sialylated glycan structures that were previously thought to be exclusive to mammals were present in avian species. Mass spectrometry proteomics shared openly.
Update on multi-disease serology and Pandemic Laboratory Preparedness at SciLifeLab
Update on multi-disease serology and Pandemic Laboratory Preparedness at SciLifeLab
Recent updates to existing sections for pandemic laboratory preparedness, and news of a new dashboard.
New editorial about leveraging genomic data to improve anthrax surveillance
New editorial about leveraging genomic data to improve anthrax surveillance
A perspective on Bacillus anthracis, a pathogen known as a biological threat, and how WGS data and surveillance can help researchers respond to cases and threats.
New editorial about friendly or disease-causing pathogens
New editorial about friendly or disease-causing pathogens
This new Editorial by Luisa W Hugerth, who is part of Portal Editorial Committee, discusses what makes a pathogen, which a focus on the microbes in our bodies.
Wastewater updates for Gothenburg
Wastewater updates for Gothenburg
The Norder group at Gothenburg University have recently updated their methods related to quantifying SARS-CoV-2 and enteric viruses in wastewater. Data collected using this new method are now available.
ISIDORe offers services for infectious disease research
ISIDORe offers services for infectious disease research
The ISIDORe project aims to accelerate research and enhance pandemic preparedness efforts across Europe by assembling and providing access to crucial research resources. This includes their state-of-the-art facilities, services, advanced equipment, and ex
New dashboard showing SARS-CoV-2 sequences in Uppsala
New dashboard showing SARS-CoV-2 sequences in Uppsala
Today we are launching a new dashboard showing information on the SARS-CoV-2 sequences detected during surveillance efforts by the section for Clinical Microbiology and Hospital Hygiene at Uppsala University Hospital.
New editorials section
New editorials section
Today, we are launching a new section containing ’editorials’. Editorials are short opinion-style articles detailing the ‘current thinking’ on a given subject.
Influenza added as a topic
Influenza added as a topic
The content of the portal is broadly organised into ’topics’ related to pathogens and pandemic preparedness. Influenza is our latest topic.
Becoming the first national node of the Pathogens Portal
Becoming the first national node of the Pathogens Portal
We are very proud to announce that we are transitioning the Portal into the first national node of the Pathogens Portal. This marks the next step in our efforts related to pandemic preparedness.
Update to include data on enteric viruses in wastewater
Update to include data on enteric viruses in wastewater
The Portal is happy to announce that the wastewater dashboard now includes data on the quantification of enteric viruses from the Norder group at Gothenburg University (GU).
Recent updates and upcoming improvements
Recent updates and upcoming improvements
An overview of recent updates and improvements, and things to look out for in future.
National COVID-19 biobank sample collection made available for research on the Portal
National COVID-19 biobank sample collection made available for research on the Portal
A unique new sample collection has been added to the COVID-19 Sample Collection Database. The collection comprises of over 1.5 million samples collected by Swedish healthcare regions and processed by the National Pandemic Centre throughout the COVID-19 pa
Update to wastewater epidemiology dashboard
Update to wastewater epidemiology dashboard
The Portal team is working closely with groups at multiple Swedish universities that are involved in wastewater epidemiology to bring you the latest research in this area.
Swedish national resources on IDTk
Swedish national resources on IDTk
The Portal is a partner in the BY-COVID project. We have added a page to the Infectious Diseases Toolkit (IDTk) related to infectious disease data in Sweden.
New section for pandemic preparedness events
New section for pandemic preparedness events
A new section has been added to promote events relevant to pandemic preparedness. This could include, for example, events related to biobanks, antibiotic resistance, or particular pathogens.
Portal welcomes editorial committee
Portal welcomes editorial committee
An editorial committee has now been established. The members will work closely with us to maximise the value of the Portal for the research community.
Dashboard on Register-based COVID-19 Vaccination Study (RECOVAC) updated & expanded
Dashboard on Register-based COVID-19 Vaccination Study (RECOVAC) updated & expanded
New information related to determinants of vaccination and vaccine effectiveness have been added to the RECOVAC dashboard. The data has also been updated.
Explore COVID-19 publications in the field of social sciences and humanities on the Portal
Explore COVID-19 publications in the field of social sciences and humanities on the Portal
The Portal contains a database of COVID-19 publications involving Swedish researchers, and an available data section that shows which share data and/or code. It has long been possible to filter both the database and available databases by certain topics.
The latest updates to the COVID-19 & Pandemic Preparedness Portal
The latest updates to the COVID-19 & Pandemic Preparedness Portal
The scope of the portal has expanded in 2022 to include other pathogens and pandemic preparedness in general. We’ve created lots of new content and features in response to this (with more planned!).
Relaunch as Swedish COVID-19 and Pandemic Preparedness Portal
Relaunch as Swedish COVID-19 and Pandemic Preparedness Portal
Today we officially relaunch the site as the Swedish COVID-19 and Pandemic Preparedness Portal. We have been gradually transitioning sections of the Portal throughout 2022. Our latest section involves a collation of resources related to pandemic preparedn
Section on Register-based COVID-19 Vaccination Study (RECOVAC) launched
Section on Register-based COVID-19 Vaccination Study (RECOVAC) launched
Data visualisations, information, and publications related to the RECOVAC project are now available on the portal. Visualisation codes are publicly available.
The Swedish COVID-19 Data Portal two year anniversary
The Swedish COVID-19 Data Portal two year anniversary
The Swedish COVID-19 Data Portal two year anniversary 2022-06-03 The national Swedish COVID-19 Data Portal was launched two years ago today. The portal has been an important part of the pandemic response in Sweden. On our anniversary, we reflect on pas
Tutorial for SARS-CoV-2 genome data submission to ENA now available
Tutorial for SARS-CoV-2 genome data submission to ENA now available
Today, we are launching a ENA tutorial on how to submit SARS-CoV2 sequences to the European Nucleotide Archive. The tutorial caters to both experienced and first time sequence submitters.
Statistics, information, and research related to COVID-19 Vaccination in Sweden now available on the Portal
Statistics, information, and research related to COVID-19 Vaccination in Sweden now available on the Portal
The Visualizations are based on data freely available from the Swedish Health Agency (Folkhälsomyndigheten).
BY-COVID – a collaborative effort to tackle data challenges that can hinder effective pandemic response BY-COVID – a collaborative effort to tackle data challenges that can hinder effective pandemic response
BY-COVID – a collaborative effort to tackle data challenges that can hinder effective pandemic response BY-COVID – a collaborative effort to tackle data challenges that can hinder effective pandemic response
The BeYond-COVID (BY-COVID) is a recently launched €12 million project funded by Horizon Europe. The Swedish COVID-19 Data Portal is one of the 53 partners from 19 countries taking part in the project.
New section on the Portal about register-based research
New section on the Portal about register-based research
The Swedish COVID-19 Data Portal is launching a section on register-based research in Sweden containing an overview of relevant registers and examples of research projects have used register data.
Statistics, information, and research about Post COVID-19 condition in Sweden now available on the Portal
Statistics, information, and research about Post COVID-19 condition in Sweden now available on the Portal
Today, for the first time, the Portal provides information and summary statistics to show the impact of ‘Post COVID-19 condition’ (‘Postcovid’ in Swedish) in Sweden, and the research underway. All data and code used on the page is publicly available.
The Swedish SARS-CoV-2 and COVID-19 research output since the beginning of the pandemic
The Swedish SARS-CoV-2 and COVID-19 research output since the beginning of the pandemic
To date, 1.400+ journal articles and preprints have been published by researchers affiliated to a Swedish university or research institute. The database of these publications is compiled by the Portal and is available for download.
The Swedish COVID-19 Data Portal one year on - focus on openly sharing data and code
The Swedish COVID-19 Data Portal one year on - focus on openly sharing data and code
One year ago today, on June 3rd 2020, the Swedish COVID-19 Data Portal was launched and became the first national node of the European data sharing platform for COVID-19 research efforts. Here, we look back at the highlights over the last year.
SARS-CoV-2 wastewater data from cities across Sweden now available
SARS-CoV-2 wastewater data from cities across Sweden now available
The Swedish COVID-19 Data Portal is launching a section with wastewater epidemiology data. Weekly data from Uppsala, Stockholm, Umeå, and Örebro is presented in graphs and available for download.
Database of COVID-19 sample collections and biobanks in Sweden launched
Database of COVID-19 sample collections and biobanks in Sweden launched
In collaboration with Biobank Sweden, today we are launching a new section of the portal: the Swedish COVID-19 Sample Collection Database. The database allows to search for available biobank sample collections.
Data on COVID-19 testing in Region Uppsala and dashboard with test positivity rate, maps, trends and more now available on the COVID-19 Data Portal
Data on COVID-19 testing in Region Uppsala and dashboard with test positivity rate, maps, trends and more now available on the COVID-19 Data Portal
The data portal is now launching a page with the CRUSH Covid dashboard with an option to download data on COVID-19 testing in each postal code of Uppsala County.
Statistics on SARS-CoV-2 antibody tests carried out by SciLifeLab now available
Statistics on SARS-CoV-2 antibody tests carried out by SciLifeLab now available
We are launching a page with statistics on the SARS-CoV-2 antibody tests carried out at the SciLifeLab Autoimmunity and Serology profiling facility.