Health data

Publications with accessible data

Data available from Swedish public agencies and large data produces

Public Health Agency of Sweden:
- Number of cases and tests: Official statistics about COVID-19 cases and tests in Sweden.
- Number of administered vaccine doses: Official statistics about the number of vaccines that have been administered in Sweden.
- Variants of concern: Official variants of concern in Sweden.
Swedish National Board of Health and Welfare (Socialstyrelsen): Statistics on COVID-19 in Sweden - underlying cause of death; infected and deceased among the elderly and among persons with disabilities and residential arrangements; inpatient care (updated every Wednesday).
Register-based research: information, tools, examples (see also our RECOVAC dashboard).
Swedish Intensive Care Register: Statistics about ICU admissions in Sweden.
Swedish Pregnancy Register: Data about all pregnant women diagnosed with COVID-19 and newborns born to mothers diagnosed with COVID-19.
SciLifeLab Autoimmunity and Serology profiling facility SARS-CoV-2 antibody test statistics: Hosted by the portal, manually updated on a weekly basis.
CRUSH Covid data and dashboard, Region Uppsala: Number of tests and % positivity in each postal code in Uppsala län.
COVID Symptom Study Sweden: National research initiative for large-scale data collection and analysis of symptoms, exposure, and risk factors associated with the COVID-19 infection.
National Pandemic Centre COVID-19 test statistics: The daily number of tests carried out between April and December 2020 as well as test results.
Statistics on post COVID-19 condition in Sweden: Information regarding the diagnoses associated with long-term affects following COVID-19 infection. Includes relevant demographic data as well as data on associated symptoms, research projects focused on the condition, and background information. Data updated monthly.
Vaccine administration and vaccine research: Visualisations of the vaccine administration in Sweden, research projects on vaccines, publications on vaccines.

The list of available data on this Portal was curated manually until February 2022. After February 2022, we instead began to use a script to query the Europe PMC database (making use of their API) in order to locate relevant publications. We only include data from publications about COVID-19/SARS-CoV-2 that BOTH involve at least one author affiliated with a Swedish research institution AND openly share reusable data and/or code. The code used for the query is written in Python and, as with all of our code, it is openly available in GitHub. We welcome others to reuse it and to repurpose it for other pathogens.

The lists of available data may not be exhaustive as the script used to generate it does not search for every possible database/repository. If you find that a dataset is missing, or that the information related to it is incorrect, please get in touch with us

Last updated: 2025-05-22

Data types

All data types (344)

Biochemistry data (35)

Drug discovery data (15)

Genomics & transcriptomics data (93)

Health data (119)

Imaging data (7)

Other data (51)

Protein data (60)

Public health data (68)

Serology data (24)

Social science and humanities data (76)

Publication	Available dataset and code
Germline variants and mosaic chromosomal alterations affect COVID-19 vaccine immunogenicity Sonehara K., Uwamino Y., Saiki R., Takeshita M., et al (2025) Elsevier BV DOI: https://doi.org/10.1016/j.xgen.2025.100783	COVID-19 GWAS in Japanese data European Genome-Phenome Archive CRYSTAL STRUCTURE OF THE INTACT HUMAN IGG B12 WITH BROAD AND POTENT ACTIVITY AGAINST PRIMARY HIV-1 ISOLATES: A TEMPLATE FOR HIV VACCINE DESIGN data Protein Data Bank: 1hzh ALFA project data National Library of Medicine: rs1043109 ALFA project data National Library of Medicine: rs1043249 ALFA project data National Library of Medicine: rs9270585 ALFA project data National Library of Medicine: rs139861548 ALFA project data National Library of Medicine: rs28472312
Distinct Omicron longitudinal memory T cell profile and T cell receptor repertoire associated with COVID-19 hospitalisation Markey G., McLaughlin J., McDaid D., Lynch S. M., et al (2025) Frontiers Media SA DOI: https://doi.org/10.3389/fimmu.2025.1549570	COVID RESPONSE STUDY (COVRES) data National Library of Medicine: NCT05548829 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/CHE/SARS-CoV-2 Omicron BA.2/2022, complete genome data European Nucleotide Archive: OR575624.1 Crystal Structure of SARS-CoV-2 NSP7-NSP8 complex data Protein Data Bank: 7jlt Omicron spike at 3.0 A (open form) data Protein Data Bank: 7tgw Crystal structure of the SARS CoV-2 Papain-like protease in complex with peptide inhibitor VIR250 data Protein Data Bank: 6wuu Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane data Protein Data Bank: 8fdw
Patients with post-COVID-19 condition show minor blood transcriptomic changes, with altered erythrocyte gene expression in a male subgroup Karisola P., Kanerva M., Vuokko A., Liira H., et al (2025) Frontiers Media SA DOI: https://doi.org/10.3389/fimmu.2025.1500997	Patients with post COVID-19 condition data Figshare
Wearable data reveals distinct characteristics of individuals with persistent symptoms after a SARS-CoV-2 infection Ledebur K., Wiedermann M., Puta C., Thurner S., et al (2025) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41746-025-01456-x	Wearable data reveals distinct characteristics of individuals with persistent symptoms after a SARS-CoV-2 infection data Biostudies: S-EPMC11920215
Plasma proteomic evidence for increased β-amyloid pathology after SARS-CoV-2 infection Duff E. P., Zetterberg H., Heslegrave A., Dehghan A., et al (2025) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41591-024-03426-4	Plasma proteomic evidence for increased β-amyloid pathology after SARS-CoV-2 infection data Biostudies: S-EPMC11922756 Code repository for Plasma proteomic evidence for increased Alzheimer’s disease-related brain pathology after SARS-CoV-2 infection code Github ALFA Allele Frequency data National Library of Medicine: rs429358 ALFA Allele Frequency data National Library of Medicine: rs7412
The COVID‐19 pandemic caused gender‐specific declines in knee surgery rates in Sweden from 2020 to 2021 Axenhus M., Magnéli M. (2024) Wiley DOI: https://doi.org/10.1002/jeo2.70030	Dataset for: Trends in Knee Surgeries and Knee Arthroplasty in Sweden: A Decade of Insights data Figshare
A combined neural ODE-Bayesian optimization approach to resolve dynamics and estimate parameters for a modified SIR model with immune memory Liu D., Sopasakis A. (2024) Elsevier BV DOI: https://doi.org/10.1016/j.heliyon.2024.e38276	Infection Dynamics code GitHub COVID-19 Projections data Institute for Health Metrics and Evaluation
A combined neural ODE-Bayesian optimization approach to resolve dynamics and estimate parameters for a modified SIR model with immune memory Liu D., Sopasakis A. (2024) Elsevier BV DOI: https://doi.org/10.1016/j.heliyon.2024.e38276	Infection Dynamics code GitHub COVID-19 Projections data Institute for Health Metrics and Evaluation
Structural brain changes in post-COVID condition and its relationship with cognitive impairment Pacheco-Jaime L., Garcia-Vicente C., Ariza M., Cano N., et al (2024) Oxford University Press (OUP) DOI: https://doi.org/10.1093/braincomms/fcaf070	Structural brain changes in post-COVID condition and its relationship with cognitive impairment data Biostudies: S-EPMC11851114
COVID-19 vaccination and birth outcomes of 186,990 women vaccinated before pregnancy: an England-wide cohort study Suseeladevi A. K., Denholm R., Retford M., Raffetti E., et al (2024) Elsevier BV DOI: https://doi.org/10.1016/j.lanepe.2024.101025	COVID-19 vaccination and birth outcomes of 186,990 women vaccinated before pregnancy: an England-wide cohort study data Biostudies: S-EPMC11838104
Differential immunometabolic responses to Delta and Omicron SARS-CoV-2 variants in golden syrian hamsters Rajaiah R., Pandey K., Acharya A., Ambikan A., et al (2024) Elsevier BV DOI: https://doi.org/10.1016/j.isci.2024.110501	Complex heatmaps for visualisation code Github Principal Component Analysis code Github
Older patients affected by COVID-19: investigating the existence of biological phenotypes Zucchelli A., Parigi M., Giliani S., Vetrano D. L., et al (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1186/s12877-024-05473-5	Frailty in Elderly Patients With COVID-19 (FRA-COVID) data National Library of Medicine: NCT04412265
Prevalent and persistent new-onset autoantibodies in mild to severe COVID-19 Jernbom A. F., Skoglund L., Pin E., Sjöberg R., et al (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41467-024-53356-5	Prevalent and persistent new-onset autoantibodies in mild to severe COVID-19 data Figshare Spike glycoprotein data UniProt: P0DTC2
Mental illness and COVID-19 vaccination: a multinational investigation of observational & register-based data Barker M. M., Kõiv K., Magnúsdóttir I., Milbourn H., et al (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41467-024-52342-1	Statistical code used for the COVIDMENT and Swedish register analysis code Github
Immunomics in one health: understanding the human, animal, and environmental aspects of COVID-19 Gao J., Zhang C., Wheelock Å. M., Xin S., et al (2024) Frontiers Media SA DOI: https://doi.org/10.3389/fimmu.2024.1450380	R scripts to analyse the CYTOF data code Github Mapping the recovery of critically ill COVID 19 patients by mass cytometry data Flowrepository
Anti-SARS-CoV-2 mRNA vaccination among patients living with SLE in Sweden: Coverage and clinical effectiveness Mageau A., Simard J. F., Svenungsson E., Arkema E. V. (2024) SAGE Publications DOI: https://doi.org/10.1177/09612033241273052	Anti-SARS-CoV-2 mRNA vaccination among patients living with SLE in Sweden: coverage progression and clinical effectiveness. data Open Science Framework
Prevalence and Determinants of Changes in Physical Activity and Sedentary Behavior during and after the COVID-19 Pandemic: A Swedish Repeated Cross-Sectional Study Kerstis B., Elvén M., Nilsson K. W., von Heideken Wågert P., et al (2024) MDPI AG DOI: https://doi.org/10.3390/ijerph21080960	Complex heatmaps for visualisation data Figshare
Socioeconomic disparities in changes to preterm birth and stillbirth rates during the first year of the COVID-19 pandemic: a study of 21 European countries Zeitlin J., Philibert M., Barros H., Broeders L., et al (2024) Oxford University Press (OUP) DOI: https://doi.org/10.1093/eurpub/ckad186	PHIRI - WP6 - Use Case C scripts for local analyses (R Markdown) code Zenodo PHIRI - WP6 - Use Case C Common Data Model & Study Protocol data Zenodo
High prevalence of long-term olfactory disorders in healthcare workers after COVID-19: A case-control study Frasnelli J., Tognetti A., Winter A. L., Thunell E., et al (2024) Public Library of Science (PLoS) DOI: https://doi.org/10.1371/journal.pone.0306290	Prevalence of olfactory dysfunction after COVID-19 /Raw Data data Open Science Framework Prevalence of olfactory dysfunction after COVID-19 /Analyses scripts code Open Science Framework
Automated surveillance of antimicrobial consumption in intensive care, northern Sweden: an observational case study Winroth A., Andersson M., Fjällström P., Johansson A. F., et al (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1186/s13756-024-01424-2	The code used for the extraction of digital data from the ICU information system accessed by the automated surveillance system code Github
Giving a Voice to Patients With Smell Disorders Associated With COVID-19: Cross-Sectional Longitudinal Analysis Using Natural Language Processing of Self-Reports Menger N. S., Tognetti A., Farruggia M. C., Mucignat C., et al (2024) JMIR Publications Inc. DOI: 10.2196/47064	Data on the open-ended comments from COVID-19 smell longhaulers and non-longhaulers on the Global Consortium for Chemosensory Research (GCCR) survey. data Open Science Framework Code to complete cross-sectional longitudinal analysis using natural language processing (primarily in R). code Open Science Framework
Assessing sickness behavior in the French: Validation of the French translation of the sickness questionnaire (SicknessQ) in a non-clinical French population Andreasson A., Tognetti A., Jones M., Lekander M., et al (2023) Elsevier BV DOI: 10.1016/j.bbih.2023.100708	Results of the Sickness Questionnaire (SicknessQ) in France, assessing symptoms of sickness behavior, including somatic, behavioral, and affective dimensions. data Open Science Framework
SARS-CoV-2 antibodies from children exhibit broad neutralization and belong to adult public clonotypes Wall S. C., Suryadevara N., Kim C., Shiakolas A. R., et al (2023) Elsevier BV DOI: 10.1016/j.xcrm.2023.101267	Raw sequence reads related to SARS-CoV-2 antibodies from children exhibiting broad neutralisation. data Sequence Read Archive: PRJNA1014462 SARS-CoV-2 spike in complex with Fab 71281-33. data Electron Microscopy Databank: EMD-41075 SARS-CoV-2 spike in complex with Fab 71281-33 (2). data Electron Microscopy Databank: EMD-41076
Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency Le Voyer T., Parent A. V., Liu X., Cederholm A., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41586-023-06717-x	Raw RNA sequence reads produced when patient whole blood samples were analysed by RNA sequencing in order to monitor global changes in transcript abundance levels post-interferon treatment. data NCBI database: PRJNA989123
Evaluation of a human mucosal tissue explant model for SARS-CoV-2 replication Gordhan B. G., Herrera C., Pillay A., Seiphetlo T., et al (2023) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0291146	Data related to PCR probes, assessments of infectivity and RNA integrity, and ex-vivo challenges are included in the study. data
Reproducibility in pharmacometrics applied in a phase III trial of BCG-vaccination for COVID-19 van Wijk R. C., Mockeliunas L., van den Hoogen G., Upton C. M., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41598-023-43412-3	Workflow developed during the COVID-19 pandemic with the purpose of COVID-19 vaccination Phase III trial data analysis and support through data quality control and automated reporting code GitHub
Predictors of the post-COVID condition following mild SARS-CoV-2 infection Reme B., Gjesvik J., Magnusson K. (2023) Springer Science and Business Media LLC DOI: 10.1038/s41467-023-41541-x	Data cannot be shared publicly, but those with appropriate ethical permissions can apply for access via helsedata.no/en. data Code used for analysis (in R) code GitHub
Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis Hartman E., Scott A. M., Karlsson C., Mohanty T., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41467-023-41146-4	AKI DIA samples for generalized peakgroup scoring model application data PRIDE: PXD038394 A time-resolved proteomic and prognostic map of COVID-19 data PRIDE: PXD025752 Olink Dataset data Figshare 56 samples from acute kidney injury patients (DIA-MS septic AKI dataset). data PRIDE: PXD044264 Biologically Informed Neural Network (BINN) code code GitHub InfectionMedicineProteomics/BINN: First release code Zenodo DE-score algorithm has been implemented into the data processing package DPKS code GitHub
Characterising information loss due to aggregating epidemic model outputs Sherratt K., Srivastava A., Ainslie K., Singh D. E., et al (2023) Cold Spring Harbor Laboratory DOI: 10.1101/2023.07.05.23292245	Data used in modelling, including location and population size. data GitHub Data processing code in R is available on Github code GitHub
Vaccine-induced correlate of protection against fatal COVID-19 in older and frail adults during waves of neutralization-resistant variants of concern: an observational study Vikström L., Fjällström P., Gwon Y., Sheward D. J., et al (2023) Elsevier BV DOI: 10.1016/j.lanepe.2023.100646	Data processing code in R is available on Github data GitHub
Sustained IFN signaling is associated with delayed development of SARS-CoV-2-specific immunity Brunet-Ratnasingham E., Morin S., Randolph H. E., Labrecque M., et al (2023) Cold Spring Harbor Laboratory DOI: 10.1101/2023.06.14.23290814	Clinical data and biobanks samples from 250 critically ill COVID-19 patients. Appropriate permits are required for access. data Figshare Data from the BQC-19 repository is available after appropriate permissions and data access agreements data BQC-19
Single-Virus Fusion Measurements Reveal Multiple Mechanistically Equivalent Pathways for SARS-CoV-2 Entry Sengar A., Cervantes M., Bondalapati S. T., Hess T., et al (2023) American Society for Microbiology DOI: 10.1128/jvi.01992-22	Movies and data to accompany the study data zenodo: 7826331 Image and time series analysis code written in MATLAB is available on GitHub code GitHub
Nucleocapsid-specific T cell responses associate with control of SARS-CoV-2 in the upper airways before seroconversion Eser T. M., Baranov O., Huth M., Ahmed M. I. M., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41467-023-38020-8	Data cannot be shared publicly, but applications can be made for access. data
Vaccine-induced correlate of protection against fatal COVID-19 in older and frail adults during waves of neutralization-resistant variants of concern: an observational study Vikström L., Fjällström P., Gwon Y., Sheward D. J., et al (2023) Elsevier BV DOI: 10.1016/j.lanepe.2023.100646	Data processing code is available on GitHub code GitHub
Regional differences in personalities account for substantial heterogeneity of loneliness change from before to during the COVID-19 Xiao S., Dang J. (2023) Frontiers Media SA DOI: 10.3389/fpsyg.2023.1124627	Data used in analysis assessing personality traits data Open Science Framework: d99ed5ce0ed641ca80965e54c11afc81 Script for data re-analysis of traits code Open Science Framework: d99ed5ce0ed641ca80965e54c11afc81
Diagnosis of COVID-19 from X-rays using combined CNN-RNN architecture with transfer learning Islam M. M., Islam M. Z., Asraf A., Al-Rakhami M. S., et al (2023) Elsevier BV DOI: 10.1016/j.tbench.2023.100088	COVID19, Pneumonia, and Normal Chest X-ray Posteroanterior Dataset data Mendeley Data Scripts used in this project to analyse the datasets code GitHub
Characteristics and outcomes of COVID-19 patients with COPD from the United States, South Korea, and Europe Moreno-Martos D., Verhamme K., Ostropolets A., Kostka K., et al (2023) F1000 Research Ltd DOI: 10.12688/wellcomeopenres.17403.3	Characteristics and outcomes of COVID-19 patients with COPD data Zenodo Aggregate data from COVID-19 patients with COPD data Code used for analysis code GitHub Archived code used for analysis code Zenodo
Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity Yoshiji S., Butler-Laporte G., Lu T., Willett J. D. S., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s42255-023-00742-w	Summary statistics related to body mass index (BMI) data Summary statistics on plasma proteome from the deCODE study data Summary statistics related to COVID-19 outcomes data Long Read RNASeq data data GTEx: phs000424.v9 Body fat percentage data data OpenGWAS: ukb-b-8909 Whole body fat mass data data OpenGWAS: ukb-b-19393 Whole body fat-free mass data data OpenGWAS: ukb-b-13354 scRNA-seq data of COVID-19 lung autopsy samples data Custom analysis codes code GitHub
How Have Physical Activity and Sedentary Behavior, Changed during the COVID-19 Pandemic? A Swedish Repeated Cross-Sectional Design Study Lindberg D., Elvén M., Nilsson K. W., Von Heideken Wågert P., et al (2023) MDPI AG DOI: 10.3390/ijerph20043642	Questionaire data on levels of physical activity and sedentary behaviour data Figshare
Monkeypox outbreaks in the context of the COVID-19 pandemic: Network and clustering analyses of global risks and modified SEIR prediction of epidemic trends Gao J., Zhou C., Liang H., Jiao R., et al (2023) Frontiers Media SA DOI: 10.3389/fpubh.2023.1052946	Information on open data sources used e.g. for socioeconomic factors, environment, biodiveristy, health, among others. data
Dynamics of COVID-19 progression and the long-term influences of measures on pandemic outcomes Lan Y., Yin L., Wang X. (2022) Springer Science and Business Media LLC DOI: 10.1186/s12982-022-00119-6	Sensitivity analysis and mortality rate data available in the paper. data Mortality rate data. data Zenodo Analysis code code Zenodo
Defining post-acute COVID-19 syndrome (PACS) by an epigenetic biosignature in peripheral blood mononuclear cells Nikesjö F., Sayyab S., Karlsson L., Apostolou E., et al (2022) Springer Science and Business Media LLC DOI: 10.1186/s13148-022-01398-1	Analysis and visualisation scripts code GitHub
Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases Lentini A., Pereira A., Winqvist O., Reinius B. (2022) Elsevier BV DOI: 10.1016/j.medj.2022.07.007	Assembled SARS-CoV-2 genomes data GISAID: EPI_ISL_11414777-11415389 and EPI_ISL_11450500-11450677 Raw sequencing data data ArrayExpress: E-MTAB-11650 Computational code code GitHub
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity Ambikan A. T., Yang H., Krishnan S., Svensson Akusjärvi S., et al (2022) Elsevier BV DOI: 10.1016/j.cels.2022.06.006	Metabolomics data data FigShare Analysis code code Zenodo
SARS-CoV-2 integral membrane proteins shape the serological responses of patients with COVID-19 Martin S., Heslan C., Jégou G., Eriksson L. A., et al (2022) Elsevier BV DOI: 10.1016/j.isci.2021.103185	Clinical and raw data related to serological assay data Mendeley
Changes in the incidence of invasive disease due to Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis during the COVID-19 pandemic in 26 countries and territories in the Invasive Respiratory Infection Surveillance Initiative: a prospective analysis of surveillance data Brueggemann A. B., Jansen van Rensburg M. J., Shaw D., McCarthy N. D., et al (2022) Elsevier BV DOI: 10.1016/S2589-7500(21)00077-7	Code for data processing, visualisation, and analysis. code GitHub
Renin–angiotensin system blockers and susceptibility to COVID-19: an international, open science, cohort analysis Morales D. R., Conover M. M., You S. C., Pratt N., et al (2022) Elsevier BV DOI: 10.1016/s2589-7500(20)30289-2	Much of the data cannot be shared publicly, but applications can be made for access data start-to-finish open and executable source code code GitHub
Risk of hydroxychloroquine alone and in combination with azithromycin in the treatment of rheumatoid arthritis: a multinational, retrospective study Lane J. C. E., Weaver J., Kostka K., Duarte-Salles T., et al (2022) Elsevier BV DOI: 10.1016/S2665-9913(20)30276-9	All analysis tools used by Observational Health Data Sciences and Informatics. code GitHub Data and results artefacts that do not include patient-level health information. data
The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19 Consiglio C. R., Cotugno N., Sardh F., Pou C., et al (2022) Elsevier BV DOI: 10.1016/j.cell.2020.09.016	Data organised by figures presented in the article. data Mendeley Plasma protein expression (Olink - NPX values), FACS, Autoantibodies. data Figshare Scripts to complete analyses and produce figures. code GitHub
Therapeutic Targets for Heart Failure Identified Using Proteomics and Mendelian Randomization Henry A., Gordillo-Marañón M., Finan C., Schmidt A. F., et al (2022) Ovid Technologies (Wolters Kluwer Health) DOI: 10.1161/CIRCULATIONAHA.121.056663	Code used in the main analysis code GitHub
Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics Tsitsiklis A., Osborne C. M., Kamm J., Williamson K., et al (2022) Elsevier BV DOI: 10.1016/s2666-5247(21)00304-9	Deidentified individual patient data and raw fastq microbial sequencing alignments data BioProject: PRJNA748764 Background correction algorithm code GitHub Rules-based model code GitHub
Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort Carapito R., Li R., Helms J., Carapito C., et al (2022) American Association for the Advancement of Science (AAAS) DOI: 10.1126/scitranslmed.abj7521	Proteomics data data ProteomeXchange: PXD025265 RNA-seq datasets data Gene Expression Omnibus: GSE172114 Code to perform classification and structural causal modeling code Zenodo
JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortality Stebbing J., Sánchez Nievas G., Falcone M., Youhanna S., et al (2022) American Association for the Advancement of Science (AAAS) DOI: 10.1126/sciadv.abe4724	RNA-seq of SARS-CoV-2-infected human primary hepatocyte-derived spheroids upon interferon a2 and baricitinib treatment. data ArrayExpress: E-MTAB-9711 Patient information are contained in the paper and supplementary information. data
COVID‐19‐specific metabolic imprint yields insights into multiorgan system perturbations Cornillet M., Strunz B., Rooyackers O., Ponzetta A., et al (2021) Wiley DOI: 10.1002/eji.202149626	Curated data are available for exploration via the Karolinska KI/K COVID-19 Immune Atlas data
ECG pathology and its association with death in critically ill COVID-19 patients, a cohort study Rosén J., Noreland M., Stattin K., Lipcsey M., et al (2021) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0261315#sec018	Data is sensitive and cannot be shared openly, but data transfer agreement could be established data Figshare
Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality Nakanishi T., Pigazzini S., Degenhardt F., Cordioli M., et al (2021) American Society for Clinical Investigation DOI: 10.1172/jci152386	Code for data management and analysis (commit 183ddb7). code GitHub Data are held in multiple international repositories. Details about gaining access are contained in the paper. data
Association between convalescent plasma treatment and mortality in COVID-19: a collaborative systematic review and meta-analysis of randomized clinical trials Axfors C., Janiaud P., Schmitt A. M., van’t Hooft J., et al (2021) Springer Science and Business Media LLC DOI: 10.1186/s12879-021-06829-7	Data from clinical trial registries used in the study data Open Science Framework
Beta RBD boost broadens antibody-mediated protection against SARS-CoV-2 variants in animal models Sheward D. J., Mandolesi M., Urgard E., Kim C., et al (2021) Elsevier BV DOI: 10.1016/j.xcrm.2021.100450	Data from clinical trial registries used in the study code GitHub
Infection of Brain Pericytes Underlying Neuropathology of COVID-19 Patients Bocci M., Oudenaarden C., Sàenz-Sardà X., Simrén J., et al (2021) MDPI AG DOI: 10.3390/ijms222111622	Data available in the supplementary material data
Diabetes, hypertension, body mass index, smoking and COVID-19-related mortality: a systematic review and meta-analysis of observational studies Mahamat-Saleh Y., Fiolet T., Rebeaud M. E., Mulot M., et al (2021) BMJ DOI: 10.1136/bmjopen-2021-052777	Data related to literature requests available in the paper and supplementary materials. data
Advances and Utility of the Human Plasma Proteome Deutsch E. W., Omenn G. S., Sun Z., Maes M., et al (2021) American Chemical Society (ACS) DOI: 10.1021/acs.jproteome.1c00657	Union of proteins in both the plasma and blood extracellular vesicle PeptideAtlas builds data
Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19 Rivero-García I., Castresana-Aguirre M., Guglielmo L., Guala D., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41598-021-99721-y	Raw and processed data available in Bitbucket data Code for data processing and figure reproduction available in Bitbucket code
Changes in Physical Activity Are Associated with Corresponding Changes in Psychological Well-Being: A Pandemic Case Study Dahlen M., Thorbjørnsen H., Sjåstad H., von Heideken Wågert P., et al (2021) MDPI AG DOI: 10.3390/ijerph182010680	Raw data on physical activity and psychological well-being. data Open Science Framework
Effects of the COVID-19 Health Crisis on Sports Practice, Life Quality, and Emotional Status in Spanish High-Performance Athletes Conde E., Martínez-Aranda L. M., Sanz G., López de Subijana C., et al (2021) Frontiers Media SA DOI: 10.3389/fpsyg.2021.736499	Descriptive data on subjects included in the study, particularly focussed on the reasons behind limitations in ability to train. data
Landscape of T‐cell repertoires with public COVID‐19‐associated T‐cell receptors in pre‐pandemic risk cohorts Simnica D., Schultheiß C., Mohme M., Paschold L., et al (2021) Wiley DOI: 10.1002/cti2.1340	COVID-19 patients’ repertoire data: AIRR-seq data (iReceptor Study ID IR-Binder-000001) data Raw FASTQ sequencing files are deposited in the European Nucleotide Archive data European Nucleotide Archive: PRJEB38339
Increased Risks of Death and Hospitalization in Influenza/Pneumonia and Sepsis for Individuals Affected by Psychotic Disorders, Bipolar Disorders, and Single Manic Episodes: A Retrospective Cross-Sectional Study Nilsson N., Bendix M., Öhlund L., Widerström M., et al (2021) MDPI AG DOI: 10.3390/jcm10194411	Data on influenza/pneumonia deaths & hospitalisations due to sepsis, subdivided by mental health condition, physical comorbidities, and demographic features. data
Dismantling internet-based cognitive behavioral therapy for tinnitus. The contribution of applied relaxation: A randomized controlled trial Beukes E. W., Andersson G., Fagelson M. A., Manchaiah V. (2021) Elsevier BV DOI: 10.1016/j.invent.2021.100402	Data and metadata from a randomised clinical trial, and the demographic questionaire data Figshare
Measuring changes in alcohol use in Finland and Norway during the COVID‐19 pandemic: Comparison between data sources Mäkelä P., Rossow I., Moan I. S., Bye E. K., et al (2021) Wiley DOI: 10.1002/mpr.1892	Database with codebook for the European Alcohol Use and COVID-19 Survey data Figshare
Acquired olfactory loss alters functional connectivity and morphology Iravani B., Peter M. G., Arshamian A., Olsson M. J., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41598-021-95968-7	Data cannot be shared publicly, but applications can be made for access. data
Perceived changes in capability during the COVID-19 pandemic: A Swedish cross-sectional study from June 2020 Meili K. W., Jonsson H., Lindholm L., Månsdotter A. (2021) SAGE Publications DOI: 10.1177/14034948211023633	Perceived changes in capability during the COVID-19 pandemic (includes data on socioeconomic position, place of birth and regional residence) data
Combined Metabolic Activators Accelerates Recovery in Mild‐to‐Moderate COVID‐19 Altay O., Arif M., Li X., Yang H., et al (2021) Wiley DOI: 10.1002/advs.202101222	Raw, patient-level characteristics and data available in Supporting Information data
COVID-19 after kidney transplantation: Early outcomes and renal function following antiviral treatment Elec A. D., Oltean M., Goldis P., Cismaru C., et al (2021) Elsevier BV DOI: 10.1016/j.ijid.2021.01.023	Patient demographics, management and outcome in 42 kidney recipients with COVID-19. data
Point of care ultrasound screening for deep vein thrombosis in critically ill COVID-19 patients, an observational study Galien S., Hultström M., Lipcsey M., Stattin K., et al (2021) Springer Science and Business Media LLC DOI: 10.1186/s12959-021-00272-z	Metadata record for PRONMED Uppsala COVID-19 ICU Biobank (facilitates data access requests) data Figshare
Seropositivity in blood donors and pregnant women during the first year of SARS‐CoV‐2 transmission in Stockholm, Sweden Castro Dopico X., Muschiol S., Christian M., Hanke L., et al (2021) Wiley DOI: 10.1111/joim.13304	Data related to discriminative bayesian seroprevalence data GitHub Code related to discriminative bayesian seroprevalence (see notebook). code GitHub Code used in analysis of seroprevalence data (R) code GitHub Seroprevalence data related to R code data GitHub
Knowledge and preventive behaviors regarding COVID-19 in Bangladesh: A nationwide distribution Hosen I., Pakpour A. H., Sakib N., Hussain N., et al (2021) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0251151	Dataset on the COVID-19 pandemic and serious psychological consequences in Bangladesh: a population-based nationwide study. data
Occupational burnout and job satisfaction among physicians in times of COVID-19 crisis: a convergent parallel mixed-method study Alrawashdeh H. M., Al-Tammemi A. B., Alzawahreh M. K., Al-Tamimi A., et al (2021) Springer Science and Business Media LLC DOI: 10.1186/s12889-021-10897-4	Individual-level demographic, occupational, COVID-19 data data Figshare
Single-Dilution COVID-19 Antibody Test with Qualitative and Quantitative Readouts Bortz R. H., Florez C., Laudermilch E., Wirchnianski A. S., et al (2021) American Society for Microbiology DOI: 10.1128/mSphere.00224-21	Input data related to ELISA tests. data GitHub Code related to modelling antibody titer quantification from single dilution points. code GitHub
Modest effects of dietary supplements during the COVID-19 pandemic: insights from 445 850 users of the COVID-19 Symptom Study app Louca P., Murray B., Klaser K., Graham M. S., et al (2021) BMJ DOI: 10.1136/bmjnph-2021-000250	ZOE COVID Study website (providing information on raw data and data visualisations). data Supplementary Information (includes information on relevant survey questions, summary statistics and flowcharts about the study). data
The Impact of Coronavirus (COVID-19) Related Public-Health Measures on Training Behaviours of Individuals Previously Participating in Resistance Training: A Cross-Sectional Survey Study Steele J., Androulakis-Korakakis P., Carlson L., Williams D., et al (2021) Springer Science and Business Media LLC DOI: 10.1007/s40279-021-01438-5	Raw data, plots, surveys data Open Science Framework
ECG with Prior Myocardial Infarction Pattern or acute ST-T Pathology is Associated with Death in Critically Ill COVID-19 Patients Rosen J., Noreland M., Stattin K., Lipcsey M., et al (2021) Research Square Platform LLC DOI: 10.21203/rs.3.rs-419853/v1	Metadata record detailing data access requirements data Figshare
Epidemiology and transmission characteristics of early COVID-19 cases, 20 January–19 March 2020, in Bavaria, Germany Böhm S., Woudenberg T., Chen D., Marosevic D. V., et al (2021) Cambridge University Press (CUP) DOI: 10.1017/S0950268821000510	Analysis code (R) code Data related to incubation period and patient. data
Assessing relative COVID-19 mortality: a Swiss population-based study Hothorn T., Bopp M., Günthard H., Keiser O., et al (2021) BMJ DOI: 10.1136/bmjopen-2020-042387	R and Stata code related to COVID-19 mortality assessment code GitLab
The effects of school closures on SARS-CoV-2 among parents and teachers Vlachos J., Hertegård E., B. Svaleryd H. (2021) Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.2020834118	Analysis code code Open Science Framework
Innate lymphoid cell composition associates with COVID‐19 disease severity García M., Kokkinou E., Carrasco García A., Parrot T., et al (2021) Wiley DOI: 10.1002/cti2.1224	Karolinska KI/K Covid19 Immune atlas. data
Elevated Angiopoietin-2 inhibits thrombomodulin-mediated anticoagulation in critically ill COVID-19 patients Hultstrom M., Fromell K., Larsson A., Quaggin S. E., et al (2021) Cold Spring Harbor Laboratory DOI: 10.1101/2021.01.13.21249429	Most data in paper, but metadata record is available as an access point for individual data requests. data Figshare
Sputum ACE2, TMPRSS2 and FURIN gene expression in severe neutrophilic asthma Kermani N. Z., Song W., Badi Y., Versi A., et al (2021) Springer Science and Business Media LLC DOI: 10.1186/s12931-020-01605-8	Data cannot be shared publicly, but applications can be made for access. data
A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2 Maricic T., Nickel O., Aximu-Petri A., Essel E., et al (2020) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0244824	Data are available in the article and supplementary materials (including Ct values & gel images). data
Risk of depression, suicide and psychosis with hydroxychloroquine treatment for rheumatoid arthritis: a multinational network cohort study Lane J. C. E., Weaver J., Kostka K., Duarte-Salles T., et al (2020) Oxford University Press (OUP) DOI: 10.1093/rheumatology/keaa771	Study protocol and analysis source code code GitHub Analysis tools used in study code GitHub Data and results artefacts that do not include patient-level health information data
Large differences in community COVID-19 testing across geographic areas in a Swedish region with 385,000 inhabitants Kennedy B., Martinell M., Hammar U., van Zoest V., et al (2020) Cold Spring Harbor Laboratory DOI: 10.1101/2020.12.15.20248247	Data cannot be made publicly available, but those with written permission from the Swedish Ethical Review Authority may be granted access. data
Screening for high amounts of SARS-CoV-2 identifies pre-symptomatic subjects among healthy healthcare workers Dillner J., Elfström K. M., Blomqvist J., Engstrand L., et al (2020) Cold Spring Harbor Laboratory DOI: 10.1101/2020.12.13.20248122	Data cannot be made publicly available, but applications can be made for individual-level pseudonymised data. data
Intracerebral endotheliitis and microbleeds are neuropathological features of COVID‐19 Kirschenbaum D., Imbach L. L., Rushing E. J., Frauenknecht K. B. M., et al (2020) Wiley DOI: 10.1111/nan.12677	Whole slide scans of ACE2 immunohistochemistry from 4 COVID-19 patients and 3 pre-pandemic controls (named PAT1-4 and CONT1-4, respectively) data Figshare R script to analyze ACE2 expression in basal ganglian from GTEx project data Figshare
Case report and systematic review suggest that children may experience similar long‐term effects to adults after clinical COVID‐19 Ludvigsson J. F. (2020) Wiley DOI: 10.1111/apa.15673	Case report of 5 Swedish children aged 9-15, as well as parental reported symptoms occurring over 2 months after diagnosis. data
Dosing of thromboprophylaxis and mortality in critically ill COVID-19 patients Jonmarker S., Hollenberg J., Dahlberg M., Stackelberg O., et al (2020) Springer Science and Business Media LLC DOI: 10.1186/s13054-020-03375-7	Data cannot be publicly shared, though it is is possible to apply for access. data
The impact of early public health interventions on SARS-CoV-2 transmission and evolution Duchene S., Featherstone L., de Blasio B. F., Holmes E. C., et al (2020) Cold Spring Harbor Laboratory DOI: 10.1101/2020.11.18.20233767	Supplementary materials include a list of GISAID accession numbers for the sequences used, and a summary of public intervention actions adopted in Nordic countries. data
Circulating bioactive adrenomedullin as a marker of sepsis, septic shock and critical illness Lundberg O. H. M., Lengquist M., Spångfors M., Annborn M., et al (2020) Springer Science and Business Media LLC DOI: 10.1186/s13054-020-03351-1	Data cannot be shared publicly due to issues with sensitivity, but it is possible to request access. data
Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series Böhmer M. M., Buchholz U., Corman V. M., Hoch M., et al (2020) Elsevier BV DOI: 10.1016/S1473-3099(20)30314-5	Data on single nucleotide polymorphisms and characteristics of 16 laboratory-confirmed COVID-19 cases included in the article. data
Inborn errors of type I IFN immunity in patients with life-threatening COVID-19 Zhang Q., Bastard P., Liu Z., Le Pen J., et al (2020) American Association for the Advancement of Science (AAAS) DOI: 10.1126/science.abd4570	Genetic Determinants of Susceptibility to Severe COVID-19 Infection. data dbGaP: phs002245.v1.p1 Plasma, cells, genomic DNA, and other materials/samples are available upon request from authors or the Amsterdam UMC Covid-19 Biobank. data All additional data are in the supplementary material. data
Autoantibodies against type I IFNs in patients with life-threatening COVID-19 Bastard P., Rosen L. B., Zhang Q., Michailidis E., et al (2020) American Association for the Advancement of Science (AAAS) DOI: 10.1126/science.abd4585	Plasma, cells, and genomic DNA, as well as other materials can be provided via material transfer agreements. data Clinical, epidemiological characteristics of 101 patients, as well as information on neutralising capacity and assays are provided in the article and supplementary materials. data
Serum-IgG responses to SARS-CoV-2 after mild and severe COVID-19 infection and analysis of IgG non-responders Marklund E., Leach S., Axelsson H., Nyström K., et al (2020) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0241104	Serum-IgG responses to SARS-CoV-2 after mild and severe COVID-19 infection. data Zenodo
Rotational thromboelastometry results are associated with care level in COVID-19 Almskog L. M., Wikman A., Svensson J., Wanecek M., et al (2020) Springer Science and Business Media LLC DOI: 10.1007/s11239-020-02312-3	All raw data underlying the study. data Swedish national dataservice
SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers in Sweden Rudberg A., Havervall S., Månberg A., Jernbom Falk A., et al (2020) Springer Science and Business Media LLC DOI: 10.1038/s41467-020-18848-0	Source data related to symptoms and some aggregated patient data. data Data cannot be made publicly available, but can be made available upon request. data
MAIT cell activation and dynamics associated with COVID-19 disease severity Parrot T., Gorin J., Ponzetta A., Maleki K. T., et al (2020) American Association for the Advancement of Science (AAAS) DOI: 10.1126/sciimmunol.abe1670	Curated flow cytometry data are available for exploration via the Karolinska COVID-19 Immune Atlas. data All other data are available in the article itself or the supplementary materials. data
Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries Bryant P., Elofsson A. (2020) PeerJ DOI: 10.7717/peerj.9879	Data required to reproduce the results. The data was largely produced using Google mobility data. data GitHub Analysis code required for modelliing (primarily using R). code GitHub
Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic Ling J., Hickman R. A., Li J., Lu X., et al (2020) MDPI AG DOI: 10.3390/v12091026	Supplementary materials include information about phylogenetic models, mutational profiles, and spatio-temporal appearance of each variant. data
Systems-Level Immunomonitoring from Acute to Recovery Phase of Severe COVID-19 Rodriguez L., Pekkarinen P. T., Lakshmikanth T., Tan Z., et al (2020) Elsevier BV DOI: 10.1016/j.xcrm.2020.100078	Raw mass cytometry data and the Olink protein data generated during this study. data Immunoglobulin G (IgG) data. data SARS-CoV2 longitudinal systems-level analyses code. data GitHub
Outcome of COVID‐19 in multiple myeloma patients in relation to treatment Susek K. H., Gran C., Ljunggren H., Alici E., et al (2020) Wiley DOI: 10.1111/ejh.13502	Provided in the article: Characteristics, treatments, COVID-19-related outcomes, additional laboratory and clinical data for 9 patients data
Natural killer cell immunotypes related to COVID-19 disease severity Maucourant C., Filipovic I., Ponzetta A., Aleman S., et al (2020) American Association for the Advancement of Science (AAAS) DOI: 10.1126/sciimmunol.abd6832	Curated flow cytometry data available via the Karolinska COVID-19 Immune Atlas. data Raw data, clinical characteristics of patients, and various results files are available in supplementary data. data
Genetic and Phenotypic Evidence for the Causal Relationship Between Aging and COVID-19 Ying K., Zhai R., Pyrkov T. V., Mariotti M., et al (2020) Cold Spring Harbor Laboratory DOI: 10.1101/2020.08.06.20169854	Supplementary information contains information on publicly available data sources used, instruments used, data on loci associated with risk factors, and genetic correlations between lifespan-related traits and COVID-19. data
Probabilistic approaches for classifying highly variable anti-SARS-CoV-2 antibody responses Dopico X. C., Hanke L., Sheward D. J., Muschiol S., et al (2020) Cold Spring Harbor Laboratory DOI: 10.1101/2020.07.17.20155937	Code for discriminative bayesian seroprevalence. code GitHub Data for discriminative bayesian seroprevalence. data GitHub Code used in analysis of seroprevalence data. code GitHub Seroprevalence data. data GitHub
The effect of opening up the US on COVID-19 spread Bryant P., Elofsson A. (2020) Cold Spring Harbor Laboratory DOI: 10.1101/2020.07.03.20145649	Code for modeling the impact of NPI implementations and lifting in all US states code GitHub Data for modeling the impact of NPI implementations and lifting in all US states data GitHub
Acute necrotizing encephalopathy with SARS-CoV-2 RNA confirmed in cerebrospinal fluid Virhammar J., Kumlien E., Fällmar D., Frithiof R., et al (2020) Ovid Technologies (Wolters Kluwer Health) DOI: 10.1212/wnl.0000000000010250	Proteomics data. data Dryad
Re-positive Cases of Nucleic Acid Tests in Discharged Patients With COVID-19: A Follow-Up Study Qiao X., Xu X., Zi H., Liu G., et al (2020) Frontiers Media SA DOI: 10.3389/fmed.2020.00349	Data are in the article, including exposure history and characterists of COVID-19 patients during hospitalisation and discharge, as well as information from a follow-up. data
Neurochemical evidence of astrocytic and neuronal injury commonly found in COVID-19 Kanberg N., Ashton N. J., Andersson L., Yilmaz A., et al (2020) Ovid Technologies (Wolters Kluwer Health) DOI: 10.1212/WNL.0000000000010111	Data cannot be publicly shared, but applications can be made for access to anonymised data. data
Hyperreninemia and low total body water may contribute to acute kidney injury in COVID-19 patients in intensive care Hultström M., von Seth M., Frithiof R. (2020) Ovid Technologies (Wolters Kluwer Health) DOI: 10.1097/HJH.0000000000002531	Biochemistry of patients ordered by days after intensive care admission (n = 9), included in the article. data
Population flow drives spatio-temporal distribution of COVID-19 in China Jia J. S., Lu X., Yuan Y., Xu G., et al (2020) Springer Science and Business Media LLC DOI: 10.1038/s41586-020-2284-y	Population outflow data from Wuhan from January 1-24, 2020; COVID-19 case counts as of February 19 and other data for 296 prefectures in mainland China (additional data in the article). data Analysis code included alongside other data in spplementary information. code
The unsynchronized changes of CT image and nucleic acid detection in COVID-19: reports the two cases from Gansu, China Gao J., Liu J., Wen H., Liu H., et al (2020) Springer Science and Business Media LLC DOI: 10.1186/s12931-020-01363-7	Provided in the article: CT images for 2 patients over 12 days. data
No impact of cancer and plague-relevant <i>FPR1</i> polymorphisms on COVID-19 Petrazzuolo A., Le Naour J., Vacchelli E., Gaussem P., et al (2020) Informa UK Limited DOI: 10.1080/2162402X.2020.1857112	Allelic frequencies of FPR1 SNPs and characteristics of patient population from Hôpital Cochin and Hôpital Européen George Pompidou data
Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells Appelberg S., Gupta S., Svensson Akusjärvi S., Ambikan A. T., et al (2020) Informa UK Limited DOI: 10.1080/22221751.2020.1799723	Raw RNAseq data data BioProject Proteomics data data Zenodo All pre-processing and analysis code code GitHub
High seroprevalence of SARS-CoV-2 in elderly care employees in Sweden Lindahl J. F., Hoffman T., Esmaeilzadeh M., Olsen B., et al (2020) Informa UK Limited DOI: 10.1080/20008686.2020.1789036	Serological responses of 1,005 employees to SARS-CoV-2 at 22 different elderly care homes in Stockholm, Sweden, and the number of employees that reported known contacts with COVID-19. data Prevalence of IgM (either only IgM or combined with IgG) or only IgG among elderly care home employees with or without reported symptoms. data Predictors for seropositivity in both univariable and multivariable analyses. data