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Published Data

Data available from research groups in Sweden

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: 2024-09-04

Data types

All data types (290)

Biochemistry data (34)

Drug discovery data (15)

Genomics & transcriptomics data (84)

Public health data (68)

Serology data (22)

Social science and humanities data (64)

Publication	Available dataset and code
Emergence of SARS-CoV-2 omicron variant JN.1 in Tamil Nadu, India - Clinical characteristics and novel mutations Selvavinayagam S. T., Sankar S., Yong Y. K., Murugesan A., et al (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41598-024-68678-z	Structure of the Axl kinase domain in complex with a macrocyclic inhibitor data Protein Data Bank: 5u6b Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 data Protein Data Bank: 6m0j Plasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) bound to basigin data Protein Data Bank: 4u0q Crystal Structure of a fragment of DC-SIGNR (containing the carbohydrate recognition domain and two repeats of the neck). data Protein Data Bank: 1xar
Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques Mandolesi M., Das H., de Vries L., Yang Y., et al (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41467-024-50286-0	IgDiscover analyses antibody repertoires and discovers new V genes from high-throughput sequencing reads. code GitLab HMM code for chimera identification. code Github SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab) data Protein Data Bank: 8p5m cryoEM structure of SARS-CoV2 Spike trimer in complex with Fab23 data Protein Data Bank: 8q5y SARS-CoV-2 Spike RBD in complex with Mab-23 (Fab) data Electron Microscopy Data Bank: EMD-17451 cryoEM structure of SARS-CoV2 Spike trimer in complex with Fab23 data Electron Microscopy Data Bank: EMD-18180
A structured course of disease dataset with contact tracing information in Taiwan for COVID-19 modelling Wu Y., Nordling T. E. M. (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41597-024-03627-z	COVID-19 Taiwan data, including individual course of disease data figshare Companion code to Wu and Nordling 2023 for visualisation of Taiwanese COVID-19 data code Github
SARS-CoV-2 brainstem encephalitis in human inherited DBR1 deficiency Chan Y., Lundberg V., Le Pen J., Yuan J., et al (2024) Rockefeller University Press DOI: https://doi.org/10.1084/jem.20231725	Lariat debranching enzyme data UniProt: Q9UK59 Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/NY-RU-NY1/2020 data European Nucleotide Archive: OM345241.1
Mammalian cell display with automated oligo design and library assembly allows for rapid residue level conformational epitope mapping Thalén N. B., Karlander M., Lundqvist M., Persson H., et al (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s42003-024-06508-8	Epitope mapping of analytes binding RBD code Github Flow cytometry data for: Mammalian cell display with automated oligo design and library assembly allows for rapid residue level conformational epitope mapping data figshare Crystal structure of the SARS-CoV-2 receptor binding domain in complex with CR3022 Fab data Protein Data Bank: 6yla Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2 data Protein Data Bank: 6vw1 Structure of SARS coronavirus spike receptor-binding domain complexed with its receptor data Protein Data Bank: 2ajf Nucleotide Sequences data European Nucleotide Archive: MK988448.1
Spike deep mutational scanning helps predict success of SARS-CoV-2 clades Dadonaite B., Brown J., McMahon T. E., Farrell A. G., et al (2024) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41586-024-07636-1	LY-CoV1404 neutralising antibody against SARS-CoV-2 data Protein Data Bank: 7mmo Structure of the SARS-CoV-2 XBB.1 spike glycoprotein (closed-2 state) data Protein Data Bank: 8iot Complex of SARS-CoV-2 receptor binding domain with the Fab fragments of two neutralising antibodies data Protein Data Bank: 6xdg Structure of SARS-CoV-2 XBB.1 spike glycoprotein in complex with ACE2 (1-up state) data Protein Data Bank: 8iou Deep mutational scanning of SARS-CoV-2 XBB.1.5 spike using a barcoded lentiviral platform data Supplementary Data Mass photometry analysis of Spike:ACE2 binding code Github SARS-CoV-2_XBB.1.5_RBD_DMS code Github Pipeline for analysing deep mutational scanning (DMS) of viral entry proteins (VEPs) code Github SARS-CoV-2_Omicron_BA.2_spike_ACE2_binding code Github SARS-CoV-2_XBB.1.5_spike_DMS code Github SARS-CoV-2_XBB.1.5_spike_DMS: SARS-CoV-2_XBB.1.5_spike_DMS-paper data Zenodo
COVID-19 knowledge and practices in Jigawa State, Nigeria: A cross-sectional survey conducted during the second wave Salako J., Bakare D., Sogbesan A., Colbourn T., et al (2024) Public Library of Science (PLoS) DOI: https://doi.org/10.1371/journal.pgph.0003386	COVID-19 knowledge, and associations with good knowledge of prevention, symptoms 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
Modulation of innate immune response to mRNA vaccination after SARS-CoV-2 infection or sequential vaccination in humans Hellgren F., Rosdahl A., Arcoverde Cerveira R., Lenart K., et al (2024) American Society for Clinical Investigation DOI: 10.1172/jci.insight.175401	Request access for metadata for the 30 study participants recruited among health-care workers at the University hospital of Örebro, Sweden. data Figshare Data points for figures, mostly comprising of serological measures (e.g. levels of B-cells) following different vaccination routines or infection experience (excludes RNASeq data). data Code for bioinformatic analysis with RNASeq analyses (primarily in R). code GitHub
Magnitude and determinants of excess total, age-specific and sex-specific all-cause mortality in 24 countries worldwide during 2020 and 2021: results on the impact of the COVID-19 pandemic from the C-MOR project Pallari C. T., Achilleos S., Quattrocchi A., Gabel J., et al (2024) BMJ DOI: 10.1136/bmjgh-2023-013018	Mortality data from 24 countries. The data includes total mortality, and sex-specific and age-specific weekly all-cause mortality for 2015–2021. data Zenodo Code used to analyse mortality data from 24 countries. code Zenodo
Proteome profiling of home-sampled dried blood spots reveals proteins of SARS-CoV-2 infections Fredolini C., Dodig-Crnković T., Bendes A., Dahl L., et al (2024) Springer Science and Business Media LLC DOI: 10.1038/s43856-024-00480-4	Protein levels obtained from dried blood spot (DBS) samples. data Figshare Data from multiplexed serology assays to determine IgG and IgM levels against several versions of SARS-CoV-2 proteins. Samples obtained from dried blood spots (DBS). data Figshare Code for the analysis and visualisation of proteome data from home-sampled dried blood spots. code GitHub
Social support predicted subsequent subjective well-being during the COVID-19 pandemic: a prospective study Mao Y., Chen J., Liu X., Dang J., et al (2024) Springer Science and Business Media LLC DOI: 10.1186/s12889-024-18473-2	Data on social support, affect balance, life satisfaction, demographics, and personality measures. data Open Science Framework
Synthetic coevolution reveals adaptive mutational trajectories of neutralizing antibodies and SARS-CoV-2 Ehling R. A., Minot M., Overath M. D., Sheward D. J., et al (2024) Cold Spring Harbor Laboratory DOI: 10.1101/2024.03.28.587189	A protein language machine learning model that predicts antibody escape to receptor binding domain variants. code GitHub
New in Town—An internet-based self-efficacy intervention for internal migrants: A randomized controlled trial Maj A., Matynia M., Michalak N., Bis A., et al (2024) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0299638	Survey data on macro-cultural dimensions, including collectivism/individualism, duty/joy, autonomy/traditionalism, and pro-fertility/individual choice norms, as well as perceived societal threats (immigration and subsistence factors) and hygiene norms of spitting. Data from 43 counties during the first 2 waves of COVID-19. data Dropbox Analysis code for survey data on macro-cultural dimensions and perceived societal threats in 43 countries during the first 2 waves of COVID-19. code Dropbox
COVID-19 pandemic waves: Identification and interpretation of global data Bali Swain R., Lin X., Wallentin F. Y. (2024) Elsevier BV DOI: 10.1016/j.heliyon.2024.e25090	Aggregated data on the COVID-19 pandemic from around the world. This repository is operated by the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE) (data available until March 2023). data GitHub
Changes in social norms during the early stages of the COVID-19 pandemic across 43 countries Andrighetto G., Szekely A., Guido A., Gelfand M., et al (2024) Springer Science and Business Media LLC DOI: 10.1038/s41467-024-44999-5	Data exploring the tightness-looseness of communities, alongside demographic and COVID-19 data. Data primarily at country level. data Open Science Framework: stkfr Analysis code exploring the tightness-looseness of communities during COVID-19 (R script). code Open Science Framework: stkfr
Assessing the effects of pandemic risk on cooperation and social norms using a before-after Covid-19 comparison in two long-term experiments Vriens E., Szekely A., Lipari F., Antonioni A., et al (2024) Springer Science and Business Media LLC DOI: 10.1038/s41598-024-53427-z	Data exploring how social norms were affected during two waves of the COVID-19 pandemic. Data available for the same population in 2 waves. data Open Science Framework: xb8a7
Evidence of COVID-19 fatalities in Swedish neighborhoods from a full population study Wixe S., Lobo J., Mellander C., Bettencourt L. M. A. (2024) Springer Science and Business Media LLC DOI: 10.1038/s41598-024-52988-3	Anonymised register data, specifically microdata on individuals or enterprises. Available after approvals from SCB. data GitHub Anonymised register data from Sweden. Available after ethical approvals from Socialstyrelsen. data GitHub
Global Transcriptomic Analysis of Placentas from Women with Gestational SARS-CoV-2 Infection during the Third Trimester of Pregnancy Tang Y., Boggavarapu N. R., Aronsson A., Gemzell-Danielsson K., et al (2024) MDPI AG DOI: 10.3390/ijms25031608	Transcriptomic analysis of the placenta in both maternal and fetal compartments was performed to investigate the impact of maternal SARS-CoV-2 infection. data Gene Expression Omnibus: GSE233557
Impact of the gut microbiome on immunological responses to COVID-19 vaccination in healthy controls and people living with HIV Ray S., Narayanan A., Vesterbacka J., Blennow O., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41522-023-00461-w	Immunological Responses after Vaccination for COVID-19 with the mRNA Vaccine Comirnaty in Immunosuppressed and Immunocompetent Individuals. An open, non-randomized , phase IV multicenter study data EU Clinical Trials Register All codes used for analysis are available in R markdown format. code GitHub
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
Early detection of the emerging SARS-CoV-2 BA.2.86 lineage through integrated genomic surveillance of wastewater and COVID-19 cases in Sweden, weeks 31 to 38 2023 Espinosa-Gongora C., Berg C., Rehn M., Varg J. E., et al (2023) European Centre for Disease Control and Prevention (ECDC) DOI: 10.2807/1560-7917.es.2023.28.46.2300595	Whole genome sequence data from individuals for all Swedish BA.2.86 cases is available on GISAID. The accession numbers are avilable in the supplementary materials (linked here). data GISAID The findings of the BA.2.86 marker specificity assessment are based on metadata associated with 13,513 sequences available on GISAID from 1 July to 19 October 2023. data GISAID Wastewater raw reads from Uppsala, Örebro, Umeå, and Kalmar. data ENA: PRJEB67638
Early mobilisation in critically ill COVID-19 patients: a subanalysis of the ESICM-initiated UNITE-COVID observational study Kloss P., Lindholz M., Milnik A., Azoulay E., et al (2023) Springer Science and Business Media LLC DOI: 10.1186/s13613-023-01201-1	Data curation pipeline for patient data extracted for medical records up to 60th day of ICU stay (written in R, Version v3.0.1 used). code Zenodo Data dictionaries associated with data curation pipeline used. data Zenodo
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
Systematic review of seroprevalence of SARS-CoV-2 antibodies and appraisal of evidence, prior to the widespread introduction of vaccine programmes in the WHO European Region, January–December 2020 Vaughan A., Duffell E., Freidl G. S., Lemos D. S., et al (2023) BMJ DOI: 10.1136/bmjopen-2022-064240	A collection of serology data created by WHO Unity Studies Global SARS-CoV2 Seroepidemiological Investigations. Includes both data published in studies and other data not used in publications. data Zenodo
Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections Sounart H., Lázár E., Masarapu Y., Wu J., et al (2023) Springer Science and Business Media LLC DOI: 10.1186/s13059-023-03080-y	Raw sequence data are available under contrlled ccess due to the sensitive nature of the data. data European Genome-Phenome Archive (EGA): EGAS00001006186 Raw sequence data are available under contrlled ccess due to the sensitive nature of the data. data European Genome-Phenome Archive (EGA): EGAC00001002635 Processed gene count matrices, related metadata, corresponding ST tissue microscopy images, and RNAScope images used in the Validation analysis. data Mendeley Dataset ISS images for SARS-CoV-2 S and E genes. data Mendeley Dataset RNAscope images for the SARS-CoV-2 S gene for sample 1C. data FigShare RNAscope images for the SARS-CoV-2 S gene for sample 2C. data FigShare RNAscope images for the SARS-CoV-2 S gene for sample 3C. data FigShare RNAscope images for the SARS-CoV-2 S gene for sample 4nC. data FigShare RNAscope images for the SARS-CoV-2 S gene for sample 5nC. data FigShare Deconvolution results as an R object data FigShare All RNAScope images for the SARS-CoV-2 S gene probe, positive control probe, and negative control probe. data Zenodo Scripts to generate the count matrices and all related R scripts used in the clustering, differential expression, colocalization analysis, and the program for the computational validation. code Github Scripts to generate the count matrices and all related R scripts used in the clustering, differential expression, colocalization analysis, and the program for the computational validation. code Zenodo
Design, structure and plasma binding of ancestral β-CoV scaffold antigens Hueting D., Schriever K., Sun R., Vlachiotis S., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41467-023-42200-x	Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein (map). data Electron Microscopy Data Bank: EMD-15475 Structure of the Ancestral Scaffold Antigen-6 of Coronavirus Spike protein (map). data Electron Microscopy Data Bank: EMD-15482 Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein (atomic coordinates). data Protein Data Bank: 8AJA Structure of the Ancestral Scaffold Antigen-6 of Coronavirus Spike protein (atomic coordinates). data Protein Data Bank: 8AJL
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
De novo design of anti-variant COVID-19 vaccine Goswami A., Kumar M., Ullah S., Gore M. M. (2023) Oxford University Press (OUP) DOI: 10.1093/biomethods/bpad021	The designed vaccine structure for Vacdeltm. data Protein Model Database: PM0084589 The designed vaccine structure for VacFL. data Protein Model Database: PM0084590
Comprehensive proteomics and meta-analysis of COVID-19 host response Babačić H., Christ W., Araújo J. E., Mermelekas G., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41467-023-41159-z	Results of the meta-analysis are available in a Shiny app. data In-depth serum proteomics of hospitalized COVID-19 patients and PCR-negative healthy controls with HiRIEF LC-MS/MS data ProteomeXchange: PXD037486 Mass-spectrometry proteomics of Calu-3 cell lines infected with SARS-CoV-2, in comparison to non-infected and UV mock-treated cell lines data ProteomeXchange: PXD037451 Mass-spectrometry phosphoproteomics of Calu-3 cell lines infected with SARS-CoV-2, in comparison to non-infected and UV mock-treated cell lines data ProteomeXchange: PXD040982 Custom code for the Nextflow proteomics workflow code GitHub R code used for analyses 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
Identification of essential genes associated with SARS-CoV-2 infection as potential drug target candidates with machine learning algorithms Taheri G., Habibi M. (2023) Springer Science and Business Media LLC DOI: 10.1038/s41598-023-42127-9	Unsupervised learning methods to Identify essential genes associated with SARS-CoV-2 data GitHub Unsupervised learning methods to Identify essential genes associated with SARS-CoV-2 code GitHub
Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets Mihalič F., Benz C., Kassa E., Lindqvist R., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41467-023-41312-8	Library designs including the proteins, peptides and statistics data
Optimal age-specific vaccination control for COVID-19: An Irish case study Zavrakli E., Parnell A., Malone D., Duffy K., et al (2023) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0290974	All vaccination data are available on Ireland's COVID-19 Data Hub data Code to simulate the evolution of the COVID-19 pandemic with and without optimal vaccination. 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
Reducing intrusive memories after trauma via an imagery-competing task intervention in COVID-19 intensive care staff: a randomised controlled trial Iyadurai L., Highfield J., Kanstrup M., Markham A., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41398-023-02578-0	Anonymised data, dictionary, analytical code, study protocol and frequentist statistical analysis plan data Open Science Framework Anonymised data, dictionary, analytical code, study protocol and frequentist statistical analysis plan code Open Science Framework
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
Cost Effectiveness of Strategies for Caring for Critically Ill Patients with COVID-19 in Tanzania Shah H. A., Baker T., Schell C. O., Kuwawenaruwa A., et al (2023) Springer Science and Business Media LLC DOI: 10.1007/s41669-023-00418-x	POETIC-COVID CEA PROJECT - R code that supports the findings of the study 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
Treating intrusive memories after trauma in healthcare workers: a Bayesian adaptive randomised trial developing an imagery-competing task intervention Ramineni V., Millroth P., Iyadurai L., Jaki T., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41380-023-02062-7	Anonymised databases with the individual participant data and the metadata for Bayesian analyses, along with a data dictionary data Open Science Framework The Study Protocol and Bayesian Statistical Analysis Plan protocol Open Science Framework
Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization Koskela von Sydow A., Lindqvist C. M., Asghar N., Johansson M., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41598-023-33168-1	Nucleotide sequence are available as assembled FASTA consensus sequences at GenBank. Accession-ID: OP585690-OP585783 data GenBank
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
Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses Pushparaj P., Nicoletto A., Castro Dopico X., Sheward D. J., et al (2023) Frontiers Media SA DOI: 10.3389/fviro.2023.1128253	The HC sequences of CAB-F52 anti-SARS-CoV-2 immunoglobulin heavy chain variable region mRNA data GenBank: ON086926 The LC sequences of CAB-F52 anti-SARS-CoV-2 immunoglobulin heavy chain variable region mRNA data GenBank: ON086941 The hydrogen–deuterium exchange mass spectrometry data data ProteomeXchange: PXD031945
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
Visiting Urban Green Space and Orientation to Nature Is Associated with Better Wellbeing during COVID-19 Lin B. B., Chang C., Andersson E., Astell-Burt T., et al (2023) MDPI AG DOI: 10.3390/ijerph20043559	Codes for analysis code Figshare
The Psychological Science Accelerator’s COVID-19 rapid-response dataset Buchanan E. M., Lewis S. C., Paris B., Forscher P. S., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41597-022-01811-7	Data used in the Shiny app for The Psychological Science Accelerator's COVID-19 Rapid-Response Project data Open Science Framework Code for the Shiny app for The Psychological Science Accelerator's COVID-19 Rapid-Response Project code Open Science Framework
Nowcasting COVID-19 Statistics Reported with Delay: A Case-Study of Sweden and the UK Altmejd A., Rocklöv J., Wallin J. (2023) MDPI AG DOI: 10.3390/ijerph20043040	Data related to development of a statistical methodology for predicting true daily quantities and their uncertainty, estimated using historical reporting delays data GitHub R code related to development of a statistical methodology for predicting true daily quantities and their uncertainty, estimated using historical reporting delays code GitHub
Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development Islam M. A., Shahi S., Marzan A. A., Amin M. R., et al (2023) Frontiers Media SA DOI: 10.3389/fphar.2023.1090717	Supplementary material including information on proteomics, mutations, T-cell epitope prediction, and much more, including accession numbers for other open data sources data
COVID-19 infection does not seem to affect cognition in college students Francis G., Thunell E. (2023) Elsevier BV DOI: 10.1016/j.concog.2023.103464	Students survey data on COVID-19 status data Open Science Framework
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
Association between long-term air pollution exposure and COVID-19 mortality in Latin America Bonilla J. A., Lopez-Feldman A., Pereda P. C., Rivera N. M., et al (2023) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0280355	Aggregated data of COVID-19 mortality and long-term air pollution concentrations data Github Stata scripts used to compile the statitics code Github
Financial incentives for vaccination do not have negative unintended consequences Schneider F. H., Campos-Mercade P., Meier S., Pope D., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41586-022-05512-4	Randomised controlled trial data from Sweden and United States for COVID-19 first dose vaccination data Zenodo Analyses were conducted using STATA 16, the code to replicate the analysis is in the article code Zenodo
Persistence of salivary antibody responses after COVID-19 vaccination is associated with oral microbiome variation in both healthy and people living with HIV Ghorbani M., Al-Manei K., Naud S., Healy K., et al (2023) Frontiers Media SA DOI: 10.3389/fimmu.2022.1079995	All genomic datasets from this project are available as part of an NCBI BioProject data NCBI: PRJNA900274
Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies Pushparaj P., Nicoletto A., Sheward D. J., Das H., et al (2023) Elsevier BV DOI: 10.1016/j.immuni.2022.12.005	Individualised IGHV Genotype Sequences of 14 SARS-CoV-2 Convalescent Donors data Figshare Mass spectrometry raw files and HDX analysis data ProteomeXchange SARS Cov2 Spike in 1-up conformation complex with Fab47 data PDB: 8A99 SARS CoV2 Spike in the 2-up state in complex with Fab47 data PDB: 8A94 SARS Cov2 Spike RBD in complex with Fab47 data PDB: 8A96 SARS Cov2 Spike in 1-up conformation complex with Fab47 data Electron Microscopy Data Bank: EMD-15273 SARS CoV2 Spike in the 2-up state in complex with Fab47 data Electron Microscopy Data Bank: EMD-15269 SARS Cov2 Spike RBD in complex with Fab47 data Electron Microscopy Data Bank: EMD-15271 Supplemental data, including Cryo-EM models data Mendeley
Familydemic Cross Country and Gender Dataset on work and family outcomes during COVID-19 pandemic Kurowska A., Barardehi I. H., Fuller S., Petts R. J., et al (2023) Springer Science and Business Media LLC DOI: 10.1038/s41597-022-01880-8	Familydemic survey data related to the work and family nexus data Open Science Framework
Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level Zhu R., Canena D., Sikora M., Klausberger M., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41467-022-35641-3	Models of SARS-CoV-2 virus spike protein bound to 1-3 of ACE2 receptors embedded in lipid nanodisks. data Zenodo Code for simulation of high speed AFM imaging. code GitHub
Preparing medical first responders for crises: a systematic literature review of disaster training programs and their effectiveness Baetzner A. S., Wespi R., Hill Y., Gyllencreutz L., et al (2022) Springer Science and Business Media LLC DOI: 10.1186/s13049-022-01056-8	Literature review data realted to disaster training programs for medical first responders. 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
Bayesian nowcasting with leading indicators applied to COVID-19 fatalities in Sweden Bergström F., Günther F., Höhle M., Britton T. (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pcbi.1010767	Analysis scripts R code GitHub COVID-19 surveillance data data GitHub
Perceived Corona virus exposure as a function of interpersonal distance and time of a conversation Svenson O. (2022) Springer Science and Business Media LLC DOI: 10.1007/s44155-022-00027-9	Results of a Qualatrics questionnaire related to perceived risk of viral infection with different social distances. data FigShare
Monitoring real-time transmission heterogeneity from incidence data Zhang Y., Britton T., Zhou X. (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pcbi.1010078	Incidence data on which the model is based. data GitHub Code for instant-individual heterogeneity model to estimate real-time transmission heterogeneity from incidence data. code GitHub
The influence of COVID-19 risk perception and vaccination status on the number of social contacts across Europe: insights from the CoMix study Wambua J., Loedy N., Jarvis C. I., Wong K. L., et al (2022) Cold Spring Harbor Laboratory DOI: 10.1101/2022.11.25.22282676	Results of a multi-country longitudinal social contact survey exploring the influence of COVID-19 vaccination status and risk perceptions related to SARS-CoV-2 on social contact. data Zenodo
Cross-protection against African swine fever virus upon intranasal vaccination is associated with an adaptive-innate immune crosstalk Bosch-Camós L., Alonso U., Esteve-Codina A., Chang C., et al (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.ppat.1010931	Raw sequencing data data Gene Expression Omnibus: GSE196472 Processed sequencing data data Gene Expression Omnibus: GSE196473
Impact of the COVID-19 pandemic on early career dementia researchers: A global online survey Bartels S. L., Shaaban C. E., Brum W. S., Welikovitch L. A., et al (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0277470	Survey data from 321 early career dementia researchers, including relevant socialdemographic characteristics data Open Science Framework
Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative Butler-Laporte G., Povysil G., Kosmicki J. A., Cirulli E. T., et al (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pgen.1010367	Single variant association studies summary statistics data GWAS Catalog: GCST90132193 Single variant association studies summary statistics data GWAS Catalog: GCST90132194 Single variant association studies summary statistics data GWAS Catalog: GCST90132195 Analysis scripts code GitHub
Acute anxiety during the COVID-19 pandemic was associated with higher levels of everyday altruism Vieira J. B., Pierzchajlo S., Jangard S., Marsh A. A., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41598-022-23415-2	All survey data and study material used in this project data Open Science Framework code Open Science Framework: Code used for analysis
Family still matters: Human social motivation across 42 countries during a global pandemic Pick C. M., Ko A., Wormley A. S., Wiezel A., et al (2022) Elsevier BV DOI: 10.1016/j.evolhumbehav.2022.09.003	Data related to social motivation data Open Science Framework
Development and cross-national investigation of a model explaining participation in WHO-recommended and placebo behaviours to prevent COVID-19 infection Kłosowska J., Bajcar E. A., Bieniek H., Brączyk J., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41598-022-17303-y	Processed and anonymised demographic and health data. data Open Science Framework
A Mendelian randomization study of genetic predisposition to autoimmune diseases and COVID-19 Li S., Yuan S., Schooling C. M., Larsson S. C. (2022) Springer Science and Business Media LLC DOI: 10.1038/s41598-022-22711-1	Exposure dataset for type 1 diabetes mellitus data MR-base: ebi-a-GCST005536 Exposure dataset for systemic lupus erythematosus data MR-base: ebi-a-GCST003156 Exposure dataset for psoriasis data MR-base: ebi-a-GCST005527 Exposure dataset for multiple sclerosis data MR-base: ieu-b-18 Exposure dataset for primary sclerosing cholangitis data MR-base: ieu-a-1112 Exposure dataset for primary biliary cirrhosis data MR-base: ebi-a-GCST005581 Outcome datasets generated in the current study. data COVID19-hg GWAS
Variations in vaccination uptake: COVID-19 vaccination rates in Swedish municipalities Larsson E. C., Wittberg E., Lundåsen S. W. (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pgph.0001204	Municipal-level vaccination data compiled from several publicly available data sources data Zenodo
A meta-epidemiological assessment of transparency indicators of infectious disease models Zavalis E. A., Ioannidis J. P. A. (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0275380	The protocol for this study protocol Open Science Framework Data used to evaluate publications and model types, and the code used for analysis. code GitHub
Treating intrusive memories after trauma in healthcare workers: a Bayesian adaptive randomised trial developing an imagery-competing task intervention Ramineni V., Millroth P., Iyadurai L., Jaki T., et al (2022) Cold Spring Harbor Laboratory DOI: 10.1101/2022.10.06.22280777	Anonymised databases with the individual participant data and the metadata for Bayesian analyses. data Open Science Framework Code used for data analysis. code Open Science Framework
SARS-CoV-2 promotes microglial synapse elimination in human brain organoids Samudyata S., Oliveira A. O., Malwade S., Rufino de Sousa N., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41380-022-01786-2	Source code to reproduce the findings code GitHub
Changes in non-communicable diseases, diet and exercise in a rural Bangladesh setting before and after the first wave of COVID-19 King C., Shaha S. K., Morrison J., Ahmed N., et al (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pgph.0001110	Fully anonymised data from two cross-sectional surveys data FigShare
Collectivism reduces objective mobility trends to public areas during the COVID-19 pandemic Dang J., Xiao S. (2022) Frontiers Media SA DOI: 10.3389/fpubh.2022.996036	Data for collectivism and mobility data Open Science Framework
Forecasting the publication and citation outcomes of COVID-19 preprints Gordon M., Bishop M., Chen Y., Dreber A., et al (2022) The Royal Society DOI: 10.1098/rsos.220440	Survey responses collected through Qualtrix data dryad Code used for analysis (in R) code dryad
Immunodeficiency syndromes differentially impact the functional profile of SARS-CoV-2-specific T cells elicited by mRNA vaccination Gao Y., Cai C., Wullimann D., Niessl J., et al (2022) Elsevier BV DOI: 10.1016/j.immuni.2022.07.005	Processed scRNA-seq data data ArrayExpress: E-MTAB-11845
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
Spatio-temporal predictions of COVID-19 test positivity in Uppsala County, Sweden: a comparative approach van Zoest V., Varotsis G., Menzel U., Wigren A., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41598-022-19155-y	Data on direct and indirect indicators of transmission e.g. mobility data, number of calls to the national healthcare advice line and vaccination coverage. data GitHub Code used to produce models. code GitHub
A universal SARS‐CoV DNA vaccine inducing highly cross‐reactive neutralizing antibodies and T cells Appelberg S., Ahlén G., Yan J., Nikouyan N., et al (2022) EMBO DOI: 10.15252/emmm.202215821	Raw time series data related to vaccine efficacy, blood testing, and histology. data
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
Over half of known human pathogenic diseases can be aggravated by climate change Mora C., McKenzie T., Gaw I. M., Dean J. M., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41558-022-01426-1	All data collected as part of the literature search (list of considered diseases, and references for empirical cases. data GitHub
Whole blood DNA methylation analysis reveals respiratory environmental traits involved in COVID-19 severity following SARS-CoV-2 infection Barturen G., Carnero-Montoro E., Martínez-Bueno M., Rojo-Rello S., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41467-022-32357-2	Genotype data generated (SPGRX cohort) data EGA: EGAS00001005304 Methylation data data Gene Expression Omnibus: GSE179325
Genome-wide spatial expression profiling in formalin-fixed tissues Gracia Villacampa E., Larsson L., Mirzazadeh R., Kvastad L., et al (2022) Elsevier BV DOI: 10.1016/j.xgen.2021.100065	Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues data Gene Expression Omnibus: GSE185715 Processed genome-wide spatial expression profiling data data Mendeley FFPE mouse brain spatial transcriptomics data explorer app code GitHub Original analysis code code Mendeley
Dynamically upregulated mast cell CPA3 patterns in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis Siddhuraj P., Jönsson J., Alyamani M., Prabhala P., et al (2022) Frontiers Media SA DOI: 10.3389/fimmu.2022.924244	Expression profiling by high throughput sequencing data Gene Expression Omnibus: GSE201772
The order of events on Avian coronavirus life cycle shapes the order of quasispecies evolution during host switches Brandão P. E., Berg M., Leite B. A., Silva S. O., et al (2022) FapUNIFESP (SciELO) DOI: 10.1590/1678-4685-gmb-2022-0034	Beaudette genome sequencing and assembly data BioProject: PRJNA736341 Avian coronavirus strain Beaudette, complete genome. data ENA: MZ368698
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 screening and evaluation of potential clinically significant HIV drug combinations against the SARS-CoV-2 virus Tomić D., Davidović D., Szasz A. M., Rezeli M., et al (2022) Elsevier BV DOI: 10.1016/j.imu.2021.100529	Results of the efficacy of FDA approved antiviral drugs on SARS-CoV-2 spike glycoprotein. data The Vini in silico model of cancer. code GitHub
Shared genetic etiology between idiopathic pulmonary fibrosis and COVID-19 severity Fadista J., Kraven L. M., Karjalainen J., Andrews S. J., et al (2022) Elsevier BV DOI: 10.1016/j.ebiom.2021.103277	Data on collaborative genetic studies of idiopathic pulmonary fibrosis. data GitHub COVID19-hg GWAS meta-analyses data. data
The effect of herd immunity thresholds on willingness to vaccinate Andersson P. A., Tinghög G., Västfjäll D. (2022) Springer Science and Business Media LLC DOI: 10.1057/s41599-022-01257-7	Data related to herd immunity, willingness to get vaccinated, and demographic factors. data Open Science Framework
Type I Interferons Promote Germinal Centers Through B Cell Intrinsic Signaling and Dendritic Cell Dependent Th1 and Tfh Cell Lineages Dahlgren M. W., Plumb A. W., Niss K., Lahl K., et al (2022) Frontiers Media SA DOI: 10.3389/fimmu.2022.932388	Expression profiling by high throughput sequencing data Gene Expression Omnibus: GSE201551
Serine Protease Inhibitors Restrict Host Susceptibility to SARS-CoV-2 Infections Rosendal E., Mihai I. S., Becker M., Das D., et al (2022) American Society for Microbiology DOI: 10.1128/mbio.00892-22	Bulk and single-cell RNA-Seq gene counts data ArrayExpress: E-MTAB-10687 R and Python code used for analysis code GitHub
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
A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process Noske G., Nakamura A., Gawriljuk V., Fernandes R., et al (2022) Elsevier BV DOI: 10.1016/j.jmb.2021.167118	7KFI SARS-CoV-2 Main protease immature form - apo structure data Protein Data Bank: 7KFI 7MBG SARS-CoV-2 Main protease in orthorhombic space group data Protein Data Bank: 7MBG 7KPH SARS-CoV-2 Main Protease in mature form data Protein Data Bank: 7KPH 7N6N SARS-CoV-2 Main protease C145S mutant in complex with N and C-terminal residues data Protein Data Bank: 7N6N 7LFE SARS-CoV-2 Main protease immature form - F2X Entry Library E03 fragment data Protein Data Bank: 7LFE 7LDX SARS-CoV-2 Main protease immature form - F2X Entry Library E06 fragment data Protein Data Bank: 7LDX 7LFP SARS-CoV-2 Main protease immature form - F2X Entry Library G05 fragment data Protein Data Bank: 7LFP 7KVL SARS-CoV-2 Main protease immature form - FMAX Library E01 fragment data Protein Data Bank: 7KVL 7N5Z SARS-CoV-2 Main protease C145S mutant data Protein Data Bank: 7N5Z 7KVR SARS-CoV-2 Main protease immature form - FMAX Library E09 fragment data Protein Data Bank: 7KVR
Agile software development one year into the COVID-19 pandemic Ågren P., Knoph E., Berntsson Svensson R. (2022) Springer Science and Business Media LLC DOI: 10.1007/s10664-022-10176-9	R code for Bayesian analysis code Zenodo
Dataset: COVID-19 epidemic policy and events timeline (Sweden) Olofsson T., Vilhelmsson A. (2022) Elsevier BV DOI: 10.1016/j.dib.2021.107698	Chronological data on Swedish Governmental COVID-19 policy/actions protocol Zenodo
Epidemic risk perceptions in Italy and Sweden driven by authority responses to COVID-19 Raffetti E., Mondino E., Di Baldassarre G. (2022) Springer Science and Business Media LLC DOI: 10.1038/s41598-022-13218-w	A comparative dataset on public perceptions of multiple risks during the COVID-19 pandemic in Italy and Sweden. data Zenodo Code for processing and visualisations code GitHub
Occurrence and transmission potential of asymptomatic and presymptomatic SARS-CoV-2 infections: Update of a living systematic review and meta-analysis Buitrago-Garcia D., Ipekci A. M., Heron L., Imeri H., et al (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pmed.1003987	Data from the systematic review on asymptomatic and presymptomatic SARS-CoV-2 infection data GitHub Code used to display and synthesise the results code GitHub
Myeloid cell‐specific topoisomerase 1 inhibition using DNA origami mitigates neuroinflammation Zhu K., Wang Y., Sarlus H., Geng K., et al (2022) EMBO DOI: 10.15252/embr.202154499	RNA-seq results data ArrayExpress: E‐MTAB‐10679
The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages Martin D. P., Weaver S., Tegally H., San J. E., et al (2022) Elsevier BV DOI: 10.1016/j.cell.2021.09.003	Initial release of SARS-CoV2 variation data data Zenodo Visualising selection analysis results for evolution of the B.1.351 clade data code Frequency trends and selection detection of subsets of sites in SARS-CoV-2 genes data code Temporal evolution of selective pressures on SARS-CoV-2 genes data code Collection of result files and underlying sequence alignments processed by the RASCL SARS-CoV-2 clade analysis pipeline code GitHub
A high-risk gut microbiota configuration associates with fatal hyperinflammatory immune and metabolic responses to SARS-CoV-2 Albrich W. C., Ghosh T. S., Ahearn-Ford S., Mikaeloff F., et al (2022) Informa UK Limited DOI: 10.1080/19490976.2022.2073131	Sequence data data ENA: PRJEB50040 Metabolite data data FigShare
Heterologous immunisation with inactivated vaccine followed by mRNA-booster elicits strong immunity against SARS-CoV-2 Omicron variant Zuo F., Abolhassani H., Du L., Piralla A., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41467-022-30340-5	Data on the effect of an mRNA vaccine booster on immunogenicity in individuals vaccinated with two doses of inactivated vaccine. data Zenodo
Characterization of the Upper Respiratory Bacterial Microbiome in Critically Ill COVID-19 Patients Bai X., Narayanan A., Skagerberg M., Ceña-Diez R., et al (2022) MDPI AG DOI: 10.3390/biomedicines10050982	Raw shotgun metagenome sequencing data data BioProject: PRJNA781460
Impact of Long COVID on health and quality of life O’ Mahony L., Buwalda T., Blair M., Forde B., et al (2022) F1000 Research Ltd DOI: 10.12688/hrbopenres.13516.1	Long COVID Survey Data data FigShare Long COVID Survey questionnaire data FigShare
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
Meteorological factors and non-pharmaceutical interventions explain local differences in the spread of SARS-CoV-2 in Austria Ledebur K., Kaleta M., Chen J., Lindner S. D., et al (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pcbi.1009973	Data time series of metereological factors, regional measures and mobility data Zenodo Scripts for the model 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
Structural and biochemical characterization of in vivo assembled Lactococcus lactis CRISPR-Csm complex Sridhara S., Rai J., Whyms C., Goswami H., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s42003-022-03187-1	Structure of the lactococcus lactis csm ctr_4:3 crispr-cas complex data PDB: 6XN3 Structure of the lactococcus lactis csm apo- crispr-cas complex data PDB: 6XN5 Structure of the lactococcus lactis csm ctr_3:2 crispr-cas complex data PDB: 6XN4 structure of the lactococcus lactis csm ntr crispr-cas complex data PDB: 6XN7
Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies Hanke L., Sheward D. J., Pankow A., Vidakovics L. P., et al (2022) American Association for the Advancement of Science (AAAS) DOI: 10.1126/sciadv.abm0220	NGS data data BioProject: PRJNA814713 Implementation of the seqUMAP algorithm code GitHub Codes for processing NGS nanobody code GitHub
Improved prediction of protein-protein interactions using AlphaFold2 Bryant P., Pozzati G., Elofsson A. (2022) Springer Science and Business Media LLC DOI: 10.1038/s41467-022-28865-w	Raw data and predicted PDB files data FigShare: 16866202.v1
Network Crosstalk as a Basis for Drug Repurposing Guala D., Sonnhammer E. L. L. (2022) Frontiers Media SA DOI: 10.3389/fgene.2022.792090	Dataset used to to assess cross-talk based approaches for drug repurposing code BitBucket Code used for analysis data BitBucket
The required size of cluster randomized trials of nonpharmaceutical interventions in epidemic settings Sheen J. K., Haushofer J., Metcalf C. J. E., Kennedy‐Shaffer L. (2022) Wiley DOI: 10.1002/sim.9365	Code and simulated data code GitHub
Molecular mechanism of inhibiting the SARS-CoV-2 cell entry facilitator TMPRSS2 with camostat and nafamostat Hempel T., Raich L., Olsson S., Azouz N. P., et al (2022) Royal Society of Chemistry (RSC) DOI: 10.1039/d0sc05064d	Structural ensembles of camostat, GBPA, and nafamostat code GitHub
Nanoscale binding site localization by molecular distance estimation on native cell surfaces using topological image averaging Kumra Ahnlide V., Kumra Ahnlide J., Wrighton S., Beech J. P., et al (2022) eLife Sciences Publications, Ltd DOI: 10.7554/elife.64709	SiteLocalization software for binding site localisation on non-homogeneous cell surfaces using topological image averaging code GitHub FluoroDist.jl - software for simulated fluorescence images with accurate surface distances code GitHub Site localisation measurements data data Dryad
Changes in Physical Activity and Sedentary Behavior before and during the COVID-19 Pandemic: A Swedish Population Study Elvén M., Kerstis B., Stier J., Hellström C., et al (2022) MDPI AG DOI: 10.3390/ijerph19052558	Dataset including variables of physical activity and sedentary behavior during the COVID-19 pandemic data FigShare
The major genetic risk factor for severe COVID-19 is associated with protection against HIV Zeberg H. (2022) Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.2116435119	Reference single nucleotide polymorphism report data dbSNP: RS17713054 Reference single nucleotide polymorphism report data dbSNP: RS17764980 Reference single nucleotide polymorphism report data dbSNP: RS17714101 Reference single nucleotide polymorphism report data dbSNP: RS17714228 Reference single nucleotide polymorphism report data dbSNP: RS71325092
Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses Luttens A., Gullberg H., Abdurakhmanov E., Vo D. D., et al (2022) American Chemical Society (ACS) DOI: 10.1021/jacs.1c08402	Information on methods, data on chemical structures and assay data data Figshare
An in silico analysis identifies drugs potentially modulating the cytokine storm triggered by SARS-CoV-2 infection Sanchez-Burgos L., Gómez-López G., Al-Shahrour F., Fernandez-Capetillo O. (2022) Springer Science and Business Media LLC DOI: 10.1038/s41598-022-05597-x	Expression profiling by array data Gene Expression Omnibus: GSE63229 Genome binding/occupancy profiling by high throughput sequencing data Gene Expression Omnibus: GSE123574
SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display Ehling R. A., Weber C. R., Mason D. M., Friedensohn S., et al (2022) Elsevier BV DOI: 10.1016/j.celrep.2021.110242	Patient VDJ data, raw FASTQ files data Enriched hybridoma NGS, raw FASTQ files data Code for analysis 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
A proteomic survival predictor for COVID-19 patients in intensive care Demichev V., Tober-Lau P., Nazarenko T., Lemke O., et al (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pdig.0000007	Protein quantities table along with the associated metadata data Input proteomics data for training machine learning models data Scripts training machine learning models code Mass spectrometry proteomics data used for survival analysis data ProteomeXchange Consortium: PXD029009
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
Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19 Huffman J. E., Butler-Laporte G., Khan A., Pairo-Castineira E., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41588-021-00996-8	COVID-19 summary statistics for individuals of African ancestry. data CADD-scores v.1.6. data Combined Annotation Dependent Depletion Genomes from the 1000 Genomes Project. data Fine-mapping association summary statistics produced in this study. data Zenodo Code used for the fine-mapping analysis. code Zenodo
Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19 Huffman J. E., Butler-Laporte G., Khan A., Pairo-Castineira E., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41588-021-00996-8	COVID-19 summary statistics for individuals of African ancestry data CADD-scores v.1.6. data Genomes from 1000 Genomes project data Summary data for OAS1/2/3 multi-ancestry fine mapping data Zenodo Source data for LD in OAS1/2/3 region data Code for fine mapping code
Swedish nationwide time series analysis of influenza and suicide deaths from 1910 to 1978 Rück C., Mataix-Cols D., Malki K., Adler M., et al (2022) BMJ DOI: 10.1136/bmjopen-2021-049302	Numbers of deaths by influenza and suicide and total population for 1910-1978 data
SARS-CoV-2 induces a durable and antigen specific humoral immunity after asymptomatic to mild COVID-19 infection Havervall S., Jernbom Falk A., Klingström J., Ng H., et al (2022) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0262169	Metadata record for dataset data Figshare
Modelling the direct virus exposure risk associated with respiratory events Wang J., Dalla Barba F., Roccon A., Sardina G., et al (2022) The Royal Society DOI: 10.1098/rsif.2021.0819	Data related to respiratory events data Figshare Code used to generate visualisations (Python) code Figshare
A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo Hanke L., Das H., Sheward D. J., Perez Vidakovics L., et al (2022) Springer Science and Business Media LLC DOI: 10.1038/s41467-021-27610-z	cryo-EM density maps data Electron Microscopy Data Bank: EMD-12561 cryo-EM density maps data Electron Microscopy Data Bank: EMD-12465 Atomic coordinates data Protein Data Bank: 7NS6 Atomic coordinates data Protein Data Bank: 7NLL Source Data for Study data
COVID-19 collateral damage—psychological burden and behavioural changes among older adults during the first outbreak in Stockholm, Sweden: a cross-sectional study Beridze G., Triolo F., Grande G., Fratiglioni L., et al (2022) BMJ DOI: 10.1136/bmjopen-2021-058422	Data are from the SNAC-K Project, a population-based study on ageing and dementia. Need approval for access. data
Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16 Kozielski F., Sele C., Talibov V. O., Lou J., et al (2022) Royal Society of Chemistry (RSC) DOI: 10.1039/D1CB00135C	Protein model data Protein Data Bank: 7ORW Protein model data Protein Data Bank: 7ORV Protein model data Protein Data Bank: 7ORU Protein model data Protein Data Bank: 7ORR Crystallographic fragment screen data Zenodo
Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor Capraz T., Kienzl N. F., Laurent E., Perthold J. W., et al (2021) eLife Sciences Publications, Ltd DOI: 10.7554/eLife.73641	Molecular models and simulation trajectories data Drug targeting modalities for COVID-19 drug discovery data
Presence of hyaluronan in lung alveoli in severe Covid-19: An opening for new treatment options? Hellman U., Karlsson M. G., Engström-Laurent A., Cajander S., et al (2021) Elsevier BV DOI: 10.1074/jbc.AC120.015967	Color light micrographs of autopsy lung tissue from the three Covid-19 cases, all included in the article. data
Potential SARS-CoV-2 infectiousness among asymptomatic healthcare workers Pimenoff V. N., Elfström M., Conneryd Lundgren K., Klevebro S., et al (2021) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0260453	Pseudonymised, individual-level data data Individual health care workers cohort data from KI Hospital data Figshare Additional data from South Hospital in Stockholm data Figshare
Differential Effect of SARS-CoV-2 Spike Glycoprotein 1 on Human Bronchial and Alveolar Lung Mucosa Models: Implications for Pathogenicity Rahman M., Irmler M., Keshavan S., Introna M., et al (2021) MDPI AG DOI: 10.3390/v13122537	Expression profiling by high throughput sequencing data Gene Expression Omnibus: GSE185657
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
1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution Agback T., Dominguez F., Frolov I., Frolova E. I., et al (2021) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0251834#sec006	Chemical shifts of full-length SARS-CoV-2 data BioMagResBank: 50915
Public perceptions of multiple risks during the COVID-19 pandemic in Italy and Sweden Mondino E., Di Baldassarre G., Mård J., Ridolfi E., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41597-020-00778-7	Raw dataset: perceived likelihoods and impacts, individual and authorities’ preparedness and knowledge, socio-demographic characteristics in August 2020 (N=2,033 in Italy, N=2,121 in Sweden) data Zenodo Code for reading, processing and graphically representing the data code GitHub
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
Accessible data curation and analytics for international-scale citizen science datasets Murray B., Kerfoot E., Chen L., Deng J., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41597-021-01071-x	Code used to generate synthetic evalutation datasets code Source code for ExeTera code
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
Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis Hober A., Tran-Minh K. H., Foley D., McDonald T., et al (2021) eLife Sciences Publications, Ltd DOI: 10.7554/eLife.70843	Proteomics data data ProteomeXchange: PXD026366 Mass spectrometry data generated data
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
A Longitudinal Study of Gambling Behaviors During the COVID-19 Pandemic in Sweden Månsson V., Wall H., Berman A. H., Jayaram-Lindström N., et al (2021) Frontiers Media SA DOI: 10.3389/fpsyg.2021.708037	R-code used for data analyses. code GitHub Data cannot be made publicly available, but access can be requested for data with some personal details removed. data
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
Priority setting and equity in COVID-19 pandemic plans: a comparative analysis of 18 African countries Kapiriri L., Kiwanuka S., Biemba G., Velez C., et al (2021) Oxford University Press (OUP) DOI: 10.1093/heapol/czab113	All data are available in the article, or in sources therein (e.g. information on healthcare and political systems). data
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
Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch O'Toole Á., Hill V., Pybus O. G., Watts A., et al (2021) F1000 Research Ltd DOI: 10.12688/wellcomeopenres.16661.2	Data underlying cov-lineages.org website. data Zenodo Accession IDs included in publication tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. data Zenodo Supplementary materials with group affiliations for tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. data Zenodo Current source code for grinch (global report investigating novel coronavirus haplotypes) software. code GitHub Data on global lineage reports (on variants of concern), lineages, and software tools. data GitHub
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
Fear and anxiety in the face of COVID-19: Negative dispositions towards risk and uncertainty as vulnerability factors Millroth P., Frey R. (2021) Elsevier BV DOI: 10.1016/j.janxdis.2021.102454	Methods used and survey results on factors related to mental health issues related to COVID-19 data Open Science Framework
DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types Das J., Idh N., Sikkeland L. I. B., Paues J., et al (2021) Informa UK Limited DOI: 10.1080/15592294.2021.1969499	R scripts to analyse Alveolar macrophages (HLA-DR+/CD3-) and lymphocytes (CD3+) specific cell types from DNA methylation analysis. code
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
The impact of a COVID-19 lockdown on work productivity under good and poor compliance Ohrnberger J., Segal A. B., Forchini G., Miraldo M., et al (2021) Oxford University Press (OUP) DOI: 10.1093/eurpub/ckab138	The code of the individual-based epidemiological model. code GitHub The raw data from the Quarterly Labour Force Survey October to December 2019 used for the labour force model. data GitHub
A phenomics approach for antiviral drug discovery Rietdijk J., Tampere M., Pettke A., Georgiev P., et al (2021) Springer Science and Business Media LLC DOI: 10.1186/s12915-021-01086-1	Data analysis code. code GitHub Images, analysis pipelines, and feature data. data Figshare
Correlates of intended COVID-19 vaccine acceptance across time and countries: results from a series of cross-sectional surveys Kerr J. R., Schneider C. R., Recchia G., Dryhurst S., et al (2021) BMJ DOI: 10.1136/bmjopen-2020-048025	Data on vaccine acceptance and code for analysis data code Open Science Framework Image data, the image analysis pipelines, and extracted features data Figshare Code for analysis code GitHub
A multi-country test of brief reappraisal interventions on emotions during the COVID-19 pandemic Wang K., Goldenberg A., Dorison C. A., Miller J. K., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41562-021-01173-x	Data (raw and processed) and analysis code related to emotion-regulation strategy testing data code Open Science Framework
Topological network based drug repurposing for coronavirus 2019 Habibi M., Taheri G. (2021) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0255270	Information on interactions between proteins & human cells, potential drug targets, genes related to potential targets. data GitHub Matlab analysis code required to process data. code GitHub
The risk for a new COVID-19 wave and how it depends on <i>R</i> <sub>0</sub> , the current immunity level and current restrictions Britton T., Trapman P., Ball F. (2021) The Royal Society DOI: 10.1098/rsos.210386	Information on Matlab files, summary statistics, R0 values, and data visualisations data Figshare
Impact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy Manica M., Guzzetta G., Riccardo F., Valenti A., et al (2021) Nature Communications DOI: https://doi.org/10.1038/s41467-021-24832-z	Data from different provinces and analysis code data code Figshare
Recurrent and persistent infection with SARS-CoV-2 – epidemiological data and case reports from Western Sweden, 2020 Ringlander J., Olausson J., Nyström K., Härnqvist T., et al (2021) Informa UK Limited DOI: 10.1080/23744235.2021.1957143	Data on subjects from first and second infection data
COVID-19 vaccine acceptance and hesitancy in low- and middle-income countries Solís Arce J. S., Warren S. S., Meriggi N. F., Scacco A., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41591-021-01454-y	Deidentified participant data, analysis code and replication files data code GitHub Analysis code and replication exercise code GitHub
Characteristics and outcomes of 627 044 COVID-19 patients living with and without obesity in the United States, Spain, and the United Kingdom Recalde M., Roel E., Pistillo A., Sena A. G., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41366-021-00893-4	Analysis code used by the CHARYBDIS study code GitHub Data produced and used by the CHARYBDIS study data
Blue Biotechnology: Computational Screening of Sarcophyton Cembranoid Diterpenes for SARS-CoV-2 Main Protease Inhibition Ibrahim M. A. A., Abdelrahman A. H. M., Atia M. A. M., Mohamed T. A., et al (2021) MDPI AG DOI: 10.3390/md19070391	All data are included in the article or supplementary material (Sarcophyton cembranoid diterpenes metabolites). data
Mapping the human genetic architecture of COVID-19 Niemi M. E. K., Karjalainen J., Liao R. G., Neale B. M., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41586-021-03767-x	Summary statistics by COVID-19 HGI. data GWAS catalog study. data GWAS: GCST011074 Code for summary statistics, PCA pipeline with precomputed loadings and meta-analyses. code GitHub Code for Mendelian randomization and genetic correlation pipeline. code GitHub
An artificial neural network approach integrating plasma proteomics and genetic data identifies PLXNA4 as a new susceptibility locus for pulmonary embolism Razzaq M., Iglesias M. J., Ibrahim-Kosta M., Goumidi L., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41598-021-93390-7	Proteomics dataset based on plasma samples from 1,388 subjects. data Zenodo
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
Virological and immunological features of SARS-CoV-2-infected children who develop neutralizing antibodies Cotugno N., Ruggiero A., Bonfante F., Petrara M. R., et al (2021) Elsevier BV DOI: 10.1016/j.celrep.2021.108852	Data required to produce the figures, includes data on proteomics and immunology data Mendeley R code for multi-omics factor analyses, correlations, and plots code GitHub
Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2 Roxhed N., Bendes A., Dale M., Mattsson C., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41467-021-23893-4	Source Data (data on antibody titer, among other things) data Code for analysis (R) code Github
Public acceptance of COVID-19 vaccines: cross-national evidence on levels and individual-level predictors using observational data Lindholt M. F., Jørgensen F., Bor A., Petersen M. B. (2021) BMJ DOI: 10.1136/bmjopen-2020-048172	Vaccine acceptance in Denmark, France, Germany, Hungary, Sweden, Italy, UK and USA; September 2020 to February 2021. data Open Science Framework
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
SARS-CoV-2 in hospital indoor environments is predominantly non-infectious Krambrich J., Akaberi D., Ling J., Hoffman T., et al (2021) Springer Science and Business Media LLC DOI: 10.1186/s12985-021-01556-6	Summary swab results, and Ct values and RT-qPCR validation results for samples all included with the article 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
Using a household-structured branching process to analyse contact tracing in the SARS-CoV-2 pandemic Fyles M., Fearon E., Overton C., Wingfield T., et al (2021) The Royal Society DOI: 10.1098/rstb.2020.0267	Data and code related to household-contact-tracing data code GitHub
Time series analysis and mechanistic modelling of heterogeneity and sero-reversion in antibody responses to mild SARS‑CoV-2 infection Manisty C., Treibel T. A., Jensen M., Semper A., et al (2021) Elsevier BV DOI: 10.1016/j.ebiom.2021.103259	Possible to apply for access to deidentified patient data and samples data
Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium Mehregan A., Pérez-Conesa S., Zhuang Y., Elbahnsi A., et al (2021) Cold Spring Harbor Laboratory DOI: 10.1101/2021.05.28.446179	Biophysical characterisation of the SARS-CoV-2 E protein. data Zenodo
Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq Yelagandula R., Bykov A., Vogt A., Heinen R., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41467-021-22664-5	Sequencing data for all experiments. data Gene Expression Omnibus: GSE163688 Primer sequences are in Supplementary Data 2. data code to analyse Next-Generation Sequencing (NGS) data. code GitHub
Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells Chen X., Saccon E., Appelberg K. S., Mikaeloff F., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41420-021-00487-z	Raw mass spectromic data. data ProteomeXchange: PXD023450 bioinformatic analysis codes. data GitHub
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
OxCOVID19 Database, a multimodal data repository for better understanding the global impact of COVID-19 Mahdi A., Błaszczyk P., Dłotko P., Salvi D., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41598-021-88481-4	OxCOVID19 Database to download data CSV extracts from the OxCOVID19 Database data GitHub Complete OxCOVID19 Database in CSV format as of 2020-07-31 data Figshare
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
Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021 Funk T., Pharris A., Spiteri G., Bundle N., et al (2021) European Centre for Disease Control and Prevention (ECDC) DOI: 10.2807/1560-7917.ES.2021.26.16.2100348	Data in supplementary materials/appendices - data on genetic data divided by demogaphic factors data
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
Mortality outcomes with hydroxychloroquine and chloroquine in COVID-19 from an international collaborative meta-analysis of randomized trials Axfors C., Schmitt A. M., Janiaud P., van’t Hooft J., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41467-021-22446-z	Source Data (includes mortality data, among other things) data Code for metaanalysis code Open Science Framework
A simple model for the total number of SARS-CoV-2 infections on a national level Blanco N., Stafford K. A., Lavoie M. C., Brandenburg A., et al (2021) Cambridge University Press (CUP) DOI: 10.1017/S0950268821000649	Datasets of the original ECDC data and the curve fits data Zenodo
Driving potent neutralization of a SARS-CoV-2 Variant of Concern with a heterotypic boost Sheward D. J., Mandolesi M., Urgard E., Kim C., et al (2021) Cold Spring Harbor Laboratory DOI: 10.1101/2021.04.03.438330	Code to acquire and analyse data code GitHub
Ultra-fast proteomics with Scanning SWATH Messner C. B., Demichev V., Bloomfield N., Yu J. S. L., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41587-021-00860-4	The data generated for the benchmarks and the drug response screen in yeast data ProteomeXchange: PXD023613 Open-source algorithms made available through the DIA–NN software suite code GitHub
A population-based nationwide dataset concerning the COVID-19 pandemic and serious psychological consequences in Bangladesh Pakpour A. H., Al Mamun F., Hosen I., Griffiths M. D., et al (2021) Elsevier BV DOI: 10.1016/j.dib.2020.106621	Raw dataset: socio-demographic characteristics, sources of information regarding COVID-19, knowledge concerning COVID-19, behavior in preventing COVID-19, etc. (n=10,067) data Harvard Dataverse Detailed description of all study variables data
Proteomic blood profiling in mild, severe and critical COVID-19 patients Patel H., Ashton N. J., Dobson R. J. B., Andersson L., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41598-021-85877-0	Proteomic data data BioStudies: S-BSST416 Application related to proteomic data analysis code Zenodo Code behind application related to proteomic data analysis code GitHub
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
Mapping the human genetic architecture of COVID-19 by worldwide meta-analysis Ganna A. (2021) Cold Spring Harbor Laboratory DOI: 10.1101/2021.03.10.21252820	Summary statistics generated by COVID-19 HGI data Code for Mendelian randomization and genetic correlation pipeline code GitHub Code for summary statistics liftover and meta-analysis and PCA pipeline code GitHub
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
Antibodies to SARS-CoV-2 and risk of past or future sick leave Dillner J., Elfström K. M., Blomqvist J., Eklund C., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41598-021-84356-w	Pseudonymised, individual-level data that allow full replication of the results in this article are freely available from joakim.dillner@sll.se or from the Karolinska University Hospital data analysis department: tableau.karolinska@sll.se. data
Ophthalmic Screening in Patients with Coronavirus Disease 2019: A Prospective Cohort Study Papazoglou A., Conen A., Haubitz S., Tschopp M., et al (2021) MDPI AG DOI: 10.3390/jcm10050896	Patient characteristics, medical treatment regiments, symptoms, laboratory findings, ophthalmic findings, systemic symtoms for each patient data
A Novel Olfactory Self-Test Effectively Screens for COVID-19 Snitz K., Honigstein D., Weissgross R., Ravia A., et al (2021) Cold Spring Harbor Laboratory DOI: 10.1101/2021.02.18.21251422	Data related to olfaction tests data Gitlab Analysis code (Matlab) code Gitlab
Mortality of the COVID-19 Outbreak in Sweden in Relation to Previous Severe Disease Outbreaks Ledberg A. (2021) Frontiers Media SA DOI: 10.3389/fpubh.2021.579948	Data held on daily death counts for Sweden from 1860 to 31.08.2020; the total population of Sweden for the years 1860 to 2019 (from Statistics Sweden). data GitHub Code to do analysis and produce figures. code GitHub
Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape Koenig P., Das H., Liu H., Kümmerer B. M., et al (2021) American Association for the Advancement of Science (AAAS) DOI: 10.1126/science.abe6230	Data generated/analysed are in the article or supplementary materials. data Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U. data Protein Data Bank: 7KN5 Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH V and antibody Fab CC12.3. data Protein Data Bank: 7KN6 Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH W and antibody Fab CC12.3. data Protein Data Bank: 7KN7 SARS-CoV-2 spike in complex with nanobodies E. data Protein Data Bank: 7KSG Nanobody E bound to Spike-RBD in a localized reconstruction. data Protein Data Bank: 7B14 SARS-CoV-spike with two RBDs up bound to VHH V on all RBDs. data Protein Data Bank: 7B11 SARS-CoV-spike bound to two neutralising nanobodies. data Protein Data Bank: 7B18 SARS-CoV-spike RBD bound to two neutralising nanobodies. data Protein Data Bank: 7B17 SARS-CoV-2 spike in complex with nanobodies E. data Electron Microscopy Data Bank: EMD-23018 Nanobody E bound to Spike-RBD in a localized reconstruction. data Electron Microscopy Data Bank: EMD-11978 SARS-CoV-spike bound to two neutralising nanobodies. data Electron Microscopy Data Bank: EMD-11981 SARS-CoV-spike RBD bound to two neutralising nanobodies. data Electron Microscopy Data Bank: EMD-11980 Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape. data BioProject: PRJNA679438
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
Community health worker knowledge, attitudes and practices towards COVID-19: Learnings from an online cross-sectional survey using a digital health platform, UpSCALE, in Mozambique Feldman M., Lacey Krylova V., Farrow P., Donovan L., et al (2021) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0244924	Knowledge, attitudes, and practices (KAP) survey results. data
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
Efficacy and tolerability of bevacizumab in patients with severe Covid-19 Pang J., Xu F., Aondio G., Li Y., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41467-021-21085-8	Raw data with demographic and clinical characteristics of the patients, progress of treatment and control groups. data Figshare All relevant codes used in SAS software for statistical analysis. code Figshare
Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples Alekseenko A., Barrett D., Pareja-Sanchez Y., Howard R. J., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41598-020-80352-8	Raw data for amplification curves, and Ct values for clinical samples. data
Surveillance of wastewater revealed peaks of SARS-CoV-2 preceding those of hospitalized patients with COVID-19 Saguti F., Magnil E., Enache L., Churqui M. P., et al (2021) Elsevier BV DOI: 10.1016/j.watres.2020.116620	Amount of SARS-CoV-2 in wastewater in Gothenburg per week between February and June 2020 (data available in the article). 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
SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice Tian J., Patel N., Haupt R., Zhou H., et al (2021) Springer Science and Business Media LLC DOI: 10.1038/s41467-020-20653-8	Source data behind study. data
Malpractice claimed calls within the Swedish Healthcare Direct: a descriptive – comparative case study Björkman A., Engström M., Winblad U., Holmström I. K. (2021) Springer Science and Business Media LLC DOI: 10.1186/s12912-021-00540-3	Data cannot be publicly shared, but applications can be made for access. data
High Rates of COVID-19 Vaccine Hesitancy and Its Association with Conspiracy Beliefs: A Study in Jordan and Kuwait among Other Arab Countries Sallam M., Dababseh D., Eid H., Al-Mahzoum K., et al (2021) MDPI AG DOI: 10.3390/vaccines9010042	Data cannot be shared publicly, but applications can be made for access. data
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
Human species D adenovirus hexon capsid protein mediates cell entry through a direct interaction with CD46 Persson B. D., John L., Rafie K., Strebl M., et al (2020) Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.2020732118	Crystal Structure of Human Adenovirus 56 Fiber Knob. data Protein Data Bank: 7AJP
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
Broadly Active Antiviral Compounds Disturb Zika Virus Progeny Release Rescuing Virus-Induced Toxicity in Brain Organoids Pettke A., Tampere M., Pronk R., Wallner O., et al (2020) MDPI AG DOI: 10.3390/v13010037	Data are available in the article and supplementary materials (effect of novel antiviral compounds against ZIKV in several cell models). data
Mechanisms of a Sustained Anti‐inflammatory Drug Response in Alveolar Macrophages Unraveled with Mathematical Modeling Nyman E., Lindh M., Lövfors W., Simonsson C., et al (2020) Wiley DOI: 10.1002/psp4.12568	Experimental data are in the supplementary material data Code for macrophage model (matlab) code GitLab
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
The MERS-CoV receptor gene is among COVID-19 risk factors inherited from Neandertals Zeberg H., Pääbo S. (2020) Cold Spring Harbor Laboratory DOI: 10.1101/2020.12.11.422139	Croatian Neandertal genome. data Croatian Neandertal genome (alternate source). data Modern human genome. data GWAS summary statistics (round 4 release: A/B2_ALL_eur_leave_23andme). data
Thermal inactivation of COVID‐19 specimens improves RNA quality and quantity Hemati M., Soosanabadi M., Ghorashi T., Ghaffari H., et al (2020) Wiley DOI: 10.1002/jcp.30206	All data are included in the paper. data
Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses Tampere M., Pettke A., Salata C., Wallner O., et al (2020) MDPI AG DOI: 10.3390/v12121423	Thermal Proteome Profiling dataset from Hazara virus infected SW13 cells treated with DMSO or antiviral inhibitor 20 µM TH6744 data Figshare Antiviral screening; Dose-response treatment of TH6744 and TH3289; List of proteins from 2D-TPP analysis in U87 cells (FDR); List of proteins from 2D-TPP analysis in U87 cells (Fold-change); Uniprot annotation of overlapping TPP-TR and 2D-TPP hits data Raw mass spectrometry data data ProteomeXchange Consortium: PXD021494
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
Impact of SARS-CoV-2 Pandemic on Patients with Primary Immunodeficiency Delavari S., Abolhassani H., Abolnezhadian F., Babaha F., et al (2020) Springer Science and Business Media LLC DOI: 10.1007/s10875-020-00928-x	General laboratory tests, immunologic investigation, computed tomographies of the chest of 17 primary immunodeficient patients infected with COVID-19 data
Social Determinants Predict Outcomes in Data From a Multi-Ethnic Cohort of 20,899 Patients Investigated for COVID-19 Lundon D. J., Mohamed N., Lantz A., Goltz H. H., et al (2020) Frontiers Media SA DOI: 10.3389/fpubh.2020.571364	Data cannot be publicly shared, though it is is possible to apply for access. 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
Global analysis of more than 50,000 SARS-CoV-2 genomes reveals epistasis between eight viral genes Zeng H., Dichio V., Rodríguez Horta E., Thorell K., et al (2020) Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.2012331117	Data & circos plots related to multiple sequence alignments data GitHub Data on GISAID accession numbers and multiple sequence alignments also available in the paper data
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy Wacker A., Weigand J. E., Akabayov S. R., Altincekic N., et al (2020) Oxford University Press (OUP) DOI: 10.1093/nar/gkaa1013	Nuclear magnetic resonance (NMR) experimental data deposited in COVID19-NMR project data Chemical shift data deposited in BMRB (multiple accession numbers, given in Table 1 in the article). data BioMagResBank
Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2 Custódio T. F., Das H., Sheward D. J., Hanke L., et al (2020) Springer Science and Business Media LLC DOI: 10.1038/s41467-020-19204-y	Microscale thermophoresis (MST) and biolayer interferometry (BLI) data. data GitHub Synthetic nanobody Sybody 23 (Sy23). data SASBDB: SASDJF4 SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD). data SASBDB: SASDJG4 SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD) bound to the synthetic nanobody Sybody 23 (Sy23). data SASBDB: SASDJH4 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23). data Electron Microscopy Data Bank: EMD-11616 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation. data Electron Microscopy Data Bank: EMD-11617 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23). data Protein Data Bank: 7A25 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation. data Protein Data Bank: 7A29 Sequences of all the selected sybodies. data Source data. 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
Dashboard of Sentiment in Austrian Social Media During COVID-19 Pellert M., Lasser J., Metzler H., Garcia D. (2020) Frontiers Media SA DOI: 10.3389/fdata.2020.00032	Data related to Austrian social media during COVID-19. 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
Modelling the dispersion of SARS-CoV-2 on a dynamic network graph Bryant P., Elofsson A. (2020) Cold Spring Harbor Laboratory DOI: 10.1101/2020.10.19.20215046	Code related to modelling the spread of COVID-19 on a dynamic social network with spread reduction according to Google mobility changes data GitHub Raw data and results related to modelling the spread of COVID-19 on a dynamic social network with spread reduction according to Google mobility changes code GitHub
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
Deep phenotyping of 34,128 adult patients hospitalised with COVID-19 in an international network study Burn E., You S. C., Sena A. G., Kostka K., et al (2020) Springer Science and Business Media LLC DOI: 10.1038/s41467-020-18849-z	Data analysis code used in the study. code GitHub Aggregated results are available. Individual patient-level data cannot be made publicly available, but requests may be submitted for access. data
Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2 Rogstam A., Nyblom M., Christensen S., Sele C., et al (2020) MDPI AG DOI: 10.3390/ijms21197375	Nonstructural protein 10 (nsp10) from SARS CoV-2, 1.58Å resolution. data Protein Data Bank: 6ZPE Nonstructural protein 10 (nsp10) from SARS CoV-2, 2.55Å resolution. data Protein Data Bank: 6ZCT Nsp10 unfolding temperatures determined by DSF. data
Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19 Sekine T., Perez-Potti A., Rivera-Ballesteros O., Strålin K., et al (2020) Elsevier BV DOI: 10.1016/j.cell.2020.08.017	All data generated during the study (predicted binding affinities, donor characteristics, sample information, and some analyses) are available in the article. data
CSF biomarkers in patients with COVID-19 and neurological symptoms Edén A., Kanberg N., Gostner J., Fuchs D., et al (2020) Ovid Technologies (Wolters Kluwer Health) DOI: 10.1212/WNL.0000000000010977	Data cannot be made publicly available, but access to anonymised data can be requested. data
The major genetic risk factor for severe COVID-19 is inherited from Neanderthals Zeberg H., Pääbo S. (2020) Springer Science and Business Media LLC DOI: 10.1038/s41586-020-2818-3	Summary statistics of the genome-wide association study are available from the COVID-19 Host Genetics Initiative (round 3, ANA_B2_V2: hospitalized patients with COVID-19 compared with population controls). data
Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR Smyrlaki I., Ekman M., Lentini A., Rufino de Sousa N., et al (2020) Springer Science and Business Media LLC DOI: 10.1038/s41467-020-18611-5	Analysis code used in the study. code GitHub Source data, including all raw data (primarily Ct values) are included in the article. 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
An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction Hanke L., Vidakovics Perez L., Sheward D. J., Das H., et al (2020) Springer Science and Business Media LLC DOI: 10.1038/s41467-020-18174-5	Sequence of Ty1. data GenBank: MT784731 Bio layer interferometry (BLI) data. data GitHub Isothermal titration calorimetry (ITC) data. data GitHub Next generation sequencing (NGS) data. data BioProject: PRJNA638614 Jupyter notebooks to reproduce next generation sequencing (NGS) data. code GitHub Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1). data Electron Microscopy Data Bank: EMD-11526 Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1). data Protein Data Bank: 6ZXN
Factors contributing to healthcare professional burnout during the COVID-19 pandemic: A rapid turnaround global survey Morgantini L. A., Naha U., Wang H., Francavilla S., et al (2020) Public Library of Science (PLoS) DOI: 10.1371/journal.pone.0238217	Number of COVID-19 deaths contributed by specific age group and population characteristics for 14 countries and 13 US states. data Healthcare professionals’ responses about perceptions, exposure, and workload during the COVID-19 pandemic. 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
Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories Su Y., Chen D., Lausted C., Yuan D., et al (2020) Cold Spring Harbor Laboratory DOI: 10.1101/2020.07.27.224063	Due to risk of de-identification, the pseudonymised RNA sequencing data will not be made publicly available, but it is possible to apply for access. data Processed data: RNA-seq of coding RNA from single cells. data ArrayExpress: E-MTAB-9357 Data are integrated for further visualization and analysis in ISB COVID-19 data explorer. 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