Genomics & transcriptomics data

Publications with accessible data

Data available on the European COVID-19 Data Portal

Published raw and assembled sequences related to the COVID-19 outbreak, including outbreak isolates and records relating to coronavirus biology:

Raw and assembled sequence and analysis of SARS-CoV-2 and other coronaviruses (>500,000 deposited items as of June 2021)
Raw and assembled sequence and analysis of human and other hosts (>15,000 deposited items as of June 2021)
European Genome-phenome Archive (EGA) - service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects.

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

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

Last updated: 2025-05-22

Data types

All data types (344)

Biochemistry data (35)

Drug discovery data (15)

Genomics & transcriptomics data (93)

Public health data (68)

Serology data (24)

Social science and humanities data (76)

Publication	Available dataset and code
Germline variants and mosaic chromosomal alterations affect COVID-19 vaccine immunogenicity Sonehara K., Uwamino Y., Saiki R., Takeshita M., et al (2025) Elsevier BV DOI: https://doi.org/10.1016/j.xgen.2025.100783	COVID-19 GWAS in Japanese data European Genome-Phenome Archive CRYSTAL STRUCTURE OF THE INTACT HUMAN IGG B12 WITH BROAD AND POTENT ACTIVITY AGAINST PRIMARY HIV-1 ISOLATES: A TEMPLATE FOR HIV VACCINE DESIGN data Protein Data Bank: 1hzh ALFA project data National Library of Medicine: rs1043109 ALFA project data National Library of Medicine: rs1043249 ALFA project data National Library of Medicine: rs9270585 ALFA project data National Library of Medicine: rs139861548 ALFA project data National Library of Medicine: rs28472312
Plasma proteomic evidence for increased β-amyloid pathology after SARS-CoV-2 infection Duff E. P., Zetterberg H., Heslegrave A., Dehghan A., et al (2025) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41591-024-03426-4	Plasma proteomic evidence for increased β-amyloid pathology after SARS-CoV-2 infection data Biostudies: S-EPMC11922756 Code repository for Plasma proteomic evidence for increased Alzheimer’s disease-related brain pathology after SARS-CoV-2 infection code Github ALFA Allele Frequency data National Library of Medicine: rs429358 ALFA Allele Frequency data National Library of Medicine: rs7412
KLRB1 expression in nasopharyngeal mucosa as a prognostic biomarker in COVID-19 patients García-Aranda M., Onieva M. Á., Martín-García D., Quirós R., et al (2025) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41598-025-86846-7	Homo sapiens transcription factor 4 (TCF4), mRNA data National Library of Medicine: NM_003199 Mus musculus RIKEN cDNA 1600014E20 gene (1600014E20Rik), mRNA data National Library of Medicine: NM_028045 Homo sapiens interferon regulatory factor 8 (IRF8), mRNA data National Library of Medicine: NM_002163 Homo sapiens killer cell lectin like receptor B1 (KLRB1), mRNA data National Library of Medicine: NM_002258
Blood DNA virome associates with autoimmune diseases and COVID-19 Sasa N., Kojima S., Koide R., Hasegawa T., et al (2025) Springer Science and Business Media LLC DOI: https://doi.org/10.1038/s41588-024-02022-z	Software of 'Blood DNA virome associates with autoimmune diseases and COVID-19 code Zenodo Human betaherpesvirus 6A, variant A DNA, complete virion genome, isolate U1102 data National Library of Medicine: NC_001664 Human herpesvirus 6B, complete genome data National Library of Medicine: NC_000898
MiMeJF: Application of Coupled Matrix and Tensor Factorization (CMTF) for Enhanced Microbiome-Metabolome Multi-Omic Analysis Ou Z., Fu X., Norbäck D., Lin R., et al (2025) MDPI AG DOI: https://doi.org/10.3390/metabo15010051	Simulation study on the effect of different data variance and data sparisity on factorization. data
Emerging mutation in SARS-CoV-2 facilitates escape from NK cell recognition and associates with enhanced viral fitness Bilev E., Wild N., Momayyezi P., Sala B. M., et al (2024) Public Library of Science (PLoS) DOI: https://doi.org/10.1371/journal.ppat.1012755	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/SWE/01/2020, complete genome. data European Nucleotide Archive: MT093571 Structure of NKG2A/CD94 bound to HLA-E data Protein Data Bank: 3cii THE HUMAN NON-CLASSICAL MAJOR HISTOCOMPATIBILITY COMPLEX MOLECULE HLA-E data Protein Data Bank: 1mhe Structure of the HLA-E-VMAPRTLIL/GF4 TCR complex data Protein Data Bank: 5w1v
Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries Akaberi D., Pourghasemi Lati M., Krambrich J., Berger J., et al (2024) American Society for Microbiology DOI: https://doi.org/10.1128/aac.00909-24	Severe acute respiratory syndrome coronavirus 2 strain FDAARGOS_983 isolate 2019-nCoV/USA-WA1/2020, complete genome. data European Nucleotide Archive: MT246667.1 SARS-CoV2 major protease in complex with a covalent inhibitor SLL12. data Protein Data Bank: 9eor SARS-CoV2 major protease in complex with a covalent inhibitor SLL11. data Protein Data Bank: 9eo6 SARS-CoV2 major protease in covalent complex with a soluble inhibitor. data Protein Data Bank: 9eox
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 analyzes 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 Protien Data Bank: 8p5m cryoEM structure of SARS-CoV2 Spike trimer in complex with Fab23 data Protien 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Defining post-acute COVID-19 syndrome (PACS) by an epigenetic biosignature in peripheral blood mononuclear cells Nikesjö F., Sayyab S., Karlsson L., Apostolou E., et al (2022) Springer Science and Business Media LLC DOI: 10.1186/s13148-022-01398-1	Analysis and visualisation scripts code GitHub
Monitoring 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort Carapito R., Li R., Helms J., Carapito C., et al (2022) American Association for the Advancement of Science (AAAS) DOI: 10.1126/scitranslmed.abj7521	Proteomics data data ProteomeXchange: PXD025265 RNA-seq datasets data Gene Expression Omnibus: GSE172114 Code to perform classification and structural causal modeling code Zenodo
JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortality Stebbing J., Sánchez Nievas G., Falcone M., Youhanna S., et al (2022) American Association for the Advancement of Science (AAAS) DOI: 10.1126/sciadv.abe4724	RNA-seq of SARS-CoV-2-infected human primary hepatocyte-derived spheroids upon interferon a2 and baricitinib treatment. data ArrayExpress: E-MTAB-9711 Patient information are contained in the paper and supplementary information. data
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series Böhmer M. M., Buchholz U., Corman V. M., Hoch M., et al (2020) Elsevier BV DOI: 10.1016/S1473-3099(20)30314-5	Data on single nucleotide polymorphisms and characteristics of 16 laboratory-confirmed COVID-19 cases included in the article. data
Inborn errors of type I IFN immunity in patients with life-threatening COVID-19 Zhang Q., Bastard P., Liu Z., Le Pen J., et al (2020) American Association for the Advancement of Science (AAAS) DOI: 10.1126/science.abd4570	Genetic Determinants of Susceptibility to Severe COVID-19 Infection. data dbGaP: phs002245.v1.p1 Plasma, cells, genomic DNA, and other materials/samples are available upon request from authors or the Amsterdam UMC Covid-19 Biobank. data All additional data are in the supplementary material. data
Autoantibodies against type I IFNs in patients with life-threatening COVID-19 Bastard P., Rosen L. B., Zhang Q., Michailidis E., et al (2020) American Association for the Advancement of Science (AAAS) DOI: 10.1126/science.abd4585	Plasma, cells, and genomic DNA, as well as other materials can be provided via material transfer agreements. data Clinical, epidemiological characteristics of 101 patients, as well as information on neutralising capacity and assays are provided in the article and supplementary materials. data
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
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
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
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
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