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Publicly available COVID-19 AIRR-seq data sets

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#1

The AIRR Community (www.airr-community.org), in response to the AIRR Community’s call to share COVID-19 AIRR-seq data, has created this page to provide a central location for finding and tracking research that is producing (or planning on producing) publicly available COVID-19 AIRR-seq data sets. By publicly available we mean data that is both available through an open data platform (such as the INSDC repositories - SRA/ENA) as well as data that is available as controlled data through a data sharing agreement with the research group and/or the data provider.

The page provides links to the papers/projects and the sources for the sequence data (SRA, ENA, etc.). If annotated AIRR-seq data are available, links to the sources for those data sets are also available (e.g. iReceptor, ImmunoAccess, Observed Antibody Space, etc.).

If you know of papers or research groups that have such data sets, please add them to this list!

There are two sections that can be found below:

  • Papers that have publicly available AIRR-seq data
  • Papers that are in pre-print and have committed to providing publicly available AIRR-seq data

Papers/projects that have publicly available AIRR-seq data:

  1. Alameh, M-G. et al. Lipid nanoparticles enhance the efficacy of mRNA and protein subunit vaccines by inducing robust T follicular helper cell and humoral responses. Immunity. 2021.
  2. Alsoussi, W. et al. A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection. J. Immunol. 2020.
  3. Bacher, P. et al. Low-Avidity CD4+ T Cell Responses to SARS-CoV-2 in Unexposed Individuals and Humans with Severe COVID-19. Immunity. 2020.
    • Paper DOI
    • Species: Homo Sapiens
    • BioProject Accession: PRJNA680539
    • SRA Accession: SRP293741
    • GEO Accession: GSE162086
    • Data availability: ScRNA-seq data generated during this study has also been deposited to FastGenomics (“https://www.fastgenomics.org”) and TCR sequences used in the single-cell analysis are provided in Table S3.
  4. Bernardes, J.P. et al. Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories. Immunity. 2020.
    • Paper DOI
    • Species: Homo Sapiens
    • BioProject Accession: PRJNA679331
    • GEO Accession: GSE161777
    • SRA Accession: SRP293160
    • Data Sharing Statement: The processed scRNA-seq and scBCR-seq data generated during this study is available in FastGenomics (Comma Soft AG).
  5. Brouwer, P. et al. Potent neutralizing antibodies from COVID-19 patients define multiple targets of vulnerability. Science. 2020.
    • Paper DOI
    • Species: Homo Sapiens
    • Data availability: Variable domain sequences of HC and LCs are available in table S1 and were uploaded on GenBank under accession numbers MT599820 to MT599987.
  6. Gaebler, C. et al. Evolution of Antibody Immunity to SARS-CoV-2. bioRxiv (Preprint).
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: Raw sequencing data associated with Figure 2 has been deposited at Github.
  7. Galson, J. et al. Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures. Front. Immunol. 2020.
  8. Goel, R. et al. Distinct antibody and memory B cell responses in SARS-CoV-2 naïve and recovered individuals following mRNA vaccination. Science Immunology. 2021.
  9. Goel, R. et al. mRNA vaccines induce durable immune memory to SARS-CoV-2 and variants of concern. Science. 2021.
  10. Hansen, J. et al. Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail. Science. 2020.
    • Paper DOI
    • Data availability: Sequences of the nine characterized antibodies have been deposited in GenBank and are available in the supplementary materials.
    • Species: Homo Sapiens
  11. Heming, M. et al. Neurological Manifestations of COVID-19 Feature T Cell Exhaustion and Dedifferentiated Monocytes in Cerebrospinal Fluid. Immunity. 2021.
  12. Joseph, M. et al. Global patterns of antigen receptor repertoire disruption across adaptive immune compartments in COVID-19. PNAS. 2022.
  13. Kim, S. et al. Stereotypic Neutralizing VH Clonotypes Against SARS-CoV-2 RBD in COVID-19 Patients and the Healthy Population. Science Translational Medicine. 2020.
  14. Kreer, C. et al. Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients. Cell. 2020.
    • Paper DOI
    • Data availability: Nucleotide sequences of all SARS-CoV-2-neutralizing antibodies were deposited at GenBank (accession numbers MT658806 - MT658861). Further antibody sequences and NGS data of healthy individuals will be shared by the Lead Contact upon request.
    • Species: Homo Sapiens
  15. Kuri-Cervantes, L. et al. Comprehensive mapping of immune perturbations associated with severe COVID-19. Science Immunology. 2020.
  16. Liao, M. et al. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19. Nat Med. 2020.
  17. Meckiff, B. et al. Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4+ T Cells in COVID-19. Cell. 2020.
  18. Minervina, A. et al. Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection. Elife. 2021.
  19. Montague, Z. et al. Dynamics of B-cell repertoires and emergence of cross-reactive responses
    in COVID-19 patients with different disease severity. MedRxiv (Preprint).
  20. Mor, M. et al. Multi-clonal SARS-CoV-2 neutralization by antibodies isolated from severe COVID-19 convalescent donors. PLoS Pathogens. 2021.
  21. Nielsen, S. et al. Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2. Cell Host & Microbe, 2020.
  22. Nolan, S et al. A large-scale database of T-cell receptor beta (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2. ResearchSquare (Preprint).
  23. Raybould, M. et al. CoV-AbDab: the Coronavirus Antibody Database (Preprint).
  24. Robbiani, D.F. et al. Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature. 2020.
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: Data are provided in SI Tables 1, 3, 4, 5 and 6; and in Figure 3 which has associated raw sequencing data deposited at Github.
  25. Schmitz, A. et al. A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Immunity. 2021.
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: Bulk sequencing reads are deposited on Sequence Read Archive under BioProject PRJNA741267. Processed B cell receptor data are deposited at Zenodo.
    • Annotated sequences:
  26. Schultheiß, C. et al. Next Generation Sequencing of T and B cell receptor repertoires from COVID-19 patients showed signatures associated with severity of disease. Immunity. 2020.
  27. Shomuradova et. al. SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors. Immunity. 2020.
  28. Sokal, A. et al. Maturation and persistence of the anti-SARS-CoV-2 memory B cell response. Cell. 2021.
    • Paper DOI
    • Preprint DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: All single cell RNA sequencing data associated with this study have been deposited to ArrayExpress and are available under the following accession number: E-MTAB-9995
    • Annotated sequences:
  29. Turner, J. et al. SARS-CoV-2 mRNA vaccines induce persistent human germinal centre responses. Nature. 2021.
  30. Wen, W. et al. Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing. Cell Discov 6, 31 (2020).
  31. Woodruff, MC. et al. Extrafollicular B cell responses correlate with neutralizing antibodies and morbidity in COVID-19. Nature Immunology. 2020
  32. Xu, G. et al. The differential immune responses to COVID-19 in peripheral and lung revealed by single-cell RNA sequencing. Cell Discovery. 2020.
  33. Zhang, J.Y. et al. Single-cell landscape of immunological responses in COVID-19 patients. Nature Immunology. 2020.
  34. Zost, S.J. et al. Rapid isolation and profiling of a diverse panel of human monoclonal antibodies targeting the SARS-CoV-2 spike protein. Nature Medicine. 2020.

Papers that are in pre-print and/or projects that have stated that they will be providing publicly available AIRR-seq data:

  1. Fan, X. et al. Single-cell RNA-seq and V(D)J profiling of immune cells in COVID-19 patients. medRxiv (Preprint).
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: The scRNA-seq data and V(D)J sequencing data used in this study have been deposited in the GSA. (Note: accession number not provided)
  2. Fischer, DS. et al. Single-cell RNA sequencing reveals in vivo signatures of SARS-CoV-2-reactive T cells through ‘reverse phenotyping’. medRxiv (Preprint).
  3. Huang, L. et al. Blood single cell immune profiling reveals the interferon-MAPK pathway mediated adaptive immune response for COVID-19, medrxiz
  4. Huang, L. et al. Profiling B cell immune responses to identify neutralizing antibodies from convalescent COVID-19 patients. Research Square (Preprint)
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: The source data of Figures 1, 2, 4, 5a, 5b, 6b and 7 in this study are provided within this paper (supplementary zip file). Patent application has been filed on the reported antibodies (PCT/CN2020/096371 and PCT/CN2020/096360). All reagents and information presented in this study are available from corresponding authors upon reasonable request.
  5. Ju, B. et al. Human neutralizing antibodies elicited by SARS-CoV-2 infection. Nature. 2020.
  6. Li, F. et al. Single cell RNA and immune repertoire profiling of COVID-19 patients reveal novel neutralizing antibody. Protein & Cell. 2020.
  7. Niu, X. et al. Longitudinal Analysis of T and B Cell Receptor Repertoire Transcripts Reveal Dynamic Immune Response in COVID-19 Patients. Front. Immunol. 2020.
    • Paper DOI
    • Species: Homo Sapiens
    • Data Availability:
      • GSA NGDC Project Accession: PRJCA003775 (Note: Not currently available)
  8. Ramaswamy, A. et al. Post-infectious inflammatory disease in MIS-C features elevated cytotoxicity signatures and autoreactivity that correlates with severity. medRxiv (Preprint).
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: Sequencing data will be made available.
  9. Ren, X. et al. Large-scale single-cell analysis reveals critical immune characteristics of COVID-19 patients. bioRxiv (Preprint).
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: The raw sequencing and processed gene expression data in this paper have been deposited into GSA (Genome Sequence Archive in BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences) and the NCBI GEO database, respectively. Visualization of this dataset can be found at http://covid19.cancer-pku.cn. (Note: accession numbers not provided)
  10. Song, E. et al. Immunologically distinct responses occur in the CNS of COVID-19 patients. bioRxiv (Preprint).
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: Gene expression and repertoire data will be available in the NCBI. (Note: SRA accession number not provided).
  11. Stephenson, E. et al. The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres. medRxiv (Preprint).
  12. Su, Y. et al. Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories. bioRxiv (Preprint).
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: Raw data will be available under controlled access in the EGA repository upon journal acceptance. All data will be integrated for further visualization and analysis in ISB COVID-19 data explorer at https://atlas.fredhutch.org/isb/covid/.
  13. Unterman, A. et al. Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19. medRxiv (Preprint).
  14. Xiang, H. et al. Landscapes and dynamic diversifications of B-cell receptor repertoires in COVID-19 patients. bioRxiv (Preprint).
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: The data that support the findings of this study have been deposited into the CNGB Sequence Archive (CNSA) of CNGBdb with accession number CNP0001106. (Note: Accession not currently available)
  15. Zhang, F. et al. Adaptive immune responses to SARS-CoV-2 infection in severe versus mild individuals. Signal Transduction and Targeted Therapy 5 (156).
  16. Zhao, X-N. et al. Longitudinal single-cell immune profiling revealed distinct innate immune response in asymptomatic COVID-19 patients. bioRxiv (Preprint).
    • Paper DOI
    • Species: Homo Sapiens
    • Data sharing statement: Raw and processed data are available on CNGB Nucleotide Sequence Archive(CNSA: CNGB Sequence Archive (CNSA)) with accession number CNP0001250. (Note: not currently available)
  17. Zhou, Y. et al. Profiling of the immune repertoire in COVID-19 patients with mild, severe, convalescent, or retesting-positive status. Journal of Autoimmunity. 2021.
    • Paper DOI
    • Species: Homo Sapiens
    • Data sharing statement: Raw data of the repertoire of immune receptors were deposited in the GSA database of national genomics data center (accession number, CRA003098). (Note: Accession not currently available)
3 Likes
Any COVID-19 AIRR-Seq data?
#2

It looks like we have a winner… The BioProject does not directly link to the paper, but the authors of the paper are the same as the creators of the BioProject, so I am assuming these are the same…

#3

Boyd-Lab at Stanford has a preprint out on AIRRseq data!

#4

Thank JP, added it above

#5

Hi, guys!

Check out (and add to the post?) our TCRalpha and TCRbeta longitudinal dataset from Minervina et. al 2020 (preprint: https://www.biorxiv.org/content/10.1101/2020.05.18.100545v1)
Github with COVID-19 associated TCR tables (pogorely/Minervina_COVID).
Raw data:
PRJNA633317
UMI-clustered and mixcr processed data (complete dataset):
https://zenodo.org/record/3835956

Thanks!

#6

We’ll release our (VH) BCR sequencing data from 19 UK COVID-19 patients upon journal publication

As part of the study we compared to the data from Nielsen et al. - if anyone wants this processed data (fully AIRR community compliant) please get in touch at opig[at]stats.ox.ac.uk

#7

Hi @mraybould I have contacted you (OPIG) separately about sharing the Nielsen et al paper (and your data when it is available) in an AIRR Covid-19 repository…

Brian

#8

Similar collation here: https://github.com/immunomind/covid19

#9

Hi @jgalson - thanks for pointing this out… We have been talking to them on how we can combine our efforts to make sure we don’t miss anything as well as reduce the amount of work involved…

#10

Annotated sequences from Nielsen et al are available for download through the OAS web platform:

OAS - Search Disease = SARS-COV-2

#11

Annotated sequences from Nielsen et al (DOI) are also available through the iReceptor Gateway. You can find all COVID-19 data available on the iReceptor Gateway by going to the Repertoire page (sorry, an account is required) and typing covid in the general text search box.

#12

The data from our study are now also available. Raw data can be found under PRJNA638224, and processed data here: https://zenodo.org/record/3886395

#13

AIRR compliant annotated sequences from Minervina, A. et al. “Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T cell memory formation after mild COVID-19 infection” bioRxiv (Preprint Paper DOI) are available in the AIRR Data Commons repository covid19-2.ireceptor.org and are searchable through the iReceptor Gateway.

1 Like
#14

Robbiani et al., Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature (2020)
https://www.nature.com/articles/s41586-020-2456-9
Characterised antibody sequences highlighted in CoV-AbDab
Data statement: “Data are provided in SI Tables 1, 3, 4, 5 and 6; and in Figure 3 has associated raw sequencing data deposited at Github (https://github.com/stratust/igpipeline).”

#15

A third AIRR-seq data set from Galson, J. et al. “Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures” (DOI) is now available on the iReceptor Gateway!

#16

Annotated sequences from Liao et al. (DOI) are now available in the AIRR Data Commons and are searchable through the iReceptor gateway!

#17

Our fifth COVID-19 AIRR-seq data set from Schultheiß, C. et al. (DOI) is now searchable on the iReceptor Gateway!

#19

https://www.cell.com/cell/pdf/S0092-8674(20)30821-7.pdf

“Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients”, Christopher Kreer et al., Cell 2020

12 individuals. Data statement: “Further antibody sequences and NGS data of healthy individuals will be shared by the Lead Contact upon request.”

#20

Our sixth and seventh COVID-19 AIRR-seq data sets from Shomuradova et al. SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors, medRxiv, and Alsoussi, et al. A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection, J. Immunol. 2020 are now searchable on the iReceptor Gateway!

1 Like
#21

“Dynamics of B-cell repertoires and emergence of cross-reactive responses in COVID-19 patients with different disease severity”. Zachary Montague et al., bioRxiv 2020

19 individuals, convergent IgG COVID-19 response tracked longitudinally.

Data Sharing Statement:

BCR repertoire data can be accessed through: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA645245

1 Like