Publicly available COVID-19 AIRR-seq data sets

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) COVID-19 AIRR-seq data sets. 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. Alsoussi, W. et al. A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection. J. Immunol. 2020.
  2. 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.
  3. Galson, J. et al. Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures. bioRxiv (Preprint).
  4. 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
  5. Kim, S. et al. Stereotypic Neutralizing VH Clonotypes Against SARS-CoV-2 RBD in COVID-19 Patients and the Healthy Population. bioRxiv (Preprint).
  6. Kreer, C. et al. Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients. Cell (Preprint).
    • 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
  7. Kuri-Cervantes, L. et al. Comprehensive mapping of immune perturbations associated with severe COVID-19. Science Immunology. 2020.
  8. Liao, M. et al. Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19. Nat Med. 2020.
  9. 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).
  10. 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).
  11. Nielsen, S. et al. Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2. Cell Host & Microbe, 2020.
  12. 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).
  13. Raybould, M. et al. CoV-AbDab: the Coronavirus Antibody Database (Preprint).
  14. Robbiani, D.F. et al. Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature (Preprint).
    • Paper DOI (Preprint)
    • Species: Homo Sapiens
    • Data 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.
  15. 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.
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: From the iReceptor Public Archive (IPA) our data will be findable as part of the AIRR Data Commons using the iReceptor Gateway (gateway.ireceptor.org; iReceptor Study ID IR-Binder-000001).
    • Annotated sequences:
  16. Shomuradova et. al. SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors, medRxiv (Preprint)
  17. Wen, W. et al. Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing. Cell Discov 6, 31 (2020).

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

  1. Huang, L. et al. Blood single cell immune profiling reveals the interferon-MAPK pathway mediated adaptive immune response for COVID-19, medrxiz
  2. Meckiff, B. et al. Single-cell transcriptomic analysis of SARS-CoV-2 reactive CD4+ T cells. bioRxiv (Preprint).
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: Sequencing data for this study is currently being deposited into the Gene Expression Omnibus and a reviewer link will be provided as soon as it is available
  3. Niu, X. et al. Analysis of Peripheral Blood T Cell Receptor and B Cell Receptor Repertoires Reveals Dynamic Adaptive Immune Responses in COVID-19 Patients. CellPress (Preprint).
    • Paper DOI
    • Species: Homo Sapiens
    • Data Sharing Statement: The raw data files were requested to Lead Contact.
  4. Zhang, F. et al. Adaptive immune responses to SARS-CoV-2 infection in severe versus mild individuals. Signal Transduction and Targeted Therapy 5 (156).
  5. Zhang, J.Y. et al. Single-cell landscape of immunological responses in COVID-19 patients . bioRxiv (Preprint).
    • Paper DOI
    • Species: Homo Sapiens
    • Beijing Institute of Genomics Accession: HRA000150 (system maintenance is in progress so the data is not currently visible)
3 Likes

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…

1 Like

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

Thank JP, added it above

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!

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

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

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

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…

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

OAS - Search Disease = SARS-COV-2

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.

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

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.

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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).”

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!

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

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

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.”

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!

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“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