COVID-19 and iReceptor

In collaboration with the AIRR Community and in response to the AIRR Community's call for sharing COVID-19 related AIRR-seq data the iReceptor Project and iReceptor Plus projects have prepared an iReceptor Turnkey Repository and the project team is curating public COVID-19 data in an AIRR COVID-19 repository on behalf of the community. In addition, we are working with our partners at VDJServer to curate other COVID-19 data. This COVID-19 data is part of the AIRR Data Commons and is searchable using the iReceptor Gateway.If you have or know of any public COVID-19 AIRR-seq data please contact us at support@ireceptor.org. If you are interested in tracking the research on COVID-19, and in particular those studies that are producing AIRR-seq data, please follow along on the b-t.cr Wiki on COVID-19 public data. This area is evolving fast, so please let us know if there are any papers or data sets available.AIRR-seq data from the following papers are available in the AIRR Data Commons:

  1. Nielsen, S. et al. B cell clonal expansion and convergent antibody responses to SARS-CoV-2. Cell Host & Microbe DOI Research Square Preprint. DOI.
  2. 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). DOI.
  3. Galson, J. et al. Deep sequencing of B cell receptor repertoires from COVID-19 patients reveals strong convergent immune signatures. bioRxiv (Preprint). DOI.
  4. Liao, M. et al. Single-cell Landscape of Bronchoalveolar Immune Cells in Patients With COVID-19, Nature Medicine, 26, 842-844, 2020. DOI.
  5. Schultheiß 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) DOI.
  6. Shomuradova et al. SARS-CoV-2 epitopes are recognized by a public and diverse repertoire of human T-cell receptors, medRxiv (Preprint). DOI.
  7. Alsoussi, W. et al. A Potently Neutralizing Antibody Protects Mice against SARS-CoV-2 Infection. J. Immunol. 2020. DOI.
  8. Kim, S et al. Stereotypic Neutralizing VH Clonotypes Against SARS-CoV-2 RBD in COVID-19 Patients and the Healthy Population. bioRxiv (Preprint). DOI.
  9. Kuri-Cervantes, L. et al. Comprehensive mapping of immune perturbations associated with severe COVID-19. Science Immunology (2020). DOI.
  10. Nolan 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). DOI.
    • Note: This data comes from the Adaptive ImmuneRace project, and is represented as 7 studies in the AIRR Data Commons, a different study for each of the data sets from the independent data sources in the ImmuneRace project. In addition, this study is stored separately in two different repositories. The iReceptor Public Archive has stored the original annotations as provided by Adaptive Biotech while VDJServer has downloaded the sequence data and re-annotated that data using igblast.
  11. Montague et al. Dynamics of B-cell repertoires and emergence of cross-reactive responses in COVID-19 patients with different disease severity, mexRxiv (Preprint). DOI.
  12. Wen et al. Immune cell profiling of COVID-19 patients in the recovery stage by single-cell sequencing, Cell Discovery, 6, 31 (2020). DOI.
  13. Mor et al. Multi-Clonal Live SARS-CoV-2 In Vitro Neutralization by Antibodies Isolated from Severe COVID-19 Convalescent Donors. PLOS Pathogens, Feb 11, 2021. DOI.
  14. Sokal et al. Maturation and persistence of the anti-SARS-CoV-2 memory B cell response. Cell, Volume 184, Issue 5, P1201-1213.E14, March 04, 2021. DOI.
  15. Goel et al. Distinct antibody and memory B cell responses in SARS-CoV-2 naïve and recovered individuals following mRNA vaccination, Science Immunology, Apr 15, 2021: Vol. 6, Issue 58. DOI.
  16. Turner et al. SARS-CoV-2 mRNA vaccines induce persistent human germinal centre responses, Nature, June 28, 2021. DOI.
  17. Goel et al. mRNA Vaccination Induces Durable Immune Memory to SARS-CoV-2 with Continued Evolution to Variants of Concern. bioRXiv preprint. DOI.
  18. Schmitz et al. A vaccine-induced public antibody protects against SARS-CoV-2 and emerging variants. Immunity, VOLUME 54, ISSUE 9, P2159-2166.E6, SEPTEMBER 14, 2021 DOI.
  19. Alameh et al. Lipid nanoparticles enhance the efficacy of mRNA and protein subunit vaccines by inducing robust T follicular helper cell and humoral responses. Immunity, VOLUME 54, ISSUE 12, P2877-2892.E7, DECEMBER 14, 2021 DOI.
  20. Joseph et al. Global patterns of antigen receptor repertoire disruption across adaptive immune compartments in COVID-19, PNAS, Volume 119, Number 34, August 9, 2022 DOI.
  21. Minervina et al. SARS-CoV-2 antigen exposure history shapes phenotypes and specificity of memory CD8+ T cells, Nature Immunology, Volume 23, Pages 781–790 (2022) DOI.

Details on the provenance of the iReceptor curated AIRR COVID-19 data can be found on the Repository Provenance page.