Cited by 540vaccines and immunoinformatics approachesSARS-CoV-2 and COVID-19 ResearchImmunotherapy and Immune Responses

Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases

Open access
Tarke, Alison, Sidney, John, Kidd, Conner K., Dan, Jennifer M., Ramirez, Sydney I., Yu, Esther Dawen, Mateus, Jose, da Silva Antunes, Ricardo +14 more·2021·Cell Reports Medicine

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Abstract

T cells are involved in control of SARS-CoV-2 infection. To establish the patterns of immunodominance of different SARS-CoV-2 antigens and precisely measure virus-specific CD4 + and CD8 + T cells, we study epitope-specific T cell responses of 99 convalescent coronavirus disease 2019 (COVID-19) cases. The SARS-CoV-2 proteome is probed using 1,925 peptides spanning the entire genome, ensuring an unbiased coverage of human leukocyte antigen (HLA) alleles for class II responses. For HLA class I, we study an additional 5,600 predicted binding epitopes for 28 prominent HLA class I alleles, accounting for wide global coverage. We identify several hundred HLA-restricted SARS-CoV-2-derived epitopes. Distinct patterns of immunodominance are observed, which differ for CD4 + T cells, CD8 + T cells, and antibodies. The class I and class II epitopes are combined into epitope megapools to facilitate identification and quantification of SARS-CoV-2-specific CD4 + and CD8 + T cells.

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Authors
Tarke, A., Sidney, J., Kidd, C. K., Dan, J. M., Ramirez, S. I., Yu, E. D., Mateus, J., da Silva Antunes, R., Moore, E., Rubiro, P., Methot, N., Phillips, E., Mallal, S., Frazier, A., Rawlings, S. A., Greenbaum, J. A., Peters, B., Smith, D. M., Crotty, S., Weiskopf, D., Grifoni, A., & Sette, A.
Affiliations
  • La Jolla Institute for Immunology (US)
  • Murdoch University (AU)
  • University of California San Diego (US)
Corresponding author
  • Grifoni, Alba
  • Sette, Alessandro
Venue
Cell Reports Medicine
Publisher
Elsevier BV
Published
2021-02
Volume
2
Issue
2
Pages
100204
ISSN
2666-3791 (ISSN-L)
OpenAlex
W3122458452
Cited by
540
References
58
Citations by year
2026: 22 · 2025: 41 · 2024: 71 · 2023: 118 · 2022: 156 · 2021: 131 · 2014: 1
FWCI
37.36
Type
journal article
Language
en
Open access
Locations
  • Cell Reports Medicine (publishedVersion, cc-by-nc-nd)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion, other-oa)
  • PubMed Central (submittedVersion)
  • Murdoch University Research Portal (submittedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
  • ImmPort
Funders
  • University of California, San Diego (AI007036and AI007384)
  • National Institute of Allergy and Infectious Diseases (75N93019C00001, AI42742, 75N9301900065)
  • National Institutes of Health (AI036214, U01 CA260541-01, AI135078)
  • John and Mary Tu Foundation
  • Gilead Sciences
  • Università degli Studi di Genova
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
  • Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
  • Life Sciences › Immunology and Microbiology › Immunology › Immunotherapy and Immune Responses
Keywords
SARS-CoV-2, COVID-19 pandemic, epitope-specific T cell responses, HLA-restricted epitopes, CD4+ T cells, CD8+ T cells, HLA class II, convalescent patients, virus-specific T cells

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