PT  - JOURNAL ARTICLE
AU  - Alison Tarke
AU  - John Sidney
AU  - Conner K Kidd
AU  - Jennifer M. Dan
AU  - Sydney I. Ramirez
AU  - Esther Dawen Yu
AU  - Jose Mateus
AU  - Ricardo da Silva Antunes
AU  - Erin Moore
AU  - Paul Rubiro
AU  - Nils Methot
AU  - Elizabeth Phillips
AU  - Simon Mallal
AU  - April Frazier
AU  - Stephen A. Rawlings
AU  - Jason A. Greenbaum
AU  - Bjoern Peters
AU  - Davey M. Smith
AU  - Shane Crotty
AU  - Daniela Weiskopf
AU  - Alba Grifoni
AU  - Alessandro Sette
TI  - Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases
AID  - 10.1101/2020.12.08.416750
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.12.08.416750
4099  - http://biorxiv.org/content/early/2020/12/09/2020.12.08.416750.short
4100  - http://biorxiv.org/content/early/2020/12/09/2020.12.08.416750.full
AB  - 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 studied epitope-specific T cell responses of approximately 100 convalescent COVID-19 cases. The SARS-CoV-2 proteome was probed using 1,925 peptides spanning the entire genome, ensuring an unbiased coverage of HLA alleles for class II responses. For HLA class I, we studied an additional 5,600 predicted binding epitopes for 28 prominent HLA class I alleles, accounting for wide global coverage. We identified several hundred HLA-restricted SARS-CoV-2-derived epitopes. Distinct patterns of immunodominance were observed, which differed for CD4+ T cells, CD8+ T cells, and antibodies. The class I and class II epitopes were combined into new epitope megapools to facilitate identification and quantification of SARS-CoV-2-specific CD4+ and CD8+ T cells.Competing Interest StatementA.S. is a consultant for Gritstone, Flow Pharma, Merck, Epitogenesis, Gilead and Avalia. S.C. is a consultant for Avalia. All other authors declare no conflict of interest. LJI has filed for patent protection for various aspects of vaccine design and identification of specific epitopes.