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Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases.
Tarke, Alison; Sidney, John; Kidd, Conner K; Dan, Jennifer M; Ramirez, Sydney I; Yu, Esther Dawen; Mateus, Jose; da Silva Antunes, Ricardo; Moore, Erin; Rubiro, Paul; Methot, Nils; Phillips, Elizabeth; Mallal, Simon; Frazier, April; Rawlings, Stephen A; Greenbaum, Jason A; Peters, Bjoern; Smith, Davey M; Crotty, Shane; Weiskopf, Daniela; Grifoni, Alba; Sette, Alessandro.
  • Tarke A; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Sidney J; Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa 16132, Italy.
  • Kidd CK; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Dan JM; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Ramirez SI; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Yu ED; Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
  • Mateus J; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • da Silva Antunes R; Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
  • Moore E; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Rubiro P; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Methot N; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Phillips E; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Mallal S; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Frazier A; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Rawlings SA; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.
  • Greenbaum JA; Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.
  • Peters B; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Smith DM; Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
  • Crotty S; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Weiskopf D; Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
  • Grifoni A; Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
  • Sette A; Division of Infectious Diseases and Global Public Health, Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
Cell Rep Med ; 2(2): 100204, 2021 02 16.
Article in English | MEDLINE | ID: covidwho-1057492
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
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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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Full text: Available Collection: International databases Database: MEDLINE Type of study: Observational study / Prognostic study Language: English Journal: Cell Rep Med Year: 2021 Document Type: Article Affiliation country: J.xcrm.2021.100204

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Full text: Available Collection: International databases Database: MEDLINE Type of study: Observational study / Prognostic study Language: English Journal: Cell Rep Med Year: 2021 Document Type: Article Affiliation country: J.xcrm.2021.100204