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Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases
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) cas...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7837622/ https://www.ncbi.nlm.nih.gov/pubmed/33521695 http://dx.doi.org/10.1016/j.xcrm.2021.100204 |
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author | 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 |
author_facet | 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 |
author_sort | Tarke, Alison |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7837622 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-78376222021-01-27 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 Cell Rep Med Article 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. Elsevier 2021-01-26 /pmc/articles/PMC7837622/ /pubmed/33521695 http://dx.doi.org/10.1016/j.xcrm.2021.100204 Text en © 2021 The Author(s) http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Article 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 Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases |
title | Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases |
title_full | Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases |
title_fullStr | Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases |
title_full_unstemmed | Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases |
title_short | Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases |
title_sort | comprehensive analysis of t cell immunodominance and immunoprevalence of sars-cov-2 epitopes in covid-19 cases |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7837622/ https://www.ncbi.nlm.nih.gov/pubmed/33521695 http://dx.doi.org/10.1016/j.xcrm.2021.100204 |
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