Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

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

View ORCID ProfileAlison Tarke, John Sidney, Conner K Kidd, View ORCID ProfileJennifer M. Dan, View ORCID ProfileSydney I. Ramirez, Esther Dawen Yu, View ORCID ProfileJose Mateus, Ricardo da Silva Antunes, Erin Moore, Paul Rubiro, Nils Methot, Elizabeth Phillips, View ORCID ProfileSimon Mallal, View ORCID ProfileApril Frazier, View ORCID ProfileStephen A. Rawlings, View ORCID ProfileJason A. Greenbaum, View ORCID ProfileBjoern Peters, View ORCID ProfileDavey M. Smith, View ORCID ProfileShane Crotty, View ORCID ProfileDaniela Weiskopf, View ORCID ProfileAlba Grifoni, View ORCID ProfileAlessandro Sette
doi: https://doi.org/10.1101/2020.12.08.416750
Alison Tarke
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
2Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, 16132, Italy
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Alison Tarke
John Sidney
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Conner K Kidd
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jennifer M. Dan
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
3Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jennifer M. Dan
Sydney I. Ramirez
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
3Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sydney I. Ramirez
Esther Dawen Yu
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jose Mateus
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jose Mateus
Ricardo da Silva Antunes
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Erin Moore
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Paul Rubiro
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Nils Methot
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Elizabeth Phillips
4Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Simon Mallal
4Institute for Immunology and Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Simon Mallal
April Frazier
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for April Frazier
Stephen A. Rawlings
3Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Stephen A. Rawlings
Jason A. Greenbaum
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jason A. Greenbaum
Bjoern Peters
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
3Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Bjoern Peters
Davey M. Smith
3Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Davey M. Smith
Shane Crotty
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
3Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Shane Crotty
Daniela Weiskopf
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Daniela Weiskopf
Alba Grifoni
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Alba Grifoni
  • For correspondence: alex@lji.org agrifoni@lji.org
Alessandro Sette
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
3Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Alessandro Sette
  • For correspondence: alex@lji.org agrifoni@lji.org
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

SUMMARY

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 Statement

A.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.

Footnotes

  • Lead Contact: alex{at}lji.org (A.S.)

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted December 09, 2020.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases
Alison Tarke, John Sidney, Conner K Kidd, Jennifer M. Dan, Sydney I. Ramirez, Esther Dawen Yu, Jose Mateus, Ricardo da Silva Antunes, Erin Moore, Paul Rubiro, Nils Methot, Elizabeth Phillips, Simon Mallal, April Frazier, Stephen A. Rawlings, Jason A. Greenbaum, Bjoern Peters, Davey M. Smith, Shane Crotty, Daniela Weiskopf, Alba Grifoni, Alessandro Sette
bioRxiv 2020.12.08.416750; doi: https://doi.org/10.1101/2020.12.08.416750
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Comprehensive analysis of T cell immunodominance and immunoprevalence of SARS-CoV-2 epitopes in COVID-19 cases
Alison Tarke, John Sidney, Conner K Kidd, Jennifer M. Dan, Sydney I. Ramirez, Esther Dawen Yu, Jose Mateus, Ricardo da Silva Antunes, Erin Moore, Paul Rubiro, Nils Methot, Elizabeth Phillips, Simon Mallal, April Frazier, Stephen A. Rawlings, Jason A. Greenbaum, Bjoern Peters, Davey M. Smith, Shane Crotty, Daniela Weiskopf, Alba Grifoni, Alessandro Sette
bioRxiv 2020.12.08.416750; doi: https://doi.org/10.1101/2020.12.08.416750

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Immunology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4383)
  • Biochemistry (9601)
  • Bioengineering (7097)
  • Bioinformatics (24868)
  • Biophysics (12621)
  • Cancer Biology (9959)
  • Cell Biology (14358)
  • Clinical Trials (138)
  • Developmental Biology (7954)
  • Ecology (12110)
  • Epidemiology (2067)
  • Evolutionary Biology (15989)
  • Genetics (10929)
  • Genomics (14745)
  • Immunology (9871)
  • Microbiology (23680)
  • Molecular Biology (9486)
  • Neuroscience (50884)
  • Paleontology (369)
  • Pathology (1540)
  • Pharmacology and Toxicology (2683)
  • Physiology (4019)
  • Plant Biology (8657)
  • Scientific Communication and Education (1510)
  • Synthetic Biology (2397)
  • Systems Biology (6439)
  • Zoology (1346)