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Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees

Alison Tarke, John Sidney, Nils Methot, View ORCID ProfileYun Zhang, View ORCID ProfileJennifer M. Dan, Benjamin Goodwin, Paul Rubiro, Aaron Sutherland, View ORCID ProfileRicardo da Silva Antunes, April Frazier, Stephen A. Rawlings, Davey M. Smith, Bjoern Peters, Richard H. Scheuermann, Daniela Weiskopf, View ORCID ProfileShane Crotty, View ORCID ProfileAlba Grifoni, Alessandro Sette
doi: https://doi.org/10.1101/2021.02.27.433180
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
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John Sidney
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
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Nils Methot
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
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Yun Zhang
4J. Craig Venter Institute, La Jolla, CA 92037, USA
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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
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Benjamin Goodwin
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
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Paul Rubiro
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
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Aaron Sutherland
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
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Ricardo da Silva Antunes
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
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April Frazier
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
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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
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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
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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
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Richard H. Scheuermann
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
4J. Craig Venter Institute, La Jolla, CA 92037, USA
5Department of Pathology, University of California, San Diego, CA 92093
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Daniela Weiskopf
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
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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
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Alba Grifoni
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
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  • 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
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  • For correspondence: alex@lji.org agrifoni@lji.org
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SUMMARY

The emergence of SARS-CoV-2 variants highlighted the need to better understand adaptive immune responses to this virus. It is important to address whether also CD4+ and CD8+ T cell responses are affected, because of the role they play in disease resolution and modulation of COVID-19 disease severity. Here we performed a comprehensive analysis of SARS-CoV-2-specific CD4+ and CD8+ T cell responses from COVID-19 convalescent subjects recognizing the ancestral strain, compared to variant lineages B.1.1.7, B.1.351, P.1, and CAL.20C as well as recipients of the Moderna (mRNA-1273) or Pfizer/BioNTech (BNT162b2) COVID-19 vaccines. Similarly, we demonstrate that the sequences of the vast majority of SARS-CoV-2 T cell epitopes are not affected by the mutations found in the variants analyzed. Overall, the results demonstrate that CD4+ and CD8+ T cell responses in convalescent COVID-19 subjects or COVID-19 mRNA vaccinees are not substantially affected by mutations found in the SARS-CoV-2 variants.

Competing Interest Statement

A.S. is a consultant for Gritstone, Flow Pharma, Oxford Immunetech, Caprion, Arcturus 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. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted March 01, 2021.
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Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees
Alison Tarke, John Sidney, Nils Methot, Yun Zhang, Jennifer M. Dan, Benjamin Goodwin, Paul Rubiro, Aaron Sutherland, Ricardo da Silva Antunes, April Frazier, Stephen A. Rawlings, Davey M. Smith, Bjoern Peters, Richard H. Scheuermann, Daniela Weiskopf, Shane Crotty, Alba Grifoni, Alessandro Sette
bioRxiv 2021.02.27.433180; doi: https://doi.org/10.1101/2021.02.27.433180
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Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees
Alison Tarke, John Sidney, Nils Methot, Yun Zhang, Jennifer M. Dan, Benjamin Goodwin, Paul Rubiro, Aaron Sutherland, Ricardo da Silva Antunes, April Frazier, Stephen A. Rawlings, Davey M. Smith, Bjoern Peters, Richard H. Scheuermann, Daniela Weiskopf, Shane Crotty, Alba Grifoni, Alessandro Sette
bioRxiv 2021.02.27.433180; doi: https://doi.org/10.1101/2021.02.27.433180

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