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SARS-CoV-2 vaccination induces immunological memory able to cross-recognize variants from Alpha to Omicron

Alison Tarke, Camila H. Coelho, Zeli Zhang, Jennifer M. Dan, Esther Dawen Yu, Nils Methot, Nathaniel I. Bloom, Benjamin Goodwin, Elizabeth Phillips, Simon Mallal, John Sidney, Gilberto Filaci, Daniela Weiskopf, View ORCID ProfileRicardo da Silva Antunes, View ORCID ProfileShane Crotty, Alba Grifoni, Alessandro Sette
doi: https://doi.org/10.1101/2021.12.28.474333
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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Camila H. Coelho
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
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Zeli Zhang
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), 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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Esther Dawen Yu
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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Nathaniel I. Bloom
1Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), 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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Elizabeth Phillips
4Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
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Simon Mallal
4Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
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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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Gilberto Filaci
2Department of Internal Medicine and Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, 16132, Italy
5Bioterapy Unit, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
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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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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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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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  • For correspondence: alex@lji.org agrifoni@lji.org shane@lji.org
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 shane@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 shane@lji.org
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SUMMARY

We address whether T cell responses induced by different vaccine platforms (mRNA-1273, BNT162b2, Ad26.COV2.S, NVX-CoV2373) cross-recognize SARS-CoV-2 variants. Preservation of at least 83% and 85% for CD4+ and CD8+ T cell responses was found, respectively, regardless of vaccine platform or variants analyzed. By contrast, highly significant decreases were observed for memory B cell and neutralizing antibody recognition of variants. Bioinformatic analyses showed full conservation of 91% and 94% of class II and class I spike epitopes. For Omicron, 72% of class II and 86% of class I epitopes were fully conserved, and 84% and 85% of CD4+ and CD8+ T cell responses were preserved. In-depth epitope repertoire analysis showed a median of 11 and 10 spike epitopes recognized by CD4+ and CD8+ T cells from vaccinees. Functional preservation of the majority of the T cell responses may play an important role as a second-level defense against diverse variants.

Competing Interest Statement

A.S. is a consultant for Gritstone Bio, Flow Pharma, Arcturus Therapeutics, ImmunoScape, CellCarta, Avalia, Moderna, Fortress and Repertoire. SC has consulted for GSK, JP Morgan, Citi, Morgan Stanley, Avalia NZ, Nutcracker Therapeutics, University of California, California State Universities, United Airlines, and Roche. All of the other authors declare no competing interests. LJI has filed for patent protection for various aspects of T cell epitope and vaccine design work.

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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SARS-CoV-2 vaccination induces immunological memory able to cross-recognize variants from Alpha to Omicron
Alison Tarke, Camila H. Coelho, Zeli Zhang, Jennifer M. Dan, Esther Dawen Yu, Nils Methot, Nathaniel I. Bloom, Benjamin Goodwin, Elizabeth Phillips, Simon Mallal, John Sidney, Gilberto Filaci, Daniela Weiskopf, Ricardo da Silva Antunes, Shane Crotty, Alba Grifoni, Alessandro Sette
bioRxiv 2021.12.28.474333; doi: https://doi.org/10.1101/2021.12.28.474333
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SARS-CoV-2 vaccination induces immunological memory able to cross-recognize variants from Alpha to Omicron
Alison Tarke, Camila H. Coelho, Zeli Zhang, Jennifer M. Dan, Esther Dawen Yu, Nils Methot, Nathaniel I. Bloom, Benjamin Goodwin, Elizabeth Phillips, Simon Mallal, John Sidney, Gilberto Filaci, Daniela Weiskopf, Ricardo da Silva Antunes, Shane Crotty, Alba Grifoni, Alessandro Sette
bioRxiv 2021.12.28.474333; doi: https://doi.org/10.1101/2021.12.28.474333

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