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Broadly-recognized, cross-reactive SARS-CoV-2 CD4 T cell epitopes are highly conserved across human coronaviruses and presented by common HLA alleles [preprint]

Becerra-Artiles, Aniuska
Calvo-Calle, J Mauricio
Co, Mary Dawn T.
Nanaware, Padma P.
Cruz, John
Weaver, Grant
Lu, Liying
Forconi, Catherine S
Finberg, Robert W.
Moormann, Ann M.
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Abstract

Sequence homology between SARS-CoV-2 and common-cold human coronaviruses (HCoVs) raises the possibility that memory responses to prior HCoV infection can impact the T cell response in COVID-19. We studied T cells recognizing SARS-CoV-2 and HCoVs in convalescent COVID-19 donors, and identified a highly conserved SARS-CoV-2 sequence S811-831, with two overlapping epitopes presented by common MHC-II proteins HLA-DQ5 and HLA-DP4. These epitopes were recognized by CD4+ T cells from convalescent COVID-19 donors, mRNA vaccine recipients, and by low-abundance CD4+ T cells in uninfected donors. TCR sequencing revealed a diverse repertoire with public TCRs. CD4+ T cell cross-reactivity was driven by the remarkably strong conservation of T cell contact residues in both HLA-DQ5 and HLA-DP4 binding frames, with distinct patterns of HCoV cross-reactivity explained by MHC-II binding preferences and substitutions at secondary TCR contact sites. These data highlight S811-831 as a highly-conserved CD4+ T cell epitope broadly recognized across human populations.

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bioRxiv 2022.01.20.477107; doi: https://doi.org/10.1101/2022.01.20.477107. Link to preprint on bioRxiv.

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10.1101/2022.01.20.477107
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This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.

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Now published in Cell Reports doi: 10.1016/j.celrep.2022.110952

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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.