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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

Becerra-Artiles, Aniuska
Calvo-Calle, J Mauricio
Co, Mary Dawn
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 affect T cell response in COVID-19. We studied T cell responses to SARS-CoV-2 and HCoVs in convalescent COVID-19 donors and identified a highly conserved SARS-CoV-2 sequence, S811-831, with overlapping epitopes presented by common MHC class II proteins HLA-DQ5 and HLA-DP4. These epitopes are recognized by low-abundance CD4 T cells from convalescent COVID-19 donors, mRNA vaccine recipients, and uninfected donors. TCR sequencing revealed a diverse repertoire with public TCRs. T cell cross-reactivity is driven by the high conservation across human and animal coronaviruses of T cell contact residues in both HLA-DQ5 and HLA-DP4 binding frames, with distinct patterns of HCoV cross-reactivity explained by MHC class 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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Becerra-Artiles A, Calvo-Calle JM, Co MD, Nanaware PP, Cruz J, Weaver GC, Lu L, Forconi C, Finberg RW, Moormann AM, Stern LJ. Broadly recognized, cross-reactive SARS-CoV-2 CD4 T cell epitopes are highly conserved across human coronaviruses and presented by common HLA alleles. Cell Rep. 2022 Jun 14;39(11):110952. doi: 10.1016/j.celrep.2022.110952. Epub 2022 May 27. PMID: 35675811; PMCID: PMC9135679.

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DOI
10.1016/j.celrep.2022.110952
PubMed ID
35675811
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This article is based on a previously available preprint in bioRxiv, https://doi.org/10.1101/2022.01.20.477107.

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Copyright 2022 The Author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).; Attribution-NonCommercial-NoDerivatives 4.0 International