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Efforts are being made worldwide to understand the immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease 2019 (COVID-19) pandemic, including the impact of T cell immunity and cross-recognition with seasonal coronaviruses. Screening of SARS-CoV-2 peptide pools revealed that the nucleocapsid (N) protein induced an immunodominant response in HLA-B7+ COVID-19-recovered individuals that was also detectable in unexposed donors. A single N-encoded epitope that was highly conserved across circulating coronaviruses drove this immunodominant response. In vitro peptide stimulation and crystal structure analyses revealed T cell-mediated cross-reactivity toward circulating OC43 and HKU-1 betacoronaviruses but not 229E or NL63 alphacoronaviruses because of different peptide conformations. T cell receptor (TCR) sequencing indicated that cross-reactivity was driven by private TCR repertoires with a bias for TRBV27 and a long CDR3β loop. Our findings demonstrate the basis of selective T cell cross-reactivity for an immunodominant SARS-CoV-2 epitope and its homologs from seasonal coronaviruses, suggesting long-lasting protective immunity.
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•ICS assay detects SARS-CoV-2-specific T cells in unexposed and recovered donors•Epitope mapping identifies one dominant HLA-B7-restricted epitope•Identical TCR clonotypes recognize SARS-CoV-2 and betacoronaviruses epitopes•Crystal structures reveal distinct peptide conformations between alpha- and betacoronaviruses
The impact of seasonal coronaviruses on immune responses to SARS-CoV-2 is an active area of research. Lineburg et al. identify CD8+ T cells specific for a conserved and immunodominant SARS-CoV-2 epitope in HLA-B7+ individuals. Furthermore, SARS-CoV-2 epitope-specific CD8+ T cells display cross-reactivity to beta- but not alphacoronaviruses because of distinct peptide-HLA conformations.