Functional characterization of CD4+ T-cell receptors cross-reactive for SARS-CoV-2 and endemic coronaviruses

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Abstract

Background. Recent studies have reported T cell immunity to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in unexposed donors, possibly due to cross-recognition by T-cells specific for common cold coronaviruses (CCCs). True T-cell cross-reactivity, defined as the recognition by a single TCR of more than one distinct peptide-MHC ligand, has never been shown in the context of SARS-CoV-2. Methods. We used the ViraFEST platform to identify T cell responses cross-reactive for the spike (S) glycoproteins of SARS-CoV-2 and CCCs at the T cell receptor (TCR) clonotype level in convalescent COVID-19 patients (CCPs) and SARS-CoV-2-unexposed donors. Confirmation of SARS-CoV-2/CCC cross-reactivity and assessments of functional avidity were performed using a TCR cloning and transfection system. Results. Memory CD4+ T-cell clonotypes that cross-recognized the S proteins of SARS-CoV-2 and at least one other CCC were detected in 65% of CCPs and unexposed donors. Several of these TCRs were shared among multiple donors. Cross-reactive T-cells demonstrated significantly impaired SARS-CoV-2-specific proliferation in vitro relative to mono-specific CD4+ T-cells, which was consistent with lower functional avidity of their TCRs for SARS CoV-2 relative to CCC. Conclusions. For the first time, our data confirm the existence of unique memory CD4+ T cell clonotypes cross-recognizing SARS-CoV-2 and CCCs. The lower avidity of cross-reactive TCRs for SARS-CoV-2 may be the result of antigenic imprinting, such that pre-existing CCC-specific memory T cells have reduced expansive capacity upon SARS-CoV-2 infection. Further studies are needed to determine how these cross-reactive T-cell responses impact clinical outcomes in COVID-19 patients.

Authors

Arbor G. Dykema, Boyang Zhang, Bezawit A. Woldemeskel, Caroline C. Garliss, Laurene S. Cheung, Dilshad Choudhury, Jiajia Zhang, Luis Aparicio, Sadhana Bom, Rufiaat Rashid, Justina X. Caushi, Emily Han-Chung Hsiue, Katherine Cascino, Elizabeth A. Thompson, Abena K. Kwaa, Dipika Singh, Sampriti Thapa, Alvaro A. Ordonez, Andrew Pekosz, Franco R. D'Alessio, Jonathan D. Powell, Srinivasan Yegnasubramanian, Shibin Zhou, Drew M. Pardoll, Hongkai Ji, Andrea L. Cox, Joel N. Blankson, Kellie N. Smith