T-Cell Receptors Cross-Reactive to Coronaviral Epitopes Homologous to the SPR Peptide

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Yana V. Serdyuk¹, Ksenia V. Zornikova¹, Dmitry V. Dianov¹, Nataliia O. Ivanova¹, Vassa D. Davydova¹, Ekaterina I. Fefelova¹, Tatiana A. Nenasheva¹, Saveliy A. Sheetikov¹, Apollinariya V. Bogolyubova^1,a*

¹National Medical Research Center for Hematology, Ministry of Health of the Russian Federation, 125167 Moscow, Russia

^* To whom correspondence should be addressed.

Received: May 15, 2024; Revised: July 26, 2024; Accepted: August 9, 2024

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The COVID-19 pandemic caused by the rapid spread of the novel coronavirus SARS-CoV-2, has promoted an interest in studying the T-cell immune response. It was found that the polyclonal and cross-reactive T-cell response against seasonal coronaviruses and other SARS-CoV-2 strains reduced disease severity. We investigated the immunodominant T-cell epitope SPRWYFYYYL from the nucleocapsid protein of SARS-CoV-2. The immune response to this epitope is characterized by the formation of highly homologous (convergent) receptors that have been found in the T-cell receptor (TCR) repertoires of different individuals. This epitope belongs to a group of highly conserved peptides that are rarely mutated in novel SARS-CoV-2 strains and are homologous to the epitopes of seasonal coronaviruses. It has been suggested that the cross-reactive response to homologous peptides contributes to the reduction of COVID-19 severity. However, some investigators have questioned this hypothesis, suggesting that the low affinity of the cross-reactive receptors reduces the strength of the immune response. The aim of this study was to evaluate the effect of amino acid substitutions in the SPR epitope on its binding affinity to specific TCRs. For this, we performed antigen-dependent cellular expansions were performed using samples from four COVID-19-transfected donors and sequenced their TCR repertoires. The resulting SPR-specific repertoire of β-chains in TCRs had a greater sequence diversity than the repertoire of α-chains. However, the TCR repertoires of all four donors contained public receptors, three of which were cloned and used to generate the Jurkat E6-1 TPR cell line. Only one of these receptors was activated by the SPR peptide and recognized with the same affinity by its mutant homologue LPRWYFYYY from seasonal coronaviruses. This indicates that the presence of the mutation did not affect the strength of the immune response, which may explain why the cross-reactive response to the SPR epitope is so frequent and contributes positively to COVID-19 infection.

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KEY WORDS: COVID-19, SARS-CoV-2, T-cell receptor, T-cell epitope, T-cell repertoire, cross-reactivity

DOI: 10.1134/S0006297924090098

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