Extensive cross-reactive T cell epitopes across SARS-CoV-2 Omicron variant spikes with finite immune evasion mutations.

Abstract

Background: The impact of spike protein mutations on T cell responses, particularly in SARS-CoV-2 Omicron variants, remains incompletely elucidated.

Methods: In this study, DNA vaccines encoding the spike protein of both the ancestral virus and Omicron variants were developed and administered in conjunction with a Th1-type adjuvant to BALB/c mice. Cross-reactive T cell responses to the spike proteins were assessed in the splenocytes of these mice using IFN-γ ELISPOT assays. Additionally, flow cytometry (FACS) was utilized to evaluate IFN-γ⁺ CD4⁺ and CD8⁺ T cell responses to various peptides covering the entire spike protein sequence.

Results: Our study demonstrated that only a limited number of mice, along with a minor subset of their splenocytes vaccinated with the DNA vaccine targeting the original spike protein, exhibited weak cross-reactivity with Omicron variants. This observation underscores the differences in T cell epitopes between Omicron variants and the prototype spikes, indicating that at least 50 and 37 mutations in Omicron variants contribute to their evasion of CD4⁺ and CD8⁺ T cell responses, respectively. Conversely, DNA vaccines encoding spike proteins from Omicron variants successfully elicited strong cross-reactive T cell responses in the immunized mice. In particular, Vaccines targeting the BA.1, BA.5, XBB.1.5, and JN.1 variants demonstrated the most robust and comprehensive T cell immune responses among Omicron variants. This efficacy is attributed to the presence of less than eleven T cell immune evasion mutations in their spike proteins, alongside numerous mutations that enhance T cell responses.

Conclusions: These findings underscore the imperative to update WHO emergency vaccine policies and contribute to the development of more effective vaccines and immunization strategies, to better control the infections caused by emerging Omicron variants.