SARS-CoV-2 T Cell Responses Elicited by COVID-19 Vaccines or Infection Are Expected to Remain Robust against Omicron

Abstract

Omicron, the most recent SARS-CoV-2 variant of concern (VOC), harbours multiple mutations in the spike protein that were not observed in previous VOCs. Initial studies suggest Omicron to substantially reduce the neutralizing capability of antibodies induced from vaccines and previous infection. However, its effect on T cell responses remains to be determined. Here, we assess the effect of Omicron mutations on known T cell epitopes and report data suggesting T cell responses to remain broadly robust against this new variant.

Keywords: COVID-19; Omicron; SARS-CoV-2; T cell epitopes; deletions; insertions; mutations; peptide-HLA binding; variants.

Figure 1

Percentage of S-specific SARS-CoV-2 T cell epitopes with and without mutations present in the five VOCs: (A) CD8⁺ T cell epitopes. (B) CD4⁺ T cell epitopes. Only epitopes of canonical lengths (CD8⁺: 8–12 residues and CD4⁺:15 residues) were included in the analysis. VOC-defining mutations (that also include deletions) were obtained from https://covariants.org (accessed on 9 December 2021). Predicted effect of Omicron mutations on peptide-HLA binding of SARS-CoV-2 (C) CD8⁺ and (D) CD4⁺ T cell epitopes. NetMHCpan-4.1 and NetMHCpanII-4.0 were employed for predicting peptide-HLA binding using the default parameters [13].

Figure 2

Percentage of SARS-CoV-2 T cell epitopes derived from proteins besides S with and without Omicron-defining mutations: (A) CD8⁺ T cell epitopes. (B) CD4⁺ T cell epitopes. Only epitopes of canonical lengths (CD8⁺: 8–12 residues and CD4⁺:15 residues) were included in the analysis. Omicron-defining mutations (that also include deletions) were obtained from https://covariants.org (accessed on 9 December 2021).