Natural heteroclitic-like peptides are generated by SARS-CoV-2 mutations

Pre-existing SARS-2-specific T cells are predicted to cross-recognize BA.2.86

Effective monitoring of evolving SARS-CoV-2 variants requires understanding the potential effect of mutations on immune evasion. Here, we predicted the impact of BA.2.86-associated mutations on SARS-CoV-2-specific T cell responses. First, evaluating the effect on known experimentally defined T cell epitopes, we found that 72% and 89% of the total SARS-CoV-2 CD4 and CD8 responses were 100% conserved, with lower rates (56% and 72%) for just spike, a major structural protein. Among the mutated spike epitopes, however, 96% and 62% still bound the same reported HLA-restricting alleles. Additional prediction analyses comparing the ancestral and BA.2 sequences with BA.2.86 mutations identified several potentially novel BA.2.86 epitopes. By simulating exposure with BA.2, the large number of epitopes conserved with BA.2.86 suggests that variant-specific epitopes induced following breakthrough infection or bivalent vaccination can bridge the gap between ancestral immunization and upcoming circulating variants, allowing for a more stable T cell response across viral evolution.

FluoroSpot assay to analyze SARS-CoV-2-specific T cell responses

Monitoring antigen-specific T cell frequency and function is essential to assess the host immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Here, we present a FluoroSpot assay for concurrently detecting ex vivo antiviral cytokine production by SARS-CoV-2-specific T cells following peptide stimulation. We then detail intracellular cytokine staining by flow cytometry to further validate the FluoroSpot assay results and define the specific T cell subpopulations. For complete details on the use and execution of this protocol, please refer to Tiezzi et al. (2023).1.