Conformational bias in SARS-CoV-2 Spike CD4+ T-cell epitope dominance

Epitope-specific T cells provide significant long-lived protection afforded by adaptive immunity to SARS-CoV-2 spike. CD4+ T-cell epitope peptides that are generated by non-ATP-dependent antigen-processing proteases bind with modest specificity to MHC class II molecules in the endo-lysosome. Studies document the influence of antigen-presenting cell type, manner of endocytosis, and antigen conformation on the strength of CD4+ T-cell response. Nevertheless, few studies report changes in epitope dominance due to circumstances of antigen exposure, which could shape proteolytic antigen processing in the class-II pathway because conformational domains limit proteolysis or MHCII binding.

Processing of SARS-CoV-2 spike was modeled using limited proteolysis of soluble spike trimer, and the effect of spike conformation on CD4+ T-cell epitope dominance was analyzed using IL-2 Elispots responding to two nine-peptide pools from conformationally stable and unstable regions of spike.

Protease-sensitive sites coincided with domain boundaries and other conformationally unstable regions, confirming that structure limits proteolysis. The ratio of CD4+ T-cell response to stable and unstable peptide pools in two non-hospitalized human subjects cohorts distinguished whether exposure was by infection or vaccination.

Circumstances of exposure to spike, e.g., spike mRNA vaccination or SARS-CoV-2 infection, could influence populations of antigen presenting cells and their levels of activation, resulting in different patterns of spike fragmentation, peptide loading, and T-cell response. Circumstances of exposure also affect spike conformational changes that contribute to distinct dominance patterns. Thus, epitope dominance patterns potentially indicate exposure history, immune imprinting, and potentially the protectiveness of the CD4+ T-cell response.