Two mRNA vaccines (V1 and V2) from our previous study, encoding different CHIKV structural proteins, exhibit distinct immune effects and protective efficacy. However, the immune mechanisms underlying these differences remain unclear. In this study, we use an integrated multi-omics approach (single-cell RNA sequencing, immune repertoire sequencing, and Olink cytokine profiling) to elucidate the differential immune cell activation states induced by the two vaccines and the potential structural basis of the antigens that may account for these differences. We find that V2 induces sustained B cell activation, predominantly IgG-type memory antibodies, and a robust recall response following viral challenge. By contrast, V1 elicits only transient B cell activation and relatively weak T cell responses. These findings delineate a mechanistic pathway linking mRNA antigen structure to immune activation, functional differentiation, immunological memory, and protective efficacy. This work enhances our understanding of the immunological mechanisms underlying CHIKV mRNA vaccination and offers insights for rational vaccine antigen design.
