Repeated exposure to a conserved antigen drives dynamic clonal and epitope succession

Defining the dynamics of T cell memory formation with epitope-level resolution can inform vaccine design. Longitudinal T cell receptor (TCR) sequencing after COVID-19 mRNA vaccination has enabled detailed tracking of T cell responses; however, connecting expanded clonotypes following antigen exposure to their cognate epitopes remains a challenge due to limited curated paired /{beta}TCR information. To fill this gap, we used TIRTL-seq to identify paired /{beta}TCRs from CD8+ T cell lineages associated with mRNA immunization in serial samples across 38 healthy donors over multiple rounds of vaccinations. Vaccine-associated paired /{beta}TCRs, identified based on their longitudinal kinetics, were grouped according to sequence similarity to infer their shared epitope specificities. We assigned epitope specificity to 1,109 clonotypes, recognizing 15 SARS-CoV-2 spike targets, identifying multiple previously undescribed responses, and confirming putative specificities experimentally. This approach uncovered a striking pattern of clonal succession in anti-spike T cell memory lineages resulting from repeated vaccination, characterized by a transition from low-avidity clones recognizing conserved coronavirus epitopes to high-avidity clones targeting epitopes unique to SARS-CoV-2. These results highlight the surprisingly dynamic responses underlying homologous boosting, suggest avenues for improving vaccine strategies, and pave the way for repertoire-based monitoring of antigen-specific T cell immunity.