Repeated mRNA vaccination and breakthrough infection reveal durable dominance but diminishing recall of vaccine-induced CD8⁺ T-cell clones

Successive mRNA vaccinations preserve SARS-CoV-2-specific T-cell immunity, but how individual CD8⁺ T-cell clones behave across repeated booster doses and breakthrough infection (BTI) remains poorly defined. We longitudinally tracked bulk CD8⁺ TCRβ repertoires and spike-specific tetramer⁺ CD8⁺ T cells in adult participants across the third and fourth vaccine doses and subsequent BTI. Each booster continued to recruit previously unexpanded "new" responder clonotypes, but both the number and summed frequency of newly engaged clones declined with successive doses. In contrast, clones first recruited by the initial prime-boost doses-particularly those expanded after dose 2-formed a durable, hierarchically dominant memory pool that persisted for more than two years yet displayed progressively attenuated recall with later boosters. BTI revealed a complementary mode of repertoire remodeling: newly engaged clones that had not responded to prior vaccinations showed the strongest, but transient, expansion, broadening the antigenic targets beyond spike. On the other hand, vaccine-induced clones showed limited recall response while sustaining their dominance in the long term. Together, these findings indicate that repeated mRNA vaccination maintains a stable pool of early-established CD8⁺ T-cell clones but progressively limits their recall capacity, whereas BTI mobilizes additional, partially distinct clonotypes that expand robustly and broaden antigenic coverage.