Repeated mRNA vaccination sequentially boosts SARS-CoV-2-specific CD8⁺ T cells in persons with previous COVID-19

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hybrid immunity is more protective than vaccination or previous infection alone. To investigate the kinetics of spike-reactive T (T_S) cells from SARS-CoV-2 infection through messenger RNA vaccination in persons with hybrid immunity, we identified the T cell receptor (TCR) sequences of thousands of index T_S cells and tracked their frequency in bulk TCRβ repertoires sampled longitudinally from the peripheral blood of persons who had recovered from coronavirus disease 2019 (COVID-19). Vaccinations led to large expansions in memory T_S cell clonotypes, most of which were CD8⁺ T cells, while also eliciting diverse T_S cell clonotypes not observed before vaccination. TCR sequence similarity clustering identified public CD8⁺ and CD4⁺ TCR motifs associated with spike (S) specificity. Synthesis of longitudinal bulk ex vivo single-chain TCRβ repertoires and paired-chain TCRɑβ sequences from droplet sequencing of T_S cells provides a roadmap for the rapid assessment of T cell responses to vaccines and emerging pathogens.