CD8+ T-cell memory induced by successive SARS-CoV-2 mRNA vaccinations is characterized by clonal replenishment [scTCR-seq, CITE-seq]]

mRNA vaccines against the Spike glycoprotein of severe acute respiratory syndrome type 2 coronavirus (SARS-CoV-2) elicit strong T-cell responses. However, it is unknown whether the repertoire of memory T cell clones changes between primary and secondary vaccinations. Here, we analyzed the kinetic profile of Spike-reactive T-cell clones before the first dose, one week after the first and second dose, and four weeks after the second dose of the BNT162b mRNA vaccine. Interestingly, a new set of Spike-reactive CD8+ T cell clones exhibited the greatest expansion following secondary vaccination and replaced the clones that had responded to the primary vaccination. Single-cell mRNA/protein/TCR analysis revealed that the first-responder clones exhibited a terminally differentiated phenotype, whereas second-responder clones exhibited an actively proliferating phenotype. These results show that Spike-reactive T cell responses induced by repetitive mRNA vaccination are augmented and maintained by replacement with newly-generated clones with proliferative potential.