Early fate bias and TCR sequence shape CD8⁺ T cell differentiation and expansion

When a naive CD8⁺ T cell encounters an antigen, it proliferates into descendants with identical T cell receptors (TCRs), termed clones. Whether their differentiation toward effector or memory fates is stochastic or TCR-dependent has remained unclear, largely because the vast diversity of TCRs makes individual clones difficult to trace over time. Using single-cell RNA and TCR sequencing in acute LCMV Armstrong infection, we found that clonal distributions in blood reflect those in lymphoid organs, enabling nonlethal longitudinal tracking of clonal evolution. Tracing hundreds of clones, we found that memory clonal distribution is surprisingly uncoupled from early dominance; instead, early central memory precursor frequency predicts memory dominance. Leveraging convergent recombination, we identified clones with identical CDR3 amino acid sequences in mice and found that these natural biological replicates were more likely than chance to adopt similar fates, although substantial clone-to-clone variation remained. Applying the TCR distance algorithm, we further identified dominant motifs associated with enhanced expansion and effector-biased transcriptional programs, extending the TCR’s role in shaping clonal differentiation.