Clone tracking through repeated malaria identifies high-fidelity memory CD4 T cell responses

Few studies have tracked human CD4⁺ T cell clones through repeated infections. We used longitudinal single-cell RNA and T cell receptor (TCR) tracking to study the functional stability and memory potential of CD4⁺ T cell clonotypes during repeated Plasmodium falciparum (Pf) infections in Ugandan children and adults. Nearly all clonotypes displayed a strong preference for one of seven CD4⁺ subsets. This phenomenon of "clonal fidelity" was influenced by clonal expansion, linking T cell polarization and proliferation in vivo. Using clone tracking, we characterized subset-specific activation trajectories and identified antigen-specific clones. Type 1 regulatory T (T_R1) cells accounted for nearly 90% of Pf-specific CD4⁺ T cells in blood. Tracking these clones longitudinally for hundreds of days, we observed malaria-induced expansion of T_R1 effectors, long-term persistence of T_R1 memory cells, and high-fidelity recall responses after reinfection. This work establishes clonal fidelity as a natural phenomenon and demonstrates the stable, long-term memory potential of T_R1 cells.