Smallpox-specific T cells in vaccinated centenarians exhibit different phenotypic and metabolic traits of long-term memory compared to SARS-CoV-2-specific memory T cells.

Long-term T cell memory is essential for durable protection against infectious diseases, yet the cellular and molecular programs that sustain antigen-specific immunity for decades in humans remain incompletely understood. Here, we combine high-dimensional single-cell approaches to dissect CD4⁺ and CD8⁺ T cell memory elicited by a remote childhood vaccination (vaccinia/smallpox) and a recent vaccine (SARS-CoV-2) across the human lifespan, including centenarians. Using multiparametric flow cytometry, VASA-seq total RNA sequencing with TCR reconstruction, and single-cell metabolic regulome profiling (scMEP), we show that antigen-specific T cell frequencies are remarkably preserved with age, whereas differentiation state, functional capacity, clonal architecture, transcriptional regulation, and metabolic programming diverge profoundly according to antigenic history. Vaccinia-specific T cells display stem-like and central memory phenotypes, preferential clonal expansion within long-lived compartments, and transcriptional and metabolic programs dominated by fatty acid oxidation and oxidative phosphorylation. In contrast, SARS-CoV-2–specific T cells are enriched in effector and transitional memory subsets with Th1–Th17/Tc1–Tc17 polarization, glycolytic metabolism, and inflammatory transcriptional signatures. Indeed, public and expanded TCR clonotypes persist across age groups, and centenarians retain robust cytotoxic competence and high-affinity antigen recognition. Together, these findings demonstrate that antigen-imprinted transcriptional, metabolic, and clonal programs, not chronological age, are the primary determinants of durable human T cell memory, providing a mechanistic framework for vaccine-induced immunity across the lifespan.