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.

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. | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article 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. Sara De Biasi, Domenico Lo Tartaro, Moritz Rau, Elena Santacroce, and 11 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8805423/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract 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. Biological sciences/Immunology/Adaptive immunity/Cellular immunity/Immunological memory Biological sciences/Immunology/Antigen processing and presentation/Cellular immunity Smallpox SARS-CoV-2 antigen-specific response polyfunctionality T cells cytokine vaccine Full Text Additional Declarations There is NO Competing Interest. Table 1 is available in the Supplementary Files section. Supplementary Files Table1.xlsx Table 1 SupplementaryTable1.xlsx Supplementary Table 1 SupplementaryTable2.xlsx Supplementary Table 2 SupplementaryTable3.xlsx Supplementary Table 3 SupplementaryTable4.xlsx Supplementary Table 4 SupplementaryfiguresmallpoxDLT2025.pdf Supplementary figures Cite Share Download PDF Status: Under Review Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8805423","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":587133322,"identity":"8bc3c564-3f9b-402f-a456-ae47335b7ba8","order_by":0,"name":"Sara De 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