Tissue localization and virus specificity shape the maintenance and function of human virus-specific memory T cells recognizing HCMV and influenza A

Abstract Generation and maintenance of memory T cells within tissue sites of infection is critical for long-term antiviral protection. Current knowledge of human antiviral responses is largely derived from studies sampling peripheral blood. Yet, little is known about human tissue-localized antiviral immunity. Utilizing our human donor tissue resource established in collaboration with LiveOnNY, we investigated how tissue, virus, and age shape T cell maintenance across diverse tissues and their function when presented with antigens derived from human cytomegalovirus (HCMV) or influenza A virus (flu). Using flow cytometry, we show that virus-specific CD8 T cells are maintained in diverse tissues with subset differentiation and distribution shaped by virus specificity and age. Compared to T cells recognizing HCMV, flu-specific T cells display higher levels of residency markers—CD69 and CD103—particularly in adult compared to pediatric donors. In contrast, HCMV-specific T cells are maintained in greater abundance as terminally-differentiated effector T cells. Sequencing of the T cell receptor CDR3b chain reveals that, while both HCMV- and flu-specific T cells demonstrate clonal overlap across multiple tissues, HCMV-specific T cells display greater clonality and less diversity. When presented with viral antigens, HCMV- and flu-specific T cells are polyfunctional. Additionally, single-cell transcriptome profiling reveals tissue localization is the primary determinant of antigen-driven responses. Together, these studies demonstrate the dynamics of T cell differentiation and maintenance throughout the human body, which is primarily driven by virus specificity, and the role of tissue localization in shaping antiviral response.