CMV-specific clonal expansion in human Th1 and GZMK⁺ CD8⁺ T cells

Abstract

Cytomegalovirus (CMV) is a common herpesvirus that establishes lifelong latency and becomes increasingly prevalent with age. To systematically delineate CMV-associated immune remodeling at single-cell resolution, we analysed six human cohorts (including two newly established cohorts) using single-cell RNA sequencing, T cell receptor (TCR) sequencing, and flow cytometry. We identified novel CMV-associated changes in cell frequencies, including increases in GZMK⁺ CD8⁺ T cells and atypical B cells, and a reduction in CD56dim NK cells, in addition to the canonical expansion of CD4⁺/CD8⁺ TEMRA and adaptive NK cells. Longitudinal profiling of an individual who seroconverted revealed rapid CMV-driven shifts in circulating immune cell frequencies. Leveraging a recently published CMV-specific TCRβ database, combined with predictive modeling (CMVerify), we identified novel CMV-specific clonal expansions that were reproduced across two independent cohorts. In the CD8⁺ lineage, CMV-specific clones were enriched in GZMK⁺ CD8⁺ T cells and CD8⁺ TEMRA cells, whereas in the CD4⁺ lineage, Th1 cells showed clonal expansion alongside CD4⁺ TEMRA cells. This multi-cohort integrative study defines the cellular and clonal signatures of latent CMV in humans and identifies GZMK⁺ CD8⁺ T cells and Th1 cells as previously underappreciated components of the CMV response.