Abstract <p>Cytomegalovirus (CMV) reactivation is a frequent complication after allogeneic hematopoietic stem cell transplantation (aHSCT) and critically shapes immune reconstitution. However, the clonal and functional dynamics of T cell responses to CMV remain insufficiently defined. In this study, we combined longitudinal single-cell RNA sequencing with paired T cell receptor sequencing to track γδ and αβ T cell clones at clonal resolution across five post-transplant time points in patients with and without CMV reactivation. This integrative approach revealed marked, patient-specific expansion of non-Vγ9Vδ2 γδ T cell clones, particularly within Vδ1⁺ and Vδ3⁺ subsets, which was associated with differentiation toward cytotoxic and antiviral effector states characterized by IFN-γ and TNF-α expression. Conventional CD8⁺ αβ T cells showed comparatively modest clonal dynamics during CMV reactivation in this cohort. Longitudinal tracking of individual clonotypes demonstrated heterogeneous but recurrent trajectories, with expanding γδ T cell clones frequently acquiring antiviral and cytotoxic phenotypes following CMV reactivation. These findings highlight the adaptive-like behavior and functional plasticity of non-Vγ9Vδ2 γδ T cells and provide a high-resolution framework for studying antiviral immune responses during immune reconstitution.</p> Key messages <p><UnorderedList Mark="Bullet"> <ItemContent> <p>Single-cell sequencing enables clonal tracking of T cells during CMV reactivation.</p> </ItemContent> <ItemContent> <p>γδ T cells show patient-specific clonal expansion after CMV reactivation.</p> </ItemContent> <ItemContent> <p>Expanding γδ T cell clones acquire antiviral and cytotoxic phenotypes.</p> </ItemContent> <ItemContent> <p>Vγ9Vδ2 γδ T cells remain stable with limited clonal expansion.</p> </ItemContent> <ItemContent> <p>αβ T cells display limited clonal responses during CMV reactivation.</p> </ItemContent> </UnorderedList></p> Graphical Abstract <p></p>