Fig. 2.

Phenotype of SARS-CoV-2-specific CD8⁺ T cells. The phenotype of SARS-CoV-2-specific CD8⁺ T cells was examined using a ex vivo stimulation-based functional assays, MHC-I multimer staining, and b single-cell RNA sequencing (scRNA-seq) following antigen-reactive T-cell enrichment (ARTE). In the acute phase, SARS-CoV-2-specific CD8⁺ T cells express activation markers (CD38 and HLA-DR), PD-1, Ki-67, and cytotoxic proteins (perforin and granzyme B). In scRNA-seq analysis of virus-reactive CD8⁺ T cells, the proportion of the “exhaustion” cluster, characterized by increased expression of exhaustion-associated genes, was higher in SARS-CoV-2-reactive CD8⁺ T cells than in influenza A virus (IAV)- or respiratory syncytial virus (RSV)-reactive CD8⁺ T cells. In addition, the proportion of the “polyfunctional” cluster expressing high levels of genes encoding cytokines was lower in SARS-CoV-2-reactive CD8⁺ T cells than in IAV- or RSV-reactive CD8⁺ T cells. AIM activation-induced marker, ICS intracellular cytokine staining