Fig. 4: Phenotypic characteristics of virus-specific CD8⁺ T cells in healthy convalescent individuals and individuals with long COVID recruited from the United Kingdom.

a, Schematic representation of the experimental design. b, Scatter dot plots showing the expression frequencies of HLA-DR and CD38 or granzyme B (GZMB) among tetramer⁺CD8⁺ T cells. c, Scatter dot plots showing the expression intensities of co-inhibitory receptors among tetramer⁺CD8⁺ T cells. d, Scatter dot plot showing co-inhibitory scores, calculated as the cumulative normalized expression intensities of the co-inhibitory receptors shown in c, among tetramer⁺CD8⁺ T cells. e, Scatter dot plots showing the expression intensities of transcription factors among tetramer⁺CD8⁺ T cells. f, UMAP visualization summarizing the phenotypic characteristics of tetramer⁺CD8⁺ T cells targeting nonspike epitopes from SARS-CoV-2. Individual marker representations are colored by expression intensity. g, Phenograph clustering (top) and cluster distribution of tetramer⁺CD8⁺ T cells (bottom). h, Scatter dot plots showing the expression intensities of co-inhibitory receptors among tetramer⁺CD8⁺ T cells targeting nonspike or spike epitopes from SARS-CoV-2. i, Scatter dot plots showing co-inhibitory scores among tetramer⁺CD8⁺ T cells targeting nonspike or spike epitopes from SARS-CoV-2. j, Scatter dot plots showing co-inhibitory scores among tetramer⁺CD8⁺ T cells targeting nonspike epitopes from SARS-CoV-2 restricted by HLA-A*02:01 or HLA-B*07:02; NC, nucleocapsid. k, Scatter dot plots showing the expression intensities of transcription factors among tetramer⁺CD8⁺ T cells targeting nonspike or spike epitopes from SARS-CoV-2. l, Scatter dot plots showing the phenotypic characteristics of tetramer⁺CD8⁺ T cells targeting lytic epitopes from EBV; healthy convalescent individuals, n = 17; individuals with long COVID, n = 15; untreated individuals infected with HIV-1, n = 14 (b–l). Horizontal bars represent median values (b–e and h–l). Significance was evaluated using a two-tailed Mann–Whitney U-test (b–e and h–l); gMFI, geometric mean fluorescence intensity.