Fig. 1

SARS-CoV-2-specific clonal T cells showed signs of long-term survival fate in circulation. a Clustering of 22,452 T cells from five patients (PA0130–34, Supplementary Table S7) at three or two consecutive time points and two healthy donors. All T cells are with both TCR and gene expression information. The cell subsets are color-coded. The labeled markers of each cluster in the UMAP are selected from the top 20 differentially expressed genes (DEGs) of each cluster. b T cell clones indicated by different colors. Clonal T cells were defined as those T cells with identical CDR3 seq/total T cells ≥1%. Non-clonal T cells are defined as those with the rate <1%. The dashed circles indicate the naive-EFF T and effector T cell population, respectively. c Expression of the selected DEGs in each cluster. d T cell clonality in five patients at the indicated time points and two healthy donors; the proportion and CDR3 amino acid sequences of the TRA and TRB of each clone across time points is shown. T cell clones are indicated by different colors. e DEGs between clonal effector (EFF) CD8+ T cells and non-expanded EFF CD8+ T cells (one cell per clone) measured by the Wilcoxon Rank Sum test. DEGs were identified based on fold change >2 and adjusted p-value < 0.01. The analyzed T cells are from an effector T cell population of five patients during virus infection (Timepoint 1). f Expression levels of six co-inhibitory molecules in the clonal CD8+ T cells; LAG3 was the dominant co-inhibitory molecule expressed by 42% of clonal T cells. g The percentages of clonal CD8+ T cells with the indicated co-inhibitory receptor expression in the entire clonal CD8+ T cell population for each patient. *P < 0.05, ** P < 0.01 according to paired t-test. h DEGs across three consecutive time points for the clonal CD8+ T cells of five patients. Wilcoxon Rank Sum test was used for differential expression analysis; DEGs were selected based on fold change >2 and adjusted p-value < 0.01 in two phases. i Flow cytometric analysis of TCR-transfected (TCR sequences from clonal T cells or non-expanded T cells) CD8+ T cells co-cultured for 48 h with Ag-APC (virus antigen loading antigen-presenting cell) or mock APC. j Representative ELISpot wells from patients PA0130 and 0131 showing granzyme B released by TCR-T cells in response to virus antigens. The experiments were technically repeated three times. The difference between groups was analyzed by unpaired t-test