Fig. 7: Single-cell transcriptome and TCR landscape of CD8 T cells specific to the top seven SARS-CoV-2 ancestral epitopes by CD8 cell activation capacity.

a, Uniform manifold approximation and projection (UMAP) visualization of the SARS-CoV-2 epitope-specific CD8 T cells, by single-cell transcriptome profiles. Clusters are named based on the cluster-specific marker genes. The numbers in parentheses indicate the number of cells in each cluster. The SARS-CoV-2 epitopes are listed in Fig. 5c. b, Dot plot of marker genes for each CD8 T cell subtypes. Color scale shows the average normalized expression of marker genes in each subtype, and dot size indicates the percentage of cells within each cell cluster expressing the marker gene. c, Same UMAP visualization as a but with total TCR sequence detection information (left), TCR clonotype expansion (clonotype frequency >1) information (middle) and the top five most frequent TCR clonotype information for the seven ancestral epitopes projection. d, Single-cell transcriptome-derived CD8 T cell naivety, proliferation and activation and cytotoxicity score comparison between cell clusters. Number of cells (n) in each tested cluster is shown in a. Gene panels used for naivety, proliferation and activation and cytotoxicity score calculation are listed in Supplementary Table 6. e, Scatter plot visualization of CD8 T cell TCR clonotype frequency versus cell naivety, proliferation and activation and cytotoxicity score, respectively. Each dot represents a CD8 T cell, with color corresponding to its annotated subtype. Blue lines are fitted by linear model, with gray error bands indicating the 95% confidence intervals. Spearman correlations (ρ) are also shown. f, Heat map visualization of numbers of TCR clonotypes shared by two CD8 T cell clusters. Only cell clusters with shared clonotypes >10 with at least one other cluster are shown. For box plots, the outlines of the boxes represent the first and third quartiles; the line inside each box represents the median; and boundaries of the whiskers are found within the 1.5× interquartile range value.