Extended Data Fig. 7: Single-cell TCR landscape and cell function scores of CD8 T cells specific to the top seven SARS-CoV-2 ancestral epitopes.

(a) Same UMAP visualization as Fig. 7c, but with TCR sequence detection information (upper), TCR clonotype expansion (clonotype frequency > 1) information (middle), and top 5 most frequent TCR clonotype information projected on and split by each SARS-CoV-2 ancestral epitope. Source of selected ancestral epitopes, epitope IDs and total TCR number of TCRs with paired chains are labeled on the top of each panel. The percent of cells with TCR detected is shown in each panel. Except B.1.1.7 ORF1a 1707-16 and B.1.1.7 ORF1a 2225-34 epitope specific CD8 T cells, the highest TCR expansion frequency of others was less than 5. For B.1.1.7 ORF1a 2230-38 and B.1.617.3 ORF1a 2240-49 epitope specific CD8 T cells, the highest clonotype frequency was 2, therefore the corresponding cells are colored in dark red. Color-mapping are exclusive to each panel. (b) Boxplot of cell function scores for each CD8 T cell cluster. The cluster IDs on x-axis is the same as Fig. 7a. Number of cells (n) in each tested cluster are shown in Fig. 7a. The genes used in each gene panel for corresponding function score evaluation are listed in Table S6. 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×IQR value.