Figure S5.

Cytotoxic T cells are silenced after a single infection. (A) Stacked bar chart showing the frequency of activated (CD38^hi Bcl2^lo) T cells at baseline, diagnosis, and T6 as well as 45 days after challenge (convalescence) during VAC063C. Each bar represents one volunteer, and individual T cell clusters are color-coded to match Fig. 6 (note that only differentially abundant clusters are included). The major CD4⁺ and CD8⁺ T cell clusters with cytotoxic features are highlighted with a black border in the key to the left of the plot. (B) Differential marker expression through time in each major T cell subset. First, T cell clusters belonging to the same lineage were merged and then CD4⁺ and CD8⁺ T cells were split into naive, effector, effector memory (EM), and central memory (CM) subsets. Next, linear models were used to independently assess differential marker expression in each subset at each time point (relative to baseline); a shift in median expression of at least 10% and an FDR < 0.05 were required for significance. Shown are all subset/marker pairs that were called as significant at T6 and data are presented as row-wise z-score marker intensities. Color codes to the left of the heatmap indicate whether markers were differentially expressed during first infection, third infection or both infections. MAIT, mucosal-associated invariant T cell; NK, natural killer; TEMRA, terminally differentiated effector memory cell re-expressing CD45RA; Treg, regulatory T cell.