Fig. 2: Mutational escape from cytotoxic T cells.
From: SARS-CoV-2 escape from cytotoxic T cells during long-term COVID-19
a Calculation of site presentation scores (adapted from Marty et al.30). b, c Change of PHBR scores caused by mutations for HLA I b and HLA II c, respectively. Dot color corresponds to PHBR fold change; the mutations that substantially (>3-fold) increase PHBR are signed. Sites that did not bind any of the patient’s HLA alleles both in ancestral and derived states are not shown. d Comparison of imBR scores for the mutated sites in their ancestral and derived states (n = 11). The level of significance is calculated by the two-sided paired Wilcoxon exact sign-rank test: Test statistic V = 0, p-value = 0.0009766, 95% confidence interval: [−11.7835; −0.3065], median estimates −4.647. Horizontal lines in a boxplot represent minima, first quartile, median, third quartile, and maxima. Source data are provided as a Source Data file.
