Extended Data Fig. 7: EpiScan of SARS-CoV-2 Spike variants and tetramer staining.

(a) SARS-CoV-2 Spike Variant EpiScan screen results for HLA-A*02:01. Scatterplot showing the difference between wildtype and mutant in EpiScan enrichment for SARS-CoV-2 Spike peptides. Negative log2(fold change) values were set to zero prior to subtraction, and peptide pairs with no difference in log2(fold change) are omitted. Orange circles represent peptides that contain a mutation present in a variant of concern. Circles are grayed out for the peptide pairs in which neither constituent was below the FDR threshold of 0.20. (b) Individual validation of HLA-A*02:01 Spike screen hits in the EpiScan assay. Data are represented as mean ± SEM of the fold change in mean fluorescence intensity (MFI) relative to the average of negative control peptides in red. Spike peptides are arranged from top to bottom by relative screen rank, with peptides on the top ranked higher by Mageck as shown on the right. Each dot represents a different biological replicate, with n = 19 for SLLNATAIAV and NLVPMVATV, n = 15 for SIINFEKL, n = 10 for FQFCNDPFLGV and KLNDLCFTNV, n = 4 for VLYQDVNCTEV, YQDVNCTEV, YLQPRTFLL and KIADYNYKL, and n = 6 for the rest. **p < 0.01, ***p < 0.001, ****p < 0.0001 for each group relative to the SIINFEKL peptide by one-way ANOVA with Dunnett’s multiple-comparison test. (c) Tetramer staining of CD8 memory T cells. Dot plot values are the percent HLA-A*02:01 tetramer positive CD8⁺ T cells for convalescent COVID-19 samples (black solid or empty circle, n = 7) and healthy control samples (red, n = 4). On left, SARS-CoV-2 peptides are shown. On the right, ELAGIGILTV and NLPMVATV are positive control peptides derived from MLANA and CMV pp65 proteins, respectively. Dots on the y-axis are zero values that would otherwise not be displayed on a log₂ axis.