Fig. 1: Measuring CD8⁺ T cell epitope-specific responses after diverse SARS-CoV-2 exposures.

a, Study design. Selected spike and non-spike SARS-CoV-2 T cell epitopes were loaded on recombinant biotinylated MHC monomers. Resulting pMHC complexes were polymerized using fluorescently labeled and DNA-barcoded dextran backbones. Next, we stained PBMC samples with pools of MHC multimers, isolated bound cells using FACS, and performed scRNA-seq, scTCR-seq and CITE-seq using the 10x Genomics platform. Created with BioRender.com. b, Time of blood sampling for each donor is shown relative to the first dose of mRNA vaccine. c, Anti-RBD IgG antibody levels in previously infected individuals increase after BNT162b2 vaccination. Anti-RBD IgG levels in the plasma were determined by ELISA. The normalized optical density (OD) is the percentage ratio of the sample OD to the OD of the positive control for each plate. Plasma was collected from previously infected donors before vaccination (purple; inf, n = 16), after one vaccine dose (pink; inf-vax1, n = 10) and after two vaccine doses (blue; inf-vax2, n = 30); from SARS-CoV-2-naive donors after the full vaccination (green; vax2, n = 16); and from donors who were infected after vaccination (yellow; breakthrough, vax2-inf, n = 9). All comparisons were done with two-sided Mann–Whitney U tests, and P values are reported after Benjamini–Hochberg correction. The central line on violin plots shows the median; upper and lower borders show maximal and minimal values. d, List of SARS-CoV-2 epitopes used in this study and summary statistics for resulting epitope-specific response. e, Total frequency of MHC dextramer-positive cells was similar in all studied groups (P > 0.05 for all pairwise comparisons, two-sided Mann–Whitney U test after Benjamini–Hochberg correction). The percentage of MHC multimer-positive cells from all CD8⁺ T cells as measured by flow cytometry is shown on a log₁₀ scale (inf, n = 16; inf-vax1, n = 10; inf-vax2, n = 30; vax2, n = 16; vax2-inf, n = 9). The central line on violin plots shows the median; upper and lower borders show maximal and minimal values. NS, not significant.