Figure 2.

Epitope Specificity of CD8⁺ T Cell Response to S Protein Differs Significantly between HLA-A^∗02:01-Positive CPs and HD

(A and B) PBMCs of HLA-A^∗02:01-positive CPs (n = 17), HD(CoV) (n = 7), and HD(BB) (n = 10) were stimulated with a mix of 13 predicted peptides and expanded for 8–12 days, followed by MHC-tetramer staining. (A) Pie charts represent fractions of wells containing tetramer-positive cells after expansion. (B) Representative MHC-tetramer staining at day 9 (patient p1445, well 3).

(C) Receiver operating characteristic (ROC) curve of the CP/HD classifier on the basis of the presence of YLQ or RLQ epitope-specific cells after expansion.

(D) MHC-tetramer-positive clones after rapid in vitro expansion were FACS-sorted, and their TCR repertoires were sequenced. Numbers of YLQ- and RLQ-specific clones in each patient are plotted (p = 0.0013 by Mann-Whitney test).

(E) YLQ- and RLQ-specific T cell clones occupy only a negligible fraction of the total repertoire. Frequencies of each antigen-specific T cell clone in the PBMCs are plotted.

(F) IFNγ-secreting CD4⁺ and CD8⁺ cells were FACS-sorted after stimulation with S protein, and their TCRβ repertoire was sequenced. A representative enrichment plot for patient p1448, showing IFNγ-secreting CD8⁺ versus total PBMCs. Red dots represent clones that are both strongly (>10×) and significantly (p < 10⁻⁸, Fisher’s exact test) enriched.

(G) Clonal structure of the CD4⁺ (blue) and CD8⁺ (orange) antigen-specific T cell populations. Numbers inside the pie charts indicate the total number of antigen-specific clones, and numbers below in parentheses indicate their combined share in the total T cell repertoire.