Fig. 2: Recognition of the immunodominant HLA-A*29:02-restricted epitope in vaccinated participants.

A Flow cytometry plots displaying the frequency of IFN-γ-producing CD8⁺ T cells from PBMC of vaccinated HLAA*29:02⁺ individuals. B Frequency of IFN-γ-producing CD8⁺ T cells following in vitro culture of PBMC from four vaccinated individuals (A*29:02 n = 3; A*29:11 n = 1) with spike overlapping peptide pools. C Frequency of IFN-γ-producing CD8⁺ T cells following in vitro stimulation with either YFPLQSYGF or YFPLRSYSF and recall with cognate peptide. D Frequency of IFN-γ-producing CD8⁺ T cells in response to serial dilutions of YFPLQSYGF. Data represents mean and standard deviation of duplicates. E Heatmap of frequency of IFN-γ-producing CD8⁺ T cells of spike peptide pool, YFPLQSYGF and published HLA-A29*02 from four vaccinated individuals (A*29:02 n = 3; A*29:11 n = 1). F Crystal structure of the HLA-A*29:02-YFPLRSYSF complex with the HLA heavy chain in white cartoon and the peptide in red cartoon and stick. The P8-Gly Cα atom is represented by a sphere, and the hydrogen bond by a red dashed line. G Model of the YFP variant peptide (blue cartoon and stick) based on the YFP peptide conformation showing the P5-Arg and P8-Ser substitutions in yellow stick. The HLA Met97, Tyr99, and Arg114 are represented as stick and transparent surface to show the steric clashes with the P5-Arg occurring if the variant adopted the same conformation as the cognate peptide. Source data are provided as a source data file.