Fig 2: YLQPRTFLL-specific T cell clonotypes from vaccinated donors do not activate with P272L-YLQLRTFLL peptide(A) Wuhan-YLQPRTFLL tetramer enriched T cell lines from 6 of the 7 vaccinees in Figure 5. HLA A*02:01-restricted SLYNTVATL peptide from HIV used as an irrelevant tetramer (Cole et al., 2017). Percentage of CD3+ cells is shown.(B) The lines were re-sorted with Wuhan-YLQPRTFLL tetramer for TCR analysis. Pie charts display the proportion (chart segments) and frequency (numbers in center) of public (blue) and private (grey) TCRs. Public or private status based on data from convalescent patient studies. Variable (V) (arc on the right) and joining (J) (arc on the left) gene rearrangements are annotated with dominant and public chains with CDR3s of interest. CDR3 sequences are listed in Figure S5A.(C) CD107a upregulation of the T cell lines with Wuhan-YLQPRTFLL or P272L-YLQLRTFLL peptides. Peptides (10-6 M) were pulsed on to T2 antigen-presenting cells prior to assay. CD3/CD28 Dynabeads used as a positive control. Error bars depict SD of duplicates. Flow cytometry data shown in Figure S5B.See also Figures S3 and S5.

Fig 3: TCRs and peptide reactivity of Wuhan-YLQPRTFLL tetramer enriched T cell lines from six vaccinated donors, related to Figures 5 and 6(A) TCR usage and CDR3 sequences of Wuhan-YLQPRTFLL specific T cells from vaccinated donors. TCRs that appear in multiple individuals highlighted as public, according to the key.(B) CD107a upregulation of the T cell lines with Wuhan and P272L-YLQLRTFLL peptides. Peptides (10-6 M) were pulsed on to T2 antigen-presenting cells prior to assay. CD3/CD28 Dynabeads used as a positive control. Performed in duplicate. Gating of positive cells shown for vaccinee 201a.