Fig. 7: SARS-CoV-2 antigen-specific T cells.
From: Adaptive immune responses to SARS-CoV-2 persist in the pharyngeal lymphoid tissue of children
a, Representative flow cytometry plots showing gating of antigen-specific CD4+ T cells from post-COV PBMCs expressing activation-induced markers (AIM+, CD40L+4-1BB+) following stimulation with SARS-CoV-2 peptide pools of S, M and N. Dimethylsulfoxide (DMSO) (vehicle, V) was the negative control, PHA-L was the positive control. b, Frequencies of AIM+CD4+ T cells from six post-COV PBMCs as in a (V versus S, P = 0.031; V versus M, P = 0.031; V versus N, P = 0.031). Significance calculated with two-sided Wilcoxon signed-rank test for paired samples from the same donor. c, Flow cytometry plots showing frequency of memory T cells (shown in box on left), CD45RA−CXCR5+PD-1+ cTFH cells and CXCR3+CCR6− cTFH cells from concatenated antigen-specific CD4+ T cells from S, M and N peptide pool stimulations from six donors compared to total CD4+ T cells in PBMC. d, Frequency of CD8+ T cells that are part of expanded clonotypes (frequency > 0.01, clone defined by identical CDR3β aa sequence) in tonsils, adenoids and PBMCs from two post-COV donors (CNMC71 and CNMC89) and one UC (CNMC99) assessed by CITE-seq and TCR sequencing. e–g, UMAP (e), tissue distribution (f) and CITE-seq surface antibody expression (g) of 16 clusters of CD95+CD8+ T cells from tonsils, adenoids and PBMCs of the three donors in d. h–i, Expanded clonotypes (h) and the distribution of expanded and non-expanded clones across clusters (i) of CD95+CD8+ T cells in e. j, Antigens recognized by four expanded CD8+ T cell clones (each represented by a slice) with CDR3β sequences matching those reported to be SARS-CoV-2-specific in public databases; percentage of cells in each clone noted. Clones recognizing spike epitopes in green and ORF1ab epitopes in red. Clones reported to recognize >1 antigen not shown. Nested epitopes recognized by spike- and ORF1ab-specific TCRs are depicted below the pie chart (Supplementary Table 8). k, Overlap of CD8+ T cell clones among PBMCs, tonsils and adenoids from two post-COV donors and one UC; degree of overlap between TCRα/β CDR3 aa sequences was calculated with the Morisita index (shown in plot), ranging from 0 to 1, with 0 indicating no sharing and 1 indicating full overlap. *P < 0.05.
