Fig. 2: TCR repertoire analysis of spike-specific CD4+ T cells at 1–3 months and 3–4 years post infection.
a, b TRAV (a) and TRBV (b) gene usage of S166–180-, S751–765- and S866–880-specific T cells at 1–3 months (red bars) and 3–4 years (blue bars) post primary infection. c TRBV genes pairing with the dominant TRAV gene for S166–180- (TRAV35), S751–765- (TRAV12-1) and S866–880- (TRAV26-1) specific cells at 1–3 months (left) and 3–4 years (right). d TCRα clonotype similarity network. Each vertex corresponds to an individual TCR clonotype, with edges connecting vertices if the CDR3 amino acid sequences show a normalised edit distance >0.9 (scRepertoire). The size of the vertex corresponds to the TCR clonotype frequency, and colour represents the timepoint at which they are found. Cluster motifs were generated using ggseqlogo and amino acid colours based on their biochemical properties. e The proportion of TCRα clonotypes classified as public (coral) or private (cyan) in our dataset. Percentages denote the proportion of cells of a particular epitope specificity classed as public or private. χ2 test of independence was used to compare proportions between 1–3 month and 3–4 years, with two-sided p-values calculated. f Proportion of TCRβ clonotypes classified as public (coral) or private (cyan) in our dataset. Percentages denote the proportion of cells of a particular epitope specificity classed as public or private. χ2 test of independence was used to compare proportions between 1–3 months and 3–4 years, with two-sided p values calculated. g Pie charts denoting the proportion of TCRα (top) and TCRβ (bottom) clonotypes found in the Observed TCR space (OTS).
