Fig. 4: gE-specific TCR usage in DR0401 individuals.

A Public TCR usage. TCR α and β amino acid CDR3 sequences are defined as a pair if they are detected in the same cell, and TCR pairs that are detected in cells across multiple donors are considered “shared.” 14 unique pairs were shared across 5 DR0401 donors, with 2 pairs shared by 4 donors, another 2 pairs shared by 3 donors and 10 pairs shared by 2 donors, as indicated. The number of cells containing each pair in each donor is depicted by the size of the dot, as shown. B V and J gene segment usage of gE-specific CD4⁺ T cells in DRB1*04:01 restricted donors. Different colors of the alluvia flowing between the strata (gene segments) indicate distinct TCR clonotypes, as determined by amino acid sequence, while width of the alluvia color indicates the number of libraries in each clonotype. TCR gene segments used in more than twenty libraries are labeled in the strata. C, D Paired T cell receptor (TCR) sequence similarity graph of VZV specific T cells identified by tetramer sort with tetramers listed in figure legend (see Methods). Network graph shows 166 unique clonotypes (defined by amino acid sequence) which form 37 clusters defined by close sequence-similarity (nearest neighbor distance 24), indicated by grey lines. Size of circle reflects the number of copies of each sequence observed. Cluster members are shaded by tetramer (C) or person (D) in which the clonotype was identified. E Logoplots demonstrating the amino acid sequences of the CDR3 sequences in clonotypes contributing to clusters 0, 1 and 2. Flanking Sankey diagrams demonstrate the V and J chain usage in each cluster. Amino acid residues are shaded by chemical characteristics.