Deep Sequencing of Antiviral T-Cell Responses to HCMV and EBV in Humans Reveals a Stable Repertoire That Is Maintained for Many Years
Figure 2
Quantification of clonal response in early response against hCMV and EBV.
(A) Anti-viral clones (identified by tetramer sorting followed by NGS). Each dot represents a different clone. The degree of expansion was determined as the frequency of the individual clonal TCRß-sequence, expressed as percentage of the total number of TCRß-sequences analyzed. (B) Frequency distribution of anti-viral CD8+ T-cell clones (median and IQR). (C) Structural variation of antiviral clones, reflected in the number of different V- and J-genes used in each epitope response (median and IQR). (D–F). Using the unique TCRß sequence of each virus specific clones, they were identified within the total CD8 population during the early response (50 most abundant CD8+ T-cell clones are shown). Red = CMV-IE-ELR(-specific clones), blue = CMV-IE-QIK, green = CMV-pp65, tangerine = EBV-BZLF, asparagus = EBV-EBNA. (G) Percentage of tetramer-specific clones that could be detected amongst the 50 most abundant CD8 clones. Grey bar show median and IQR. (H) Comparison of percentage of CD8+ T cells that was tetramer specific as identified by FACS (black bars) to percentage of TCRß-reads that was attributable to tetramer-specific clones as determined by NGS (white bars). (I) Wilcoxon matched pairs test comparing the frequency of the 56 tetramer+ clones (all 6 tetramers combined) before and after infection (clones that were not detected were given a frequency of 1∶10,000 which was the lower detection limit).