Fig. 5. Productive HIV infection is preferentially established in previously expanded and disseminated clonotypes.

A. Frequency of TRBV and TRBJ segment usage for the clonotypes identified by TCRβ sequencing in p24⁺ cells and in total CD4⁺ cells in both blood and lymph nodes from 17 participants. Significant differences between p24⁺ and total CD4⁺ T cells are highlighted with a red or blue background depending on the trend (see Fig. S6c). B. Venn diagrams showing the number of unique and shared clonotypes in the four subsets: blood and lymph node total CD4⁺ T cells and p24⁺ cells for all participants C. Example (Participant PID#11, data from other participants are shown in Fig. S7d) of frequency distribution (based on bulk deep sequencing data and single-cell sorting/Sanger sequencing) of the clonotypes corresponding to the clones that were found in a single subset (empty circles) and in multiple subsets including p24⁺ cells (colored circles). Frequencies are shown as percentage of total reads for total CD4⁺ T cells and as the frequency of cells determined by HIV-Flow for p24⁺ cells. D. Median frequency of reads of CD4⁺ T cells clonotypes from blood and lymph node in which p24⁺ cells were identified (p24⁺) or not (p24⁻) (data from n=9 participants with at least n=3 p24⁺ clonotypes shared with blood or lymph nodes are shown). E. Pie charts representing the median frequency of p24⁺ cells and total CD4⁺ T cells clonotypes from a given compartment (blood or lymph node) that were shared with the other compartment (lymph node or blood), respectively (data from n=9 participants). The total number of cells (p24⁺ cells) and median number of reads (total CD4⁺ T cells) per condition is indicated at the center of the pie. Significant differences are highlighted (Wilcoxon or Fisher’s exact test; p<0.05, *; p<0.01**; p<0.001, ***; p<0.0001 ****).