Fig. 4: Phenotype of clonally expanded cells harboring inducible and translation-competent proviruses.

Levels of expression of PD-1, TIGIT, HLA-DR, ICOS, α4, β1, CD45RA and CCR7 is represented by the ratio between the fluorescence intensity of a cellular marker on each p24+ single sorted-cell and the mean fluorescence intensity of this marker on all CD4+ T cells from the same participant. A normalized expression level above or below 1 (dotted line) reflects a higher or lower expression of this marker on a given p24+ cell compared to all CD4+ T cells, respectively. Each dot represents a single-sorted cell and is color-coded by the participant. a Normalized expression levels of each marker for all clonally expanded p24+ cells (n = 239 independent clonally expanded proviruses). Mean fold differences in levels of expression and standard deviations are indicated at the top of the graph. Grey bars indicate the mean normalized expression level for each marker. b Normalized expression levels of individual p24-expressing cells belonging to each individual clone. Single-sorted cells belonging to the same clone are grouped in each column and color-coded by the participant. c Pie charts representing the proportions of unique (light grey) and clonally expanded (dark grey) proviral sequences expressing each marker. The numbers of proviral sequences retrieved from p24+ cells expressing each marker are indicated in the center of the pie chart. Differences in the frequency of clonal proviruses between each subset were assessed by a two-sided Chi-square t-test (*p < 0.05; **p < 0.01; ***p < 0.001).