Fig. 5

Genetic diversity of the peripheral HIV-1 reservoir in patients from Uganda and the U.S. A Intra-patient HIV-1 diversity of inducible cell-associated spliced HIV-1 RNA and proviral DNA in resting memory CD4⁺ T cells based on the p-distance model [56]. Unpaired t test was used to assess the statistical significance between the reservoir diversity in both cohorts of patients and between individuals infected with subtype B (U.S.) and non-B (Uganda) HIV-1 subtypes. Median substitutions/site and interquartile range are depicted. ***p < 0.001, ****p < 0.0001, n.s., not significant. B Genetic diversity of the inducible cell-associated spliced HIV-1 RNA and proviral DNA based on the number of viral haplotypes using CliqueSNV (103). Unpaired t test was used to compare the number of unique HIV-1 variants (viral haplotypes) between the reservoir diversity in both cohorts of patients and between individuals infected with subtype B (U.S.) and non-B (Uganda) HIV-1 subtypes. Median substitutions/site and interquartile range are depicted. *p < 0.05, n.s., not significant. C Comparison of the frequency of viral haplotypes in resting memory CD4⁺ T cells from Ugandan and U.S. patients. Each dot represents the frequency (proportional contribution) of the viral haplotype within the HIV-1 population when present as only one variant in the reservoir (1.0) or part of two or up to a maximum of nine unique sequences (> 0 to < 1) within each sample. Unpaired t test was used to compare the frequency of each viral haplotype present as one or more unique HIV-1 variant in each sample between both cohorts of patients. **p < 0.01, n.s., not significant