Fig. 2

Overall longitudinal HIV 5′-LTR methylation profiles from total CD4⁺ T cells of 12 participants with short-term antiretroviral treatment. Each group represents a single participant on short-term antiretroviral treatment (24 to 30 months), followed up for 2 years at 3-month intervals. Each line depicts a summary of all variants observed per time point. CpG sites are shown as pie charts indicating the proportion of methylated (black), unmethylated (light gray) or mutated (dark gray) variants in the sample. Canonical HXB2 CpG positions are numbered. Additional CpG, CHG, and CHH methylation-susceptible sites, not observed in the HXB2 sequence, are also included (marked with *). The number of reads and the total number of variants obtained per time point, after filtering and aligning, are shown. Additionally, measurements of residual plasma viral load, proviral load and proportion of memory (CD3⁺/CD4⁺/CD28⁺⁻/CD95⁺; black) and naïve (CD3⁺/CD4⁺/CD45RO⁻/CCR7⁺/CD28+/CD95⁻; light gray) CD4⁺ T cells per time point are shown