Fig. 2.

HIV-1 deep-sequencing in the Rakai Community Cohort, Uganda. Individuals aged 15–49 years were surveyed from August 2011 to January 2015 in 40 communities. In all, 5142 men and women were found positive (circles). Of those, 1264 self-reported using antiretrovirals (grey area of circles), and were not considered further as sequencing is challenging when virus is suppressed by treatment. Samples from 3878 individuals were deep-sequenced (see Methods). Of those, samples from 1226 (31.6%) individuals were not of sufficient quality for analysis (blue area of circles). Specifically, for phylogeny reconstruction, only paired-end merged reads of at least 250 base pairs (bp) in length were used, and subsequent deep-sequence inferences were performed on individuals whose reads covered the HIV-1 genome at a depth of at least 30 reads for 750 bp or more. Thus, samples from 2652 individuals (red area of circles) were used for molecular epidemiological analyses, corresponding to an estimated 45.1% of eligible and infected individuals with unsuppressed virus in RCCS communities