We measured the HIV proviral reservoir in genomic DNA from CD4+ T cells and from central memory, effector memory, and naïve T-cell subsets. We also measured HIV in rectal biopsies. Methods used for isolating and sorting T-cell subsets are described in the Supplementary Methods. We used the Bio-Rad ddPCR platform to run an assay targeting 3 regions in the HIV genome (within gag, pol, and env). This assay provides a good approximation of intact and defective provirus copy numbers, has been validated in a clinical laboratory, and is described in detail in 2 prior publications [31 (link), 32 (link)]. A determination of proviral “intactness” by this method requires the detection of all 3 HIV targets in a single droplet. To avoid false negatives from true intact provirus being mechanically sheared and distributed into different droplets, we used a method modified from Wiegand et al. to extract high–molecular weight genomic DNA [33 (link)]. For rectal biopsies, we used the adapted Wiegand protocol and a Qiagen QIAamp DNA micro kit. Additional details are available in the Supplementary Methods.