Identification of a reservoir for HIV-1 in individuals on highly active antiretroviral therapy. HIV data units spanning a median of 19.5 years (range, 10 to 20 years) per participant. We inferred a distribution of within-host phylogenies for each participant, from which we characterized proviral age groups, phylogenetic diversity, and genetic compartmentalization between CD4+ T cell subsets. While three of five participants exhibited some degree of proviral compartmentalization between CD4+ T cell subsets, combined analyses exposed no evidence that any particular CD4+ T cell subset harbored the longest persisting, most genetically diverse, and/or most genetically special HIV reservoir. In one participant, varied proviruses archived within naive T cells were significantly more youthful than those in memory space subsets, while for three additional participants we observed no significant variations in proviral age groups between subsets. In one participant, older proviruses were recovered from all subsets, and included one sequence, estimated to be 21.5?years old, that dominated (>93%) their effector memory space subset. HIV eradication strategies will need to conquer within- and between-host genetic difficulty of proviral landscapes, possibly via personalized approaches. IMPORTANCE The main barrier to HIV treatment is the ability of a genetically varied pool of proviruses, integrated into the genomes of infected CD4+ T cells, to persist despite long-term suppressive combination antiretroviral therapy (cART). CD4+ T cells, however, constitute a heterogeneous human population because of the maturation across a developmental continuum, and the genetic landscapes of latent proviruses archived within them remains incompletely recognized. We applied phylogenetic techniques, mainly novel to HIV persistence study, to reconstruct within-host HIV evolutionary history and characterize proviral diversity in CD4+ T cell subsets in five individuals on long-term cART. Participants assorted widely in terms of proviral burden, genetic diversity, and age distribution between CD4+ T cell subsets, exposing that proviral landscapes can differ between individuals and between infected cell types within an individual. Our findings expose each within-host latent reservoir as unique in its genetic difficulty and support customized strategies for HIV eradication. (20, 21). Recent longitudinal studies confirm this: proviral sequences dating as far back as transmission are present in many individuals reservoirs (20,C22) though some are enriched for proviruses seeded around the time of cART (20, 22). Populations of cells harboring identical proviruses or identical integration sites also feature prominently in the reservoir, indicating that clonal development of latently infected cells also drives HIV persistence (15, 23,C29). HIV eradication will therefore require an in-depth understanding of latent HIV genetic composition and persistence in CD4+ T cells, but this is complicated by the fact that CD4+ T cells adult along a program of development Methylphenidate and thus constitute a heterogeneous human population (30, 31). Upon encountering their cognate antigen, naive T (TN) cells develop into effector and memory space cell subsets which include, from least to most differentiated, stem-cell-like memory space (TSCM), central memory space (TCM), transitional memory space (TTM), effector memory space (TEM), and finally terminally differentiated (TTD) cells (31). Though HIV DNA is Rabbit Polyclonal to ASC definitely reproducibly detected in all of these subsets during long-term cART (13, 32,C38), it has been hypothesized that less differentiated memory space T cell subsets may represent probably the most durable sites for long-term HIV persistence in peripheral blood (32, 34, 35, 37). This is an intuitive notion, given that the longevity of CD4+ T cell subsets (30) and the half-life of proviral DNA in these cells (34, 39) decrease with differentiation, but studies analyzing proviral sequences within CD4+ T cell subsets are Methylphenidate Methylphenidate limited and have yielded somewhat conflicting observations. Buzon et al. observed that proviruses isolated from less differentiated, longer-lived memory space CD4+ T cells, in particular, TSCM and TCM cells, were phylogenetically most closely related to early pre-cART plasma sequences, suggesting that HIV strains circulating in early illness were more likely to persist in these cell subsets (34). Chomont et al. hypothesized that, because of the differential.