HPCs from HIV-infected NSG-BLT mice generate colonies that harbor proviral DNA. (A) The total number of colonies that develops from each infected mouse is significantly less than those from uninfected mice. Each mark represents the average of triplicate assays in a single mouse; the total data represent the pooled mean ± SEM from all mice. (B) Phenotypic analysis of colonies indicates significant differences in lineage commitment from HSC derived from infected mice compared with uninfected mice. (C) Erythroid lineage development is particularly impaired in the HSC derived from HIV-1–infected mice. Each mark represents the average of triplicate assays in a single mouse; the total data represent the pooled mean ± SEM from all mice. (D) Colonies derived from human CD34+ cells isolated from the bone marrow of infected and uninfected mice were assayed by qRT-PCR for the presence of full-length viral DNA. Colonies were first phenotyped visually by light microscopy. E, erythroid; G, granulocyte; GM, granulocyte-macrophage mixed; M, macrophage. Percentages are of that particular colony type in which HIV was detected compared with the total number of that colony type assayed. (E) HIV+ colonies were assayed by alu-Gag PCR to determine integration site. Following successful amplification, amplicons were sequenced to determine the gene into which the virus integrated. Four different mice were assayed, representing infection by each of the 3 viral strains.