Research Articles

HIV replication is suppressed by combination antiretroviral therapy (cART), but infected cells persist in patients and are a critical obstacle to curing HIV infection (1, 2). Analysis of HIV populations in vivo shows that, after long-term suppressive cART, genetically identical HIV vari-ants emerge (3, 4). The source and mechanisms involved in the emer-gence of these identical variants are not understood. One possibility is that the identical variants arise from cells that have clonally expanded. Because HIV DNA integrates at many sites in the human genome, the site of integration can be used to identify clonally expanded cells that arose from a single infected progenitor. Clonal expansion of HIV infected cells in patients We analyzed the integration sites in peripheral blood mononuclear cells (PBMCs) or CD4+ T-cells from patients on prolonged cART ob-tained by negative selection using a previously described technique (5– 7). DNA from PBMCs or CD4+ T-cells was randomly sheared t