Phenotypic analysis of productively SIV-infected cells in blood and lymphoid tissues of rhesus macaques.

Simian immunodeficiency virus (SIV) primarily infects CD4+ T cells, yet the relative contribution of different subsets to viral production in blood and tissues remains unclear. We develop SIV-Flow, a flow cytometry-based assay, to quantify and characterize the phenotype of productively infected cells in blood, spleen, and multiple lymph nodes from eight chronically SIV-infected rhesus macaques. We measured a consistent average of ∼1,000 infected cells per million CD4+ T cells, with limited variation by the anatomical site. Most productively infected cells displayed a memory phenotype, dominated by the effector memory subset. Despite modest tissue-specific differences, infected cells were uniformly enriched for the activation (PD-1 and CD69), integrin (VLA-4), and proliferation (Ki-67) markers. A unique subset of memory cells expressing high levels of Ki67 and PD-1 represented 44% of all infected cells. These data identify proliferating effector memory CD4+ T cells as key contributors to viral production and suggest that their phenotypic profile is conserved across diverse tissues.