Latently infected CD4+ T cells, thought to be the main barrier to HIV cure, are indistinguishable from uninfected cells and are exceedingly rare, rendering the study of HIV latency in vivo particularly challenging. The development of more tractable systems such as in vitro primary cell models of latency has greatly advanced our understanding of the establishment, maintenance and reactivation of HIV latency, since these models permit higher infection frequencies and some employ reporter viruses to readily distinguish latent and productively infected populations. However, the precise mechanisms that underlie latency remain unclear. The objective of this study is to identify the molecular signatures associated with HIV infection to enable us to distinguish latent infected, reactivated, and productively infected cells from uninfected cells. The long-term goal of these studies is to provide insight needed to design new therapies to disrupt latency and/or target latently infected cells as a part of a cure strategy, which is a highly significant contribution. The central hypothesis is that despite differences in primary cell models, latently infected cells will be distinguished from reactivated and productively infected cells by transcriptional blocks to HIV, which are governed by expression of distinct human cellular factors. Our specific aims are to test three prominent primary cell models of HIV latency (Greene, Planelles/Bosque and Verdin) at the single cell level to probe underlying mechanisms of latency. Using a dual approach of single cell multiplex qRT-PCR assaying 96 cellular and HIV targets (Specific Aim 1) and single cell total RNAseq (Specific Aim 2), this study seeks to uncover the molecular signatures that distinguish latent and productively infected cells and distinguish these from uninfected cells. The proposed research is innovative because it employs complementary cutting-edge single cell methods to probe the transcriptomes of HIV infected cells.