In this project we aim to understand the mechanisms by which the HIV reservoir is established in resting and activated T cells. This work involves identifying and quantifying infected cells in vivo as well as exploring mechanisms of infection of primary T cells in vitro. We place particular emphasis on CD4 T cell infection in tissues such as gut and lymph node. Our findings suggest a single model in which HIV persists despite natural virologic control by three interrelated mechanisms: (1) ongoing infection of cells in lymphoid tissue, (2) survival and recirculation of some of these cells, and (3) long-term persistence of proviruses in clonally expanded cells. However, the initial establishment of the reservoir in vivo should require the infection of resting T cells as these are predominant. We used whole transcriptome sequencing, HIV sequencing and in vitro infection with mutated reporter viruses to address this question. We found that resting non-dividing CD4 T cells are efficiently infected. We are working to understand which pool of cellular nucleotides is used by the virus during the reverse transcription step and how this affects the stability of the integrated virus genome.