Project 2 - Identification of the source of viral rebound using SIV proviral genome analysis

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Abstract The key to developing successful strategies to delay and ultimately prevent viral rebound upon treatment interruption is to identify the source and mechanisms of viral rebound. Ongoing debates regarding the source of rebound include 1) whether CD4+ T cells or tissue macrophages are the dominant source of rebound, 2) whether ongoing cycles of replication in the lymphoid tissue contribute to rebound, 3) whether HIV-1 infection may actively drive the clonal expansion of infected cells through integration into proliferation-related genes. We propose here to explore these issues in collaborative studies in the SIV model using a new technology developed by our group. Using full length, single genome sequencing of HIV-1 proviruses, we have recently shown that the vast majority (>95%) of HIV-1 proviruses in patient cells are defective. This discovery greatly complicates analysis of issues such as the source of rebound viremia, the possibility of ongoing viral evolution during treatment, and the role of clonal expansion in viral persistence. In preliminary studies, we have shown that most SIV proviruses are also defective. By focusing on those proviruses that are not defective, we will be able to better understand the cellular sources of viral rebound and to address controversies regarding ongoing viral replication during treatment and reservoir expansion through proliferation of infected cells. This studies will be carried out in conjunction with Hopkins colleagues who will employ other novel assays for replication-competent SIV in the cohorts of treated macaques described in the application. Together these studies should provide new insights into the sources of viral rebound.