HIV Integration Profiling and Viral Persistence in Children and Youth

Johns Hopkins University, Baltimore MD

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Abstract

Despite highly active antiretroviral therapy (HAART), HIV persists in a small, stable pool of resting memory CD4+ T cells and at low levels in plasma, even in children treated before 6 weeks of age, precluding cure or treatment discontinuation. Identifying strategies to purge persistent HIV-reservoirs is a high priority for HIV research, but will require better understanding of their source. Current methods to study HIV persistence have provided significant insights, but new approaches are required to make leaps forward. One promising possibility is the use of new high-throughput deep sequencing technologies, which our preliminary data show can detect HIV integration events and conduct viral genome sequencing, revealing changes over time. We hypothesize that HIV integration profiling coupled with whole viral genome sequencing will allow us to better examine longitudinally the contribution of: 1) intrinsically long-lived memory CD4+ T cells, 2) clonal expansion of memory CD4+ T cells, and 3) ongoing viral replication to establishment and maintenance of HIV reservoirs in children and youth. To test this hypothesis, we propose to:1) Establish new metrics using high throughput deep sequencing to detect clonally expanding and newly generated infected cells over a time course to assess HIV persistence in children and youth;2) Use the new metrics to characterize HIV persistence in early-treated infants and youth, including therapeutic vaccinees;and 3) Examine whether the new metrics can predict success of treatment simplification. Achievement of these aims will dramatically improve our ability to reveal the origins and mechanisms of HIV persistence, help shape potentially curative treatment approaches, and assess completely the abilities of newer treatment approaches to control virus replication, including those aimed at achieving functional cure for HIV in children and youth.