Characterizing proviral populations in brain tissues

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 DESCRIPTION: This study is designed to meet the goals of the RFA-DA-15-018: Developing Technologies and Tools to Monitor HIV Brain Reservoirs and How They May be Altered by Exposure to Substances of Abuse. To meet this challenge in the R21 phase, we propose to develop and validate a combined next generation sequencing (Pacific Biosciences single-molecule, real time (SMRT) sequencing) and bioinformatics platform to accurately measure and characterize HIV DNA populations in brain and lymph node tissues. In particular, this platform will be able to measure and identify proviral populations that are (i) intact and replication competent, (ii) intact but replication incompetent, and (iii) not intact. We will develop and validate the proposed platform based on international standard procedures for diagnostic molecular methods (i.e. CAP and OIE) using brain and lymph node tissues from HIV-infected individuals on optimized antiretroviral therapy for at least 2 years before death. Once developed and validated, we will use this technology in the R33 phase to determine how HIV DNA populates the brains of stimulant users and non-users.