HIV-associated neurocognitive disorder (HAND) continues to be a debilitating disorder affecting the aging HIV patient population. This is despite the fact that currently available highly active antiretroviral therapy (HAART) is capable of suppressing HIV RNA to undetectable levels in both blood and cerebrospinal fluid (CSF). The persistence of HAND is likely due to a complex interplay between poorly understood virologic factors and natural aging processes. Understanding the biological determinants at the core of this complex interplay, and how they lead to the development of HAND even in the presence of suppressive HAART, will require a more detailed investigation of virologic factors and how they compound various human aging pathways. To better understand the biological correlates of HAND, we propose to use an analysis that combines clinical, neuromedical, and laboratory data with ultradeep sequencing (UDS) technology. We have identified a group of 56 individuals from the CNS HIV Antiretroviral Therapy Effects Research (CHARTER) cohort who are older than 50 years in age, have been followed longitudinally for at least four years, and have been suppressed with HAART throughout this time. Using UDS, we propose to sequence the env, gag, pro and reverse transcriptase coding regions of HIV-1 DNA populations in peripheral blood mononuclear cells (PBMCs) and CSF cell pellets (approximately 400 samples and 6.5 million sequences in total). These data will then be co-analyzed with clinical, antiretroviral, host geneti, and bio-marker data currently available in CHARTER. Specifically, we will investigate how the age of a subject and the presence or absence of HAND are associated with HIV-1 DNA levels in PBMCs and CSF cell pellets (Aim 1), the frequency of viral populations with differing co-receptor usage and drug resistance (Aim 2), anatomic compartmentalization and viral diversity between blood and CSF (Aim 3), and the rate of viral evolution during HAART (Aim 4). These analyses will be accomplished using a combination of phylogenetic, computational, and statistical techniques we developed and employ as part of our research at UCSD to better understand aspects of viral dynamics within human hosts. Collectively, this study will yield a more complete understanding of how various virologic factors impact natural aging processes and thereby lead to HAND within the context of HAART.
There is a growing body of literature into how viral dynamics and aging influence neurologic disease during HIV infection, but these studies are often limited by small numbers of participants, lack of standardized neurologic and clinical assessments, and practical restrictions of the virologic assays. Using data and samples collected from a large cohort designed to investigate neurologic dysfunction during HIV infection, this project aims to use novel next- generation ultradeep sequencing methods to better evaluate how human aging and HIV dynamics influence neurologic disease.
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