Dynamics of the HIV-1 Latent Reservoir

Thesis (Ph.D.)--University of Washington, 2019Human immunodeficiency virus type 1 (HIV) has caused more than 35 million deaths world-wide and contributes significantly to the global burden of disease. Currently, the only effective treatment to suppress viral replication and prevent HIV transmission is combination antiretroviral therapy (ART), which prevents HIV from infecting new cells. Despite the efficacy of ART, long lived latently infected cells persist, with an estimated half-life of 44 months, and circulate throughout the infected host necessitating life-long treatment. These cells, known as the latent reservoir, contain an integrated form of the HIV genome (HIV DNA) that is transcriptionally silent, but can reactivate to produce virus. Therefore, interruption of ART inevitably leads to viral recrudescence stemming from the latent reservoir. Studying the latent reservoir is difficult because these cells contain no known biomarkers and do not always produce replication competent virus upon cellular activation. Additionally, latent reservoir cells are rare, and many proviral genomes contain defects that prevent them from producing replication competent virus. They do however confound efforts to measure the replication competent reservoir. Understanding the dynamics and correlates of reservoir seeding will be essential to develop novel cure strategies that target this latent reservoir. There is limited data on the dynamics of reservoir seeding throughout HIV infection, the impact of treatment interruption on reservoir size, and whether antibodies can play a role in limiting reservoir seeding. I focused my thesis on characterizing the seeding dynamics of latent reservoir cells containing HIV DNA (HIV DNA Reservoir) to better understand when the latent reservoir was generated and how it changed following treatment interruption. In the first part of this thesis I adapt, optimize, and validate a molecular based assay to quantitate HIV DNA from latently infected cells, as well as develop a novel cell line to detect replication competent HIV reactivated from latent reservoirs. In the second part of this thesis I demonstrate that the HIV DNA reservoir is limited by early ART and does not significantly increase following randomization to short treatment interruption in a cohort of Kenyan infants, suggesting that short treatment interruption studies may pose little risk to reservoir reseeding. I also examine the role of ADCC activity in preventing re-seeding of the latent reservoir and demonstrate that ADCC activity does not correlate with change in HIV DNA reservoir size following treatment interruption. Finally, I demonstrate that the HIV DNA reservoir is comprised mostly of viral variants circulating just prior to ART initiation, suggesting that during untreated infection the HIV DNA reservoir decays at a much faster rate than during suppressive ART. Together, these data demonstrate that the HIV DNA reservoir is limited by early ART, is not significantly reseeded with short treatment interruption, and that contrary to previous assumptions about reservoir dynamics, is decaying at a significantly faster rate pre-ART than after ART initiation, and suggest that targeting the HIV latent reservoir prior to early ART initiation may be an effective strategy to limit reservoir size, and that short treatment interruption can limit re-seeding of the latent reservoir