Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)

Graduate Group

Genomics & Computational Biology

First Advisor

Frederic D. Bushman


HIV is a deadly virus responsible for the AIDS pandemic, which has claimed countless lives since its origins in the early 1980s. A cure for HIV is still elusive - HIV can exist as a diverse and dynamic population that adapts quickly to immune and drug pressures, making elimination of infection difficult. Advances in antiretroviral (ARV) therapy have resulted in effective control of HIV for some but not all patients. This dissertation reports case studies of the response of viral populations to selection pressures exerted by emerging anti-HIV therapies. Deep sequencing technology was used to probe viral swarms at high-resolution, which helped make clinically relevant conclusions. Further, novel computational approaches were implemented to control procedural noise and carefully interpret signal. In one study, we examine HIV integrase inhibitors (INIs), which are among the latest ARV drugs. INIs act at a pre-integration level by aborting viral integration, which would normally lead to lasting infection. Raltegravir (RAL) is the only FDA-approved INI to date. Investigating drug resistance is crucial to informing future course of ARV therapy. We describe evolving HIV swarms in patients exhibiting a switch in RAL-resistance profiles. To understand implications of RAL administration, we analyzed the pre-therapy or treatment-naïve context for the viral populations in-depth. Our findings suggest that predominant mutations arise only in presence of RAL - in its absence, they do not constitute fit polymorphisms. For all their effectiveness, drugs have not eradicated HIV. A recent clinical case, however, involving transfer of HIV-resistant cells to an infected patient, resulted for the first time in possible cure. This emphasized the importance of gene-modification and cell-based therapies to treat HIV. One such strategy showing promise uses an antisense to target HIV. The approach has been safe although clinical efficacy has not been fully determined. In support of one such study, we deep-sequenced viral swarms in the presence of antisense-modified cells. Encouragingly, we observed minority strains harboring evidence of antisense pressure in vivo, demonstrating the potential of alternative therapy. Finally, this dissertation underscores the significance of rare signatures in HIV populations, and outlines methods to investigate them.

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