HIV proviral evolutionary dynamics and genetic compartmentalization during long-term suppressive antiretroviral therapy

Antiretroviral therapy (ART) effectively inhibits Human Immunodeficiency Virus (HIV) replication, but it is not curative. This is because HIV persists as an integrated, genomically-intact provirus in a small pool of infected cells that reside in blood and tissue. These cells, referred to as HIV reservoir cells (or, simply, "the HIV reservoir"), can reactivate at any time to produce infectious HIV. As a result, ART needs to be taken for life. One of the many barriers to achieving an HIV cure is our incomplete understanding of the genetic diversity, evolutionary dynamics, and anatomical distribution of the viral genomes that make up the within-host HIV reservoir. We also incompletely understand the large and diverse pool of genetically-defective proviruses that persist during long-term ART. Even though defective proviruses cannot produce infectious HIV, they can nevertheless contribute to chronic inflammation through viral antigen presentation. This thesis comprises three original research chapters that address knowledge gaps in our understanding of HIV proviral genetic diversity and evolutionary dynamics in blood, as well as an understudied anatomical site: the lung. The first research chapter reconstructs within-host HIV evolutionary histories in blood from participants of the Women's Interagency HIV Study. It then leverages this information to infer the lineage origins and integration dates of proviruses persisting during ART, as well as HIV RNA sequences emerging from the reservoir into blood when ART is interrupted. Notably, this study lessens the underrepresentation of women living with HIV subtype B strain in proviral evolutionary dynamics research. The second research chapter applies a variety of genetic and phylogenetic tests to investigate the extent of proviral genetic compartmentalization in blood and lung, an understudied site of HIV persistence. The third research chapter develops methods to study the evolutionary dynamics of hypermutated proviruses, which persist in abundance during ART, but that are routinely excluded from such studies because of a lack of validated approaches to properly incorporate them into phylogenies. The methods developed in this thesis, and the resulting insights into proviral genetic diversity and dynamics in blood and tissue, advance our understanding of HIV persistence towards the ultimate goal of an HIV cure.