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Doctor of Philosophy


Microbiology and Immunology


Barr, Stephen D.


An important event during infection by retroviruses such as human immunodeficiency virus type 1 (HIV-1) is the permanent integration of the viral genome into the host genome. This event leads to life-long infection and is accompanied by a period of quiescence/latency ranging from a few years to >10 years where HIV-1 expression is barely detectable or undetectable. Despite the use of combination antiretroviral therapy (cART) which controls HIV-1 infection, quiescent/latent virus presents a major obstacle towards a functional cure. Integration site location in the genome is thought to contribute to latent infections and has the potential to confound anti-latency treatments, necessitating a greater understanding of the effects of integration site location on latency. To examine the global preference for integration location, we performed an extensive bioinformatics analysis on the integration site profile of HIV-1 and other retroviruses. We found that HIV-1 integration sites and that of other retroviruses are enriched in and/or near non-B DNA motifs. Non-B DNA are secondary structures in our genome formed by specific nucleotide sequences that exhibit non-canonical DNA base pairing. We demonstrated a strong correlation between integration sites in and near guanine-quadruplex (G4) motifs, a type of non-B DNA associated with transcriptional silencing, and reactivation of latent proviruses with latency reversal agents. Additionally, integration site studies have focused on HIV-1 subtype B infections; however, infections with other subtypes exist worldwide. A comparative analysis of 62 infected individuals with different HIV-1 subtypes showed significant differences in the integration site profiles between different subtypes, which was further altered by cART. Finally, we examined HIV-1 integration site profiles in anatomical sites and showed distinct integration profiles from peripheral blood, brain, and the gastrointestinal tract. Overall, our findings identified similarities and differences in the integration site profiles among evolutionarily diverse retroviruses. Notably, we have implicated non-B DNA as a new factor that influences integration site targeting and may play an important role in the establishment of HIV-1 latency and/or disease progression.