Studies on the Molecular Determinants of Human Retrovirus Diversity

Abstract

The human immunodeficiency viruses (HIVs) are two species (HIV type 1, HIV-1; HIV type 2, HIV-2) in the Lentivirus genus of the Retroviridae family of viruses and are the etiological agents of acquired immunodeficiency syndrome (AIDS). Nearly 75 million people have been infected with HIV-1 and HIV-2 since their emergence in the human population and they are responsible for the deaths of almost 32 million individuals to date. One of the key drivers of the HIV-1 pandemic is the extreme genetic diversity of the virus, which drives the development of antiviral drug resistance and frustrates vaccine development. Retroviruses also exhibit considerable structural diversity, which may have important implications for infectivity and replication. Human T-cell leukemia virus type 1 (HTLV-1), within the Deltaretrovirus genus, is also a major pathogenic human retrovirus. HIV-2 and HTLV-1 exhibit markedly reduced rates of transmissibility and potentially evolution compared with HIV-1 and are therefore understudied relative to their pandemic counterpart. The overarching goal of this thesis was to characterize the viral and cellular determinants of the molecular diversity of human retroviruses, with an emphasis on HTLV-1 and HIV-2. To this end, experiments were conducted which 1) characterized the structural diversity of authentic HTLV-1 particles derived from the chronically infected SP cell line, demonstrating that intact capsid cores are relatively rare among HTLV-1 particles; and 2) examined the contribution of host apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) proteins to HIV-2 mutagenesis, which revealed that despite their role as potent mutagens of HIV-1, APOBEC3-mediated mutagenesis of HIV-2 is limited. Additionally, a user-friendly sequence analysis workflow was developed that enables the ultra-accurate detection of mutations within HIV-1 and HIV-2, which reduces the background error rate of traditional Illumina next-generation sequencing by approximately 100-fold. This workflow is already being employed to characterize the contributions of additional cellular proteins to retroviral mutagenesis, including the host protein SAM domain and HD domain- containing protein 1 (SAMHD1). Taken together, these studies provide new insights into the structural and genetic diversity of human retroviruses, particularly those which have historically been poorly characterized and underappreciated.