Assessment of genetic and functional diversity among natural HIV-1 Nef and Vpu isolates

Despite over 40 years of research and clinical investigation, there is still no vaccine or cure for HIV-1. Highly effective antiretroviral therapy (ART) has dramatically reduced illness due to HIV-1 infection, but ART is still not available universally. The enormous diversity of global HIV-1 sequences poses significant challenges to understanding mechanisms of viral pathogenesis, and also to developing new vaccines or therapies. The HIV-1 accessory proteins Nef and Vpu, which enhance viral pathogenesis and immune evasion, are encoded by highly polymorphic genes, but little is known about the functional impact of natural genetic variability in these proteins on HIV-1 infection. Furthermore, although Sub-Saharan Africa (SSA) harbours most HIV-1 infections globally, studies on viral subtypes prevalent in this region of the world are still limited. In this thesis, I assessed the genetic diversity and in vitro functional activity of nef and vpu sequences isolated from ART-naïve individuals living with HIV-1, including participants from SSA. In an analysis of 332 vpu sequences representing major HIV-1 group M subtypes (A, B, C and D and several unique recombinants), I observed substantial variability in CD4 and Tetherin downregulation functions among the clones and between the HIV-1 subtypes. Additionally, in an analysis of nef and vpu sequences isolated from untreated HIV-1 long term survivors (LTS) and progressors living with HIV-1 subtype A, I found that an impaired ability of nef to downregulate CD4 and HLA was associated with the LTS phenotype. Finally, in an analysis of nef sequences isolated from individuals living with untreated HIV-1 subtype A, I observed that TIM-3 upregulation function was associated with a faster rate of CD4 cell decline, suggesting a link between this Nef activity and disease progression. For each study, I also identified viral sequence polymorphisms associated with variable nef and vpu function that may inform future mechanistic studies. Overall, my thesis research provides new scientific insights into the impacts of HIV-1 nef and vpu sequence diversity on the function of these important viral accessory proteins. Potential links between these viral proteins and disease may support ongoing efforts to target nef and vpu using novel antiviral therapies and to inform the design of an HIV-1 vaccine for the African context.