Early Treatment Initiation and Outcomes in Perinatally HIV-infected Infants and Young Children in Johannesburg, South Africa

The 2013 case report of the “Mississippi baby,” who was started on antiretroviral therapy (ART) within 30 hours of life and maintained off-treatment remission for 27 months before HIV was once again detectable, generated renewed interest in the benefits of early ART, as well as optimism that HIV remission is a possibility if ART is started very early. The overarching goal of this dissertation was to advance our understanding of the relationship between early ART and three outcomes – the possibility of HIV remission, improved viral outcomes, and epigenetic changes – in HIV-infected infants and young children. First, a systematic review was conducted to assess current published data in support of the possibility of very early ART leading to HIV remission in infants. Evidence from this review suggested that although early ART does appear to be associated with better sustained virological control and smaller reservoir size, there are limited data at this time to support a strong link between early ART and HIV remission. Second, the association between age at ART initiation and virologic outcomes after ART initiation was empirically assessed using data from five cohorts of HIV-infected infants and young children initiating ART before 2 years of age in Johannesburg, South Africa. In three cohorts, there was no consistent evidence of an association between early ART initiation and rates of initial viral suppression. However, there was a consistent benefit of early treatment initiation on long-term viral control in two cohorts. Finally, an epigenome-wide association study was conducted to identify differential DNA methylation patterns between ART-treated HIV-infected and HIV-uninfected South African children. A total of 1,309 differentially methylated CpG sites associated with HIV status were selected (FDR q-value <0.05; |Δβ| >0.05), after adjustment for age, sex, and cell type proportions. In addition, 315 differentially methylated regions associated with HIV status were selected (Stouffer p-value <0.05, maximum |Δβ| change in the region >0.05, and containing at least two or more CpG sites). Many of the genes identified in both the site and region approaches were located in the major histocompatibility complex (MHC) region on chromosome 6, a region that plays an important role in the adaptive immune system. This novel study provided evidence of an association between perinatally-acquired HIV infection and a large number of changes in DNA methylation in school-aged children on ART, and highlighted potential new lines of investigation into the biologic pathways influenced by HIV and its treatment. Overall, this dissertation increased our understanding of the timing of early ART initiation in HIV-infected infants and addressed gaps in our knowledge relevant to outcomes associated with early ART initiation. As public health practice continues to move towards infant diagnosis of HIV at birth and early life initiation of ART, these findings help to inform future research that will guide HIV care in infants.