Inferring HIV-1 epidemiological dynamics from next-generation sequencing data

One of the major barriers to successful interventions for the prevention of premature viral failure and ageing in HIV-1 patients on combination antiviral therapy (cART) and for finding curative strategies, is our limited understanding of residual viremia and low-level viremia during cART. In this study, we will characterize the longitudinal viral haplotypes by next-generation sequencing. Sequencing results will be compared between patients who display sustained viral response and patients who display persistent low-level viremia during cART. We will explore the association of viral diversity, dual infections and recombination before therapy initiation to persistent low-level viremia on cART and will determine the temporal origin of viral variants isolated during episodes of persistent low-level viremia. The mutation profile of these variants will assist in the identification of pathways and factors that contribute to viral escape and can assist in the exploration of novel strategies that enhance the clearance of infected cells and virions.