Population genomic analysis of HIV transmission fitness

HIV evolves to maximize replication within hosts and transmit to new uninfected individuals, but we currently lack a detailed understanding of how changes in the HIV genome alter the ability of HIV to reproduce and spread. To understand how beneficial mutations spread at the epidemic level requires a deeper understanding of how mutations impact transmissibility of the virus. We will develop new bioinformatic methods to estimate fitness along multiple dimensions associated with replication and transmission. We will identify new mutations which are associated with gain or loss of transmission fitness. These methods will be applied to new large population-based samples of whole HIV genomes across sub-Saharan Africa. These findings will have relevance for vaccine design and forecasting the future evolution of the HIV epidemic, and the potential for therapeutic vaccines to modify the transmissibility of HIV will be explored.