The roles of chance and spatial structure within host evolution of HIV

The way in which HIV evolves varies greatly between different infected hosts. I will discuss the role of deterministic factors, such as the viral genotype and the strength of immune responses, and stochastic factors in generating this variation. In particular, I will consider the processes of genetic drift, stochastic fluctuations in gene frequencies due to finite population size, and genetic draft, stochastic fluctuations in gene frequencies due to linkage to positively selected mutations. The bulk of viral replication occurs in highly spatially structured lymphoid tissues. I will discuss the impact of spatial structure on genetic drift and draft.