Deep sequence analysis of HIV adaptation following vertical transmission reveals the impact of immune pressure on the evolution of HIV

Highly mutable pathogens utilise genetic variations within T cell epitopes as a mechanism of immune escape (viral adaptation). The diversity of HLA in human populations partially protects against rapid population-level accumulation of HIV adaptations through horizontal transmissions. In contrast vertical transmissions occur between haploidentical maternal-child pairs, and potentially include adaptive changes through a paternal-maternal-child transmission chain, representing a pathway to complete pre-adaptation to HLA in child hosts over only two transmission events. We utilised next generation sequencing to examine HIV evolution in the unique setting of vertical HIV transmission. We predict the in vivo replicative cost and immune benefit of specific HIV adaptations that could be used to inform vaccine designs to combat the issue of immune escape.