Viral sequence evolution
Our longitudinal sampling of maternal and child virus in the babycure study has provided a wealth of full-length and gag-pro sequence data to accompany the in-vitro IFN-sensitivity and VRC data. Through detailed bioinformatic analysis run by Nicholas Grayson we are working to elucidate the evolutionary requirements for IFN-resistance at both nucleic acid and peptide levels, and whether there is a relationship with VRC. Additionally, we are looking into the mother-to-child transmission bottleneck at the sequence level. We are also monitoring the in-host evolution of child virus to see whether it reverts from the transmission genotype back towards the maternal genotype or is influenced by HLA type. In close collaboration with the Wellcome Trust Centre for Human Genomics in Oxford we use high throughput bait capture techniques to specifically enrich HIV samples and generate next generation sequence data to allow us to look at viral diversity and drug resistance.