Pathogen Genomics, Phenotype and Immunity (PGPI) & Basic Sciences Programme

This programme aims to conduct research that will lead to better understanding of pathogen genomics in order to characterise diseases and epidemics for better control and to investigate virological, immunological and genetic factors required for the development of effective interventions against HIV-1 and other infections. Advantage will be taken of a) well characterised cohorts and biobanks b) Unit track record in intervention trials c) investment in new technologies in genomics, immunological assays and bioinformatics and d) established collaborations. We propose to monitor the HIV epidemic by characterising the circulating HIV-1 subtypes especially in recent infections and use full length genome sequencing to understand better the increasing recombinant viruses using better bioinformatics tools. We will use molecular in combination with social-epidemiological and modelling approaches to provide novel avenues to monitor epidemic trends and transmission dynamics, and to contribute to targeted interventions through the identification of transmission clusters and hotspots. HIV drug resistance (HIVDR) is emerging as one of the most important challenges to ART roll out for both care and prevention, more so in resource limited areas characterized by the use of limited ARV regimens, stock outs, regimen change based on available supply and often limited use of viral load (VL) testing to monitor treatment outcomes. We will expand our drug resistance studies to contribute to improved interventions. HIV superinfection (SI) investigations will utilise a large collection of specimens from high risk populations to study host and viral factors associated with SI.