Final Report Summary - VIRALPHYLOGEOGRAPHY (Evolutionary reconstruction of viral spread in time and space)
With the objective to assist in designing effective intervention and prevention strategies, we have developed a comprehensive statistical framework for uncovering the spatial and temporal dynamics of pathogen genomes. To this aim, we designed and extended a series of computationally tractable models that use the rapidly proliferating viral genome data to their full potential, connect molecular evolution to underlying spatial processes, and pave the path to rigorous and powerful phylogeographic hypothesis testing. The framework includes models for phylogenetic diffusion in discrete and continuous space. These models and the associated inference methodologie have been implemented in a popular and freely available Bayesian statistical software package (BEAST: http://beast.bio.ed.ac.uk). Armed with these tools, we have investigated how genetic variation within important viral pathogens, such as influenza, rabies, Ebola and HIV, arises and persists across a diverse range of hosts and environments.