University of Cambridge
I will revisit data from experimental phylogenetics studies and in vivo challenge studies, in order to evaluate methods for source attribution. These experiments represent cases where the transmission history is known, but the evolution of the pathogen is not, and are particularly useful for validating methods for densely sampled outbreaks. I will present examples that illustrate three different types of data; bulk sequences, clonal sequences, and short read data, to show the potential and challenges of using within-host diversity to help understand who infected whom. In particular, in order to harness within-host data to guide transmission studies, we need good within-host models of viral evolution, both during and following transmission. I have set up a repository of data and resources, http://molecular-epidemiolo.gy, which I hope will facilitate the broader comparison of methods of source attribution. Finally, I discuss how in principle, an experimental approach may be applied to help evaluate a broader range of inferential approaches, including those for sparsely sampled epidemics.