An analytical journey from pathogen genetics to epidemiology. Prof Xavier Didelot, University of Warwick.

Recent years have seen a fantastic increase in the practicality of sequencing whole pathogen genomes. The availability of this data has huge potential to help us learn more about the evolution and epidemiology of pathogens, but the analytical methodology has been lacking behind the sequencing technology, with evolutionary and epidemiological fields remaining unduly separate. Here we present a whole pipeline for such analysis, from genomes to epidemiological interpretations, bridging the gap between evolution and epidemiology.

A central component of this pipeline is the dated phylogeny, which is a phylogenetic tree with branch lengths measured in units of time. We will describe how dated phylogenies can be constructed, and how they can be used for both fine scale and large scale epidemiological analysis.