Abstract

Rapidly evolving viruses such as HIV , HCV and Influenza virus are of major interest in phylogenetics. They are special in that their ecological and evolutionary processes act on the same timescale and are therefore entangled. The cross-reaction of the two processes must be accounted for when inferring epidemiological parameters and/or phylogenetic history.

Our aim is a joint epidemiological phylogenetic, i.e. phylodynamic, analysis of genomic data by incorporating the dynamics of an SIR model into Bayesian phylogenetic inference. A new version of the birth-death model (Stadler, 2010) that incorporates sampling-through-time and can also be extended to allow birth and death rates to change over time can be parameterized to facilitate modeling SIR -like population dynamics while reconstructing phylogenetic history and simultaneously estimating epidemiological parameters.

References Stadler, T., 2010. Sampling-through-time in birth-death trees. Journal of Theoretical Biology.