Phylogenetic Methods for Infectious Models

Here, we adopt the maximum-likelihood framework based on a multi-type branching process (MTBP) for heterogeneous population where each host is assigned to a type (subpopulation). We extend this multi-type birth-death branching model to a tree-based SIR model which also incorporates contact tracing. On a rooted known phylogenetic tree where only the root node is infected and infectious, we investigate the probability density of a sampled tree given some epidemiological parameters. The maximum-likelihood parameter estimation of the basic model is combined with the results for contact tracing. We expect that the tracing events incorporate information about the heterogeneity in the contact structure, while the phylogenetic methods are better to estimate the timing of the infectious process. In that, we hope that the combined method will improve the estimations of the parameters of the epidemic process, as well as on the underlying contact structure.