Epidemic reconstruction in a phylogenetics framework: transmission trees as partitions

Abstract

The reconstruction of transmission trees for epidemics from genetic data has been the subject of some recent interest. It has been demonstrated that the transmission tree structure can be investigated by augmenting internal nodes of a phylogenetic tree constructed using pathogen sequences from the epidemic with information about the host that held the corresponding lineage. In this paper, we note that this augmentation is equivalent to a correspondence between transmission trees and partitions of the phylogenetic tree into connected subtrees each containing one tip, and provide a framework for Markov Chain Monte Carlo inference of phylogenies that are partitioned in this way, giving a new method to co-estimate both trees. The procedure is integrated in the existing phylogenetic inference package BEAST.

40 pages, 3 figures

Cited by in corpus (3)

• SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
• Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees
• Bayesian reconstruction of HIV transmission trees from viral sequences and uncertain infection times