Epidemic reconstruction in a phylogenetics framework: transmission trees as partitions

TL;DR

This paper introduces a novel method for reconstructing epidemic transmission trees by partitioning phylogenetic trees, enabling joint inference of phylogenies and transmission dynamics within the BEAST software.

Contribution

It establishes a new framework linking transmission trees to phylogenetic partitions and integrates a Markov Chain Monte Carlo approach into BEAST for co-estimation.

Findings

Provides a new partition-based method for transmission tree inference

Integrates the approach into the BEAST phylogenetic software

Enables joint estimation of phylogenies and transmission trees

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.