Comparing the pathogen genomes from several cases of an infectious disease has the potential to help us understand and control outbreaks. Many methods exist to reconstruct a phylogeny from such genomes, which represents how the genomes are related to one another. However, such a phylogeny is not directly informative about transmission events between individuals. TransPhylo is a software tool implemented as an R package designed to bridge the gap between pathogen phylogenies and transmission trees. TransPhylo is based on a combined model of transmission between hosts and pathogen evolution within each host. It can simulate both phylogenies and transmission trees jointly under this combined model. TransPhylo can also reconstruct a transmission tree based on a dated phylogeny, by exploring the space of transmission trees compatible with the phylogeny. A transmission tree can be represented as a coloring of a phylogeny where each color represents a different host of the pathogen, and TransPhylo provides convenient ways to plot these colorings and explore the results. This article presents the basic protocols that can be used to make the most of TransPhylo.
Bibliographical noteFunding Information:
The authors acknowledge funding from the Medical Research Council (grant MR/N010760/1) and the National Institute for Health Research (NIHR) Health Protection Research Unit in Genomics and Enabling Data (NIHR200892). P.J.W. thanks the NIHR HPRU in Modelling and Health Economics, a partnership between Public Health England, Imperial College London and LSHTM, for funding (NIHR200908). P.J.W. also acknowledges support from the MRC Centre (MR/R015600/1); this award is jointly funded by the U.K. Medical Research Council (MRC) and the U.K. Foreign, Commonwealth & Development Office (FCDO) under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 program supported by the European Union (EU). The views expressed are those of the authors and not necessarily those of the Department of Health and Social Care, EU, FCDO, MRC, NHS, NIHR, or Public Health England.
© 2021 The Authors.
- genomic epidemiology
- infectious disease outbreak
- transmission analysis