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Genomic epidemiology analysis of infectious disease outbreaks using transPhylo

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Didelot, Xavier, Kendall, Michelle, Xu, Yuanwei, White, Peter J. and McCarthy, Noel D. (2021) Genomic epidemiology analysis of infectious disease outbreaks using transPhylo. Current Protocols, 1 (2). e60. doi:10.1002/cpz1.60

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Official URL: http://dx.doi.org/10.1002/cpz1.60

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Abstract

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.

Item Type: Journal Article
Subjects: R Medicine > RA Public aspects of medicine
R Medicine > RC Internal medicine
Divisions: Faculty of Science > Life Sciences (2010- )
Faculty of Medicine > Warwick Medical School
Library of Congress Subject Headings (LCSH): Communicable diseases, Communicable diseases -- Epidemiology, Communicable diseases -- Transmission -- Mathematical models, Phylogeny
Journal or Publication Title: Current Protocols
Publisher: Wiley-Blackwell Publishing Ltd.
ISSN: 2691-1299
Official Date: 22 February 2021
Dates:
DateEvent
22 February 2021Available
15 January 2021Accepted
Volume: 1
Number: 2
Article Number: e60
DOI: 10.1002/cpz1.60
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
MR/N010760/1[MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265
NIHR200892National Institute for Health Researchhttp://dx.doi.org/10.13039/501100000272
NIHR200908[NIHR] National Institute for Health Researchhttp://dx.doi.org/10.13039/501100000272
MR/R015600/1[MRC] Medical Research Councilhttp://dx.doi.org/10.13039/501100000265

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