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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
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. © 2021 The Authors.
| Item Type: | Journal Article | |||||||||||||||
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| Subjects: | R Medicine > RA Public aspects of medicine R Medicine > RC Internal medicine |
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| Divisions: | Faculty of Science > Life Sciences (2010- ) Faculty of Medicine > Warwick Medical School |
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| 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: |
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| Date of first compliant deposit: | 25 February 2021 | |||||||||||||||
| 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: |
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