Effects of memory on the shapes of simple outbreak trees
File(s)
Author(s)
Plazzotta, G
Kwan, C
Boyd, M
Colijn, C
Type
Journal Article
Abstract
Genomic tools, including phylogenetic trees derived from sequence data, are increasingly used to understand outbreaks of infectious diseases. One challenge is to link phylogenetic trees to patterns of transmission. Particularly in bacteria that cause chronic infections, this inference is a ected by variable infectious periods and infectivity over time. It is known that non-exponential infectious periods can have substantial e ects on pathogens' transmission dynamics. Here we ask how this non-Markovian nature of an outbreak process a ects the branching trees describing that process, with particular focus on tree shapes. We simulate Crump-Mode-Jagers branching processes and compare di erent patterns of infectivity over time. We nd that memory (non-Markovian-ness) in the process can have a pronounced e ect on the shapes of the outbreak's branching pattern. However, memory also has a pronounced e ect on the sizes of the trees, even when the duration of the simulation is xed. When the sizes of the trees are constrained to a constant value, memory in our processes has little direct e ect on tree shapes, but can bias inference of the birth rate from trees. We compare simulated branching trees to phylogenetic trees from an outbreak of tuberculosis in Canada, and discuss the relevance of memory to this dataset.
Date Issued
2016-02-18
Date Acceptance
2016-01-07
Citation
Scientific Reports, 2016, 6
ISSN
2045-2322
Publisher
Nature Publishing Group
Journal / Book Title
Scientific Reports
Volume
6
Copyright Statement
This work is licensed under a Creative Commons Attribution 4.0 International License. The images
or other third party material in this article are included in the article’s Creative Commons license,
unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license,
users will need to obtain permission from the license holder to reproduce the material. To view a copy of this
license, visit http://creativecommons.org/licenses/by/4.0/
or other third party material in this article are included in the article’s Creative Commons license,
unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license,
users will need to obtain permission from the license holder to reproduce the material. To view a copy of this
license, visit http://creativecommons.org/licenses/by/4.0/
License URL
Sponsor
Engineering & Physical Science Research Council (EPSRC)
Grant Number
EP/K026003/1
Publication Status
Published
Article Number
21159