Paper Info
Title
Phylodynamics on local sexual contact networks.
Abstract
Phylodynamic models are widely used in infectious disease epidemiology to infer the dynamics and structure of pathogen populations. However, these models generally assume that individual hosts contact one another at random, ignoring the fact that many pathogens spread through highly structured contact networks. We present a new framework for phylodynamics on local contact networks based on pairwise epidemiological models that track the status of pairs of nodes in the network rather than just individuals. Shifting our focus from individuals to pairs leads naturally to coalescent models that describe how lineages move through networks and the rate at which lineages coalesce. These pairwise coalescent models not only consider how network structure directly shapes pathogen phylogenies, but also how the relationship between phylogenies and contact networks changes depending on epidemic dynamics and the fraction of infected hosts sampled. By considering pathogen phylogenies in a probabilistic framework, these coalescent models can also be used to estimate the statistical properties of contact networks directly from phylogenies using likelihood-based inference. We use this framework to explore how much information phylogenies retain about the underlying structure of contact networks and to infer the structure of a sexual contact network underlying a large HIV-1 sub-epidemic in Switzerland.
Year
DOI
Venue
2017
10.1371/journal.pcbi.1005448
PLOS COMPUTATIONAL BIOLOGY
Field
DocType
Volume
Coalescent theory,Pairwise comparison,Biology,Inference,Viral phylodynamics,Epidemic dynamics,Bioinformatics,Infectious Disease Epidemiology,Probabilistic framework,Network structure
Journal
13
Issue
ISSN
Citations 
3
1553-734X
1
PageRank 
References 
Authors
0.36
10
4
Name
Order
Citations
PageRank
David A. Rasmussen1224.05
Roger D Kouyos2185.57
Huldrych F. Günthard3101.89
Tanja Stadler4122.82