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Phylodynamics on local sexual contact networks.

  • Rasmussen DA Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
  • Kouyos R Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland.
  • Günthard HF Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland.
  • Stadler T Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
  • 2017-03-29
Published in:
  • PLoS computational biology. - 2017
Biological Evolution
Computer Simulation
Disease Outbreaks
Genetic Variation
HIV Infections
HIV-1
Humans
Models, Statistical
Phylogeny
Prevalence
Sexual Partners
Switzerland
English 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.
Language
  • English
Open access status
gold
Identifiers
Persistent URL
https://sonar.ch/global/documents/277388
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