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Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses.

  • Müller NF Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; nicola.felix.mueller@gmail.com timothy.vaughan@bsse.ethz.ch.
  • Stolz U Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
  • Dudas G Department of Biological and Environmental Sciences, University of Gothenburg, SE-40530 Gothenburg, Sweden.
  • Stadler T Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland.
  • Vaughan TG Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland; nicola.felix.mueller@gmail.com timothy.vaughan@bsse.ethz.ch.
  • 2020-07-08
Published in:
  • Proceedings of the National Academy of Sciences of the United States of America. - 2020
BEAST
MCMC
infectious diseases
phylodynamics
phylogenetics
Algorithms
Evolution, Molecular
Genome, Viral
Humans
Influenza, Human
Models, Genetic
Models, Statistical
Orthomyxoviridae
Phylogeny
Reassortant Viruses
English Reassortment is an important source of genetic diversity in segmented viruses and is the main source of novel pathogenic influenza viruses. Despite this, studying the reassortment process has been constrained by the lack of a coherent, model-based inference framework. Here, we introduce a coalescent-based model that allows us to explicitly model the joint coalescent and reassortment process. In order to perform inference under this model, we present an efficient Markov chain Monte Carlo algorithm to sample rooted networks and the embedding of phylogenetic trees within networks. This algorithm provides the means to jointly infer coalescent and reassortment rates with the reassortment network and the embedding of segments in that network from full-genome sequence data. Studying reassortment patterns of different human influenza datasets, we find large differences in reassortment rates across different human influenza viruses. Additionally, we find that reassortment events predominantly occur on selectively fitter parts of reassortment networks showing that on a population level, reassortment positively contributes to the fitness of human influenza viruses.
Language
  • English
Open access status
hybrid
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Persistent URL
https://sonar.ch/global/documents/77347
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