Phylodynamics on local sexual contact networks.

Détails

Ressource 1Télécharger: 28350852_BIB_C51F01784241.pdf (2410.23 [Ko])
Etat: Public
Version: Final published version
Licence: CC BY 4.0
ID Serval
serval:BIB_C51F01784241
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
Phylodynamics on local sexual contact networks.
Périodique
PLoS computational biology
Auteur⸱e⸱s
Rasmussen D.A., Kouyos R., Günthard H.F., Stadler T.
ISSN
1553-7358 (Electronic)
ISSN-L
1553-734X
Statut éditorial
Publié
Date de publication
03/2017
Peer-reviewed
Oui
Volume
13
Numéro
3
Pages
e1005448
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: epublish
Résumé
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.
Pubmed
Open Access
Oui
Création de la notice
04/04/2017 18:30
Dernière modification de la notice
30/04/2021 7:14
Données d'usage