Phylodynamics on local sexual contact networks

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.Author summary: Phylodynamic models relate the branching pattern of a pathogen’s phylogenetic tree to the tree-like growth of an epidemic as it spreads through a host population. Such models are increasingly used to learn about the epidemiology of different pathogens. We extend current models to consider the structure of host contact networks—the web of physical interactions through which pathogens spread. By considering how local interactions among hosts shape the phylogeny of a pathogen, our models offer a “pathogen’s eye view” of these networks. Our models also provide a statistical framework that can be used to infer network structure directly from phylogenies, which we use to estimate the properties of a sexual contact network in Switzerland from a HIV phylogeny.