Uncovering Epidemiological Dynamics in Heterogeneous Host Populations Using Phylogenetic Methods

Overview

Journal Philos Trans R Soc Lond B Biol Sci

Specialty Biology

Date 2013 Feb 6

PMID 23382421

Citations 69

Authors

Tanja Stadler

Sebastian Bonhoeffer

Affiliations

Soon will be listed here.

Abstract

Host population structure has a major influence on epidemiological dynamics. However, in particular for sexually transmitted diseases, quantitative data on population contact structure are hard to obtain. Here, we introduce a new method that quantifies host population structure based on phylogenetic trees, which are obtained from pathogen genetic sequence data. Our method is based on a maximum-likelihood framework and uses a multi-type branching process, under which each host is assigned to a type (subpopulation). In a simulation study, we show that our method produces accurate parameter estimates for phylogenetic trees in which each tip is assigned to a type, as well for phylogenetic trees in which the type of the tip is unknown. We apply the method to a Latvian HIV-1 dataset, quantifying the impact of the intravenous drug user epidemic on the heterosexual epidemic (known tip states), and identifying superspreader dynamics within the men-having-sex-with-men epidemic (unknown tip states).

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