Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods

作者：Stadler Tanja^*; Bonhoeffer Sebastian

来源：Philosophical Transactions of the Royal Society B-Biological Sciences, 2013, 368(1614): 20120198.

DOI：10.1098/rstb.2012.0198

• phylogenetics
• epidemiology
• heterogeneous population
• parameter inference

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 super-spreader dynamics within the men-having-sex-with-men epidemic (unknown tip states).

• 出版日期2013-3-19