期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 110, 期 1, 页码 228-233出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1207965110
关键词
birth-death prior; epidemiological dynamics; phylodynamics
资金
- Swiss National Science Foundation
- Royal Society of New Zealand [UOA0809]
Phylogenetic trees can be used to infer the processes that generated them. Here, we introduce a model, the Bayesian birth-death skyline plot, which explicitly estimates the rate of transmission, recovery, and sampling and thus allows inference of the effective reproductive number directly from genetic data. Our method allows these parameters to vary through time in a piecewise fashion and is implemented within the BEAST2 software framework. The method is a powerful alternative to the existing coalescent skyline plot, providing insight into the differing roles of incidence and prevalence in an epidemic. We apply this method to data from the United Kingdom HIV-1 epidemic and Egyptian hepatitis C virus (HCV) epidemic. The analysis reveals temporal changes of the effective reproductive number that highlight the effect of past public health interventions.
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