2-AIN-505, 2-AIN-251: Seminár z bioinformatiky (1) a (3)
Zima 2019
Abstrakt

Tanja Stadler, Denise Kuhnert, Sebastian Bonhoeffer, Alexei J. Drummond. Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proceedings of the National Academy of Sciences of the United States of America, 110(1):228-233. 2013. The website links to a blog post applying this method to SARS-CoV-2.

Download preprint: not available

Download from publisher: https://dx.doi.org/10.1073%2Fpnas.1207965110 PubMed

Related web page: http://virological.org/t/phylodynamic-analyses-of-outbreaks-in-china-italy-washington-state-usa-and-the-diamond-princess/439

Bibliography entry: BibTeX

Abstract:

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.