tetano
Editor, Senior Moderator
Biol Lett. 2013 Jul 24;9(5):20130331. doi: 10.1098/rsbl.2013.0331. Print 2013.
Real-time characterization of the molecular epidemiology of an influenza pandemic.
Hedge J, Lycett SJ, Rambaut A.
Source
Institute of Evolutionary Biology, University of Edinburgh, , Ashworth Laboratories, Edinburgh, UK.
Abstract
Early characterization of the epidemiology and evolution of a pandemic is essential for determining the most appropriate interventions. During the 2009 H1N1 influenza A pandemic, public databases facilitated widespread sharing of genetic sequence data from the outset. We use Bayesian phylogenetics to simulate real-time estimates of the evolutionary rate, date of emergence and intrinsic growth rate (r0) of the pandemic from whole-genome sequences. We investigate the effects of temporal range of sampling and dataset size on the precision and accuracy of parameter estimation. Parameters can be accurately estimated as early as two months after the first reported case, from 100 genomes and the choice of growth model is important for accurate estimation of r0. This demonstrates the utility of simple coalescent models to rapidly inform intervention strategies during a pandemic.
KEYWORDS:
Bayesian phylogenetics, influenza, pandemic, parameter estimation, real-time
PMID:
23883574
[PubMed - in process]
http://www.ncbi.nlm.nih.gov/pubmed/23883574
Real-time characterization of the molecular epidemiology of an influenza pandemic.
Hedge J, Lycett SJ, Rambaut A.
Source
Institute of Evolutionary Biology, University of Edinburgh, , Ashworth Laboratories, Edinburgh, UK.
Abstract
Early characterization of the epidemiology and evolution of a pandemic is essential for determining the most appropriate interventions. During the 2009 H1N1 influenza A pandemic, public databases facilitated widespread sharing of genetic sequence data from the outset. We use Bayesian phylogenetics to simulate real-time estimates of the evolutionary rate, date of emergence and intrinsic growth rate (r0) of the pandemic from whole-genome sequences. We investigate the effects of temporal range of sampling and dataset size on the precision and accuracy of parameter estimation. Parameters can be accurately estimated as early as two months after the first reported case, from 100 genomes and the choice of growth model is important for accurate estimation of r0. This demonstrates the utility of simple coalescent models to rapidly inform intervention strategies during a pandemic.
KEYWORDS:
Bayesian phylogenetics, influenza, pandemic, parameter estimation, real-time
PMID:
23883574
[PubMed - in process]
http://www.ncbi.nlm.nih.gov/pubmed/23883574