Format

Send to

Choose Destination
Mol Biol Evol. 2012 Jan;29(1):347-57. doi: 10.1093/molbev/msr217. Epub 2011 Sep 2.

Estimating the basic reproductive number from viral sequence data.

Author information

1
Institute of Integrative Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland. tanja.stadler@env.ethz.ch

Abstract

Epidemiological processes leave a fingerprint in the pattern of genetic structure of virus populations. Here, we provide a new method to infer epidemiological parameters directly from viral sequence data. The method is based on phylogenetic analysis using a birth-death model (BDM) rather than the commonly used coalescent as the model for the epidemiological transmission of the pathogen. Using the BDM has the advantage that transmission and death rates are estimated independently and therefore enables for the first time the estimation of the basic reproductive number of the pathogen using only sequence data, without further assumptions like the average duration of infection. We apply the method to genetic data of the HIV-1 epidemic in Switzerland.

PMID:
21890480
DOI:
10.1093/molbev/msr217
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Silverchair Information Systems
Loading ...
Support Center