Institute of Integrative Biology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland.
Mol Biol Evol. 2012 Jan;29(1):347-57. doi: 10.1093/molbev/msr217. Epub 2011 Sep 2.
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.
流行病学过程在病毒种群的遗传结构模式中留下了指纹。在这里，我们提供了一种从病毒序列数据中直接推断流行病学参数的新方法。该方法基于使用出生-死亡模型（BDM）进行系统发育分析，而不是通常使用的合并作为病原体传播的流行病学模型。使用 BDM 的优点是，传输率和死亡率是独立估计的，因此首次能够仅使用序列数据估计病原体的基本繁殖数，而无需进一步假设感染的平均持续时间等。我们将该方法应用于瑞士 HIV-1 流行的遗传数据。
