Estimating the Basic Reproductive Number from Viral Sequence Data
Estimating the Basic Reproductive Number from Viral Sequence Data
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DOI：
10.1093/molbev/msr217
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发表时间：
2012-01-01
影响因子：
10.7
通讯作者：
Bonhoeffer, Sebastian
中科院分区：
文献类型：
--
作者：
Stadler, Tanja;Kouyos, Roger;Bonhoeffer, Sebastian
流行病学进程在病毒种群的遗传结构模式中留下了印记。本文提供了一种从病毒序列数据直接推断流行病学参数的新方法。该方法基于系统发育分析，采用出生-死亡模型（BDM），而不是常用的聚结模型作为病原体流行病学传播的模型。使用BDM的优点是可以独立估计传播率和死亡率，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，如平均感染持续时间。我们将该方法应用于瑞士HIV-1流行病的遗传数据。
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.