Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages - Application to rabies virus spread in Iran
Using phylogeographic approaches to analyse the dispersal history, velocity and direction of viral lineages - Application to rabies virus spread in Iran
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DOI：
10.1111/mec.15222
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发表时间：
2019-09-01
影响因子：
4.9
通讯作者：
Bourhy, Herve
中科院分区：
文献类型：
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作者：
Dellicour, Simon;Troupin, Cecile;Bourhy, Herve
近年来，人们广泛使用系统地理学方法来揭示病毒流行的传播历史。病毒传播的空间明确重建是谱系运动数据的宝贵来源，可用于研究潜在环境层对病原体传播的影响。在这里，我们进行了系统地理学推断，并应用不同的post - hoc方法来分析一个新的和全面的病毒基因组数据集，以阐明狂犬病毒（RABV）在伊朗的传播历史和动态，这在很大程度上仍然是未知的。我们首先分析了环境因素与世系间扩散速度变化之间的关系。其次，我们提出、测试并应用了一种新的方法来研究环境条件与谱系扩散方向之间的联系。通过仿真对新方法的统计性能（检测功率、假阳性率）进行了评估。我们对RABV基因组进行了系统地理学分析，使我们能够描述伊朗RABV的巨大多样性，并确认该国几个分支的共循环。总的来说，我们估计谱系传播速度相对较高，类似于先前对北非犬狂犬病病毒传播的估计。最后，我们强调RABV谱系在与高人口密度相关的可达地区传播的趋势。我们的分析工作流程说明了如何使用系统地理学方法来研究环境因素对病毒传播动力学的几个方面的影响。
Recent years have seen the extensive use of phylogeographic approaches to unveil the dispersal history of virus epidemics. Spatially explicit reconstructions of viral spread represent valuable sources of lineage movement data that can be exploited to investigate the impact of underlying environmental layers on the dispersal of pathogens. Here, we performed phylogeographic inference and applied different post hoc approaches to analyse a new and comprehensive data set of viral genomes to elucidate the dispersal history and dynamics of rabies virus (RABV) in Iran, which have remained largely unknown. We first analysed the association between environmental factors and variations in dispersal velocity among lineages. Second, we present, test and apply a new approach to study the link between environmental conditions and the dispersal direction of lineages. The statistical performance (power of detection, false-positive rate) of this new method was assessed using simulations. We performed phylogeographic analyses of RABV genomes, allowing us to describe the large diversity of RABV in Iran and to confirm the cocirculation of several clades in the country. Overall, we estimate a relatively high lineage dispersal velocity, similar to previous estimates for dog rabies virus spread in northern Africa. Finally, we highlight a tendency for RABV lineages to spread in accessible areas associated with high human population density. Our analytical workflow illustrates how phylogeographic approaches can be used to investigate the impact of environmental factors on several aspects of viral dispersal dynamics.