Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data.
Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data.
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DOI：
10.1093/molbev/msw064
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发表时间：
2016-08
影响因子：
10.7
通讯作者：
Drummond AJ
中科院分区：
文献类型：
--
作者：
Kühnert D;Stadler T;Vaughan TG;Drummond AJ
当病毒传播时，可能会在以前未受影响的地区爆发疫情。根据传入的时间和方式，每个地区的疫情都有自己的流行动态。迁移和系统动力学过程通常是相互交织的，在分析时空结构化病毒数据时需要予以考虑。在本文中，我们提出了一种基于多类型出生-死亡过程的结构化种群（例如地理结构）中系统动力学历史联合重建的完全概率方法。这种方法可用于量化病原体在结构化人群中的传播。亚人群内流行病动态随时间的变化是通过传播参数的分段持续变化来体现的。我们分析了来自地理结构宿主群体的全球人类流感 H3N2 病毒数据集，以证明如何在系统发育和迁移过程的同时推断季节性动态。我们的结果表明，这里分析的样本中所代表的北部、热带和南部地区之间的主要迁徙路径是从热带到北部地区的路径。此外，还对拉脱维亚艾滋病毒流行中两个艾滋病毒高危人群（异性恋者和注射吸毒者）之间和内部的时间依赖性传播动态进行了调查。我们的分析证实，拉脱维亚艾滋病毒流行在 2001 年左右达到顶峰，主要是由注射吸毒者风险群体推动的。
When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth–death process. This approach can be used to quantify the spread of a pathogen in a structured population. Changes in epidemic dynamics through time within subpopulations are incorporated through piecewise constant changes in transmission parameters. We analyze a global human influenza H3N2 virus data set from a geographically structured host population to demonstrate how seasonal dynamics can be inferred simultaneously with the phylogeny and migration process. Our results suggest that the main migration path among the northern, tropical, and southern region represented in the sample analyzed here is the one leading from the tropics to the northern region. Furthermore, the time-dependent transmission dynamics between and within two HIV risk groups, heterosexuals and injecting drug users, in the Latvian HIV epidemic are investigated. Our analyses confirm that the Latvian HIV epidemic peaking around 2001 was mainly driven by the injecting drug user risk group.