新型病毒景观系统发育地理学方法的比较性能
Comparative performance of novel viral landscape phylogeography approaches.
作者信息
Dellicour Simon, Gámbaro Fabiana, Jacquot Maude, Lequime Sebastian, Baele Guy, Gilbert Marius, Pybus Oliver G, Suchard Marc A, Lemey Philippe
机构信息
Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium.
Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
出版信息
bioRxiv. 2025 Mar 27:2025.03.24.645003. doi: 10.1101/2025.03.24.645003.
The fast rate of evolution in RNA viruses implies that their evolutionary and ecological processes occur on the same time scale. Genome sequences of these pathogens can therefore contain information about the processes that govern their transmission and dispersal. In particular, landscape phylogeographic approaches use phylogeographic reconstructions to investigate the impact of environmental factors and variables on the spatial spread of viruses. Here, we extend and improve existing approaches and develop three novel landscape phylogeographic methods that can test the impact of continuous environmental factors on the diffusion velocity of viral lineages. In order to evaluate the different methods, we also implemented two simulation frameworks to test and compare their statistical performance. The results enable us to formulate clear guidelines for the use of three complementary landscape phylogeographic approaches that have sufficient statistical power and low rates of false positives. Our open-source methods are available to the scientific community and can be used to investigate the drivers of viral spread, with potential benefits for understanding virus epidemiology and designing tailored intervention strategies.
RNA病毒快速的进化速度意味着它们的进化和生态过程在同一时间尺度上发生。因此,这些病原体的基因组序列可以包含有关控制其传播和扩散过程的信息。特别是,景观系统发育地理学方法利用系统发育地理学重建来研究环境因素和变量对病毒空间传播的影响。在这里,我们扩展并改进了现有方法,并开发了三种新颖的景观系统发育地理学方法,这些方法可以测试连续环境因素对病毒谱系扩散速度的影响。为了评估不同的方法,我们还实施了两个模拟框架来测试和比较它们的统计性能。结果使我们能够为使用三种具有足够统计效力和低误报率的互补景观系统发育地理学方法制定明确的指导方针。我们的开源方法可供科学界使用,可用于研究病毒传播的驱动因素,对理解病毒流行病学和设计量身定制的干预策略具有潜在益处。
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