Phylogenies increase power to detect highly transmissible viral genome variants.
Phylogenies increase power to detect highly transmissible viral genome variants.
复制标题
系统发育增强了检测高传染性病毒基因组变异的能力。
DOI：
10.1101/2023.07.28.23293332
复制
发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Rannala,Bruce
中科院分区：
文献类型：
--
作者：
May,MichaelR;Rannala,Bruce
正如SARS-CoV-2大流行所表明的那样，传播率增加的新病毒株的出现对全球健康构成了重大威胁。病毒基因组序列与序列进化的统计模型相结合，可能为这些毒株的早期检测提供关键工具。使用一种新的统计模型，将传播率与整个病毒基因组序列联系起来，我们研究了系统进化方法--使用与病毒样本相关的系统发育树--和基于计数的方法--使用随时间变化的变异病例计数--来检测增加的传播率，并识别致病突变。我们发现，特别是系统发育学可以在新变种起源后很快发现它们，并可能有助于开发用于暴发监测的早期检测系统。
As demonstrated by the SARS-CoV-2 pandemic, the emergence of novel viral strains with increased transmission rates poses a significant threat to global health. Viral genome sequences, combined with statistical models of sequence evolution, may provide a critical tool for early detection of these strains. Using a novel statistical model that links transmission rates to the entire viral genome sequence, we study the power of phylogenetic methods—using a phylogenetic tree relating viral samples—and count-based methods—using case-counts of variants over time—to detect increased transmission rates, and to identify causative mutations. We find that phylogenies in particular can detect novel variants very soon after their origin, and may facilitate the development of early detection systems for outbreak surveillance.