DYNAMITE: a phylogenetic tool for identification of dynamic transmission epicenters
DYNAMITE: a phylogenetic tool for identification of dynamic transmission epicenters
复制标题
DYNAMITE：一种用于识别动态传播震中的系统发育工具
DOI：
--
复制
发表时间：
2021
期刊：
影响因子：
--
通讯作者：
M. Prosperi
中科院分区：
文献类型：
--
作者：
B. R. Magalis;S. Marini;M. Salemi;M. Prosperi
当流行病学监测有问题时，分子数据分析对于理解快速传播的病毒种群的整体行为是非常有价值的。在描述种群内的亚群(通常被识别为系统发育树中的分支)时，它也特别有用，这些亚群代表通过直接传播或通过病毒传播中的不同风险因素传播而联系在一起的个体。然而，不应期望这些较小群体内的传播模式或病毒动态随着时间的推移表现出同质性行为。因此，根据汇总统计数据(例如，支系上的中位数遗传距离)识别集群的标准系统发育方法将不会被期望捕捉到动态的传播集群。为此，我们开发了Dynamite(动态识别传输震中)，这是一种基于分支(而不是传统的分支)搜索集群标准的集群识别算法，允许将部分分支识别为集群。使用不同集群类型和动态的模拟病毒爆发，我们表明，在检测静态和动态传播集群方面，Dynamite始终比现有工具更敏感。Dynamite已经在R中实现，并以开放源码的形式在：githorb.com/ProsperiLab/Dynamite上发布。
Molecular data analysis is invaluable in understanding the overall behavior of a rapidly spreading virus population when epidemiological surveillance is problematic. It is also particularly beneficial in describing subgroups within the population, often identified as clades within a phylogenetic tree, that represent individuals connected via direct transmission or transmission via differing risk factors in viral spread. However, transmission patterns or viral dynamics within these smaller groups should not be expected to exhibit homogeneous behavior over time. As such, standard phylogenetic approaches that identify clusters based on summary statistics (e.g., median genetic distance over the clade) would not be expected to capture dynamic clusters of transmission. For this purpose, we have developed DYNAMITE (DYNAMic Identification of Transmission Epicenters), a cluster identification algorithm based on a branch-wise (rather than traditional clade-wise) search for cluster criteria, allowing partial clades to be recognized as clusters. Using simulated viral outbreaks with varying cluster types and dynamics, we show that DYNAMITE is consistently more sensitive than existing tools in detecting both static and dynamic transmission clusters. DYNAMITE has been implemented in R and released as open source at: github.com/ProsperiLab/DYNAMITE.
影响因子：
10.7
作者：
Hoang DT;Chernomor O;von Haeseler A;Minh BQ;Vinh LS
通讯作者：
Vinh LS