Phylogenetic tree shapes resolve disease transmission patterns
Phylogenetic tree shapes resolve disease transmission patterns
复制标题
系统发育树形状解决疾病传播模式
DOI：
10.1101/003194
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发表时间：
2014
期刊：
影响因子：
--
通讯作者：
Colijn C
中科院分区：
文献类型：
--
作者：
Colijn C
背景和目的全基因组测序作为了解传染病暴发的一种工具正变得越来越流行，系统发育树被用于识别个体传播事件或表征暴发水平的总体传播动态。从序列数据推断传播动力学的现有方法依赖于充分表征的感染期、流行病学和临床元数据，这些元数据可能并不总是可用的，并且通常需要集中于系统发育树中的分支长度的计算密集型分析。我们试图确定系统发育树的拓扑结构是否包含签名的传输模式的基础outbreak.MethodologyWe使用模拟爆发训练，然后测试计算分类。我们测试的方法，从两个真实世界的outbreaks.ResultsWe的数据表明，不同的传输模式导致定量不同的系统发育树的形状。我们描述的拓扑特征，总结了一个暴发的结构，并发现基于这些计算分类器能够预测爆发的传播动态。该方法是强大的传输参数和网络类型的变化，并概括了已知的流行病学以前的特点，现实世界outbreaks.Conclusions和implicationsThere是简单的结构特性的系统发育树，当结合起来，可以区分传染病爆发的超级传播者，同质传播和链的传播。仅使用基因组数据就可以做到这一点，并且可以在疫情爆发期间完成。我们讨论了疫情管理的影响。
Background and ObjectivesWhole-genome sequencing is becoming popular as a tool for understanding outbreaks of communicable diseases, with phylogenetic trees being used to identify individual transmission events or to characterize outbreak-level overall transmission dynamics. Existing methods to infer transmission dynamics from sequence data rely on well-characterized infectious periods, epidemiological and clinical metadata which may not always be available, and typically require computationally intensive analysis focusing on the branch lengths in phylogenetic trees. We sought to determine whether the topological structures of phylogenetic trees contain signatures of the transmission patterns underlying an outbreak.MethodologyWe use simulated outbreaks to train and then test computational classifiers. We test the method on data from two real-world outbreaks.ResultsWe show that different transmission patterns result in quantitatively different phylogenetic tree shapes. We describe topological features that summarize a phylogeny’s structure and find that computational classifiers based on these are capable of predicting an outbreak’s transmission dynamics. The method is robust to variations in the transmission parameters and network types, and recapitulates known epidemiology of previously characterized real-world outbreaks.Conclusions and implicationsThere are simple structural properties of phylogenetic trees which, when combined, can distinguish communicable disease outbreaks with a super-spreader, homogeneous transmission and chains of transmission. This is possible using genome data alone, and can be done during an outbreak. We discuss the implications for management of outbreaks.
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影响因子：
4.3
作者：
Leventhal GE;Kouyos R;Stadler T;Wyl Vv;Yerly S;Böni J;Cellerai C;Klimkait T;Günthard HF;Bonhoeffer S
通讯作者：
Bonhoeffer S
系统发育学回顾：系统发育系统学的理论与实践
DOI：
--
发表时间：
1982
期刊：
影响因子：
--
作者：
D. H. Colless
通讯作者：
D. H. Colless
DOI：
10.1098/rstb.2012.0198
发表时间：
2013-03-19
影响因子：
6.3
作者：
Stadler, Tanja;Bonhoeffer, Sebastian
通讯作者：
Bonhoeffer, Sebastian
影响因子：
10.7
作者：
Stadler, Tanja;Kouyos, Roger;Bonhoeffer, Sebastian
通讯作者：
Bonhoeffer, Sebastian
影响因子：
30.8
作者：
Croucher, Nicholas J.;Finkelstein, Jonathan A.;Pelton, Stephen I.;Mitchell, Patrick K.;Lee, Grace M.;Parkhill, Julian;Bentley, Stephen D.;Hanage, William P.;Lipsitch, Marc
通讯作者：
Lipsitch, Marc