Features that matter: evolutionary signatures that predict viral transmission routes
Features that matter: evolutionary signatures that predict viral transmission routes
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重要的特征：预测病毒传播途径的进化特征
DOI：
10.1101/2023.11.22.568327
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Wardeh M
中科院分区：
文献类型：
--
作者：
Wardeh M
宿主之间的病毒传播途径是理解病毒流行病学的关键。不同的传播途径对病毒生态、传播的可能性和速度有很大影响;例如，呼吸道和病媒传播的病毒共同涵盖了大多数快速暴发和严重后果的动植物流行病。然而，确定具体的传播途径可能需要数月至数年的时间，从而延误了缓解工作。在这里，我们确定了预测病毒传播途径的病毒特征和进化特征，并使用它们来快速预测完全测序的病毒的潜在途径，无论是没有观察到路线的病毒，还是缺少路线的病毒。这是通过编译一个包含24，953个病毒-宿主关联的数据集和81个定义的传播途径，构建一个包含这些途径和42个高阶模式的病毒传播层次结构，并从三个互补的角度设计446个预测特征来实现的。我们整合了这些数据和特征，训练了98个独立的LightGBM分类器。我们发现，所有功能都有助于预测至少一种传播途径和/或模式，这证明了我们广泛的多视角方法的实用性。我们的框架在所有包括的传播途径和模式中实现了ROC-AUC = 0.991，F1评分= 0.855，并且能够实现高后果呼吸（ROC-AUC = 0.990，F1评分= 0.864）和媒介传播（ROC-AUC = 0.997，F1评分= 0.921）的高水平预测性能。我们的框架将病毒特征按其对预测的贡献排序，每种传播途径，从而确定与每种途径相关的基因组进化特征。结合更成熟的病毒宿主范围预测领域，我们的预测框架可以：提供对病毒传播潜力和模式的早期见解;通过适当的措施促进快速反应;并显著分流耗时的调查，以确认可能的传播途径。
Routes of virus transmission between hosts are key to understanding viral epidemiology. Different routes have large effects on viral ecology, and likelihood and rate of transmission; for example, respiratory and vector-borne viruses together encompass the majority of rapid outbreaks and high-consequence animal and plant epidemics. However, determining the specific transmission route(s) can take months to years, delaying mitigation efforts. Here, we identify the viral features and evolutionary signatures which are predictive of viral transmission routes and use them to predict potential routes for fully-sequenced viruses in silico and rapidly, for both viruses with no observed routes, as well as viruses with missing routes. This was achieved by compiling a dataset of 24,953 virus-host associations with 81 defined transmission routes, constructing a hierarchy of virus transmission encompassing those routes and 42 higher-order modes, and engineering 446 predictive features from three complementary perspectives. We integrated those data and features to train 98 independent ensembles of LightGBM classifiers. We found that all features contributed to the prediction for at least one of the routes and/or modes of transmission, demonstrating the utility of our broad multi-perspective approach. Our framework achieved ROC-AUC = 0.991, and F1-score = 0.855 across all included transmission routes and modes, and was able to achieve high levels of predictive performance for high-consequence respiratory (ROC-AUC = 0.990, and F1-score = 0.864) and vector-borne transmission (ROC-AUC = 0.997, and F1-score = 0.921). Our framework ranks the viral features in order of their contribution to prediction, per transmission route, and hence identifies the genomic evolutionary signatures associated with each route. Together with the more matured field of viral host-range prediction, our predictive framework could: provide early insights into the potential for, and pattern of viral spread; facilitate rapid response with appropriate measures; and significantly triage the time-consuming investigations to confirm the likely routes of transmission.
猴痘病毒有可能感染欧洲各地的多种本土动物物种，表明该地区流行的风险很高
DOI：
10.1101/2022.08.13.503846
发表时间：
2022
期刊：
--
影响因子：
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作者：
Blagrove M
通讯作者：
Blagrove M
水库*
DOI：
10.1201/9781003062103-8
发表时间：
2021
期刊：
Water Quality Assessments
影响因子：
--
作者：
D. Chapman
通讯作者：
D. Chapman
影响因子：
4.3
作者：
Folly, Arran J.;Sewgobind, Sanam;Hernandez-Triana, Luis M.;Mansfield, Karen L.;Lean, Fabian Z. X.;Lawson, Becki;Seilern-Moy, Katharina;Cunningham, Andrew A.;Spiro, Simon;Wrigglesworth, Ethan;Pearce-Kelly, Paul;Herdman, Trent;Johnston, Colin;Berrell, Morgan;Vaux, Alexander G. C.;Medlock, Jolyon M.;Johnson, Nicholas
通讯作者：
Johnson, Nicholas