Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints.
Simultaneously reconstructing viral cross-species transmission history and identifying the underlying constraints.
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DOI：
10.1098/rstb.2012.0196
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发表时间：
2013-03-19
期刊：
影响因子：
--
通讯作者：
Lemey P
中科院分区：
文献类型：
--
作者：
Faria NR;Suchard MA;Rambaut A;Streicker DG;Lemey P
对于大多数人类病原体来说，决定跨物种传播事件起源和结局的因素仍然不清楚，尽管这些因素对于开发预测模型和评估预防策略的有效性至关重要。在这里，我们描述了一个灵活的贝叶斯统计框架，以重建病毒基因序列的基础上不同的宿主物种之间的病毒传播，同时测试和估计跨物种传播的几个潜在的预测因素的贡献。具体来说，我们采用广义线性模型扩展的系统发育扩散进行贝叶斯模型平均候选预测。通过进一步扩展这个模型与分支分区，我们允许不同的主机过渡过程的外部和内部分支，从而区分最近的跨物种传输，其中许多可能会导致死端感染，和主机转移，反映成功向前传输的新的宿主物种。我们的方法证实了宿主之间的遗传距离是北美蝙蝠狂犬病病毒宿主转移和跨物种传播的关键决定因素。此外，我们的研究结果表明，地理范围重叠是一个温和的预测跨物种传播，但不是主机转移。尽管我们的进化框架重点关注蝙蝠狂犬病病毒的多宿主宿主动态，但它也适用于其他病原体和其他离散状态转变过程。
The factors that determine the origin and fate of cross-species transmission events remain unclear for the majority of human pathogens despite being central for the development of predictive models and assessing the efficacy of prevention strategies. Here, we describe a flexible Bayesian statistical framework to reconstruct virus transmission between different host species based on viral gene sequences while simultaneously testing and estimating the contribution of several potential predictors of cross-species transmission. Specifically, we employ a generalized linear model extension of phylogenetic diffusion to perform Bayesian model averaging over candidate predictors. By further extending this model with branch partitioning, we allow for distinct host transition processes on external and internal branches, thus discriminating between recent cross-species transmissions, many of which are likely to result in dead-end infections, and host shifts that reflect successful onwards transmission in the new host species. Our approach corroborates genetic distance between hosts as a key determinant of both host shifts and cross-species transmissions of rabies virus in North American bats. Furthermore, our results indicate that geographical range overlap is a modest predictor for cross-species transmission but not for host shifts. Although our evolutionary framework focused on the multi-host reservoir dynamics of bat rabies virus, it is applicable to other pathogens and to other discrete state transition processes.
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DOI：
10.1016/j.cub.2011.05.058
发表时间：
2011-08-09
期刊：
Current biology : CB
影响因子：
--
作者：
Edwards CJ;Suchard MA;Lemey P;Welch JJ;Barnes I;Fulton TL;Barnett R;O'Connell TC;Coxon P;Monaghan N;Valdiosera CE;Lorenzen ED;Willerslev E;Baryshnikov GF;Rambaut A;Thomas MG;Bradley DG;Shapiro B
通讯作者：
Shapiro B
DOI：
10.1073/pnas.0700741104
发表时间：
2007-05-08
影响因子：
11.1
作者：
Biek, Roman;Henderson, J. Caroline;Real, Leslie A.
通讯作者：
Real, Leslie A.
DOI：
10.1073/pnas.0607968104
发表时间：
2007-03-20
影响因子：
11.1
作者：
Gilbert, Gregory S.;Webb, Campbell O.
通讯作者：
Webb, Campbell O.
影响因子：
10.7
作者：
O'Brien, John D.;Minin, Vladimir N.;Suchard, Marc A.
通讯作者：
Suchard, Marc A.
影响因子：
9.8
作者：
Hampson K;Dushoff J;Cleaveland S;Haydon DT;Kaare M;Packer C;Dobson A
通讯作者：
Dobson A