Evolutionary dynamics of West Nile virus in the United States, 1999-2011: phylogeny, selection pressure and evolutionary time-scale analysis.
Evolutionary dynamics of West Nile virus in the United States, 1999-2011: phylogeny, selection pressure and evolutionary time-scale analysis.
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DOI：
10.1371/journal.pntd.0002245
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发表时间：
2013
影响因子：
3.8
通讯作者：
Rios M
中科院分区：
文献类型：
--
作者：
Añez G;Grinev A;Chancey C;Ball C;Akolkar N;Land KJ;Winkelman V;Stramer SL;Kramer LD;Rios M
西尼罗河病毒(WNV)是一种存在于鸟类-蚊子地方性流行病循环中的虫媒病毒，可感染包括人类在内的其他脊椎动物。西尼罗河病毒于1999年在美国首次报告，迄今已描述了三种属于西尼罗河病毒谱系I的基因类型(NY99、WN02、Sw/WN03)。我们在这里报告了从2006-2011年美国疫情期间从两只鸟、一只蚊子和29个精选人类样本中获得的西尼罗河病毒序列，并检查了1999-2011年报告的西尼罗河病毒分离株的公开阅读框架中的进化动力学。系统发育分析采用最大似然法和贝叶斯方法，选择压力分析采用HYPHY软件包。系统发育分析确定了在美国流行的主要西尼罗河病毒基因型中的人西尼罗河病毒分离物。在基因Sw/WN03中，我们已经确定了来自2006-2007年收集的来自爱达荷州和北达科他州的献血者和鸟类的菌株的一个簇，在这里称为MW/WN06。使用不同的基于密码子的模型和分支位置选择模型，我们在西尼罗河病毒基因中检测到了一些承受正压力的密码子。从人源分离的西尼罗河病毒分离株的平均核苷酸替换率为5.06×10−4替换/位/年(S/S/y)。贝叶斯天际线图显示，在西尼罗河病毒引入美国后，经过一段时间的高度遗传变异，西尼罗河病毒种群似乎已经达到了遗传稳定。西尼罗河病毒在美国的建立为了解虫媒病毒如何在幼稚的环境中适应和进化提供了一个独特的机会。我们描述了一个由来自爱达荷州和北达科他州的人和鸟的毒株组成的新的、得到良好支持的西尼罗河病毒群。充分的基因监测对公众健康至关重要，因为新的突变株可能会潜在地影响病毒的致病机理，降低诊断分析的性能，并对疫苗的有效性和特定疗法的开发产生负面影响。西尼罗河病毒(WNV)是一种起源于非洲的蚊媒病毒，在世界各地传播。西尼罗河病毒的生命周期涉及蚊子和鸟类，但人和其他动物可能会被感染，尽管他们不被认为是传播周期中的重要参与者。临床上，大多数西尼罗河病毒感染是不明显的，但病毒可以传播到中枢神经系统，导致一种潜在的致命神经系统疾病，特别是在包括老年人和免疫功能低下的易感人群中。西尼罗河病毒还可以通过器官移植以及输血和血液成分传播。与其他虫媒病毒一样，西尼罗河病毒具有在无脊椎动物载体和脊椎动物宿主所代表的不同微环境中生长的非凡能力。从进化的角度来看，1999年西尼罗河病毒在美国的到来是一个独特的机会，可以探索虫媒病毒在幼稚环境中的适应和传播过程。通过对西尼罗河病毒序列的研究，我们不仅可以了解虫媒病毒的进化机制，还可以更新依赖于在发生突变时检测病毒基因组的诊断测试，并研究可能导致临床病例增加及其严重程度的遗传标记的存在。
West Nile virus (WNV), an arbovirus maintained in a bird-mosquito enzootic cycle, can infect other vertebrates including humans. WNV was first reported in the US in 1999 where, to date, three genotypes belonging to WNV lineage I have been described (NY99, WN02, SW/WN03). We report here the WNV sequences obtained from two birds, one mosquito, and 29 selected human samples acquired during the US epidemics from 2006–2011 and our examination of the evolutionary dynamics in the open-reading frame of WNV isolates reported from 1999–2011. Maximum-likelihood and Bayesian methods were used to perform the phylogenetic analyses and selection pressure analyses were conducted with the HyPhy package. Phylogenetic analysis identified human WNV isolates within the main WNV genotypes that have circulated in the US. Within genotype SW/WN03, we have identified a cluster with strains derived from blood donors and birds from Idaho and North Dakota collected during 2006–2007, termed here MW/WN06. Using different codon-based and branch-site selection models, we detected a number of codons subjected to positive pressure in WNV genes. The mean nucleotide substitution rate for WNV isolates obtained from humans was calculated to be 5.06×10−4 substitutions/site/year (s/s/y). The Bayesian skyline plot shows that after a period of high genetic variability following the introduction of WNV into the US, the WNV population appears to have reached genetic stability. The establishment of WNV in the US represents a unique opportunity to understand how an arbovirus adapts and evolves in a naïve environment. We describe a novel, well-supported cluster of WNV formed by strains collected from humans and birds from Idaho and North Dakota. Adequate genetic surveillance is essential to public health since new mutants could potentially affect viral pathogenesis, decrease performance of diagnostic assays, and negatively impact the efficacy of vaccines and the development of specific therapies. West Nile Virus (WNV) is a mosquito-borne virus of African origin that is widespread around the world. The WNV life-cycle involves mosquitoes and birds, but humans and other animals can be infected, although they are not considered to be important players in the transmission cycle. Clinically, most WNV infections are unapparent, but the virus can disseminate to the central nervous system causing a potentially fatal neurological disease, especially in susceptible populations including elderly and immunocompromised individuals. West Nile virus can also be transmitted by organ transplant and by transfusion of blood and blood components. Like other arboviruses, WNV has the extraordinary capacity of growing in the different microenvironments represented by the invertebrate vector and the vertebrate hosts. From an evolutionary standpoint, the arrival of WNV in the US in 1999 represents a unique opportunity to explore the processes involved in the adaptation and dissemination of an arbovirus in a naïve environment. From the study of WNV sequences, we can not only learn about the evolutionary mechanisms that govern arboviruses, but also update diagnostic tests that rely on the detection of the viral genome upon the occurrence of mutations and study the existence of genetic markers that may be responsible for increases in clinical cases and their severity.
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影响因子：
11.8
作者：
Grinev A;Daniel S;Stramer S;Rossmann S;Caglioti S;Rios M
通讯作者：
Rios M
影响因子：
11.8
作者：
Davis, C Todd;Beasley, David W C;Guzman, Hilda;Raj, Rushker;D'Anton, Mary;Novak, Robert J;Unnasch, Thomas R;Tesh, Robert B;Barrett, Alan D T
通讯作者：
Barrett, Alan D T
影响因子：
5.4
作者：
Holmes, EC
通讯作者：
Holmes, EC
影响因子：
3.7
作者：
Beasley, DWC;Davis, CT;Barrett, ADT
通讯作者：
Barrett, ADT
影响因子：
3.8
作者：
Berthet, FX;Zeller, HG;Deubel, V
通讯作者：
Deubel, V