Phylogeography and Re-Evaluation of Evolutionary Rate of Powassan Virus Using Complete Genome Data.
Phylogeography and Re-Evaluation of Evolutionary Rate of Powassan Virus Using Complete Genome Data.
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DOI：
10.3390/biology10121282
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发表时间：
2021-12-06
期刊：
影响因子：
4.2
通讯作者：
Bukin YS
中科院分区：
文献类型：
--
作者：
Bondaryuk AN;Peretolchina TE;Romanova EV;Yudinceva AV;Andaev EI;Bukin YS
人类致病性病毒的进化是现代生物学的紧迫问题之一，直接关系到公众健康。病毒进化的许多重要方面（例如，进化速度、种群规模和迁徙历史）对研究人员的肉眼来说是“隐藏”的。现代生物信息学方法使评估和可视化病毒的这种进化特性成为可能。在本文中，我们重建的迁移历史，并估计最危险的神经侵入性和嗜神经蜱传黄病毒-Powassan病毒（POWV）-分布在北美和俄罗斯远东地区的进化速度。使用获得的日期，我们假设，最近的共同祖先的POWV到两个独立的遗传谱系的分歧最有可能发生，因为冰川融化，开始在11.72 KYA在全新世由于气候变暖引起的洪水的地峡之间的欧亚大陆和北美。在这篇论文中，我们揭示了基于NCBI和ViPR数据库（2021年6月访问）中提供的25个完整基因组重建的Powassan病毒（POWV）的遗传结构和迁移历史。使用这个数据集使我们能够对这种病毒的进化速度进行更精确的评估。此外，我们提出了一个简单的贝叶斯技术的评价和可视化的“时间信号动态”沿着系统发育树。我们发现，POWV的进化速率值为每年每个位点3.3 × 10−5个核苷酸替换（95%HPD，2.0 × 10−5-4.7 × 10−5），这低于以前的研究报道的值。POWV最近的共同祖先（MRCA）分化成两个独立的遗传谱系最有可能发生在2600年至6030年前。我们假设病毒谱系的分化是由于大约12，000年前冰川融化，导致欧亚大陆和北美（现代阿拉斯加领土）之间的白令陆桥消失，病毒区域在空间上分为两部分。基因组数据提供了病毒在两个大陆之间迁移的证据。从俄罗斯远东到北美的平均迁移率为每1750年一次。向相反方向的迁移大约每475年发生一次。
The evolution of human pathogenic viruses is one of the pressing problems of modern biology and directly relevant to public health. Many important aspects of virus evolution (e.g., evolutionary rate, population size, and migration history) are ‘hidden’ from the naked eye of a researcher. Modern bioinformatics methods make it possible to evaluate and visualize such evolutionary particularities of viruses. In this paper, we reconstructed the migration history and estimated the evolutionary rate of one of the most dangerous neuroinvasive and neurotropic tick-borne flaviviruses—Powassan virus (POWV)—distributed in North America and the Far East of Russia. Using the dates obtained, we hypothesized that the divergence of the most recent common ancestor of POWV into two independent genetic lineages most likely occurred because of the melting of glaciers that began at 11.72 Kya in the Holocene due to the climate warming-caused flooding of the isthmus between Eurasia and North America. In this paper, we revealed the genetic structure and migration history of the Powassan virus (POWV) reconstructed based on 25 complete genomes available in NCBI and ViPR databases (accessed in June 2021). The usage of this data set allowed us to perform a more precise assessment of the evolutionary rate of this virus. In addition, we proposed a simple Bayesian technique for the evaluation and visualization of ‘temporal signal dynamics’ along the phylogenetic tree. We showed that the evolutionary rate value of POWV is 3.3 × 10−5 nucleotide substitution per site per year (95% HPD, 2.0 × 10−5–4.7 × 10−5), which is lower than values reported in the previous studies. Divergence of the most recent common ancestor (MRCA) of POWV into two independent genetic lineages most likely occurred in the period between 2600 and 6030 years ago. We assume that the divergence of the virus lineages happened due to the melting of glaciers about 12,000 years ago, which led to the disappearance of the Bering Land Bridge between Eurasia and North America (the modern Alaskan territory) and spatial division of the viral areal into two parts. Genomic data provide evidence of the virus migrations between two continents. The mean migration rate detected from the Far East of Russia to North America was one event per 1750 years. The migration to the opposite direction occurred approximately once per 475 years.
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影响因子：
3.2
作者：
Adelshin, Renat V.;Sidorova, Elena A.;Balakhonov, Sergey V.
通讯作者：
Balakhonov, Sergey V.
影响因子：
10.7
作者：
Nguyen LT;Schmidt HA;von Haeseler A;Minh BQ
通讯作者：
Minh BQ
影响因子：
13.2
作者：
Pettersson JH;Bohlin J;Dupont-Rouzeyrol M;Brynildsrud OB;Alfsnes K;Cao-Lormeau VM;Gaunt MW;Falconar AK;de Lamballerie X;Eldholm V;Musso D;Gould EA
通讯作者：
Gould EA
影响因子：
4.4
作者：
Ogden, N. H.;Lindsay, L. R.;Thompson, R. A.
通讯作者：
Thompson, R. A.
DOI：
10.1093/bioinformatics/bty406
发表时间：
2018-11-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Müller NF;Rasmussen D;Stadler T
通讯作者：
Stadler T