Comprehensive Evolutionary Analysis of Complete Epstein-Barr Virus Genomes from Argentina and Other Geographies.
Comprehensive Evolutionary Analysis of Complete Epstein-Barr Virus Genomes from Argentina and Other Geographies.
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DOI：
10.3390/v13061172
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发表时间：
2021-06-18
期刊：
影响因子：
--
通讯作者：
Preciado MV
中科院分区：
文献类型：
--
作者：
Blazquez AC;Berenstein AJ;Torres C;Izquierdo A;Lezama C;Moscatelli G;De Matteo EN;Lorenzetti MA;Preciado MV
在过去的几年里，人们在不同地理区域的分离株中对EB病毒的序列变异性进行了广泛的研究，并描述了随后在遗传和基因组水平上的变异。然而，来自南美的分离株在这些研究中没有得到充分的代表。在这里，我们通过定制的生物信息学管道，对来自全球其他地区的199株EBV分离株进行了15个完整的EBV基因组测序，并与公开可用的原始NGS数据一起进行了分析。评估了基因组的系统发育关系，数据集的地理结构和变异性，以及整个基因组和每个基因的进化率。目前的工作有助于克服南美洲EBV全基因组稀缺的问题，是最全面的与地理相关的变异性研究，涉及确定每个EBV基因对整个基因组地理分离的实际贡献。此外，据我们所知，我们首次基于宿主-病毒共散度无关的假设建立了整个EBV基因组的进化速率，并在逐个基因的基础上评估了它们的进化速率，这与编码的蛋白质功能有关。用共散度无关的方法考虑dsDNA病毒的进化可能为未来EBV进化的研究奠定基础。对这个新的数据集进行的详尽的生物信息学分析使我们能够得出一组关于EBV基因组进化的新结论。
The sequence variability of the Epstein–Barr virus has been extensively studied throughout previous years in isolates from various geographic regions and consequent variations at both genetic and genomic levels have been described. However, isolates from South America were underrepresented in these studies. Here, we sequenced 15 complete EBV genomes that we analyzed together with publicly available raw NGS data for 199 EBV isolates from other parts of the globe by means of a custom-built bioinformatic pipeline. The phylogenetic relations of the genomes, the geographic structure and variability of the data set, and the evolution rates for the whole genome and each gene were assessed. The present work contributes to overcoming the scarcity of complete EBV genomes from South America and is the most comprehensive geography-related variability study, which involved determining the actual contribution of each EBV gene to the geographic segregation of the entire genome. Moreover, to the best of our knowledge, we established for the first time the evolution rate for the entire EBV genome based on a host–virus codivergence-independent assumption and assessed their evolution rates on a gene-by-gene basis, which were related to the encoded protein function. Considering the evolution of dsDNA viruses with a codivergence-independent approach may lay the basis for future research on EBV evolution. The exhaustive bioinformatic analysis performed on this new dataset allowed us to draw a novel set of conclusions regarding the genome evolution of EBV.
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影响因子：
6.4
作者：
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通讯作者：
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影响因子：
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作者：
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作者：
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影响因子：
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作者：
Katoh K;Standley DM
通讯作者：
Standley DM
DOI：
10.1098/rstb.2018.0299
发表时间：
2019-05-27
影响因子：
6.3
作者：
Bridges, Ray;Correia, Samantha;Farrell, Paul J.
通讯作者：
Farrell, Paul J.