Beyond the whole genome consensus: unravelling of PRRSV phylogenomics using next generation sequencing technologies.
Beyond the whole genome consensus: unravelling of PRRSV phylogenomics using next generation sequencing technologies.
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DOI：
10.1016/j.virusres.2014.10.004
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发表时间：
2014-12-19
期刊：
影响因子：
5
通讯作者：
Ait-Ali T
中科院分区：
文献类型：
--
作者：
Lu ZH;Archibald AL;Ait-Ali T
NGS允许在没有任何先验知识的情况下对PRRSV进行全基因组测序。可以检测到共同进化准种内的低频变体。使用NGS可以跟踪宏观和微观进化事件。高度异质性的猪繁殖与呼吸综合征病毒（PRRSV）是引起经济上重要的猪疾病的病原体，其特征性症状是繁殖母猪的繁殖损失和仔猪的呼吸道疾病。该病毒可大致分为欧洲和北美样基因型1和2分别。除了这种株内变异性，共存的病毒准种对疾病发展的影响最近得到了很多关注;这在很大程度上是由于下一代测序（NGS）技术的出现。NGS的大规模测序能力产生的基因组数据使PRRSV的研究以前所未有的速度和细节成为可能。与需要保守区域知识的常规测序方法不同，NGS允许从头组装完整的病毒基因组。从不同基因型毒株获得的进化变异为病毒的重要功能区域提供了有价值的见解。随着先进的生物信息学工具的发展，超深NGS技术使低频共同进化准种的检测成为可能。这篇简短的综述概述了使用NGS在宏观和微观进化水平上探索PRRSV遗传多样性的方法，包括建议的工作流程。
NGS allows the whole genome sequencing of PRRSV without any prior knowledge. Low frequency variants within the co-evolving quasispecies can be detected. Both macro- and micro-evolutionary events can be followed using NGS. The highly heterogeneous porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent responsible for an economically important pig disease with the characteristic symptoms of reproductive losses in breeding sows and respiratory illnesses in young piglets. The virus can be broadly divided into the European and North American-like genotype 1 and 2 respectively. In addition to this intra-strains variability, the impact of coexisting viral quasispecies on disease development has recently gained much attention; owing very much to the advent of the next-generation sequencing (NGS) technologies. Genomic data produced from the massive sequencing capacities of NGS have enabled the study of PRRSV at an unprecedented rate and details. Unlike conventional sequencing methods which require knowledge of conserved regions, NGS allows de novo assembly of the full viral genomes. Evolutionary variations gained from different genotypic strains provide valuable insights into functionally important regions of the virus. Together with the advancement of sophisticated bioinformatics tools, ultra-deep NGS technologies make the detection of low frequency co-evolving quasispecies possible. This short review gives an overview, including a proposed workflow, on the use of NGS to explore the genetic diversity of PRRSV at both macro- and micro-evolutionary levels.
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