Complete genomic analysis and molecular characterization of Japanese porcine sapeloviruses
Complete genomic analysis and molecular characterization of Japanese porcine sapeloviruses
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日本猪萨佩洛病毒的完整基因组分析和分子表征
DOI：
10.1007/s11262-019-01640-8
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发表时间：
2019
期刊：
影响因子：
1.6
通讯作者：
Nagai M.
中科院分区：
文献类型：
--
作者：
Sunaga F;Masuda T;Ito M;Akagami M;Naoi Y;Sano K;Katayama Y;Omatsu T;Oba M;Sakaguchi S;Furuya T;Yamasato H;Ouchi Y;Shirai J;Mizutani T;Nagai M.
猪囊病毒(PSV)是一种猪肠道病毒，可引起各种疾病。然而，很少有报道描述PSV基因组的分子特征。在这项研究中，利用生物信息学对在日本猪身上检测到的23个PSV的几乎整个基因组进行了分析。对顺式活性RNA元件的分析表明，预测的5‘非翻译区内部核糖体进入位点和2C编码区的Acis复制元件的二级结构在PSV之间是保守的。相反，不同PSV在3‘UTR上的结构是不同的；然而，结构域之间的三级结构在所有PSV中都是保守的。对VP1区核苷酸序列的系统发育分析表明，PSV具有序列多样性，但由于簇的引导支持度较低，它们不能划分为不同的基因型。C-末端VP1区的插入和/或缺失模式与VP1树的拓扑结构无关。3CD系统发育树与VP1系统树在拓扑结构上不同，同一国家的PSV相互独立聚类。重组分析表明，重组事件发生在P2区上游，一些重组断裂点涉及C-末端VP1区的插入和/或缺失。这些发现表明，PSV表现出遗传多样性和频繁的重组事件，特别是在P2区上游区域；然而，PSV目前不能被归类为基因型，并且在所有PSV中都观察到了保守的顺式活性RNA元件的遗传结构特征。
ThePorcine Sapelovirus(PSV) is an enteric virus of pigs that can cause various disorders. However, there are few reports that describe the molecular characteristics of the PSV genome. In this study, almost the entire genomes of 23 PSVs detected in Japanese pigs were analyzed using bioinformatics. Analysis of thecis-active RNA elements showed that the predicted secondary structures of the internal ribosome entry site in the 5′ untranslated region (UTR) and acis-replication element in the 2C coding region were conserved among PSVs. In contrast, those at the 3′ UTR were different for different PSVs; however, tertiary structures between domains were conserved across all PSVs. Phylogenetic analysis of nucleotide sequences of the complete VP1 region showed that PSVs exhibited sequence diversity; however, they could not be grouped into genotypes due to the low bootstrap support of clusters. The insertion and/or deletion patterns in the C-terminal VP1 region were not related to the topology of the VP1 tree. The 3CD phylogenetic tree was topologically different from the VP1 tree, and PSVs from the same country were clustered independently. Recombination analysis revealed that recombination events were found upstream of the P2 region and some recombination breakpoints involved insertions and/or deletions in the C-terminal VP1 region. These findings demonstrate that PSVs show genetic diversity and frequent recombination events, particularly in the region upstream of the P2 region; however, PSVs could currently not be classified into genotypes and conserved genetic structural features of thecis-active RNA elements are observed across all PSVs.