Complete genome analysis of porcine kobuviruses from the feces of pigs in Japan
Complete genome analysis of porcine kobuviruses from the feces of pigs in Japan
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DOI：
10.1007/s11262-017-1464-9
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发表时间：
2017-08-01
期刊：
影响因子：
1.6
通讯作者：
Nagai, Makoto
中科院分区：
文献类型：
--
作者：
Akagami, Masataka;Ito, Mika;Nagai, Makoto
猪柯布病毒(PoKov)广泛存在于世界各地的猪群中，被认为是猪的肠道病毒。虽然在日本的猪身上检测到了PoKov，但还没有关于日本PoKov的完整基因组数据。本研究利用元基因组学方法对从10个腹泻猪粪便和14个非腹泻猪粪便中获得的24个PoKoV基因组的近全序列进行了分析。日本的PoKov与其他国家的PoKov的核苷酸序列同源性为85.2-100%，与其他国家的PoKov的同源性最近，为85.1-98.3%。在24个日本PoKov中，有20个在2B编码区有90个核苷酸缺失。系统进化树分析表明，PoKov没有按其地理区域进行分类，L、P1、P2和P3基因区的系统发育树显示出不同的拓扑结构。对来自同一农场的菌株进行的相似性图谱分析显示，来自相同农场来源的菌株之间存在部分不同的相似性模式，这表明重组事件已经发生。这些结果表明，PoKoV毒株在世界各地的养猪场中普遍存在，且不受地理限制，多个毒株的共存导致了PoKoV的重组事件，并有助于PoKoV的遗传多样性和进化。
Porcine kobuviruses (PoKoVs) are ubiquitously distributed in pig populations worldwide and are thought to be enteric viruses in swine. Although PoKoVs have been detected in pigs in Japan, no complete genome data for Japanese PoKoVs are available. In the present study, 24 nearly complete or complete sequences of the PoKoV genome obtained from 10 diarrheic feces and 14 non-diarrheic feces of Japanese pigs were analyzed using a metagenomics approach. Japanese PoKoVs shared 85.2-100% identity with the complete coding nucleotide (nt) sequences and the closest relationship of 85.1-98.3% with PoKoVs from other countries. Twenty of 24 Japanese PoKoVs carried a deletion of 90 nt in the 2B coding region. Phylogenetic tree analyses revealed that PoKoVs were not grouped according to their geographical region of origin and the phylogenetic trees of the L, P1, P2, and P3 genetic regions showed topologies different from each other. Similarity plot analysis using strains from a single farm revealed partially different similarity patterns among strains from identical farm origins, suggesting that recombination events had occurred. These results indicate that various PoKoV strains are prevalent and not restricted geographically on pig farms worldwide and the coexistence of multiple strains leads to recombination events of PoKoVs and contributes to the genetic diversity and evolution of PoKoVs.