Detection and genetic characterization of bovine kobuvirus from calves in Egypt
Detection and genetic characterization of bovine kobuvirus from calves in Egypt
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DOI：
10.1007/s00705-018-3758-1
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发表时间：
2018-06-01
影响因子：
2.7
通讯作者：
Goyal, Sagar M.
中科院分区：
文献类型：
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作者：
Mohamed, Fakry F.;Mansour, Shimaa M. G.;Goyal, Sagar M.
Kobuvirus是一种小型无包膜RNA病毒，可能导致牛和猪腹泻。自2003年发现以来，很少有研究涉及牛科布病毒（BKoV;艾奇病毒B的一种）感染。BKoV已在欧洲、亚洲和南美洲报告，表明其在全球范围内分布。为了调查埃及是否存在BKoV，通过RT-PCR对埃及两个不同省份（开罗和Sharkia）的36份来自埃及犊牛的粪便标本进行了筛查，发现24份（66.7%）BKoV呈阳性。对其中一份阳性样本（BKoV/Egy-1/KY 407744）的RNA进行下一代测序，以确定完整的BKoV基因组序列。当与唯一记录的BKoV基因组序列（BKoV/U-1/AB 084788）比较时，所研究的菌株显示通过其整个多蛋白（2463 aa）的94个氨基酸（aa）替换，在2B基因中的一个核苷酸（nt）插入和一个nt缺失以及在UTR中的4-nt缺失（各2个）。另外，通过RT-PCR和桑格测序，从其他样品中获得了5个VP 1和7个3D序列。观察到VP 1和3D的系统发育地形图存在差异，其中埃及VP 1序列被归类为拟议谱系1（基因型A）内的一个独特簇，其中还包含来自英国、巴西和日本的菌株。然而，来自开罗的3D序列与中国菌株的3D序列相关，而不像Sharkia菌株更接近韩国菌株。据我们所知，这是在埃及或非洲首次检测到BKoV并对其进行基因组表征。
Kobuviruses are small non-enveloped RNA viruses that probably cause diarrhea in cattle and swine. Since its discovery in 2003, few studies have addressed bovine kobuvirus (BKoV; a species of Aichivirus B) infections. BKoV has been reported in Europe, Asia, and South America, suggesting a worldwide distribution. To investigate the presence of BKoV in Egypt, 36 fecal specimens from diarrheic calves in two different Egyptian provinces (Cairo and Sharkia) were screened by RT-PCR and 24 (66.7%) were found positive for BKoV. RNA from one of the positive samples (BKoV/Egy-1/KY407744) was subjected to next-generation sequencing to determine the complete BKoV genome sequence. When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Additionally, five VP1 and seven 3D sequences were obtained from other samples by using RT-PCR and Sanger sequencing. A discrepancy in the phylogenetic topography of VP1 and 3D was observed, where the Egyptian VP1 sequences were classified as a distinct cluster within the proposed lineage 1 (genotype A), which also contained strains from the UK, Brazil, and Japan. While, the 3D sequences from Cairo were related to those of Chinese strains unlike Sharkia ones that were more closer to Korean strains. To the best of our knowledge, this is the first detection and genomic characterization of BKoV in Egypt or indeed Africa.