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    贾荣荣, 汪祥斌, 贾坤. 广东省牛流行热病毒分离株JM 2020的全基因组测序及进化分析[J]. 华南农业大学学报, 2023, 44(3): 382-390. doi: 10.7671/j.issn.1001-411X.202204028
    引用本文: 贾荣荣, 汪祥斌, 贾坤. 广东省牛流行热病毒分离株JM 2020的全基因组测序及进化分析[J]. 华南农业大学学报, 2023, 44(3): 382-390. doi: 10.7671/j.issn.1001-411X.202204028
    shu
    JIA Rongrong, WANG Xiangbin, JIA Kun. Whole genome sequencing and evolutionary analysis of bovine ephemeral fever virus isolate JM 2020 in Guangdong Province[J]. Journal of South China Agricultural University, 2023, 44(3): 382-390. doi: 10.7671/j.issn.1001-411X.202204028
    Citation: JIA Rongrong, WANG Xiangbin, JIA Kun. Whole genome sequencing and evolutionary analysis of bovine ephemeral fever virus isolate JM 2020 in Guangdong Province[J]. Journal of South China Agricultural University, 2023, 44(3): 382-390. doi: 10.7671/j.issn.1001-411X.202204028
    shu

    广东省牛流行热病毒分离株JM 2020的全基因组测序及进化分析

    Whole genome sequencing and evolutionary analysis of bovine ephemeral fever virus isolate JM 2020 in Guangdong Province

      摘要
    • 摘要:
      目的  分析广东省牛流行热病毒(Bovine ephemeral fever virus，BEFV)分离株JM 2020与其他地区毒株的进化关系，阐明遗传进化与全基因组的特征，为中国乃至世界对牛流行热疾病的流行情况以及预防该疾病提供有用信息。
      方法  根据从GenBank下载的BEFV毒株的全基因组序列信息，设计引物PCR扩增糖蛋白(Glycoprotein，G)基因；另设计10对引物用于扩增全基因组，送测序得到10个片段的基因序列，运用DNAStar软件中的EditSeq手动编辑和拼接获得全基因组序列。运用MEGA 6.0分别构建G基因和全基因组进化树进行进化分析。
      结果  JM 2020毒株的G基因和全基因组与泰国毒株的核苷酸序列相似性均最高，分别为94.9%~99.3%和99.0%，进化分析表明JM 2020与2013—2017年泰国毒株处于同一小分支，而与JB76H、JT02L等国内毒株有一定进化距离。全基因组测序结果表明，JM 2020全基因组长度为14 902个核苷酸(nt)，包括50 nt的前导序列，1 296 nt的核蛋白(Nucleoprotein，N)基因，837 nt的磷蛋白(Phosphoprotein，P)基因，672 nt的基质蛋白(Matrixprotein，M)基因，1 872 nt的G基因，1 812 nt的非结构糖蛋白II (Non-structural glycoprotein II，GNS)基因，618 nt的α1、α2基因，444 nt的β基因，345 nt的γ基因，444 nt的RNA依赖性聚合酶(Large multi-functional enzyme，L)基因和73 nt的尾随序列，且分别被21、47、68、67、23、64、59、79和35 nt的区域隔开。JM 2020、qy2017及泰国毒株均出现P′基因(P基因多顺反子产物)截断的特征。
      结论  JM 2020毒株与2017年分离毒株qy2017序列相似性高且均与泰国毒株进化关系较近，与JB76H等我国其他地区毒株有一定进化距离。该研究丰富了中国BEFV流行株的基因组信息，为牛流行热疫病综合防控及开发新疫苗奠定了基础。

       

      Abstract:
      Objective  The purpose of this study was to analyze the evolutionary relationship between bovine ephemeral fever virus (BEFV) isolate JM 2020 in Guangdong Province and other strains from other regions, and clarify the characteristics of genetic evolution and whole genome, so as to provide information for the epidemic situation and prevention of bovine ephemeral fever disease in China and the world.
      Method  According to the whole genome sequence information of BEFV strain downloaded from GenBank, primers were designed to amplify glycoprotein (G) gene by PCR. The 10 pairs of primers were designed to amplify the whole genome, and the gene sequences of 10 fragments were obtained by sequencing. The whole genome sequences were manually edited and spliced by EditSeq in DNAStar software. Using MEGA 6.0 to construct G gene and whole genome evolutionary tree respectively for evolutionary analysis.
      Result  The G gene and whole genome of the JM 2020 strain had the highest nucleotide sequence similarity with the Thai strain, which were 94.9%−99.3% and 99.0% respectively. The evolutionary analysis showed that JM 2020 was in the same small branch with the 2013 to 2017 Thai strains, while there was a certain evolutionary distance from domestic virus strains such as JB76H and JT02L. Whole genome sequencing results showed that whole genome of JM 2020 was 14 902 nucleotides (nt) in length, including 50 nt leader sequence, 1 296 nt nucleoprotein (N) gene, and 837 nt phosphoprotein (P) gene, 672 nt matrixprotein (M) gene, 1 872 nt G gene, 1 812 nt non-structural glycoprotein II (GNS) gene, 618 nt α1 and α2 gene, 444 nt β gene, 345 nt γ gene, 6 444 nt large multi-functional enzyme (L) gene and tail sequence of 73 nt, which was separated by 21, 47, 68, 67, 23, 64, 59, 79 and 35 nt intergenic regions. The P′ gene (polycistronic product of P gene) of JM 2020 was truncated like qy2017 and the Thai strain.
      Conclusion  The JM 2020 strain is highly similar with the qy2017 strain isolated in 2017 and they are closely related to the evolution of the Thai strain. They have some evolutionary distance with JB76H strain etc. from other regions of China. This study enriches the genome information of BEFV epidemic strains in China and lays a foundation for the prevention and control of bovine ephemeral fever and the research of new vaccines.

       

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