中国农业科学Issue(7)：1445-1452,8.DOI:10.3864/j.issn.0578-1752.2015.07.19
大熊猫源犬瘟热病毒基因组遗传特征分析
Genomic Characterization of the Newly Emerged Canine Distemper Virus in Giant Panda
金艺鹏 1刘巧荣 2孙明 2乔雁超 1乔明明 2刘伯华 2林德贵 1陈西钊2
作者信息
- 1. 中国农业大学动物医学院，北京 100193
- 2. 北京世纪元亨动物防疫技术有限公司，北京 100094
- 折叠
摘要
Abstract
[Objective] The objective of this study is to analyze the genetic variation of the newly emerged giant panda canine distemper virus by sequencing its full-length genome, thereby to track the source of infection and provide a theoretical basis for the prevention and control of giant panda CDV infection. [Method] According to the CDV genomic sequences published in GenBank, 17 pairs of oligonucleotide primers were designed, the overlapping fragments spanning whole genome of CDV were amplified by RT-PCR from lung exudate of the infected giant panda and then cloned into vector pMD19-T and sequenced, respectively, the determined sequences were spliced and assembled by using biological software DNAman. Based on above efforts, the first complete genome sequence of P-CDV isolated from giant panda was accomplished, and was further characterized by alignment with 20 published CDV whole-genome sequences from GenBank. Moreover, to track the source of infection, different phylogenetic trees were constructed according to complete genome as well as genes H, F, P and M, respectively.[Result]The genome of the giant panda CDV is 15 690 nucleotides in length (GenBank accession No. KP677502), and mainly encodes six genes in the order of 3′-N-P-M-F-H-L-5′. No nucleotides insert and deletion were observed in encoding and intergenic regions compared to other CDV complete genome sequences. Phylogenetic analysis of the giant panda CDV genome showed 91.5%-98.7% nucleotide identity with 20 representative CDV isolates. Along with virulent strains MKY-KM08 (accession no. HM852904), PS, HLJ1-06 (accession no. JX681125), Hebei (accession no. KC427278) and AC96I-H358 (accession no. AB753776), P-CDV belongs to one large homogeneous clade, and is phylogenetically most closely related to the isolate PS with 98.7% identity at nucleotide. It shares 95.7% nucleotide identity with wild strain A75-17, and exhibits the lowest nucleotide similarity with standard vaccine strain CDV3 (91.5%). Sequence analysis based on H gene indicates that the giant panda CDV is a virulent strain, it belongs to genotype Asia-I. There are a total of nine amino acid (aa) substitutions, among them three amino acid substitutions were firstly found and are unique to the giant panda CDV. Of these 3 aa substitutions, 2 substitutions (N/K208S, S215A) occur in F open reading frame (ORF), one substitution (Q58K) occurs in P ORF. [Conclusion]The complete genomic sequence of this newly emerged giant panda CDV was successfully characterized, the key site mutations in F and P genes were recognized. The data will provide valuable theoretical reference for the prevention and control of giant panda CDV infection.关键词
犬瘟热病毒/大熊猫/全基因组测序/序列分析Key words
canine distemper virus/giant panda/genomic characterization/gene sequence analysis引用本文复制引用
金艺鹏,刘巧荣,孙明,乔雁超,乔明明,刘伯华,林德贵,陈西钊..大熊猫源犬瘟热病毒基因组遗传特征分析[J].中国农业科学,2015,(7):1445-1452,8.
