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.

Key words: canine distemper virus, giant panda, genomic characterization, gene sequence analysis