Abstract: To understand the genetic variation of Canine distemper virus (CDV) in Shanghai,the full-length genome of CDV SH202003 strain was sequenced by RT-PCR with 11 pairs of over lapping primers.PCR fragments were obtained and sequenced repeatedly to ensure the mostly possible sequences.The sequenced 11 fragments were spliced to obtain the full-length genomes sequences of CDV SH202003 strain.Alignment analysis of the full-length genome and H gene sequences of SH202003 strain and other CDV sequences published in GenBank was analyzed with Lasergene 7.0 and Mega 6.0 software,and the phylogenetic tree was constructed.The results showed that total length of SH202003 strain was 15 690 bp,encoding 6 structural proteins (N,P,M,F,H and L).The gene interval sequences were CUA between H and L,and CAA between L and 5' trailer,respectively.The SH202003 strain had 98.6% nucleotide sequence similarity and 96.6% amino acid similarity with Hebei strain,and had 92.2% to 94.3% nucleotide sequence similarity and 82.7% to 87.0% amino acid similarity with vaccine strains.Phylogenetic tree analysis showed that SH202003 strain was in the same branch with prevalent virulent strains and distant from the vaccine strains.H gene had 98.7% nucleotide sequence similarity and 99.5% amino acid similarity with Hebei strain,and was distant from the vaccine strains such as Snyder Hill,CDV3,Convac and Onderstepoort.SH202003 strain belonged to Asia-1 subtype (Asia-1 virulent strain).SH202003 strain contained 9 potential N-glycosylation sites,which was consistent with Hebei strain.The results indicated that SH202003 strain was virulent and belonged to Asia-1 type.H gene sequences were relatively conservative and had 9 potential N-glycosylation sites.However,SH202003 strain had many mutations in the full-length genome and low homology with the vaccine strains,which might be the main reason for canine distemper in immunized dogs.

Key words: Canine distemper virus (CDV); genomic; sequencing analysis