Sequencing and analysis genome of a VIb subgenotype of Newcastle disease virus isolated from Semi-Muscovy duck.

Based on the genome sequence of newcastle disease virus(NDV) published in GenBank,nine pairs of gene-specific primers were designed to amplify cDNA of FJ-SMD-03 strain isolated from Semi-Muscovy duck in Fuzhou,Fujian,then sequecing and analysis were performed.The results showed that FJ-SMD-03 was 15 192 nucleotides in length which consisted of six ORFs in the order of 3′leader-NP-P-M-F-HN-L-5′trailer and it had six nucleotides longer than Lasota strain in non-coding region of NP gene.The genome shared the highest similarity of the nucleotide with 1.3,carrier-pigeon/Guangdong/2008,pigeon/Italy/1166/00,AV324/96 and dove/Italy/2736/00(94.9%-98.5%),and shared the lowest similarity of the nucleotide with vaccine strain Lasota,Mukteswar and B1(80.7%-83.3%),whereas it shared lower similarity of the nucleotide with strain F48E8 and Muscovy duck/China(Fujian)/FP1/02,Subgenotype VIId,velogenic,isolated from Muscovy duck in Fujian during 2002 for 82.5% and 87.1% respectively.The motif of cleavage site region of F gene was 112R-R-Q-K-R-F117,which was the sequence signature of virulent strain.Phylogenetic analysis revealed that FJ-SMD-03 belonged to subgenotype VIb,Class Ⅱ,which was the first report of the subgenotype VIb virulent NDV strain isolated from Semi-Muscovy duck.FJ-SMD-03 was closely associated with 1.3,carrier-pigeon/Guangdong/2008 and pigeon/Italy/1166/00 and formed a secondary branch in the phylogenetic tree with carrier-pigeon/Guangdong/2008,which suggested that FJ-SMD-03,carrier-pigeon/Guangdong/2008 and pigeon/Italy/1166/00 came from the same origin,which might be due to virus carried by pigeons.