Phylogenetic characterization of Newcastle disease virus isolated in the mainland of China during 2001–2009

Twenty Newcastle disease virus (NDV) isolates from infected chicken flocks during 2001 to 2009 in China were biologically and genetically characterized. All the 20 NDVs were categorized into velogenic (n = 17) and lentogenic (n = 3) viruses, respectively, according to the mean death time (MDT) of chicken embryos. Velogenic viruses carry the motif 112R-R-Q-K-R/F117 (n = 14) or 112G-R-Q-G-R/L117 (n = 3) at the F0 cleavage site, while all the lentogenic virus had a sequence motif of 112G-R-Q-G-R/L117 (n = 3) at the same site. Phylogenetic analysis revealed that at least three distinct genotypes (genotypes I, II and VII) existed in chicken flocks in China and VIId of genotype VII were mainly responsible for the present ND panzootic. Two natural recombinants (XD/Shandong/08 and QG/Hebei/07) were supposed and identified by the SimPlot program, and their two parental-like strains might be from the NDV vaccine lineage and VIId velogenic lineage respectively. The results indicate that recombination play a role in NDV evolution and the live vaccines have capacity to boost NDV evolution by homologous recombination with circulating virus.