Characterization of complete genome sequence of genotype VI and VII velogenic Newcastle disease virus from Japan

Abstract

The complete genome sequences of three strains of Newcastle disease virus (NDV) isolated from vaccinated commercial layer flocks in Japan in the span of three decades were characterized. All strains had genome lengths of 15,192 nucleotides consisting of six genes in the order of 3'-NP-P/V/W-M-F-HN-L-5'. The general genomic characteristics of the Japanese field strains were consistent with previously characterized class II NDV, except for those belonging to early genotypes (genotype I-IV), which lack the six nucleotide insertion at nucleotide positions 1,648-1,653 of the nucleoprotein (NP) gene. Phylogenetic analysis showed that the Japanese strains could be classified into genotypes VIc and VIIe using the complete genome sequence and the complete coding sequence of the fusion (F) gene according to the unified NDV classification system. Characterization of functional domains and neutralizing epitopes of the F and hemagglutinin-neuraminidase (HN) proteins of Japanese field strains revealed a total of 31 amino acid substitutions, as compared to vaccine strains Ishii and B1, which were widely used in Japan. Although virus neutralization (VN) test showed that poor flock immunity due to vaccination failure or partial and non-uniform immunization maybe the major factors involved in the mechanism of breakthrough infection of the Japanese field strains, approximately two to threefold decrease in the VN titers of the field NDV strains possessing a point mutation (E347K or E347G) at the linear epitope of the HN protein was observed, as compared to vaccine strain B1 and field strain 2440/69, which lack the point mutation. This study may be a useful reference in characterizing future ND outbreaks in vaccinated chickens and as a genetic map for future investigations regarding vaccine designs, reverse genetics systems, and development of molecular diagnostic tools to prevent future ND outbreaks in vaccinated poultry flocks.

Genomic Characterizations of Six Pigeon Paramyxovirus Type 1 Viruses Isolated from Live Bird Markets in China during 2011 to 2013

“…The major transmembrane region of six isolates was not conserved, with differences at position 502, 506, 509, 516 and 517 ( Table 3 ). Compared with consensus amino acid sequences derived from NDV strains of different genotypes [ 33 ], the six isolates all had 2 substitutions (V121I, A132S) in fusion peptide ( Table 3 ). Analysis of the three heptad repeat region (HR) showed 2 substitutions in HRa (143–185 aa) and 2 in HRc (471–500 aa) ( Table 3 ).…”

“…Comparison of functional domains of F and HN proteins between consensus sequences derived from NDV strains of different genotypes and six PPMV-1 isolates identified several amino acid substitutions. As reported, in the F protein, amino acid substitutions at fusion peptide and HR region, or replacement of transmembrane domain of NDV could affect the fusion activity of F protein [ 33 ]. In HN protein, seven substitutions were identified in neutralizing epitopes, some (N263K, E347G, I514V) of which also appeared in other NDV isolates [ 33 ].…”

Pathobiology of Avian avulavirus 1: special focus on waterfowl

“…Many virulent isolates from the domestic poultry cannot cause disease in waterfowl [21,53]. Most prevalent virulent genotype VII causing the endemics in China, Japan, Korea [18,60,65] are co circulating into the ducks and chicken [66]. This coevolution was further confirmed when the results of Huang et al [67] declared that some of the circulating APMV-1 had the multiple homologous genomes from chicken, ducks and geese.…”

Molecular characterization of a Class I Newcastle disease virus strain isolated from a pigeon in China

“…Epitopes 1 and 1-4 are linear epitopes, whereas 2, 3, 4, 1-2 and 2-3 are conformational ones. Those epitopes were separated into several completely different domains on the linear structure but aggregated together in the three-dimensional structure (Iorio et al, 1991(Iorio et al, , 1992Connaris et al, 2002;Umali et al, 2014). Figure 2.…”