Identification of a Genotype IX Newcastle Disease Virus in a Guangxi White Duck.

We report the complete genomic sequence of a novel Newcastle disease virus (NDV) strain, duck/China/Guangxi19/2011, isolated from a white duck in Guangxi Province, southern China. Phylogenetic analysis based on a fusion gene comparison with different NDV strains revealed that duck/China/Guangxi19/2011 is phylogenetically close to genotype IX NDV, and the deduced amino acid sequence of the fusion protein cleavage site was 112R-R-Q-R-R-F117. The whole nucleotide sequence had the highest homology (99.7%) to the sequence of strain F48E8 (GenBank accession number FJ436302). This study will help us understand the epidemiology and molecular characteristics of genotype IX Newcastle disease virus in ducks.

GENOME ANNOUNCEMENT

Newcastle disease virus (NDV) is a single-stranded, negative-strand RNA virus. The full genome of NDV has three sequence types, with lengths of 15,198 nucleotides, 15,192 nucleotides, and 15,186 nucleotides. NDVs of 15,198 nucleotides belong to class I (containing 9 genotypes), and NDVs of 15,192 nucleotides and 15,186 nucleotides belong to class II (containing 11 genotypes) (1–3). The NDV genome sequence contains six open reading frames, which encode 6 kinds of proteins (3′-NP-P-M-F-HN-L-5′), nucleocapsid proteins, phosphoproteins, matrix proteins, fusion proteins, hemagglutinin-neuraminidase proteins, and large polymerases (4–6).

In December 2011, NDV was isolated from a white duck in Guangxi Province, southern China. The isolate was named duck/China/Guangxi19/2011. Nucleotide sequences of duck/China/Guangxi19/2011 were amplified by PCR. The amplified products were purified and cloned into the pMD18-T vector (TaKaRa) and then sequenced (TaKaRa, Dalian, China). Sequences were assembled and manually edited to generate the final genome sequence.

Sequence analysis showed that the full genome sequence of duck/China/Guangxi19/2011 is 15,192 nucleotides and has the highest homology (99.7%) to the sequence of strain F48E8 (GenBank accession number FJ436302, class II, genotype IX). The amino acid sequence identities of the NP, P, M, F, HN, and L proteins between duck/China/Guangxi19/2011 and F48E8 are 99.6%, 99.0%, 98.6%, 99.3%, 99.1%, and 99.6%, respectively. The amino acid sequence identities of the NP, P, M, F, HN, and L proteins between duck/China/Guangxi/2011 and strain LaSota (GenBank accession number AF077761, class II, genotype II) are 91.5%, 86.5%, 90.2%, 91.9%, 90.6%, and 93.4%, respectively. The amino acid sequence identities of the NP, P, M, F, HN, and L proteins between duck/China/Guangxi/2011 and the Newcastle disease virus isolate SDWF02 (GenBank accession number HM188399, class II, genotype VII) are 94.5%, 80.8%, 89.2%, 90.3%, 88.3%, and 93.6%, respectively.

The sequence at the fusion protein cleavage site is a major determinant of NDV pathogenicity (7–9). The F gene of duck/China/Guangxi19/2011 has the highest sequence homology (99.8%) to strain F48E8, and its virulence fusion protein cleavage site sequence (112R–R-Q-R-R-F117) (10) is in accord with the detected biological characteristics (mean death time, 51.4 h; intracerebral pathogenicity index, 1.80; intravenous pathogenicity index, 2.82).

The first to 21st amino acid sites of the F protein are the signal peptide areas of the N terminus and comprise one of the main variant areas of the F protein (11). There are four amino acid mutations in duck/China/Guangxi19/2011 compared with strain F48E8. The sites of amino acid mutations are the third amino acid, for which proline (hydrophobic) in F48E8 is mutated to serine (hydrophilic) in duck/China/Guangxi19/2011; the fourth amino acid, for which lysine (alkaline) in F48E8 is mutated to arginine (basic) in duck/China/Guangxi19/2011; the 380th amino acid, for which threonine (hydrophilic) is mutated to alanine (hydrophobic) in duck/China/Guangxi19/2011; and the 553rd amino acid, for which methionine (hydrophobic) is mutated to isoleucine (hydrophobic) in duck/China/Guangxi19/2011. Further study is needed to determine whether these variations affect viral fusion.

This report of the phylogenetic analysis of the whole-genome sequence of genotype IX NDV isolated from a white duck will further understanding of the epidemiology and molecular characteristics of NDV in duck.

Nucleotide sequence accession number.

The GenBank accession number for duck/China/Guangxi19/2011 is KC920893.