Abstract
BackgroundTo investigate the relationship between the selective pressure and the sequence variation of the hemagglutinin-neuraminidase (HN) protein, we performed the positive selection analysis by estimating the ratio of non-synonymous to synonymous substitutions with 132 complete HN gene sequences of Newcastle disease viruses (NDVs) isolated in China.ResultsThe PAML software applying a maximum likelihood method was used for the analysis and three sites (residues 266, 347 and 540) in the HN protein were identified as being under positive selection. Codon 347 was located exactly in a recognized antigenic determinant (residues 345-353) and codon 266 in a predicted linear B-cell epitope. Substitutions at codon 540 contributed to the N-linked glycosylation potential of residue 538. To further evaluate the effect of positively selected sites on the vaccine efficacy, we constructed two recombinant fowlpox viruses rFPV-JS6HN and rFPV-LaSHN, expressing the HN proteins from a genotype VII field isolate Go/JS6/05 (with A266, K347 and A540) and vaccine strain La Sota (with V266, E347 and T540), respectively. Two groups of SPF chickens, 18 each, were vaccinated with the two recombinant fowlpox viruses and challenged by Go/JS6/05 at 3 weeks post-immunization. The results showed that rFPV-JS6HN could elicit more effective immunity against the prevalent virus infection than rFPV-LaSHN in terms of reducing virus shedding.ConclusionsThe analysis of positively selected codons and their effect on the vaccine efficacy indicated that the selective pressure on the HN protein can induce antigenic variation, and new vaccine to control the current ND epidemics should be developed.
Highlights
To investigate the relationship between the selective pressure and the sequence variation of the hemagglutinin-neuraminidase (HN) protein, we performed the positive selection analysis by estimating the ratio of non-synonymous to synonymous substitutions with 132 complete HN gene sequences of Newcastle disease viruses (NDVs) isolated in China
Sequence analysis The full coding region of the 132 HN genes analyzed in this study exhibited diverse phylogenetic phenotypes in Chinese poultry flocks, containing six of the nine recognized genotypes (II, III, VI, VII, VIII and IX), with the overwhelming majority (113/132) belonged to genotype VII (Additional file 1, Table S1)
The phylogenetic tree (Figure 1) showed that our 26 sequences belonged to four different genotypes as follows: III (Ch/ JS7/05 and Go/JS9/05), VI (NDV05-028 and NDV05029), VIII (QH-1/79 and QH-4/85) and the remaining 20 fell into genotype VII
Summary
To investigate the relationship between the selective pressure and the sequence variation of the hemagglutinin-neuraminidase (HN) protein, we performed the positive selection analysis by estimating the ratio of non-synonymous to synonymous substitutions with 132 complete HN gene sequences of Newcastle disease viruses (NDVs) isolated in China. The causative agent, Newcastle disease virus (NDV), known as avian paramyxovirus serotype 1, is a member of the family Paramyxoviridae [1]. The virus genome is a non-segmented, single-strand, negative sense RNA which codes for six major proteins including nucleocapsid protein (NP), phosphoprotein (P), matrix protein (M), fusion protein (F), hemagglutinin-neuraminidase (HN), and large RNA-directed RNA polymerase (L), in the order from the. The genotype VII NDV is still prevalent in China [4,8,9,10]
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