Genetic evolution and substitutions frequency of F and HN gene of Newcastle disease virus isolates from poultry in China

Abstract:

[Objective] Newcastle disease virus (NDV) is one of the most serious infection problems in China in the last two decades, resulting in huge economic losses for the poultry industry. The genetic evolution of NDV strain is a very important topic for controlling ND. In this study, the evolution of NDV under the immune pressure of vaccine was further assessed by comparing the molecular characteristics and genetic variation frequency of F and HN genes of different genotypes of NDV. [Methods] NDV sequences of F gene and HN gene including 89 NDV isolates in our laboratory, 364 NDV pandemic strains worldwide and 15 classical strains, were collected and downloaded from the GenBank, and further genetically analyzed to determine their evolution, molecular characteristic and substitution rate by using Lasergene 7.1 and MEGA 5.1 software. [Results] Phylogenetic tree analysis suggested that NDV evolved into 15 distinct genotypes from genotype I to XV. Most NDV pandemic isolates during 1997?2015 belonged to sub-genotype VII d, suggesting that this genotype was the dominate isolate in China in the last two decades. Furthermore, comparison based on homologies of the nucleotide and amino acid sequence of F and HN gene of NDV showed that different genotypes had their own distinct characteristics, and significant accumulation of amino acid variation was also found. In addition, in comparing F and HN gene with reference Go/GD/QY/1997, which was the first genotype VII in China, average annual substitution frequencies of NDV pandemic strain nucleotide (amino acid) were 2.31×10?3 (2.26×10?3) and 3.37×10?3 (2.35×10?3), respectively. Substitution rates of F and HN during 1997?2001 were 4.72×10?3 and 8.28×10?3, higher than that during 2002?2015 (1.6×10?3 and 1.84×10?3), when the genotype VII vaccine was initially applied in the field. [Conclusion] Bioinformatics analysis proved that matching NDV vaccine strain with epidemic strains in genotype is an important factor in mitigating NDV variability.