Molecular Characterization and Epitope Mapping of Fusion (F) and Hemagglutinin (HN) Genes of Avian Paramyxovirus Serotype I from Peacocks in Pakistan

Effective diagnosis and control measures for Newcastle disease virus (NDV) requires continuous disease surveillance and understanding of field NDV strains. The NDVs, a prototype of Avian Paramyxoviruses (APMV-1), have been reported previously both in chicken and feral birds (natural reservoirs) in Pakistan; however, their molecular characterization is largely inadequate and requires continuous evaluation. In this study, sequencing and molecular analysis of fusion (F) and hemagglutinin (HN) genes of NDV strain isolated from an outbreak in a peacock flock was undertaken. Proteolytic cleavage site of F-0 showed a cleavage motif ((112)RRQKR down arrow F-117), representative of a velogenic serotype. Moreover, based on F and HN, gene nucleotide sequence analysis, the isolate clustered as genotype VII closely associated to those reported from Indonesia. Further sequence analysis of hyper-variable region within F gene revealed its clustering to sub-genotype VIIe. The inferred residue analysis of the virus revealed a number of substitution mutations in the structural and functional domains when compared to the representative strains of each genotype, including the vaccine strains (genotype II and III). Interestingly, some of these mutations were found exclusive to the study isolate. Not only do these prime findings improve our understanding about currently circulating strains of NDVs but they also help us to envisage potential efforts to avoid future outbreaks in wild birds, as well as in commercial and backyard poultry.