Genetic characterization and phylogeny of pigeon paramyxovirus isolate (PPMV-1) from Pakistan

Background: Knowing the genome characteristics of circulating Newcastle disease viruses [avian paramyxoviruses (APMV-1) and pigeon paramyxoviruses (PPMV-1)] is important to devise appropriate diagnostics and control strategies. APMVs originating from chicken and wildlife in Pakistan are well-elucidated; nevertheless, molecular characterization for the circulating PPMV-1 is largely unknown. Findings: Here, we have performed fusion (F) and hemagglutinin (HN) gene based characterization of PPMV-1 isolated from an outbreak in a pigeon flock. With F-0 proteolytic cleavage site ((112)RRQKR down arrow F-117), characteristic of velogenic/mesogenic serotype, the complete F and HN gene based sequence analysis of the isolate revealed evolutionary relationship to genotype VI. Further analysis of hyper-variable region of F-gene demonstrated clustering of the study isolate with genotype VIb. The deduced residue analysis for both F and HN protein showed a number of substitution mutations in the functional domains distinct from representative strains of each genotype including the vaccine strains; some of them were found exclusive to the study isolate. Conclusions: Though limited and preliminary data, the findings enhance our knowledge towards circulating strains of PPMVs in Pakistan. Further studies are needed to ascertain its potential for transmission in the wild birds, commercial and backyard poultry and its subsequent shedding into the environment.