Molecular phylogenetics of Newcastle disease viruses isolated from vaccinated flocks during outbreaks in Southern India reveals circulation of a novel sub‐genotype

Newcastle disease (ND) is an economically important, contagious poultry viral disease reported across the globe. In India, ND is endemic and episodes of ND outbreaks despite strict vaccinations are not uncommon. We isolated and characterized seven ND viruses from vaccinated commercial poultry farms during severe disease outbreaks in Tamil Nadu, in Southern India, between April 2015 and June 2016. All the seven isolates were categorized as virulent by mean death time (48–54 hr) in embryonated chicken eggs. Also, their sequences carried the virulence signature of multi‐basic amino acid residues in their fusion protein cleavage site (RRQ/RR/KRF). Phylogenetic and evolutionary distance analyses revealed circulation of a novel sub‐genotype of genotype XIII, class II ND viruses, herein proposed as sub‐genotype XIIIe. The genetic divergence between the circulating virulent strains and the vaccine strains could possibly explain the disease outbreak in the vaccinated flocks. Further, our study signifies the need to implement routine epidemiological surveillance and to revisit the current vaccination program.