Molecular Characterisation and Dynamics of the Fusion Protein of an Emerging Genotype VIIi of Newcastle Disease Virus

Abstract

The viral strains of the Newcastle disease virus have exhibited genetic and pathogenic diversity since their discovery, which is mainly influenced by mutations in the Fusion gene. This study focussed on describing the circulating Newcastle disease virus strain based on the Fusion gene sequencing of three isolates: JKND01, JKND02, and JKND03, which were isolated from commercial poultry in Kashmir. Phylogenetic analysis identified the isolates as Genotype VIIi with the virulent fusion cleavage site motif (¹¹³RQKRF¹¹⁷). Homology analysis of amino acid sequences identified amino acid substitutions in the Fusion protein of the isolates compared to the reference strains. In silico mutational analysis revealed that the amino acid changes impact the structure of the protein, potentially affecting the functional behaviour of the virus. Moreover, predictive analysis of potential post-translational modification motifs showed a loss of an N-glycosylation site and the acquisition of a phosphorylation site in JKND02 compared to the reference Fusion glycoprotein. This study reports the first presence of the fifth panzootic vNDV genotype VIIi in Kashmir, highlighting the need for further epidemiological and surveillance studies to better understand the distribution and spread of the virus and to develop effective control measures.