ANTIGENIC DIVERSITY IN THE IMMUNODOMINANT PROTEIN OF NEWCASTLE DISEASE VIRUS

Newcastle Disease Virus (NDV) is a highly contagious viral pathogen affecting domestic and wild birds, with major importance in poultry production. The Hemagglutinin-Neuraminidase (HN) protein is an important surface and immunodominant protein of NDV because it participates in receptor binding, neuraminidase activity, viral attachment and release. The present internship study was undertaken to investigate the antigenic diversity of the HN protein using a combination of sequence analysis, protein structure prediction, structural visualisation, structure validation and phylogenetic analysis. HN protein sequences from selected NDV isolates were retrieved from the NCBI GenBank database in FASTA format. Homologous sequences and conserved regions were examined using BLAST. The three-dimensional structure of the HN protein was obtained from the AlphaFold Protein Structure Database and visualised using PyMOL. Structural features including alpha-helices, beta-sheets, loops, surface-exposed regions and flexible segments were examined. BIOVIA Discovery Studio was used for structural validation through Ramachandran plot analysis and for assessing the stereochemical quality of the predicted model. Multiple sequence alignment was performed using ClustalW in MEGA, followed by phylogenetic analysis to investigate sequence similarity, genetic divergence and clustering among selected isolates. The structural model showed an organised arrangement of secondary structural elements with exposed and flexible regions. The Ramachandran analysis indicated that most residues were located in favoured and additionally allowed regions, supporting acceptable structural quality. Phylogenetic analysis revealed distinct clusters and genetic diversity among the selected isolates, with closely related Indian isolates forming related groups. The combined analysis demonstrates how sequence, structural and evolutionary approaches can be used to characterise HN protein diversity and to support molecular surveillance and future vaccine-related investigations of Newcastle Disease Virus.

 

Keywords: Newcastle Disease Virus, HN protein, antigenic diversity, immunodominant protein, GenBank, BLAST, AlphaFold, PyMOL, BIOVIA Discovery Studio, Ramachandran plot, MEGA, ClustalW, phylogenetic analysis

Newcastle Disease Virus HN protein antigenic diversity immunodominant protein GenBank BLAST AlphaFold PyMOL BIOVIA Discovery Studio Ramachandran plot MEGA ClustalW phylogenetic analysis