Genome-Wide Diversity and Evolutionary Insights into Newcastle Disease Virus

Newcastle Disease virus (NDV) is a single-stranded, non-segmented RNA virus that encodes six structural and two non-structural proteins. It belongs to the genus Avulavirus of the family Paramyxoviridae and is divided into class I and class II groups. Class I isolates are classified as a single genotype with four sub-genotypes, while class II isolates were found to be much more diverse, divided into 18 genotypes. Several complete whole-genome sequences have been reported from different parts of the world. However, despite attempts to capture the evolutionary dynamics of NDV at regional levels, there is limited research on comparative genomic and evolutionary analysis worldwide. Therefore, this study examined overall nucleotide diversity and genomic characteristics to deduce an evolutionary relationship among strains representing diverse geographical regions worldwide, utilizing various bioinformatics tools. A total of 935 whole-genome NDV sequences from 48 countries were included in this study, comprising 132 class I and 797 class II, with the remaining six classified as unknown. The nucleotide diversity(π) and the haplotype diversity among the whole genome sequences were 0.162 and 0.999, respectively. Based on RDP4 analysis, the highest number of recombination events was found in gene L, followed by genes NP, HN, and P and F, M genes, respectively. Although different algorithmic approaches reveal the number of positive selection sites in each gene, none of them exhibited a mean dN/dS greater than 1. In conclusion, this study enhances our understanding of ongoing phylogenomic and evolutionary dynamics, providing a more profound comprehension of NDVs and informing effective disease control interventions.