Decoding the diversity: a comprehensive sequence analysis of accessory viral protein W of Newcastle disease virus

Newcastle disease virus (NDV) is an avian paramyxovirus that has a significant impact on the global poultry industry. The accessory W protein (W) of NDV is generated by RNA editing of the phosphoprotein (P) gene; however, its precise function remains elusive. Consequently, we conducted an in-silico analysis of the W sequences from 1,011 NDV strains, utilizing the data from GenBank. Our investigation revealed 24 W-length variants ranging between 135 and 231 amino acids (aa), with variant 227 aa being the most prevalent. Further, the W-length variants were distinct for class I and class II NDV strains. We observed no apparent correlation between W lengths and genotype or pathogenicity of NDV. However, a nuclear localization signal (NLS) in the W seemed to be associated with virulence, with 55.9% of virulent strains having an NLS, compared to 38.9% of avirulent strains. Geographical analysis indicated region-specific evolutionary factors, with Asia showing the most W diversity. The lengths of W were more specific to the bird species from which they were isolated/sequenced, suggesting possible adaptation to the host. Molecular clock analysis showed varied evolutionary rates among W types, with variant 185 aa evolving the fastest. Selection pressure analysis indicated that most types are under negative selection, but some presented signs of relaxed or positive selection. Our study provides a broad view of W diversity in NDV, highlighting its complex evolutionary history and possible implications for host adaptation and virulence.