Comparative Genomics of Virulent and Attenuated Strains of Newcastle Disease Virus Isolated from Poultry in Sokoto and Kebbi States

Newcastle disease (ND) remains a major economic constraint in poultry production across Nigeria, with virulent velogenic and mesogenic strains co-circulating alongside vaccine strains in Sahelian Northwest states. Comparative genomic analysis of virulent and attenuated NDV strains provides mechanistic insight into pathogenicity determinants and informs vaccine strain selection strategies. This study performed comparative genomics on NDV isolates recovered from commercial and backyard poultry flocks in Sokoto and Kebbi States, Northwest Nigeria. Tracheal and cloacal swabs were collected from 140 birds with clinical ND signs. RT-PCR and Sanger sequencing of the fusion (F) gene were used for initial virulence classification. Whole-genome sequences of 18 selected isolates (12 velogenic, 6 vaccine-like) were obtained using Illumina MiSeq. Genome assemblies were annotated with RAST, and phylogenetic trees were constructed from complete genome alignments. Comparative analysis focused on the F-gene cleavage site, HN receptor-binding domain, and polymerase (L) gene variations. Velogenic isolates contained polybasic cleavage sites (112R-R-Q-K/R-F117) and distinct HN antigenic site substitutions compared to attenuated strains. L gene analysis identified a cluster of mutations in the catalytic domain unique to Northwest Nigerian velogenic strains not previously reported in GenBank reference sequences. These novel L gene variants may represent regionally evolved molecular pathogenicity signatures with implications for diagnostic assay design and vaccine efficacy assessment. Keywords: Newcastle disease virus, comparative genomics, velogenic, fusion gene, Northwest Nigeria.