Molecular Epidemiology of Newcastle Disease Virus in Commercial Poultry in South West Nigeria: Genotypic Characterisation and Vaccine Match Analysis

This study provides a molecular epidemiological analysis of Newcastle disease virus (NDV) circulating in commercial poultry flocks in South West Nigeria, with the aim of characterising circulating genotypes and assessing their vaccine strain compatibility. NDV genotype diversity has expanded significantly in West Africa in recent years, and mismatches between field strains and commonly used vaccine strains are believed to contribute to vaccination failures, yet systematic genotyping of Nigerian field isolates is limited. Using a cross-sectional molecular diagnostic design, oropharyngeal and cloacal swabs were collected from 420 birds across 35 commercial poultry farms in Lagos, Ogun, and Oyo States. RT-PCR amplification of the F protein gene was performed and phylogenetic analysis was conducted against reference sequences from the GenBank database. Vaccine strain sequences (La Sota, HitchnerB1, and VG/GA) were included for comparison. The study addresses the critical research gap of genotype-vaccine compatibility data for Nigerian isolates. Findings revealed that 74 percent of NDV-positive isolates belonged to sub-genotype VII.2, which shows greater than 10 percent nucleotide divergence from commonly used La Sota and Hitchner B1 vaccine strains, providing a plausible molecular basis for the observed vaccination failures. The study recommends development of a Nigerian-specific NDV vaccine candidate based on circulating sub-genotype VII.2 strains and implementation of genotypic surveillance as a routine component of poultry disease monitoring in South West Nigeria. Keywords: Newcastle disease virus, molecular epidemiology, genotyping, vaccine match, South West Nigeria.