Detection and molecular characterisation of subtype B avian metapneumovirus in commercial chickens and co-infection with bacteria pathogens in Nigeria

Avian metapneumovirus (aMPV) significantly impacts turkey and chicken production, though its prevalence in chickens is often underestimated due to a lack of systematic diagnostic surveys. This study aimed to detect and characterise aMPV and determine the prevalence of secondary bacterial pathogens present during aMPV infection in commercial chickens raised in three climatic zones in Nigeria. Tissue samples were collected from carcasses of 42 flocks with suspected aMPV cases accounting for 420 chickens. These samples were obtained from veterinary diagnostic facilities in three climatic zones of Nigeria: near-temperate (Plateau, n = 140), rainforest (Oyo, n = 140), and semi-arid (Sokoto, n = 140). Virus detection was performed using RT-PCR to amplify the N- and G-genes, followed by Sanger sequencing. Multiple sequence alignment and phylogenetic analysis were used to infer the subtypes to which sequences belong. Secondary bacterial pathogens associated with aMPV-positive tissues were isolated and identified using standard methods. RT-PCR results indicated that 11.90% (5/42) of the flocks were positive for aMPV strains. aMPV detected belongs to subtype B. The Amino acids mutations (K183R and H224Y) observed in the sequence obtained from this study differentiate the strain from A, C, and D subtypes. Phylogenetic analysis showed that the isolated aMPV strain (GenBank accession number MZ408311) was closely related to Subtype B strains from Europe and Asia. Prominent secondary bacterial pathogens isolated included Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae. This study highlights the necessity for enhanced surveillance and targeted vaccination to reduce the prevalence of aMPV and associated secondary bacterial infections, potentially decreasing antibiotic reliance.