Comparative analysis of codon usage bias and host adaptation across avian metapneumovirus genotypes

Avian metapneumovirus (aMPV) is a significant pathogen affecting poultry worldwide, causing respiratory disease and economic losses. This study investigated the genetic and evolutionary differences among aMPV genotypes through codon usage bias analysis. Using whole-genome and F gene sequences, we assessed phylogenetic relationships, codon usage patterns, evolutionary pressures, and host adaptation. Our results indicate clear genotype differentiation in the phylogenetic tree, with Group C identified as the earliest diverging lineage of aMPV. The F gene exhibits independent evolutionary trajectories, reflecting distinct selective pressures. Codon usage bias varies across genotypes and is primarily driven by selection pressure, with Groups B and C experiencing stronger selective constraints. The F gene, crucial for viral entry and adaptation, undergoes intense selection, optimising codon usage for host adaptation. Host adaptation analysis reveals that aMPV is most suited to chickens. Additionally, Group B exhibits the largest population size; however, recent declines, particularly in this genotype, suggest that vaccine-driven selection pressure may be influencing aMPV population dynamics. These findings provide critical insights into aMPV evolution, highlighting the role of codon usage bias and selection pressure in shaping viral adaptation. Understanding these evolutionary mechanisms may aid in vaccine development and disease control strategies.