Shi Shuiqin, Gao Jiahui, Gai Mengrui, Pan Yue, Cao Jichun, Peng Tianyi, Liu Yannan, Yang Kankan
School of Life Sciences, Anqing Normal University, Anqing, Anhui, 246133, PR China; Anqing Yongqiang Agricultural Technology Co., Anqing, Anhui, 246133, PR China.
School of Life Sciences, Anqing Normal University, Anqing, Anhui, 246133, PR China.
Poult Sci. 2025 Jun 11;104(9):105428. doi: 10.1016/j.psj.2025.105428.
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.
禽偏肺病毒（aMPV）是一种影响全球家禽的重要病原体，可导致呼吸道疾病和经济损失。本研究通过密码子使用偏好分析，调查了aMPV基因型之间的遗传和进化差异。利用全基因组和F基因序列，我们评估了系统发育关系、密码子使用模式、进化压力和宿主适应性。我们的结果表明，在系统发育树中存在明显的基因型分化，C组被确定为aMPV最早分化的谱系。F基因呈现出独立的进化轨迹，反映出不同的选择压力。密码子使用偏好在不同基因型之间存在差异，主要由选择压力驱动，B组和C组受到更强的选择限制。对病毒进入和适应至关重要的F基因经历了强烈的选择，优化密码子使用以适应宿主。宿主适应性分析表明，aMPV最适合鸡。此外，B组的种群规模最大；然而，最近的下降，尤其是该基因型的下降，表明疫苗驱动的选择压力可能正在影响aMPV的种群动态。这些发现为aMPV的进化提供了关键见解，突出了密码子使用偏好和选择压力在塑造病毒适应性中的作用。了解这些进化机制可能有助于疫苗开发和疾病控制策略。
