Department of Veterinary Medicine, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou 225300, China.
Viruses. 2024 Aug 29;16(9):1380. doi: 10.3390/v16091380.
Duck hepatitis virus 1 (DHV-1) is a major threat to the global poultry industry, causing significant economic losses due to high mortality rates in young ducklings. To better understand the evolution and host adaptation strategies of DHV-1, we conducted a comprehensive codon usage analysis of DHV-1 genomes. Our phylogenetic analysis revealed three well-supported DHV-1 phylogroups (Ia, Ib, and II) with distinct genetic diversity patterns. Comparative analyses of the codon usage bias and dinucleotide abundance uncovered a strong preference for A/U-ended codons and a biased pattern of dinucleotide usage in the DHV-1 genome, with CG dinucleotides being extremely underrepresented. Effective number of codons (ENC) analysis indicated a low codon usage bias in the DHV-1 ORF sequences, suggesting adaptation to host codon usage preferences. PR2 bias, ENC plot, and neutrality analyses revealed that both mutation pressure and natural selection influence the codon usage patterns of DHV-1. Notably, the three DHV-1 phylogroups exhibited distinct evolutionary trends, with phylogroups Ia and Ib showing evidence of neutral evolution accompanied by selective pressure, while the phylogroup II evolution was primarily driven by random genetic drift. Comparative analysis of the codon usage indices (CAI, RCDI, and SiD) among the phylogroups highlighted significant differences between subgroups Ia and Ib, suggesting distinct evolutionary pressures or adaptations influencing their codon usage. These findings contribute to our understanding of DHV-1 evolution and host adaptation, with potential implications for the development of effective control measures and vaccines.
鸭肝炎病毒 1（DHV-1）是全球家禽业的主要威胁，由于雏鸭死亡率高，造成了巨大的经济损失。为了更好地了解 DHV-1 的进化和宿主适应策略，我们对 DHV-1 基因组进行了全面的密码子使用分析。我们的系统发育分析揭示了三个具有明显遗传多样性模式的支持良好的 DHV-1 进化枝（Ia、Ib 和 II）。对密码子使用偏性和二核苷酸丰度的比较分析揭示了 DHV-1 基因组中强烈偏好 A/U 结尾的密码子和二核苷酸使用的偏性模式，CG 二核苷酸的出现频率极低。有效密码子数（ENC）分析表明，DHV-1 ORF 序列中的密码子使用偏性较低，表明适应了宿主的密码子使用偏好。PR2 偏性、ENC 图和中性分析表明，突变压力和自然选择都影响了 DHV-1 的密码子使用模式。值得注意的是，三个 DHV-1 进化枝表现出不同的进化趋势，进化枝 Ia 和 Ib 显示出中性进化伴随着选择压力的证据，而进化枝 II 的进化主要是由随机遗传漂变驱动的。对进化枝间密码子使用指数（CAI、RCDI 和 SiD）的比较分析突出了亚群 Ia 和 Ib 之间的显著差异，表明不同的进化压力或适应影响了它们的密码子使用。这些发现有助于我们理解 DHV-1 的进化和宿主适应，对开发有效的控制措施和疫苗具有潜在意义。
