Beijing Institute of Radiation Medicine, Beijing, 100850, China.
Virol Sin. 2010 Oct;25(5):329-40. doi: 10.1007/s12250-010-3123-3. Epub 2010 Oct 8.
A novel subtype of influenza A virus 09H1N1 has rapidly spread across the world. Evolutionary analyses of this virus have revealed that 09H1N1 is a triple reassortant of segments from swine, avian and human influenza viruses. In this study, we investigated factors shaping the codon usage bias of 09H1N1 and carried out cluster analysis of 60 strains of influenza A virus from different subtypes based on their codon usage bias. We discovered that more preferentially used codons of 09H1N1 are A-ended or U-ended, and the intra-genomic codon usage bias of 09H1N1 is quite low. Base composition constraint, dinucleotide biases and translational selection are the main factors influencing the codon usage bias of 09H1N1. At the genome level, we find that the codon usage bias of 09H1N1 is similar to H1N1 (A/swine/Kansas/77778/2007H1N1), H9N2 from Asia, H1N2 from Asia and North America and H3N2 from North America. Our results provide insight for understanding the processes governing evolution, regulation of gene expression, and revealing the evolution of 09H1N1.
一种新型的甲型流感病毒 09H1N1 已经在全球范围内迅速传播。对这种病毒的进化分析表明，09H1N1 是猪流感、禽流感和人流感病毒片段的三重重组体。在这项研究中，我们调查了影响 09H1N1 密码子使用偏性的因素，并基于其密码子使用偏性对来自不同亚型的 60 株甲型流感病毒进行了聚类分析。我们发现，09H1N1 中更多被优先使用的密码子是 A 结尾或 U 结尾的，而 09H1N1 内部基因组的密码子使用偏性相当低。碱基组成约束、二核苷酸偏性和翻译选择是影响 09H1N1 密码子使用偏性的主要因素。在基因组水平上，我们发现 09H1N1 的密码子使用偏性与 H1N1（A/swine/Kansas/77778/2007H1N1）、来自亚洲的 H9N2、来自亚洲和北美的 H1N2 以及来自北美的 H3N2 相似。我们的结果为理解进化、基因表达调控以及揭示 09H1N1 的进化过程提供了深入的认识。
