Zhang Hua, Cao Hong-Wei, Li Feng-Qi, Pan Zi-Ye, Wu Zhi-Jun, Wang Yan-Hong, Cui Yu-Dong
College of Biological Science and Technology, HeiLongJiang BaYi Agricultural University, DaQing, 163319 China.
Virusdisease. 2014;25(2):243-8. doi: 10.1007/s13337-014-0215-y. Epub 2014 May 21.
Enterovirus 71 (EV71) is the major cause of hand-foot-and-mouth disease in children. In our study, using the complete genome sequences of 42 EV71 representing all three genotypes, we analyzed synonymous codon usage and the relative dinucleotide abundance in EV71 genome. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in EV71 genome. Furthermore, we observed that the relative abundance of dinucleotides in EV71 is independent of the overall base composition but is still the result of differential mutational pressure, which also shapes codon usage. In addition, other factors, such as hydrophobicity and aromaticity, also influence the codon usage variation among the genomes of EV71. This study represents the most comprehensive analysis of EV71 codon usage patterns and provides a basic understanding of the mechanisms for codon usage bias.
肠道病毒71型（EV71）是导致儿童手足口病的主要病因。在我们的研究中，利用代表所有三种基因型的42株EV71的全基因组序列，我们分析了EV71基因组中的同义密码子使用情况和相对二核苷酸丰度。碱基组成与密码子使用偏好之间的总体相关性表明，突变压力而非自然选择是决定EV71基因组中密码子使用偏好的主要因素。此外，我们观察到EV71中二核苷酸的相对丰度与总体碱基组成无关，但仍是不同突变压力的结果，这也影响了密码子的使用。此外，其他因素，如疏水性和芳香性，也影响EV71基因组间的密码子使用差异。本研究是对EV71密码子使用模式最全面的分析，并为密码子使用偏好机制提供了基本认识。
