The characteristics of the synonymous codon usage in enterovirus 71 virus and the effects of host on the virus in codon usage pattern.
The characteristics of the synonymous codon usage in enterovirus 71 virus and the effects of host on the virus in codon usage pattern.
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DOI：
10.1016/j.meegid.2011.02.018
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发表时间：
2011-07
期刊：
影响因子：
--
通讯作者：
Zhang J
中科院分区：
文献类型：
--
作者：
Liu YS;Zhou JH;Chen HT;Ma LN;Pejsak Z;Ding YZ;Zhang J
EV71在进化过程中存在突变压力和自然选择。EV71的同义密码子使用模式与宿主的同义密码子使用模式是一致和拮抗的混合。⑶观察EV71毒株的遗传多样性。同时还观察了EV71病毒部分同义密码子选择的地理因素。为了从一个新的角度探讨肠道病毒71型（EV 71）的进化特征及其宿主的自然选择对病毒密码子使用模式的影响，对EV 71的相对同义密码子使用（RSCU）值、密码子使用偏好（CUB）值、计算有效密码子数（ENC）值和核苷酸含量以实施比较分析，从而评估病毒进化的动力学。EV71的同义密码子使用模式和核苷酸含量的特征以及EV71全编码序列和病毒蛋白编码序列的ENC值的比较均表明，在EV71的进化过程中，存在着来自病毒的突变压力和来自宿主的自然选择之间的相互作用。EV71的同义密码子使用模式与宿主细胞的同义密码子使用模式是一致和拮抗的混合。此外，还观察到EV71毒株的遗传多样性以及不同流行地区EV71毒株对某些同义密码子的偏好性选择，提示地理和社会因素可能在影响该病毒进化过程中发挥作用。
► The mutation pressure and natural selection exists in the processes of evolution of EV71. ► The synonymous codon usage pattern of EV71 is a mixture of coincidence and antagonism to that of host. ► The genetic diversity of EV71 strains was observed. ► The geographic factors of selection of some synonymous codons in EV71 was also observed. To give a new perspective on the evolutionary characteristics shaping the genetic diversity of enterovirus 71 (EV71) and the effects of natural selection from its host on the codon usage pattern of the virus, the relative synonymous codon usage (RSCU) values, codon usage bias (CUB) values, effective number of codons (ENCs) values and nucleotide contents were calculated to implement a comparative analysis to evaluate the dynamics of the virus evolution. The characteristics of the synonymous codon usage patterns and nucleotide contents of EV71 and the comparison between ENC values for the whole coding sequence of EV71 and that of coding sequences for viral proteins of EV71 all indicate that the interaction between mutation pressure from virus and natural selection from host exists in the processes of evolution of EV71. The synonymous codon usage pattern of EV71 is a mixture of coincidence and antagonism to that of host cell. In addition, the genetic diversity of EV71 strains and the preferential selection of some synonymous codons in EV71 strains based on the different epidemic areas were observed, suggesting that geographic and social factors may play roles in influencing the evolution of this virus.
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