Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses.
Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses.
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DOI：
10.1371/journal.pone.0154376
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Virmani N
中科院分区：
文献类型：
--
作者：
Kumar N;Bera BC;Greenbaum BD;Bhatia S;Sood R;Selvaraj P;Anand T;Tripathi BN;Virmani N
H3 N8亚型马流感病毒（EIV）是马严重急性呼吸道感染的罪魁祸首，并且仍然是全球重大疫情的罪魁祸首。流感病毒对特定宿主的适应性受到其密码子使用偏好的显著影响，这是由于其复制完全依赖于宿主细胞机制。在本研究中，我们分析了92个EIV株，包括H3 N8和H7 N7亚型的全基因组密码子使用模式，通过计算几个密码子使用指数和应用多元统计方法。相对同义密码子使用（RSCU）分析显示，偏好的同义密码子偏向A/U-末端密码子。EIV的总体密码子使用偏倚略低，主要受RSCU和有效密码子数（ENc）分析推断的核苷酸组成限制的影响。我们的数据表明，EIV的密码子使用模式是由突变压力，从其宿主的自然选择和不确定因素的相互作用。与H3 N8相比，H7 N7亚型具有更高的密码子偏好性，更低的突变压力和更少的对马细胞tRNA库的适应性，因此被发现对其宿主（马）的适应性较差。据我们所知，这是第一份描述EIV全基因组密码子使用分析的报告。我们的研究结果可能会增强我们对病毒适应，进化和适应宿主的因素的理解。
Equine influenza viruses (EIVs) of H3N8 subtype are culprits of severe acute respiratory infections in horses, and are still responsible for significant outbreaks worldwide. Adaptability of influenza viruses to a particular host is significantly influenced by their codon usage preference, due to an absolute dependence on the host cellular machinery for their replication. In the present study, we analyzed genome-wide codon usage patterns in 92 EIV strains, including both H3N8 and H7N7 subtypes by computing several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis disclosed bias of preferred synonymous codons towards A/U-ended codons. The overall codon usage bias in EIVs was slightly lower, and mainly affected by the nucleotide compositional constraints as inferred from the RSCU and effective number of codon (ENc) analysis. Our data suggested that codon usage pattern in EIVs is governed by the interplay of mutation pressure, natural selection from its hosts and undefined factors. The H7N7 subtype was found less fit to its host (horse) in comparison to H3N8, by possessing higher codon bias, lower mutation pressure and much less adaptation to tRNA pool of equine cells. To the best of our knowledge, this is the first report describing the codon usage analysis of the complete genomes of EIVs. The outcome of our study is likely to enhance our understanding of factors involved in viral adaptation, evolution, and fitness towards their hosts.