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    黄蔚虹, 陈永杰, 孙彦阔, 等. H9N2禽流感病毒全基因组密码子使用偏好性及影响因素分析[J]. 华南农业大学学报, 2020, 41(3): 15-22. doi: 10.7671/j.issn.1001-411X.201908020
    引用本文: 黄蔚虹, 陈永杰, 孙彦阔, 等. H9N2禽流感病毒全基因组密码子使用偏好性及影响因素分析[J]. 华南农业大学学报, 2020, 41(3): 15-22. doi: 10.7671/j.issn.1001-411X.201908020
    shu
    HUANG Weihong, CHEN Yongjie, SUN Yankuo, et al. Codon usage bias of H9N2 avian influenza virus complete genomes and its influence factors[J]. Journal of South China Agricultural University, 2020, 41(3): 15-22. doi: 10.7671/j.issn.1001-411X.201908020
    Citation: HUANG Weihong, CHEN Yongjie, SUN Yankuo, et al. Codon usage bias of H9N2 avian influenza virus complete genomes and its influence factors[J]. Journal of South China Agricultural University, 2020, 41(3): 15-22. doi: 10.7671/j.issn.1001-411X.201908020
    shu

    H9N2禽流感病毒全基因组密码子使用偏好性及影响因素分析

    Codon usage bias of H9N2 avian influenza virus complete genomes and its influence factors

      摘要
    • 摘要:
      目的  探究H9N2禽流感病毒(AIV)全基因组的密码子使用偏好性及影响因素。
      方法  选取2010—2018年国内H9N2 AIV流行毒株的全基因组为研究对象，分析其碱基组成特性、最优密码子、密码子使用偏好性的影响因素以及病毒对宿主密码子使用模式的适应性。
      结果  H9N2 AIV的全基因组中AU含量高于GC。大部分最优密码子以A或U结尾，有效密码子数(ENC)平均值为52.86，提示存在密码子使用偏好性但偏好性较低。密码子使用偏好性主要受到突变压力和自然选择的共同作用，其中自然选择(所占比例为61.79%~76.15%)作用大于突变压力(所占比例为23.85%~38.21%)。H9N2 AIV对人Homo sapiens的密码子适应指数平均值为0.739~0.741，提示H9N2 AIV禽流感病毒可能已适应人类的密码子使用模式。
      结论  本研究为H9N2 AIV的基因进化分析、已有疫苗的密码子优化和新型疫苗(密码子去优化疫苗)研制提供了理论依据。

       

      Abstract:
      Objective  To study codon usage bias of H9N2 avian influenza virus (AIV) complete genomes and its influence factors.
      Method  The complete genomes of Chinese epidemic H9N2 AIV strains from 2010 to 2018 were selected. The characteristics of base composition, optimal codons, influence factors of codon usage bias and adaption to the codon usage patterns of the host were analyzed.
      Result  AU content was higher than GC content in the whole genomes of H9N2 AIV. Most of the optimal codons ended with A or U, and the average of effective number of codons (ENC) was 52.86, suggesting that codon usage bias existed, but the bias was low. The codon usage bias was mainly affected by mutation pressure and natural selection. Natural selection (accounting for 61.79%−76.15%) played a greater role than mutation pressure (accounting for 23.85%−38.21%). In addition, the average codon adaptation ind ex of H9N2 AIV to Homo sapiens ranged from 0.739 to 0.741, suggesting that H9N2 AIV might have adapted to human codon usage patterns.
      Conclusion  The study provides a theoretical basis for genetic evolution analysis of H9N2 AIV, codon optimization of existing vaccines and development of new vaccines (codon deoptimization vaccine).

       

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