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Volume 25 Issue 5
October 2010
    Citation: Zhen-peng LI, De-quan YING, Peng LI, Fei LI, Xiao-chen BO, Sheng-qi WANG. Analysis of Synonymous Codon Usage Bias in 09H1N1 .VIROLOGICA SINICA, 2010, 25(5) : 329-340.  http://dx.doi.org/10.1007/s12250-010-3123-3
    shu

    Analysis of Synonymous Codon Usage Bias in 09H1N1

    • Beijing Institute of Radiation Medicine, Beijing 100850, China

    • Corresponding author: Xiao-chen BO, boxc@bmi.ac.cn
      Sheng-qi WANG, sqwang@bmi.ac.cn
    • These authors contributed equally to this work.
    • Received Date: 05 January 2010
      Accepted Date: 30 April 2010
      Available online: 01 October 2010
    • 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.
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      Analysis of Synonymous Codon Usage Bias in 09H1N1

        Corresponding author: Xiao-chen BO, boxc@bmi.ac.cn
        Corresponding author: Sheng-qi WANG, sqwang@bmi.ac.cn
      • Beijing Institute of Radiation Medicine, Beijing 100850, China
      • Received Date: 05 January 2010
      • Accepted Date: 30 April 2010

      Abstract: 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.

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