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

Analysis of Synonymous Codon Usage Bias in 09H1N1

  • Corresponding author: Xiao-chen BO, boxc@bmi.ac.cn
    Sheng-qi WANG, sqwang@bmi.ac.cn
  • 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

    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.