Virologica Sinica

, Volume 25, Issue 5, pp 329–340

Analysis of synonymous codon usage bias in 09H1N1


DOI: 10.1007/s12250-010-3123-3

Cite this article as:
Li, Z., Ying, D., Li, P. et al. Virol. Sin. (2010) 25: 329. doi:10.1007/s12250-010-3123-3


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.

Key words

09H1N1 Correspondence analysis Codon usage bias 

Copyright information

© Wuhan Institute of Virology, CAS and Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  1. 1.Beijing Institute of Radiation MedicineBeijingChina

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