Analysis of codon usage preference in hemagglutinin genes of the swine-origin influenza A (H1N1) virus

Sheng Fan Wang, Ming Wei Su, Sung Pin Tseng, Ming Chun Li, Ching Han Tsao, Szu Wei Huang, Woei Chyn Chu, Wu Tse Liu, Yi Ming Arthur Chen, Jason C. Huang

研究成果: 雜誌貢獻文章同行評審

6 引文 斯高帕斯(Scopus)


Background The swine-origin influenza A (H1N1) virus (S-OIV) has come to the forefront since 2009 and was identified as a new reassortant strain. The hemagglutinin (HA) glycoprotein mediates virus binding, contains antigenic regions recognized by neutralizing antibodies, and is associated with viral cross-species infection and adaption. The comparison study of codon usage preferences in influenza viral genomes was less extensive. In this study, we used codon usage pattern analyses to validate the adaption and origins of S-OIV. Methods Codon usage pattern was used to estimate the host adaption of S-OIVs. Phylogenetic analysis of the HA gene was conducted to understand the phylogeny of H1N1 viruses isolated from different hosts. Amino acid signature pattern on antigenic sites of HA was analyzed to understand the antigenic characteristics. Results Results of phylogenetic analyses of HA gene indicate that S-OIVs group in identical clusters. The synonymous codon usage pattern analyses indicate that the effective number of codons versus GC content at the third codon position in the HA1 gene slightly differ from those in swine H1N1 and gradually adapted to human. Our data indicate that S-OIV evolution occurred according to positive selection within these antigenic regions. A comparison of antigenic site amino acids reveals similar signature patterns between S-OIV and 1918 human influenza strains. Conclusion This study proposes a new and effective way to gain a better understanding of the features of the S-OIV genome and evolutionary processes based on the codon usage pattern. It is useful to trace influenza viral origins and cross-species virus transmission.
頁(從 - 到)477-486
期刊Journal of Microbiology, Immunology and Infection
出版狀態已發佈 - 8月 1 2016

ASJC Scopus subject areas

  • 免疫學和過敏
  • 一般免疫學和微生物學
  • 微生物學(醫學)
  • 傳染性疾病


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