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

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)477-486
Number of pages10
JournalJournal of Microbiology, Immunology and Infection
Volume49
Issue number4
DOIs
Publication statusPublished - Aug 1 2016
Externally publishedYes

Fingerprint

H1N1 Subtype Influenza A Virus
Hemagglutinins
Codon
Genes
Human Influenza
Virus Attachment
Amino Acids
Viral Genome
Base Composition
Phylogeny
Cross Infection
Neutralizing Antibodies
Glycoproteins
Swine
Genome
Viruses

Keywords

  • antigenic sites
  • phylogenetic tree
  • S-OIV
  • synonymous codon usage

ASJC Scopus subject areas

  • Immunology and Allergy
  • Immunology and Microbiology(all)
  • Microbiology (medical)
  • Infectious Diseases

Cite this

Analysis of codon usage preference in hemagglutinin genes of the swine-origin influenza A (H1N1) virus. / Wang, Sheng Fan; Su, Ming Wei; Tseng, Sung Pin; Li, Ming Chun; Tsao, Ching Han; Huang, Szu Wei; Chu, Woei Chyn; Liu, Wu Tse; Chen, Yi Ming Arthur; Huang, Jason C.

In: Journal of Microbiology, Immunology and Infection, Vol. 49, No. 4, 01.08.2016, p. 477-486.

Research output: Contribution to journalArticle

Wang, Sheng Fan ; Su, Ming Wei ; Tseng, Sung Pin ; Li, Ming Chun ; Tsao, Ching Han ; Huang, Szu Wei ; Chu, Woei Chyn ; Liu, Wu Tse ; Chen, Yi Ming Arthur ; Huang, Jason C. / Analysis of codon usage preference in hemagglutinin genes of the swine-origin influenza A (H1N1) virus. In: Journal of Microbiology, Immunology and Infection. 2016 ; Vol. 49, No. 4. pp. 477-486.
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AU - Tsao, Ching Han

AU - Huang, Szu Wei

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