title: Analysis of codon usage preference in hemagglutinin genes of the swine-origin influenza A (H1N1) virus.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan; AIDS Prevention and Research Center, National Yang-Ming University, Taipei, Taiwan; Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.
authors.forename: Sheng-Fan
authors.initials: SF
authors.lastname: Wang
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Institute of Biomedical Engineering, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Ming-Wei
authors.initials: MW
authors.lastname: Su
authors.affiliation: Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan.
authors.forename: Sung-Pin
authors.initials: SP
authors.lastname: Tseng
authors.affiliation: Department of Pediatrics, Taipei City Hospital, Yang-Ming Branch, Taipei, Taiwan.
authors.forename: Ming-Chun
authors.initials: MC
authors.lastname: Li
authors.affiliation: Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Ching-Han
authors.initials: CH
authors.lastname: Tsao
authors.affiliation: Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Szu-Wei
authors.initials: SW
authors.lastname: Huang
authors.affiliation: Institute of Biomedical Engineering, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Woei-Chyn
authors.initials: WC
authors.lastname: Chu
authors.affiliation: Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan.
authors.forename: Wu-Tse
authors.initials: WT
authors.lastname: Liu
authors.affiliation: Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Microbiology, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan. Electronic address: arthur@kmu.edu.tw.
authors.forename: Yi-Ming Arthur
authors.initials: YM
authors.lastname: Chen
authors.affiliation: AIDS Prevention and Research Center, National Yang-Ming University, Taipei, Taiwan; Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan. Electronic address: jchuang2@ym.edu.tw.
authors.forename: Jason C
authors.initials: JC
authors.lastname: Huang
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D000818:Animals; D001482:Base Composition / Q000235:genetics; D003062:Codon / Q000235:genetics; D016679:Genome, Viral / Q000235:genetics; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics*; D058507:Host Specificity / Q000235:genetics*; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics*; D007251:Influenza, Human / Q000821:virology*; D010802:Phylogeny; D013552:Swine; D013553:Swine Diseases / Q000821:virology; D053585:Virus Attachment
chemical_list: D003062:Codon; D019267:Hemagglutinin Glycoproteins, Influenza Virus
keywords: S-OIV; antigenic sites; phylogenetic tree; synonymous codon usage