title: Codon volatility of hemagglutinin genes of H5N1 avian influenza viruses from different clades.
abstract: Codon volatility is a method recently developed to estimate selective pressures on proteins on the basis of their synonymous codon usage. Volatility of a codon was defined as the fraction of single nucleotide substitutions that would be nonsynonymous. Higher volatility may indicate that the gene has been under more positive selection in the recent past. We analyzed volatility of hemagglutinin genes of H5N1 viruses in the recent outbreaks and observed differences in the volatility among viruses of different clades. The codon volatility of subclade 2.1 viruses from Indonesia was the lowest among all H5N1 clades and subclades. Time series analyses since the beginning of the epidemic in 2004 showed that codon volatility of subclade 2.1 has gradually decreased, while those of other major clades have been increasing. This may reflect differences in the recent evolution of these viruses.
authors.affiliation: Department of Microbiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, 2 Prannok Road, Bangkok Noi, Bangkok, 10700, Thailand. sipaw@mahidol.ac.th
authors.forename: Prasert
authors.initials: P
authors.lastname: Auewarakul
authors.forename: Sunisa
authors.initials: S
authors.lastname: Chatsurachai
authors.forename: Alita
authors.initials: A
authors.lastname: Kongchanagul
authors.forename: Pumaree
authors.initials: P
authors.lastname: Kanrai
authors.forename: Sikarin
authors.initials: S
authors.lastname: Upala
authors.forename: Prapat
authors.initials: P
authors.lastname: Suriyaphol
authors.forename: Pilaipan
authors.initials: P
authors.lastname: Puthavathana
mesh_terms: D000818:Animals; D001717:Birds; D003062:Codon / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics*; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics* / Q000302:isolation & purification; D005585:Influenza in Birds / Q000453:epidemiology / Q000821:virology*; D012641:Selection, Genetic
chemical_list: D003062:Codon; D019267:Hemagglutinin Glycoproteins, Influenza Virus; C109963:hemagglutinin, avian influenza A virus