title: Computational model for analyzing the evolutionary patterns of the neuraminidase gene of influenza A/H1N1.
abstract: In this study, we performed computer simulations to evaluate the changes of selection potentials of codons in influenza A/H1N1 from 1999 to 2009. We artificially generated the sequences by using the transition matrices of positively selected codons over time, and their similarities against the database of influenzavirus A genus were determined by BLAST search. This is the first approach to predict the evolutionary direction of influenza A virus (H1N1) by simulating the codon substitutions over time. We observed that the BLAST results showed the high similarities with pandemic influenza A/H1N1 in 2009, suggesting that the classical human-origin influenza A/H1N1 isolated before 2009 might contain some selection potentials of swine-origin viruses. Computer simulations using the time series codon substitution patterns resulted dramatic changes of BLAST results in influenza A/H1N1, providing a possibility of developing a method for predicting the viral evolution in silico.
authors.affiliation: Supercomputing Center, Korea Institute of Science and Technology Information, 245 Daehangno, Yuseong-Gu, Daejon 305-806, Republic of Korea.
authors.forename: Insung
authors.initials: I
authors.lastname: Ahn
authors.forename: Hyeon Seok
authors.initials: HS
authors.lastname: Son
mesh_terms: D000818:Animals; D001483:Base Sequence; D001717:Birds; D003062:Codon; D003198:Computer Simulation; D030541:Databases, Genetic; D019143:Evolution, Molecular; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype / Q000235:genetics*; D008957:Models, Genetic; D009439:Neuraminidase / Q000235:genetics*; D009976:Orthomyxoviridae Infections / Q000235:genetics*; D013552:Swine; D014764:Viral Proteins / Q000235:genetics*
chemical_list: D003062:Codon; D014764:Viral Proteins; D009439:Neuraminidase