Computational model for analyzing the evolutionary patterns of the neuraminidase gene of influenza A/H1N1

Abstract

Inthisstudy,weperformedcomputersimulationstoevaluatethechangesofselectionpotentialsof codonsininfluenzaA/H1N1from1999to2009.Weartificiallygeneratedthesequencesbyusingthe transitionmatricesofpositivelyselectedcodonsovertime,andtheirsimilaritiesagainstthedatabase ofinfluenzavirusAgenusweredeterminedbyBLASTsearch.Thisisthefirstapproachtopredictthe evolutionarydirectionofinfluenzaAvirus(H1N1)bysimulatingthecodonsubstitutionsovertime.We observedthattheBLASTresultsshowedthehighsimilaritieswithpandemicinfluenzaA/H1N1in2009,suggestingthattheclassicalhuman-origininfluenzaA/H1N1isolatedbefore2009mightcontainsomeselectionpotentialsofswine-originviruses.ComputersimulationsusingthetimeseriescodonsubstitutionpatternsresulteddramaticchangesofBLASTresultsininfluenzaA/H1N1,providingapossibilityofdevelopingamethodforpredictingtheviralevolutioninsilico.