Detecting Transmission And Reassortment Events For Influenza A Viruses With Genotype Profile Method

Background and objectives:Influenza A virus had caused four global pandemics, in1918,1957,1968and2009, whichthreatened human health greatly. The reason that changed virus antigenicity periodically was thatthe evolutionary events such as the transmission of avian viruses or a reassortment between humanand avian viruses renewed the antigenicity constantly. At the end of2008or the beginning of2009,a novel swine reassortant was transmitted to humans, and a global pandemic broke out in Mexicoand USA in April2009. Researchers confirmed that the reassorted virus consisted of six genesegments that emerged from triple-reassortant viruses circulating in North American swine and twogene segments from Eurasian avian-like swine H1N1viruses. This pandemic implied theimportance of the researching on the genome reassortment of influenza A viruses again. Based onthis background, we studied the mechanism of virus genomic evolution with the Bioinformaticsand statistical genetics tools, in order to provide the theoretical and the technical supports for thecenters for disease control (CDC).Material and methods:We downloaded the genotype information for all influenza A viruses of humans, swine andavian species from FluGenome database (http://www.FluGenome.org) on Sep10th,2010. Based onthe epidemiological knowledge for the influenza A virus, we constructed the genotype profiles andproposed a reassortment detecting method based on our genotype profiles. Furthermore, wedeveloped a software tool called IVEE version2.0(Tool for Influenza A Virus Evolutionary Events,IVEE) that implemented the genotype profile method on Windows platform with C++Builderdevelopment tools.Results:In our genotype profiles, there are four basic genotypes for human influenza A viruses:[A, A,A/B,1B, A,1A, B,1A] and [C, D, E,1A, A,1F, F,1A] for subtype H1N1,[A, E, B,2A, A,2A, B,1A] for H2N2and [A, D, B,3A, A,2A, B,1A] for H3N2as well as three basic genotypes forswine influenza A viruses: Classic swine [B, A, C,1A, A,1B, A,1A]，the avian-like [F, G, I,4, F,6, F,1E] and the novel triple reassortant [C, D, E,3A, A,2A, A,1A]. Avian influenza A viruses hadtwo basic genotypes:[C, F, E/H,4, H,6, E,1D/2B] for waterfowl and [K/G, G, D/E,4, F,6, F,1E/1F/2A] for domestic poultry. Using the genotype profile method, we further found that most ofthe viruses that had rare genotypes were transmitting viruses or reassortants that emerged fromcombinations of basic genotypes, which was confirmed by many previous reports. An applicationcalled IVEE2.0that implementing the genotype profile method was available for all academicusers from the website http://snptransformer.sourceforge.net.ConclusionsThe genotype profile method and the application IVEE2.0could be used to detect virustransmission and reassortment events and were useful for the basic research on the mechanism ofthe viral evolution or influenza A virus surveillance in practice.