plosone-phylo
pone.0017293.g001.png
Genome analysis.
We apply our method to analyze 59 influenza viruses based on their whole genomes. The natural vector and the hierarchical clustering methods are used to reconstruct the phylogenetic tree for nucleotide sequences of the whole genome sequences of selected influenza viruses. The selected viruses are chosen to be representative from among all available relevant sequences in GenBank. Sequences have both high and low divergence to avoid biasing the distribution of branch lengths. Strains are representative of the major gene lineages from different hosts. The robustness of individual nodes of the tree is assessed using a bootstrap resampling analysis with 1000 replicates shown in Supporting Information S1. From this figure, we can clearly see that new influenza A (H1N1) viruses originate from North American triple-reassortant swine virus and Eurasian classical swine virus lineage. We note that (A/swine/Nakhon pathom/NIAH586-1/2005(H3N2)), (A/duck/Nanchang/4-165/2000(H4N6)) and American avian (A/blue-winged teal/Ohio/1864/2006(H3N8)) are not clustered with A (H1N1) genomes from the same geographical regions respectively. This result is caused by the different structures of these genomes and the traditional A (H1N1) subtypes. In addition, we check the distance matrix of these genomes obtained by natural vectors and the result shows that (A/duck/Nanchang/4-165/2000(H4N6)) is the closest to A/duck/NY/185502/2002(H5N2). Meanwhile, A/blue-winged teal/Ohio/1864/2006(H3N8) is the closest to A/chicken/Korea/ES/03(H5N1) and A/egret/Hong Kong/757.2/2003(H5N1) respectively, which means that A/blue-winged teal/Ohio/1864/2006(H3N8) is evolutionary related with H5N1 avian virus outbreak in Asian countries from 2003 to 2006. As for A/swine/Nakhon pathom/NIAH586-1/2005(H3N2), it is the closest to A/swine/Tianjin/01/2004(H1N1) and then to A/swine/Ontario/55383/04(H1N2) with and A/swine/OH/511445/2007(H1N1). This H3N2 is the closest related to Eurasian swine even if it is clustered within American swine clade (The large distance matrix data is not shown and available upon request).
pone.0017293.g001.png
Genome analysis.
We apply our method to analyze 59 influenza viruses based on their whole genomes. The natural vector and the hierarchical clustering methods are used to reconstruct the phylogenetic tree for nucleotide sequences of the whole genome sequences of selected influenza viruses. The selected viruses are chosen to be representative from among all available relevant sequences in GenBank. Sequences have both high and low divergence to avoid biasing the distribution of branch lengths. Strains are representative of the major gene lineages from different hosts. The robustness of individual nodes of the tree is assessed using a bootstrap resampling analysis with 1000 replicates shown in Supporting Information S1. From this figure, we can clearly see that new influenza A (H1N1) viruses originate from North American triple-reassortant swine virus and Eurasian classical swine virus lineage. We note that (A/swine/Nakhon pathom/NIAH586-1/2005(H3N2)), (A/duck/Nanchang/4-165/2000(H4N6)) and American avian (A/blue-winged teal/Ohio/1864/2006(H3N8)) are not clustered with A (H1N1) genomes from the same geographical regions respectively. This result is caused by the different structures of these genomes and the traditional A (H1N1) subtypes. In addition, we check the distance matrix of these genomes obtained by natural vectors and the result shows that (A/duck/Nanchang/4-165/2000(H4N6)) is the closest to A/duck/NY/185502/2002(H5N2). Meanwhile, A/blue-winged teal/Ohio/1864/2006(H3N8) is the closest to A/chicken/Korea/ES/03(H5N1) and A/egret/Hong Kong/757.2/2003(H5N1) respectively, which means that A/blue-winged teal/Ohio/1864/2006(H3N8) is evolutionary related with H5N1 avian virus outbreak in Asian countries from 2003 to 2006. As for A/swine/Nakhon pathom/NIAH586-1/2005(H3N2), it is the closest to A/swine/Tianjin/01/2004(H1N1) and then to A/swine/Ontario/55383/04(H1N2) with and A/swine/OH/511445/2007(H1N1). This H3N2 is the closest related to Eurasian swine even if it is clustered within American swine clade (The large distance matrix data is not shown and available upon request).