Phylogenetic trees of H1N1 influenza viruses. ML phylogenies reconstructed from (A) HA gene; (B) NA gene; (C) PA gene. Human lineage is showed in red; while swine and avian are characterized in green and blue, respectively. Only the topological supports for major lineage or sublineages and reassortant viruses are showed and summarized from 1,000 ML bootstrap replicates. Transmissions among swine, avian and human viruses between 1988 and 1992 are highlighted in blue. The closest related swine viruses of 2009 H1N1 viruses are highlighted in red. Phylogenetic trees for five other gene segments can be found in Additional file 1.