Fig. 1

The jpHMM-derived mosaic structure and confirmation by sub-region phylogenetic trees. a The jpHMM-derived mosaic structure. The predicted genotype recombination is represented in the outer ring. Posterior probabilities of the genotypes at each sequence position were calculated using jpHMM and are plotted in the second inner ring. P, C, S, and X indicate polymerase, core, surface, and X genes. b ML (GTR + I + G4) phylogenetic tree of regions derived from major parent (1–1898 and 2526–3215 of the strain). c ML (GTR + I + G4) phylogenetic tree of the region spanning 1899–2295 of the strain. d ML (GTR + I + G4) phylogenetic tree of the region spanning 2296–2525 of the strain. Phylogenetic trees were constructed using the PhyML 3.0 implemented in RDP4. The reliability of the phylogenetic tree analysis was assessed by bootstrap resampling with 1000 replicates. Genotypes and GenBank accession numbers are indicated. Values at the nodes indicate the bootstrap numbers by which the cluster was supported. Branch lengths are drawn to scale