Recombination between CyHV-3 lineages. An alignment of the 11 CyHV-3 genomes listed in Table 1 was analysed using the RDP4 software. Three potential recombination events were identified for strains GZ11/GZ11-SC (illustrated by A–I, respectively). The left part illustrates the results of RDP analyses (A, D and G). The right part presents phylogenetic analyses based on the full-length genome (excluding one of the terminal direct repeats) excluding the region of recombination (B, E and H) or based on the recombination region only (C, F and I) using UPGMA in MEGA6 with 1000 replicates. Values on internal branches refer to the percentage of bootstrap replicates in which the branch was found; only values greater than 50% are shown. The scales illustrate the number of substitutions per nucleotide. The color code used is described at the top.