Phylogenies of individual and concatenated genes were reconstructed after the removal of the five putative recombinant isolates and chimeric vaccine strain EU140955 (Figure 4 ). Consistent with Figure 1A and 1B, genotypes III -VII clustered together as a monophyletic group in all trees. All taxa were consistently affiliated with a single genotype and there were no long branches associated with any genotype. Two of the three original patterns of phylogenetic affiliation were retained following removal of recombinant sequences. The placement of genotypes based on HN and L was the same with or without recombinants; genotype I and II were sister groups to genotype III, IV, V, VI, and VII ( Figure 1A; Figure 4 ). All of the remaining trees presented a topology similar to that of the P gene-tree before recombinant removal, which placed genotype I with III-VII. It is noteworthy that in the absence of recombinant sequences, genotype II is never clustered with genotypes III-VII, as was seen with trees based on M and F in the presence of recombinant sequences ( Figure 1A ).