Phylogenetic structure of cDNA clones.

<p>A) Phylogenetic structure of the cDNA clone population (tree reconstructed using MrBayes). All viable clones are labelled as either infectious (fully functional) or replicating (capable of replicating in PK-15 cells, but do not produce infectious viral particles). Unlabelled leafs were non-functional. Different haplotypes are shown as coloured clades. B) Haplotype mutation frequency distribution. The plot shows the frequency of SNVs that define the major haplotypes from the NGS deep sequencing. The colour coding corresponds to the respective haplotypes in Fig 2.