Fig 2. Median-joining haplotype network showing Prunus necrotic ringspot virus (PNRSV) intra-specific diversity of RNA1, RNA2 and RNA3 sequence variants in sample Q15.

Each of the blue, green and orange circles represents a PNRSV methyl transferase (MT), RNA dependent RNA polymerase (RdRp) and coat protein (CP) amplicon sequence variant of RNA1, RNA2 and RNA3 respectively. The yellow circles represent the largest sequence variants (variant made up of highest copy number of reads) of each phylo-group (labeled I, II or III) of RNA1, RNA2 and RNA3 present in sample Q15. The hatch mark indicates the number of mutations separating the haplotypes and the black circles (median vectors) are hypothetical missing intermediates connecting the haplotype groups. Multiple median vectors connecting phylo-groups were collapsed for ease of presentation.