Fig 1. Maximum likelihood relationship phylogeny obtained from alignment of 5,040, 2,083 and 5,486 amplicon sequence variants of methyl transferase (MT), RNA dependent RNA polymerase (RdRp) and coat protein (CP) gene segments on PNRSV RNA1, RNA2 and RNA3 respectively.

The alignments were generated using Muscle version 3.8.31 and the phylogenetic trees constructed with RAxML version 8.0.19 using GTRGAMMA model with 1000 bootstrap replicates. The trees were visualized in FigTree version 1.4.2 with branches having less than 90% bootstrap support collapsed and are indicated by the black circles. Sequence variant labels were removed for ease of presentation and major variant groups colour coded with phylo-group II on RNA3 (shown in green colour), which had the largest number of variants, collapsed for ease of presentation. The number of samples and number of sequence variants forming each major group of each RNA are shown.