Taxonomic relationships between distinct potato virus Y isolates based on detailed comparisons of the viral coat proteins and 3′-nontranslated regions

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Abstract
Detailed comparisons were made of the sequences of the coat protein (CP) cistrons and 3′-nontranslated regions (3′-NTR) of 21 (geographically) distinct isolates of potato virus Y (PVY) and a virus isolate initially described as pepper mottle virus (PepMoV). Multiple sequence alignments and phylogenetic relationships based on these alignments resulted into a subgrouping of virus isolates which largely corresponded with the historical strain differentiation based on biological criteria as host range, symptomatology and serology. Virus isolates belonging to the same subgroup shared a number of characteristic CP amino acid and 3′-NTR nucleotide residues indicating that, by using sequences from the 3′-terminal region of the potyvirus genome, a distinction could be made between different isolates of one virus species as well as between different virus species. RNA secondary structure analysis of the 3′-NTR of twelve PVY isolates revealed four major stem-loop structures of which, surprisingly, the loop sequences gave a similar clustering of isolates as resulting from the overall comparisons of CP and 3′-NTR sequences. This implies a biological significance of these structural elements.