Sequence analysis of isolates of the Canadian Plum pox virus, and comparisons to isolates from Europe and the United States

Abstract

The complete genome sequences of seven isolates of Canadian Plum pox virus (PPV) obtained from infected peach, plum, and flowering almond have been determined. All sequences were most similar to PPV-D strain. Comparison of the sequences of nucleotides and amino acids of the seven isolates indicate that Canadian isolates fall into two main subgroups, I and II, with subgroup I isolates being most closely related to European PPV-D isolates. All isolates of subgroup I (two) were from plum, whereas for isolates of subgroup II, four were obtained from peach and one isolate from flowering almond. Comparisons of complete PPV-D isolates from Canada, Europe, and the United States show that these fall into distinct groupings based on geographic origin. Alignments of Canadian, European, and United States PPV-D isolates revealed that there were only 13 positions in the PPV polyprotein where a variant amino acid exists in more than one isolate. A diagnostic RsaI site, often used to assign strain-D status to an isolate, was found to be absent in several Canadian PPV-D isolates, suggesting that caution should be exerted when employing this restriction site polymorphism for strain identification

Keywords:

• Plum pox virus
• sharka
• peach
• plum
• full genome sequence
• potyvirus