title: Genome Sequence Analysis of New Isolates of the Winona Strain of Plum pox virus and the First Definitive Evidence of Intrastrain Recombination Events.
abstract: Plum pox virus (PPV) is genetically diverse with nine different strains identified. Mutations, indel events, and interstrain recombination events are known to contribute to the genetic diversity of PPV. This is the first report of intrastrain recombination events that contribute to PPV's genetic diversity. Fourteen isolates of the PPV strain Winona (W) were analyzed including nine new strain W isolates sequenced completely in this study. Isolates of other strains of PPV with more than one isolate with the complete genome sequence available in GenBank were included also in this study for comparison and analysis. Five intrastrain recombination events were detected among the PPV W isolates, one among PPV C strain isolates, and one among PPV M strain isolates. Four (29%) of the PPV W isolates analyzed are recombinants; one of which (P2-1) is a mosaic, with three recombination events identified. A new interstrain recombinant event was identified between a strain M isolate and a strain Rec isolate, a known recombinant. In silico recombination studies and pairwise distance analyses of PPV strain D isolates indicate that a threshold of genetic diversity exists for the detectability of recombination events, in the range of approximately 0.78×10(-2) to 1.33×10(-2) mean pairwise distance. RDP4 analyses indicate that in the case of PPV Rec isolates there may be a recombinant breakpoint distinct from the obvious transition point of strain sequences. Evidence was obtained that indicates that the frequency of PPV recombination is underestimated, which may be true for other RNA viruses where low genetic diversity exists.
authors.affiliation: First, second, and third authors: Centre for Plant Health-Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, British Columbia, V8L 1H3, Canada; and fourth and fifth authors: Department of Virology, Biology Faculty, Lomonosov Moscow State University, Leninskie Gory MSU 1/12, Moscow, 119991, Russia.
authors.forename: Delano
authors.initials: D
authors.lastname: James
authors.affiliation: First, second, and third authors: Centre for Plant Health-Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, British Columbia, V8L 1H3, Canada; and fourth and fifth authors: Department of Virology, Biology Faculty, Lomonosov Moscow State University, Leninskie Gory MSU 1/12, Moscow, 119991, Russia.
authors.forename: Dan
authors.initials: D
authors.lastname: Sanderson
authors.affiliation: First, second, and third authors: Centre for Plant Health-Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, British Columbia, V8L 1H3, Canada; and fourth and fifth authors: Department of Virology, Biology Faculty, Lomonosov Moscow State University, Leninskie Gory MSU 1/12, Moscow, 119991, Russia.
authors.forename: Aniko
authors.initials: A
authors.lastname: Varga
authors.affiliation: First, second, and third authors: Centre for Plant Health-Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, British Columbia, V8L 1H3, Canada; and fourth and fifth authors: Department of Virology, Biology Faculty, Lomonosov Moscow State University, Leninskie Gory MSU 1/12, Moscow, 119991, Russia.
authors.forename: Anna
authors.initials: A
authors.lastname: Sheveleva
authors.affiliation: First, second, and third authors: Centre for Plant Health-Sidney Laboratory, Canadian Food Inspection Agency, 8801 East Saanich Road, North Saanich, British Columbia, V8L 1H3, Canada; and fourth and fifth authors: Department of Virology, Biology Faculty, Lomonosov Moscow State University, Leninskie Gory MSU 1/12, Moscow, 119991, Russia.
authors.forename: Sergei
authors.initials: S
authors.lastname: Chirkov
mesh_terms: D001483:Base Sequence; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology*; D017801:Plum Pox Virus / Q000235:genetics* / Q000302:isolation & purification; D000068242:Prunus domestica / Q000821:virology*; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D012367:RNA, Viral