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Chirkov S, Sheveleva A, Ivanov P, Zakubanskiy A. Analysis of Genetic Diversity of Russian Sour Cherry Plum pox virus Isolates Provides Evidence of a New Strain. PLANT DISEASE 2018; 102:569-575. [PMID: 30673474 DOI: 10.1094/pdis-07-17-1104-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plum pox virus (PPV) exists as a complex of nine strains adapted to different Prunus hosts. Unusual PPV isolates that do not belong to the known cherry-adapted strains were discovered on sour cherry in Russia. Here, two complete genomes of isolates Tat-2 and Tat-4 were determined by sequencing on the Illumina HiSeq 2500 platform. Both were composed of 9,792 nucleotides, excluding the poly(A) tail, with the organization typical of PPV and had 99.4 and 99.7% identity between each other at the nucleotide and amino acid levels. The sequence identities between Tat-2/Tat-4 and known PPV strains ranged from 77.6 to 83.3% for genomic RNA and from 80.0 to 93.8% for polyprotein. Phylogenetic analysis placed Tat-2 and Tat-4 in a separate clade, distinct from the C and CR strains. Three more Tat-2/Tat-4-like isolates were detected in local cherry plantings using the newly developed, specific RT-PCR assay. Based on the phylogenetic analysis, sequence identities, and environmental distribution, Tat-2, Tat-4, and related isolates represent a new cherry-adapted PPV strain for which the name PPV-CV (Cherry Volga) is proposed.
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Affiliation(s)
- Sergei Chirkov
- Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Anna Sheveleva
- Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Peter Ivanov
- Lomonosov Moscow State University, 119234 Moscow, Russia
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James D, Sanderson D, Varga A, Sheveleva A, Chirkov S. Genome Sequence Analysis of New Isolates of the Winona Strain of Plum pox virus and the First Definitive Evidence of Intrastrain Recombination Events. PHYTOPATHOLOGY 2016; 106:407-416. [PMID: 26667187 DOI: 10.1094/phyto-09-15-0211-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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.
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Affiliation(s)
- Delano James
- 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
| | - Dan Sanderson
- 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
| | - Aniko Varga
- 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
| | - Anna Sheveleva
- 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
| | - Sergei Chirkov
- 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
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García JA, Glasa M, Cambra M, Candresse T. Plum pox virus and sharka: a model potyvirus and a major disease. MOLECULAR PLANT PATHOLOGY 2014; 15:226-41. [PMID: 24102673 PMCID: PMC6638681 DOI: 10.1111/mpp.12083] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
TAXONOMIC RELATIONSHIPS Plum pox virus (PPV) is a member of the genus Potyvirus in the family Potyviridae. PPV diversity is structured into at least eight monophyletic strains. GEOGRAPHICAL DISTRIBUTION First discovered in Bulgaria, PPV is nowadays present in most of continental Europe (with an endemic status in many central and southern European countries) and has progressively spread to many countries on other continents. GENOMIC STRUCTURE Typical of potyviruses, the PPV genome is a positive-sense single-stranded RNA (ssRNA), with a protein linked to its 5' end and a 3'-terminal poly A tail. It is encapsidated by a single type of capsid protein (CP) in flexuous rod particles and is translated into a large polyprotein which is proteolytically processed in at least 10 final products: P1, HCPro, P3, 6K1, CI, 6K2, VPg, NIapro, NIb and CP. In addition, P3N-PIPO is predicted to be produced by a translational frameshift. PATHOGENICITY FEATURES PPV causes sharka, the most damaging viral disease of stone fruit trees. It also infects wild and ornamental Prunus trees and has a large experimental host range in herbaceous species. PPV spreads over long distances by uncontrolled movement of plant material, and many species of aphid transmit the virus locally in a nonpersistent manner. SOURCES OF RESISTANCE A few natural sources of resistance to PPV have been found so far in Prunus species, which are being used in classical breeding programmes. Different genetic engineering approaches are being used to generate resistance to PPV, and a transgenic plum, 'HoneySweet', transformed with the viral CP gene, has demonstrated high resistance to PPV in field tests in several countries and has obtained regulatory approval in the USA.
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Affiliation(s)
- Juan Antonio García
- Departmento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049, Madrid, Spain
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Jarocka U, Wąsowicz M, Radecka H, Malinowski T, Michalczuk L, Radecki J. Impedimetric Immunosensor for Detection of Plum Pox Virus in Plant Extracts. ELECTROANAL 2011. [DOI: 10.1002/elan.201100152] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Maejima K, Himeno M, Komatsu K, Takinami Y, Hashimoto M, Takahashi S, Yamaji Y, Oshima K, Namba S. Molecular epidemiology of Plum pox virus in Japan. PHYTOPATHOLOGY 2011; 101:567-574. [PMID: 21198358 DOI: 10.1094/phyto-10-10-0280] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
For a molecular epidemiological study based on complete genome sequences, 37 Plum pox virus (PPV) isolates were collected from the Kanto region in Japan. Pair-wise analyses revealed that all 37 Japanese isolates belong to the PPV-D strain, with low genetic diversity (less than 0.8%). In phylogenetic analysis of the PPV-D strain based on complete nucleotide sequences, the relationships of the PPV-D strain were reconstructed with high resolution: at the global level, the American, Canadian, and Japanese isolates formed their own distinct monophyletic clusters, suggesting that the routes of viral entry into these countries were independent; at the local level, the actual transmission histories of PPV were precisely reconstructed with high bootstrap support. This is the first description of the molecular epidemiology of PPV based on complete genome sequences.
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Affiliation(s)
- Kensaku Maejima
- Department of Agricultural and Environmental Biology, University of Tokyo, Tokyo, Japan
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