RFLP mapping of the whole genome of ten viral isolates representative of different biological groups of potato virus Y

The importance of potato has increased dramatically in Indonesia over the last three decades. During this period, ‘Granola’, a potato cultivar originally from Germany, has become the most common cultivar for fresh consumption in Indonesia. In August 2014, a survey was conducted in Sulawesi, where potato fields cultivated with Granola and its selection, ‘Super John’, were sampled for Potato virus Y (PVY) presence. PVY was found in Sulawesi for the first time. Samples determined to be positive for PVY were subsequently typed to strain using reverse-transcription polymerase chain reaction assays. All PVY isolates sampled were identified as PVYNTN recombinants, with three recombination junctions in P3, VPg, and CP regions of the genome. Three local PVY isolates were subjected to whole-genome sequencing and subsequent sequence analysis. The whole genomes of the Indonesian PVYNTN isolates I-6, I-16, and I-17 were found to be closely related to the European PVYNTN-A. This recombinant type was shown previously to cause potato tuber necrotic ringspot disease (PTNRD) in susceptible potato cultivars. The dependence of potato farmers on mostly a single cultivar, Granola, may have given a competitive advantage to PVYNTN over other PVY strains, resulting in the predominance of the PVYNTN recombinant. The dominance of PVYNTN in Sulawesi, and possibly in Indonesia as a whole, represents a potential risk to any newly introduced potato cultivar to the country, especially cultivars susceptible to PTNRD.

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Genetic Diversity of the Ordinary Strain of Potato virus Y (PVY) and Origin of Recombinant PVY Strains

Phytopathology ◽

10.1094/phyto-10-10-0284 ◽

2011 ◽

Vol 101 (7) ◽

pp. 778-785 ◽

Cited By ~ 73

Author(s):

Alexander V. Karasev ◽

Xiaojun Hu ◽

Celeste J. Brown ◽

Camille Kerlan ◽

Olga V. Nikolaeva ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Tree ◽

Potato Virus ◽

Potato Virus Y ◽

Molecular Study ◽

The United States ◽

Whole Genome ◽

Whole Genome Analysis ◽

Severe Stunting ◽

Ordinary Strain

The ordinary strain of Potato virus Y (PVY), PVYO, causes mild mosaic in tobacco and induces necrosis and severe stunting in potato cultivars carrying the Ny gene. A novel substrain of PVYO was recently reported, PVYO-O5, which is spreading in the United States and is distinguished from other PVYO isolates serologically (i.e., reacting to the otherwise PVYN-specific monoclonal antibody 1F5). To characterize this new PVYO-O5 subgroup and address possible reasons for its continued spread, we conducted a molecular study of PVYO and PVYO-O5 isolates from a North American collection of PVY through whole-genome sequencing and phylogenetic analysis. In all, 44 PVYO isolates were sequenced, including 31 from the previously defined PVYO-O5 group, and subjected to whole-genome analysis. PVYO-O5 isolates formed a separate lineage within the PVYO genome cluster in the whole-genome phylogenetic tree and represented a novel evolutionary lineage of PVY from potato. On the other hand, the PVYO sequences separated into at least two distinct lineages on the whole-genome phylogenetic tree. To shed light on the origin of the three most common PVY recombinants, a more detailed phylogenetic analysis of a sequence fragment, nucleotides 2,406 to 5,821, that is present in all recombinant and nonrecombinant PVYO genomes was conducted. The analysis revealed that PVYN:O and PVYN-Wi recombinants acquired their PVYO segments from two separate PVYO lineages, whereas the PVYNTN recombinant acquired its PVYO segment from the same lineage as PVYN:O. These data suggest that PVYN:O and PVYN-Wi recombinants originated from two separate recombination events involving two different PVYO parental genomes, whereas the PVYNTN recombinants likely originated from the PVYN:O genome via additional recombination events.

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Occurrence of Diverse Recombinant Strains of Potato virus Y Circulating in Potato Fields in Egypt

Plant Disease ◽

10.1094/pdis-02-17-0275-re ◽

2017 ◽

Vol 101 (8) ◽

pp. 1463-1469 ◽

Cited By ~ 10

Author(s):

Esraa A. Elwan ◽

Engy E. Abdel Aleem ◽

Faiza A. Fattouh ◽

Kelsie J. Green ◽

Lisa T. Tran ◽

...

Keyword(s):

Potato Tuber ◽

Potato Virus ◽

Potato Virus Y ◽

Molecular Properties ◽

Whole Genome ◽

The Novel ◽

Limited Information ◽

Genome Sequences ◽

Recombinant Strains ◽

Virus Strains

Potato is one of the staple crops in Egypt, grown under irrigation almost continuously year-round. Potato virus Y (PVY) has been reported as one of the main viruses affecting potatoes in Egypt, but limited information is available on PVY strains circulating in potato fields in the country. From 2014 to 2016, virus surveys were conducted in several potato-growing governorates of Egypt, and PVY-positive samples were found to represent at least five distinct recombinant PVY strains, including PVYNTN and PVYN-Wi. Whole genome sequences were determined for four isolates representing strains PVY-SYR-III (Egypt7), PVY-261-4 (Egypt11), PVYNTNa (Egypt35), and a novel recombinant named Egypt24 that combined molecular properties of strains PVY-261-4 and PVY-Wilga156var. At least three recombinants found in Egypt in potato were previously found associated with potato tuber necrotic ringspot disease (PTNRD). The identification of multiple recombinant types of PVY in potato in Egypt, including the novel recombinant Egypt24, suggests a wide presence of PTNRD-inducing virus strains in the country.

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Identification and Molecular Characterization of Recombinant Potato Virus Y (PVY) in Potato from South Korea, PVYNTN Strain

Plant Disease ◽

10.1094/pdis-05-18-0715-re ◽

2019 ◽

Vol 103 (1) ◽

pp. 137-142 ◽

Cited By ~ 3

Author(s):

Mohamad Chikh-Ali ◽

Mariana Rodriguez-Rodriguez ◽

Kelsie J. Green ◽

Dong-Jun Kim ◽

Sang-Min Chung ◽

...

Keyword(s):

South Korea ◽

Whole Genome Sequencing ◽

Molecular Characterization ◽

Genome Sequencing ◽

Potato Virus ◽

Potato Virus Y ◽

Potato Production ◽

Whole Genome ◽

Rt Pcr

Potato is an important source of food in South Korea, and viruses represent a significant threat to sustainable and profitable potato production. However, information about viruses affecting the potato crop in South Korea is limited. In 2017, potato plants of five cultivars exhibiting foliar mosaic, crinkling, and mottle were collected in two seed potato production areas, in Gangwon-do and Jeollabuk-do Provinces, and subjected to virus testing and characterization. Potato virus Y (PVY) was found associated with mosaic symptoms, and samples were characterized using reverse transcription polymerase chain reaction (RT-PCR) and whole genome sequencing. All analyzed PVY-positive samples were found to represent the same recombinant PVY strain: PVYNTN. Three PVY isolates were subjected to whole genome sequencing using overlapping RT-PCR fragments and Sanger methodology, and all three were confirmed to represent strain PVYNTNa after a recombination analysis of the complete genomes. In phylogenetic analysis, the three South Korean isolates were placed most closely to several PVYNTNa isolates reported from Japan and Vietnam, suggesting a common source of infection. This is the first report and complete molecular characterization of a PVYNTN strain present in the country, and because this strain induces tuber necrotic ringspot disease in susceptible cultivars of potato, appropriate management tools need to be implemented to mitigate potential tuber quality losses.

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Whole genome characterization of Potato virus Y isolates collected in the western USA and their comparison to isolates from Europe and Canada

Archives of Virology ◽

10.1007/s00705-005-0707-6 ◽

2006 ◽

Vol 151 (6) ◽

pp. 1055-1074 ◽

Cited By ~ 87

Author(s):

J. H. Lorenzen ◽

T. Meacham ◽

P. H. Berger ◽

P. J. Shiel ◽

J. M. Crosslin ◽

...

Keyword(s):

Potato Virus ◽

Potato Virus Y ◽

Whole Genome ◽

Genome Characterization ◽

Western Usa

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Sequence characteristics of potato virus Y recombinants

Journal of General Virology ◽

10.1099/vir.0.014142-0 ◽

2009 ◽

Vol 90 (12) ◽

pp. 3033-3041 ◽

Cited By ~ 45

Author(s):

Xiaojun Hu ◽

Alexander V. Karasev ◽

Celeste J. Brown ◽

Jim H. Lorenzen

Keyword(s):

Secondary Structure ◽

Potato Virus ◽

Plant Pathogens ◽

Potato Virus Y ◽

Rna Virus ◽

Template Switching ◽

Whole Genome ◽

Evolutionary Mechanisms ◽

Stem Loop ◽

Two Factors

Potato virus Y (PVY) is one of the most economically important plant pathogens. The PVY genome has a high degree of genetic variability and is also subject to recombination. New recombinants have been reported in many countries since the 1980s, but the origin of these recombinant strains and the physical and evolutionary mechanisms driving their emergence are not clear at the moment. The replicase-mediated template-switching model is considered the most likely mechanism for forming new RNA virus recombinants. Two factors, RNA secondary structure (especially stem–loop structures) and AU-rich regions, have been reported to affect recombination in this model. In this study, we investigated the influence of these two factors on PVY recombination from two perspectives: their distribution along the whole genome and differences between regions flanking the recombination junctions (RJs). Based on their distributions, only a few identified RJs in PVY genomes were located in lower negative FORS-D, i.e. having greater secondary-structure potential and higher AU-content regions, but most RJs had more negative FORS-D values upstream and/or higher AU content downstream. Our whole-genome analyses showed that RNA secondary structures and/or AU-rich regions at some sites may have affected PVY recombination, but in general they were not the main forces driving PVY recombination.

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