Characterization of a Novel Far-Eastern Potato Virus Y Isolates

Potato virus Y (PVY) is one of the most severe viruses affecting the production of potato (Solanum tuberosum) in the world. This study presents a detailed molecular analysis using nextgeneration sequencing (NGS), IC-RT-qPCR and RT-PCR on the PVY isolates infecting seed-tubers and foliage of potato plants cv. Diacol-Capiro in La Union (Antioquia, Colombia). Analysis of incidence by IC-RT-qPCR in 15 random leaf samples of three cultivation plots and fifteen sprouting tuber eye-buds reveal infection levels between 13.4 and 80%; a higher incidence of 86.7% was observed in seed-tuber samples with threshold cycle (Ct) values as low as 24.3. Genome assembly from a bulk of foliage samples resulted in a consensus PVY genome (PVY_LaUnionF) of 9,702 nt and 399 polymorphic sites within the polyprotein ORF; while the assembled genome from sprouts of tubers has 9,704 nt (PVY_LaUnionT) and contained only six polymorphic nucleotide sites. Phylogenetic analysis demonstrates that the PVY isolates from leaf samples are in the recombinant PVYNTN group (sequence identity >99%); while those from tuber sprouts are in the PVYN/NTN group with identities above 95%. Sanger sequencing of viral capsid suggests the presence of a third variant related to PVYO, a prevalent strain reported in potato fields worldwide.

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The Recombinant Potato virus Y (PVY) Strain, PVYNTN, Identified in Potato Fields in Victoria, Southeastern Australia

Plant Disease ◽

10.1094/pdis-05-20-0961-sc ◽

2020 ◽

Vol 104 (12) ◽

pp. 3110-3114

Author(s):

Mariana Rodriguez-Rodriguez ◽

Mohamad Chikh-Ali ◽

Steven B. Johnson ◽

Stewart M. Gray ◽

Nellie Malseed ◽

...

Keyword(s):

Potato Virus ◽

Potato Virus Y ◽

Strain Typing ◽

Rt Pcr ◽

Growing Seasons ◽

Fta Cards ◽

Southeastern Australia ◽

Whole Genomes ◽

Pcr Assays

Potato virus Y (PVY) is one of the main viruses affecting potato in Australia. However, molecular characterization of PVY isolates circulating in potato in different states of Australia has not yet been thoroughly conducted. Only nonrecombinant isolates of three biological PVY strains collected from potato were reported previously from Western Australia and one from Queensland. Here, PVY isolates collected from seed potato originating in Victoria, Australia, and printed on FTA cards, were subjected to strain typing by RT-PCR, with three isolates subjected to whole genome sequencing. All the 59 PVY isolates detected during two growing seasons were identified to be recombinants based on two RT-PCR assays. No nonrecombinant PVY isolates were identified. All the RT-PCR typed isolates belonged to the PVYNTN strain. Sequence analysis of the whole genomes of three isolates suggested a single introduction of the PVYNTN strain to Australia but provided no clues as to where this introduction originated. Given the association of the PVYNTN strain with potato tuber damage, growers in Australia should implement appropriate strategies to manage PVYNTN in potato.

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Occurrence and Molecular Characterization of Recombinant Potato virus YNTN Isolates from Sulawesi, Indonesia

Plant Disease ◽

10.1094/pdis-07-15-0817-re ◽

2016 ◽

Vol 100 (2) ◽

pp. 269-275 ◽

Cited By ~ 11

Author(s):

Mohamad Chikh-Ali ◽

Nilsa A. Bosque-Pérez ◽

Dalton Vander Pol ◽

Dantje Sembel ◽

Alexander V. Karasev

Keyword(s):

Potato Virus ◽

Potato Virus Y ◽

Potato Cultivar ◽

Whole Genome ◽

Chain Reaction ◽

Recombinant Type ◽

Whole Genomes ◽

Polymerase Chain ◽

First Time

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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