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Title: Pepino mosaic virus genotype shift in North America and development of a loop-mediated isothermal amplification for rapid genotype identification

Author
item Ling, Kai-Shu
item Li, Rugang
item BLEDSOE, MICHAEL - Village Farms

Submitted to: Virology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/2/2013
Publication Date: 4/12/2013
Citation: Ling, K., Li, R., Bledsoe, M. 2013. Pepino mosaic virus genotype shift in North America and development of a loop-mediated isothermal amplification for rapid genotype identification. Virology Journal. 10:117.

Interpretive Summary: Tomato is the world’s second most important vegetable, and the U.S. is a leading tomato producing country. Greenhouse tomato production has increased significantly in recent years with nearly 40% of U.S. fresh tomato supplies produced from greenhouses. The unique growing conditions and intensive production practices can promote certain plant pathogens to spread quickly resulting in disease epidemics. In the last decade, Pepino mosaic virus (PepMV) has evolved from an emerging to endemic disease on greenhouse tomatoes in North America. Several distinct genotypes of PepMV have been identified, which share only about 80% nucleotide sequence identity. A simple and accurate detection of a specific genotype is important, as each genotype of PepMV causes different symptoms and must be managed by different strategies. In the present study, a simple and sensitive genotype-specific molecular detection method, combined with a collaborative surveillance system in North America, was developed and used to effectively monitor the field samples for their genetic diversity. Using this surveillance system, we detected a major genotype shift in North America since 2010. There was a strong indication that this genotype shift was induced from the use of contaminated tomato seed. Thorough understanding of a genetic diversity of PepMV will lead us to make an accurate disease prediction, and thus to recommend an effective strategy for disease management.

Technical Abstract: Pepino mosaic, once an emerging disease a decade ago, has become endemic on greenhouse tomatoes worldwide in recent years. Three distinct genotypes of Pepino mosaic virus (PepMV), including EU, US1 and CH2 have been recognized. Our earlier study conducted in 2006-2007 demonstrated a predominant EU genotype in Canada and United States. The objective of the present study was to monitor the dynamic of PepMV genetic composition and its current status in North America. Through yearly monitoring efforts in 2009-2012, we detected a dramatic shift in the prevalent genotype of PepMV from the genotype EU to CH2 in North America since early 2010, with another shift from CH2 to US1 occurring in Mexico only two years later. Through genetic diversity analysis using the coat protein gene, such genotype shifting of PepMV in North America was linked to the positive identification of similar sequence variants in two different commercial tomato seed sources used for scion and rootstock, respectively. To allow for a quick identification, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) system was developed and demonstrated to achieve a rapid identification for each of the three genotypes of PepMV, EU, US1 and CH2. Through systemic yearly monitoring and genetic diversity analysis, we identified a linkage between the field epidemic isolates and those from commercial tomato seed lots as the likely sources of initial PepMV inoculum that resulted in genetic shifting as observed on greenhouse tomatoes in North America. Application of the genotype-specific reverse transcription Loop-mediated isothermal amplification (RT-LAMP) system would allow growers to efficiently determine the genetic diversity of PepMV on their crops.