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ARS Home » Southeast Area » Charleston, South Carolina » Vegetable Research » Research » Publications at this Location » Publication #291817
Title: Pepino mosaic virus genotype shift in North America and rapid genotype identification using loop-mediated isothermal amplification

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

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/1/2013
Publication Date: 8/25/2013
Citation: Ling, K., Li, R., Bledsoe, M. 2013. Pepino mosaic virus genotype shift in North America and rapid genotype identification using loop-mediated isothermal amplification. Acta phytopathologica sinica 43 (suppl.). p. 402.

Interpretive Summary: N/A

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 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 during 2009-2012, we detected a dramatic shift in the prevalent genotype of PepMV from EU to CH2 in North America since early 2010 and an additional shift from CH2 to US1 in Mexico only 2 years later. We demonstrated that for detection of PepMV-infested commercial tomato seeds a previously developed real-time reverse transcription polymerase chain reaction (RT-PCR) was more sensitive than traditional enzyme-linked immunosorbent assay (ELISA). According to coat protein gene, PepMV variants with identical or similar genomic sequence were identified using RT-PCR from commercial tomato seed sources used for scion or rootstock. A reverse transcription loop-mediated isothermal amplification (RT-LAMP) system was developed and shown to achieve rapid genotype identification for the respective genotypes (EU, US1 and CH2). Through systemic monitoring and genetic diversity analysis, we demonstrated that PepMV genotype shift in North America was likely resulted from the introduction of contaminated tomato seed lots. Therefore, it is recommended that seed health test should be conducted using more sensitive RT-PCR or real-time RT-PCR to complement ELISA, and if necessary, using RT-LAMP to determine the specific genotype.