ARS | Publication request: Genetic diversity and phylogenetic analysis revealed Pepino Mosaic Virus in North-America has shifted to a more aggressive CH2 genotype

Submitted to: Phytopathology
Publication Type: Abstract Only
Publication Acceptance Date: May 8, 2012
Publication Date: August 4, 2012
Citation: Ling, K., Li, R. 2012. Genetic diversity and phylogenetic analysis revealed Pepino Mosaic Virus in North-America has shifted to a more aggressive CH2 genotype. Phytopathology. 102:S4.71.

Technical Abstract: In nearly a decade, Pepino mosaic virus (PepMV) has become endemic on greenhouse tomatoes in North America. Several distinct genotypes of PepMV have been identified and three of them confirmed, including EU, US1, and CH2. Previous population genetic studies conducted in 2006-2007 revealed a predominant EU genotype in Canada and the U.S., with US1 and CH2 genotypes also detected in some localities. In early 2010, a more aggressive disease in a greenhouse in British Columbia, Canada, was observed and the CH2 genotype of PepMV was identified. At the same time, another disease epidemic was reported in a greenhouse facility near Mexico City, Mexico, and shown also to be infected by CH2 genotype. The objective of this study was to assess the current status of genetic diversity of PepMV in North America. Surveys were conducted in 2011-2012 on several greenhouse facilities. As expected, nearly 100% of symptomatic samples collected were infected by PepMV in ELISA or RT-PCR test. To allow for an efficient assessment of genetic diversity of PepMV, a genotype-specific loop-mediated isothermal amplification (LAMP) technology was developed. The phylogenetic relationship of PepMV population was evaluated through nucleotide sequencing of selected genomic regions. Results showed that the predominant genotype of PepMV in North America has shifted to CH2. How this new genotype was introduced to these facilities was not determined. The fact that the CH2 genotype was originally identified in the U.S. from an imported commercial seed lot suggests the possibility of seed sources.