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Genetic Composition of Pepino mosaic virus Population in North American Greenhouse Tomatoes

In just a few short years, pepino mosaic disease has quickly become endemic in greenhouse tomatoes around the world. Although three genotypes of Pepino mosaic virus (PepMV) were identified in the United States, genetic composition of PepMV in greenhouse tomato crops in North America has not been determined. In this study, genetic variability and population structure of PepMV were evaluated through nucleotide sequence comparison and phylogenetic analysis of two genomic regions (helicase domain and TGB2-3) derived from 91 cDNA clones that were derived from 31 field-collected samples. These samples were collected from several major greenhouse tomato facilities in five states in the United States and two provinces in Canada. All four major genotypes of PepMV (EU, US1, US2, and CH2) were found in North America. Three distinct genotypes (EU, US1, and US2) were found in mixed infection in samples collected from Arizona and Colorado, two genotypes (EU and CH2) in Texas, and a single genotype (EU) in Alabama and California and the provinces of British Columbia and Ontario in Canada. The complexity of population genetics of PepMV in the United States poses an additional challenge to the greenhouse tomato industry because a tomato cultivar with durable resistance to multiple genotypes of PepMV may be harder to develop.