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United States Department of Agriculture

Agricultural Research Service

Research Project: Characterization, Etiology, and Disease Management for Vegetable Crops

Location: Vegetable Research

Title: Molecular and biological properties of tomato necrotic stunt virus and development of a sensitive real-time RT-PCR assay

Authors
item Li, Rugang
item Fei, Zhangjun -
item Ling, Kai-Shu

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 10, 2013
Publication Date: February 1, 2014
Citation: Li, R., Fei, Z., Ling, K. 2014. Molecular and biological properties of tomato necrotic stunt virus and development of a sensitive real-time RT-PCR assay. Archives of Virology. 159(2):353-358.

Interpretive Summary: Tomato is the second most economically important vegetable crop in the world. In the U.S., with a total production of 14.1 million tons in 2009, tomato has a value over $10.86 billion. Greenhouse tomato production has increased steadily in recent years with nearly 40% of fresh tomatoes in the U.S. supermarket produced in greenhouses. Viral diseases caused by new or emerging viruses are a major limiting factor in tomato production. Using small RNA (sRNA) deep sequencing technology, we previously identified a novel potyvirus in Mexico, named Tomato necrotic stunt virus (ToNSV). In the present study, we characterized biological and molecular properties of this new virus. The results showed that ToNSV is a typical potyvirus with only a limited sequence identity (60%) to known viruses. Using a newly developed molecular detection, we were able to show that this virus was distributed in at least two separate locations in Mexico, but not in the U.S. or Canada. Understanding the virus molecular and biological properties and development of the sensitive detection method may lead us to devise an effective disease management strategy to combat this virus. Such new strategies should prove invaluable to producers of greenhouse tomatoes.

Technical Abstract: Using small RNA (sRNA) deep sequencing technology, we previously identified a novel potyvirus, named Tomato necrotic stunt virus (ToNSV), in Mexico. In the present study, we characterized the biological and molecular properties of this virus. A ToNSV infected tomato plant was badly stunted, with yellowish, rusty or necrotic appearance on leaves. In a host range study using 36 plant species from 7 families, ToNSV was confirmed to infect numerous plant species in two families: Amaranthaceae and Solanaceae. ToNSV shared less than 60% identity in nucleotide or amino acid sequences to all known viruses, with the highest similarity to potyviruses. Predicted polyprotein organization also showed its typical structural characteristic of a potyvirus. A sensitive molecular detection using reverse transcription polymerase chain reaction (RT-PCR) was developed and used to screen 165 tomato samples collected in recent years in various locations in North America. Our results showed that this emerging virus was localized in at least two separate locations in Mexico (state of Mexico and Jalisco). Comparative analysis of genome sequences showed only minor genetic diversity between the two Mexican isolates of ToNSV. In conclusion, understanding of its molecular and biological properties and development of the sensitive detection method may lead us to devise an effective disease management strategy.

Last Modified: 10/1/2014
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