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Virus Detection, Heavy Weather

Posted by | July 6, 2011

Optimizing Virus Detection Using the Power of Attraction

Dr. Ken Eastwell
Dr. Ken Eastwell

To determine if a fruit tree has a virus, it currently takes a minimum of nine separate laboratory tests in combination with several biological assays, and even these can identify only known viruses. Scientists dream of being able to run a single test that will determine all the plant viruses in a sample. That imaginative idea is closer to reality thanks to the Washington Tree Fruit Research Commission, which has funded a two-year project to evaluate a universal plant virus microarray test. Potentially, such a test might even be able to detect previously unknown viruses.

“This research could lead to quicker and cheaper testing that gives us more detailed answers than current laboratory methods,” said WSU’s Ken Eastwell, who will serve as the principle investigator on the project. Eastwell, based at WSU’s Irrigated Agriculture Research and Extension Center in Prosser, is a plant pathologist and director of the Clean Plant Center of the Northwest. “This will benefit fruit tree growers and nurseries by getting clean plant material to them sooner and at lower cost. Additionally, it will help growers because we will be able to unravel emerging disease situations in orchards much faster.”

Originally designed to detect viruses in humans and animals, microarray technology was modified to detect plant viruses by the USDA’s Agricultural Research Service. The new project enables a team of WSU and USDA scientists to further modify testing protocols and find ways to optimize testing conditions for fruit trees diseases.

“We know the technology works,” said James Susaimuthu of the National Clean Plant Network–Fruit Trees program, also based at WSU’s research center in Prosser. He will serve as a co-principle investigator on the project. “We’ll be determining what changes need to be made to existing testing procedures to allow the microarray to give us clear results for fruit tree viruses.”

Dr. James Susaimuthu
Dr. James Susaimuthu

The microarray process takes advantage of the power of attraction and starts with a slide outfitted with 10,000 micro probes. Each probe is designed to attract different types of viruses. RNA is extracted from the suspect plant and also from a healthy control plant. The RNA is then copied into DNA, a more stable molecule. The DNA from the suspect plant is colorized with a red florescent dye, while the control DNA is dyed green. The two are mixed together and a drop of the DNA-rich solution is pipetted onto the microarray chip.

In a manner similar to the way negative and positive magnets are attracted to each other, the DNA molecules seek out those probes in the microarray that are complementary to its sequence. When the molecule finds one it is attracted to, it sticks or binds to it. Once this binding or “hybridization” is completed, excess dyed DNA is washed off and the slide is scanned in a microarray reader. The reader scans and records the red and green florescent color of each of the spots on the slide. Software analysis then compares this color pattern to that produced by known virus sequences to indicate the family, genus and species of virus.

The first phase of the project has started with the printing of the universal plant virus microarray slides. This fall the research team will start training and optimizing methods and data analysis techniques. The second year of the project will be spent evaluating the effectiveness of the test.

By Terri Reddout

To learn more about this research project and get periodic updates, go to and click the research link.

By the Numbers: Worst Spring in 20 Years

Heavy weather in central Washington
Heavy weather in central Washington

Following a winter of wild weather extremes, spring weather in central Washington was the wettest and windiest since 1990, according to data recently analyzed by Washington State University meteorologist Nic Loyd and Gerrit Hoogenboom, director of WSU AgWeatherNet. Following periods of unusual warmth in January and February, a large-scale pattern change occurred in late February and yielded one of the coolest springs (March through May) in central Washington in 20 years. The most notable aspect of the anomalous spring weather was the longevity of the cool weather and the consistency of the large-scale pattern.

“People talk subjectively about it being wet and cold, but we agro-meteorologists always want to see the numbers. And what those numbers show is that it was indeed cold, wet and windy,” said Hoogenboom.

March, April, and May all featured below normal temperatures and unsettled conditions over the region. A strong jet stream transporting cool north Pacific Ocean air masses into the region, coupled with cloud cover and evaporative cooling caused by rainfall into dry air, led to very cool average daily maximum temperatures of 60°F. In contrast, daily minimum temperatures were relatively less cool due to many cloudy, moist, and windy nights that inhibited surface heat loss. At an average of 6 mph, wind speeds were unusually strong during the 2011 spring.

A consequence of the unusual spring weather has been a late season for a variety of Washington crops. The spring wheat crop is more than one week behind its normal progression, and many growers were unable to plant due to saturated or flooded fields. The cherry crop is about two weeks behind schedule, but is expected to be larger than normal. The progression at area vineyards is lagging a normal year by one to two weeks, but a warm summer may allow the crop to catch up from a late bloom.

The cool and wet spring, which included significant late-season snowfall in the Cascade Mountains, was somewhat expected due to the presence of La Niña. La Niña is the negative phase of the El Niño-Southern Oscillation (ENSO). ENSO is characterized by variations in the phase and strength of the Walker Circulation. The Walker Circulation involves a coupled ocean-atmosphere circulation in the equatorial Pacific Ocean that varies in phase over several years. La Niña is characterized by strong east winds and cool sea-surface temperatures in the eastern equatorial Pacific Ocean. Although ENSO generally moves between positive, neutral, and negative phases over two to five year intervals, it cannot be forecast more than a few months in advance, and so the magnitude and duration of individual events cannot be estimated beyond one year.

By Brian Clark

Loyd and Hoogenbooom’s report is available at

A Web-based, publicly available system, AgWeatherNet provides access to near real-time weather data and value-added products from WSU’s statewide weather network, along with decision aids for agricultural producers and other users. It includes 134 weather stations located mostly in the irrigated regions of eastern Washington state, but the network recently has undergone significant expansion in western Washington and dryland regions of the state. AgWeatherNet is available at

Check out a short YouTube video featuring Gerrit Hoogenboom talking about AgWeatherNet at