Fighting Pathogens:

A New Test to Save Crops

By Rita Waimer

Every year, viruses kill millions of dollars of crops in Florida alone. Add to that the other tropical and subtropical regions of the world where these viruses spread and you see that they’re an immense problem, especially in areas like West and Central Africa where vegetables are essential to people’s livelihood.

Many of these viruses belong to the genus Begomovirus, which emerged over the last 30 years and infects a wide range of dicotyledonous plants, including crops like tomatoes, beans, squash and cotton. When one of these viruses infects a crop, usually spread from one plant to another by insects like whiteflies, the grower must treat the plants and manage the outbreak as quickly as possible to minimize losses. If left unchecked, the virus could substantially reduce the yields of the plants it has infected. But even if a grower notices viral symptoms early, it still takes time to run tests and then manage the outbreak.

Finding the Virus

The challenge here is that many pathogens cause the same symptoms, so you can’t simply look at the symptoms a plant is exhibiting and recognize what pathogen has infected it. While the symptoms may give the grower an idea of what’s wrong, the only way to be sure is to run a few tests. So growers must take a sample from an infected plant and send it to a lab, where it can be tested to see exactly which virus is the culprit.

“Knowing which pathogen is causing the symptoms is essential to knowing what to do to minimize its spread to other plants and other crops, and reduce yield losses,” said Polston.

With fungus and bacteria, simply culturing the sample is all it takes to get an accurate identification. But viruses can’t be cultured, so the lab must use polymerase chain reaction tests in the hopes of identifying part of the virus. But these tests take a lot of time, and beyond that they’re expensive. As a result many diagnostic labs decide against testing, leaving many outbreaks managed incorrectly or not managed at all. Even if they do run the tests, answers are not always guaranteed: there are 1,600 known plant viruses, and assays exist for only a fraction of them. Many growers are left with inconclusive or inaccurate results and a field of dying crops — a hefty expense.

A Better Way

Thankfully, the days of slow, expensive tests that may not even produce meaningful results could be numbered: In a new study published in the Virology Journal, Jane Polston revealed that recombinase polymerase amplification can identify the cause of a disease faster and cheaper than PCR tests. Working at the University of Florida Institute of Food and Agricultural Sciences — home to one of the best plant disease diagnostic facilities in the country — she and her colleagues modified the test to check for viruses transmitted by whiteflies in Florida. Their new test makes it easier for labs to identify viruses in plants and crops, which in turn makes it easier for growers to quickly respond to and manage

an outbreak, giving them a better chance to save their crops and avoid losses. The UF/IFAS Plant Diagnostic Center officially adopted the new test in the summer of 2016 to benefit Florida’s growers, and Polston and her team hope that other clinics will follow suit and use the test to better equip themselves to diagnose plant viruses.