Plant scientists continue to study ‘phantom pathogens’
by January 27, 2025 9:00 am 74 views

Ioannis Tzanetakis, Professor of Plant Virology and Director of the Arkansas Clean Plant Center for Berries (U of A System Division of Agriculture photo by Fred Miller)
German agricultural chemist Adolf Eduard Mayer made a startling discovery in 1886. He was studying mosaic disease on tobacco leaves when he noticed that if sap from the leaves touched healthy leaves the disease would spread.
According to News Medical Life Sciences, he could not identify what exactly caused the disease and its spread, but through observation it became clear to him and other plant scientists of the era that something was lurking underneath the surface.
The science of plant virology was born.
In the decades following this discovery, many pathogens in plants were thought to be identified, and regulations were sculpted based on what scientists thought at the time was good science around these mysterious “agents.”
There is only one problem.
Many of these “phantom pathogens” may not exist, and using them as a guide for international plant regulations negatively impacts the worldwide agriculture industry, said Ioannis Tzanetakis, professor of plant virology for the Arkansas Agricultural Experiment Station and director of the Arkansas Clean Plant Center.
The Arkansas Clean Plant Center led the efforts of a team of 185 agricultural scientists from more than 40 countries that test for plant pathogens. They are calling for the removal of more than 120 phantom agents from regulation lists because they are outdated and impede access to plant materials clean of pathogens. Clean plants are needed for the sustainable production of crops.
Most of these phantom agents were “discovered” before modern molecular techniques, and there are no samples or genome sequences available to study them. Despite the lack of evidence of their existence, the suspected pathogens made their way into international regulations that control the shipment of plant materials.
For example, among the list of phantom agents is “Strawberry band mosaic virus,” something described as a disease once in Hungary in the 1960s on an old cultivar by its display of symptoms based on a single picture present in a publication. This could lead to other countries not allowing strawberry plants into their country based on a report and one picture and with no scientific inquiry at all.
“Given the limited information provided in the single report, the agent cannot be studied further,” Tzanetakis and his co-authors said.
The result, Tzanetakis said, is a confusing mix of real and phantom agents on regulatory lists that must be ruled out by the sender before plants can be shipped from country to country.
“We have tried to clean the list of regulated pathogens to make this process much more mainstream,” Tzanetakis said. “What we call phantom agents are names where there’s not really any knowledge of what they are, nor are there any places on this planet where you can go pick this plant and say it is infected with agent X.”
In a plant disease article recently published by the “American Phytopathological Society,” Tzanetakis and a broad host of co-authors identify phantom agents in eight crops that still appear on regulated pathogen lists even though there is no way to accurately test for them.
“With today’s technology, if an indicator plant shows symptoms, it would undergo analysis by high-throughput sequencing, also known as HTS,” Tzanetakis explained. “If this process identifies a novel agent, it’s unlikely to be attributed to a phantom. Instead, it would be recognized as a new pathogen of the host. As a result, phantom agents tend to persist indefinitely.”
High-throughput sequencing is a scientific method that allows researchers to quickly sequence DNA from a large number of samples and/or organisms simultaneously.
The Arkansas Clean Plant Center, or ACPC, is the newest center for berries in the National Clean Plant Center Network. The network, also known as the NCPC, was created to protect U.S. specialty crops from the spread of economically harmful plant pests and diseases. The U.S. Department of Agriculture funds the NCPC, which includes scientists, educators, state and federal regulators, nurseries and growers who work together to make sure plant propagation material is clean and available.
Labs like the Arkansas Clean Plant Center conduct testing to identify and verify the presence of plant pathogens like those on regulatory lists. The ACPC also provides “clean-up” services to ensure that plant material is the best quality possible before providing it to nurseries, breeding companies and growers.
Tzanetakis said cleaning plant material might be responsible for the elimination of some of the pathogens on the list of phantom agents. Suspected pathogens could also be caused by either a single or multiple viruses now known under a different name, or possibly even eliminated through resistance in modern cultivars.
The ACPC lab is one of only two in the National Clean Plant Center Network with in-house HTS capabilities, which streamlines the testing and cleanup processes for breeding lines that improve quality control in pathogen testing.
The goal, Tzanetakis said, is to improve crop production and ensure that farmers have access to high-quality, disease-free plants without unnecessary obstacles. He said NCPC labs like the Arkansas Clean Plant Center are designed to test for and eliminate viruses from plants.
“Those regulations are in place even though we have so many better tools to test for a disease,” Tzanetakis said.