1. Published research

Researchers are trying to determine the impact the recently discovered Snake River Alfalfa Virus will have on farmers and dairy producers in south-central Idaho.

University of Idaho plant virologist Alexander Karasev and UI Extension entomologist Erik Wenninger recently received a three-year, $300,000 National Institute of Food and Agriculture grant to study the virus.

They will determine how economically important it is to growers, how it is transmitted, foliar symptoms of infection and the crops it can infect.

“Alfalfa is one of the largest crops grown in the state but is one of the least-studied…,” Karasev said in a UI press release. “You have a crop that stays in the same place for four years. It acts like a sponge — any type of pathogens and diseases tend to make a stop in this crop.”

Snake River, which appears to be the first flavi-like virus detected in plants, likely will become the “founding member” of a new virus family or order once additional related viruses are discovered, according to a paper published in June 2022 by Karasev, Wenninger and several colleagues.

Its unique features might have evolved as an adaptation to reproduction in plants, or in both plants and insects, according to the research. Genome sequences also were identified in thrips, suggesting the insects might be vectors.

Flaviviruses are in the same genus as yellow fever. The Snake River virus shouldn’t threaten human health, according to UI.

Karasev discovered it in 2020 while collecting symptomatic foliage in a field at the future site of UI’s dairy-anchored Idaho Center for Agriculture, Food and the Environment near Rupert.

He chose the field due to prevalence of foliage with common symptoms of viral diseases, including mosaic leaf discoloration and vein clearing.

He was seeking to test deep sequencing, a new diagnostic genetic sequencing methodology, and associated laboratory equipment. Researchers with the National Center for Biotechnology Information, in Maryland, compared his results against their database and determined Snake River was a new virus.

Based on subsequent testing of south-central Idaho fields, the virus is widespread in the region. It is possible that the virus is long-established but discovered recently thanks to new diagnostic technology, according to the university.

Karasev suspects the Snake River virus is spread by thrips. Some thrips that Wenninger collected from UI research fields in Kimberly were confirmed to have it.

Wenninger plans to have a graduate student research if it is transmitted by thrips. The student also will conduct tests related to insect control, and alfalfa yield and quality.

In Rupert, sample testing also confirmed infection by six other viral diseases. Four are transmitted only by seed and are considered benign, according to UI. The others, the alfalfa mosaic and bean leafroll viruses, can be transmitted by aphids and may be contributing to diminished yield and quality in older plantings.

Karasev’s hypothesis is virus pressure reduces production by the fourth year, prompting most farmers to rotate to a different crop.

“The assumption was viruses in general caused very little harm to alfalfa,” he said. “We’re trying to get some data to confirm or refute it. Until you start studying it, you may not realize it’s a problem.”