The blueberries that show up in summer pies, roadside fruit stands, and u-pick fields across the Lower Mainland have been under threat from a diagnostic puzzle: plants showing clear viral symptoms were testing negative for both known pathogens. Farmers faced impossible decisions about whether to remove crops or wait for recovery, all while an economically critical sector hung in the balance.

A research team has found the answer.

A collaboration between the BC Blueberry Council, Simon Fraser University, and Phyto Diagnostics Company Ltd., funded by Genome BC, used genomic sequencing to uncover why standard tests were failing. Both major blueberry viruses—Scorch and Shock—had evolved into new variants that existing diagnostic methods couldn't detect.

"We took hundreds of samples from fields in the Fraser Valley in 2020 and up to 30% of sick plant samples came back negative for the viruses that are known to affect blueberry bushes," said Dr. Eric Gerbrandt, research director at the BC Blueberry Council and project co-lead. "These inconclusive results led to uncertainty for our farmers."

B.C. produces more than 90% of Canada's highbush blueberries, a crop that was the province's highest-value agricultural export in 2019, worth $236 million in exports by 2020. The two viral threats present fundamentally different management challenges: Scorch-infected plants must be removed entirely, while Shock-infected plants can recover over time. Diagnostic uncertainty transforms every infected plant into a costly decision point for growers.

The research team, led by Dr. Jim Mattsson from SFU's Department of Biological Sciences and Dr. Gerbrandt, applied genomic sequencing to map the viral landscape affecting B.C. blueberry fields.

"This was a complex biological puzzle that traditional diagnostic methods couldn't solve," said Dr. Mattsson. "By applying the power of genomic sequencing, we discovered that both the Shock and Scorch viruses had evolved into new variants, which is why the diagnostic test wasn't successfully identifying the cause of the sick plants."

The sequencing work also revealed four previously undetected viruses in BC fields, though researchers determined these pose no threat to growers as they don't cause disease in blueberry plants.

The team is developing updated diagnostic methods expected to be available by next growing season. These include an updated ELISA test for the evolved virus variants and more sensitive PCR tests capable of detecting lower virus levels in young plants before they're used to establish new crops.

The improved diagnostics will enable farmers to accurately identify Scorch-infected plants requiring removal—essential for containing the spread of this economically damaging disease.

"These viruses are one of the most economically significant challenges we face, and this work has helped bring the importance of viruses to growers' attention so they can better manage infected fields," Dr. Gerbrandt said.

The findings underscore a broader challenge in agriculture: plant viruses naturally evolve new strains over time, making disease management an ongoing challenge requiring continuous adaptation from both farmers and researchers.

"This project is a perfect example of how genomics can be a powerful tool for solving real-world challenges facing our industries," said Suzanne Gill, president and CEO of Genome BC. "By connecting researchers with industry partners, we're helping to turn a frustrating problem into a workable, data-driven solution that protects a vital part of our province's economy."