A team of researchers from the universities of Waterloo and Oxford developed a highly targeted approach to identify the presence of Tomato Brown Rugose Fruit virus (ToBRFV) genomes in municipal wastewater in Ontario, Canada. 

The devastating plant pathogen infects tomato and pepper plants with nearly 100% disease incidence. It can easily spread through contact with contaminated equipment and soil, or infected plants and seeds.

The virus can survive a long time on various surfaces: at least 2 hours on skin and gloves, at least 3 hours on hard plastics, and at least 1 month on glass, aluminum, and stainless steel.

Symptoms are commonly expressed on leaves, flowers, and fruit during the developmental stages of a plant. Leaves show early symptoms of discoloration, mosaic, and shoestring or fern-like appearance.

New research

Scientists used a novel tiled amplicon sequencing assay to track the evolution of ToBRFV genomes in municipal wastewater. They found ToBRFV to be “widespread and one of the most abundant virus species in Ontario.”

Moreover, the “closely related ToBRFV may also be transmissible in reclaimed wastewater used in crop irrigation.” This, researchers say, could facilitate the transmission of active ToBRFV virions to crops, causing viral outbreaks.

Amplicon sequencing enables researchers to analyze genetic variation in specific genomic regions. The ultra-deep sequencing of PCR products (amplicons) allows efficient variant identification and characterization. 

This method uses oligonucleotide probes designed to target and capture regions of interest, followed by next-generation sequencing (NGS).

Researchers Delaney Nash and Isaac Ellmet used this technique to “aid in global ToBRFV surveillance efforts,” as it causes massive crop and financial losses to farmers.

The earliest cases of ToBRFV were reported following a 2015 outbreak in Jordan. Shortly thereafter, ToBRFV was identified as the causative agent of a 2014 tomato disease outbreak in Israel. 

Since then, it has spread to at least 35 countries, including major tomato producers such as China, Turkey, and Mexico. It was first reported in Ontario in 2019.

In March 2023, Essex County greenhouse growers were reportedly struggling to develop a resistant tomato strain to fight off the disease. However, no cultivars resistant to ToBRFV have been identified to date.