PART 1. Genomic diversity of ToBRFV: What’s happening in Canada?

Published on by Cara McCreary

Authors: Greg Fougere (MSc candidate, Brock University), Jonathan Griffiths (Research Scientist – Virology, Agriculture and Agri-Food Canada) and Cara McCreary (Greenhouse Vegetable IPM Specialist, OMAFA)

For several years now tomato brown rugose fruit virus (ToBRFV) has reared its ugly tomato head in Canadian greenhouses and across the world (Zhang et al., 2022). The greenhouse sector and all its allies including greenhouse employees, grower organizations, suppliers and researchers have worked diligently to understand mitigation and management. Biosecurity has improved. Detection has improved. Seed suppliers have developed ToBRFV-resistant cultivars at a rapid pace. But we are not out of the woods quite yet.

In an effort to understand the situation in Canada and compare ToBRFV to other parts of the world, researchers from AAFC, Brock University, and OMAFA have recently published an article detailing the genomic diversity of ToBRFV in Canadian tomato greenhouses (access article here). The purpose of the study was to:

  • Examine the diversity of the virus in Canada.
  • Understand how it is moving into and between greenhouses.
  • Understand how the virus is responding to new resistant cultivars.

All this information can help us determine if the virus is adapting, if and how it persists, and inform management decisions.

SYMPTOMATIC SAMPLING

Researchers collected 15 samples from symptomatic plants from three separate greenhouses in Ontario. Symptoms were typical of ToBRFV-positive tomato plants. Each sample included at least one of the following symptoms (Fig. 1):

  • deformed leaves
  • crinkled leaves
  • mosaic patterns on leaves
  • mottling or flecking on leaves
  • severe chlorosis of leaves
  • brown patches (rugose) on fruit

Figure 1. Images of ToBRFV symptoms. (A) Uninfected tomato fruit. (B) Brown rugose symptoms on fruit. (C) Fruit deformations. (D) Uninfected leaf. (E) Leaf blistering, curling, and deformations. (F) Leaf chlorosis and bleaching (Fougere et al., 2025).

GENOMIC DIVERSITY OF ToBRFV IN CANADA

They extracted RNA from these plant samples and determined the genome of the virus from multiple plants and greenhouses. They compared Canadian genomes to other genomes from around the world. They were able to show that Canadian populations were fairly unique but group closely with other North American isolates in most cases, suggesting circulation of the virus within North America (Fig. 2).

Figure 2: Phylogeny showing the relation of international isolates of ToBRFV. Canadian isolates are highlighted in blue and pink (Fougere et al., 2025).

Two isolates, Qc-47900 from Quebec, and GRT3 from a greenhouse in Ontario were distantly related to most other genomes identified in Ontario. In addition, some isolates from different greenhouses were very highly related.

What does this tell us? With this information, we suspect that:

  • The virus could have entered Canada on at least three separate occasions.
  • Related isolates from different greenhouses suggests the virus could be moving locally.

This could be due to the same virus being introduced through plants, or the virus could have moved between greenhouses, potentially transmitted by humans, containers or tools, insects, or even water. Samples from the same greenhouse show how difficult it is to eliminate ToBRFV once established. If it keeps re-occurring the virus can adapt to new cultivars (more will be discussed on the matter of adaptation in Part 2). This study highlights the importance of continued biosecurity around ToBRFV.

What does this mean for your farm? Once ToBRFV has infested a greenhouse it is difficult to eradicate it. Viral loads increase the longer a plant is infected and with the number of infected plants. Higher viral loads are more difficult to eliminate from a greenhouse and re-infections are more likely to occur in new crops. There may be multiple routes of entry which means greenhouses need multiple points of protection.

THE TAKE HOMES

1) ToBRFV may be introduced into the greenhouse through multiple avenues. Reduce the opportunity for early introductions through:

    1. Clean seed.
    2. Clean seedlings.
    3. Clean water.
    4. Strict hygiene of employees and visitors.
    5. Monitor plants for symptoms.

    Monitoring suggestions:

    • Sample and test seeds and seedlings.
    • Isolate new seedlings, sample and test leachate from these plants before transplanting.

    2) Sanitation is still necessary. In addition to measures listed above:

    1. Conduct thorough clean outs.
    2. Regularly clean surfaces, tools and equipment.
    3. Disinfect recirculated nutrient solution.

    Suggestions:

    • Clean first, then disinfect.
    • Focus on high-risk areas by regularly cleaning surfaces that hands touch (door knobs, steering wheels, etc.).

    3) The virus is persisting within the greenhouse. Reduce viral loads by:

    1. Use resistant cultivars whenever possible.
    2. Quarantine and eradicate infected plants immediately.

    Genetic resistance has become widely available and the situation has improved. But rugose has not gone away. Diligent monitoring and management are still required. Stay tuned for Part 2 where we will discuss genetic host resistance and how ToBRFV is responding to this type of protection in Canadian greenhouses.

    References

    Fougere, G. C., D. Xu, J.R.Gaiero, C. McCreary, G. Marchand, C. Despres, A. Wang, M. L. Fall & J. S. Griffiths. (2025). Genomic Diversity of Tomato Brown Rugose Fruit Virus in Canadian Greenhouse Production Systems. Viruses, 17(5), 696. https://www.mdpi.com/1999-4915/17/5/696

    Zhang, S., Griffiths, J.S., Marchand, G., Bernards, M.A., Wang, A. (2022). Tomato brown rugose fruit virus: an emerging and rapidly spreading plant RNA virus that threatens tomato production worldwide. Molecular Plant Pathology, 23(9), 1239-1398.