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

Part 1 explained how we suspect ToBRFV was entering into Canada and moving between greenhouses (access post here). Here we will explore mutations, adaptations and how the virus is responding to the protection offered by genetic host resistance.

Before we go any further, let’s explain what these terms mean.

Mutation: random change in the viral genome that occurs when the virus replicates inside a host plant. Plant viruses with RNA genomes (like ToBRFV) are especially prone to mutations.

Adaptation: heritable trait that becomes common in a virus population because it improves survival or transmission in a specific environment.

Adaptation occurs through natural selection acting on mutations. This can happen over multiple infection cycles.

SUCCESSIVE ADAPTATIONS

Because we collected samples from susceptible and resistant cultivars at one greenhouse on 5 different dates from September 2023 until November 2024, we could track changes to the genome over time. The greenhouse had separate compartments, grew multiple different susceptible and resistant cultivars sometimes adjacent and most of the crops had ToBRFV-outbreaks. The crops were removed, the greenhouse was decontaminated and replanted multiple times during the sampling period.

Successive adaptations of ToBRFV to multiple different resistance genes were tracked over time through genomic analysis. This suggests that the virus can mutate and escape some of the new resistant cultivars that were in production in 2023-2024.

To summarize, successive samples from the same greenhouse show persistence and adaptation through:

• Mutations in multiple regions.
• Mutations found in susceptible and resistant tomato hosts.
• The same mutations (identical genomes) found in different greenhouses.
• Multiple adaptations in a single greenhouse.

What does this tell us?

1. It is difficult to eliminate ToBRFV once established.
2. If it keeps re-occurring the virus can adapt to new cultivars (even those with resistance genes).

The introduction of genetic host resistance into commercial varieties has grown rapidly. At this point, many growers are exclusively growing newly commercialized resistant cultivars. There is a lot of uncertainty about new resistance traits, and they are protected as intellectual property. We don’t know much about what these new resistance genes might even be. But it’s safe to say most (or all) of the commercially available cultivars offer protection through resistance, but not immunity.

TOMATO RESISTANCE – THE PAST

One gene which has been important in the past for preventing Tobamovirus infections and has previously been used by seed companies is Tm-1. Tm-1 was useful for preventing Tobamovirus infections but was replaced by the much more stable and efficient Tm-2² gene.

The heavy reliance on Tm-2² for many decades was damaged when ToBRFV evaded this resistance and rapidly spread across the world.

Two resistance genes, two different defense strategies

• Tm-2² functions through recognizing the viral movement protein and initiates a hypersensitive response, which results in cell death and prevention of viral spread and replication.
• Tm-1 functions through a different mechanism, by recognizing the viral replication protein and stopping it from replicating viral RNA.

However, Tomato mosaic virus was able to mutate and escape Tm-1 mediated resistance, while Tm-2² mediated resistance was more durable and effective. Therefore, Tm-2² was the dominant resistance gene in use in tomato production for over 60 years and help to prevent Tobamovirus infection until the rise of ToBRFV.

TOMATO RESISTANCE – THE PRESENT

Tm-1 slows ToBRFV, but doesn’t stop it

Since Tm-2² is ineffective against ToBRFV, seed companies worldwide have been searching for genes that can provide some resistance to ToBRFV. Tm-1 in particular has seen renewed interest. But recent reports, including by Fougere and colleagues, suggest that Tm-1 alone cannot prevent ToBRFV infections and that the resistance can break down, particularly at higher temperatures. But Tm-1 can help slow down infection, and maybe reduce symptoms, but it won’t prevent it.

An unknown gene, similar vulnerabilities

A different resistance gene, which hasn’t been extensively studied but has been reported in patents from some seed companies, also does not appear to be as stable as Tm-2². ToBRFV isolates breaking this resistance gene have been described in two different scientific reports. This gene can also break down at higher temperatures, which is why the virus can seem to suddenly show up during heat waves.

It isn’t clear how well these genes will work, but generally the attitude towards ToBRFV has improved lately. With more and more resistant cultivars being in grown, there does seem to be a reduction in losses due to this devastating virus. Seed companies have become better at screening their seed sources and reducing spread of ToBRFV through the seed pathway.

Less virus, less spread

This is all good news. But we don’t have the tools to eliminate ToBRFV outbreaks yet.

This recent report about ToBRFV in Canada does suggest that this virus could escape multiple resistance genes and continue to be an issue in greenhouse production for the long term. These are only two resistance genes, and other unknown genes have been reported in the scientific literature. Any of these genes could end up being a solution to this virus. Further study of these new resistance genes and how they work will help us to design better tomato cultivars and reduce losses associated with ToBRFV.

But for now, we suggest growers continue to be vigilant and take steps to reduce virus spread in their greenhouses. There is resistance available, but no known immunity.

ToBRFV has a history of overcoming other genetic resistance such as Tm-2². So, with these new resistant cultivars it’s important to minimize the opportunity of the virus to escape resistance. One of the best ways to mitigate this risk is to minimize the crops exposure to ToBRFV.

THE TAKE HOMES

1. ToBRFV is still here, can mutate and escape resistance. Genetic host resistance has improved the incidence and severity of ToBRFV outbreaks in Canada but there is evidence of ToBRFV mutations and resistance escape.
2. The higher the disease pressure, the more opportunities for mutations. To preserve the success of genetic host resistance, growers should minimize the opportunity of ToBRFV resistance-escape by reducing ToBRFV pressure in the greenhouse.
   1. Use as much resistant seed as possible.
   2. Avoid growing resistant cultivars next to susceptible cultivars.
   3. Monitor for ToBRFV throughout the production cycle.
   4. Remove infected plants and quarantine areas of known infection.
   5. Do not replant into infected growing media.
   6. Thorough clean outs between crops are vital.

Host resistance is the ultimate form of protection, but we need to dampen our expectations since the protection that Tm-2² offered previously is unprecedented. And the ToBRFV beast overcame it.

Further studies could be aimed at improved durability of genetic host resistance to ToBRFV. Knowledge of the identity of these new resistance genes and how they work will help us better protect greenhouse production in the future.

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.

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.

Zisi Z, Ghijselings L, Vogel E, Vos C, Matthijnssens J. 2024. Single amino acid change in tomato brown rugose fruit virus breaks virus-specific resistance in new resistant tomato cultivar. Frontiers in plant science, 15: 1382862.