Plants and Viruses: Biotechnology, the Arms Race, and Agriculture

Introduction

Plants are the heart and soul of our ecosystem. Plants help run the lifecycle of our planet by keeping atmospheric balance between static and dynamic life. It has been said that among most plant diseases, viral illness is the most common, affecting half of the plant population. 47% pathogen borne diseases are virus-borne. The virus-borne conditions can have detrimental impacts on the plant, resulting in the loss of crop production through a decrease in quality, corresponding to damages of global trade on the order of billions of dollars in losses. Consequences of plant viral disease can hardly be ignored, as an increase in global population and its growing demand will make it increasingly more complicated to manage. More than anything, now is the time when plant biosystems will need our attention and understanding the most.

Some of the infections are easily visible, like mosaic patterns, leaf curling, or tissue necrosis on the plant, whereas others are harder to locate. Endornaviruses, for example, infect crops such as rice, beans, barley and several capsicum species and are not visible with the naked eye, even as sometimes the severity of the infection fluctuates over time (Escalante & Valverde, 2015). In grapevines, grapevine red blotch-associated virus (GRBaV) causes symptoms that vary with cultivar and developmental stages (DeShields & KC, 2023).

Due to high mutation rates, plant viruses evolve rapidly and can easily adapt to host plant defences. By taking over the immune machinery and deceiving the plant to think it still governs the system, viruses can overcome plant resistance and make disease management more difficult. These challenges demand a more modern outlook and also emphasize the need for precise techniques for diagnosis, even as some modern methods are already transforming plant viruses into a source for molecular farming, advanced tools for gene editing, and nanotechnology (Mohammed Riyaz et al. 2021).

Plant viruses are traditionally seen as destructive pathogens that cause disease and reduce crop yields. However, their unique biology is now being harnessed for good. This shift in perspective explores how the very features that make plant viruses effective pathogens, like their rapid replication and simple structure, are being repurposed as powerful tools in biotechnology for gene expression, vaccine production, and nanotechnology (Gleba et al., 2007, Love et al., 2014).

 

Viral Properties that Enable Biotechnology
Several key features of plant viruses make them ideal platforms for biotechnology:

• High-Speed Replication & Gene Expression: Unlike plant cells, which rely on the cell’s nucleus to read genes, many plant viruses (like tobacco mosaic virus, TMV) replicate directly in the cell’s cytoplasm. This allows them to produce massive amounts of viral protein very quickly.
• Systemic Spread: Viruses naturally move from cell to cell and throughout the plant’s vascular system. Biotechnologists can exploit this to rapidly and uniformly produce a protein of interest in all leaves.
• Genetic Plasticity: Viruses exhibit high tolerance for genetic modifications, such as foreign gene insertions or peptide displays on capsid surfaces.
• Programmable Structure: A virus particle is essentially a protein shell (capsid) that protects its genetic material. This shell can be genetically modified to display new proteins or to carry different genetic instructions.

 

Exploiting Replication for Protein Production
The high replication rate of plant viruses can be used as a factory system to produce large amounts of a desired protein. Researchers create “viral vectors” by modifying a virus’s genome, removing disease-causing parts, and inserting a gene for a useful protein (like a vaccine antigen).

This method is far more efficient than standard non-replicating techniques. For example, when a viral vector is delivered alongside a gene that suppresses the plant’s natural defence (RNA silencing), protein levels skyrocket. One study co-delivered the TMV system with a suppressor protein called P19, resulting in nearly complete infection of leaves within days and producing 600-1200 micrograms of protein per gram of plant tissue, far exceeding standard methods (Lindbo, 2007a). By further optimizing the viral vector, some proteins have reached concentrations as high as 5 milligrams per gram of tissue (Lindbo, 2007b).

 

Plant Virus-Made Pharmaceuticals and Vaccines
The efficiency of viral vectors makes plants viable factories for producing pharmaceuticals, a field known as molecular pharming. Using plants and their associated viruses for this purpose offers significant advantages:

• Cost & Scale: Leveraging agricultural infrastructure enables scalable, cost-effective production. Producing proteins in plants can be 10 to 50 times cheaper than using traditional bacterial fermentation in coli (Kusnadi et al., 1997).
• Safety: Plants do not harbour human pathogens (like viruses or prions), drastically reducing contamination risks and simplifying purification.
• Speed & Flexibility: The system is rapid. For instance, antibodies against SARS-CoV-2 were produced and harvested just four days after introducing the viral vectors into tobacco plants (Nicotiana benthamiana) (Taeye et al., 2024).
• Complex Product Formation: Plants can correctly assemble complex proteins, including multi-part antibodies and Virus-Like Particles (VLPs). VLPs are empty, non-infectious shells that mimic a real virus, making them excellent and safe vaccine candidates. Some plant-made vaccines also show improved heat stability, easing cold-storage requirements (Eidenberger et al., 2023).

 

Building Blocks for Nanotechnology

While using plants as bioreactors leverages a virus’s replication machinery, a distinct approach repurposes the virus particle itself as a sophisticated nanomaterial. Once purified, empty viral capsids, or virus-like particles (VLPs), serve as uniform, programmable scaffolds. Their surfaces can be chemically or genetically modified to display functional groups (like enzymes or binding sites) in a highly ordered, repeating pattern. Plant viruses such as Cowpea Mosaic Virus (CPMV), Cowpea Chlorotic Mottle Virus (CCMV), and TMV are ideal for this purpose. They can be produced at scale in plants, easily purified, and used as precise nanotemplates to organize metals, minerals, and other molecules (Zhang et al., 2018). Their advantages include a homogeneous size, well-defined atomic structure, and remarkable stability across a wide range of pH, temperature, and solvent conditions.

 

This “bottom-up” nanotechnology approach unlocks several key applications:

• Templated Nanomaterial Synthesis: The repeating protein structure of a capsid provides a perfect surface for nucleating and organizing inorganic materials. For example, scaffolding gold nanoparticles on the surface of cowpea mosaic virus has been used to create uniform, conductive nanowires with potential uses in next-generation electronics, sensors, and biomedical devices (Blum et al., 2005).
• Nanoscale Catalysis: By positioning catalytic molecules (like enzymes or metals) in a controlled, high-density array on a viral scaffold, their collective activity is amplified. This turns a plant virus nanoparticle into a highly efficient nanoreactor, significantly boosting catalytic performance for industrial chemical reactions (Koch et al., 2015).
• Enhanced Drug Delivery Systems: Plant-based VLPs offer significant advantages as drug carriers, including cost-effective production, scalability, and a strong safety profile (Peralta-Cuevas et al., 2025). Their small, uniform size facilitates efficient cellular uptake, while their modifiable surface enables targeting of specific tissues.
• Advanced Materials for Energy: Viral templates can organize light-sensitive molecules (dyes or quantum dots) and inorganic nanoparticles into precise geometries (Medintz et al., 2005). This ordered arrangement can dramatically improve charge transport and light absorption, with direct applications in the development of more efficient photovoltaic (solar) devices.

 

 

 

 

 

 

 

 

 

 

Challenges and Future Directions:

Although plant viruses have many potential uses in biotechnology, there are some limitations to how they can be used. These challenges span biological, technical, biosafety and containment, and regulatory areas and need to be adequately considered while progressing with viral-based biotechnology.

 

• Plant viruses exhibit significant genetic diversity and high mutation rates; estimates of the mutation rate range from 10^-8 to 10^-4 substitutions per nucleotide per cell infection (Sanjuán et al., 2010). This genetic instability during replication can reduce vector reliability and payload delivery efficiency.
• Unintended spread or recombination of synthesized vectors can pose unforeseen ecological risks.
• Systemic movement within plants is often inefficient, reducing the efficiency of processes such as vaccine or antibody production. Proteolytic degradation, resistance genes, and cellular barriers all make viral movement through a plant more difficult (Hipper et al., 2013).
• There are stringent regulations for virus-based products which delay commercialization, especially for edible crops used in vaccine production. The US Department of Agriculture, for example, has put in place strict requirements to prevent recombinant proteins from entering the food chain or environment (Streatfield, 2005).

 

Future progress hinges on engineering more stable viral vectors, improving biosafety protocols, and navigating regulatory pathways. As these challenges are addressed, the true breadth of plant virus use will be revealed.

 

Plant-Pathogen Coevolution: The Never-Ending Molecular Arms Race

You can see the struggle between plants and viruses in nature, such as the yellow patches on tobacco leaves, stunted cassava plants, and curled papaya leaves (Shimura et al., 2011). This is more than a simple predator-prey relationship: it is a complex molecular battle that has shaped both plants and viruses over millions of years (Han, 2019). When we see a sick plant, we are witnessing just a small part of a long story of coevolution (Scholthof and Scholthof 2023). As we learn more about this genetic process, we uncover clues that help us create stronger, more sustainable crops (Paul et al., 2025).

 

Mechanisms of Interaction – Locks, Keys, and Zigzags

For decades, scientists explained the plant-virus coevolution struggle using the gene-for-gene hypothesis (Flor 1971). In this model, a plant has a special lock called a resistance (R) gene, and a virus has a matching key, known as an avirulence (Avr) protein. If the key fits the lock, the plant detects the virus and starts an immune response, sometimes sacrificing a few cells to protect the rest of the plant (Figure X).

However, evolutionary processes are complex. The gene-for-gene model leads to the Red Queen effect, in which both plants and viruses must continuously evolve to maintain their relative positions (Figure X). As plants develop more robust resistance mechanisms, viruses in parallel must adapt their strategies to overcome these defences (Clay and Kover, 1996).

The Zigzag Model increased our understanding of the complexity of this struggle, showing that there are multiple layers to plant immunity (Jones and Dangl, 2006). First, plants have a general barrier, called pattern-triggered immunity (PTI) that blocks most threats. Some viruses get past this barrier using specialised effector proteins that act like molecular bolt cutters. In response, plants develop new defences called effector-triggered immunity (ETI) that recognise these proteins and mount a stronger defence (Yu et al., 2024). The virus then changes its approach, and the cycle repeats. This ongoing struggle has led to many new genetic changes in both plants and viruses (Fraile and García-Arenal, 2010).

Figure X: The Red Queen’s race describes an endless cycle of adaptation. Plants and viruses are caught in a constant evolutionary battle, where new viral tactics push plants to develop better defences and plant responses lead viruses to find new ways to adapt to survive. Neither side ever wins for good; both must keep changing to survive (Roossinck, 2008). The figure was created using Biorender.com.

 

Evolutionary intelligence and molecular innovations

Researchers have made surprising discoveries about how plants defend themselves in clever ways. Plant immune proteins, often called nucleotide-binding and leucine-rich repeats (NLRs), do not work by themselves. Instead, they form complex networks that share information, similar to a team working together (Wu et al., 2018).

Additionally, plants have another clever defence: they sometimes add pieces of viral DNA to their own genomes. These pieces, called endogenous viral elements (EVEs), were once thought to be useless. We now know they help plants remember and fight off future viruses (Geering et al., 2014). In some cases, plants use these viral fragments as decoys to trick viruses into triggering the plant’s own alarm systems (Kourelis and Van Der Hoorn, 2018).

 

The CRISPR counterstrike and viral trickery

Now, we have a new tool called CRISPR, which is homologous to some bacterial anti-viral pathways. Thanks to this technology, we are no longer just watching this battle- we can actively make changes ourselves.

With CRISPR, viral DNA can be cut inside plant cells to stop infections. Plant immunity can also be enhanced by improving the function of native immune receptors known as NLRs.. Another approach is to insert harmless pieces of viral DNA that prepare the plant’s defences in advance.

Viruses possess a significant evolutionary advantage due to their rapid mutation rates (Roossinck, 1997). They have evolved proteins known as RNAi suppressors, which can inhibit key plant antiviral defence mechanisms (Preising et al., 2025). This ongoing molecular arms race results in plants developing new defences, followed by viral adaptations that circumvent these barriers (Fraile and García-Arenal, 2010).

 

Lessons for the field – breeding smarter, not harder

The history of coevolution shows that relying on a single resistance gene only works for a short time (Cowger and Brown, 2019). Using one strong R gene in large fields gives the virus a chance to adapt and overcome it, leading to mass infection of the field.

Based on what we have learned at the molecular level, a new approach focuses on creating long-lasting resistance:

• Pyramiding genes: Stacking multiple R genes in one crop variety, forcing the virus to solve several evolutionary puzzles at once (Mundt, 2018).
• Editing for resilience: Using CRISPR to tweak essential host factors (like the eIF4E protein that viruses can hijack) so the virus can’t get a foothold, mimicking natural, durable recessive resistance (Zaidi et al., 2020).
• Embracing diversity: The most important lesson is ecological. Growing only one type of crop accelerates viral evolution (Muscatt, Hilton et al., 2022). Fields with many different crop varieties and their wild relatives harbour a wide range of R genes and slow the rate of viral adaptation. This diversity acts as a living library of resilience built over millions of years (Dempewolf, Baute, et al., 2017).

 

The bigger picture – from warfare to wary coexistence

The ongoing struggle against viruses now faces novel challenges, including climate change and food security. As temperatures rise, insects that spread viruses move to new area,s bringing new viruses with them. Stressed plants are more likely to get sick (van Munster et al., 2017). Our solutions need to be as adaptable as the viruses themselves.

The most mind-bending twist is the shift from viewing viruses purely as pathogens to recognising their potential as symbionts. Some captured viral fragments (EVEs) appear to help regulate plant development or stress tolerance. The line between enemy and ally blurs, suggesting a future in which we might harness viral mechanisms not just to fight but to fortify (Wang et al., 2024).

The relationship between plants and viruses will never end with a clear winner. Instead, it is about managing a balance that is both constant and changing. By learning about this long struggle, its patterns, and its challenges, we gain valuable knowledge rather than a single answer.

We learn to breed smarter, creating crops with layered, evolutionary-informed defences. We learn to design agricultural systems that work with biological principles rather than against them. Importantly, we also learn humility, recognising that our interventions are just the latest moves in a billion-year-old game.

So, the next time you see a leaf that is not perfect, remember that you are seeing the result of evolution at work- a moment in the ongoing struggle that shapes all life. By understanding this process, we may also learn how to protect our own future.

 

Plant viruses as a pathogen in Agriculture

Infection caused by plant viruses can immensely disrupt the physiological and biological processes of plants, which impedes plant growth in a multitude of ways, affecting activities such as photosynthesis, metabolism, and development and leading to symptoms including chlorosis, deformation, necrosis, and reduced vigor (Kanapiya et al, 2024).

Viruses corrupt the biological processes of plants, which hurt the crop yield and economy.  The virus citrus tristeza virus (CTV), found in citrus species like orange, grapefruit, and lime, can cause stem pitting and seedlings to turn yellow, and also pose threats from strain evolution and vector-mediated spread (Moreno et al, 2008). Perennial crops like cassava, which are a primary food source for a billion people worldwide, have seen a 70% decline in production because of cassava mosaic disease (CMD), which affects the leaves and can make the plant unsuitable to eat. Cassava brown streak disease (CBSD), caused by another cassava virus, infect the whole plant, including the roots, stems, leaves and seed capsules (Rey & Vanderschuren, 2017, Chikoti & Tembo, 2022). Other infection-causing viruses, such as the potato virus (PVY), are transmitted easily from field to field by aphids. The virus can cause declines in the yield of the third most important crop in the world, as the virus severely worsens tuber quality. Occasionally, these outbreaks can lead to yield declines exceeding 80% (Torrance & Taliansky, 2020). Tuber-borne and aphid-transmitted viruses present aerial and seed-based threats to plants, while the wheat soil-borne mosaic virus (SBWMV) presents as more of an earth-bound threat, which could corrupt the agricultural landscape. SBWMV causes mosaic mottling and chlorotic striping of leave,s and the virus severely limits the plant’s physiological development, leading to reduced tillering and overall stunted growth, slashing yield up to 50% (Hou et al, 2025).

The above viruses illustrate the danger they present and highlight the importance of modern diagnostic tools for surveillance, on which recent advances in plant virology continue to build.

 

Recent Advances in Plant Virology & Impact on Global Agroeconomics and Trade

Plant viruses are hard to ignore, especially in rural areas where agriculture is the backbone of the economy. Plant viruses directly threaten food security and trade and cause approximately US$30 billion in annual crop losses globally, posing a serious risk to the sustainability and productivity of agriculture (Jones, 2021). Rice tungro disease reduces rice productivity up to  70-90% in Southeast Asia and accounts for a US$1.5 billion loss annually (Hore et al, 2022). Viral diseases of maize are equally as severe — maize streak virus alone is responsible for  US$120–480 million in annual losses in Africa (Benjamin et al., 2024).  Similarly, a banana bunchy top virus (BBTV) outbreak caused up to 100% yield loss in India, amounting to almost 30 million tons of lost bananas (Jekayinoluwa et al., 2020). Along with citrus tristeza virus, plum pox virus, cucumber mosaic virus, and tomato yellow leaf curl virus, viruses play a major role in global crop losses and negatively affect market sales, thereby hindering trade through quarantine restrictions and the removal of orchards.

Opportunities to leverage viruses for biotech, using plant immunity agents, CRISPR gene editing, and advanced diagnostics for novel controls, and understanding their ecological roles to enhance crop resilience allows us to transform would-be threats into tools for food security. Modern plant virology follows a sort of discover–detect–deploy approach, where we discover new viruses and uses for them, detect their strengths and test the possibilities, and then deploy them where needed.

Present-day advances in virology have enabled the development of powerful analytical, diagnostic, and control technologies that are transforming how plant–virus interactions are studied and managed:

Metabolomics: This field allows us to understand how metabolites change in response to stimuli. For example, we can see precisely how CCYV modifies the host’s chemical profile by suppressing defensive metabolites while concurrently increasing nutrient-rich amino acids and lipids to alter whitefly feeding behavior and optimize its own replication (Zhang et al. 2022).

Genome Wide Association Studies (GWAS) and co-GWAS: These studies have become valuable approaches in plants to map host and viral resistance and virulence loci. One example is the identification of key resistance loci & candidate genes conferring resistance to soybean mosaic virus (SMV) and joint host–virus QTLs in the melon–watermelon mosaic virus system (He et al., 2025, Boubacar-Abdou et al., 2025).

Lateral Flow Immunoassays (LFIA) and LAMP (Loop-Mediated Isothermal Amplification): These tools can be effectively used in the field for portable, low-cost, rapid detection of banana bract virus, cassava brown streak virus, and many other viruses. This helps to reduce the delay between detection and response and supports faster, better informed quarantine decisions (Song et al., 2024, Selvarajan et al, 2020).

RNA interference: RNA interference has expanded both the effectiveness and practicality of antiviral strategies. From early transgenic RNAi against potato viruses to spray-induced gene silencing (SIGS) approaches that suppress barley yellow dwarf viruses to multivalent edsRNAs that provide strong, non-transgenic protection against rapidly mutating cucumber mosaic virus, there is a growing potential of RNAi for sustainable virus control. A significantly greater immunological response in the plant can be obtained with less substance. Finally, durable resistance delivered through genetic modification and non-genetic modification RNAi approaches stabilize yields and marketability (Derbal et al., 2025, Knoblich et al., 2025).

CRISPR/Cas: Using this powerful genome editing technique allows for target engineering of virus resistance. For example, TYLCV replication in tomatoes can be disrupted through this genome editing technique. Cas12- and Cas13-based diagnostic platforms provide for additional rapid, field deployable detection and allow sensitive, sequence-specific identification of viral infections within minutes. Ultimately, they help to prevent outbreaks and trade disruption (Jaybhaye et al., 2024).

 

Bioinformatics and Machine Learning: Machine learning is another powerful tool, where data-driven models facilitate early disease detection, and precise sequence analysis enables reliable viral identification. One example of how computational methods are improving virus diagnosis and crop protection is the effective application of a mobile-based CNN model for cassava brown streak disease weeks before symptoms become apparent (Ramcharan et al., 2019).

Workflows based on high-throughput sequencing provide the opportunity to detect both known and unknown substances in germplasm and quarantined samples, decreasing the risk that contaminated material crosses the border undetected (Villamor et al., 2019). For instance, post-entry quarantine (PEQ) for Fragaria imports into Australia used to require a minimum period of 24 months utilizing multiple indicator plants and bioassays; however, the use of high-throughput sequencing as a routine PEQ assay considerably shortened the quarantine period (Whattam et al., 2021).

The global trade system can be preserved,and the rural economy strengthened as advanced techniques are continued to be used to diagnose viruses more quickly, allowing for a rapid response and preventing the virus from spreading from one area to another. By reducing the risk of virus-driven supply chain disruptions and border rejections, these developments promote more stable global circulation of planting material and crop products, strengthen phytosanitary systems, and safeguard staple yields.

 

Conclusion

Plant viruses occupy a paradoxical position in biology: they are both incredible agents of disease and powerful tools for innovation. As we have shown, viral pathogens continue to impose immense pressures on global agriculture through yield losses, trade disruptions, and heightened vulnerability under climate change. At the same time, the decades of research into plant-virus coevolution have revealed incredible evolutionary logic, such as immune receptors, resistance networks, and viral countermeasures, that can all be deliberately harnessed. Advances in molecular farming, viral nanotechnology, CRISPR editing, RNA interference, and high-throughput surveillance are changing plant virology from a reactive field of study to a predictive and design-oriented science. An important lesson is that viruses are not defeated, but by working with evolutionary principles we can help plants to layer defences, preserve genetic diversity, and anticipate viral adaptation. By reframing viruses not just as enemies but as systems to be understood, managed, and repurposed we can protect crops, stabilize food systems, and innovate responsibly. In doing so, plant virology becomes a cornerstone of sustainable agriculture and a model for navigating broader challenges of living in a rapidly changing world.

 

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About the Authors

Jahed Ahmed

Jahed is a Marie Curie Postdoctoral Fellow at the Laboratory of Membrane Biogenesis, CNRS/University of Bordeaux and a 2026 Plantae Fellow . His research focuses on deciphering the roles of reactive oxygen species and calcium signaling in plant-virus interactions, exploring how pathogens hijack host membrane nanodomains to facilitate infection.

Kavita Joshi

Kavita is a 2026 Plantae Fellow with a background in plant biology who is passionate about plant science research, science communication, and education.She is interested in creating content for ASPB that makes plant science accessible and engaging for both the general public and the broader plant science community through simple and approachable communication. In her free time, she enjoys crafting, gardening, and exploring nature as an eco-enthusiast.

Trevor Melusen

Trevor is currently a researcher at Plasmidsaurus and a 2026 Plantae Fellow. He focuses on making Next-Generation Sequencing faster and more affordable for all researchers. . You can find him on X: @trevor_melusen