Invisible to the eye yet devastating in the field, viroids are inspiring breakthrough research to safeguard sustainable agriculture and future food security
The greatest threats to agriculture are not always the ones we can see. Some are invisible, silent and astonishingly small. Viroids, the smallest infectious particles known to science, are often mistaken for viruses, yet these tiny circles of RNA can devastate crops, reduce yields and inflict millions of euros in economic losses. As climate change and global trade reshape the spread of plant diseases, scientists are uncovering new ways to detect, understand, and, utlimately, defeat these elusive pathogens.
Understanding the challenge viroids present
Their story began over a century ago. In the 1920s, potato growers in the United States faced a mysterious disease that produced elongated, misshapen tubers and reduced yields by up to 60%. The cause remained elusive until 1971, when plant pathologist Theodor Otto Diener identified an entirely new type of pathogen: a tiny circular RNA molecule that could make copies of itself and damage host cells without producing proteins. It also lacked the protective protein coat typical of viruses. These tiny infectious molecules continue to challenge agriculture and have profound biological and economic consequences.
Today, around 45 different viroids are known to infect vegetables, fruit trees, grapevines, hops, and ornamental plants. Infected plants may become stunted, develop yellow or distorted leaves, produce poor quality fruit, or even die. Yet some infections produce no visible symptoms at all, allowing apparently healthy plants to spread disease unnoticed through commercial production systems, while wild plants can act as hidden reservoirs. Viroids spread efficiently through contaminated pruning and harvesting tools, direct plant contact, seeds, pollen, and even insects. With no chemical cure and very limited natural resistance available, early detection, disease-free planting material, and strict hygiene remain the most effective crop protection measures. Recent outbreaks in new crops and regions demonstrate how global trade and climate change are reshaping their dynamics and distribution, highlighting the urgent need for new approaches to disease prevention and control.
ViroiDoc: A collaborative effort focused on sustainable crop protection against viroids
Meeting that challenge is ViroiDoc, a Marie Skłodowska-Curie Doctoral Network, which brings together 22 academic and industrial partners from 11 countries across Europe and the Americas. Ten doctoral students, supported by leading experts, are tackling viroids from every angle, combining expertise in molecular biology, genomics, biotechnology, diagnostics, and plant pathology to reveal how these pathogens infect plants and how they can be stopped. Together, their work is building a scientific toolkit for the next generation of sustainable crop protection.
The first step is understanding the enemy. At the University of Ljubljana, researchers are analysing large genomic and transcriptomic datasets to identify plant proteins and biological pathways that either promote or restrict viroid infection. In Italy, scientists at the National Research Council and the University of Bari ‘Aldo Moro’ are comparing symptomatic and symptomless infections in tomato and chrysanthemum plants to understand why some plants develop disease while others remain apparently unaffected.
Meanwhile, at the University of Crete, researchers are investigating host proteins required for viroid replication, while at the Centre National de la Recherche Scientifique in Strasbourg they are developing advanced methods to visualise viroid movement inside living plant cells and identify the proteins that transport these pathogens throughout the plant. Together, these studies are exposing the molecular weak points that could be exploited to engineer crops with improved resistance and develop more effective disease management strategies.
From chasing the invisible culprits to rapid and reliable detection
Understanding infection is only half the battle. Detecting viroids before they spread is equally critical. Researchers at the Spanish National Research Council and the Polytechnic University of València have developed a CRISPR-Cas13a-based assay capable of detecting viroids directly without RNA amplification, laying the groundwork for rapid field diagnostics of plant RNA pathogens.
At the National Institute of Chemistry in Slovenia, another team is developing a portable electrochemical genosensor designed to detect viroids during the earliest stages of infection. The prototype has already demonstrated reliable performance and is now being refined to improve sensitivity and selectivity. Faster and more accessible diagnostics could transform routine disease surveillance by allowing infections to be identified before they become costly outbreaks.
Breaking new ground: Antiviroidal drugs and RNA-based plant protection
While better diagnostics help contain disease, ViroiDoc researchers are also pioneering entirely new ways of crop protection. At the Polytechnic University of València, scientists have engineered a tobacco cell system that supports viroid replication, creating a powerful platform for screening the first antiviroidal compounds and simultaneously monitoring compound cytotoxicity. More broadly, this model system can also reveal how plants recognise foreign RNA.
At the University of Regensburg, researchers are harnessing the plant’s natural process of RNA interference to design highly specific RNA sprays that either directly target viroid RNA and interfere with viroid replication or intracellular trafficking or temporarily suppress plant genes required for infection. Because these RNA-based approaches are non-transgenic, highly specific and environmentally compatible, they offer an attractive alternative to conventional chemical crop protection.
These innovations point towards a future where viroid plant diseases can be managed with greater precision and a smaller environmental footprint.
Climate-driven viroid risks and new opportunity for fungal biocontrol
At the Slovenian Institute of Hop Research and Brewing, researchers are examining how rising temperatures and drought influence viroid transmission and plant susceptibility, with early observations suggesting that warmer conditions may favour disease spread. Meanwhile, scientists at the National Research Council and the University of Bari ‘Aldo Moro’ are exploring newly discovered viroid-like RNAs in fungi to determine whether these naturally occurring molecules could one day contribute to biological control of fungal crop diseases. By anticipating future risks and uncovering unexpected biological opportunities, these projects are helping agriculture prepare for a changing world.
Although viroids remain largely unknown outside specialist scientific circles, their impact on global food production is becoming increasingly difficult to ignore. By combining fundamental research with practical innovation, the ViroiDoc network is delivering new knowledge, diagnostic technologies and sustainable protection strategies that could reshape the way growers manage these invisible pathogens.
Disclaimer
The ViroiDoc – Advanced research on viroid pathogenesis and control for agricultural sustainability is a project coordinated by the University of Ljubljana, Slovenia and funded by the European Union within the Horizon Europe MSCA Doctoral Networks (Grant Agreement Number: 101169421).
Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or European Research Executive Agency. Neither the European Union nor the granting authority can be held responsible for them.
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