Diseases caused by emerging viruses have become more and more important over the last few decades in terms of their incidence and economic impact. Currently, the most economically important emerging virus is the tobamovirus tomato brown rugose fruit virus (ToBRFV), which emerged in Israel around 2014. Since then, outbreaks of ToBRFV have occurred around the world, including recent outbreaks in several European countries. This endangers tomato and pepper production, the main host plants for ToBRFV. The same crops can be severely infected also by other emerging tobamoviruses, such as tomato mottle mosaic virus (ToMMV), which was first described in 2013 in Mexico, and was subsequently found in the Americas, Asia and Europe. Due to their physical and biological properties, tobamoviruses can spread rapidly and have high epidemic potential. Similarly, as for coronaviruses in wild animals, a search for yet unknown tobamoviruses in different plant species and in different environmental sample matrices should provide us with valuable information, possibly before the emergence of such species as crop pathogens. This would enable quicker development of tests and it should provide better understanding of the possible points of origin of such viruses. The latter can help us to better understand the possible future spread of such viruses in crops, and consequently, it provides us with better means for containment of any further spread.

Modern agriculture requires the use of irrigation in plant production and global food security can be threatened by the severe shortage of water that arises from shifts in climate patterns. Hydroponic systems are now commonly used for production of some plant species, and as they require significantly less water, they can contribute to the solution of the global problem of water shortage. On the other hand, the use of circulating nutrient solutions in hydroponic systems holds the potential for rapid and effective spread of water-transmissible plant pathogens throughout a whole crop, thus increasing the chance of pathogen outbreaks if the system is not managed intensively. It has already been shown that waters used for irrigation represent a source of inoculum for some environmentally stable viruses. However, it is worth noting that survival in water has been studied for only a few plant pathogenic viruses, with even fewer studies carried out to assess the potential for water-mediated transmission of such viruses. To date, no studies have investigated how long ToBRFV can survive in a water environment, nor the possibility and/or efficiency of its transmission to plants through irrigation water. This knowledge is essential for future epidemiology and risk assessment studies. Similar studies to fill the gaps in the knowledge of epidemiology are needed also for ToMMV, and also for other newly discovered (re)emerging tobamoviruses.

The outcomes of the proposed project will certainly serve to expand the current knowledge on plant viruses, their epidemiology and the burden they pose for important field crops, such as tomato, pepper, cucurbits, and others. Searching for known and novel tobamoviruses in already published sequence datasets from wastewater samples, human or animal gut samples, and transcriptomes of different plant species, along with the phylogenetic characterisation of the tobamoviral genomes found, will help to update the member composition of the genus Tobamovirus and trigger studies on the potential impact on crops of any newly found member(s). The catalogue of sequences of known and likely also novel tobamoviruses that they expect to deliver within the project will also serve as baseline for the assessment of future new tobamovirus emergences as crop pathogens. Assessing water as a route of transmission of emergent tobamoviruses and providing efficient methods for their concentration and detection in this matrix will help to determine the relevance of water as a potentially important modulator of tobamovirus epidemiology. This is especially relevant for arid regions, where water is scarce and where in many cases treated reclaimed wastewater is used for irrigation. This is relevant also for plants growing in hydroponic systems, as the use of circulating nutrient solutions in hydroponic systems might facilitate rapid spread of water-transmissible plant pathogens throughout the whole crop. This can increase the chances of epidemics if it is not managed appropriately. ToBRFV is one of the major actual threats to tomato as it can overcome the resistance of most commonly used tomato cultivars, and it is rapidly spreading from its present regions (Jordan, Israel) to Europe. Taking into consideration the high environmental resilience of tobamoviruses, water is an important suspect for a role in the epidemiology of ToBRFV and other emerging tobamoviruses. However, this has not been demonstrated yet. In the proposed project, we will aim to expand the knowledge on the epidemiology and behaviour of these important plant pathogens, and to devise novel efficient strategies for plant protection through prevention and improved diagnostics.