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Lettuce ring necrosis virus (LRNV), genus Ophiovirus, was detected by the Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP) in June and November of 2021 in two samples of chili pepper fruits (Capsicum spp.), both in mixed infection with other viruses. The first sample originated from a production site in Belgium (Sample ID: 40009704) and the second from a production site in the Netherlands (Sample ID: 41115269). One of the fruits of 40009704 showed a light purple circular pattern, while fruits from 41115269 showed colored (ring)spots. The samples were analyzed using Illumina sequencing on a NovaSeq 6000 platform (PE 150) as described previously (Hammond et al., 2021), obtaining 39.9M and 22.8M total reads for 40009704 and 41115269. The corresponding sequence read archives (SRA) were deposited in the NCBI SRA database under BioProject accession number PRJNA917231. From both samples, the nearly complete genome of LRNV (RNA1-4) was obtained and deposited in GenBank (40009704, OQ160823- OQ160826 (7616, 1799, 1502, 1382 nt, mapped reads: 40K, 12K, 114K, 12K , average read coverage (ARC): 0.8K, 0.9K, 11.3K and 1.1K); 41115269, OQ160827- OQ160830 (7616, 1801, 1518, 1389 nt, mapped reads: 112K, 7K, 357K, 55K reads, ARC: 2.2K, 0.6K, 34K and 5.8K)). The shared sequence identities with the Genbank reference sequence of LRNV (NC_006051-NC_006051) were 99.2 and 99.2% (RNA1), 99.1 and 99.1% (RNA2), 98.3 and 98.8% (RNA3), 99.0 and 98.9% (RNA4) for 40009704 and 41115269 respectively. The shared sequence identities between 40009704 and 41115269 were 99.9 (RNA1), 99.0 (RNA2), 99.1 (RNA3) and 99.5% (RNA4). In addition to LRNV, the ophiovirus ranunculus white mottle virus (RWMV) was detected in both samples (OQ160831-OQ160834; OQ160835-OQ160838), while the tobamovirus pepper mild mottle virus (PMMoV) was present in the fruits of 41115269 (OQ160839). Since RWMV has been associated with leaf symptoms in pepper (Gambley et al., 2019; Rivarez et al., 2022) and the colored (ring)spots of 41115269 were very similar to reported symptoms of PMMoV-infected pepper fruits (Martínez-Ochoa et al., 2003), it remains unclear whether LRNV contributed to the observed symptoms. Additionally, LRNV was detected in tomato (Solanum lycopersicum) in Belgium in 2020. In the frame of a metagenomic survey using Virion-Associated Nucleic Acids (VANA)-based protocol (Maclot et al., 2021) on a Nextseq 500 platform (PE 150), partial genome sequences of LRNV were detected in two pools of tomato plants. One pool was made of 44 asymptomatic cultivars from a non-commercial grower (one sample per cultivar) yielding 118K total reads of which 84, 59, 335, and 18 reads mapped on RNA1, 2, 3, and 4, covering 35%, 69%, 100% and 55% of the genome, respectively. The other pool consisted of 15 plants from one cultivar from a production site yielding 3.1M total reads of which 6 and 5 reads mapped on RNA3 and 4, respectively. The detection of LRNV was confirmed for both pooled samples using the real-time RT-PCR method, targeting the CP gene, as described by Maachi et al. (2021). To our knowledge this is the first report of LRNV in pepper anywhere in the world. Additionally, although the disease lettuce ring necrosis in lettuce (Lactuca sativa) has been described in Belgium and the Netherlands before the causal agent was identified (Bos & Huijberts, 1996), this is the first official report of this virus in Belgium and the Netherlands. This publication resulted from pre-publication data sharing of sequences and biological data among plant virologists to provide more context to two independent findings (Hammond et al., 2021). Bos, L., & Huijberts, N. (1996). Lettuce ring necrosis, caused by a chytrid-borne agent distinct from lettuce big-vein ‘virus’. European Journal of Plant Pathology, 102(9), 867-873. https://doi.org/10.1007/bf01877057 Gambley, C., Persley, D., & Thomas, J. E. (2019). First record of Ranunculus white mottle virus from Australia. New Disease Reports, 40(1), 13-13. https://doi.org/10.5197/j.2044-0588.2019.040.013 Hammond, J., Adams, I. P., Fowkes, A. R., McGreig, S., Botermans, M., Oorspronk, J. J. A., Westenberg, M., Verbeek, M., Dullemans, A. M., Stijger, C. C. M. M., Blouin, A. G., Massart, S., De Jonghe, K., Heyneman, M., Walsh, J. A., & Fox, A. (2021). Sequence analysis of 43‐year old samples of Plantago lanceolata show that Plantain virus X is synonymous with Actinidia virus X and is widely distributed. Plant Pathology, 70, 249-258. https://doi.org/10.1111/ppa.13310 Maachi, A., Torre, C., Sempere, R. N., Hernando, Y., Aranda, M. A., & Donaire, L. (2021). Use of High-Throughput Sequencing and Two RNA Input Methods to Identify Viruses Infecting Tomato Crops. Microorganisms, 9(5). https://doi.org/10.3390/microorganisms9051043 Maclot, F. J., Debue, V., Blouin, A. G., Fontdevila Pareta, N., Tamisier, L., Filloux, D., & Massart, S. (2021). Identification, molecular and biological characterization of two novel secovirids in wild grass species in Belgium. Virus Res, 298, 198397. https://doi.org/10.1016/j.virusres.2021.198397 Martínez-Ochoa, N., Langston, D. B., Mullis, S. W., & Flanders, J. T. (2003). First Report of Pepper mild mottle virus in Jalapeno Pepper in Georgia. Plant Health Progress, 4(1). https://doi.org/10.1094/php-2003-1223-01-hn Rivarez, M. P. S., Kogej, Z., Jakos, N., Pecman, A., Seljak, G., Vucurovic, A., Ravnikar, M., Mehle, N., & Kutnjak, D. (2022). First Report of Ranunculus White Mottle Ophiovirus in Slovenia in Pepper with Yellow Leaf Curling Symptom and in Tomato. Plant Dis, PDIS08211624PDN. https://doi.org/10.1094/PDIS-08-21-1624-PDN

With the emergence of high throughput sequencing (HTS) technologies, the discovery of new plant viruses has outpaced their biological characterization. However, it is crucial to understand the biology of these viruses to evaluate the risks they pose for the production of crops and natural ecosystems and to manage them properly. In 2018, Physostegia chlorotic mottle virus (PhCMoV) was detected in Austria in aPhysostegiaplant (Lamiaceae) using HTS, and subsequent prepublication data sharing associated the presence of the virus with severe fruit symptoms on important crops like tomato, eggplant, and cucumber across nine European countries. This discovery led to a collaborative effort to understand better the virus’s genetic diversity, host range, symptomatology, and distribution. Still, specific knowledge gaps remained. In this study, the authors address these gaps by examining the transmission mode, prevalence, and disease severity of PhCMoV. Bioassay and field survey confirmed the causal association between the presence of the virus and symptoms on tomato and eggplant. The investigation also mapped out the historical and geographic footprint of the virus, spanning back 30 years and including a new location, Switzerland. Based on field survey, PhCMoV was found to naturally infect 11 new host plant species across seven families, extending the host range of PhCMoV to 20 plant species across 14 plant families. Greenhouse assays with mechanical inoculation showed that yield losses could reach 100% depending on the phenological stage of the plant at the time of infection. The study also identified a polyphagous leafhopper species (Anaceratagalliasp.) as the natural vector of PhCMoV. PhCMoV was widespread in diversified vegetable farms in Belgium where tomato is grown in soil, occurring in approximately one-third of such farms. However, outbreaks were sporadic and it can be suggested that they were associated with specific cultural practices, such as the cultivation of perennial plants in tomato tunnels that can serve as a host for both the virus and its vector. To further explore this phenomenon and better manage the virus, studying the ecology of theAnaceratagalliaevector would be beneficial.

The number of small-scale diversified vegetable growers in industrialized countries has risen sharply over the last ten years. The risks associated with plant viruses in these systems have been barely studied in Europe, yet dramatic virus emergence events, such as tomato brown fruit rugose virus, sometimes occur. We developed a methodology that aimed to understand better the implications related to viruses for tomato production in Belgian’s vegetable farms by comparing growers’ perception of the presence of viral symptoms (visual inspection) with non targeting detection of nearly all viruses present in the plants by high throughput sequencing technologies (HTS). Virus presence and impact were interpreted considering the farm’s typology and cultural practices, the grower’s professional profiles, and visual inspection of plant-viral-like symptoms. Overall, The data indicated that most growers have limited understanding of tomato viruses and are not concerned about them. Field observations were correlated to this perception as the prevalence of symptomatic plants was usually lower than 1%. However, important and potentially emergent viruses, mainly transmitted by insects, were detected in several farms. Noteworthy, the presence of these viruses was correlated with the number of plant species grown per site (diversity) but not with a higher awareness of the growers regarding plant viral diseases or a higher number of symptomatic plants. In addition, both HTS and perception analysis underlined the rising incidence and importance of an emergent virus: Physostegia chlorotic mottle virus. Overall, the original methodology developed here, combining social science with HTS technologies, could be applied to other crops in other systems to identify emergent risks associated with plant viruses and can highlight the communication needed toward growers to mitigate epidemics.

Susceptibility to fungal pathogens and plant immunity in rice and wheat can be modulated by the presence of intraspecific neighbours and does not require the neighbours to be infected., As part of a trend towards diversifying cultivated areas, varietal mixtures are subject to renewed interest as a means to manage diseases. Besides the epidemiological effects of varietal mixtures on pathogen propagation, little is known about the effect of intraspecific plant–plant interactions and their impact on responses to disease. In this study, genotypes of rice (Oryza sativa) or durum wheat (Triticum turgidum) were grown with different conspecific neighbours and manually inoculated under conditions preventing pathogen propagation. Disease susceptibility was measured together with the expression of basal immunity genes as part of the response to intra-specific neighbours. The results showed that in many cases for both rice and wheat susceptibility to pathogens and immunity was modified by the presence of intraspecific neighbours. This phenomenon, which we term ‘neighbour-modulated susceptibility’ (NMS), could be caused by the production of below-ground signals and does not require the neighbours to be infected. Our results suggest that the mechanisms responsible for reducing disease in varietal mixtures in the field need to be re-examined.

Application of high throughput sequencing (HTS) technologies enabled the first identification of Physostegia chlorotic mottle virus (PhCMoV) in 2018 in Austria. Subsequently, PhCMoV was detected in Germany and Serbia on tomatoes showing severe fruit mottling and ripening anomalies. We report here how prepublication data-sharing resulted in an international collaboration across eight laboratories in five countries, enabling an in-depth characterization of PhCMoV. The independent studies converged toward its recent identification in eight additional European countries and confirmed its presence in samples collected 20 years ago (2002). The natural plant host range was expanded from two to nine species across seven families, and we confirmed the association of PhCMoV presence with severe fruit symptoms on economically important crops such as tomato, eggplant, and cucumber. Mechanical inoculations of selected isolates in the greenhouse established the causality of the symptoms on a new indexing host range. In addition, phylogenetic analysis showed a low genomic variation across the 29 near-complete genome sequences available. Furthermore, a strong selection pressure within a specific ecosystem was suggested by nearly identical sequences recovered from different host plants through time. Overall, this study describes the European distribution of PhCMoV on multiple plant hosts, including economically important crops on which the virus can cause severe fruit symptoms. This work demonstrates how to efficiently improve knowledge on an emergent pathogen by sharing HTS data and provides a solid knowledge foundation for further studies on plant rhabdoviruses. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .