During summer and autumn 2019, virus-like disease symptoms were observed in tomato (Solanum lycopersicum) grown in several greenhouses in Chania (Crete, Greece) and Kyparissia (Messenia, Peloponnes...

Quinone outside inhibitors (QoI) are powerful fungicides, which have been reported, additionally to their fungicide activity, to increase plant capacity to activate cellular defense responses and to promote plant growth. In this work, the effect of the QoI class fungicide pyraclostrobin was examined against Cucumber mosaic virus (CMV), Potato virus Y (PVY) and Pseudomonas syringae pv. tomato in tomato plants following artificial inoculation of the plants with the pathogens. Under controlled environmental conditions, pyraclostrobin delayed viral and bacterial disease development, even if P. syringae pv. tomato internal population levels were not affected significantly. In contrast, under field conditions in commercial greenhouses, a reduced CMV disease incidence throughout the tomato cultivation period was recorded. Gene expression analysis indicated an effect of pyraclostrobin application on tomato MAPKs transcript levels and a possible interference with plant stress responses.

High-throughput sequencing (HTS) technologies and bioinformatic analyses are of growing interest to be used as a routine diagnostic tool in the field of plant viruses. The reliability of HTS workflows from sample preparation to data analysis and results interpretation for plant virus detection and identification must be evaluated (verified and validated) to approve this tool for diagnostics. Many different extraction methods, library preparation protocols, and sequence and bioinformatic pipelines are available for virus sequence detection. To assess the performance of plant virology diagnostic laboratories in using the HTS of ribosomal RNA depleted total RNA (ribodepleted totRNA) as a diagnostic tool, we carried out an interlaboratory comparison study in which eight participants were required to use the same samples, (RNA) extraction kit, ribosomal RNA depletion kit, and commercial sequencing provider, but also their own bioinformatics pipeline, for analysis. The accuracy of virus detection ranged from 65% to 100%. The false-positive detection rate was very low and was related to the misinterpretation of results as well as to possible cross-contaminations in the lab or sequencing provider. The bioinformatic pipeline used by each laboratory influenced the correct detection of the viruses of this study. The main difficulty was the detection of a novel virus as its sequence was not available in a publicly accessible database at the time. The raw data were reanalysed using Virtool to assess its ability for virus detection. All virus sequences were detected using Virtool in the different pools. This study revealed that the ribodepletion target enrichment for sample preparation is a reliable approach for the detection of plant viruses with different genomes. A significant level of virology expertise is needed to correctly interpret the results. It is also important to improve and complete the reference data.

Citrus impietratura disease (CID) is a graft transmissible, virus-like disease observed in old-line citrus trees; its characteristic symptom is the appearance of gum in the albedo of the affected fruits. To identify the causal agent of the disease, high-throughput sequencing (HTS) was performed on symptomatic orange fruits. The analysis of the obtained data revealed in all samples mixed infections of viroids commonly found in citrus trees together with the recently described citrus virus A (CiVA). Examination of additional symptomatic fruits with conventional reverse transcription PCR led to the identification of a single CiVA infection in one tree, which was verified by HTS. Indexing of the single CiVA-infected tree on indicator plants resulted in the appearance of characteristic symptoms in the leaves that were correlated with virus accumulation. Moreover, a comparative analysis among symptomatic and asymptomatic fruits derived from the same trees was performed and included the single CiVA-infected orange tree. The analysis revealed a positive correlation between the appearance of symptoms and the accumulation of CiVA RNAs. To facilitate CiVA detection during certification programs of propagation material, a quantitative RT-PCR targeting the movement protein of the virus was developed and evaluated for reliable and sensitive detection of the virus. To the best of our knowledge this is the first study that associates CiVA with the appearance of CID symptoms.

The disease “sharka”, caused by Potyvirus plumpoxi (plum pox virus), is the most harmful viral disease affecting stone fruits. The virus spreads over long distances through illegal and insufficiently controlled exchange of infected propagative plant material. Once established in an area, the virus spreads locally through vegetative propagation of infected plant material, and naturally through aphid-vectors. Previously considered a European problem, sharka has now been reported in 54 Prunus-growing countries in all continents except Oceania, although the disease has been eradicated from the United States of America. The economic cost of the disease in the 28 years from 1995 to 2023 is estimated to be €2.4 × 109, equivalent to approx. 0.17% of the stone fruit industry’s value. This includes more than over €2 × 109 in direct fruit losses, €1.4 million from international rejection of symptomatic fruit, and over €100 million in eradication and disease limitation costs. Indirect costs include €137 million, mainly associated with ELISA analyses, and approx. €130 million in costs related to research and science networks. Cumulative global losses from the sharka pandemic since the decade 1910/20 probably surpass €13 × 109. These outlays exclude indirect trade costs, economic losses, genetic erosion of traditional cultivars, and the costs of developing new cultivars tolerant or resistant to plum pox virus. The decline in these costs compared to the previously evaluated €10 billion from the 1970s to 2006 is analyzed. Four case studies (for Spain, Turkey, Chile, and Greece) illustrate different sharka scenarios and management strategies.

Tomato brown rugose fruit virus (ToBRFV; Tobamovirus fructirugosum) is a harmful virus significantly reducing yield and fruit quality in tomato. It was first detected in Israel and Jordan in 2015 and quickly reached a near-global distribution. Following the outbreak of ToBRFV in the Netherlands in 2019, the Dutch National Plant Protection Organization (NPPO-NL) created a Nextstrain build, which was updated in 2021 and 2023. Here, we announce the release of 82 new (near) complete ToBRFV genomes with associated metadata and the fourth version of the ToBRFV Nextstrain build, which has expanded from 179 to 336 (near) complete genomes. This ToBRFV Nextstrain build is a powerful tool for gaining more insight into the epidemiology of ToBRFV, i.e., on pathways of introduction and the spread and possible origin of the rapidly emerging clade 7 sequence type isolates. The ToBRFV Nextstrain build is available at https://nextstrain.nrcnvwa.nl/ToBRFV/20240205 . [ ] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .