An outbreak of a new disease infecting tomatoes occurred in October-November 2014 at the Ohad village in Southern Israel. Symptomatic plants showed a mosaic pattern on leaves accompanied occasionally by narrowing of leaves and yellow spotted fruit. The disease spread mechanically and rapidly reminiscent of tobamovirus infection. Epidemiological studies showed the spread of the disease in various growing areas, in the South and towards the Southeast and Northern parts of the country within a year. Transmission electron microscope (TEM) analysis showed a single rod-like form characteristic to the Tobamovirus genus. We confirmed Koch’s postulates for the disease followed by partial host range determination and revealed that tomato cultivars certified to harbor the Tm-22 resistance gene are susceptible to the new viral disease. We further characterized the viral source of the disease using a range of antisera for serological detection and analyzed various virus genera and families for cross-reactivity with the virus. In addition, next generation sequencing of total small RNA was performed on two cultivars grown in two different locations. In samples collected from commercial cultivars across Israel, we found a single virus that caused the disease. The complete genome sequence of the new Israeli tobamovirus showed high sequence identity to the Jordanian isolate of tomato brown rugose fruit virus.

The effect of tomato yellow leaf curl virus (TYLCV) on total yield and yield components of various resistant F1 tomato cultivars and new breeding lines was evaluated in the field. Seeds of the F1 hybrids 8484, 3761, Fiona, and Tyking and the new breeding lines TY172 and TY197 were sown in an insect-proof greenhouse. When the seedlings reached the first-leaf stage, they were inoculated with TYLCV by means of the whitefly vector Bemisia tabaci. Noninoculated plants of the same cultivar or line which were exposed to nonviruliferous whiteflies served as controls. After a short recovery period, the plants were transplanted to the field. The inoculated plants of each cultivar or line were compared with their respective control, noninoculated plants, in terms of total yield, average fruit weight and number, and plant fresh weight. Disease symptom development and virus accumulation in the inoculated plants were monitored. There were substantial differences among the different entries tested in the extent of yield loss relative to the corresponding noninoculated control plants as well as viral DNA accumulation levels. Plants of TY172 and TY197 suffered the least relative yield loss and contained the lowest level of viral DNA. Therefore, these two lines exhibited the highest level of resistance. These results clearly demonstrate the ability of the various resistant tomato cultivars and lines to inhibit the effects of the virus, even following inoculation at a very early stage of plant development.

The bumblebee Bombus terrestris is a beneficial pollinator extensively used in tomato production. Our hypothesis was that bumblebee hives collected from a Tomato brown rugose fruit virus (ToBRFV) infected tomato greenhouse, preserve an infectious primary inoculum. Placing a bumblebee hive collected from a ToBRFV contaminated greenhouse, in a glass-/net-house containing only uninfected healthy tomato plants, spread ToBRFV disease. Control uninfected tomato plants grown in a glass-/net-house devoid of any beehive remained uninfected. ToBRFV-contaminated hives carried infectious viral particles as demonstrated in a biological assay on laboratory test plants of virus extracted from hive components. Viral particles isolated from a contaminated hive had a typical tobamovirus morphology observed in transmission electron microscopy. Assembly of ToBRFV genome was achieved by next generation sequencing analysis of RNA adhering to the bumblebee body. Bumblebee dissection showed that ToBRFV was mostly present in the abdomen suggesting viral disease spread via buzz pollination. These results demonstrate that bumblebee hives collected from ToBRFV-contaminated greenhouses carry a primary inoculum that reflects the status of viruses in the growing area. This new mode of ToBRFV spread by pollinators opens an avenue for detection of viruses in a growing area through analysis of the pollinators, as well as emphasizes the need to reevaluate the appropriate disease management protocols.

Reliable detection and identification of plant pathogens are essential for disease control strategies. Diagnostic methods commonly used to detect plant pathogens have limitations such as requirement of prior knowledge of the genome sequence, low sensitivity and a restricted ability to detect several pathogens simultaneously. The development of advanced DNA sequencing technologies has enabled determination of total nucleic acid content in biological samples. The possibility of using the single‐molecule sequencing platform of Oxford Nanopore as a general method for diagnosis of plant diseases was examined. It was tested by sequencing DNA or RNA isolated from tissues with symptoms from plants of several families inoculated with known pathogens (e.g. bacteria, viruses, fungi, phytoplasma). Additionally, samples of groups of 200 seeds containing one infected seed of each of two or three pathogens, as well as samples with symptoms but unidentified pathogens were tested. Sequencing results were analysed with Nanopore data analysis tools. In all the inoculated plants, pathogens were identified in real time within 1–2 h of running the Nanopore sequencer and were classified to the species or genus level. DNA sequencing or direct RNA sequencing of samples with unidentified disease agents were validated by conventional diagnostic procedures (e.g. PCR, ELISA, Koch test), which supported the results obtained by Nanopore sequencing. The advantages of this technology include: long read lengths, fast run times, portability, low cost and the possibility of use in every laboratory. This study indicates that adoption of the Nanopore platform will be greatly advantageous for routine laboratory diagnosis.

Tobamoviruses induce crop diseases that are responsible for significant economic losses around the world. Like other tobamoviruses, Cucumber green mottle mosaic virus (CGMMV) forms highly stable particles that can persist for long periods on plant debris, in soil and on seed surfaces. These particles serve as a primary source of infection, infecting seedlings from which the virus can then be mechanically transmitted to other neighbouring plants. Contaminated seeds also provide a route for the movement of the virus between countries and its introduction into new areas. Effective seed disinfection treatments and the use of uncontaminated seed may reduce the global prevalence of this virus. Several treatments based on the use of heat or chemicals have been reported to effectively eliminate CGMMV and other tobamoviruses from seeds. An evaluation of these treatments on highly contaminated seed lots revealed inconsistent results, which encouraged the construction of a more accurate detection method that combines morphological, serological, molecular and biological analyses in one protocol. The detection of viable (infectious) viral particles in seed treated with heat, trisodium phosphate or a combined treatment, indicates that these treatments are insufficient. The serological detection of CGMMV in the inner parts of infected seeds provides a possible explanation for the inconsistent efficacy of these treatments.