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Tomato (Solanum lycopersicum) plants from a commercial glasshouse were identified with symptoms compatible with a tomato brown rugose fruit virus (ToBRFV) infection. Reverse transcription-PCR and quantitative PCR confirmed the presence of ToBRFV. Subsequently, the same RNA sample and a second from tomato plants infected with a similar tobamovirus, tomato mottle mosaic virus (ToMMV), were extracted and processed for high-throughput sequencing with the Oxford Nanopore Technology (ONT). For the targeted detection of ToBRFV, the two libraries were synthesized by using six ToBRFV sequence-specific primers in the reverse transcription step. This innovative target enrichment technology enabled deep coverage sequencing of ToBRFV, with 30% of the total reads mapping to the target virus genome and 57% mapping to the host genome. The same set of primers applied to the ToMMV library generated 5% of the total reads mapping to the latter virus, indicating that sequencing of similar, non-target viral sequences was also allowed. Further, the complete genome of pepino mosaic virus (PepMV) was also sequenced from the ToBRFV library, thus suggesting that, even using multiple sequence-specific primers, a low rate of off-target sequencing can usefully provide additional information on unexpected viral species coinfecting the same samples in an individual assay. These results demonstrate that targeted nanopore sequencing can specifically identify viral agents and has sufficient sensitivity towards non-target organisms to provide evidence of mixed virus infections.

Mosaic diseases caused by tobamoviruses have posed significant threats to tomato production. In this review, we overview studies of tomato mosaic diseases published over the past century, which have led to several important discoveries in plant virology, such as the application of attenuated strains. A resistance breeding program established in the 1970s successfully controlled tomato mosaic virus for over 40 years; however, newly emerging tobamoviruses are posing serious challenges in current tomato production. We introduce recent biotechnological attempts to engineer tobamovirus-resistant tomato plants, which offer promising technologies for eradicating the current outbreak.

Many countries have identified tomato mottle mosaic virus (ToMMV) as a serious threat to tomato production. Here, we constructed and characterized infectious clones of ToMMV isolated from Japanese sweet pepper seeds. The genome of the Japanese isolate is 6399 nucleotides in length and exhibits the highest identity with previously characterized isolates. For example, it is 99.7% identical to that of the Mauritius isolate, which occurs worldwide. Phylogenetic analysis based on complete genome sequences revealed that the Japanese isolates clustered in the same clade as those from other countries. When homozygous tomato cultivars with tobamovirus resistance genes were inoculated with an infectious cDNA clone of ToMMV, the virus systemically infected tomato plants with symptoms typical of Tm-1-carrying tomato cultivars. In contrast, tomato cultivars carrying Tm-2 or Tm-22 showed symptoms only on the inoculated leaves. Furthermore, when commercial cultivars of Tm-22 heterozygous tomato were inoculated with ToMMV, systemic infections were observed in all cultivars, with infection frequencies ranging from 25 to 100%. Inoculation of heterozygous sweet pepper cultivars with tobamovirus resistance genes (L1, L3, and L4) with ToMMV resulted in an infection frequency of about 70%, but most of the infected L1, L3, and L4 cultivars were symptomless, and 10-20% showed symptoms of necrosis and yellowing. Tomato mosaic virus strain L11A, an attenuated virus, did not provide cross-protection against ToMMV and led to systemic infection with typical symptoms. These results suggest that ToMMV might cause extensive damage to existing tomato and sweet pepper cultivars commonly grown in Japan.

Tomato mottle mosaic virus (ToMMV) is a tobamovirus found in a Solanum lycopersicum sample collected in Mexico in 2009. To assess the possible presence of ToMMV in Europe, accessions from a historic seed collection were tested by real-time RT-PCR and Illumina sequencing. ToMMV was identified in historical seed accessions produced in France, the Netherlands and Spain. Three different near complete genome sequences were obtained, each corresponding to the country in which the seeds had been produced. Positive samples from France and Spain could be related to the same production location and year, respectively, while the identical genome sequences from the Netherlands were obtained from samples produced in different locations and years between 1981 and 2007. The latter could be due to the fact that the Dutch seed accessions had been repacked in the past at the same location and time as accessions with a relatively high virus load from 2007. This indicates that possibly only the seeds from 2007 originated from ToMMV-infected plants, while the detection of ToMMV in the older seed accessions resulted from cross contamination. This data shows that ToMMV has been around in Europe before its first description and is possibly more widespread than currently known.

The solanaceous-infecting tobamoviruses are closely related and hence it can be challenging to detect them using serological or molecular methods, particularly when present in a mixed infection. Tomato mottle mosaic virus (ToMMV) is a newly identified tobamovirus that poses serious risk to tomato ( Solanum lycopersicum L.) and pepper ( Capsicum annuum L.) production worldwide. Species-specific identification is crucial to prevent the entry and establishment of plant pathogens and protect the billion-dollar tomato industry. In this study, we report the validation of a previously described reverse transcription polymerase chain reaction (RT-PCR) assay that amplifies a 289 bp fragment of the coat protein coding region of ToMMV genome. This assay has 100% specificity for ToMMV. Inclusivity tests were performed against a diverse collection of six ToMMV isolates in North America. Exclusivity tests showed no cross reaction with eleven non-target viruses and seven viroids commonly found on tomato and pepper host plants. The detection limit of the one-step RT-PCR was determined to be at 10 -5 (or 0.25pg/μl) dilution in plant samples, with its amplicon sequence confirmed by Sanger sequencing. The RT-PCR can detect ToMMV consistently on contaminated seed or leaf tissues. This validated assay could serve as a standard method for detecting ToMMV in seed health testing and for plant disease diagnosis, thus to prevent inadvertent introduction and spread of this emerging and economically important tobamovirus in tomato and pepper fields.

Seed lots of tomato and capsicum (Solanum lycopersicon and Capsicum annuum, respectively) are required to be free of quarantine pests before their entry to Australia is permitted. Testing of samples from 118 larger seed lots in the period 2019–2021 revealed that 31 (26.3%) carried one or more of four Tobamovirus species, including tomato mottle mosaic virus (ToMMV), which is a quarantine pest for Australia. Testing of samples from a further 659 smaller seed lots showed that 123 (18.7%) carried a total of five Tobamovirus species, including ToMMV and tomato brown rugose fruit virus (ToBRFV), which is also a quarantine pest for Australia. Estimated prevalence of contamination by tobamoviruses ranged from 0.388% to 0.004% in contaminated larger seed lots. Analyses of these data allow us to estimate probabilities of detection of contamination under different regulatory settings.

Abstract Tomato mottle mosaic virus (ToMMV) poses a threat to production and quality of tomato fruits. The Tm-2 2 gene confers resistance to some tobamoviruses by recognizing viral movement proteins. However, Tm-2 2 -mediated resistance against ToMMV is not well known. Here, we found that ToMMV could infect wild-type but not Tm-2 2 transgenic Nicotiana benthamiana plants and could also infect tomato cultivar Moneymaker but not resistant cultivar Jili with homozygous Tm-2 2 . Chimeric viral ToMMVToBRFV−MP with swapped ToMMV MP to MP of tomato brown rugose fruit virus could systemically infect Tm-2 2 transgenic N. benthamiana and tomato cultivars Jili plants. Further, transient expression of ToMMV MP in the leaves of Tm-2 2 transgenic N. benthamiana plants induced hypersensitive response-associated cell death, suggesting that the MP of ToMMV was the avirulent factor for the Tm-2 2 resistance gene. ToMMV could infect Tm-2 2 -containing cultivar Jinpeng 1 but not Chaobei. Sequence analysis revealed that cultivars Chaobei and Jinpeng 1 were heterozygous, where Chaobei consists of Tm-2 2 and Tm-2 genes, while Jinpeng 1 consists of Tm-2 2 and tm-2 genes. Transient co-expression assays showed that both Tm-2 2 and Tm-2 but not tm-2 could recognize ToMMV MP and induce hypersensitivity response-associated cell death in N. benthamiana leaves, suggesting that homozygous tomato harboring Tm-2 2 and heterozygous tomato containing Tm-2 2 and Tm-2 may exhibit more durable resistance to ToMMV than heterozygous tomato carrying Tm-2 2 and tm-2. Further, Tm-2 2 transgenic N. benthamiana and tomato cultivar Jili plants with silenced Tm-2 2 gene were susceptible to ToMMV. Also, silencing type-I J-domain MIP1 gene compromised Tm-2 2 -mediated resistance to ToMMV in Tm-2 2 transgenic N. benthamiana and tomato cultivar Jili. Moreover, we found that viral RNA could accumulate in the systemic leaves of Tm-2 2 transgenic N. benthamiana plants and tomato cultivar Jili at 35°C, but not at 20, 25, or 30°C. Altogether, our findings reveal that the Tm-2 2 confers resistance to ToMMV by recognizing MP, and the resistance is regulated by the allele combinations, accumulation levels of Tm-2 2 , MIP1, and the temperature.

Tomato is known to be a natural and experimental reservoir host for many plant viruses. In the last few years a new tobamovirus species, Tomato mottle mosaic virus (ToMMV), has been described infecting tomato and pepper plants in several countries worldwide. Upon observation of symptoms in tomato plants growing in a greenhouse in Valencia, Spain, we aimed to ascertain the etiology of the disease. Using standard molecular techniques, we first detected a positive sense single-stranded RNA virus as the probable causal agent. Next, we amplified and sequenced its full-length genomic RNA which identified the virus as a new ToMMV isolate. Through extensive assays on distinct plant species, we investigated the host range of the Spanish ToMMV isolate. Several plant species were locally and/or systemically infected by the virus, some of which had not been previously reported as ToMMV hosts despite they are commonly used in research greenhouses. Finally, two reliable molecular diagnostic techniques were developed and used to assess the presence of ToMMV. This is the first observation of ToMMV in tomato plants in Europe. We discuss the possibility that, given the high sequence homology between ToMMV and Tomato mosaic virus , the former may have been mistakenly diagnosed as the latter by serological methods.

Background Tomato mottle mosaic virus (ToMMV) is a recently identified species in the genus Tobamovirus and was first reported from a greenhouse tomato sample collected in Mexico in 2013. In August 2013, ToMMV was detected on peppers ( Capsicum spp.) in China. However, little is known about the molecular and biological characteristics of ToMMV. Methods Reverse transcription-polymerase chain reaction (RT-PCR) and rapid identification of cDNA ends (RACE) were carried out to obtain the complete genomic sequences of ToMMV. Sap transmission was used to test the host range and pathogenicity of ToMMV. Results The full-length genomes of two ToMMV isolates infecting peppers in Yunnan Province and Tibet Autonomous Region of China were determined and analyzed. The complete genomic sequences of both ToMMV isolates consisted of 6399 nucleotides and contained four open reading frames (ORFs) encoding 126, 183, 30 and 18 kDa proteins from the 5’ to 3’ end, respectively. Overall similarities of the ToMMV genome sequence to those of the other tobamoviruses available in GenBank ranged from 49.6% to 84.3%. Phylogenetic analyses of the sequences of full-genome nucleotide and the amino acids of its four proteins confirmed that ToMMV was most closely related to Tomato mosaic virus (ToMV). According to the genetic structure, host of origin and phylogenetic relationships, the available 32 tobamoviruses could be divided into at least eight subgroups based on the host plant family they infect: Solanaceae-, Brassicaceae-, Cactaceae-, Apocynaceae-, Cucurbitaceae-, Malvaceae-, Leguminosae-, and Passifloraceae-infecting subgroups. The detection of ToMMV on some solanaceous, cucurbitaceous, brassicaceous and leguminous plants in Yunnan Province and other few parts of China revealed ToMMV only occurred on peppers so far. However, the host range test results showed ToMMV could infect most of the tested solanaceous and cruciferous plants, and had a high affinity for the solanaceous plants. Conclusions The complete nucleotide sequences of two Chinese ToMMV isolates from naturally infected peppers were verified. The tobamoviruses were divided into at least eight subgroups, with ToMMV belonging to the subgroup that infected plants in the Solanaceae. In China, ToMMV only occurred on peppers in the fields till now. ToMMV could infect the plants in family Solanaceae and Cucurbitaceae by sap transmission.

Tomato mottle mosaic virus (ToMMV) is an emerging seed-transmissible tobamovirus that infects tomato and pepper. Since the first report in 2013 in Mexico, ToMMV has spread worldwide, posing a serious threat to the production of both crops. To prevent the spread of this virus, early and accurate detection of infection is required. In this study, we developed a detection method for ToMMV based on reverse-transcription loop-mediated isothermal amplification (RT-LAMP). A LAMP primer set was designed to target the genomic region spanning the movement protein and coat protein genes, which is a highly conserved sequence unique to ToMMV. This RT-LAMP detection method achieved 10-fold higher sensitivity than conventional RT-polymerase chain reaction methods and obtained high specificity without false positives for closely related tobamoviruses or healthy tomato plants. This method can detect ToMMV within 30 min of direct sampling of an infected tomato leaf using a toothpick and therefore does not require RNA purification. Given its high sensitivity, specificity, simplicity, and rapidity, the RT-LAMP method developed in this study is expected to be valuable for point-of-care testing in field surveys and for large-scale testing.