First Report of Tomato torrado virus on Weed Hosts in Spain

A Novel Distinct Genetic Variant of Tomato Torrado Virus with Substantially Shorter RNA1-Specific 3’Untranslated Region (3’UTR)

Tomato torrado virus (ToTV) induces severe systemic necrosis in Solanum lycopersicum. This work aimed at describing the genetic variability of necrosis-inducing ToTV-Wal’17 collected in 2017, derived from the ToTV-Wal’03 after long-term passages in plants. Sequence analyses of the ToTV-Wal’17 indicated twenty-eight single nucleotide substitutions in coding sequence of both RNAs, twelve of which resulted in amino acid changes in viral polyproteins. Moreover the sequencing data revealed that the 3’UTR of ToTV-Wal’17 RNA1 was 394 nts shorter in comparison to Wal’03. The performed sequence analyses revealed that 3’UTR of RNA1 of ToTV-Wal’17 is the most divergent across all previously described European isolates.

Detection of Four New Tomato Viruses in Serbia Using Post Hoc High-Throughput Sequencing Analysis of Samples From a Large-Scale Field Survey

Tomato production worldwide is affected by numerous plant virus species. The early and accurate detection of viruses is a critical step for disease control. However, the simultaneous detection of the most known tomato viruses can be difficult because of the high number and diversity of tomato-infecting viruses. Here, we have identified four new viruses in Serbia by applying target-independent small RNA high-throughput sequencing (HTS). HTS was applied on pools of samples and separate samples, in total comprising 30 tomato samples that exhibited (severe) virus-like symptoms and were collected in Serbia during three annual surveys (2011 to 2013). These samples had previously tested negative for the presence of 16 tomato viruses using targeted detection methods. Three divergent complete genome sequences of Physostegia chlorotic mottled virus were obtained from different localities, indicating for the first time that this virus is widespread in Serbia and might represent an emergent viral pathogen of tomato. The tomato torrado virus was detected at one locality with devastating yield losses. The southern tomato virus was detected at two localities, and the spinach latent virus was detected at one locality. In addition, we detected the presence of one already-known virus in Serbia, the tomato spotted wilt orthotospovirus. All the HTS results were subsequently confirmed by targeted detection methods. In this study, the successful application of post hoc HTS testing of a limited number of pooled samples resulted in the discovery of new viruses. Thus, our results encourage the use of HTS in research and diagnostic laboratories, including laboratories that have limited resources to resolve disease etiology.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing

Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato.

Contribution of Tomato torrado virus Vp26 coat protein subunit to systemic necrosis induction and virus infectivity in Solanum lycopersicum

BACKGROUND

Tomato torrado virus (ToTV) infection manifests with burn-like symptoms on leaves, leaflets and upper stem parts of susceptible infected plants. The symptoms caused by ToTV may be considered as one of the most severe virus-induced forms of systemic necrosis, which spreads within the whole plant and leads to a lethal phenotype. However, to date there are no data revealing which viral genes encode for a specific pathogenicity determinant that triggers the plant necrotic response for any torradovirus. In this study we evaluated the influence of three coat protein subunits of ToTV: Vp23, Vp26 and Vp35, transiently expressed from a PVX-based vector, and checked their association with the induction of systemic necrosis in infected Solanum lycopersicum L. (cv. Beta Lux), a natural host of ToTV.

METHODS

To estimate how ToTV coat protein subunits might contribute in plant response to virus infection we over-expressed the proteins from PVX-based vector in tomato and analyzed enzymatic activities related with plant defense response. By doing protein qualitative analysis performed by mass spectrometry we indicated the PR10 in protein fraction with induced ribonuclease activity.

RESULTS

We observed that only the Vp26 enhanced PVX pathogenicity causing severe necrosis of the infected plant. Moreover, we indicated increased RNase and oxidative activities in plants infected with PVX-Vp26 chimeras only. Importantly, we suspected that this increased RNase activity is associated with increased accumulation of PR10 mRNA and products of its translation.

CONCLUSIONS

On the basis of the obtained results, we indicated that Vp26 acts as the elicitor of hypersensitive response-like reactions of PVX-Vp26 manifesting with enhanced pathogenicity of the recombined PVX. This might be the first described suspected necrosis determinant of torradoviruses infecting tomatoes.

Detection and transmission of Carrot torrado virus, a novel putative member of the Torradovirus genus

A new Torradovirus tentatively named Carrot torrado virus (CaTV) was an incidental finding following a next generation sequencing study investigating internal vascular necrosis in carrot. The closest related viruses are Lettuce necrotic leaf curl virus (LNLCV) found in the Netherlands in 2011 and Motherwort yellow mottle virus (MYMoV) found in Korea in 2014. Primers for reverse transcriptase-PCR (RT-PCR) and RT-qPCR were designed with the aim of testing for the presence of virus in plant samples collected from the field. Both methods successfully amplified the target from infected samples but not from healthy control samples. The specificity of the CaTV assay was also checked against other known carrot viruses and no cross-reaction was seen. A comparative study between methods showed RT-qPCR was the most reliable method, giving positive results in samples where RT-PCR fails. Evaluation of the Ct values following RT-qPCR and a direct comparison demonstrated this was due to improved sensitivity. The previous published Torradovirus genus specific RT-PCR primers were tested and shown to detect CaTV. Also, virus transmission experiments carried out suggest that unlike other species of the same genus, Carrot torrado virus could be aphid-transmitted.

A single amino acid substitution in movement protein of tomato torrado virus influences ToTV infectivity in Solanum lycopersicum

Tomato torrado virus (ToTV), which is a tomato-infecting member of the genus Torradovirus, induces severe systemic necrosis in Solanum lycopersicum cv. Beta Lux as well as leaf malformation and chlorosis in Nicotiana benthamiana. To date, neither the tomato gene conferring resistance to the pathogen nor the ToTV-encoded necrosis determinant have been characterized. We herein revealed that the phenylalanine 210 residue in the movement protein domain encoded by ToTV RNA2 is a necrosis-inducing pathogenicity determinant during tomato infection. Using a ToTV infectious RNA2 clone, we performed site-directed mutagenesis of the phenylalanine 210 residue, confirming its importance during ToTV infection and symptom manifestation in S. lycopersicum cv. Beta Lux, but not in N. benthamiana.

Torradoviruses

Torradoviruses are an example of a group of recently discovered plant viruses. The first description of Tomato torrado virus, now the type member of the newly established genus Torradovirus within the family Secoviridae, was published in 2007 and was quickly followed by findings of other torradoviruses, initially all on tomato. Their characterization led to the development of tools that allowed recognition of still other torradoviruses, only very recently found on non-tomato crops, which indicates these viruses have a much wider host range and diversity than previously believed. This review describes the characteristics of this newly emerged group of plant viruses. It looks in detail at taxonomic relationships and specific characteristics in their genomes and encoded proteins. Furthermore, it discusses their epidemiology, including host range, semipersistent transmission by whitefly vectors, and impact on diverse cropping systems.

Two generic PCR primer sets for the detection of members of the genus Torradovirus

Two degenerate primer pairs were designed for the universal detection of members of the genus Torradovirus. Primer pair Torrado-1F/Torrado-1R was designed based on the RNA-dependent RNA polymerase region located in RNA1 and primer pair Torrado-2F/Torrado-2R based on a region overlapping the two first coat proteins Vp35 and Vp26 in RNA2. The primers were used in two-step and one-step RT-PCR protocols. Both primer pairs were able to detect 14 out of 15 isolates belonging to the two torradovirus species Tomato torrado virus (ToTV) and Tomato marchitez virus (ToMarV) and the two tentative species Tomato chocolate spot virus (ToChSV) and Tomato chocolàte virus (ToChV). Due to poor sample quality, one isolate of ToTV was detected with primer pair Torrado-2F/Torrado-2R and not with primer pair Torrado-1F/Torrado-1R, suggesting that the latter primer pair was less sensitive. Nevertheless, both primer pairs proved to be suitable for the universal RT-PCR detection of torradoviruses and can be deployed for the detection of all currently known torradoviruses and possibly for the detection of new members of this group.

Pepino mosaic virus and Tomato torrado virus: two emerging viruses affecting tomato crops in the Mediterranean basin

The molecular biology, epidemiology, and evolutionary dynamics of Pepino mosaic virus (PepMV) are much better understood than those of Tomato torrado virus (ToTV). The earliest descriptions of PepMV suggest a recent jump from nontomato species (e.g., pepino; Solanum muricatum) to tomato (Solanum lycopersicum). Its stability in contaminated plant tissues, its transmission through seeds, and the global trade of tomato seeds and fruits may have facilitated the global spread of PepMV. Stability and seed transmission also probably account for the devastating epidemics caused by already-established PepMV strains, although additional contributing factors may include the efficient transmission of PepMV by contact and the often-inconspicuous symptoms in vegetative tomato tissues. The genetic variability of PepMV is likely to have promoted the first phase of emergence (i.e., the species jump) and it continues to play an important role as the virus becomes more pervasive, progressing from regional outbreaks to pandemics. In contrast, the long-term progression of ToTV outbreaks is not yet clear and this may reflect factors such as the limited accumulation of the virus in infected plants, which has been shown to be approximately two orders of magnitude less than PepMV. The efficient dispersion of ToTV may therefore depend on dense populations of its principal vectors, Bemisia tabaci and Trialeurodes vaporariorum, as has been proposed for the necrogenic satellite RNA of Cucumber mosaic virus.

Major tomato viruses in the Mediterranean basin

Tomato (Solanum lycopersicum L.) originated in South America and was brought to Europe by the Spaniards in the sixteenth century following their colonization of Mexico. From Europe, tomato was introduced to North America in the eighteenth century. Tomato plants show a wide climatic tolerance and are grown in both tropical and temperate regions around the world. The climatic conditions in the Mediterranean basin favor tomato cultivation, where it is traditionally produced as an open-field plant. However, viral diseases are responsible for heavy yield losses and are one of the reasons that tomato production has shifted to greenhouses. The major tomato viruses endemic to the Mediterranean basin are described in this chapter. These viruses include Tomato yellow leaf curl virus, Tomato torrado virus, Tomato spotted wilt virus, Tomato infectious chlorosis virus, Tomato chlorosis virus, Pepino mosaic virus, and a few minor viruses as well.

Emerging virus diseases transmitted by whiteflies

Virus diseases that have emerged in the past two decades limit the production of important vegetable crops in tropical, subtropical, and temperate regions worldwide, and many of the causal viruses are transmitted by whiteflies (order Hemiptera, family Aleyrodidae). Most of these whitefly-transmitted viruses are begomoviruses (family Geminiviridae), although whiteflies are also vectors of criniviruses, ipomoviruses, torradoviruses, and some carlaviruses. Factors driving the emergence and establishment of whitefly-transmitted diseases include genetic changes in the virus through mutation and recombination, changes in the vector populations coupled with polyphagy of the main vector, Bemisia tabaci, and long distance traffic of plant material or vector insects due to trade of vegetables and ornamental plants. The role of humans in increasing the emergence of virus diseases is obvious, and the effect that climate change may have in the future is unclear.

Emerging viral diseases of tomato crops

Viral diseases are an important limiting factor in many crop production systems. Because antiviral products are not available, control strategies rely on genetic resistance or hygienic measures to prevent viral diseases, or on eradication of diseased crops to control such diseases. Increasing international travel and trade of plant materials enhances the risk of introducing new viruses and their vectors into production systems. In addition, changing climate conditions can contribute to a successful spread of newly introduced viruses or their vectors and establishment of these organisms in areas that were previously unfavorable. Tomato is economically the most important vegetable crop worldwide and many viruses infecting tomato have been described, while new viral diseases keep emerging. Pepino mosaic virus is a rapidly emerging virus which has established itself as one of the most important viral diseases in tomato production worldwide over recent years. Begomovirus species and other whitefly-transmitted viruses are invading into new areas, and several recently described new viruses such as Tomato torrado virus and new Tospovirus species are rapidly spreading over large geographic areas. In this article, emerging viruses of tomato crops are discussed.