Potato Mop-top Virus Research Articles

Investigating the Roles of Coat Protein and Triple Gene Block Proteins of Potato Mop-Top Virus Using a Heterologous Expression System.

Potato mop-top virus (PMTV) is an emerging viral pathogen that causes tuber necrosis in potatoes. PMTV is composed of three single-stranded RNA segments: RNA1 encodes RNA-dependent RNA polymerase, RNA2 contains the coat protein (CP), and RNA3 harbors a triple gene block (TGB 1, TGB2, and TGB3). CP plays a role in viral transmission, while TGB is known to facilitate cell-to-cell and long-distance systemic movement. The role of CP in symptom development, specifically in the presence of TGB genes, was investigated using potato virus X (PVX) as a delivery vehicle to express PMTV genes in the model plant Nicotiana benthamiana. Plants expressing individual genes showed mild symptoms that included leaf curling and crumpling. Interestingly, symptom severity varied among plants infected with three different combinations: CP with TGB1, CP with TGB2, and CP with TGB3. Notably, the combination of CP and TGB3 induced a hypersensitive response, accompanied by stunted growth and downward curling and crumpling. These results suggest the potential role of TGB co-expressed with CP in symptom development during PMTV infection. Additionally, this study demonstrates the use of the PVX-based expression system as a valuable platform for assessing the role of unknown genes in viral pathogenicity.

Potato mop-top virus: knowledge review, and evaluation of the biosecurity response to ‘incursion’ of this virus in New Zealand

Pomovirus solani (common name: potato mop-top virus, PMTV) was first recorded in New Zealand on 11 September 2018. In contrast, Spongospora subterranea, the vector of PMTV, was first recorded in New Zealand in 1909, and is widespread causing important diseases of potato. PMTV causes distortion on potato leaves, shoots and tubers, and was designated at the time of first record as an Unwanted Organism by the New Zealand Ministry for Primary Industries. Spongospora subterranea and PMTV can survive for long periods in soil and in alternative hosts, so multi-year non-potato crop rotations are important for limiting the diseases caused by these pathogens. Both pathogens can also survive in wastes from potato processing factories, so disposal of processing effluent should be avoided on paddocks likely to be used for potato crops. The first observation and timely reporting of PMTV symptoms by a potato processing company instigated an official biosecurity response to the virus ‘incursion’, although PMTV may have been present 1 or 2 years prior to this first record. Rapid establishment of a PMTV Technical Advisory Group, including relevant international expertise, and the advice it provided, effectively directed the prompt response to the PMTV ‘incursion’, and the Ministry for Primary Industries and Potatoes New Zealand (Inc.) swiftly and effectively developed capability for monitoring and management of the ‘incursion’. Efforts since then by the New Zealand potato industry have reduced potential impacts of PMTV in this country, as demonstrated by low incidence of the virus in seed potato crops in 2019/20 and 2020/21. This low incidence indicates that PMTV is not adversely affecting potato productivity in New Zealand, and that management of the virus ‘incursion’ has been effective.

Spongospora subterranea f. sp. subterranea Affects Plant Susceptibility to Subsequent Pathogen Infections Under Controlled-Environment Conditions.

Spongospora subterranea f. sp. subterranea (Sss) is a soilborne potato pathogen responsible for causing powdery scab on tubers and galls on roots, reducing root water uptake through colonizing root hairs, and vectoring of Potato mop-top virus (PMTV). However, effects of Sss on overall plant susceptibilities against subsequent infections of potato pathogens above ground have not been previously reported. This study aimed to investigate the effects of Sss on root and tuber disease expression, yield, and susceptibilities to subsequent late blight and white mold infections across six potato varieties. Sss-infected Silverton plants had 28.3% less total tuber yield and 29% fewer tubers compared to noninfected Silverton plants. We did not find a correlation across the varieties between root colonization and root gall formation. Sss-infected Silverton plants were more susceptible to hemibiotrophic late blight and less susceptible to necrotrophic white mold. Sss infection also increased susceptibilities of Goldrush and Atlantic plants to white mold. We also evaluated prevalence of asymptomatic Sss infections across the six varieties. Between 50 and 92% of the asymptomatic tubers tested positive for Sss DNA, depending on the variety. Further research is required to understand the possibility and extent of these asymptomatic infections to the spread of Sss in the field. These findings highlight the complexity of Sss-host interactions and give precedence that the lack of disease expression does not necessarily indicate resistance of a variety to Sss.

Production of Double-Stranded RNA in Planta by a Potato Mop-Top Virus (PMTV)-Based Vector for Inducing Gene Silencing.

RNA silencing (also known as gene silencing) is an evolutionary conserved mechanism that is involved in regulating gene expression, suppressing mobile elements, and defensing virus infection. RNA silencing is triggered by double-stranded RNA via Dicer or Dicer-like riboendonucleases. DsRNAs are also the replication intermediates of all RNA viruses; as a result, plant RNA viruses are ideal candidates to induce RNA silencing. A large body of plant viruses have been modified into vectors for RNA silencing in varied plant species. Here, we described a simple, time-saving, and operable system for gene function and genetic breeding study of potato and Nicotiana benthamiana using a potato mop-top (MPTV)-based vector.

A Genome Wide Association Study (GWAS) Identifies SNPs Associated with Resistance to Tobacco Rattle Virus (TRV) and Potato Mop-Top Virus (PMTV) in a Tetraploid Mapping Population of Potato

A Genome Wide Association Study (GWAS) Identifies SNPs Associated with Resistance to Tobacco Rattle Virus (TRV) and Potato Mop-Top Virus (PMTV) in a Tetraploid Mapping Population of Potato

AN OVERVIEW REGARDING THE INCIDENCE OF SOME NECROTIC VIRUSES IN SEVERAL ROMANIAN AREAS

PMTV (Potato Mop-Top Virus ) and PAMV (Potato Aucuba Mosaic Virus) are new damaging pathogens of potato crop in Romania. They can cause serious reduced yield and decrease of the tuber’s quality. In case of these viruses, infected plants do not allways show signs of disease and the symptoms depend on potato cultivar, virus strain and the environment. PMTV and PAMV infection of material plants can produce spraing in tubers of sensitive varieties. PMTV causes heavy losses in northen Europe and it is very difficult to control. PAMV is a helping virus for the development of dangerous potyvirus like Potato Virus Y (PVY). Elimination of all these pathogens from the potato supply chain is essential for potato production and choosing resistant varieties to the infection with these viruses could be one of the measures recommended for farmers and producers. The results of this preliminary study shows that PMTV and PAMV were not found in the material collected from the following varieties: Armonia, Azaria, Christian and Millenium (samples collected from the counties Braşov, Covasna, Harghita, Suceava in 2019, 2020 and 2021).

Detection of Potato Mop-Top Virus in Potato Seed Lots Entering Washington State

Detection of Potato Mop-Top Virus in Potato Seed Lots Entering Washington State

INCIDENCE OF APHID BORNE VIRUSES AND THEIR VECTOR DYNAMICS INFECTING POTATO CROP IN DIFFERENT DISTRICTS OF AZAD JAMMU AND KASHMIR, PAKISTAN

Potato crop production is hampered by several fungal, viral, and bacterial diseases. Among the viral Potato leaf roll virus (PLRV), Potato virus Y (PVY), Potato-mop-top-virus (PMTV), Potato virus S (PVS) and Potato virus X (PVX) are the most important. Potato growing fields were surveyed during 2016 and 2017 to determine the incidence of two aphid-borne viruses, PVY and PLRV and to explore the dynamics of potato aphids in four potato-producing district of Azad Jammu & Kashmir (AJK), Pakistan. During survey 930 leaf samples were collected from various locations of Bagh, Sudhnoti, Poonch and Neelum. Parameters determined included aphid population, symptomology, DAC-ELISA based virus incidence, rate of co-infection and disease severity. Overall relative disease incidence of PLRV and PVY was 48.71% and 53.23% respectively. The highest average aphid’s population per field was 390.27 in Sudhnoti due to the low altitude of the surveyed locations. Three aphid species Myzuspersicae Myzusornatusand, Macrosiphum euphorbiaewere identified in AJK potato fields. Themaximum co-infection was recorded from Poonch. It was found that aphid populations decreased with the increase of altitude. The incidence of PLRV and PVY were high where aphid population was high. Therefore, it is necessary to promote awareness among the farmers on virus and aphid symptoms identification and to recommend use of healthy, uncontaminated certified potato seed.

Genomes of Potato Mop-Top Virus (Virgaviridae: Pomovirus) Isolates from New Zealand and Their Impact on Diagnostic Methods.

Following the detection of potato mop-top virus (PMTV) in New Zealand in 2018, three near-complete PMTV genomes (AS22, AS99, AS144) were assembled from soil samples taken from potato fields in Canterbury. Phylogenetic analysis revealed that these genomes form a distinct lineage, with limited genetic diversity, within the PMTV species. This analysis supports the hypothesis that these genomes share a common origin, possibly resulting from a single (or limited) incursion of PMTV into New Zealand. A single nucleotide polymorphism was identified in the region where a key diagnostic primer binds. The mismatch of the diagnostic primer has implications for the effectiveness of the Mumford diagnostic protocol currently recommended for use in New Zealand; we recommend that the alternative Pandey assay, for which no primer mismatch was detected, be validated and optimized for use on the viral genomes present in New Zealand.

An on-site adaptable test for rapid and sensitive detection of Potato mop-top virus, a soil-borne virus of potato (Solanum tuberosum).

Potato mop-top virus (PMTV) is considered an emerging threat to potato production in the United States. PMTV is transmitted by a soil-borne protist, Spongospora subterranean. Rapid, accurate, and sensitive detection of PMTV in leaves and tubers is an essential component in PMTV management program. A rapid test that can be adapted to in-field, on-site testing with minimal sample manipulation could help in ensuring the sanitary status of the produce in situations such as certification programs and shipping point inspections. Toward that goal, a rapid and highly sensitive recombinase polymerase amplification (RPA)-based test was developed for PMTV detection in potato tubers. The test combines the convenience of RPA assay with a simple sample extraction procedure, making it amenable to rapid on-site diagnosis of PMTV. Furthermore, the assay was duplexed with a plant internal control to monitor sample extraction and RPA reaction performance. The method described could detect as little as 10 fg of PMTV RNA transcript in various potato tissues, the diagnostic limit of detection (LOQ) similar to that of traditional molecular methods.

Comparison of Potato Viromes Between Introduced and Indigenous Varieties.

Viral disease in potatoes has been a major problem in potato production worldwide. In addition to the potential risk of introducing new diseases in new areas, viral-disease epidemics/pandemics can be initiated by “spillover” of indigenous viruses from infected alternative hosts into introduced cultivars. To investigate the tendency of potential viral infection/resistance, we analyzed the viromes of introduced and indigenous varieties of potatoes among different tissues using RNA-seq libraries. Bioinformatics analyses revealed that potato viruses PVM, PVY, and PVS were dominant and the most frequently identified viruses infecting potato virus-free plants in the field, and showed an infection bias between introduced and indigenous cultivars. PVY and PVS were the major viruses in introduced varieties, whereas PVM showed an extraordinarily high percentage in the indigenous variety. Other three common viruses, PVH, potato mop-top virus, and potato leafroll virus were identified specifically in the indigenous variety. There was a tendency for tissue-specific infection and sequence variation in viruses: underground parts (tubers, roots) harbored more unusual viruses, and tubers harbored relatively more variation with a high frequency of single nucleotide polymorphisms than other tissues. Taken together, our study provides a comprehensive overview of the composition, distribution, and sequence variation of viruses between introduced and indigenous varieties of potatoes.

Detection of Major Soil-Borne Viruses and Assessment of Virus-Vector Association in Potato Growing Areas of North-Western Pakistan (Khyber Pakhtunkhwa) and Azad Jammu and Kashmir

Soil-borne potato viruses are an increasing economic threat to crop yield in the future. Potato mop-top virus (PMTV) and Tobacco rattle virus (TRV) and their vector association in field infection in North-western region of Pakistan and Azad Jammu and Kashmir were surveyed in this study. Incidence and distribution of these soil-borne viruses were estimated by field sample collection from Malakand and Hazara divisions of KPK and selected areas of Azad Kashmir. PMTV incidence was 22% in Malakand (highest of 40% in Swat II and Swat V), 24% in Hazara (highest 50% in Galliyat), and 23% from selected areas of Azad Jammu and Kashmir (AJK) (Highest with 40% in Rawalakot and Trarkhal). TRV incidence was 49% in AJK (100% highest field incidence in Khaigala Rawalakot), 53% in Malakand division (80% highest field incidence in Swat II), and 24% in Hazara division (70% highest field incidence in Abbottabad and Mansehra districts). PMTV, TRV vectors are Spongospora subterranea and Trichodorus, Paratrichodorus spp. were found distributed in all surveyed areas. Eighty percent (80%) fields were found infested with S. subterranean, while Trichodorus and Paratrichodorus were found in 64% in Malakand. In Hazara, 84% of surveyed fields were found infested with S. subterranea while 65% were found to be infested with Trichodorus, Paratrichodorus. In AJK S. subterranea was found distributed in 79% of fields. A significant relationship (P value=0.000) between viruses (PMTV and TRV) and their respective vectors were detected in proportionate. The corresponding R2 (0.70 and 0.82) indicates positive relation between viruses and their vectors. Positive Pearson correlation was found among incidence and severity of virus infection (PMTV and TRV) and vectors (S. subterranea; Trichodorus minor, Paratrichodorus), indicating increased disease severity with vector presence and activity. The study will be a tool in vector virus management to economical potato harvest

Development of High-Resolution DNA Melting Analysis for Simultaneous Detection of Potato Mop-Top Virus and Its Vector, Spongospora subterranea, in Soil.

In this study, a set of duplex reverse transcription PCR (RT-PCR)-mediated high-resolution DNA melting (HRM) analyses for simultaneous detection of potato mop-virus (PMTV) and its protist vector, Spongospora subterranea f. sp. subterranea (Sss), was developed. The infestation of soil by PMTV was detected with a tobacco-based baiting system. Total RNA extracted from the soil led to successful RT-PCR gel electrophoresis detection of both PMTV and Sss. To facilitate more efficient detection, newly designed primer pairs for PMTV RNA species (i.e., RNA-Rep, RNA-CP, and RNA-TGB) were analyzed together with the existing Sss primers via real-time RT-PCR. The resulting amplicons exhibited melting profiles that could be readily differentiated. Under duplex RT-PCR format, all PMTV and Sss primer combinations led to successful detection of respective PMTV RNA species and Sss in the samples by HRM analyses. When the duplex HRM assay was applied to soil samples collected from six fields at four different sites in New Brunswick, Canada, positive detection of PMTV or Sss was found in 63 to 100% samples collected from fields in which PMTV-infected tubers had been observed. In contrast, the samples from fields where neither PMTV- nor Sss-infected tubers had been observed resulted in negative detection by the assay. Bait tobacco bioassay for PMTV and Sss produced similar results. Of the soil samples collected from PMTV-infested fields, 63 to 83% and 100% led to PMTV and Sss infections in the bait tobacco plants, respectively, whereas no PMTV- or Sss-infected plants were obtained from soil samples collected from PMTV- and Sss-free fields.

Detection of RNA viruses in Solanum quitoense by high-throughput sequencing (HTS) using total and double stranded RNA inputs

Solanum quitoense Lam. is a solanaceous fruit shrub native to South America that produces a tomato-sized fruit popular in the preparation of fresh juice, fermented beverages, nectars, ice cream and fruit concentrates. Unfortunately, this crop is highly susceptible to insects, nematodes, fungi, oomycetes, bacteria, and a wide range of viral diseases. With the arrival of High-Throughput Sequencing (HTS) methods, our understanding of the viruses affecting this crop has increased at a steady pace. In this work, we investigate the virome of S. quitoense in Antioquia (Colombia) using the Illumina HTS platform and analyze the effect of using ribosomal RNA depleted total RNA and dsRNA templates. Our results suggest that total RNA outputs a larger amount of viral sequences but fails to detect viruses present at lower loads. Both templates allowed detection and assembly of Potato leafroll virus (PLRV), Potato yellow vein virus (PYVV), and Potato mop-top virus (PMTV); however, the dsRNA input was more sensitive for detection of Potato virus Y (PVY), Potato virus X (PVX), Potato virus S (PVS), and Bell pepper alphaendornavirus (BPEV). These results suggest that the combination of different RNA inputs in HTS studies of plant viromes can give a more complete picture of the real virus diversity.

Evaluation of Effects of Chemical Soil Treatments and Potato Cultivars on Spongospora subterranea Soil Inoculum and Incidence of Powdery Scab and Potato Mop-Top Virus in Potato.

Spongospora subterranea is a soilborne plasmodiophorid that causes powdery scab in potato. It also transmits potato mop-top virus (PMTV), which causes necrotic arcs (spraing) in potato tubers. Three field experiments were conducted in naturally S. subterranea-infested soil to investigate the effects of two chemicals, Omega 500F (fluazinam) and FOLI-R-PLUS RIDEZ (biological extract), on powdery scab, PMTV, and changes in S. subterranea inoculum with six different potato cultivars. The efficacy of soil treatment with these two chemicals on tuber lesions, root galling, and pathogen population was also assessed in greenhouse trials. The chemical treatments did not reduce powdery scab, root gall formation, or S. subterranea inoculum in the field or greenhouse trials. Postharvest S. subterranea soil inoculum in fields varied across farms and among potato cultivars but the pathogen population consistently increased by the end of the growing season. The evaluated russet cultivars were more tolerant to powdery scab than the yellow- or red-skinned cultivars but all were susceptible to PMTV. In the field, powdery scab indices and soil inoculum changes were positively correlated, while postharvest S. subterranea inoculum was positively correlated with root galling in both greenhouse trials. Powdery scab and PMTV occurred in noninoculated potting mix, indicating that peat-based potting mix is a source for both pathogens. These results demonstrate that chemical management methods currently used by farmers are ineffective, that S. subterranea and PMTV in potting mix can cause severe epidemics in greenhouses, and that potato cultivar choices impact inoculum increases in soil.

Detection of RNA viruses in Cape gooseberry (Physalis peruviana L.) by RNAseq using total RNA and dsRNA inputs

Physalis peruviana L. is a herbaceous solanaceous plant native to the South American Andes that produces a small yellow fruit of about 1-2 cm in diameter with high demand in the international markets. Currently, Colombia is the largest worldwide exporter of this fruit crop but, due to the emergence of several phytosanitary problems, yields have experienced a steady declined in recent years. Viruses are not included in current disease management programs of P. peruviana but, evidence suggest that viruses might play an important role in decreasing the productivity of this crop. High-throughput sequencing (HTS) has allowed a deeper understanding of the P. peruviana genome and promises to become a routine technique in future integrated disease management programs. Here, we evaluate the influence of the RNA input (total RNA vs dsRNA) on the sensitivity of HTS as a virus detection tool. Our results suggest that, total RNA can produce a high number of viral sequences but fails to detect viruses present at low concentrations and detectable using dsRNA. In particular, infection by potato mop-top virus (PMTV) was detected using both inputs. In addition to PMTV, dsRNA also allowed the assembly of a complete Potato yellow vein virus (PYVV) genome and scaffolds of Potato yellowing virus (PYV), Southern tomato virus (STV) and Potato virus S (PVS). Evidence for the presence of Potato virus X (PVX), Potato virus V (PVV), Potato virus Y (PVY), Bell pepper alphaendornavirus (BPEV) and a putative mycovirus was also obtained from the dsRNA dataset.

Correction to: Genetic diversity in potato mop-top virus populations in the United States and a global analysis of the PMTV genome

Correction to: Genetic diversity in potato mop-top virus populations in the United States and a global analysis of the PMTV genome

Genetic diversity in potato mop-top virus populations in the United States and a global analysis of the PMTV genome

Potato mop-top virus (PMTV; Genus: Pomovirus; Family: Virgaviridae) is a soil-borne RNA virus that is an emerging issue impacting potato production in the US. PMTV is known to exist as two distinct strains; however, there is limited information on the population structure, strain incidence and distribution in the U.S. The complete genome of six isolates of PMTV collected from three states in the USA were sequenced, analyzed, and compared with a previously characterized isolate from Washington and all known PMTV sequences available in GenBank. Genome-wide nucleotide sequence identities of the U.S. isolates ranged from 96% to 100%. Based on the CPRT amino acid sequence, all the U.S. isolates clustered with known severe (S) strains. Genetic diversity test showed that the S strain to be more diverse than the mild (M) strain and the PMTV recombinant strain. Population selection analysis revealed that most of the codons were generally negatively selected in the PMTV isolates studied. However, positive selection was detected at codon 689 in the RT domain, which could be an adaptation to facilitate vector transmission and to overcome host plant resistance. The sequence characteristics and the observed genetic diversity would be useful in developing improved virus diagnostics to detect virus in aerial plant parts, tubers, soil and the soil-borne vector.

Recombinase Polymerase Amplification (RPA) for the Rapid Isothermal Detection of Spongospora subterranea f. sp. subterranea and Potato Mop-Top Virus

The amplification of specific nucleic acid sequences with high specificity and sensitivity is an essential technique for pathogen detection. Recombinase polymerase amplification (RPA) is a rapid isothermal amplification method. Here, we demonstrate the end-point and real-time detection of Spongospora subterranea f. sp. subterranea (Sss) using RPA and potato mop-top virus (PMTV) using reverse transcription (RT)-RPA. Oligonucleotide primers were designed for amplification that target the internal transcribed spacer 1 (ITS1) region and the coat protein readthrough (CP-RT) domain for the detection of Sss and PMTV, respectively. Our data showed that real-time RPA can detect 100 of Sss sporosori per gram of soil, while real-time RT-RPA could detect in ~1 ng total RNA of the PMTV-infected tuber. For Sss detection, the R2 value for real-time RPA and real-time PCR was 98.0% by linear regression analysis in the concentration range of 100–34,000 sporosori per gram of soil. The developed RPA assay here may provide a useful alternative tool for the rapid, simple and reliable detection of Sss and PMTV in diagnostic laboratories and in-field testing.

Development and Application of a Real-Time Reverse-Transcription PCR and Droplet Digital PCR Assays for the Direct Detection of Potato mop top virus in Soil.

Potato mop top virus (PMTV) is a continuing threat to potato production throughout the world. It has the potential to persist in the soil for long periods in the sporosori of its vector Spongospora subterranea f. sp. subterranea, which is as an important source for PMTV infection and dissemination. In this study, we used real-time quantitative reverse-transcription PCR (qRT-PCR) and reverse-transcription droplet digital PCR (RT-ddPCR) assays of the total RNA extracted directly from the soil to develop a simple, fast, and sensitive method to detect PMTV in soil samples using a specific primer with high efficiency despite a minimal amount of viral RNA. The designed primers are resilient in the presence of various PCR inhibitors in the soil when RNA is extracted. Both assays detected PMTV in all soil types used and supported the detection of <10 PMTV copies µl-1 in the RNA sample. With qRT-PCR, detection was linear, with amplification efficiencies ranging from 93.3 to 105.3% for silt loam, loamy sand, sand, and sandy loam in various experiments with R2 > 0.99. Furthermore, the RT-ddPCR assay also demonstrated a high degree of linearity (R2 > 0.99 and P < 0.0001) with the RNA extracted from the soil samples representing different textures and physiochemical characteristics that were artificially spiked with infested S. subterranea f. sp. subterranea sporosori. Additionally, both assays successfully detected PMTV in different types of naturally infested soil with PMTV carrying S. subterranea f. sp. subterranea sporosori levels ranging from 6.2 × 102 g-1 to 1.2 × 106 g-1 in soils with pH ranging from 4.9 to 7.5 and organic matter ranging from 0.9 to 5.1%, demonstrating the potential to detect PMTV in a wide variety of soils. To our knowledge, this is the first report of the development of real-time PCR and ddPCR methods for the direct detection of a soilborne virus in soil.