Pea Necrotic Yellow Dwarf Virus Research Articles

Comparison of Sequencing Methods for Obtaining a Whole Genome of Pea Necrotic Yellow Dwarf Virus from U.K. Peas

During a project investigating pea viruses in the United Kingdom and developing a workflow for high-throughput sequencing in crop surveillance, pea necrotic yellow dwarf virus (PNYDV) was identified at one site, along with pea enation mosaic virus-1, pea enation mosaic virus-2, pea enation mosaic virus satellite RNA, pea seedborne mosaic virus, and turnip yellows virus. Following an initial finding of small PNYDV contigs by an RNA sequencing protocol on MiSeq (Illumina), confirmation and prevalence testing by PCR and Sanger sequencing determined the average PNYDV prevalence to be 3%. This is the first report of PNYDV, and a nanovirus, in the United Kingdom. Initial characterization of the octopartite genome by PCR revealed that component DNA N had a truncated sequence that differed from those previously reported. This led to confirmation testing using rolling circle amplification (RCA) into MiSeq and then MinION (Oxford Nanopore). Sequences were obtained by both RCA-MiSeq and RCA-MinION, with MinION producing more complete genomes than RCA-MiSeq. Data obtained from sequencing were used to provide an initial estimation of the genomic formula of PNYDV. Previous work has looked into comparing each method; however, this study shows how these methods can be used together. The truncated sequence for DNA N was also found by RCA-MiSeq and RCA-MinION and confirmed by specific primers, but further work is required to understand the impact of this truncation. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Impact of Pea necrotic yellow dwarf virus (PNYDV) on nodulation, N2 fixation and yield in faba bean (Vicia faba, L.)

Pea necrotic yellow dwarf virus (PNYDV) is a novel nanovirus in Europe, affecting various grain legumes. The impact of PNYDV on nodulation, symbiotic N2 fixation and yield parameters in faba bean (Vicia faba L.) was investigated at controlled conditions in the greenhouse (2017), on-farm in natural infection foci (2018, 2019) and in a small-scale field experiment (2020). In the latter, the standard variety ‘Fuego’ was compared with the variety ‘GL Sunrise’ in early and late infections. In addition, the analogous effects for Pea enation mosaic virus (PEMV) were investigated under greenhouse conditions and the naturally occurring virus spectrum was recorded on-farm and in the field experiment. Results showed a much more severe impact of PNYDV than PEMV on nodulation, leghemoglobin status, N2 fixation and finally yield, especially in early infections. Although ‘GL Sunrise’ was rated for a less symptomatic field performance toward PNYDV than ‘Fuego’, it showed a similar susceptibility in our field experiment where PNYDV was artificially inoculated to individual plants. Further research on the effect of plant varieties on susceptibility toward PNYDV infection and its spread in single or co-infection mainly with PEMV as a function of climate change acting upon their common aphid vector is required.

Pea necrotic yellow dwarf virus

This datasheet on Pea necrotic yellow dwarf virus covers Identity, Distribution, Hosts/Species Affected, Vectors & Intermediate Hosts, Further Information.

Investigating the Pea Virome in Germany-Old Friends and New Players in the Field(s).

Peas are an important legume for human and animal consumption and are also being used as green manure or intermediate crops to sustain and improve soil condition. Pea production faces constraints from fungal, bacterial, and viral diseases. We investigated the virome of German pea crops over the course of three successive seasons in different regions of pea production to gain an overview of the existing viruses. Pools from 540 plants, randomly selected from symptomatic and asymptomatic peas, and non-crop plants surrounding the pea fields were used for ribosomal RNA-depleted total RNA extraction followed by high-throughput sequencing (HTS) and RT-PCR confirmation. Thirty-five different viruses were detected in addition to nine associated nucleic acids. From these viruses, 25 are classified as either new viruses, novel strains or viruses that have not been reported previously from Germany. Pea enation mosaic virus 1 and 2 were the most prevalent viruses detected in the pea crops, followed by pea necrotic yellow dwarf virus (PNYDV) and turnip yellows virus which was also found also in the surrounding non-legume weeds. Moreover, a new emaravirus was detected in symptomatic peas in one region for two successive seasons. Most of the identified viruses are known to be aphid transmissible. The results revealed a high virodiversity in the German pea fields that poses new challenges to diagnosticians, researchers, risk assessors and policy makers, as the impact of the new findings are currently unknown.

Symptomology and yield impact of pea necrotic yellow dwarf virus (PNYDV) in faba bean (Vicia faba L. minor)

We surveyed 33 symptomatic faba bean sites in central Germany towards the end of the growing season 2016 to analyse the suspected virus spectrum. All sites displayed plants with characteristic symptoms and had distinct funnel-shaped patches with a severely affected centre. The central core consisted of stunted, prematurely senescent plants. Symptomatic foci were scattered at random over a largely symptomless field. At two exemplary investigation sites we combined ground based yield assessments with remote sensing techniques to describe disease-loss relationships. Based on low altitude true-colour aerial imaging data, symptomatic patches were categorised into: (i) severely affected blackish core region, (ii) yellowish symptomatic periphery, and (iii) a corresponding non-symptomatic reference patch. Serological tests revealed PNYDV (Pea necrotic yellow dwarf virus) together with PEMV (Pea enation mosaic virus) as dominant and equally abundant viruses. However, because PNYDV was significantly more restricted to the focal core than PEMV, we perceived PNYDV to be the causal agent for this apparently new symptom pattern in faba bean. As both viruses are vectored persistently by leguminous aphids, the observed symptom gradient within individual foci mirrored the epidemiological development over time, starting from an initial infection point and expanding towards the periphery via secondary virus spread to successively maturing and less susceptible plants. For each investigation site the segmented symptomatic surface of category (i) was 0.8 and 0.4%, for (ii) 20.5 and 6.4%, respectively. Combining the relative yield level for each symptom category with its respective surface, the overall yield gap at the field scale was extrapolated to 4.1 and 9.2% for grain yield and for 3.9 and 1.2% for crude protein. In the symptomatic core category, TKWs (thousand kernel weights) were halved due to enhanced proportions of shriveled grain. Because PNYDV-related yield decline was determined by the number, relative surface and disease intensity of individual foci, remote sensing techniques can offer valuable options for monitoring, loss assessment and agricultural decision-making.

Pea necrotic yellow dwarf virus. [Distribution map

Abstract A new distribution map is provided for Pea necrotic yellow dwarf virus. Nanoviridae: Nanovirus. Hosts: pea ( Pisum sativum ), faba bean ( Vicia faba ) and lentil ( Lens culinaris ). Information is given on the geographical distribution in Europe (Austria, Denmark, Germany and Netherlands).

Nanovirus DNA-N encodes a protein mandatory for aphid transmission

Nanoviruses possess a multipartite single-stranded DNA genome and are naturally transmitted to plants by various aphid species in a circulative non-propagative manner. Using the cloned genomic DNAs of faba bean necrotic stunt virus (FBNSV) for reconstituting nanovirus infections we analyzed the necessity of different virus components for infection and transmission by aphids. We found that in the absence of DNA-U1 and DNA-U2 symptom severity decreased, and in the absence of DNA-U1 the transmission efficiency decreased. Most significantly, we demonstrated that the protein encoded by DNA-N (NSP) is mandatory for aphid transmission. Moreover, we showed that the NSP of FBNSV could substitute for that of a distantly related nanovirus, pea necrotic yellow dwarf virus. Altering the FBNSV NSP by adding 13 amino acids to its carboxy-terminus resulted in an infectious but non-transmissible virus. We demonstrate that the NSP acts as a nanovirus transmission factor, the existence of which had been hypothesized earlier.

Molecular characterisation of the first occurrence of Pea necrotic yellow dwarf virus in Denmark

Pea necrotic yellow dwarf virus (PNYDV), a member of the Nanovirus genus, has been reported from numerous European countries causing yield loss in peas, faba beans, vetches and lentils (Grigoras et al., 2010; Grigoras et al., 2014; Gaafar…

Analyses of pea necrotic yellow dwarf virus-encoded proteins.

Pea necrotic yellow dwarf virus (PNYDV) is a multipartite, circular, single-stranded DNA plant virus. PNYDV encodes eight proteins and the function of three of which remains unknown-U1, U2, and U4. PNYDV proteins cellular localization was analyzed by GFP tagging and bimolecular fluorescence complementation (BiFC) studies. The interactions of all eight PNYDV proteins were tested pairwise in planta (36 combinations in total). Seven interactions were identified and two (M-Rep with CP and MP with U4) were characterized further. MP and U4 complexes appeared as vesicle-like spots and were localized at the nuclear envelope and cell periphery. These vesicle-like spots were associated with the endoplasmatic reticulum. In addition, a nuclear localization signal (NLS) was mapped for U1, and a mutated U1 with NLS disrupted localized at plasmodesmata and therefore might also have a role in movement. Taken together, this study provides evidence for previously undescribed nanovirus protein-protein interactions and their cellular localization with novel findings not only for those proteins with unknown function, but also for characterized proteins such as the CP.

First report of Pea necrotic yellow dwarf virus in The Netherlands

Pea necrotic yellow dwarf virus (PNYDV) is a nanovirus that was first detected in pea crops ( Pisum sativum ) in Saxony-Anhalt, Germany in 2009 (Grigoras et al ., 2010). In 2016, PNYDV was detected countrywide in both Germany and Austria not…

The stress granule component G3BP is a novel interaction partner for the nuclear shuttle proteins of the nanovirus pea necrotic yellow dwarf virus and geminivirus abutilon mosaic virus

Stress granules (SGs) are structures within cells that regulate gene expression during stress response, e.g. viral infection. In mammalian cells assembly of SGs is dependent on the Ras-GAP SH3-domain–binding protein (G3BP). The C-terminal domain of the viral nonstructural protein 3 (nsP3) of Semliki Forest virus (SFV) forms a complex with mammalian G3BP and sequesters it into viral RNA replication complexes in a manner that inhibits the formation of SGs. The binding domain of nsP3 to HsG3BP was mapped to two tandem ‘FGDF’ repeat motifs close to the C-terminus of the viral proteins. It was speculated that plant viruses employ a similar strategy to inhibit SG function. This study identifies an Arabidopsis thaliana NTF2-RRM domain-containing protein as a G3BP-like protein (AtG3BP), which localizes to plant SGs. Moreover, the nuclear shuttle protein (NSP) of the begomovirus abutilon mosaic virus (AbMV), which harbors a ‘FVSF’-motif at its C-terminal end, interacts with the AtG3BP-like protein, as does the ‘FNGSF’-motif containing NSP of pea necrotic yellow dwarf virus (PNYDV), a member of the Nanoviridae family. We therefore propose that SG formation upon stress is conserved between mammalian and plant cells and that plant viruses may follow a similar strategy to inhibit plant SG function as it has been shown for their mammalian counterparts.

Vicia faba, V. sativa and Lens culinaris as new hosts for Pea necrotic yellow dwarf virus in Germany and Austria

Pea necrotic yellow dwarf virus (PNYDV) was identified in green peas ( Pisum sativum ) in Germany in 2009 (Grigoras et al ., 2010). In subsequent years, sampling of symptomatic green peas showed that PNYDV was restricted to Saxony and…

Virus surveys of process vegetable crops pea beetroot and dwarf bean

In a survey of 14 processing crops and 7 pea seed crops throughout Canterbury Cucumber mosaic virus (CMV) was the most widespread with crop incidences of up to 20 Alfalfa mosaic virus (AMV) up to 11 Pea seedborne mosaic virus (PSbMV) up to 9 Soybean dwarf virus (SDV) up to 2 Turnip yellows virus (TuYV) up to 2 and Bean yellow mosaic virus (BYMV) up to 35 Red clover vein mosaic virus (RCVMV) was detected in peas for the first time in New Zealand with incidences of up to 35 Pea necrotic yellow dwarf virus (PNYDV) Faba bean necrotic yellows virus (FBNYV) and Broad bean stain virus (BBSV) were not detected In a survey of 8 beetroot crops TuYV was detected in Auckland at 1 incidence but not in Hawkes Bay Beet mosaic virus was detected at 1 incidence in both regions Fungal leaf spotting pathogens appear a greater concern in beetroot In 12 dwarf bean processing crops throughout Canterbury virus was only detected in early sown crops AMV and RCVMV were most widespread with incidences of up to 9; CMV with up to 7 incidence; then BYMV TuYV and SDV each with 1 incidence No Bean common mosaic virus was detected

Genome diversity and evidence of recombination and reassortment in nanoviruses from Europe

The recent identification of a new nanovirus, pea necrotic yellow dwarf virus, from pea in Germany prompted us to survey wild and cultivated legumes for nanovirus infections in several European countries. This led to the identification of two new nanoviruses: black medic leaf roll virus (BMLRV) and pea yellow stunt virus (PYSV), each considered a putative new species. The complete genomes of a PYSV isolate from Austria and three BMLRV isolates from Austria, Azerbaijan and Sweden were sequenced. In addition, the genomes of five isolates of faba bean necrotic yellows virus (FBNYV) from Azerbaijan and Spain and those of four faba bean necrotic stunt virus (FBNSV) isolates from Azerbaijan were completely sequenced, leading to the first identification of FBNSV occurring in Europe. Sequence analyses uncovered evolutionary relationships, extensive reassortment and potential remnants of mixed nanovirus infections, as well as intra- and intercomponent recombination events within the nanovirus genomes. In some virus isolates, diverse types of the same genome component (paralogues) were observed, a type of genome complexity not described previously for any member of the family Nanoviridae. Moreover, infectious and aphid-transmissible nanoviruses from cloned genomic DNAs of FBNYV and BMLRV were reconstituted that, for the first time, allow experimental reassortments for studying the genome functions and evolution of these nanoviruses.

First Report of a Nanovirus Disease of Pea in Germany.

During the growing season of 2009, a disease consisting of leaf rolling, top yellows, and plant stunting affected pea (Pisum sativum) in fields near Aschersleben, Saxony-Anhalt, Germany. Samples from symptomatic plants collected in July 2009 were analyzed at the JKI in Braunschweig for infections by various legume viruses by ELISA, immunoelectron microscopy, and transmission assays by sap and aphids. Of 23 samples, 9 were shown to contain Pea enation mosaic virus and three samples each contained Bean leafroll virus and Soybean dwarf virus. From two further samples that had tested negative for the aforementioned viruses, we succeeded in transferring a disease agent to faba bean (Vicia faba) seedlings by giving 50 to 100 individuals of the pea aphid (Acyrthosiphon pisum) acquisition and inoculation access feedings each of ~48 h. Following vector transmission, the agent caused severe yellowing and stunting in pea and faba bean, sometimes followed by necrosis. Attempts at mechanical transmission of the agent failed, and isolation of double-stranded RNA from infected tissue was not successful. Therefore, we considered the possible presence of a nanovirus (4). When using polyclonal antibodies (PAbs) against Faba bean necrotic yellows virus (FBNYV) for double-antibody sandwich (DAS)-ELISA analysis of the two isolates of the disease agent we observed weak but clearly positive reactions. To confirm these weak DAS-ELISA reactions, we used all available monoclonal antibodies (MAbs) raised against FBNYV (1) and faba bean necrotic stunt virus (FBNSV) (3) individually in triple-antibody sandwich (TAS)-ELISA in combination with the FBNYV PAbs for plate coating. Six of 26 MAbs reacted from weak to strong with the two pea isolates, with MAbs FBNYV-3-1F7 and FBNSV-5-1G8 giving the strongest reactions and none of the MAbs giving a differential reaction with the two pea isolates. Employing rolling circle amplification of total DNA extracted from symptomatic leaves of one of the pea isolates yielded a substantial amount of high molecular weight DNA, whereas little or no amplification occurred when using DNA from noninoculated pea leaves. Restriction of the amplified DNA in a nanovirus iteron-specific manner by AatII endonuclease yielded a predominant and abundant product of ~1 kb (3). Sequence comparisons of eight cloned DNAs of 1,002 nucleotides long unequivocally identified them as complete DNA-R component of a new member of the genus Nanovirus (2,4). Its DNA-R sequence (GenBank No. GU553134) is nearly equidistant from the DNA-R sequences of FBNYV (Y11405), FBNSV (GQ150778), Milk vetch dwarf virus (MDV) (AB027511) and Subterranean clover stunt virus (SCSV) (AJ290434), sharing with them respective sequence identities of 79, 78, 79, and 73%. Moreover, it is more distinct from the DNA-R sequences of FBNYV, FBNSV, and MDV than the three latter are from each other (86 to 91%). This together with the serological data relating to the capsid protein properties of this virus strongly suggest that it is distinct from the hitherto described nanoviruses FBNYV, MDV, FBNSV, and SCSV. Therefore, we propose the name pea necrotic yellow dwarf virus (PNYDV) for this new nanovirus naturally infecting pea in Germany.