Leafroll Virus Research Articles

Molecular Characterization of a Novel Polerovirus Infecting Soybean in China.

Poleroviruses are positive-sense, single-stranded viruses. In this study, we describe the identification of a novel polerovirus isolated from soybean displaying curled leaves. The complete viral genome sequence was identified using high-throughput sequencing and confirmed using rapid amplification of cDNA ends (RACE), RT-PCR and Sanger sequencing. Its genome organization is typical of the members of genus Polerovirus, containing seven putative open reading frames (ORFs). The full genome is composed of single-stranded RNA of 5822 nucleotides in length, with the highest nucleotide sequence identity (79.07% with 63% coverage) for cowpea polerovirus 2 (CPPV2). Amino acid sequence identities of the protein products between the virus and its relatives are below the threshold determined by the International Committee of Taxonomy of Viruses (ICTV) for species demarcation, and this strongly supports this virus’ status as a novel species, for which the name soybean chlorotic leafroll virus (SbCLRV) is proposed. Recombination analysis identified a recombination event in the ORF5 of the 3’ portion in the genome. Phylogenetic analyses of the genome and encoded protein sequences revealed that the new virus is closely related to phasey bean mild yellows virus, CPPV2 and siratro latent polerovirus. Subsequently, we demonstrated the infectivity of SbCLRV in Nicotiana benthamiana via infectious cDNA clone generation and agroinoculation.

Genome editing (CRISPR-Cas)-mediated virus resistance in potato (Solanum tuberosum L.).

Plant viruses are the major pathogens that cause heavy yield loss in potato. The important viruses are potato virus X, potato virus Y and potato leaf roll virus around the world. Besides these three viruses, a novel tomato leaf curl New Delhi virus is serious in India. Conventional cum molecular breeding and transgenics approaches have been applied to develop virus resistant potato genotypes. But progress is slow in developing resistant varieties due to lack of host genes and long breeding process, and biosafety concern with transgenics. Hence, CRISPR-Cas mediated genome editing has emerged as a powerful technology to address these issues. CRISPR-Cas technology has been deployed in potato for several important traits. We highlight here CRISPR-Cas approaches of virus resistance through targeting viral genome (DNA or RNA), host factor gene and multiplexing of target genes simultaneously. Further, advancement in CRISPR-Cas research is presented in the area of DNA-free genome editing, virus-induced genome editing, and base editing. CRISPR-Cas delivery, transformation methods, and challenges in tetraploid potato and possible methods are also discussed.

A Novel Flavi-like Virus in Alfalfa (Medicago sativa L.) Crops along the Snake River Valley.

Alfalfa is an important perennial forage crop in Idaho supporting dairy and cattle industries that is typically grown in the same field for as many as 4 years. Alfalfa stands of different ages were subjected to screening for viruses using high-throughput sequencing and RT-PCR. The two most common viruses found were alfalfa mosaic virus and bean leafroll virus, along with Medicago sativa amalgavirus, two alphapartitiviruses, and one deltapartitivirus. Additionally, a new flavi-like virus with an unusual genome organization was discovered, dubbed Snake River alfalfa virus (SRAV). The 11,745 nt, positive-sense (+) RNA genome of SRAV encodes a single 3835 aa polyprotein with only two identifiable conserved domains, an RNA-dependent RNA polymerase (RdRP) and a predicted serine protease. Notably, unlike all +RNA virus genomes in the similar size range, the SRAV polyprotein contained no predicted helicase domain. In the RdRP phylogeny, SRAV was placed inside the flavi-like lineage as a sister clade to a branch consisting of hepaci-, and pegiviruses. To the best of our knowledge, SRAV is the first flavi-like virus identified in a plant host. Although commonly detected in alfalfa crops in southern Idaho, SRAV sequences were also amplified from thrips feeding in alfalfa stands in the area, suggesting a possible role of Frankliniella occidentalis in virus transmission.

Metagenomic analysis for detection and discovery of plant viruses in wild Solanum spp. in South Africa

AbstractWild plant species play an important role in plant virus epidemiology, mainly by harbouring viruses pathogenic to cultivated plant species. The genus Solanum includes important crop species as well as some highly abundant and widely distributed wild plant species. The aim of the present study was to profile the viromes of 11 wild Solanum spp. found in five provinces of South Africa. Metatranscriptomic analysis of pooled RNA samples from each of the Solanum spp. detected viruses belonging to 13–19 families. Reverse transcription PCR confirmed the detection of potato virus Y (PVY), potato leaf roll virus (PLRV), tomato torrado virus (ToTV) and tomato chlorosis virus (ToCV) for the first time in some of the Solanum spp. studied. Phylogenetic analyses indicated that the PVY and PLRV strains from the wild Solanum spp. were divergent from those reported in cultivated crops, while there was limited divergence among ToTV and ToCV isolates. Viruses detected for the first time in South Africa included tobacco mild green mosaic virus, tomato matilda virus, a pepper enamovirus from Rwanda and a cytorhabdovirus from potato in Kenya. Potentially novel viruses were also detected in S. lichtensteinii, S. mauritianum and S. viarum. This study demonstrates the role of Solanum spp. in harbouring viruses pathogenic to solanaceous crops, and in the emergence of new virus strains. It may therefore inform strategies for virus disease management by control of wild solanums that harbour viruses pathogenic to important Solanum crops.

Identification of New Chickpea Virus and Control of Chickpea Virus Disease

Objective The objective of the study was to discuss the classification, virus characteristics, detection methods, and control measures of chickpea virus, with an aim to provide a theoretical basis for identification of new chickpea virus and control of chickpea virus disease. Methods The domestic and foreign studies were reviewed, and the virus coat protein or nucleic acid sequence was identified by immunological and molecular diagnostic techniques. Results There were 14 main types of chickpea viruses attacking, and seven Luteoviridae viruses were reported, namely, chickpea chlorotic stunt virus (CpCSV), bean leafroll virus (BLRV), beet western yellows virus (BWYV), soybean dwarf virus (SbDV), cotton leafroll dwarf virus (CLRDV), cucurbit aphid-borne yellows virus (CABYV), and phasey bean mild yellows virus (PhBMYV). The family Geminiviridae includes chickpea chlorotic dwarf virus (CpCDV), chickpea chlorosis virus (CpCV), chickpea redleaf virus (CpRLV), chickpea yellows virus (CpYV), and mastrevirus. The family Nanoviridae is dominated by the faba bean necrotic yellows virus (FBNYV). The family Bromoviridae includes cucumber mosaic virus (CMV) and alfalfa mosaic virus (AMV). Conclusion At present, there are mainly 12 types of viruses infecting chickpeas, which are transmitted by leafhoppers or aphids and are associated with symptoms such as yellowing, chlorosis, and stunted pod development, resulting in serious yield loss. Correct use of various molecular diagnostic tools to detect and identify chickpea virus can accurately assess chickpea virus infection and provide a basis for the prevention and treatment of chickpea virus disease.

Diversity of the virome associated with alfalfa (Medicago sativa L.) in the U.S. Pacific Northwest

Alfalfa (Medicago sativa L.) is one of the most extensively cultivated forage legumes in the world. It is currently the third most valuable field crop in the United States with an estimated value of over $9.3 billion. Alfalfa productivity is limited by various infectious diseases that can reduce forage yield and quality and shorten stand life. The crop can frequently be infected with a diverse array of pathogens and other organisms that have distinct life cycles, biology, and mode of action. Among them are many coinfecting viruses, that greatly contribute to the heterogeneity of within-host pathogenic communities, representing a ubiquitous and abundant background for all other host–pathogen interactions. Regrettably, the impact of viral diseases, their role in alfalfa health and involvement in the severity of multi-pathogen infections are often underestimated and not well understood. As high-throughput sequencing approaches have been developed, opportunities to delve into these complex interactions can be realized. In this work, we have characterized a diversity of viral populations in several commercial alfalfa production fields located in the U.S. Pacific Northwest. At least 45 distinct viruses have been identified in all alfalfa samples. Among them some were known to infect the crop prior to this study, and others were designated as emerging, novel and viruses integrated into the alfalfa genome. Known viruses included alfalfa mosaic virus, pea streak virus and bean leafroll virus, while among emerging and novel agents were alfalfa virus S, cherry virus Trakiya, several rhabdoviruses and others. Additional biological and impact studies will be needed to determine if newly identified viruses, especially those that have not been reported from alfalfa before, should be considered pathogens of this crop.

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.

Advances in RNA-Silencing-Related Resistance against Viruses in Potato.

Potato is a major food crop that has the potential to feed the increasing global population. Potato is the fourth most important crop and a staple food for many people worldwide. The traditional breeding of potato poses many challenges because of its autotetraploid nature and its tendency toward inbreeding depression. Moreover, potato crops suffer considerable production losses because of infections caused by plant viruses. In this context, RNA silencing technology has been successfully applied in model and crop species. In this review, we describe the RNA interference (RNAi) mechanisms, including small-interfering RNA, microRNA, and artificial microRNA, which may be used to engineer resistance against potato viruses. We also explore the latest advances in the development of antiviral strategies to enhance resistance against potato virus X, potato virus Y, potato virus A, potato leafroll virus, and potato spindle tuber viroid. Furthermore, the challenges in RNAi that need to be overcome are described in this review. Altogether, this report would be insightful for the researchers attempting to understand the RNAi-mediated resistance against viruses in potato.

Regression Modeling Strategies to Predict and Manage Potato Leaf Roll Virus Disease Incidence and Its Vector

The potato leaf roll virus (PLRV) disease is a serious threat to successful potato production and is mainly controlled by integrated disease management; however, the use of chemicals is excessive and non-judicious, and it could be rationalized using a predictive model based on meteorological variables. The goal of the present investigation was to develop a disease predictive model based on environmental responses viz. minimum and maximum temperature, rainfall and relative humidity. The relationship between epidemiological variables and PLRV disease incidence was determined by correlation analysis, and a stepwise multiple regression was used to develop a model. For this purpose, five years (2010–2015) of data regarding disease incidence and epidemiological variables collected from the Plant Virology Section Ayub Agriculture Research Institute (AARI) Faisalabad were used. The model exhibited 94% variability in disease development. The predictions of the model were evaluated based on two statistical indices, residual (%) and root mean square error (RMSE), which were ≤±20, indicating that the model was able to predict disease development. The model was validated by a two-year (2015–2017) data set of epidemiological variables and disease incidence collected in Faisalabad, Pakistan. The homogeneity of the regression equations of the two models, five years (Y = −47.61 − 0.572x1 + 0.218x2 + 3.78x3 + 1.073x4) and two years (Y = −28.93 − 0.148x1 + 0.510x2 + 0.83x3 + 0.569x4), demonstrated that they validated each other. Scatter plots indicated that minimum temperature (5–18.5 °C), maximum temperature (19.1–34.4 °C), rainfall (3–5 mm) and relative humidity (35–85%) contributed significantly to disease development. The foliar application of salicylic acid alone and in combination with other treatments significantly reduced the PLRV disease incidence and its vector population over control. The salicylic acid together with acetamiprid proved the most effective treatment against PLRV disease incidence and its vector M. persicae.

Knockdown of capsid protein encoding novel ATPase domain inhibits genome packaging in potato leafroll virus.

Potato leafroll virus (PLRV) uses powerful molecular machines to package its genome into a viral capsid employing ATP as fuel. Although, recent bioinformatics and structural studies have revealed detailed mechanism of DNA packaging, little is known about the mechanochemistry of genome packaging in small plant viruses such as PLRV. We have identified a novel P-loop-containing ATPase domain with two Walker A-like motifs, two arginine fingers, and two sensor motifs distributed throughout the polypeptide chain of PLRV capsid protein (CP). The composition and arrangement of the ATP binding and hydrolysis domain of PLRV CP is unique and rarely reported. The discovery of the system sheds new light on the mechanism of viral genome packaging, regulation of viral assembly process, and evolution of plant viruses. Here, we used the RNAi approach to suppress CP gene expression, which in turn prevented PLRV genome packaging and assembly in Solanum tuberosum cv. Khufri Ashoka. Potato plants agroinfiltrated with siRNA constructs against the CP with ATPase domain exhibited no rolling symptoms upon PLRV infection, indicating that the silencing of CP gene expression is an efficient method for generating PLRV-resistant potato plants. In addition, molecular docking study reveals that the PLRV CP protein has ATP-binding pocket at the interface of each monomer. This further confirms that knockdown of the CP harboring ATP-binding domain could hamper the process of viral genome packaging and assembly. Moreover, our findings provide a robust approach to generate PLRV-resistant potato plants, which can be further extended to other species. Finally, we propose a new mechanism of genome packaging and assembly in plant viruses.

The Carboxyl Terminal Regions of P0 Protein Are Required for Systemic Infections of Poleroviruses.

P0 proteins encoded by poleroviruses Brassica yellows virus (BrYV) and Potato leafroll virus (PLRV) are viral suppressors of RNA silencing (VSR) involved in abolishing host RNA silencing to assist viral infection. However, other roles that P0 proteins play in virus infection remain unclear. Here, we found that C-terminal truncation of P0 resulted in compromised systemic infection of BrYV and PLRV. C-terminal truncation affected systemic but not local VSR activities of P0 proteins, but neither transient nor ectopic stably expressed VSR proteins could rescue the systemic infection of BrYV and PLRV mutants. Moreover, BrYV mutant failed to establish systemic infection in DCL2/4 RNAi or RDR6 RNAi plants, indicating that systemic infection might be independent of the VSR activity of P0. Partially rescued infection of BrYV mutant by the co-infected PLRV implied the functional conservation of P0 proteins within genus. However, although C-terminal truncation mutant of BrYV P0 showed weaker interaction with its movement protein (MP) when compared to wild-type P0, wild-type and mutant PLRV P0 showed similar interaction with its MP. In sum, our findings revealed the role of P0 in virus systemic infection and the requirement of P0 carboxyl terminal region for the infection.

Manipulation of Vector Host Preference by Pathogens: Implications for Virus Spread and Disease Management.

Some plant pathogens manipulate the behavior and performance of their vectors, potentially enhancing pathogen spread. The implications are evolutionary and epidemiological but also economic for pathogens that cause disease in crops. Here we explore with models the effects of vector manipulation on crop yield loss to disease and on the economic returns for vector suppression. We use two frameworks, one that simulates the proportional occurrence of the pathogen in the vector population with the option to eliminate vectors by a single insecticidal treatment, and one that includes vector population dynamics and the potential for multiple insecticidal sprays in a season to suppress vectors. We parameterize the models with published data on vector manipulation, crop yields as affected by the age of the plant at infection, commodity prices and costs of vector control for three pathosystems. Using the first framework, maximum returns for treating vectors are greater with vector manipulation than without it by approximately US$10 per acre (US$24.7/ha) in peas infected by Pea enation mosaic virus and Bean leaf roll virus, and approximately US$50 per acre (US$124/ha) for potatoes infected by Potato leaf roll virus. Using the second framework, maximum returns for controlling the psyllid vectors of Candidatus Liberibacter solanacearum are 50% greater (approximately US$400/acre, US$988/ha) but additional returns for multiple weekly sprays diminish more with vector manipulation than without it. These results suggest that the economics of vector manipulation can be substantial and provide a framework that can inform management decisions.

Cherry leaf roll virus (walnut ringspot)

Cherry leaf roll virus (walnut ringspot)

Potato leafroll virus

Potato leafroll virus

Potato leafroll virus

This datasheet on Potato leafroll virus covers Identity, Overview, Distribution, Dispersal, Hosts/Species Affected, Vectors & Intermediate Hosts, Diagnosis, Biology & Ecology, Seedborne Aspects, Impacts, Prevention/Control, Further Information.

Antiviral Potential of Plant Activators and Nutrients for the Management of Potato Leaf Roll Virus

Antiviral Potential of Plant Activators and Nutrients for the Management of Potato Leaf Roll Virus

First Report of Papaya ring spot virus (PRSV) Infecting Jute (Corchorus olitorius) in India.

Jute is the most important bast fibre crop of the world, which is mainly cultivated in India, Nepal, Bangladesh, China, Indonesia and South American countries. The fibre is utilized for making apparels, ropes, bags, carpets etc (Biswas et al. 2014). This bio-fibre is gaining importance due to growing environmental consciousness worldwide. In June 2019, we noticed jute plants (less than 2%) showing virus like symptoms viz., downward curling, puckering, angular brownish to yellowish spots etc in a farmer's field at Amdanga Block, North 24 Paraganas, West Bengal, India. To identify the virus, five symptomatic leaves from five different plants were used for high throughput sequencing (HTS). We extracted total RNA from each leaf which was subjected to construction of cDNA libraries. Sequencing was done on Illumina Hiseq 4000 (CytoScan, Thermo Fisher). Approximately 46 million 105 nt paired end reads were generated. Raw reads were trimmed and filtered to perform de novo assembly as described previously by (Grabherr et al. 2013). The obtained contig was 10,326 bp nucleotides (nt) long and in BLASTn against GenBank showed highest identity with papaya ring spot virus (PRSV) with the contig covering 99.6% of the viral genome. The obtained contig shared 99.33% sequence similarity with PRSV strain P (Accession No. MT470188). The selected leaf samples were also tested by double-antibody sandwich (DAS)- enzyme linked immunosorbent assay (ELISA) for papaya ring spot virus (PRSV) along with some common viruses, viz., Potato leaf roll virus (PLRV), Watermelon mosaic virus, Cowpea mosaic virus and Cucumber mosaic virus with the help of commercial diagnostic kits (Agdia). However, only the test with PRSV gave positive reaction for the symptomatic samples. The major symptoms of PRSV on papaya are severe mosaic, chlorosis, reduced lamina with curling and puckering (Gonsalves et al. 2010). To confirm PRSV infection, five symptomatic leaf samples (used for HTS) were collected and whole RNA was extracted from the samples using RNeasy plant minikit (Qiagen, USA). Reverse transcriptase polymerase chain reaction (RT-PCR) was conducted by using isolated RNA. One pair of PRSV specific primer (PSRV1F: 5' TTAAATCTGATTCGTC 3' PRSV 1R: 5'GAAATTCACGCAAAGTCGA3') was developed by using primer BLAST software and was used in RT-PCR assays. Amplified fragments were cloned and sequenced and all the fragments shared 98% sequence identity with PRSV. One of the amplicons was deposited in NCBI (Accession No. MN615832). Crude sap was prepared by homogenizing PRSV-infected jute leaf tissues in 0.1 M sodium phosphate buffer and 2% carborundum dust was added as abrasive (Holkar et al. 2018). The sap was then gently rubbed on to the healthy papaya leaves for inoculation. Typical PRSV like symptoms appeared in inoculated leaves 10 days post inoculation which confirmed the presence of PRSV-P. PRSV was detected by RT-PCR as well as (DAS)-ELISA from all inoculated infected papaya leaf tissues, but could not be detected from uninoculated healthy papaya tissues. To the best of our knowledge, this is the first report of PRSV-P infecting jute in India.

Grapes recovery from viruses during reproduction by biotechnological method

Grape regenerant plants obtained from apical meristems were assessed for the presence of the viruses using PCR and enzyme-linked immunosorbent assay (ELISA). The vast majority of the samples studied for the presence of the most common viruses (Grapevine Leafroll-Associated Virus – 1 (GLRaV-1); Grapevine yellow mosaic virus; Grapevine vein banding; virus; Grapevine Leafroll Virus; Grapevine stemm pitting) by ELISA showed negative results. Testing of regenerant plants of the Augustine variety clones showed that only one plant out of 80 plants showed a positive reaction to the presence of this virus. Analysis of 80 plants of the Moldova variety clones revealed a positive reaction to the yellow mosaic virus (Grapevine yellow mosaic virus) in 1 plant as well as in the original donor plant (Moldova variety). The rest of the regenerated plants (79 pcs.) were absolutely healthy. PCR analysis showed that the spectrum of fragments of the original genotypes of Moldova varieties (lanes 1–4) and Augustin (lanes 5–8) contained DNA fragments of 450 bps, corresponding to Candidatus Phytoplasma vitis Flavescence doree. In Bart variety (lanes 9–11), no pathogen was detected. Analysis of the spectrum of fragments of grape regenerant plants obtained from apical meristems (lanes 1–4) and Augustine (lanes 5–8) showed the absence of the pathogen Candidatus Phytoplasma vitis Flavescence doree.

Survey for Legume and Cereal Viruses in Libya

Abukraa, H., S.G. Kumari and F. Bshia. 2022. Survey for Legume and Cereal Viruses in Libya. Arab Journal of Plant Protection, 40(3): 222-230. https://doi.org/10.22268/AJPP-40.3.222230 A field survey was conducted during March and April 2010, to identify viral diseases affecting cereal and legume crops in different regions of Libya. A total of 3706 barley and wheat samples were collected randomly in addition to 187 symptomatic samples from 22 barley and 20 wheat fields. Moreover, 34 symptomatic legume samples were collected from two faba bean fields and one field each of of lentil, chickpea, Vicia sativa, Vicia ervillia and Vicia narbonesis. All samples were tested at ICARDA Virology Laboratory by tissue blot immunoassay (TBIA) using specific antibodies. Results of random cereal samples showed that Barley yellow dwarf virus-PAV (BYDVPAV) was more common (12.6%) in wheat and barley samples, followed by Wheat dwarf virus (WDV) (1.1%). In symptomatic samples, BYDV-PAV was also the most common (45 out of 187 samples tested were infected: 45/187), followed by WDV (23/187), Barley yellow striate mosaic virus (BYSMV) (40/187) and Maize streak virus (MSV) (7/187). In legume fields, Soybean dwarf virus (SbDV) 13 out of 34 samples tested were infected (13/34) was the most common, followed by Bean leafroll virus (BLRV) (12/34), Chickpea chlorotic stunt virus (CpCSV) (5/34) and Beet western yellows virus (BWYV) (4/34). Serological results were confirmed by amplification with polymerase chain reaction (PCR) using specific primers. This is the first report of WDV, MSV and BYSMV on cereal crops, and BLRV, BWYV, SbDV and CpCSV on legume crops in Libya. Keywords: Libya, Cereals, Legumes, Viruses, TBIA, PCR

Potato infection with viruses in the Republic of Bashkortostan and ribonuclease activity in tubers

The paper presents the results of enzyme immunoassay (ELISA) of the presence of potato viruses S (PVS), M (PVM), Y (PVY), X (PVX), and Potato Leaf Roll Virus (PLRV) in tubers of various potato varieties grown in 2019 in the Republic of Bashkortostan. PVS, PVM, PVY, PVX were detected, the VSLK virus was not detected. The greatest infection with PVS, PVM, and PVX was observed in samples of tubers of early-maturing varieties. Tubers of mid-early and late-maturing varieties were more often affected by PVY than early-maturing ones, and PVX was not detected in plants of those varieties. Ribonuclease (RNase) activity in potato tubers of 14 varieties depended on the earliness of the variety, regardless of the soil and climatic conditions. A statistically significant positive correlation (P<0.05) was found between the abundance of PVS and PVM viruses and RNase activity in tubers of medium-early and late-maturing varieties, whereas, on the contrary, a negative correlation between PVM and RNase activity was revealed when analyzing tubers of early-maturing varieties. It is concluded that the prevalence of potato viruses in the territory of the Republic of Bashkortostan and the activity of RNase in tuber seedlings depend on the potato variety and the type of viruses.