Detection Of Plant Viruses Research Articles

Virus Occurrence and Survival in Reusable Resources: A Minireview

This work covers important aspects of the occurrence and viability of various viruses in the two most common reusable waste resources: wastewater and biomass waste. Detection of human, bacterial and plant viruses in these wastes are summarized. Historically, human viruses have been monitored in wastewater for decades. Evidence suggests that wastewater mostly contains fecal-orally transmitted viruses, which are abundant and diverse. Recently, an increasing occurrence of SARS-CoV2 in sewage water with the spreading epidemics has been confirmed but lacking biological proof of infectivity yet. Besides human pathogens, wastewater is shown to be rich in bacteriophages and plant viruses as well, which supposedly enter the water from human guts. Viruses serving as water quality indicators are also discussed here. Lastly, we focus on biomass waste treatment, showing the presence of some common and stable plant viruses which may supposedly survive the technological process.

Potato viruses in Kazakhstan and methods for obtaining virus-free seed material

Potato (Solanum tuberosum L.) is a staple food worldwide, including in Kazakhstan. The potato yield in 2021 in the country was only 20 tonnes per ha, which is a rather low indicator. One of the main reasons for the insufficient yield of potatoes in Kazakhstan is the low quality of seed material, and the main requirement for high-quality seed material is the absence of viral diseases. Viral diseases in crops are a major impediment to sustainable potato production, as they cause large losses in crop quantity and quality. To date, 40 viral potato diseases have been discovered worldwide. Depending on the infection of viral diseases, the yield can be reduced by up to 90% in crop production. In this review, we discuss in detail the current state of potato viral diseases in Kazakhstan and characterise the most common potato viruses in the country, including potato virus M (PVM), potato virus (PVS), potato virus X (PVX), potato virus Y (PVY) and potato leafroll virus (PLRV). To ensure food security of the country and prevent the spread of infection with viral diseases, popular methods (ELISA, RT-PCR and detection of specific types of targets using microarrays) for the early detection of potato plant viruses in seed and field material are considered. For the mass production of virus-free potato plant material, the use of temporary immersion bioreactors is discussed, as well as the use of modern genetic engineering methods to obtain plant varieties resistant to the most common viral diseases.

PM 7/153 (1) Mechanical inoculation of test plants

PM 7/153 (1) Mechanical inoculation of test plants

The transmission of plant viruses

Abstract Plant viruses are a threat to a sustainable economy because they cause economic losses in yields. The epidemiology of plant viruses is of particular interest because of their dynamic spread by insect vectors and their transmission by seeds. The speed and direction of viral evolution are determined by the selective environment in which they are found. Knowledge of the ecology of plant viruses is critical to the transmission of many plant viruses. Accurate and timely detection of plant viruses is an essential part of their control. Rapid climate change and the globalization of trade through free trade agreements encourage the transmission of vectors and viruses from country to country. Another factor affecting the emergence of viruses is the cultivation of monocultures with low genetic diversity a nd high plant density. Trade in plant material (germplasm and living plants) also cause the emergence of new viruses. Viruses have a fast adaptation and development in a new environment. Aphids are the most widespread and important vectors of plant viruses. Myzus persicae transmits more than 100 different plant viruses. In nature plant viruses are transmitted also by nematodes, fungi, mites, leafhoppers, whiteflies, beetles, and planthoppers. The symptoms of viral diseases are very diverse and are often confused with symptoms of abiotic stress. Control of viral diseases is based on two strategies: i) immunization (genetic resistance acquired by plant transformation, breeding, or cross-protection), ii) prophylaxis to limit viruses (removal of infected plants and control of their vectors). For management, we rely on quick and accurate identification of the disease.

Colloidal gold immunochromatographic test strip for virus detection: a review

Colloidal gold immunochromatographic strip is a fast, sensitive and accurate solid-phase labeling detection technology, which has the advantages of low price, easy operation, rapid detection and high specificity, with the potential to qualitatively detect the relevant viruses in a short time with desired sensitivity and accuracy. It effectively addresses the disadvantages of long detection time, equipment inconvenience and professionalism requirement of the traditional detection methods used in the medical, veterinary, animal, plant virus detection, pesticide residue detection and other areas. Presently, the technology has been applied in the detection of bacterial diseases, viral diseases and prevention of extensive spread of infectious diseases, and has sufficient room for further development. This review summarizes the application of colloidal gold immunochromatography strip for biological virus detection, followed by prospecting future perspectives.

Detection and discovery of plant viruses in soybean by metagenomic sequencing

BackgroundViruses negatively impact soybean production by causing diseases that affect yield and seed quality. Newly emerging or re-emerging viruses can also threaten soybean production because current control measures may not be effective against them. Furthermore, detection and characterization of new plant viruses requires major efforts when no sequence or antibody-based resources are available.MethodsIn this study, soybean fields were scouted for virus-like disease symptoms during the 2016–2019 growing seasons. Total RNA was extracted from symptomatic soybean parts, cDNA libraries were prepared, and RNA sequencing was performed using high-throughput sequencing (HTS). A custom bioinformatic workflow was used to identify and assemble known and unknown virus genomes.ResultsSeveral viruses were identified in single or mixed infections. Full- or nearly full-length genomes were generated for tobacco streak virus (TSV), alfalfa mosaic virus (AMV), tobacco ringspot virus (TRSV), soybean dwarf virus (SbDV), bean pod mottle virus (BPMV), soybean vein necrosis virus (SVNV), clover yellow vein virus (ClYVV), and a novel virus named soybean ilarvirus 1 (SIlV1). Two distinct ClYVV isolates were recovered, and their biological properties were investigated in Nicotiana benthamiana, broad bean, and soybean. In addition to infections by individual viruses, we also found that mixed viral infections in various combinations were quite common.ConclusionsTaken together, the results of this study showed that HTS-based technology is a valuable diagnostic tool for the identification of several viruses in field-grown soybean and can provide rapid information about expected viruses as well as viruses that were previously not detected in soybean.

Nanopore sequencing technology and its application in plant virus diagnostics.

Plant viruses threaten crop yield and quality; thus, efficient and accurate pathogen diagnostics are critical for crop disease management and control. Recent advances in sequencing technology have revolutionized plant virus research. Metagenomics sequencing technology, represented by next-generation sequencing (NGS), has greatly enhanced the development of virus diagnostics research because of its high sensitivity, high throughput and non-sequence dependence. However, NGS-based virus identification protocols are limited by their high cost, labor intensiveness, and bulky equipment. In recent years, Oxford Nanopore Technologies and advances in third-generation sequencing technology have enabled direct, real-time sequencing of long DNA or RNA reads. Oxford Nanopore Technologies exhibit versatility in plant virus detection through their portable sequencers and flexible data analyses, thus are wildly used in plant virus surveillance, identification of new viruses, viral genome assembly, and evolution research. In this review, we discuss the applications of nanopore sequencing in plant virus diagnostics, as well as their limitations.

Onsite detection of plant viruses using isothermal amplification assays.

SummaryPlant diseases caused by viruses limit crop production and quality, resulting in significant losses. However, options for managing viruses are limited; for example, as systemic obligate parasites, they cannot be killed by chemicals. Sensitive, robust, affordable diagnostic assays are needed to detect the presence of viruses in plant materials such as seeds, vegetative parts, insect vectors, or alternative hosts and then prevent or limit their introduction into the field by destroying infected plant materials or controlling insect hosts. Diagnostics based on biological and physical properties are not very sensitive and are time‐consuming, but assays based on viral proteins and nucleic acids are more specific, sensitive, and rapid. However, most such assays require laboratories with sophisticated equipment and technical skills. By contrast, isothermal‐based assays such as loop‐mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) are simple, easy to perform, reliable, specific, and rapid and do not require specialized equipment or skills. Isothermal amplification assays can be performed using lateral flow devices, making them suitable for onsite detection or testing in the field. To overcome non‐specific amplification and cross‐contamination issues, isothermal amplification assays can be coupled with CRISPR/Cas technology. Indeed, the collateral activity associated with some CRISPR/Cas systems has been successfully harnessed for visual detection of plant viruses. Here, we briefly describe traditional methods for detecting viruses and then examine the various isothermal assays that are being harnessed to detect viruses.

Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants.

High-throughput sequencing (HTS) of host plant small RNA (sRNA) is a popular approach for plant virus and viroid detection. The major bottlenecks for implementing this approach in routine virus screening of plants in quarantine include lack of computational resources and/or expertise in command-line environments and limited availability of curated plant virus and viroid databases. We developed: (1) virus and viroid report web-based bioinformatics workflows on Galaxy Australia called GA-VirReport and GA-VirReport-Stats for detecting viruses and viroids from host plant sRNA extracts and (2) a curated higher plant virus and viroid database (PVirDB). We implemented sRNA sequencing with unique dual indexing on a set of plants with known viruses. Sequencing data were analyzed using GA-VirReport and PVirDB to validate these resources. We detected all known viruses in this pilot study with no cross-sample contamination. We then conducted a large-scale diagnosis of 105 imported plants processed at the post-entry quarantine facility (PEQ), Australia. We detected various pathogens in 14 imported plants and discovered that de novo assembly using 21–22 nt sRNA fraction and the megablast algorithm yielded better sensitivity and specificity. This study reports the successful, large-scale implementation of HTS and a user-friendly bioinformatics workflow for virus and viroid screening of imported plants at the PEQ.

Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses.

Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

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.

Systematic Comparison of Nanopore and Illumina Sequencing for the Detection of Plant Viruses and Viroids Using Total RNA Sequencing Approach.

High-throughput sequencing (HTS) has become an important tool for plant virus detection and discovery. Nanopore sequencing has been rapidly developing in the recent years and offers new possibilities for fast diagnostic applications of HTS. With this in mind, a study was completed, comparing the most established HTS platform (MiSeq benchtop sequencer—Illumina), with the MinION sequencer (Oxford Nanopore Technologies) for the detection of plant viruses and viroids. Method comparisons were performed on five selected samples, containing two viroids, which were sequenced using nanopore technology for the first time and 11 plant viruses with different genome organizations. For all samples, sequencing libraries for the MiSeq were prepared from ribosomal RNA-depleted total RNA (rRNA-depleted totRNA) and for MinION sequencing, direct RNA sequencing of totRNA was used. Moreover, for one of the samples, which contained five different plant viruses and a viroid, three additional variations of sample preparation for MinION sequencing were also used: direct RNA sequencing of rRNA-depleted totRNA, cDNA-PCR sequencing of totRNA, and cDNA-PCR sequencing of rRNA-depleted totRNA. Whilst direct RNA sequencing of total RNA was the quickest of the tested approaches, it was also the least sensitive: using this approach, we failed to detect only one virus that was present in a sample at an extremely low titer. All other MinION sequencing approaches showed improved performance with outcomes similar to Illumina sequencing, with cDNA-PCR sequencing of rRNA-depleted totRNA showing the best performance amongst tested nanopore MinION sequencing approaches. Moreover, when enough sequencing data were generated, high-quality consensus viral genome sequences could be reconstructed from MinION sequencing data, with high identity to the ones generated from Illumina data. The results of this study implicate that, when an appropriate sample and library preparation are selected, nanopore MinION sequencing could be used for the detection of plant viruses and viroids with similar performance as Illumina sequencing. Taken as a balance of practicality and performance, this suggests that MinION sequencing may be an ideal tool for fast and affordable virus diagnostics.

​Techniques for Detection and Diagnosis of Plant Viruses: A Review

Plant viruses are famed for serious economic losses to most of the agricultural and horticultural crops all around the world. The losses caused by plant viruses are estimated to be several billion bucks per year and are therefore a major threat to global crop production and food security. Traditional diagnostic methods based on biological and physical properties of virus such as appearance of symptoms, bioassay on indicator plants, vector borne and virus particle morphology by electron microscopy are cumbersome, time-consuming and expensive. Recognition of disease based on the symptoms indicated by virus affected plants, can invariably be the first process in several cases, however it’s confusing additionally as a result of the symptoms are changeable and depends on several factors like abiotic conditions. There are several sensitive and effective diagnostic methods developed during the last four decades based on virus protein e.g., immunosorbent electron microscopy (ISEM), enzyme-linked immunosorbent assay (ELISA) and nucleic acid e.g., nucleic acid hybridization, isothermal and thermostable PCRs, for plant virus detection, each having its own advantage and disadvantage. This review provides an update on the progress made on the techniques that are useful for early, sensitive, accurate and reliable detection and diagnosis of plant viruses.

Potato viruses of 7 commercial cultivars grown in field Primorsky Krai of Russia

Scientific relevance. Plant viruses cause a significant economic loss to potato production, especially if plants are infected at early growth stages and infections are mixed. Viral diseases reduce both yield and quality of harvested crops. Detection and identification of plant viruses are key important to prevent their spreading and to achieve potential yield predetermined by characteristics of varieties.Research methods. Seven potato varieties, bred in Russia and overseas, were used in the field experiment: Smak, Avgustin, Yantar, Laperla, Labella, Red Lady, Sante, Belmonda. Viral infection rate was measured by the percent of plants with symptoms to the total number of plants. In addition to infection frequency, a disease rate was described after visual estimation. Total RNA was isolated from the collected leaves according to Bekesiova I. et al. 1999 [13]. Qualitative and quantitative estimation of plant viruses in the samples were conducted by single-step real-time RT-PCR with fluorescent detection with the Applied Biosystems QuantStudio 5 and commercial kits “Potato Virus X, Y, M, L, S, A, PSTVd-RT” (Syntol Company) according to the official protocol of the kits.Results. As a result of our research, symptoms of mixed viral infection were described for potato varieties depending on concentrations and proportions of these viruses in a plant. Mixed viral infection in the potato field in Primorsky Krai comprised PVY, PVX, PVA, PVS, PVM, also PLRV and PSTVd.

Effect of neural network structure in accelerating performance and accuracy of a convolutional neural network with GPU/TPU for image analytics.

BackgroundIn deep learning the most significant breakthrough in the field of image recognition, object detection language processing was done by Convolutional Neural Network (CNN). Rapid growth in data and neural networks the performance of the DNN algorithms depends on the computation power and the storage capacity of the devices.MethodsIn this paper, the convolutional neural network used for various image applications was studied and its acceleration in the various platforms like CPU, GPU, TPU was done. The neural network structure and the computing power and characteristics of the GPU, TPU was analyzed and summarized, the effect of these on accelerating the tasks is also explained. Cross-platform comparison of the CNN was done using three image applications the face mask detection (object detection/Computer Vision), Virus Detection in Plants (Image Classification: agriculture sector), and Pneumonia detection from X-ray Images (Image Classification/medical field).ResultsThe CNN implementation was done and a comprehensive comparison was done on the platforms to identify the performance, throughput, bottlenecks, and training time. The CNN layer-wise execution in GPU and TPU is explained with layer-wise analysis. The impact of the fully connected layer and convolutional layer on the network is analyzed. The challenges faced during the acceleration process were discussed and future works are identified.

RECOMBINANT ANTIBODY PRODUCTION BY CLONING OF Pepper yellow leaf curl Indonesia virus (PepYLCIV) COAT PROTEIN GENE

Pepper yellow leaf curl Indonesia virus (PepYLCIV) is an important pathogen on chili cultivation and is transmitted through the seed. Serological tests are sensitive, accurate, efficient and it has been widely used for the detection of seed-transmitted plant viruses. This study aimed to produce PepYLCIV recombinant protein as a material to produce recombinant antibodies PepYLCIV. DNA was extracted from infected chili leaves collected from Congkrang, Muntilan, Central Java verified using primer PepYLCIV-BamHI and PepYLCIV-EcoRI and produced an amplicon at 840 bp. The amplified fragments were cloned into the pET32a then transformed to Escherichia coli BL21. The percentage of nucleotide sequence identity and sequence of amino acid, PepYLCIV CK-6 isolates had the highest similarity of nucleotide and amino acid sequences to of chili isolates from Bandung. The expressed recombinant protein was obtained with IPTG concentration 0,5 mM and harvested at 6 hours after IPTG induction. SDS PAGE analysis of the recombinant plasmid Begomovirus CK-6 showed that the coat protein size was about 29 kDa. Immunization was carried out on rabbits by injecting 150 µg of recombinant protein 4 times with an interval of 1 week to produce crude antiserum and pure antiserum capable of detecting PepYLCIV in chili and Ageratum conyzoides using I-ELISA and DIBA tests.

Direct identification of fungi associated with indoor and outdoor ornamental plants by utilizing PCR assay

Direct identification of fungi associated with indoor and outdoor ornamental plants by utilizing PCR assay

Advanced and Commonly Used Serological Techniques for Detection and Diagnosis of Plant Virus: Review

Plant diseases caused by viruses are the most menace to sustainable agriculture, leading to numerous billion dollars in losses annually. Proper and accurate detection of plant viruses is always the key to developing appropriate solutions to manage the economic losses caused by them. Advances in technology have simplified the tools available to detect and diagnose viruses at a time when control measures should be used. Currently, nucleic acid and serological based diagnostic methods are widely used for plant viral identifications. Serological techniques which based on antibody and antigen reaction is broadly used for the detection of plant viruses because of its simplicity, adaptability and sensitivity. A large number of advanced serological tests are available such as enzyme-linked immunosorbent assay (ELISA), dot immunobinding assay, tissue blotting immunoassay and Lateral flow assay. Various ELISA varieties such as double-antibody sandwich- ELISA, triple-antibody sandwich-ELISA, and antigen-coated-ELISA are widely used in the detection and testing of plant viruses. Dot immunobinding assay performed on a nitrocellulose that the plant extracts are spotted onto a membrane while tissue blotting immunoassay is an easy method that the crude sap from plants is directly blotted and used for detection through immunology. Lateral flow assay is the latest and the only serological method used for the detection of viruses without the aid of laboratory and skilled personnel. It is an onsite and quick assay that can be performed by anyone and suitable for the detection of viruses that occur in high concentrations in plants. Keywords : Antibody, Antigen, ELISA, Plant virus, Detection, Serology DOI: 10.7176/ALST/91-02 Publication date: January 31 st 2022

Electron microscopy as a tool for detection of plant Viruses

Electron microscopy as a tool for detection of plant Viruses

CRISPR-Cas-Led Revolution in Diagnosis and Management of Emerging Plant Viruses: New Avenues Toward Food and Nutritional Security.

Plant viruses pose a serious threat to agricultural production systems worldwide. The world's population is expected to reach the 10-billion mark by 2057. Under the scenario of declining cultivable land and challenges posed by rapidly emerging and re-emerging plant pathogens, conventional strategies could not accomplish the target of keeping pace with increasing global food demand. Gene-editing techniques have recently come up as promising options to enable precise changes in genomes with greater efficiency to achieve the target of higher crop productivity. Of genome engineering tools, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) proteins have gained much popularity, owing to their simplicity, reproducibility, and applicability in a wide range of species. Also, the application of different Cas proteins, such as Cas12a, Cas13a, and Cas9 nucleases, has enabled the development of more robust strategies for the engineering of antiviral mechanisms in many plant species. Recent studies have revealed the use of various CRISPR-Cas systems to either directly target a viral gene or modify a host genome to develop viral resistance in plants. This review provides a comprehensive record of the use of the CRISPR-Cas system in the development of antiviral resistance in plants and discusses its applications in the overall enhancement of productivity and nutritional landscape of cultivated plant species. Furthermore, the utility of this technique for the detection of various plant viruses could enable affordable and precise in-field or on-site detection. The futuristic potential of CRISPR-Cas technologies and possible challenges with their use and application are highlighted. Finally, the future of CRISPR-Cas in sustainable management of viral diseases, and its practical utility and regulatory guidelines in different parts of the globe are discussed systematically.