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An easy, rapid and inexpensive method of preparing RNA template for a reverse transcription qPCR assay for avocado sunblotch viroid (ASBVd) is described. This method depends on the principle of reversible binding of viroid RNA to filter paper under different concentrations of monovalent cation. Lysis buffers containing either sodium chloride or lithium chloride were compared, and 1.5 M lithium chloride was shown to be optimal for the adsorption of the viroid RNA to the filter paper. The extraction method was validated using field samples and equivalent yields of viroid RNA were obtained using this method and either a commercial RNA extraction kit or a dsRNA chromatography method. The filter paper method of RNA extraction is ideally suited for the large-scale surveillance for ASBVd., (Copyright © 2022 Elsevier B.V. All rights reserved.)

This method originated due to the need to quickly and sensitively detect Avocado sunblotch viroid (ASBVd) in nursery and field trees in California. Optimum sampling protocols were developed for leaf collection from different sized trees based on size and branching as well as for fruit. An ethanol containing buffered extract from 1 g of ground leaf tissue was used as the source of RNA. The extract was absorbed onto small pieces (disks) of Whatman No. 1 filter paper which were then washed and dried. RNA was eluted from the filter paper using sterile water and used as a template in a standard single-tube RT-PCR reaction. The RNA adsorbed on the filter paper disks was quite stable, and the disks could be stored for over 1 year and shipped worldwide at ambient temperature with no noticeable decline in the quality or quantity of the resulting RT-PCR products. The filter paper capture method was expanded to the detection of other viroids including Potato spindle tuber viroid, Peach latent mosaic viroid, and Chrysanthemum stunt viroid and was tested with some viruses as well with minor modifications of the standard protocol., (© 2022. Springer Science+Business Media, LLC, part of Springer Nature.)

Paper-based electrochemical analytical devices (ePADs) have gained significant interest as promising analytical units in recent years because they can be fabricated in simple ways, are low-cost, portable, and disposable platforms that can be applied in various fields. In this sense, paper-based electrochemical biosensors are attractive analytical devices since they can promote diagnose several diseases and potentially allow decentralized analysis. Electrochemical biosensors are versatile, as the measured signal can be improved by using mainly molecular technologies and nanomaterials to attach biomolecules, resulting in an increase in their sensitivity and selectivity. Additionally, they can be implemented in microfluidic devices that drive and control the flow without external pumping and store reagents, and improve the mass transport of analytes, increasing sensor sensitivity. In this review, we focus on the recent developments in electrochemical paper-based devices for viruses' detection, including COVID-19, Dengue, Zika, Hepatitis, Ebola, AIDS, and Influenza, among others, which have caused impacts on people's health, especially in places with scarce resources. Also, we discuss the advantages and disadvantages of the main electrode's fabrication methods, device designs, and biomolecule immobilization strategies. Finally, the perspectives and challenges that need to be overcome to further advance paper-based electrochemical biosensors' applications are critically presented. [ABSTRACT FROM AUTHOR]

In an attempt of reducing the cost of tissue blot immunoassay (TBIA), some kinds of papers as alternative solid phases in place of nitrocellulose membrane (NCM), were tested for detection of three viruses: Cowpea mosaic virus (CPMV), Tomato mosaic virus (ToMV) and Zucchini yellow mosaic virus (ZYMV). Most of the examined papers developed positive reaction with all tested viruses. Canson paper (150g/m² and 300g/m²) were sensitive for detection of the tested viruses as NCM and persist in good condition during the processing. Filter paper (Whatman No. 1), local drawing paper (60g/m2), photocopy paper (80g/m²), (56g/m²) and (70g/m²) were very weak and need to taking care in handling. High glossy photo paper (200g/m²) was not effective however, it did not show any infected or healthy tissue print. Good results were obtained when both faces of NCM and Canson paper (300g/m-2) were printed with all tested viruses. TBIA could detect CPMV in infected leaves using the unused face of NCM previously processed with 7 or 11 years ago. CPMV, ToMV and ZYMV were detected 2, 4, 6, 8 and16 days after inoculation with NCM and Canson paper (300g/m-2). Also, the tested viruses were detected in leaf, petiole, stem and root of infected plants. ToMV could be detected using NCM and Canson paper (300g/m-2) in naturally infected tomato plant samples. [ABSTRACT FROM AUTHOR]

In 2022, the outbreak of the monkeypox virus occurred in many non-endemic countries, and the World Health Organization (WHO) assessed that this outbreak was "atypical". The establishment of a rapid and effective assay that can be used for the early diagnosis of monkeypox virus infection is crucial for outbreak prevention and control. In this study, the monkeypox virus A29 protein and the homologous vaccinia virus A27 protein and cowpox virus 162 protein were expressed in Escherichia coli BL21 for screening. We synthesized the monkeypox virus A2917–49 peptide as the immunogen and obtained 25 monoclonal antibodies (mAbs) against the A29 protein using mouse hybridoma techniques. Then an immunochromatographic test strip method for detecting A29 was established. The strips utilizing mAb-7C5 and 5D8 showed the best sensitivity and lowest limit of detection: 50 pg mL−1 for purified A29 and specificity tests showed that the strips did not cross-react with other orthopox viruses (vaccinia virus or cowpox virus) as well as common respiratory pathogens (SARS-CoV-2, influenza A and influenza B). Therefore, this method can be used for early and rapid diagnosis of monkeypox virus infection by antigen detection. [ABSTRACT FROM AUTHOR]

Since April 2022, a large number of monkeypox (MPX) cases have emerged across the globe in regions that are known to be totally free of zoonotic reservoir. The High Council for Public Health is a national institute commissioned to provide guidelines to the French Ministry of Health. The objective of these guidelines and recommendations is to inform the public, people at risk of severe MPX infection, infected patients and their families and contacts and healthcare workers in charge of infected patients. A review of the literature from the MEDLINE database was carried out using the single keyword 'monkeypox', including recent and older articles from January 2000 to June 2022. There was no filter for the type of study, except English language. The titles and summaries of all the articles were read by the experts to select articles of interest. The High Council for Public Health brought together specialists with expertise in the field to analyse the scientific literature and international recommendations. Recommendations were classified with clinical practice methodology using four levels (strong recommendation, recommendation, optional recommendation and no recommendation) without grading the level of evidence. To develop and methodologically validate the recommendations, the Appraisal of Guidelines for Research and Evaluation Instrument (AGREE-II)chart was partially used. (a) What are the therapeutic management measures for hospitalized patients with severe forms of MPX infection, and what are the preventive measures to protect healthcare professionals? (b) What are the isolation and prevention measures in the community for patients with mild or moderate severity MPX infection? (c) what are the preventive measures for contacts of an MPX-infected person? (d) Who should be vaccinated? (e) What are the specific prevention measures for children and schools? [ABSTRACT FROM AUTHOR]

A technique for the detection of plant virus coat proteins in plant sap is described. The method entails the electroblotting of sodium dodecyl sulphate-polyacrylamide gel electrophoresis-fractionated plant extracts onto nitrocellulose paper, probing the paper with virus-specific rabbit antisera, and indirect detection of virus proteins with horseradish peroxidase-conjugated goat anti-rabbit globulins. The sensitivity and specificity of the technique were tested using brome mosaic and barley stripe mosaic viruses. As little as 1 ng per track of virus protein was detectable, either as pure virus or when mixed with plant sap. Distant serological relationships were detected amongst tobamoviruses, and amongst the bromoviruses, with single antisera. The uses of the technique in probing capsid configuration in a presumed aphid picornavirus, and in routine diagnostic practice, are described.

[Display omitted] • A novel ChF/ZnO/CNT nano-hybrid was fabricated for detection of COVID-19. • Paper based aptasensor with colorimetric detection approach was developed. • Oxidation of TMB substrate by biosensor was detectable by naked eye sensitively. • The LOD of method was 0.05 pg/mL in colorimetric and 8 pg/mL in paper-based platform. Corona Virus Disease 2019 (COVID-19) as the infectious disease caused the pandemic disease around the world through infection by SARS-CoV-2 virus. The common diagnosis approach is Quantitative RT-PCR (qRT-PCR) which is time consuming and labor intensive. In the present study a novel colorimetric aptasensor was developed based on intrinsic catalytic activity of chitosan film embedded with ZnO/CNT (ChF/ZnO/CNT) on 3,3′,5,5′-tetramethylbenzidine (TMB) substrate. The main nanocomposite platform was constructed and functionalized with specific COVID-19 aptamer. The construction subjected with TMB substrate and H 2 O 2 in the presence of different concentration of COVID-19 virus. Separation of aptamer after binding with virus particles declined the nanozyme activity. Upon addition of virus concentration, the peroxidase like activity of developed platform and colorimetric signals of oxidized TMB decreased gradually. Under optimal conditions the nanozyme could detect the virus in the linear range of 1–500 pg mL and LOD of 0.05 pg mL. Also, a paper-based platform was used for set up the strategy on applicable device. The paper-based strategy showed a linear range between 50 and 500 pg mL with LOD of 8 pg mL. The applied paper based colorimetric strategy showed reliable results for sensitive and selective detection of COVID-19 virus with the cost-effective approach. [ABSTRACT FROM AUTHOR]

[Display omitted] • A rotational paper-based analytical device was designed for differential detection of SARS-CoV-2 and influenza A H1N1 virus. • The tetrahedral DNA framework could fix aptamer in a straightforward direction and well-defined spacing. • The strong affinity of aptamer toward target S protein and H1N1 ensured the specificity of this strategy. • The developed platform exhibited excellent analysis performance in terms of simple, rapid, low cost, disposability and high sensitivity. Coronavirus disease 2019 (COVID-19) and influenza A are two respiratory infectious diseases with similar clinical manifestations. Because of the complex global epidemic situation of COVID-19, the distinction and diagnosis of COVID-19 and influenza A infected persons is crucial for epidemic prevention and control. In this study, tetrahedral DNA framework (TDF) was combined with a rotational paper-based analytical device, and the color change generated by the reaction between horseradish peroxidase (HRP) and 3,3′5,5′-tetramethylbenzidine (TMB)–H 2 O 2 was used for grayscale signal analysis by ImageJ software. The quantitative detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A H1N1 virus were realized simultaneously. Under the optimal conditions, the paper-based analytical device showed a good linear relationship between the two viruses in the range of 10-14-10-8g/mL, and the two viruses were not affected by cross reaction. This sensor provides a convenient and reliable method for clinical rapid differentiation and diagnosis of COVID-19 and influenza A. [ABSTRACT FROM AUTHOR]

• Importance of improved approaches to viral pathogen detection for human health care. • Limitations of traditional human virus detecting methods have been compared with biosensors. • Recent progresses towards paper-based diagnostic chips for detecting human viruses are reviewed. • Challenges and prospects of paper-based diagnostic chips for detecting viruses were summarized. Viruses cause various diseases in humans, and pose serious health risks to individuals and populations worldwide. As a result, various diagnostic procedures and methods have been developed to prevent, manage, and reduce the burden of viral diseases, each with its own benefits and drawbacks. Among these, paper-based diagnostic chips are becoming increasingly common because of their speed, accuracy, convenience, and economical and environmental friendliness. These paper-based diagnostic tests have ideal point-of-care (POC) diagnostic applications, particularly in personalized healthcare. Paper-based diagnostics have emerged as innovative and low-cost solutions for diagnosing viral diseases in remote and underdeveloped regions where traditional diagnostic methods are not readily available. These tests are easy to use, require minimal equipment, and can be performed by nonspecialized personnel, making them accessible even in resource-constrained settings. In this review, we discuss recent developments in paper-based diagnostic chips, the importance of improved methods for identifying viral pathogens, drawbacks of traditional detection techniques, and challenges and prospects of paper-based diagnostic chips for the detection of viruses. [ABSTRACT FROM AUTHOR]

Viruses cause many severe diseases in both plants and animals, urging us to explore new antiviral strategies. In their natural reservoirs, viruses live and replicate while causing mild or no symptoms. Some animals, such as bats, are the predicted natural reservoir of multiple viruses, indicating that they possess broad-spectrum antiviral capabilities. Mechanisms of host defenses against viruses are generally studied independently in plants and animals. In this article, we speculate that some antiviral strategies of natural reservoirs are conserved between kingdoms. To verify this hypothesis, we created null mutants of 10-formyltetrahydrofolate synthetase (AtTHFS), an Arabidopsis thaliana homologue of methylenetetrahydrofolate dehydrogenase, cyclohydrolase and formyltetrahydrofolate synthetase 1 (MTHFD1), which encodes a positive regulator of viral replication in bats. We found that disruption of AtTHFS enhanced plant resistance to three different types of plant viruses, including the tomato spotted wilt virus (TSWV), the cucumber mosaic virus (CMV) and the beet severe curly top virus (BSCTV). These results demonstrate a novel antiviral strategy for plant breeding. We further discuss the approaches used to identify and study natural reservoirs of plant viruses, especially those hosting many viruses, and highlight the possibility of discovering new antiviral strategies from them for plant molecular breeding and antiviral therapy., (© 2022 Institute of Botany, Chinese Academy of Sciences.)

Geminiviruses are a group of plant viruses that cause severe diseases in many economically important crops worldwide, leading to devastating losses to agricultural production. Here we summarize the occurrence and distribution of geminiviruses in China, which provides valuable information for further epidemiological studies and supports the development of effective disease management strategies., (© 2022. Science China Press and Springer-Verlag GmbH Germany, part of Springer Nature.)

Rupert Jethro Best (1903–91), working alone at the Waite Agricultural Research Institute in Adelaide between 1934 and 1937, was among the first to purify tobacco mosaic virus (TMV) and to propose that it was a complex macromolecule containing protein and another reactive group that was responsible for infectivity of the virus. However, his research was completely overshadowed by that of Wendell Stanley and the duo of Frederick Bawden and Norman (aka Bill) Pirie, working in the United States of America and Great Britain, respectively, to the point where Best is not even mentioned in modern histories of TMV. Many factors have contributed to this lack of recognition for Best. Professor James Prescott, a soil scientist and Best's supervisor at the Waite Institute, failed to appreciate the significance of his research, leading to critical delays in publication that prevented him from claiming precedence for purifying TMV. When Best's research was eventually published, it was in Australian journals that were not broadly distributed, resulting in minimal international exposure for his research. The plant virology community within which he worked in Australia was very small and entirely focused on plant disease control, and not concerned with fundamental questions about the composition of viruses. Communication with similarly interested scientists in the Northern Hemisphere was hindered by the great distances involved. In this paper, pioneering research done by Best on TMV is reviewed, and placed in context with that undertaken by Stanley and by Bawden and Pirie, who are best remembered for purifying TMV and characterising its physicochemical properties. Rupert Jethro Best, working alone in Adelaide at the Waite Agricultural Research Institute, was among the first to purify tobacco mosaic virus and to provide evidence that it was a heterogeneous macromolecule, composed mainly of protein but also small prosthetic groups with the properties of a weak acid, wherein lay the activity of the virus. This paper describes the contributions of Rupert Best to early theories on the material nature and mode of reproduction of viruses. Photographer unknown, State Library of South Australia. [ABSTRACT FROM AUTHOR]

We improved a multiple rapid immunofilter paper assay (multi-RIPA) to simultaneously detect three major viruses of cucumber, Cucumber mosaic virus, Melon yellow spot virus and Zucchini yellow mosaic virus. When we increased the concentration of bovine serum albumin (BSA) in the extraction buffer, a positive band for each virus developed in the multi-RIPA, regardless of the order that the three sensitized white latex particles were immobilized on the strip. The increase in BSA concentration also strengthened the sensitivity of each RIPA. In addition, using a mixture of commercially available, red and blue, sensitized latex solutions as a tracer, purple bands could be produced on the strips. Because each virus yielded an unique color for a positive reaction, the three viruses were easy to distinguish. [ABSTRACT FROM AUTHOR]

The rapid immunofilter paper assay (RIPA) was developed to detect Tomato spotted wilt virus (TSWV), Groundnut ringspot virus (GRSV), and Tomato chlorotic spot virus (TCSV) using antisera against recombinant nucleocapsid (N) proteins of each tospovirus. The two-step RIPA was sensitive enough to detect each pecies specifically in only 30 min. This technique is proposed as an excellent tool for routine Tospovirus diagnosis and field epidemiological studies. [ABSTRACT FROM AUTHOR]

The adaptation and improvement of serological assays for the detection of plant viruses has steadily developed. A filter paper immunobinding assay, Western blotting and the double sandwich ELISA were compared for the detection and quantification of wheat streak mosaic virus. ELISA was a more quantitative assay, but the filter paper immunobinding assay and Western blotting were more conservative of antiserum when only a few assays were required and could be run in a shorter period of time. [ABSTRACT FROM AUTHOR]

The second paper in this series [[2]] concerned an examination of two subgroups of the cytorhabdovirus lettuce necrotic yellows virus (LNYV), a virus apparently endemic to the Australia/New Zealand region. The Special Issue "State-of-the-Art Plant Virus Research in Australasia" in I Viruses i provided a fascinating snapshot of plant and fungus virus research being undertaken in Australasia during the final year of the official COVID-19 pandemic. In contrast to papers 2 and 3, where indigenous viruses were adapting to new hosts, in this paper, exotic viruses were shown to be evolving in exotic hosts under selection pressures present in their new geographical location of Tasmania. Paper seven [[7]] reported research into mycoviruses (viruses that infect fungi), not plant viruses as such, although in this case, the virus-infected fungus originated from inside the root of an Australian indigenous orchid. [Extracted from the article]

Presents paper models that can help biology students understand the concept of icosahedral symmetry in small virus capsids. Instructions for construction the models; General principles of symmetry in viruses; Disposition of protein subunits in plant viruses and the picornaviruses.

An introduction is presented in which the editor discusses various reports within the issue on topics including genomics, plant viruses, and pathogenic microorganisms.

Cross-protection is a phenomenon in which a plant that is infected with a virus becomes immune to a secondary infection by the same or related viruses. Although molecular mechanisms underlying this phenomenon are not completely understood, cross-protection induced by an attenuated strain with mild symptoms has been successfully used to prevent damage by more severe strains. In the development and selection of an effective attenuated strain among candidate isolates, evaluating their infectivity and efficiency of cross-protection is important. We describe two protocols to check the infection efficiency and distribution in a plant based on immunostaining results. In addition, a practical inoculation method that uses a spray gun to apply attenuated viruses to a large number of seedlings is presented.

Plant viruses threaten global food security by infecting commercial crops, highlighting the critical need for efficient virus detection to enable timely preventive measures. Current techniques rely on polymerase chain reaction (PCR) for viral genome amplification and require laboratory conditions. This review explores the applications of CRISPR-Cas assisted diagnostic tools, specifically CRISPR-Cas12a and CRISPR-Cas13a/d systems for plant virus detection and analysis. The CRISPR-Cas12a system can detect viral DNA/RNA amplicons and can be coupled with PCR or isothermal amplification, allowing multiplexed detection in plants with mixed infections. Recent studies have eliminated the need for expensive RNA purification, streamlining the process by providing a visible readout through lateral flow strips. The CRISPR-Cas13a/d system can directly detect viral RNA with minimal preamplification, offering a proportional readout to the viral load. These approaches enable rapid viral diagnostics within 30 min of leaf harvest, making them valuable for onsite field applications. Timely identification of diseases associated with pathogens is crucial for effective treatment; yet developing rapid, specific, sensitive, and cost-effective diagnostic technologies remains challenging. The current gold standard, PCR technology, has drawbacks such as lengthy operational cycles, high costs, and demanding requirements. Here we update the technical advancements of CRISPR-Cas in viral detection, providing insights into future developments, versatile applications, and potential clinical translation. There is a need for approaches enabling field plant viral nucleic acid detection with high sensitivity, specificity, affordability, and portability. Despite challenges, CRISPR-Cas-mediated pathogen diagnostic solutions hold robust capabilities, paving the way for ideal diagnostic tools. Alternative applications in virus research are also explored, acknowledging the technology's limitations and challenges., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Agriculture and global food security encounter significant challenges due to viral threats. In the following decades, several molecular studies have focused on discovering biosynthetic pathways of numerous defensive and signaling compounds, as key regulators of plant interactions, either with viruses or their associated vectors. Nevertheless, the complexities of specialized metabolites mediated plant-virus-vector tripartite viewpoint and the identification of their co-evolutionary crossroads toward antiviral defense system, remain elusive. The current study reviews the various roles of plant-specialized metabolites (PSMs) and how plants use these metabolites to defend against viruses. It discusses recent examples of specialized metabolites that have broad-spectrum antiviral properties. Additionally, the study presents the co-evolutionary basis of metabolite-mediated plant-virus-insect interactions as a potential bioinspired approach to combat viral threats. The prospects also show promising metabolic engineering strategies aimed at discovering a wide range of PSMs that are effective in fending off viruses and their related vectors. These advances in understanding the potential role of PSMs in plant-virus interactions not only serve as a cornerstone for developing plant antiviral systems, but also highlight essential principles of biological control., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

This review describes the enhanced classification of polyphenols into flavonoids, lignans, phenolic acids, stilbenes, and tannins. Its focus is the natural sources of polyphenols and an in-depth discussion of their antibacterial, antifungal, and antiviral activity. Besides a broad literature overview, this paper contains authors' experimental data according to some daily consumed vegetables such as tomatoes, different varieties of onion, garlic, parsley, and cayenne pepper and the probable relation of these activities to polyphenols. The isolation of polyphenols via conventional and ultrasonic, pressurized liquids and pulse-field extractions, as well as their methods for detection and determination, are interpreted as well. The main mechanisms by which polyphenols inhibit the growth of bacteria, fungi, and viruses, such as protein synthesis, cell membrane destabilization, and ROS production induction, are in focus. Data on polyphenol concentrations and their respective MIC or the inhibition zone diameters of different bacterial and fungal species and suppressing viral replication are depicted. The toxicity of polyphenols in vitro, ex vivo, and in vivo towards microorganisms and human/animal cells, and the safety of the polyphenols applied in clinical and industrial applications are expanded. This review also characterizes the antimicrobial effects of some chemically synthesized polyphenol derivatives. Biotechnological advances are also reported, especially the entrapment of polyphenols in biocompatible nanoparticles to enhance their bioavailability and efficacy. Polyphenols are promising for exploring molecules' novel antimicrobial substances and paving the path for effective novel antimicrobial agents' discovery, taking into consideration their positives and negatives. [ABSTRACT FROM AUTHOR]

Juglans sigillata Dode is one of the important tree species in southwest China, and it has significant economic and ecological value. However, there is still a lack of effective methods to identify the functional genes of J. sigillata. By verifying the model plant tobacco, the pTRV2::JsPDS vector was able to cause photobleaching. This study showed that photobleaching occurred 24 and 30 d after the silencing vector was infected with aseptic seedlings and fruits of J. sigillata, respectively. When the OD 600 was 0.6, and the injection dose was 500 μL, the gene silencing efficiency of aseptic seedlings was the highest at 16.7 %, significantly better than other treatments. Moreover, when the OD 600 was 0.8, and the injection dose was 500 μL, the gene silencing efficiency in the walnut fruit was the highest (20 %). In addition, the VIGS system was successfully used to silence JsFLS2 and JsFLS4 genes in J. sigillata. This study also showed that the flavonol content and gene expression in the treatment group were decreased compared to the control group. In addition, the proteins transcribed and translated from the JsFLS4 gene may have higher catalytic activity for dihydroquercetin. The above results indicate that the TRV-mediated VIGS system can be an ideal tool for studying J. sigillata gene function., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The major citrus species include several economically important fruits, such as orange, mandarin, lemon, limes, grapefruit and pomelos. Since the 1980 s, total production and consumption of citrus has grown strongly with the current annual worldwide production at over 105 million tonnes. New Zealand's citrus exports, for instance, had an estimated worth of NZ$ 11.6 million (approx. US$ 7 million) in 2020. Citrus plants are prone to viral diseases, which can lead to substantial economic losses. In New Zealand, the citrus Import Health Standard (IHS) has identified 22 viruses and viroids that are subject to regulation and requires citrus nursery stock to be free of these pathogens. As such, there is a need for reliable, sensitive, and rapid detection methods to screen for these viruses and viroids during post entry quarantine. In this study, we developed TaqMan RT-qPCR assays for the detection of nine of these regulated viruses and viroids, namely citrus leaf rugose virus (CiLRV), citrus leprosis virus C (CiLV-C), citrus leprosis virus C2 (CiLV-C2), citrus leprosis virus N (CiLV-N), citrus psorosis virus (CPsV), citrus yellow mosaic virus (CYMV), citrus bent leaf viroid (CBLVd), citrus viroid V (CVd-V), and citrus viroid VI (CVd-VI). These assays have been validated and found to be highly sensitive, specific, and reliable. The implementation of these assays will facilitate the safe importation of citrus nursery stock, thus safeguarding the country's horticultural and economic interests., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Fig mosaic virus (FMV) is recognized as the main viral agent associated with the mosaic disease (MD) of fig trees (Ficus carica). Due to its worldwide occurrence, FMV represents the most significant global threat to the production of fig fruit. A disease management strategy against the MD in fig orchards has never been effective; and therefore, expression of recombinant antibody in plant cells could provide an alternative approach to suppress FMV infections. In this study we focused on expressing a specific recombinant antibody, a single-chain variable fragment (scFv), targeting the nucleocapsid protein (NP) of FMV in planta. To accomplish this objective, we inserted the scFv gene into a plant expression vector and conducted transient expression in leaves of Nicotiana tabacum cv. Samson plants. The construct was transiently expressed in tobacco plants by agroinfiltration, and antibody of the anticipated size was detected by immunoblotting. The produced plantibody was then assessed for specificity using ELISA and confirmed by Western blot analysis. In this study, the plantibody developed against FMV could be considered as a potential countermeasure to the infection by conferring resistance to MD., Competing Interests: Declaration of Competing Interest The authors (Mahsa Jahandideh; Farshad Rakhshandehroo; Mohammadreza Safarnejad; Amir Sahraroo and Toufic Elbeaino) declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Background: Groundnut (Arachis hypogaea L.) is the 13th most important global crop grown throughout the tropical and subtropical regions of the world. One of the major constraints to groundnut production is viruses, which are also the most economically important and most abundant pathogens among cultivated legumes. Only a few studies have reported the characterization of RNA viruses in cultivated groundnuts in western Kenya, most of which deployed classical methods of detecting known viruses., Methods: We sampled twenty-one symptomatic and three asymptomatic groundnut leaf samples from farmers' fields in western Kenya. Total RNA was extracted from the samples followed by First-strand cDNA synthesis and sequencing on the Illumina HiSeq 2500 platform. After removing host and rRNA sequences, high-quality viral RNA sequences were de novo assembled and viral genomes annotated using the publicly available NCBI virus database. Multiple sequence alignment and phylogenetic analysis were done using MEGA X., Results: Bioinformatics analyses using as low as ∼3.5 million reads yielded complete and partial genomes for Cauliflower mosaic virus (CaMV), Cowpea polerovirus 2 (CPPV2), Groundnut rosette assistor virus (GRAV), Groundnut rosette virus (GRV), Groundnut rosette virus satellite RNA (satRNA) and Peanut mottle virus (PeMoV) falling within the species demarcation criteria. This is the first report of CaMV and the second report of CPPV2 on groundnut hosts in the world. Confirmation of the detected viruses was further verified through phylogenetic analyses alongside reported publicly available highly similar viruses. PeMoV was the only seed-borne virus reported., Conclusion: Our findings demonstrate the power of Next Generation Sequencing in the discovery and identification of novel viruses in groundnuts. The detection of the new viruses indicates the complexity of virus diseases in groundnuts and would require more focus in future studies to establish the effect of the viruses as sole or mixed infections on the crop. The detection of PeMoV with potential origin from Malawi indicates the importance of seed certification and cross-boundary seed health testing., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Plant virus detection and identification in crops is a pillar for disease management, import of crop material, production of clean stock plants and basic plant virology studies. In this report, we present a platform for the enrichment and isolation of known or unknown viruses. This platform is based on carbon nanotube arrays inside a microfluidic device that can be a solution for the identification of low titer viruses from plants. Using our microfluidic devices, we achieved enrichment of two economically important viruses, the orthotospovirus, tomato spotted wilt orthotospovirus (TSWV) and the potyvirus, zucchini yellow mosaic virus (ZYMV). The carbon nanotube arrays integrated in these microfluidic devices are capable of trapping viruses discriminated by their size; the virus rich arrays can be then analyzed by common downstream techniques including immunoassays, PCR, HTS and electron microscopy. This procedure offers a simple to operate and portable sample preparation device capable of trapping viruses from raw plant extracts while reducing the host contamination., Competing Interests: Declaration of Competing Interest M.T. and N.P.L. hold equity in Virolock Technologies LLC; a company engaged in the commercialization of CNTMDs. C. R., F. I., C. V., and E. R. declare that they have no known competing financial interests or personal relationships that could have influenced the research reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Plant virus-based sgRNA delivery strategy has been widely applied for efficient genome editing across various plant species, leveraging its significant advantages in the rapid expression and expansion of sgRNA through virus replication and movement. However, the efficacy of the virus-induced gene editing (VIGE) tool in tomato has yet to be explored. In this paper, we established a TRV-mediated CRISPR/Cas9 genome editing system in the somatic cells of tomato, reporting the validation of VIGE and evaluating the mutagenesis efficiency in both tomato leaves and fruits using high-throughput sequencing. The results demonstrated an approximate 65% efficiency of VIGE in tomato leaves for the selected target genes, with VIGE efficiency reaching up to 50% in tomato fruits. This research not only introduces an efficient tool for reverse genetics but also reveals substantial potential of VIGE in surpassing traditional tissue culture techniques for creating heritable mutations in tomato., (© 2024 Wiley‐VCH GmbH.)

Food security is a basic human right that guarantees humans an adequate amount of nutritious food. However, plant viruses and agricultural pests cause real damage to food sources, leading to negative impacts on meeting the human right of obtaining a sufficient amount of food. Understanding infectious disease dynamics can help us to design appropriate control and prevention strategies. Although cassava is among the most produced and consumed crops and greatly contributes to food security, cassava mosaic disease causes a decrease in photosynthesis and reduces cassava yield, resulting in a lack of crops. This paper developed a fractional model for cassava mosaic disease (CMD) dynamics based on the Caputo–Fabrizio (CF) fractional derivative to decrease cassava plant infection. We used fixed-point theory to study the existence of a unique solution in the form of the CMD model. A stability analysis of the model was conducted by using fixed-point theory and the Picard technique. A new numerical scheme was proposed for solving the nonlinear system of a fractional model in the sense of the CF-derivative and applied to obtain numerical simulations for a fractional model of the dynamics of CMD. The obtained results are described using figures that show the dynamics and behaviors of the compartments of CMD, and it is concluded that decreasing the population of whitefly vectors can prevent cassava plants from becoming infected better than increasing the recovery rate of the infected cassava plants. [ABSTRACT FROM AUTHOR]

Summary: In the world of intelligent agriculture, agricultural disease picture detection plays a critical role. Plant disease identification must be efficient if agricultural production is to be increased sustainably. Anomalies in plants affected by viruses, insects, nutritional deficiencies, or poor weather conditions have traditionally been diagnosed by human experts. Deep learning (DL) and transfer learning, two sophisticated machine learning techniques synonymous with the advancement of artificial intelligence technologies in recent years, have started to be used for the identification of agricultural diseases. However, a variety of significant obstacles exist in the way of widespread use of these approaches. This paper looks at DL and transfer learning in particular, and discusses recent developments in using these advanced technologies to recognize agricultural disease images. Many DL architectures have recently been adopted, along with visualization tools, which are critical for identifying signs and classifying plant diseases. The analysis and evaluation of these two approaches show that transfer learning is the better choice given existing agricultural disease data tools. The paper then looks at the key problems that need to be addressed for research in this area to advance, such as image dataset creation, the collection of big data auxiliary domains, and the optimization of the transfer learning process. The construction of technically feasible agricultural disease image recognition systems requires the creation of image datasets collected under real cultivation conditions. This survey aims to learn more about DL capabilities in plant disease detection to increase device efficiency and accuracy in future research. [ABSTRACT FROM AUTHOR]

Potatoes are developed vegetatively from tubers, and therefore potato virus transmission is always a possibility. The potato leafroll virus (PLRV) is a highly devastating virus of the genus Polerovirus and family Luteoviridae and is regarded as the second-most destructive virus after Potato virus Y. Multiple species of aphids are responsible for the persistent and non-propagating transmission of PLRV. Due to intrinsic tuber damage (net necrosis), the yield and quality are drastically diminished. PLRV is mostly found in phloem cells and in extremely low amounts. Therefore, we have attempted to detect PLRV in both potato tuber and leaves using a highly sensitive, reliable and cheap method of one-step reverse transcription-recombinase polymerase amplification (RT-RPA). In this study, an isothermal amplification and detection approach was used for efficient results. Out of the three tested primer sets, one efficiently amplified a 153-bp product based on the coat protein gene. In the present study, there was no cross-reactivity with other potato viruses and the optimal amplification reaction time was thirty minutes. The products of RT-RPA were amplified at a temperature between 38 and 42 °C using a simple heating block/water bath. The present developed protocol of one-step RT-RPA was reported to be highly sensitive for both leaves and tuber tissues equally in comparison to the conventional reverse transcription-polymerase chain reaction (RT-PCR) method. By using template RNA extracted employing a cellular disc paper-based extraction procedure, the method was not only simplified but it detected the virus as effectively as purified total RNA. The simplified one-step RT-RPA test was proven to be successful by detecting PLRV in 129 samples of various potato cultivars (each consisting of leaves and tubers). According to our knowledge, this is the first report of a one-step RT-RPA performed using simple RNA extracted from cellular disc paper that is equally sensitive and specific for detecting PLRV in potatoes. In terms of versatility, durability and the freedom of a highly purified RNA template, the one-step RT-RPA assay exceeds the RT-PCR assay, making it an effective alternative for the certification of planting materials, breeding for virus resistance and disease monitoring. [ABSTRACT FROM AUTHOR]

A mathematical analysis by computations performed in [[4]] succeeded to predict that the RNA editing mechanism by a conformational switch in HDV genotype 3 occurs in HDV genotype 7 as well. Mathematical and computational biology of viruses at the molecular or cellular levels are more difficult to accurately address than at the population level. The HDV paper in [[4]] already mentions addressing HDV viral kinetics across the different genotypes through the use of a simple differential equation model (transitioning from the molecular to the cellular level), and from here on, the Special Issue is devoted to the cellular level. 32422927 6 Casey J.L. RNA editing in hepatitis delta virus genotype III requires a branched double-hairpin RNA structure. [Extracted from the article]

Simple Summary: As COVID-19 shifts from pandemic to endemic, emerging variants may be more or less virulent. Predicting whether an emerging COVID-19 variant has of high risk of causing severe disease is needed to plan for potential burdens on hospital capacity and protecting vulnerable populations. However, it takes time to do laboratory and animal experiments to determine whether a new genetic variant might be more severe, and the results may not be representative of when the virus infects humans. By the time there is epidemiological data on the severity of disease associated with a new variant, it can be too late for designing an optimal public health response. There is a critical need for computer models that can predict severe disease risk from genetic sequence data, which can be obtained from just the first few infections in a potential incoming wave. Two key challenges make computer modeling difficult: (1) sequence changes are complex, and (2) using historical data to predict future disease requires accounting for the confounding effects of changing patient demographics, improving therapeutics, and increased vaccination. In this paper, we introduce a novel interpretable deep learning architecture to solve this problem, demonstrating that it can make robust predictions for emerging variants. Through the COVID-19 pandemic, SARS-CoV-2 has gained and lost multiple mutations in novel or unexpected combinations. Predicting how complex mutations affect COVID-19 disease severity is critical in planning public health responses as the virus continues to evolve. This paper presents a novel computational framework to complement conventional lineage classification and applies it to predict the severe disease potential of viral genetic variation. The transformer-based neural network model architecture has additional layers that provide sample embeddings and sequence-wide attention for interpretation and visualization. First, training a model to predict SARS-CoV-2 taxonomy validates the architecture's interpretability. Second, an interpretable predictive model of disease severity is trained on spike protein sequence and patient metadata from GISAID. Confounding effects of changing patient demographics, increasing vaccination rates, and improving treatment over time are addressed by including demographics and case date as independent input to the neural network model. The resulting model can be interpreted to identify potentially significant virus mutations and proves to be a robust predctive tool. Although trained on sequence data obtained entirely before the availability of empirical data for Omicron, the model can predict the Omicron's reduced risk of severe disease, in accord with epidemiological and experimental data. [ABSTRACT FROM AUTHOR]

Plant viruses are responsible for nearly 47 % of all crop losses brought by plant diseases, which have a considerable negative impact on agricultural output. Nanoparticles have the potential to greatly raise agricultural output due to their wonderful applications in the fields of highly sensitive biomolecular detection, disease diagnostics, antimicrobials, and therapeutic compounds. The application of nanotechnology in plant virology is known as nanophytovirology, and it involves biostimulation, drug transport, genetic manipulation, therapeutic agents, and induction of plant defenses. The inactivation and denaturation of capsid protein, nucleic acids (RNA or DNA), and other protein constituents are involved in the underlying mechanism. To determine the precise mechanism by which nanoparticles affect viral mobility, reproduction, encapsidation, and transmission, more research is however required. Nanoparticles can be used to precisely detect plant viruses using nanobiosensors or as biostimulants. The varieties of nanoparticles employed in plant virus control and their methods of virus suppression are highlighted in this review., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Viral nanoparticles (VNPs) are self-assembling, adaptable delivery systems for vaccines and other therapeutic agents used in a variety of biomedical applications. The potential of viruses to invade and infect various hosts and cells renders them suitable as potential nanocarriers, possessing distinct functional characteristics, immunogenic properties, and improved biocompatibility and biodegradability. VNPs are frequently produced through precise genetic or chemical engineering, which involves adding diverse sequences or functional payloads to the capsid protein (CP). Several spherical and helical plant viruses, bacteriophages, and animal viruses are currently being used as VNPs, or non-infectious virus-like particles (VLPs). In addition to their broad use in cancer therapy, vaccine technology, diagnostics, and molecular imaging, VNPs have made important strides in the realms of tissue engineering, biosensing, and antimicrobial prophylaxis. They are also being used in energy storage cells due to their binding and piezoelectric properties. The large-scale production of VNPs for research, preclinical testing, and clinical use is fraught with difficulties, such as those relating to cost-effectiveness, scalability, and purity. Consequently, many plants- and microorganism-based platforms are being developed, and newer viruses are being explored. The goal of the current review is to provide an overview of these advances., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.)

Plant viruses pose a significant threat to agriculture. Several are stable outside their hosts, can enter water bodies and remain infective for prolonged periods of time. Even though the quality of irrigation water is of increasing importance in the context of plant health, the presence of plant viruses in irrigation waters is understudied. In this study, we conducted a large-scale high-throughput sequencing (HTS)-based virome analysis of irrigation and surface water sources to obtain complete information about the abundance and diversity of plant viruses in such waters. We detected nucleic acids of plant viruses from 20 families, discovered several novel plant viruses from economically important taxa, like Tobamovirus and observed the influence of the water source on the present virome. By comparing viromes of water and surrounding plants, we observed presence of plant viruses in both compartments, especially in cases of large-scale outbreaks, such as that of tomato mosaic virus. Moreover, we demonstrated that water virome data can extensively inform us about the distribution and diversity of plant viruses for which only limited information is available from plants. Overall, the results of the study provided extensive insights into the virome of irrigation waters from the perspective of plant health. It also suggested that an HTS-based water virome surveillance system could be used to detect potential plant disease outbreaks and to survey the distribution and diversity of plant viruses in the ecosystem., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023. Published by Elsevier Ltd.)

Soybean pests are one of the major factors limiting yield improvement. With the expansion of area and changes in cropping patterns, a number of new pests have been identified in the main soybean production areas of China. The common brown leafhopper, Orosius orientalis, is a new pest associated with soybean stay-green virus that has been discovered on cultivated soybean crop in the Yellow-Huai-hai region of China in recent years. The polyphagous insect has a wide feeding range and infests a variety of important grain and cash crops. This paper presents the basic information, geographical distribution, hosts, damage characteristics, plant virus transmission, occurrence patterns, and prevention and control measures O. orientalis. This review also provides insights into integrated prevention and control of the genus Orosius as an insect vector. [ABSTRACT FROM AUTHOR]

Virus attacks have had devastating effects on mankind. The prominent viruses such as Ebola virus (2012), SARS-CoV or Severe acute respiratory syndrome, Middle East respiratory syndrome-related coronavirus called as the MERS (EMC/2012), Spanish flu (H1N1 virus-1918) and the most recent COVID-19(SARS-CoV-2) are the ones that have created a difficult situation for the survival of the human race. Currently, throughout the world, a global pandemic situation has put economy, livelihood and human existence in a very pathetic situation. Most of the above-mentioned viruses exhibit some similar characteristics and genetic pattern. Analysing such characteristics and genetic pattern can help the researchers to get a deeper insight into the viruses and helps in finding appropriate medicine or cure. To address these issues, this paper proposes an experimental analysis of the above-mentioned viruses data using correlation methods. The virus data considered for the experimental analysis include the distribution of various amino acids, protein sequences, 3D modelling of viruses, pairwise alignment of proteins that comprise the DNA genome of the viruses. Furthermore, this comparative analysis can be used by the researchers and organizations like WHO(World Health Organization), computational biologists, genetic engineers to frame a layout for studying the DNA sequence distribution, percentage of GC (guanine–cytosine) protein which determines the heat stability of viruses. We have used the Biopython to illustrate the gene study of prominent viruses and have derived results and insights in the form of 3D modelling. The experimental results are more promising with an accuracy rate of 96% in overall virus relationship calculation. [ABSTRACT FROM AUTHOR]

Plant viruses have been engineered to express proteins and induce gene silencing for decades. Recently, plant viruses have also been used to deliver components into plant cells for genome editing, a technique called virus-induced genome editing (VIGE). Although more than a dozen plant viruses have been engineered into VIGE vectors and VIGE has been successfully accomplished in some plant species, application of VIGE to crops that are difficult to tissue culture and/or have low regeneration efficiency is still tough. This paper discusses factors to consider for an ideal VIGE vector, including insertion capacity for foreign DNA, vertical transmission ability, expression level of the target gene, stability of foreign DNA insertion, and biosafety. We also proposed a step-by-step schedule for excavating the suitable viral vector for VIGE., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Cancer therapy requires sophisticated treatment strategies to obtain the highest success. Nanotechnology is enabling, revolutionizing, and multidisciplinary concepts to improve conventional cancer treatment modalities. Nanomaterials have a central role in this scenario, explaining why various nanomaterials are currently being developed for cancer therapy. Viral nanoparticles (VNPs) have shown promising performance in cancer therapy due to their unique features. VNPs possess morphological homogeneity, ease of functionalization, biocompatibility, biodegradability, water solubility, and high absorption efficiency that are beneficial for cancer therapy applications. In the current review paper, we highlight state-of-the-art properties and potentials of plant viruses, strategies for multifunctional plant VNPs formulations, potential applications and challenges in VNPs-based cancer therapy, and finally practical solutions to bring potential cancer therapy one step closer to real applications. This article is categorized under: Therapeutic Approaches and Drug Discovery > Nanomedicine for Oncologic Disease Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Protein and Virus-Based Structures., (© 2022 Wiley Periodicals LLC.)

Background: Sequence variation has been attributed to symptom variations but has not been investigated in Orange Spotting-Coconut cadang-cadang viroid (OS-CCCVd) infected palms. Likewise, the relationship between Coconut cadang-cadang viroid (CCCVd) variants, Orange Spotting (OS) severity and the accumulation of the viroid in the palms have not been elucidated. This paper describes the characterization of CCCVd variants by cloning and sequencing, followed by correlation with symptom expression., Methods and Results: Total nucleic acids were extracted from leaf samples harvested from frond 20 of seven Dura × Pisifera (D × P) African oil palm (Elaeis guineensis Jacq.) aged between 13 and 21 years old collected from local plantations. The nucleic acids were fractionated using 5% non-denaturing polyacrylamide gel electrophoresis (PAGE) before being subjected to detection by reverse transcribed polymerase chain reaction (RT-PCR). The PCR products were cloned into a plasmid vector and the sequence of the clones was analyzed. CCCVd variants were quantified using real-time qPCR assay with CCCVd specific primers. Sixteen randomly selected clones of (OP 246 ) had an arbitrary 100% identity with CCCVd OP246 (GeneBank Accession No: HQ608513). Meanwhile, four clones had >93% similarity with several minor sequence variations forming variants of OP 234 , OP 235 , OP 251 and OP 279 ., Conclusion: The OS symptoms observed in the field were characterized into three categories based on the size and morphology of the orange spots on the affected fronds. In addition, there was no direct correlation between disease severity and the accumulation of CCCVd variants in oil palm. This finding is the first report describing the sequence variation of the CCCVd RNA and symptom variation in OS oil palm field samples., (© 2023. The Author(s), under exclusive licence to Springer Nature B.V.)