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Shang P, Xu L, Cheng T. Serological and Molecular Detection of Citrus Tristeza Virus: A Review. Microorganisms 2024; 12:1539. [PMID: 39203383 PMCID: PMC11356770 DOI: 10.3390/microorganisms12081539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 07/13/2024] [Accepted: 07/20/2024] [Indexed: 09/03/2024] Open
Abstract
Citrus tristeza virus (CTV) is a globally pervasive and economically significant virus that negatively impacts citrus trees, leading to substantial reductions in fruit yield. CTV occurs within the phloem of infected plants, causing a range of disease phenotypes, such as stem pitting (SP), quick decline (QD), and other detrimental diseases. Research on CTV is challenging due to the large size of its RNA genome and the diversity of CTV populations. Comparative genomic analyses have uncovered genetic diversity in multiple regions of CTV isolates' genomes, facilitating the classification of the virus into distinct genotypes. Despite these challenges, notable advancements have been made in identifying and controlling CTV strains through serological and molecular methods. The following review concentrates on the techniques of nucleic acid identification and serological analysis for various CTV isolates, assisting in the comparison and evaluation of various detection methods, which are crucial for the effective management of CTV diseases, and so contributes to the innovation and development of CTV detection methods.
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Affiliation(s)
- Pengxiang Shang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, China;
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Longfa Xu
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, China;
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
| | - Tong Cheng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Life Sciences, School of Public Health, Xiamen University, Xiamen 361102, China;
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen 361102, China
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Lei Y, Yang F, Yu Z, Xu T, Zhang W, Tian F, Chen X. One-Step Reverse-Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Assay for the Detection of Canna Yellow Streak Virus. PLANT DISEASE 2023:PDIS04220780RE. [PMID: 36480737 DOI: 10.1094/pdis-04-22-0780-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Canna yellow streak virus (CaYSV) is a potyvirus that causes severe damage to the ornamental plant canna in the United Kingdom and Brazil. Here, we identified CaYSV in China by isolating total RNA from an infected plant, amplifying the virus genome segments, and cloning and sequencing the amplicons. After assembly, the full-length genome of the virus was obtained and uploaded to the NCBI database. Phylogenetic analysis results showed that the Guizhou isolate (OL546222) was most closely related to the KS isolate (MG545919.1). Virus detection is essential for virus disease control but the subclinical infection of CaYSV on canna in its early development increases the difficulty of CaYSV diagnosis. The goal of this study was to develop an efficient method for detection of CaYSV. We designed the primers, optimized the reaction conditions, and finally established a one-step reverse-transcription loop-mediated isothermal amplification (RT-LAMP) method. The product of RT-LAMP can be analyzed by both agarose gel electrophoresis and visible color change. The established one-step RT-LAMP assay showed high specificity and sensitivity in detecting CaYSV. This RT-LAMP method was also applied in analysis of 61 field samples collected from Guizhou and Jiangsu Provinces. The results showed that the infection rates of CaYSV on canna samples from these two provinces were very high (63 and 96% respectively).
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Affiliation(s)
- Yunting Lei
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Fuhan Yang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Zhaoyao Yu
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Tengzhi Xu
- College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Wene Zhang
- College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Fenghua Tian
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
| | - Xiangru Chen
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, P.R. China
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Wallis CM, Gorman Z, Rattner R, Hajeri S, Yokomi R. Amino acid, sugar, phenolic, and terpenoid profiles are capable of distinguishing Citrus tristeza virus infection status in citrus cultivars: Grapefruit, lemon, mandarin, and sweet orange. PLoS One 2022; 17:e0268255. [PMID: 35536831 PMCID: PMC9089872 DOI: 10.1371/journal.pone.0268255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/26/2022] [Indexed: 11/18/2022] Open
Abstract
Citrus tristeza virus (CTV) is the most severe viral disease for citrus production. Many strains of CTV have been characterized and their symptomology widely varies, ranging from asymptomatic or mild infections to severe symptomology that results in substantial yield loss or host death. The capacity of the different CTV strains to affect the biochemistry of different citrus species has remained largely unstudied, despite that associated metabolomic shifts would be relevant toward symptom development. Thus, amino acid, sugar, phenolic, and terpenoid levels were assessed in leaves of healthy and CTV-infected grapefruit, lemon, mandarin, and two different sweet orange cultivars. Both mild [VT-negative (VT-)] and severe [VT-positive (VT+)] CTV genotype strains were utilized. When looking at overall totals of these metabolite classes, only amino acid levels were significantly increased by infection of citrus with severe CTV strains, relative to mild CTV strains or healthy plants. No significant trends of CTV infection on summed amounts of all sugar, phenolic, or terpenoid compounds were observed. However, individual compound levels were affected by CTV infections. Subsequent canonical discriminant analysis (CDA) that utilized profiles of individual amino acids, terpenoids, or phenolics successfully distinguished leaf samples to specific citrus varieties and identified infection status with good accuracy. Collectively, this study reveals biochemical patterns associated with severity of CTV infections that can potentially be utilized to help identify in-field CTV infections of economic relevance.
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Affiliation(s)
- Christopher M. Wallis
- Crop Diseases, Pests and Genetics Research Unit, United States Department of Agriculture—Agricultural Research Service San Joaquin Valley Agricultural Sciences Center, Parlier, California, United States of America
| | - Zachary Gorman
- Crop Diseases, Pests and Genetics Research Unit, United States Department of Agriculture—Agricultural Research Service San Joaquin Valley Agricultural Sciences Center, Parlier, California, United States of America
| | - Rachel Rattner
- Crop Diseases, Pests and Genetics Research Unit, United States Department of Agriculture—Agricultural Research Service San Joaquin Valley Agricultural Sciences Center, Parlier, California, United States of America
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, California, United States of America
| | - Raymond Yokomi
- Crop Diseases, Pests and Genetics Research Unit, United States Department of Agriculture—Agricultural Research Service San Joaquin Valley Agricultural Sciences Center, Parlier, California, United States of America
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Tarazi R, Vaslin MFS. The Viral Threat in Cotton: How New and Emerging Technologies Accelerate Virus Identification and Virus Resistance Breeding. FRONTIERS IN PLANT SCIENCE 2022; 13:851939. [PMID: 35449884 PMCID: PMC9016188 DOI: 10.3389/fpls.2022.851939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/07/2022] [Indexed: 05/12/2023]
Abstract
Cotton (Gossypium spp. L., Malvaceae) is the world's largest source of natural fibers. Virus outbreaks are fast and economically devasting regarding cotton. Identifying new viruses is challenging as virus symptoms usually mimic nutrient deficiency, insect damage, and auxin herbicide injury. Traditional viral identification methods are costly and time-consuming. Developing new resistant cotton lines to face viral threats has been slow until the recent use of molecular virology, genomics, new breeding techniques (NBT), remote sensing, and artificial intelligence (AI). This perspective article demonstrates rapid, sensitive, and cheap technologies to identify viral diseases and propose their use for virus resistance breeding.
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Affiliation(s)
- Roberto Tarazi
- Plant Molecular Virology Laboratory, Department of Virology, Microbiology Institute, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Programa de Pós-graduação em Biotecnologia e Bioprocessos da UFRJ, Rio de Janeiro, Brazil
| | - Maite F. S. Vaslin
- Plant Molecular Virology Laboratory, Department of Virology, Microbiology Institute, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Programa de Pós-graduação em Biotecnologia e Bioprocessos da UFRJ, Rio de Janeiro, Brazil
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Hajeri S, Yokomi R. Immunocapture-Reverse Transcriptase Loop-Mediated Isothermal Amplification Assay for Detection of Plant RNA Viruses. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2400:245-252. [PMID: 34905207 DOI: 10.1007/978-1-0716-1835-6_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Loop-mediated isothermal amplification (LAMP) is a sensitive method that can rapidly amplify a specific nucleic acid target with high specificity. The LAMP reaction process has no denaturation step, instead DNA amplification occurs by strand displacement activity of the Bacillus stearothermophilus (Bst) DNA polymerase under isothermal conditions. It utilizes three sets of forward and reverse oligonucleotide primers specific to six distinct sequences on the target gene. These primers are used to generate amplification products that contain single-stranded loops, thereby allowing primers to bind to these sequences without the need for repeated cycles of thermal denaturation. For diagnosis of pathogens with RNA genome, LAMP has been merged with reverse transcription (RT) step to create RT-LAMP. To further reduce the cost of diagnosis and increase the throughput, immunocapture (IC) step was added to develop IC-RT-LAMP assay. Hence, this chapter focuses on utilizing IC-RT-LAMP assay to specifically identify severe strain of a plant virus from field samples.
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Affiliation(s)
- Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, Tulare, CA, USA.
| | - Raymond Yokomi
- USDA-ARS, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, USA
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Khalilzadeh M, Weber KC, Dutt M, El-Mohtar CA, Levy A. Comparative transcriptome analysis of Citrus macrophylla tree infected with Citrus tristeza virus stem pitting mutants provides new insight into the role of phloem regeneration in stem pitting disease. FRONTIERS IN PLANT SCIENCE 2022; 13:987831. [PMID: 36267951 PMCID: PMC9577373 DOI: 10.3389/fpls.2022.987831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 08/24/2022] [Indexed: 05/21/2023]
Abstract
Stem pitting is a complex and economically important virus-associated disease of perennial woody plants. Molecular mechanisms and pathways occurring during virus-plant interaction that result in this phenomenon are still obscure. Previous studies indicated that different Citrus tristeza virus (CTV) mutants induce defined stem pitting phenotypes ranging from mild (CTVΔp13) to severe (CTVΔp33) in Citrus macrophylla trees. In this study, we conducted comparative transcriptome analyses of C. macrophylla trees infected with CTV mutants (CTVΔp13 and CTVΔp33) and a full-length virus in comparison to healthy plants as control. The mild CTV stem pitting mutant had very few differentially expressed genes (DEGs) related to plant defense mechanism and plant growth and development. In contrast, substantial gene expression changes were observed in plants infected with the severe mutant and the full-length virus, indicating that both the p13 and p33 proteins of CTV acted as a regulator of symptom production by activating and modulating plant responses, respectively. The analysis of transcriptome data for CTVΔp33 and the full-length virus suggested that xylem specification has been blocked by detecting several genes encoding xylem, cell wall and lignin degradation, and cell wall loosening enzymes. Furthermore, stem pitting was accompanied by downregulation of transcription factors involved in regulation of xylem differentiation and downregulation of some genes involved in lignin biosynthesis, showing that the xylem differentiation and specification program has been shut off. Upregulation of genes encoding transcription factors associated with phloem and cambium development indicated the activation of this program in stem pitting disease. Furthermore, we detected the induction of several DEGs encoding proteins associated with cell cycle re-entry such as chromatin remodeling factors and cyclin, and histone modification. This kind of expression pattern of genes related to xylem differentiation and specification, phloem and cambium development, and cell cycle re-entry is demonstrated during secondary vascular tissue (SVT) regeneration. The microscopy analysis confirmed that the regeneration of new phloem is associated with stem pitting phenotypes. The findings of this study, thus, provide evidence for the association between stem pitting phenotypes and SVT regeneration, suggesting that the expression of these genes might play important roles in development of stem pitting symptoms. Overall, our findings suggest that phloem regeneration contributes to development of stem pitting symptoms.
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Affiliation(s)
- Maryam Khalilzadeh
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Kyle Clark Weber
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Manjul Dutt
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Choaa Amine El-Mohtar
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Amit Levy
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
- *Correspondence: Amit Levy
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Raeisi H, Safarnejad MR, Sadeghkhani F. A new single-chain variable fragment (scFv) antibody provides sensitive and specific detection of citrus tristeza virus. J Virol Methods 2021; 300:114412. [PMID: 34896452 DOI: 10.1016/j.jviromet.2021.114412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 09/17/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022]
Abstract
Citrus tristeza virus (CTV) is the most economically important virus disease of citrus worldwide. To develop a specific serological assay for CTV, a Tomlinson phage display antibody library of single chain variable fragments (scFv) was screened with a recombinant CTV coat protein (CTV-CP) heterologously expressed in Escherichia coli. The phage clones were checked by ELISA to identify clones with high specificity for CTV-CP. Eight clones were strongly reactive with CTV-CP. Nucleotide sequencing of these clones revealed that all of them contained the same sequence. Thus, the phage-displayed scFv antibody was termed scFvF10. Evaluation of scFvF10 binding to CTV-CP by plate-trapped antigen ELISA (PTA-ELISA) and immunoblotting, showed that it was specific and allowed sensitive detection of CTV-CP. Homology-based molecular modeling and docking analysis confirmed that the interaction between CTV-CP and scFvF10, with a binding energy of -738 kj mol-1, occurred mainly by 12 intermolecular hydrogen bonds. Moreover, triple-antibody sandwich (TAS)-ELISA using scFvF10 as second antibody showed high sensitivity in the detection of CTV infected samples. The CTV detection limit of scFvF10 by PTA-ELISA and TAS-ELISA were 0.05 and 0.01 μg CP/mL, respectively. Our results with different diagnostic assays demonstrated that scFvF10 has the potential to be used as an efficient tool for CTV-infected plant diagnosis.
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Affiliation(s)
- Hamideh Raeisi
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Safarnejad
- Department of Plant Viruses, Iranian Research Institute of Plant Protection, Agricultural Research Education and Extension Organization of Iran, Tehran, Iran
| | - Farideh Sadeghkhani
- Department of Life Sciences Engineering, Faculty of New Sciences and Technologies, Tehran University, Tehran, Iran
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Uke A, Khin S, Kobayashi K, Satou T, Kim OK, Hoat TX, Natsuaki KT, Ugaki M. Detection of Sri Lankan cassava mosaic virus by loop-mediated isothermal amplification using dried reagents. J Virol Methods 2021; 299:114336. [PMID: 34656701 DOI: 10.1016/j.jviromet.2021.114336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 10/02/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022]
Abstract
Recently, the widespread occurrence of Sri Lankan cassava mosaic virus (SLCMV), genus Begomovirus, family Geminiviridae, which causes a mosaic disease in cassava (Manihot esculenta Crantz) in South-East Asia have, become a serious economic issue. Since cassava is propagated through vegetative cuttings, a rapid virus diagnostic method is crucial for generating virus-free planting materials. In this study, a loop-mediated isothermal amplification (LAMP) assay using six primers was developed and validated for the rapid detection of SLCMV in cassava leaves. This SLCMV assay had a detection sensitivity that was up to 10,000 times higher than that of the conventional polymerase chain reaction assay and can detect the virus from symptomless stem cutting, which is a potential long-distance spreader of the virus. Furthermore, a practical LAMP protocol using stable dried reagents from a commercial kit was established so that the assay could be performed in the field by incubating the reactions in water at 60-65 °C instead of using a thermal cycler. The primer sequences and the LAMP protocol described here should be useful for the rapid and sensitive on-site detection of SLCMV.
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Affiliation(s)
- Ayaka Uke
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8562, Japan.
| | - Sophary Khin
- National University of Battambang (UBB), National Road 5, Sangkat Preaek Preah Sdach, Battambang City, Battambang Province, 02352, Cambodia
| | - Kohei Kobayashi
- Department of Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa, 243-0034, Japan
| | - Takuma Satou
- Department of Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa, 243-0034, Japan
| | - Ok-Kyung Kim
- Department of Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa, 243-0034, Japan
| | - Trinh Xuan Hoat
- Plant Protection Research Institute (PPRI), Duc Thang Ward, Bac Tu Liem District, Ha Noi, 100000, Viet Nam
| | - Keiko T Natsuaki
- Department of International Agricultural Development, Graduate School of Agriculture, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo 156-8502, Japan
| | - Masashi Ugaki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa City, Chiba, 277-8562, Japan
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Development of a real-time RT-PCR method for the detection of Citrus tristeza virus (CTV) and its implication in studying virus distribution in planta. 3 Biotech 2021; 11:431. [PMID: 34603909 DOI: 10.1007/s13205-021-02976-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/23/2021] [Indexed: 12/26/2022] Open
Abstract
Tristeza is an economically important disease of the citrus caused by Citrus tristeza virus (CTV) of genus Closterovirus and family Closteroviridae. The disease has caused tremendous losses to citrus industry worldwide by killing millions of trees, reducing the productivity and total production. Enormous efforts have been made in many countries to prevent the viral spread and the losses caused by the disease. To understand the reason behind this scenario, studies on virus distribution and tropism in the citrus plants are needed. Different diagnostic methods are available for early CTV detection but none of them is employed for in planta virus distribution study. In this study, a TaqMan RT-PCR-based method to detect and quantify CTV in different tissues of infected Mosambi plants (Citrus sinensis) has been standardized. The assay was very sensitive with the pathogen detection limit of > 0.0595 fg of in vitro-transcribed CTV-RNA. The assay was implemented for virus distribution study and absolute CTV titer quantification in samples taken from Tristeza-infected trees. The highest virus load was observed in the midribs of the symptomatic leaf (4.1 × 107-1.4 × 108/100 mg) and the lowest in partial dead twigs (1 × 103-1.7 × 104/100 mg), and shoot tip (2.3 × 103-4.5 × 103/100 mg). Interestingly, during the peak summer months, the highest CTV load was observed in the feeder roots (3 × 107-1.1 × 108/100 mg) than in the midribs of symptomatic leaf. The viral titer was highest in symptomatic leaf midrib followed by asymptomatic leaf midrib, feeder roots, twig bark, symptomatic leaf lamella, and asymptomatic leaf lamella. Overall, high CTV titer was primarily observed in the phloem containing tissues and low CTV titer in the other tissues. The information would help in selecting tissues with higher virus titer in disease surveillance that have implication in Tristeza management in citrus.
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Current Developments and Challenges in Plant Viral Diagnostics: A Systematic Review. Viruses 2021; 13:v13030412. [PMID: 33807625 PMCID: PMC7999175 DOI: 10.3390/v13030412] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/24/2022] Open
Abstract
Plant viral diseases are the foremost threat to sustainable agriculture, leading to several billion dollars in losses every year. Many viruses infecting several crops have been described in the literature; however, new infectious viruses are emerging frequently through outbreaks. For the effective treatment and prevention of viral diseases, there is great demand for new techniques that can provide accurate identification on the causative agents. With the advancements in biochemical and molecular biology techniques, several diagnostic methods with improved sensitivity and specificity for the detection of prevalent and/or unknown plant viruses are being continuously developed. Currently, serological and nucleic acid methods are the most widely used for plant viral diagnosis. Nucleic acid-based techniques that amplify target DNA/RNA have been evolved with many variants. However, there is growing interest in developing techniques that can be based in real-time and thus facilitate in-field diagnosis. Next-generation sequencing (NGS)-based innovative methods have shown great potential to detect multiple viruses simultaneously; however, such techniques are in the preliminary stages in plant viral disease diagnostics. This review discusses the recent progress in the use of NGS-based techniques for the detection, diagnosis, and identification of plant viral diseases. New portable devices and technologies that could provide real-time analyses in a relatively short period of time are prime important for in-field diagnostics. Current development and application of such tools and techniques along with their potential limitations in plant virology are likewise discussed in detail.
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Srivastava S, Upadhyay DJ, Srivastava A. Next-Generation Molecular Diagnostics Development by CRISPR/Cas Tool: Rapid Detection and Surveillance of Viral Disease Outbreaks. Front Mol Biosci 2020; 7:582499. [PMID: 33425987 PMCID: PMC7785713 DOI: 10.3389/fmolb.2020.582499] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 11/04/2020] [Indexed: 12/26/2022] Open
Abstract
Virus disease spreads effortlessly mechanically or through minute insect vectors that are extremely challenging to avoid. Emergence and reemergence of new viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), H1N1 influenza virus, avian influenza virus, dengue virus, Citrus tristeza virus, and Tomato yellow leaf curl virus have paralyzed the economy of many countries. The cure for major viral diseases is not feasible; however, early detection and surveillance of the disease can obstruct their spread. Therefore, advances in the field of virus diagnosis and the development of new point-of-care testing kits become necessary globally. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is an emerging technology for gene editing and diagnostics development. Several rapid nucleic acid diagnostic kits have been developed and validated using Cas9, Cas12, and Cas13 proteins. This review summarizes the CRISPR/Cas-based next-generation molecular diagnostic techniques and portability of devices for field-based utilization.
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Affiliation(s)
- Sonal Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, India
| | | | - Ashish Srivastava
- Amity Institute of Virology and Immunology, Amity University Uttar Pradesh, Noida, India
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Leichtfried T, Reisenzein H, Steinkellner S, Gottsberger RA. Transmission studies of the newly described apple chlorotic fruit spot viroid using a combined RT-qPCR and droplet digital PCR approach. Arch Virol 2020; 165:2665-2671. [PMID: 32638117 PMCID: PMC7547948 DOI: 10.1007/s00705-020-04704-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/15/2020] [Indexed: 01/17/2023]
Abstract
The transmission of the apscaviroid tentatively named apple chlorotic fruit spot viroid (ACFSVd) was investigated using a one-step reverse-transcription (RT) droplet digital PCR assay for absolute quantification of the viroid, followed by quantification of relative standard curves by RT-qPCR. Our results indicate that ACFSVd is effectively transmitted by grafting, budding and seeds. No transmission has yet been observed to the viroid-inoculated pome fruit species Pyrus sp. and Cydonia sp. ACFSVd was detected in viruliferous aphids (Myzus persicae, Dysaphis plantaginea) and in codling moths (Cydia pomonella). The viroid was also detected systemically in the infected hemiparasitic plant Viscum album subsp. album (mistletoe).
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Affiliation(s)
- Thomas Leichtfried
- Institute for Sustainable Plant Protection, Austrian Agency for Health and Food Safety, 1220, Vienna, Austria
| | - Helga Reisenzein
- Institute for Sustainable Plant Protection, Austrian Agency for Health and Food Safety, 1220, Vienna, Austria
| | - Siegrid Steinkellner
- Institute of Plant Protection, University of Natural Resources and Life Sciences, 3430, Tulln an der Donau, Austria.
| | - Richard A Gottsberger
- Institute for Sustainable Plant Protection, Austrian Agency for Health and Food Safety, 1220, Vienna, Austria
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Kokane SB, Kokane AD, Misra P, Warghane AJ, Kumar P, Gubyad MG, Sharma AK, Biswas KK, Ghosh DK. In-silico characterization and RNA-binding protein based polyclonal antibodies production for detection of citrus tristeza virus. Mol Cell Probes 2020; 54:101654. [PMID: 32866661 DOI: 10.1016/j.mcp.2020.101654] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/22/2020] [Accepted: 08/28/2020] [Indexed: 01/31/2023]
Abstract
Citrus tristeza virus (CTV) is the etiologic agent of the destructive Tristeza disease, a massive impediment for the healthy citrus industry worldwide. Routine indexing of CTV is an essential component for disease surveys and citrus budwood certification for production of disease-free planting material. Therefore, the present study was carried out to develop an efficient serological assay for CTV detection based on the RNA binding protein (CTV-p23), which is translated from a subgenomic RNA (sgRNA) that accumulates at higher levels in CTV-infected plants. CTV-p23 gene was amplified, cloned and polyclonal antibodies were raised against recombinant CTV-p23 protein. The efficacy of the produced polyclonal antibodies was tested by Western blots and ELISA to develop a quick, sensitive and economically affordable CTV detection tool and was used for indexing of large number of plant samples. The evaluation results indicated that the developed CTV-p23 antibodies had an excellent diagnostic agreement with RT-PCR and would be effective for the detection of CTV in field samples. Furthermore, CTV-p23 gene specific primers designed in the present study were found 1000 times more sensitive than the reported coat protein (CTV-p25) gene specific primers for routine CTV diagnosis. In silico characterizations of CTV-p23 protein revealed the presence of key conserved amino acid residues that involved in the regulation of protein stability, suppressor activity and protein expression levels. This would provide precious ground information towards understanding the viral pathogenecity and protein level accumulation for early diagnosis of virus.
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Affiliation(s)
- Sunil B Kokane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, Maharashtra, India; Department of Molecular & Cellular Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh, India
| | - Amol D Kokane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, Maharashtra, India
| | - Pragati Misra
- Department of Molecular & Cellular Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, Uttar Pradesh, India
| | - Ashish J Warghane
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, Maharashtra, India; Faculty of Life Sciences, Mandsaur University, Mandsaur, Madhya Pradesh, India
| | - Pranav Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Mrugendra G Gubyad
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, Maharashtra, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Kajal Kumar Biswas
- Plant Pathology Division, ICAR- Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Dilip Kumar Ghosh
- Plant Virology Laboratory, ICAR-Central Citrus Research Institute, Nagpur, Maharashtra, India.
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14
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Yokomi RK, Sisterson MS, Hajeri S. Spread of Citrus Tristeza Virus in Citrus Orchards in Central California. PLANT DISEASE 2020; 104:1925-1931. [PMID: 32396051 DOI: 10.1094/pdis-08-19-1791-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In California, citrus tristeza virus (CTV) is regulated by a State Interior Quarantine. In CTV abatement districts in central California, trees with CTV that react to MCA13 (MCA13-positive [MCA13+]), a strain-discriminating monoclonal antibody, are rogued to prevent virus spread. The Tulare County Pest Control District, however, does not participate in this abatement program except for a 1.6-km2 zone around the Lindcove Research and Extension Center, Exeter, CA. To quantify CTV spread under these two disparate management programs, CTV surveys were conducted in abatement plots with mandatory aphid control and nonabatement plots. Abatement plot surveys used hierarchical sampling of 25% of trees with samples pooled from four adjacent trees. Detection of MCA13+ CTV in a sample prompted resampling and testing of individual trees. From 2008 to 2018, incidence of CTV increased by an average of 3.9%, with only two MCA13+ samples detected. In contrast, in nonabatement plots, incidence of CTV increased by an average of 4.6% between 2015 and 2018. Increase in MCA13-negative (MCA-) isolates was 11 times greater than that of MCA13+ isolates, with the number of MCA13+ trees increasing by 19 trees between 2015 and 2018. MCA13- isolates were more randomly distributed, suggesting primary spread, whereas MCA13+ CTV isolates were more aggregated, suggesting some secondary spread. These results suggest that spread of MCA13+ isolates was limited by a combination of tree removal and aphid vector suppression. MCA13+ samples were VT isolates with some mixtures with T30 isolates. Despite the presence of VT isolates, all CTV-infected trees were asymptomatic.
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Affiliation(s)
- Raymond K Yokomi
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757, U.S.A
| | - Mark S Sisterson
- United States Department of Agriculture-Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA 93648-9757, U.S.A
| | - Subhas Hajeri
- Citrus Pest Detection Program, Central California Tristeza Eradication Agency, 22847 Road 140, Tulare, CA 93274-9367, U.S.A
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15
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Panno S, Matić S, Tiberini A, Caruso AG, Bella P, Torta L, Stassi R, Davino S. Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E461. [PMID: 32268586 PMCID: PMC7238132 DOI: 10.3390/plants9040461] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.
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Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Slavica Matić
- Department of Agricultural, Forestry and Food Sciences, University of Turin, 10095 Turin, Italy;
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification, 00156 Rome, Italy;
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Livio Torta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Raffaele Stassi
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Turin, Italy
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