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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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Zindović J, Čizmović M, Vučurović A, Margaria P, Škorić D. Increased Diversity of Citrus Tristeza Virus in Europe. PLANT DISEASE 2024; 108:1344-1352. [PMID: 37990525 DOI: 10.1094/pdis-09-23-1718-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
This study investigated the genetic diversity of Citrus tristeza virus (CTV) isolates from Montenegro and Croatia, European countries with the northernmost citrus-growing regions situated on the Eastern Adriatic coast. Fifteen complete or nearly complete CTV genomes were reconstructed by high-throughput sequencing of samples collected in distinct municipalities in Montenegro and Opuzen municipality in Croatia. Phylogenetic analyses assigned some of the sequences to VT and T30 strains, previously recorded in Europe, while remarkably other isolates were placed in S1 and RB groups, which have not been reported in Europe so far. In addition, a new phylogenetic lineage comprising only isolates from Montenegro was delineated and tentatively proposed as the MNE cluster. Recombination analysis revealed evidence of 11 recombination events in the sequences obtained in this study, between isolates of related strains, within isolates of the same strain, and between distant strains. These findings show that CTV diversity in Europe is higher than reported before and calls for the reevaluation of management strategies.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jelena Zindović
- Department for Plant Protection, Biotechnical Faculty, University of Montenegro, 81000 Podgorica, Montenegro
| | - Miroslav Čizmović
- Department for Plant Protection, Biotechnical Faculty, University of Montenegro, 81000 Podgorica, Montenegro
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Paolo Margaria
- Plant Virus Department, Leibniz-Institute DSMZ, 38124 Braunschweig, Germany
| | - Dijana Škorić
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
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Bester R, Maree HJ. Validation of High-Throughput Sequencing (HTS) for Routine Detection of Citrus Viruses and Viroids. Methods Mol Biol 2024; 2732:199-219. [PMID: 38060127 DOI: 10.1007/978-1-0716-3515-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
The management of plant diseases relies on the accurate identification of pathogens that requires a robust and validated tool in terms of specificity, sensitivity, repeatability, and reproducibility. High-throughput sequencing (HTS) has become the method of choice for virus detection when either a complete viral status of a plant is required in a single assay or if an unknown viral agent is expected. To ensure that the most accurate diagnosis is made from an HTS data analysis, a standardized protocol per pathosystem is required. This chapter presents a detailed protocol for the detection of viruses and viroids infecting citrus using HTS. The protocol describes all the steps from sample processing, nucleic acid extraction, and bioinformatic analyses validated to be an efficient method for detection in this pathosystem. The protocol also includes a section on citrus tristeza virus (CTV) genotype differentiation using HTS data.
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Affiliation(s)
- Rachelle Bester
- Citrus Research International, Stellenbosch, South Africa
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Hans J Maree
- Citrus Research International, Stellenbosch, South Africa.
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa.
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Bester R, Steyn C, Breytenbach JHJ, de Bruyn R, Cook G, Maree HJ. Reproducibility and Sensitivity of High-Throughput Sequencing (HTS)-Based Detection of Citrus Tristeza Virus and Three Citrus Viroids. PLANTS 2022; 11:plants11151939. [PMID: 35893644 PMCID: PMC9330035 DOI: 10.3390/plants11151939] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/01/2022] [Accepted: 07/19/2022] [Indexed: 11/16/2022]
Abstract
The credibility of a pathogen detection assay is measured using specific parameters including repeatability, specificity, sensitivity, and reproducibility. The use of high-throughput sequencing (HTS) as a routine detection assay for viruses and viroids in citrus was previously evaluated and, in this study, the reproducibility and sensitivity of the HTS assay were assessed. To evaluate the reproducibility of HTS, the same plants assayed in a previous study were sampled again, one year later, and assessed in triplicate using the same analyses to construct the virome profile. The sensitivity of the HTS assay was compared to routinely used RT-PCR assays in a time course experiment, to compensate for natural pathogen accumulation in plants over time. The HTS pipeline applied in this study produced reproducible and comparable results to standard RT-PCR assays for the detection of CTV and three viroid species in citrus. Even though the limit of detection of HTS can be influenced by pathogen concentration, sample processing method and sequencing depth, detection with HTS was found to be either equivalent or more sensitive than RT-PCR in this study.
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Affiliation(s)
- Rachelle Bester
- Citrus Research International, P.O. Box 2201, Matieland 7602, South Africa;
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
| | - Chanel Steyn
- Citrus Research International, P.O. Box 28, Nelspruit 1200, South Africa; (C.S.); (J.H.J.B.); (G.C.)
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | | | - Rochelle de Bruyn
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
- Citrus Research International, P.O. Box 28, Nelspruit 1200, South Africa; (C.S.); (J.H.J.B.); (G.C.)
| | - Glynnis Cook
- Citrus Research International, P.O. Box 28, Nelspruit 1200, South Africa; (C.S.); (J.H.J.B.); (G.C.)
| | - Hans J. Maree
- Citrus Research International, P.O. Box 2201, Matieland 7602, South Africa;
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
- Correspondence: ; Tel.: +27-21-808-9579
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Britt K, Gebben S, Levy A, Achor D, Sieburth P, Stevens K, Al Rwahnih M, Batuman O. Analysis of Citrus Tristeza Virus Incidences within Asian Citrus Psyllid ( Diaphorina citri) Populations in Florida via High-Throughput Sequencing. INSECTS 2022; 13:275. [PMID: 35323573 PMCID: PMC8954720 DOI: 10.3390/insects13030275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/04/2022] [Accepted: 03/07/2022] [Indexed: 11/17/2022]
Abstract
The destructive citrus disease, Huanglongbing (HLB) or citrus greening, continues to devastate Florida's citrus industry. A hemipteran insect, the Asian citrus psyllid (ACP), disperses Candidatus Liberibacter asiaticus, one of the putative bacterial pathogens of HLB. This study builds upon ongoing research utilizing high-throughput sequencing to analyze the virome of ACP populations collected from citrus groves throughout Florida. Following the widespread detection of sequences aligning to the genome of citrus tristeza virus (CTV) across consecutive years in the Florida ACP virome, we continued to detect a pervasive amount of CTV in Florida ACPs during subsequent years. Simultaneously, we also detected mixed infections of CTV strains in pooled ACPs from different Florida regions. Predating the HLB epidemic, CTV has been present in Florida for many years and our results confirm its widespread and diverse persistence in Florida citrus groves through a unique lens, the ACP. CTV presence in the ACP likely results from feeding on CTV-infected citrus trees in Florida citrus groves, which may help to understand an overlapping presence of CTV and HLB, both endemic citrus pathosystems in the state, and their role in future integrated pest management strategies.
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Affiliation(s)
- Kellee Britt
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL 34142, USA; (K.B.); (S.G.)
| | - Samantha Gebben
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL 34142, USA; (K.B.); (S.G.)
| | - Amit Levy
- Department of Plant Pathology, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA; (A.L.); (D.A.); (P.S.)
| | - Diann Achor
- Department of Plant Pathology, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA; (A.L.); (D.A.); (P.S.)
| | - Peggy Sieburth
- Department of Plant Pathology, Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33850, USA; (A.L.); (D.A.); (P.S.)
| | - Kristian Stevens
- Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA;
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA;
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA;
| | - Ozgur Batuman
- Department of Plant Pathology, Southwest Florida Research and Education Center, University of Florida, Immokalee, FL 34142, USA; (K.B.); (S.G.)
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Bester R, Cook G, Breytenbach JHJ, Steyn C, De Bruyn R, Maree HJ. Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids. Virol J 2021; 18:61. [PMID: 33752714 PMCID: PMC7986492 DOI: 10.1186/s12985-021-01523-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/02/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND High-throughput sequencing (HTS) has been applied successfully for virus and viroid discovery in many agricultural crops leading to the current drive to apply this technology in routine pathogen detection. The validation of HTS-based pathogen detection is therefore paramount. METHODS Plant infections were established by graft inoculating a suite of viruses and viroids from established sources for further study. Four plants (one healthy plant and three infected) were sampled in triplicate and total RNA was extracted using two different methods (CTAB extraction protocol and the Zymo Research Quick-RNA Plant Miniprep Kit) and sent for Illumina HTS. One replicate sample of each plant for each RNA extraction method was also sent for HTS on an Ion Torrent platform. The data were evaluated for biological and technical variation focussing on RNA extraction method, platform used and bioinformatic analysis. RESULTS The study evaluated the influence of different HTS protocols on the sensitivity, specificity and repeatability of HTS as a detection tool. Both extraction methods and sequencing platforms resulted in significant differences between the data sets. Using a de novo assembly approach, complemented with read mapping, the Illumina data allowed a greater proportion of the expected pathogen scaffolds to be inferred, and an accurate virome profile was constructed. The complete virome profile was also constructed using the Ion Torrent data but analyses showed that more sequencing depth is required to be comparative to the Illumina protocol and produce consistent results. The CTAB extraction protocol lowered the proportion of viroid sequences recovered with HTS, and the Zymo Research kit resulted in more variation in the read counts obtained per pathogen sequence. The expression profiles of reference genes were also investigated to assess the suitability of these genes as internal controls to allow for the comparison between samples across different protocols. CONCLUSIONS This study highlights the need to measure the level of variation that can arise from the different variables of an HTS protocol, from sample preparation to data analysis. HTS is more comprehensive than any assay previously used, but with the necessary validations and standard operating procedures, the implementation of HTS as part of routine pathogen screening practices is possible.
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Affiliation(s)
- Rachelle Bester
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Glynnis Cook
- Citrus Research International, P.O. Box 28, Nelspruit, 1200, South Africa
| | | | - Chanel Steyn
- Citrus Research International, P.O. Box 28, Nelspruit, 1200, South Africa
- Department of Plant Pathology, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
| | - Rochelle De Bruyn
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa
- Citrus Research International, P.O. Box 28, Nelspruit, 1200, South Africa
| | - Hans J Maree
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland, 7602, South Africa.
- Citrus Research International, P.O. Box 2201, Matieland, 7602, South Africa.
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