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Kumar R, Gupta N, Sharma SK, Kishan G, Srivastava N, Khan ZA, Kumar A, Baranwal VK. Mixed infection of two mandariviruses identified by high-throughput sequencing in Kinnow mandarin and development of their specific detection using duplex RT-PCR. 3 Biotech 2024; 14:170. [PMID: 38828101 PMCID: PMC11143089 DOI: 10.1007/s13205-024-04011-9] [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: 01/17/2024] [Accepted: 05/18/2024] [Indexed: 06/05/2024] Open
Abstract
In the current study, high-throughput sequencing (HTS) was used to identify viruses associated with the Kinnow mandarin (Citrus reticulata) plants exhibiting yellow vein clearing, mottling, and chlorosis symptoms at experimental farm of ICAR-Indian Agricultural Research Institute, New Delhi, India. During November 2022, leaf samples of symptomatic and asymptomatic Kinnow mandarin trees were collected, subjected to HTS and one of the representative symptomatic samples was subjected to leaf-dip electron microscopy (EM). In the EM results, flexuous virus particles typical of mandarivirus were observed. Ribosomal RNA was depleted from total RNA of pooled samples and RNA sequencing was done using NovaSeq 6000. Host unaligned reads were de novo assembled into contigs, which were annotated through BLASTn using database of plant viruses/viroids reference genomes (NCBI). Results of assembled contigs revealed near-complete genomes of two mandariviruses, i.e., citrus yellow vein clearing virus (CYVCV) and citrus yellow mottle-associated virus (CiYMaV). The values of fragments per kilo base transcript length per million fragments mapped estimation indicated the dominance of CYVCV in HTS data and it was also confirmed through krona plot distribution of viruses in the pooled samples. A rapid and reliable duplex RT-PCR assay was also developed and standardized for the simultaneous detection of both CYVCV and CiYMaV in a pooled Kinnow mandarin sample. The developed duplex RT-PCR was then validated for the presence of these viruses in individual Kinnow mandarin samples. The specificity and sensitivity results confirmed that primers were highly specific to their targets and able to detect viruses up to 10-2 dilutions of RNA in standard and duplex RT-PCR. Therefore, the developed rapid duplex RT-PCR can be used for virus indexing and production of virus-free Kinnow mandarin plants for certification programs. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04011-9.
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Affiliation(s)
- Rakesh Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Nitika Gupta
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Susheel Kumar Sharma
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Gopi Kishan
- ICAR-Indian Institute of Seed Science, Uttar Pradesh, Kushmaur, Mau, 275101 India
| | - Nishant Srivastava
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Zainul A. Khan
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Ashwini Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
| | - Virendra Kumar Baranwal
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012 India
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Abrahamian P, Tian T, Posis K, Guo Y, Yu D, Blomquist CL, Wei G, Adducci B, Vidalakis G, Bodaghi S, Osman F, Roy A, Nunziata SO, Nakhla M, Mavrodieva V, Rivera Y. Genetic Analysis of the Emerging Citrus Yellow Vein Clearing Virus Reveals a Divergent Virus Population in American Isolates. PLANT DISEASE 2024; 108:1544-1554. [PMID: 38127632 DOI: 10.1094/pdis-09-23-1963-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: 12/23/2023]
Abstract
Citrus yellow vein clearing virus is a previously reported citrus virus from Asia with widespread distribution in China. In 2022, the California Department of Food and Agriculture conducted a multipest citrus survey targeting multiple citrus pathogens including citrus yellow vein clearing virus (CYVCV). In March 2022, a lemon tree with symptoms of vein clearing, chlorosis, and mottling in a private garden in the city of Tulare, California, tested positive for CYVCV, which triggered an intensive survey in the surrounding areas. A total of 3,019 plant samples, including citrus and noncitrus species, were collected and tested for CYVCV using conventional reverse transcription polymerase chain reaction, reverse transcription quantitative polymerase chain reaction, and Sanger sequencing. Five hundred eighty-six citrus trees tested positive for CYVCV, including eight citrus species not previously recorded infected under field conditions. Comparative genomic studies were conducted using 17 complete viral genomes. Sequence analysis revealed two major phylogenetic groups. Known Asian isolates and five California isolates from this study made up the first group, whereas all other CYVCV isolates from California formed a second group, distinct from all worldwide isolates. Overall, the CYVCV population shows rapid expansion and high differentiation indicating a population bottleneck typical of a recent introduction into a new geographic area.
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Affiliation(s)
- Peter Abrahamian
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Tongyan Tian
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Katie Posis
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Ying Guo
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Doris Yu
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Cheryl L Blomquist
- Plant Pest Diagnostics Center, California Department of Food and Agriculture, Sacramento, CA 95832
| | - Gang Wei
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Benjamin Adducci
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Georgios Vidalakis
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521
| | - Sohrab Bodaghi
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521
| | - Fatima Osman
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - Avijit Roy
- Molecular Plant Pathology Laboratory, Beltsville Agriculture Research Center, USDA-ARS, Beltsville, MD 20705
| | - Schyler O Nunziata
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Mark Nakhla
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Vessela Mavrodieva
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
| | - Yazmín Rivera
- Plant Pathogen Confirmatory Diagnostics Laboratory, PPQ S&T, USDA-APHIS, Laurel, MD 20708
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Fontdevila Pareta N, Khalili M, Maachi A, Rivarez MPS, Rollin J, Salavert F, Temple C, Aranda MA, Boonham N, Botermans M, Candresse T, Fox A, Hernando Y, Kutnjak D, Marais A, Petter F, Ravnikar M, Selmi I, Tahzima R, Trontin C, Wetzel T, Massart S. Managing the deluge of newly discovered plant viruses and viroids: an optimized scientific and regulatory framework for their characterization and risk analysis. Front Microbiol 2023; 14:1181562. [PMID: 37323908 PMCID: PMC10265641 DOI: 10.3389/fmicb.2023.1181562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/25/2023] [Indexed: 06/17/2023] Open
Abstract
The advances in high-throughput sequencing (HTS) technologies and bioinformatic tools have provided new opportunities for virus and viroid discovery and diagnostics. Hence, new sequences of viral origin are being discovered and published at a previously unseen rate. Therefore, a collective effort was undertaken to write and propose a framework for prioritizing the biological characterization steps needed after discovering a new plant virus to evaluate its impact at different levels. Even though the proposed approach was widely used, a revision of these guidelines was prepared to consider virus discovery and characterization trends and integrate novel approaches and tools recently published or under development. This updated framework is more adapted to the current rate of virus discovery and provides an improved prioritization for filling knowledge and data gaps. It consists of four distinct steps adapted to include a multi-stakeholder feedback loop. Key improvements include better prioritization and organization of the various steps, earlier data sharing among researchers and involved stakeholders, public database screening, and exploitation of genomic information to predict biological properties.
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Affiliation(s)
| | - Maryam Khalili
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
- EGFV, Univ. Bordeaux, INRAE, ISVV, Villenave d’Ornon, France
| | | | - Mark Paul S. Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- College of Agriculture and Agri-Industries, Caraga State University, Butuan, Philippines
| | - Johan Rollin
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- DNAVision (Belgium), Charleroi, Belgium
| | - Ferran Salavert
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Coline Temple
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Miguel A. Aranda
- Department of Stress Biology and Plant Pathology, Center for Edaphology and Applied Biology of Segura, Spanish National Research Council (CSIC), Murcia, Spain
| | - Neil Boonham
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive Plants and Plant Health (NIVIP), Wageningen, Netherlands
| | | | - Adrian Fox
- School of Natural and Environmental Sciences, Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, United Kingdom
- Fera Science Ltd, York Biotech Campus, York, United Kingdom
| | | | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | | | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ilhem Selmi
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Rachid Tahzima
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Plant Sciences Unit, Institute for Agricultural, Fisheries and Food Research (ILVO), Merelbeke, Belgium
| | - Charlotte Trontin
- European and Mediterranean Plant Protection Organization, Paris, France
| | - Thierry Wetzel
- DLR Rheinpfalz, Institute of Plant Protection, Neustadt an der Weinstrasse, Germany
| | - Sebastien Massart
- Plant Pathology Laboratory, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Bioversity International, Montpellier, France
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Yang C, Zhang S, Sun J, Wang J, Zhang S, Cao M. Complete genome sequence of a distinct rosadnavirus isolated from Viola plants in China. Arch Virol 2022; 167:607-609. [PMID: 34988695 DOI: 10.1007/s00705-021-05316-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/16/2021] [Indexed: 11/29/2022]
Abstract
In 2019, plants of the genus Viola showing yellow mottling symptoms were collected in Liaoning, China. RNA sequencing and PCR both confirmed the presence of a reverse-transcribing DNA virus. The novel virus was named "viola yellow mottle virus" (VYMV), and its 9,872-bp genome was found to contain eight open reading frames. The polymerase (RT + RNase H) gene shared the most similarity (31.6% nucleotide and 41.6% amino acid sequence identity) with that of rose yellow vein virus (RYVV, NC_020999), which is currently the only member of the genus Rosadnavirus. Phylogenetic analysis indicated a close relationship between these viruses, suggesting that VYMV should be considered a new member of the genus Rosadnavirus.
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Affiliation(s)
- Caixia Yang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China.
| | - Shunyan Zhang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China
| | - Jia Sun
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China
| | - Junzhu Wang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Engineering, Shenyang University, Dadong, Shenyang, 110044, Liaoning, China
| | - Song Zhang
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing, 400712, China.
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Hou W, Li S, Massart S. Is There a "Biological Desert" With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses. Front Microbiol 2020; 11:592816. [PMID: 33329473 PMCID: PMC7710903 DOI: 10.3389/fmicb.2020.592816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
High throughput sequencing technologies accelerated the pace of discovery and identification of new viral species. Nevertheless, biological characterization of a new virus is a complex and long process, which can hardly follow the current pace of virus discovery. This review has analyzed 78 publications of new viruses and viroids discovered from 32 fruit tree species since 2011. The scientific biological information useful for a pest risk assessment and published together with the discovery of a new fruit tree virus or viroid has been analyzed. In addition, the 933 publications citing at least one of these original publications were reviewed, focusing on the biology-related information provided. In the original publications, the scientific information provided was the development of a detection test (94%), whole-genome sequence including UTRs (92%), local and large-scale epidemiological surveys (68%), infectivity and indicators experiments (50%), association with symptoms (25%), host range infection (23%), and natural vector identification (8%). The publication of a new virus is cited 2.8 times per year on average. Only 18% of the citations reported information on the biology or geographical repartition of the new viruses. These citing publications improved the new virus characterization by identifying the virus in a new country or continent, determining a new host, developing a new diagnostic test, studying genome or gene diversity, or by studying the transmission. Based on the gathered scientific information on the virus biology, the fulfillment of a recently proposed framework has been evaluated. A baseline prioritization approach for publishing a new plant virus is proposed for proper assessment of the potential risks caused by a newly identified fruit tree virus.
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Affiliation(s)
- Wanying Hou
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Institute of Tobacco Research, Chinese Academy of Agricultural Sciences, Qingdao, China
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shifang Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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