1
|
Temple C, Blouin AG, Boezen D, Botermans M, Durant L, De Jonghe K, de Koning P, Goedefroit T, Minet L, Steyer S, Verdin E, Zwart M, Massart S. Biological Characterization of Physostegia Chlorotic Mottle Virus, an Emergent Virus Infecting Vegetables in Diversified Production Systems. PHYTOPATHOLOGY 2024; 114:1680-1688. [PMID: 38648112 DOI: 10.1094/phyto-06-23-0194-r] [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: 04/25/2024]
Abstract
In 2014, Physostegia chlorotic mottle virus (PhCMoV) was discovered in Austria in Physostegia virginiana. Subsequent collaborative efforts established a link between the virus and severe fruit symptoms on important crops such as tomato, eggplant, and cucumber across nine European countries. Thereafter, specific knowledge gaps, which are crucial to assess the risks PhCMoV can pose for production and how to manage it, needed to be addressed. In this study, the transmission, prevalence, and disease severity of PhCMoV were examined. This investigation led to the identification of PhCMoV presence in a new country, Switzerland. Furthermore, our research indicates that the virus was already present in Europe 30 years ago. Bioassays demonstrated PhCMoV can result in up to 100% tomato yield losses depending on the phenological stage of the plant at the time of infection. PhCMoV was found to naturally infect 12 new host plant species across eight families, extending its host range to 21 plant species across 15 plant families. The study also identified a polyphagous leafhopper (genus Anaceratagallia) as a natural vector of PhCMoV. Overall, PhCMoV was widespread in small-scale diversified vegetable farms in Belgium where tomato is grown in soil under tunnels, occurring in approximately one-third of such farms. However, outbreaks were sporadic and were associated at least once with the cultivation in tomato tunnels of perennial plants that can serve as a reservoir host for the virus and its vector. To further explore this phenomenon and manage the virus, studying the ecology of the vector would be beneficial.
Collapse
Affiliation(s)
- Coline Temple
- Plant Pathology Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Arnaud G Blouin
- Plant Protection Department, Agroscope, 1260, Nyon, Switzerland
| | - Dieke Boezen
- Department of Microbial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6700 AB, The Netherlands
| | - Marleen Botermans
- Netherlands Institute for Vectors, Invasive plants and Plant health, Netherlands Food and Product Safety Authority, Wageningen, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Laurena Durant
- Plant Pathology Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, 9820, Belgium
| | - Pier de Koning
- Netherlands Institute for Vectors, Invasive plants and Plant health, Netherlands Food and Product Safety Authority, Wageningen, P.O. Box 9102, 6700 HC Wageningen, The Netherlands
| | - Thomas Goedefroit
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke, 9820, Belgium
| | - Laurent Minet
- Hortiforum asbl/Centre Technique Horticole de Gembloux, Gembloux, Belgium
| | - Stephan Steyer
- Crops and Forest Health Unit, Walloon Agricultural Research Centre (CRA-W), Gembloux, Belgium
| | - Eric Verdin
- Unité de Pathologie Végétale, Institut National de Recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Avignon, 84000, France
| | - Mark Zwart
- Department of Microbial Ecology, Netherlands Institute for Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, 6700 AB, The Netherlands
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| |
Collapse
|
2
|
Ontiveros I, Diaz-Pendón JA, López-Moya JJ. Experimental Transmission of Plant Viruses by Aphids or Whiteflies. Methods Mol Biol 2024; 2724:165-179. [PMID: 37987905 DOI: 10.1007/978-1-0716-3485-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Numerous species of plant viruses are naturally transmitted by insect vectors, mainly homopterans like aphids and whiteflies. Depending on the vector specificity and the mode of transmission, different durations of the periods for acquisition, retention, and inoculation are required for a successful transmission. Therefore, the experimental setup to perform controlled transmission experiments under laboratory conditions involves handling the vector organisms and managing the times for the different steps of the process to optimize and standardize the results. This chapter describes some basic procedures that can be applied to vector-mediated transmission experiments with selected viruses using aphids or whiteflies and different host plants.
Collapse
Affiliation(s)
- Irene Ontiveros
- Centre for Research in Agricultural Genomics (CRAG, CSIC-IRTA-UAB-UB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
- Institute for Mediterranean and Subtropical Horticulture La Mayora (IHSM), CSIC-UMA, Málaga, Spain
| | - Juan Antonio Diaz-Pendón
- Institute for Mediterranean and Subtropical Horticulture La Mayora (IHSM), CSIC-UMA, Málaga, Spain
| | - Juan José López-Moya
- Centre for Research in Agricultural Genomics (CRAG, CSIC-IRTA-UAB-UB), Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain.
- Institute for Mediterranean and Subtropical Horticulture La Mayora (IHSM), CSIC-UMA, Málaga, Spain.
| |
Collapse
|
3
|
Rivarez MPS, Faure C, Svanella-Dumas L, Pecman A, Tušek-Žnidaric M, Schönegger D, De Jonghe K, Blouin A, Rasmussen DA, Massart S, Ravnikar M, Kutnjak D, Marais A, Candresse T. Diversity and Pathobiology of an Ilarvirus Unexpectedly Detected in Diverse Plants and Global Sequencing Data. PHYTOPATHOLOGY 2023; 113:1729-1744. [PMID: 37399026 DOI: 10.1094/phyto-12-22-0465-v] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
High-throughput sequencing (HTS) and sequence mining tools revolutionized virus detection and discovery in recent years, and implementing them with classical plant virology techniques results in a powerful approach to characterize viruses. An example of a virus discovered through HTS is Solanum nigrum ilarvirus 1 (SnIV1) (Bromoviridae), which was recently reported in various solanaceous plants from France, Slovenia, Greece, and South Africa. It was likewise detected in grapevines (Vitaceae) and several Fabaceae and Rosaceae plant species. Such a diverse set of source organisms is atypical for ilarviruses, thus warranting further investigation. In this study, modern and classical virological tools were combined to accelerate the characterization of SnIV1. Through HTS-based virome surveys, mining of sequence read archive datasets, and a literature search, SnIV1 was further identified from diverse plant and non-plant sources globally. SnIV1 isolates showed relatively low variability compared with other phylogenetically related ilarviruses. Phylogenetic analyses showed a distinct basal clade of isolates from Europe, whereas the rest formed clades of mixed geographic origin. Furthermore, systemic infection of SnIV1 in Solanum villosum and its mechanical and graft transmissibility to solanaceous species were demonstrated. Near-identical SnIV1 genomes from the inoculum (S. villosum) and inoculated Nicotiana benthamiana were sequenced, thus partially fulfilling Koch's postulates. SnIV1 was shown to be seed-transmitted and potentially pollen-borne, has spherical virions, and possibly induces histopathological changes in infected N. benthamiana leaf tissues. Overall, this study provides information to better understand the diversity, global presence, and pathobiology of SnIV1; however, its possible emergence as a destructive pathogen remains uncertain. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
Collapse
Affiliation(s)
- Mark Paul Selda Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Chantal Faure
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Laurence Svanella-Dumas
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Magda Tušek-Žnidaric
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Deborah Schönegger
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Merelbeke, 9820, Belgium
| | - Arnaud Blouin
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - David A Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, 27606, U.S.A
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, 1000, Slovenia
| | - Armelle Marais
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| | - Thierry Candresse
- University of Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, Villenave d'Ornon, 33882, France
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Khalili M, Candresse T, Koloniuk I, Safarova D, Brans Y, Faure C, Delmas M, Massart S, Aranda MA, Caglayan K, Decroocq V, Drogoudi P, Glasa M, Pantelidis G, Navratil M, Latour F, Spak J, Pribylova J, Mihalik D, Palmisano F, Saponari A, Necas T, Sedlak J, Marais A. The Expanding Menagerie of Prunus-Infecting Luteoviruses. PHYTOPATHOLOGY 2023; 113:345-354. [PMID: 35972890 DOI: 10.1094/phyto-06-22-0203-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Members of the genus Luteovirus are responsible for economically destructive plant diseases worldwide. Over the past few years, three luteoviruses infecting Prunus trees have been characterized. However, the biological properties, prevalence, and genetic diversity of those viruses have not yet been studied. High-throughput sequencing of samples of various wild, cultivated, and ornamental Prunus species enabled the identification of four novel species in the genus Luteovirus for which we obtained complete or nearly complete genomes. Additionally, we identified another new putative species recovered from Sequence Read Archive data. Furthermore, we conducted a survey on peach-infecting luteoviruses in eight European countries. Analyses of 350 leaf samples collected from germplasm, production orchards, and private gardens showed that peach-associated luteovirus (PaLV), nectarine stem pitting-associated virus (NSPaV), and a novel luteovirus, peach-associated luteovirus 2 (PaLV2), are present in all countries; the most prevalent virus was NSPaV, followed by PaLV. The genetic diversity of these viruses was also analyzed. Moreover, the biological indexing on GF305 peach indicator plants demonstrated that PaLV and PaLV2, like NSPaV, are transmitted by graft at relatively low rates. No clear viral symptoms have been observed in either graft-inoculated GF305 indicators or different peach tree varieties observed in an orchard. The data generated during this study provide a broader overview of the genetic diversity, geographical distribution, and prevalence of peach-infecting luteoviruses and suggest that these viruses are likely asymptomatic in peach under most circumstances.
Collapse
Affiliation(s)
- Maryam Khalili
- Université de Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | | | - Igor Koloniuk
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Dana Safarova
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Yoann Brans
- Laboratoire de Virologie et de Biologie Moléculaire, CTIFL, Prigonrieux, France
| | - Chantal Faure
- Université de Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| | - Marine Delmas
- INRAE, Unité Expérimentale Arboricole, Toulenne, France
| | - Sébastien Massart
- Laboratory of Plant Pathology, TERRA, Gembloux Agro-Bio Tech, Liège University, Gembloux, Belgium
| | - Miguel A Aranda
- Department of Stress Biology and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura, CSIC, Murcia, Spain
| | - Kadriye Caglayan
- Department of Plant Protection, Hatay Mustafa Kemal University, Antakya, Hatay, Turkey
| | | | - Pavlina Drogoudi
- Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Naoussa, Greece
| | - Miroslav Glasa
- Biomedical Research Center of the Slovak Academy of Sciences, Institute of Virology, Bratislava, Slovakia
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Trnava, Slovakia
| | - George Pantelidis
- Department of Deciduous Fruit Trees, Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Naoussa, Greece
| | - Milan Navratil
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - François Latour
- Laboratoire de Virologie et de Biologie Moléculaire, CTIFL, Prigonrieux, France
| | - Josef Spak
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Jaroslava Pribylova
- Department of Plant Virology, Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Daniel Mihalik
- Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Trnava, Slovakia
| | - Francesco Palmisano
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura "Basile Caramia", Locorotondo, Italy
| | - Antonella Saponari
- Centro di Ricerca, Sperimentazione e Formazione in Agricoltura "Basile Caramia", Locorotondo, Italy
| | - Tomas Necas
- Department of Fruit Science, Faculty of Horticulture, Mendel University, Lednice, Czech Republic
| | - Jiri Sedlak
- Vyzkumny A Slechtitelsky Ustav Ovocnarsky, Holovousy, Czech Republic
| | - Armelle Marais
- Université de Bordeaux, INRAE, UMR BFP, Villenave d'Ornon, France
| |
Collapse
|
6
|
Pasin F. Assembly of plant virus agroinfectious clones using biological material or DNA synthesis. STAR Protoc 2022; 3:101716. [PMID: 36149792 PMCID: PMC9519601 DOI: 10.1016/j.xpro.2022.101716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/29/2022] [Accepted: 08/26/2022] [Indexed: 01/26/2023] Open
Abstract
Infectious clone technology is universally applied for biological characterization and engineering of viruses. This protocol describes procedures that implement synthetic biology advances for streamlined assembly of virus infectious clones. Here, I detail homology-based cloning using biological material, as well as SynViP assembly using type IIS restriction enzymes and chemically synthesized DNA fragments. The assembled virus clones are based on compact T-DNA binary vectors of the pLX series and are delivered to host plants by Agrobacterium-mediated inoculation. For complete details on the use and execution of this protocol, please refer to Pasin et al. (2017, 2018) and Pasin (2021).
Collapse
Affiliation(s)
- Fabio Pasin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València (CSIC-UPV), 46011 Valencia, Spain.
| |
Collapse
|
7
|
Robson M, Chooi KM, Blouin AG, Knight S, MacDiarmid RM. A National Catalogue of Viruses Associated with Indigenous Species Reveals High-Throughput Sequencing as a Driver of Indigenous Virus Discovery. Viruses 2022; 14:v14112477. [PMID: 36366575 PMCID: PMC9693408 DOI: 10.3390/v14112477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Viruses are important constituents of ecosystems, with the capacity to alter host phenotype and performance. However, virus discovery cued by disease symptoms overlooks latent or beneficial viruses, which are best detected using targeted virus detection or discovered by non-targeted methods, e.g., high-throughput sequencing (HTS). To date, in 64 publications, 701 viruses have been described associated with indigenous species of Aotearoa New Zealand. Viruses were identified in indigenous birds (189 viruses), bats (13 viruses), starfish (4 viruses), insects (280 viruses), and plants (126 viruses). HTS gave rise to a 21.9-fold increase in virus discovery rate over the targeted methods, and 72.7-fold over symptom-based methods. The average number of viruses reported per publication has also increased proportionally over time. The use of HTS has driven the described national virome recently by 549 new-to-science viruses; all are indigenous. This report represents the first catalogue of viruses associated with indigenous species of a country. We provide evidence that the application of HTS to samples of Aotearoa New Zealand's unique fauna and flora has driven indigenous virus discovery, a key step in the process to understand the role of viruses in the biological diversity and ecology of the land, sea, and air environments of a country.
Collapse
Affiliation(s)
- Merlyn Robson
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
- Bio-Protection Research Centre, Lincoln University, P.O. Box 85084, Lincoln 7674, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | - Kar Mun Chooi
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
| | | | - Sarah Knight
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Robin Marion MacDiarmid
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand
- Bio-Protection Research Centre, Lincoln University, P.O. Box 85084, Lincoln 7674, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 92169, Auckland 1142, New Zealand
- Correspondence:
| |
Collapse
|
8
|
Temple C, Blouin AG, De Jonghe K, Foucart Y, Botermans M, Westenberg M, Schoen R, Gentit P, Visage M, Verdin E, Wipf-Scheibel C, Ziebell H, Gaafar YZA, Zia A, Yan XH, Richert-Pöggeler KR, Ulrich R, Rivarez MPS, Kutnjak D, Vučurović A, Massart S. Biological and Genetic Characterization of Physostegia Chlorotic Mottle Virus in Europe Based on Host Range, Location, and Time. PLANT DISEASE 2022; 106:2797-2807. [PMID: 35394335 DOI: 10.1094/pdis-12-21-2800-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: 06/14/2023]
Abstract
Application of high throughput sequencing (HTS) technologies enabled the first identification of Physostegia chlorotic mottle virus (PhCMoV) in 2018 in Austria. Subsequently, PhCMoV was detected in Germany and Serbia on tomatoes showing severe fruit mottling and ripening anomalies. We report here how prepublication data-sharing resulted in an international collaboration across eight laboratories in five countries, enabling an in-depth characterization of PhCMoV. The independent studies converged toward its recent identification in eight additional European countries and confirmed its presence in samples collected 20 years ago (2002). The natural plant host range was expanded from two to nine species across seven families, and we confirmed the association of PhCMoV presence with severe fruit symptoms on economically important crops such as tomato, eggplant, and cucumber. Mechanical inoculations of selected isolates in the greenhouse established the causality of the symptoms on a new indexing host range. In addition, phylogenetic analysis showed a low genomic variation across the 29 near-complete genome sequences available. Furthermore, a strong selection pressure within a specific ecosystem was suggested by nearly identical sequences recovered from different host plants through time. Overall, this study describes the European distribution of PhCMoV on multiple plant hosts, including economically important crops on which the virus can cause severe fruit symptoms. This work demonstrates how to efficiently improve knowledge on an emergent pathogen by sharing HTS data and provides a solid knowledge foundation for further studies on plant rhabdoviruses.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Coline Temple
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège (ULIEGE), Gembloux 5030, Belgium
| | - Arnaud G Blouin
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège (ULIEGE), Gembloux 5030, Belgium
- Plant Protection Department, Agroscope, 1260 Nyon, Switzerland
| | - Kris De Jonghe
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke 9820, Belgium
| | - Yoika Foucart
- Plant Sciences Unit, Research Institute for Agriculture, Fisheries and Food (ILVO), Merelbeke 9820, Belgium
| | - Marleen Botermans
- National Reference Centre of Plant Health, National Plant Protection Organization of the Netherlands, 6700 HC Wageningen, the Netherlands
| | - Marcel Westenberg
- National Reference Centre of Plant Health, National Plant Protection Organization of the Netherlands, 6700 HC Wageningen, the Netherlands
| | - Ruben Schoen
- National Reference Centre of Plant Health, National Plant Protection Organization of the Netherlands, 6700 HC Wageningen, the Netherlands
| | - Pascal Gentit
- Laboratoire de santé des végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Angers 49100, France
| | - Michèle Visage
- Laboratoire de santé des végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Angers 49100, France
| | - Eric Verdin
- Unité de Pathologie Végétale, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Avignon 84000, France
| | - Catherine Wipf-Scheibel
- Unité de Pathologie Végétale, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Avignon 84000, France
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Yahya Z A Gaafar
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Amjad Zia
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Xiao-Hua Yan
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | - Katja R Richert-Pöggeler
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig 38104, Germany
| | | | - Mark Paul S Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana 1000, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana 1000, Slovenia
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Ljubljana 1000, Slovenia
| | - Sébastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liège (ULIEGE), Gembloux 5030, Belgium
| |
Collapse
|
9
|
Várallyay E, Přibylová J, Galbacs ZN, Jahan A, Varga T, Špak J, Lenz O, Fránová J, Sedlák J, Koloniuk I. Detection of Apple Hammerhead Viroid, Apple Luteovirus 1 and Citrus Concave Gum-Associated Virus in Apple Propagation Materials and Orchards in the Czech Republic and Hungary. Viruses 2022; 14:v14112347. [PMID: 36366445 PMCID: PMC9695845 DOI: 10.3390/v14112347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 02/01/2023] Open
Abstract
Grafting cultivars onto rootstocks is a widely used practice by the apple industry predominantly aimed at faster fruit bearing. Using high-throughput sequencing, we revealed the presence of recently described viral agents, namely apple hammerhead viroid (AHVd), apple luteovirus 1 (ALV-1), and citrus concave gum-associated virus (CCGaV), in germplasm collections and production orchards in the Czech Republic and Hungary. The HTS results were validated with RT-(q)PCR, and Northern blotting techniques. To obtain further insight about the presence of these agents, RT-PCR based surveys were carried out and showed their widespread presence alone or in mixed infections. The pathogens were present both in production areas and in feral samples. In addition, rootstock-to-scion transmission of ALV-1 and CCGaV was confirmed using commercial rootstock materials. Phylogenetic relationships based on partial sequences of distinct variants were also investigated. Furthermore, the rosy apple aphid was found to be ALV-1-positive, suggesting that it might be a potential vector of the virus.
Collapse
Affiliation(s)
- Eva Várallyay
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Gödöllő, Hungary
- Correspondence: (E.V.); (I.K.)
| | - Jaroslava Přibylová
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Zsuzsanna Nagyne Galbacs
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Gödöllő, Hungary
| | - Almash Jahan
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Gödöllő, Hungary
| | - Tunde Varga
- Genomics Research Group, Department of Plant Pathology, Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Szent-Gyorgyi Albert Street 4, 2100 Gödöllő, Hungary
| | - Josef Špak
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Ondřej Lenz
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jana Fránová
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Jiří Sedlák
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 50801 Holovousy, Czech Republic
| | - Igor Koloniuk
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Branišovská 31, 37005 České Budějovice, Czech Republic
- Correspondence: (E.V.); (I.K.)
| |
Collapse
|
10
|
Reynard JS, Brodard J, Zufferey V, Rienth M, Gugerli P, Schumpp O, Blouin AG. Nuances of Responses to Two Sources of Grapevine Leafroll Disease on Pinot Noir Grown in the Field for 17 Years. Viruses 2022; 14:1333. [PMID: 35746804 PMCID: PMC9227476 DOI: 10.3390/v14061333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 11/25/2022] Open
Abstract
Grapevine leafroll disease (GLD) is one of the most economically damaging virus diseases in grapevine, with grapevine leafroll-associated virus 1 (GLRaV-1) and grapevine leafroll-associated virus 3 (GLRaV-3) as the main contributors. This study complements a previously published transcriptomic analysis and compared the impact of two different forms of GLD to a symptomless control treatment: a mildly symptomatic form infected with GLRaV-1 and a severe form with exceptionally early leafroll symptoms (up to six weeks before veraison) infected with GLRaV-1 and GLRaV-3. Vine physiology and fruit composition in 17-year-old Pinot noir vines were measured and a gradient of vigor, yield, and berry quality (sugar content and berry weight) was observed between treatments. Virome composition, confirmed by individual RT-PCR, was compared with biological indexing. Three divergent viromes were recovered, containing between four to seven viruses and two viroids. They included the first detection of grapevine asteroid mosaic-associated virus in Switzerland. This virus did not cause obvious symptoms on the indicators used in biological indexing. Moreover, the presence of grapevine virus B (GVB) did not cause the expected corky bark symptoms on the indicators, thus underlining the important limitations of the biological indexing. Transmission of GLRaV-3 alone or in combination with GVB by Planococcus comstocki mealybug did not reproduce the strong symptoms observed on the donor plant infected with a severe form of GLD. This result raises questions about the contribution of each virus to the symptomatology of the plant.
Collapse
Affiliation(s)
| | - Justine Brodard
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland; (J.B.); (P.G.); (O.S.)
| | - Vivian Zufferey
- Groupe Viticulture, Agroscope, 1009 Pully, Switzerland; (J.-S.R.); (V.Z.)
| | - Markus Rienth
- Changins College for Viticulture and Oenology, University of Sciences and Art Western Switzerland, 1260 Nyon, Switzerland;
| | - Paul Gugerli
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland; (J.B.); (P.G.); (O.S.)
| | - Olivier Schumpp
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland; (J.B.); (P.G.); (O.S.)
| | - Arnaud G. Blouin
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland; (J.B.); (P.G.); (O.S.)
| |
Collapse
|
11
|
Viromes of Hungarian Peach Trees Identified by High-Throughput Sequencing of Small RNAs. PLANTS 2022; 11:plants11121591. [PMID: 35736743 PMCID: PMC9230589 DOI: 10.3390/plants11121591] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/06/2022] [Accepted: 06/13/2022] [Indexed: 11/17/2022]
Abstract
Peach trees can be infected with viruses and viroids. As we do not have efficient plant protection methods against these pathogens, the prevention of infection is crucial. Fruit trees are maintained by vegetative propagation. Planting material such as certified mother trees and rootstocks should be free from viruses and viroids, and this status has to be regularly checked to prevent infections. We surveyed certified peach trees for the presence of viruses and viroids using small RNA high-throughput sequencing (HTS), an unbiased virus diagnostic method. The results of the bioinformatic analysis of HTS were validated by other molecular methods including RT-PCR, Northern blot hybridization and loop-mediated isothermal amplification (LAMP). We found the presence of plum pox virus and peach latent mosaic viroid (PLMVd) in the vector-free isolator houses, whose presence should be regularly tested. Moreover, we detected frequent infection with recently described viruses such as nectarine stem pitting-associated virus and peach-associated luteovirus (PaLV). During the survey, PLMVd and PaLV were detected for the first time in Hungary. The analysis of the presenting virus variants and possible sources of infection suggests that the source of the viral infection could be the infected propagating material. Our study emphasizes the importance of using sensitive and trustworthy diagnostic techniques to be able to detect viral infections and successfully prevent their spread by propagation material.
Collapse
|
12
|
Bettoni JC, Fazio G, Carvalho Costa L, Hurtado-Gonzales OP, Rwahnih MA, Nedrow A, Volk GM. Thermotherapy Followed by Shoot Tip Cryotherapy Eradicates Latent Viruses and Apple Hammerhead Viroid from In Vitro Apple Rootstocks. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050582. [PMID: 35270052 PMCID: PMC8912313 DOI: 10.3390/plants11050582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 05/06/2023]
Abstract
Virus and viroid-free apple rootstocks are necessary for large-scale nursery propagation of apple (Malus domestica) trees. Apple stem grooving virus (ASGV) and Apple chlorotic leaf spot virus (ACLSV) are among the most serious apple viruses that are prevalent in most apple growing regions. In addition to these viruses, a new infectious agent named Apple hammerhead viroid (AHVd) has been identified. We investigated whether thermotherapy or cryotherapy alone or a combination of both could effectively eradicate ACLSV, ASGV, and AHVd from in vitro cultures of four apple rootstocks developed in the Cornell-Geneva apple rootstock breeding program (CG 2034, CG 4213, CG 5257, and CG 6006). For thermotherapy treatments, in vitro plants were treated for four weeks at 36 °C (day) and 32 °C (night). Plant vitrification solution 2 (PVS2) and cryotherapy treatments included a shoot tip preculture in 2 M glycerol + 0.8 M sucrose for one day followed by exposure to PVS2 for 60 or 75 min at 22 °C, either without or with liquid nitrogen (LN, cryotherapy) exposure. Combinations of thermotherapy and PVS2/cryotherapy treatments were also performed. Following treatments, shoot tips were warmed, recovered on growth medium, transferred to the greenhouse, grown, placed in dormancy inducing conditions, and then grown again prior to sampling leaves for the presence of viruses and viroids. Overall, thermotherapy combined with cryotherapy treatment resulted in the highest percentage of virus- and viroid-free plants, suggesting great potential for producing virus- and viroid-free planting materials for the apple industry. Furthermore, it could also be a valuable tool to support the global exchange of apple germplasm.
Collapse
Affiliation(s)
- Jean Carlos Bettoni
- The New Zealand Institute for Plant and Food Research Limited, Batchelar Road, Palmerston North 4410, New Zealand
- Correspondence:
| | - Gennaro Fazio
- USDA-ARS Plant Genetic Resources Unit, 630 W. North Street, Geneva, NY 14456, USA; (G.F.); (A.N.)
| | - Larissa Carvalho Costa
- USDA-APHIS Plant Germplasm Quarantine Program, 9901 Powder Mill Road, Bldg 580, BARC-East, Beltsville, MD 20705, USA; (L.C.C.); (O.P.H.-G.)
| | - Oscar P. Hurtado-Gonzales
- USDA-APHIS Plant Germplasm Quarantine Program, 9901 Powder Mill Road, Bldg 580, BARC-East, Beltsville, MD 20705, USA; (L.C.C.); (O.P.H.-G.)
| | - Maher Al Rwahnih
- Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA;
| | - Abby Nedrow
- USDA-ARS Plant Genetic Resources Unit, 630 W. North Street, Geneva, NY 14456, USA; (G.F.); (A.N.)
| | - Gayle M. Volk
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 S. Mason Street, Fort Collins, CO 80521, USA;
| |
Collapse
|
13
|
Oberemok V, Laikova K, Golovkin I, Kryukov L, Kamenetsky-Goldstein R. Biotechnology of virus eradication and plant vaccination in phytobiome context. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:3-8. [PMID: 34569131 DOI: 10.1111/plb.13338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
A plant's associated biota plays an integral role in its metabolism, nutrient uptake, stress tolerance, pathogen resistance and other physiological processes. Although a virome is an integral part of the phytobiome, a major contradiction exists between the holobiont approach and the practical need to eradicate pathogens from agricultural crops. In this review, we discuss grapevine virus control, but the issue is also relevant for numerous other crops, including potato, cassava, citrus, cacao and other species. Grapevine diseases, especially viral infections, cause main crop losses. Methods have been developed to eliminate viruses and other microorganisms from plant material, but elimination of viruses from plant material does not guarantee protection from future reinfection. Elimination of viral particles in plant material could create genetic drift, leading in turn to an increase in the occurrence of pathogenic strains of viruses. A possible solution may be a combination of virus elimination and plant propagation in tissue culture with in vitro vaccination. In this context, possible strategies to control viral infections include application of plant resistance inducers, cross protection and vaccination using siRNA, dsRNA and viral replicons during plant 'cleaning' and in vitro propagation. The experience and knowledge accumulated in human immunization can help plant scientists to develop and employ new methods of protection, leading to more sustainable and healthier crop production.
Collapse
Affiliation(s)
- V Oberemok
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
- Nikita Botanical Gardens - National Scientific Centre Russian Academy of Sciences, Yalta, Russia
| | - K Laikova
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
- Research Institute of Agriculture of Crimea, Simferopol, Russia
| | - I Golovkin
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
| | - L Kryukov
- V.I. Vernadsky Crimean Federal University, Simferopol, Russia
- Lobachevsky State University of Nizhni Novgorod, Nizhni Novgorod, Russia
| | | |
Collapse
|
14
|
Liu Z, Dong Z, Zhan B, Li S. Characterization of an Isolate of Citrus Concave Gum-Associated Virus from Apples in China and Development of an RT-RPA Assay for the Rapid Detection of the Virus. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112239. [PMID: 34834603 PMCID: PMC8621397 DOI: 10.3390/plants10112239] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 05/17/2023]
Abstract
Apple (Malus domestica) fruits exhibiting bright stripe symptoms were identified in Weihai City, Shandong Province, China. To investigate the virome in the apple samples, the method of high throughput sequencing (HTS) was used to identify the viruses. It was found that the sequence of citrus concave gum-associated virus (CCGaV) was involved in the apple transcriptome dataset. The full-length genome of the CCGaV-Weihai isolate contained two segments, the RNA1 was 6674 nt in size containing a conserved RNA-dependent RNA polymerase (RdRp), and the RNA2 was ambisense, 2706 nt in length, encoding a movement protein (MP) and a coat protein (CP). Sequence alignment and phylogenetic analyses indicated that CCGaV-Weihai was more closely related to CCGaV-H2799 isolated from the apple host in the United States and distantly related to CCGaV-CGW2 from Citrus sinensis in Italy, indicating a possibly geographical and host differentiation of CCGaV isolates. This was the first identification and characterization of CCGaV infecting apples in China. Additionally, a rapid and sensitive reverse transcription recombinase polymerase amplification (RT-RPA) assay technique was established for CCGaV detection in apple plants. The RT-RPA of CCGaV was not affected by other common viruses in apple plants and is about 10-fold more sensitive than the conventional reverse transcription polymerase chain reaction method, which can be used in large-scale testing.
Collapse
Affiliation(s)
- Zhen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.L.); (Z.D.)
| | - Zhenfei Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.L.); (Z.D.)
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Binhui Zhan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.L.); (Z.D.)
- Correspondence: (B.Z.); (S.L.)
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.L.); (Z.D.)
- Correspondence: (B.Z.); (S.L.)
| |
Collapse
|
15
|
Aljabali AAA, Hassan S, Pabari RM, Shahcheraghi SH, Mishra V, Charbe NB, Chellappan DK, Dureja H, Gupta G, Almutary AG, Alnuqaydan AM, Verma SK, Panda PK, Mishra YK, Serrano-Aroca Á, Dua K, Uversky VN, Redwan EM, Bahar B, Bhatia A, Negi P, Goyal R, McCarron P, Bakshi HA, Tambuwala MM. The viral capsid as novel nanomaterials for drug delivery. Future Sci OA 2021; 7:FSO744. [PMID: 34737885 PMCID: PMC8558853 DOI: 10.2144/fsoa-2021-0031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/14/2021] [Indexed: 12/11/2022] Open
Abstract
The purpose of this review is to highlight recent scientific developments and provide an overview of virus self-assembly and viral particle dynamics. Viruses are organized supramolecular structures with distinct yet related features and functions. Plant viruses are extensively used in biotechnology, and virus-like particulate matter is generated by genetic modification. Both provide a material-based means for selective distribution and delivery of drug molecules. Through surface engineering of their capsids, virus-derived nanomaterials facilitate various potential applications for selective drug delivery. Viruses have significant implications in chemotherapy, gene transfer, vaccine production, immunotherapy and molecular imaging.
Collapse
Affiliation(s)
- Alaa AA Aljabali
- Faculty of Pharmacy, Department of Pharmaceutics & Pharmaceutical Technology, Yarmouk University, Irbid, 21163, Jordan
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Paschim Medinipur, India
| | - Ritesh M Pabari
- School of Pharmacy, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Seyed H Shahcheraghi
- Infectious Diseases Research Center, Shahid Sadoughi Hospital, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Nitin B Charbe
- Department of Pharmaceutical Sciences, Rangel College of Pharmacy, Texas A&M University, Kingsville, TX 78363, USA
| | - Dinesh K Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur, 57000, Malaysia
| | - Harish Dureja
- Department of Pharmaceutical Sciences, Maharshi Dayanand University, Rohtak, 124001, India
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur, 302017, India
| | - Abdulmajeed G Almutary
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Saudi Arabia
| | - Abdullah M Alnuqaydan
- Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Saudi Arabia
| | - Suresh K Verma
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics & Astronomy, Uppsala University, Uppsala, 75120, Sweden
| | - Pritam K Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics & Astronomy, Uppsala University, Uppsala, 75120, Sweden
| | - Yogendra Kumar Mishra
- University of Southern Denmark, Mads Clausen Institute, NanoSYD, Alsion 2, Sønderborg 6400, Denmark
| | - Ángel Serrano-Aroca
- Biomaterials & Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, Valencia, 46001, Spain
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology, Sydney, Australia
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Elrashdy M Redwan
- King Abdulazizi University, Faculty of Science, Department of Biological Science, Saudi Arabia
| | - Bojlul Bahar
- International Institute of Nutritional Sciences & Food Safety Studies, School of Sport & Health Sciences, University of Central Lancashire, Preston, Lancashire, PR1 2HE, UK
| | - Amit Bhatia
- Maharaja Ranjit Singh Punjab Technical University Dabwali Road, Bathinda, Punjab, 151001, India
| | - Poonam Negi
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology & Management Sciences, Solan, 173229, India
| | - Rohit Goyal
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology & Management Sciences, Solan, 173229, India
| | - Paul McCarron
- School of Pharmacy & Pharmaceutical Science, Ulster University, Coleraine, County Londonderry, Northern Ireland, BT52 1SA, UK
| | - Hamid A Bakshi
- School of Pharmacy & Pharmaceutical Science, Ulster University, Coleraine, County Londonderry, Northern Ireland, BT52 1SA, UK
| | - Murtaza M Tambuwala
- School of Pharmacy & Pharmaceutical Science, Ulster University, Coleraine, County Londonderry, Northern Ireland, BT52 1SA, UK
| |
Collapse
|
16
|
Beris D, Ioanna M, Vassilakos N, Theologidis I, Rampou A, Kektsidou O, Massart S, Varveri C. Association of Citrus Virus A to Citrus Impietratura Disease Symptoms. PHYTOPATHOLOGY 2021; 111:1782-1789. [PMID: 33703919 DOI: 10.1094/phyto-01-21-0027-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Citrus impietratura disease (CID) is a graft transmissible, virus-like disease observed in old-line citrus trees; its characteristic symptom is the appearance of gum in the albedo of the affected fruits. To identify the causal agent of the disease, high-throughput sequencing (HTS) was performed on symptomatic orange fruits. The analysis of the obtained data revealed in all samples mixed infections of viroids commonly found in citrus trees together with the recently described citrus virus A (CiVA). Examination of additional symptomatic fruits with conventional reverse transcription PCR led to the identification of a single CiVA infection in one tree, which was verified by HTS. Indexing of the single CiVA-infected tree on indicator plants resulted in the appearance of characteristic symptoms in the leaves that were correlated with virus accumulation. Moreover, a comparative analysis among symptomatic and asymptomatic fruits derived from the same trees was performed and included the single CiVA-infected orange tree. The analysis revealed a positive correlation between the appearance of symptoms and the accumulation of CiVA RNAs. To facilitate CiVA detection during certification programs of propagation material, a quantitative RT-PCR targeting the movement protein of the virus was developed and evaluated for reliable and sensitive detection of the virus. To the best of our knowledge this is the first study that associates CiVA with the appearance of CID symptoms.
Collapse
Affiliation(s)
- Despoina Beris
- Laboratory of Virology, Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Malandraki Ioanna
- Laboratory of Virology, Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Nikon Vassilakos
- Laboratory of Virology, Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Ioannis Theologidis
- Laboratory of Virology, Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Aggeliki Rampou
- Laboratory of Virology, Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Oxana Kektsidou
- Laboratory of Virology, Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, Athens 14561, Greece
| | - Sebastien Massart
- Laboratory of Plant Pathology, TERRA, Gembloux Agro-Bio Tech, University of Liège, Gembloux 5030, Belgium
| | - Christina Varveri
- Laboratory of Virology, Scientific Directorate of Phytopathology, Benaki Phytopathological Institute, Athens 14561, Greece
| |
Collapse
|
17
|
Rumbou A, Vainio EJ, Büttner C. Towards the Forest Virome: High-Throughput Sequencing Drastically Expands Our Understanding on Virosphere in Temperate Forest Ecosystems. Microorganisms 2021; 9:microorganisms9081730. [PMID: 34442809 PMCID: PMC8399312 DOI: 10.3390/microorganisms9081730] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022] Open
Abstract
Thanks to the development of HTS technologies, a vast amount of genetic information on the virosphere of temperate forests has been gained in the last seven years. To estimate the qualitative/quantitative impact of HTS on forest virology, we have summarized viruses affecting major tree/shrub species and their fungal associates, including fungal plant pathogens, mutualists and saprotrophs. The contribution of HTS methods is extremely significant for forest virology. Reviewed data on viral presence in holobionts allowed us a first attempt to address the role of virome in holobionts. Forest health is dependent on the variability of microorganisms interacting with the host tree/holobiont; symbiotic microbiota and pathogens engage in a permanent interplay, which influences the host. Through virus–virus interplays synergistic or antagonistic relations may evolve, which may drastically affect the health of the holobiont. Novel insights of these interplays may allow practical applications for forest plant protection based on endophytes and mycovirus biocontrol agents. The current analysis is conceived in light of the prospect that novel viruses may initiate an emergent infectious disease and that measures for the avoidance of future outbreaks in forests should be considered.
Collapse
Affiliation(s)
- Artemis Rumbou
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, 14195 Berlin, Germany;
- Correspondence:
| | - Eeva J. Vainio
- Natural Resources Institute Finland, Forest Health and Biodiversity, Latokartanonkaari 9, 00790 Helsinki, Finland;
| | - Carmen Büttner
- Faculty of Life Sciences, Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, 14195 Berlin, Germany;
| |
Collapse
|
18
|
Demian E, Holczbauer A, Galbacs ZN, Jaksa-Czotter N, Turcsan M, Olah R, Varallyay E. Variable Populations of Grapevine Virus T Are Present in Vineyards of Hungary. Viruses 2021; 13:1119. [PMID: 34200935 PMCID: PMC8230486 DOI: 10.3390/v13061119] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/09/2021] [Indexed: 12/02/2022] Open
Abstract
Grapevine virus T (GVT) is a recently described foveavirus, which was identified from a transcriptome of a Teroldego grapevine cultivar in 2017. Recently, we surveyed vineyards and rootstock plantations in Hungary using small RNA (sRNA) high-throughput sequencing (HTS), at a time when GVT had not yet been described. A re-analysis of our sRNA HTS datasets and a survey of grapevines by RT-PCR revealed the presence of GVT in most of the vineyards tested, while at rootstock fields its presence was very rare. The presence and high variability of the virus in the country was confirmed by sequence analysis of strains originating from different vineyards. In this study, we demonstrate the presence of GVT in Hungary and show its high diversity, suggesting that GVT presence may not seriously affect grapevine health and that it could have been present in European vineyards for a long time as a latent infection.
Collapse
Affiliation(s)
- Emese Demian
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| | - Aliz Holczbauer
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| | - Zsuzsanna Nagyne Galbacs
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| | - Nikoletta Jaksa-Czotter
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| | - Mihaly Turcsan
- Institute for Viticulture and Oenology, Hungarian University of Agriculture and Life Sciences, Villányi Str. 29-43, H-1118 Budapest, Hungary; (M.T.); (R.O.)
| | - Robert Olah
- Institute for Viticulture and Oenology, Hungarian University of Agriculture and Life Sciences, Villányi Str. 29-43, H-1118 Budapest, Hungary; (M.T.); (R.O.)
| | - Eva Varallyay
- Institute of Plant Protection, Hungarian University of Agriculture and Life Sciences, Ménesi Road 44, H-1118 Budapest, Hungary; (E.D.); (A.H.); (Z.N.G.); (N.J.-C.)
| |
Collapse
|
19
|
Rivarez MPS, Vučurović A, Mehle N, Ravnikar M, Kutnjak D. Global Advances in Tomato Virome Research: Current Status and the Impact of High-Throughput Sequencing. Front Microbiol 2021; 12:671925. [PMID: 34093492 PMCID: PMC8175903 DOI: 10.3389/fmicb.2021.671925] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/12/2021] [Indexed: 11/30/2022] Open
Abstract
Viruses cause a big fraction of economically important diseases in major crops, including tomato. In the past decade (2011–2020), many emerging or re-emerging tomato-infecting viruses were reported worldwide. In this period, 45 novel viral species were identified in tomato, 14 of which were discovered using high-throughput sequencing (HTS). In this review, we first discuss the role of HTS in these discoveries and its general impact on tomato virome research. We observed that the rate of tomato virus discovery is accelerating in the past few years due to the use of HTS. However, the extent of the post-discovery characterization of viruses is lagging behind and is greater for economically devastating viruses, such as the recently emerged tomato brown rugose fruit virus. Moreover, many known viruses still cause significant economic damages to tomato production. The review of databases and literature revealed at least 312 virus, satellite virus, or viroid species (in 22 families and 39 genera) associated with tomato, which is likely the highest number recorded for any plant. Among those, here, we summarize the current knowledge on the biology, global distribution, and epidemiology of the most important species. Increasing knowledge on tomato virome and employment of HTS to also study viromes of surrounding wild plants and environmental samples are bringing new insights into the understanding of epidemiology and ecology of tomato-infecting viruses and can, in the future, facilitate virus disease forecasting and prevention of virus disease outbreaks in tomato.
Collapse
Affiliation(s)
- Mark Paul Selda Rivarez
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Ana Vučurović
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,Faculty of Agriculture, University of Belgrade, Belgrade, Serbia
| | - Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia.,School for Viticulture and Enology, University of Nova Gorica, Nova Gorica, Slovenia
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| |
Collapse
|