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Lelwala RV, LeBlanc Z, Gauthier MEA, Elliott CE, Constable FE, Murphy G, Tyle C, Dinsdale A, Whattam M, Pattemore J, Barrero RA. Implementation of GA-VirReport, a Web-Based Bioinformatics Toolkit for Post-Entry Quarantine Screening of Virus and Viroids in Plants. Viruses 2022; 14:v14071480. [PMID: 35891459 PMCID: PMC9317486 DOI: 10.3390/v14071480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 02/01/2023] Open
Abstract
High-throughput sequencing (HTS) of host plant small RNA (sRNA) is a popular approach for plant virus and viroid detection. The major bottlenecks for implementing this approach in routine virus screening of plants in quarantine include lack of computational resources and/or expertise in command-line environments and limited availability of curated plant virus and viroid databases. We developed: (1) virus and viroid report web-based bioinformatics workflows on Galaxy Australia called GA-VirReport and GA-VirReport-Stats for detecting viruses and viroids from host plant sRNA extracts and (2) a curated higher plant virus and viroid database (PVirDB). We implemented sRNA sequencing with unique dual indexing on a set of plants with known viruses. Sequencing data were analyzed using GA-VirReport and PVirDB to validate these resources. We detected all known viruses in this pilot study with no cross-sample contamination. We then conducted a large-scale diagnosis of 105 imported plants processed at the post-entry quarantine facility (PEQ), Australia. We detected various pathogens in 14 imported plants and discovered that de novo assembly using 21–22 nt sRNA fraction and the megablast algorithm yielded better sensitivity and specificity. This study reports the successful, large-scale implementation of HTS and a user-friendly bioinformatics workflow for virus and viroid screening of imported plants at the PEQ.
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Affiliation(s)
- Ruvini V. Lelwala
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Zacharie LeBlanc
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
| | - Marie-Emilie A. Gauthier
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
| | - Candace E. Elliott
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Fiona E. Constable
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia;
| | - Greg Murphy
- Technology Infrastructure Branch, Information Services Division, Department of Agriculture, Fisheries and Forestry, Canberra, ACT 2601, Australia; (G.M.); (C.T.)
| | - Callum Tyle
- Technology Infrastructure Branch, Information Services Division, Department of Agriculture, Fisheries and Forestry, Canberra, ACT 2601, Australia; (G.M.); (C.T.)
| | - Adrian Dinsdale
- Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (A.D.); (M.W.)
| | - Mark Whattam
- Plant Innovation Centre, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (A.D.); (M.W.)
| | - Julie Pattemore
- Science and Surveillance Group, Post Entry Quarantine, Department of Agriculture, Fisheries and Forestry, Mickleham, VIC 3064, Australia; (C.E.E.); (J.P.)
| | - Roberto A. Barrero
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane, QLD 4001, Australia; (R.V.L.); (Z.L.); (M.-E.A.G.)
- Correspondence:
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Gaafar YZA, Westenberg M, Botermans M, László K, De Jonghe K, Foucart Y, Ferretti L, Kutnjak D, Pecman A, Mehle N, Kreuze J, Muller G, Vakirlis N, Beris D, Varveri C, Ziebell H. Interlaboratory Comparison Study on Ribodepleted Total RNA High-Throughput Sequencing for Plant Virus Diagnostics and Bioinformatic Competence. Pathogens 2021; 10:pathogens10091174. [PMID: 34578206 PMCID: PMC8469820 DOI: 10.3390/pathogens10091174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
High-throughput sequencing (HTS) technologies and bioinformatic analyses are of growing interest to be used as a routine diagnostic tool in the field of plant viruses. The reliability of HTS workflows from sample preparation to data analysis and results interpretation for plant virus detection and identification must be evaluated (verified and validated) to approve this tool for diagnostics. Many different extraction methods, library preparation protocols, and sequence and bioinformatic pipelines are available for virus sequence detection. To assess the performance of plant virology diagnostic laboratories in using the HTS of ribosomal RNA depleted total RNA (ribodepleted totRNA) as a diagnostic tool, we carried out an interlaboratory comparison study in which eight participants were required to use the same samples, (RNA) extraction kit, ribosomal RNA depletion kit, and commercial sequencing provider, but also their own bioinformatics pipeline, for analysis. The accuracy of virus detection ranged from 65% to 100%. The false-positive detection rate was very low and was related to the misinterpretation of results as well as to possible cross-contaminations in the lab or sequencing provider. The bioinformatic pipeline used by each laboratory influenced the correct detection of the viruses of this study. The main difficulty was the detection of a novel virus as its sequence was not available in a publicly accessible database at the time. The raw data were reanalysed using Virtool to assess its ability for virus detection. All virus sequences were detected using Virtool in the different pools. This study revealed that the ribodepletion target enrichment for sample preparation is a reliable approach for the detection of plant viruses with different genomes. A significant level of virology expertise is needed to correctly interpret the results. It is also important to improve and complete the reference data.
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Affiliation(s)
- Yahya Z. A. Gaafar
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Messeweg 11/12, 38104 Braunschweig, Germany;
| | - Marcel Westenberg
- National Reference Centre of Plant Health, Dutch National Plant Protection Organization, Geertjesweg 15, 6706 EA Wageningen, The Netherlands; (M.W.); (M.B.)
| | - Marleen Botermans
- National Reference Centre of Plant Health, Dutch National Plant Protection Organization, Geertjesweg 15, 6706 EA Wageningen, The Netherlands; (M.W.); (M.B.)
| | - Krizbai László
- Plant Health Diagnostics National Reference Laboratory, Directorate of Food Chain Safety Laboratory, National Food Chain Safety Office, Budaörsi út 141–145, H-1118 Budapest, Hungary;
| | - Kris De Jonghe
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Burgemeester Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (Y.F.)
| | - Yoika Foucart
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Burgemeester Van Gansberghelaan 96, 9820 Merelbeke, Belgium; (K.D.J.); (Y.F.)
| | - Luca Ferretti
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, Via C.G. Bertero 22, 00156 Rome, Italy;
| | - Denis Kutnjak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia; (D.K.); (A.P.); (N.M.)
| | - Anja Pecman
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia; (D.K.); (A.P.); (N.M.)
- Jožef Stefan International Postgraduate School, SI-1000 Ljubljana, Slovenia
| | - Nataša Mehle
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia; (D.K.); (A.P.); (N.M.)
| | - Jan Kreuze
- Health and Quarantine Unit, International Potato Center (CIP), Av. La Molina 1895 La Molina, Lima 15023, Peru; (J.K.); (G.M.)
| | - Giovanna Muller
- Health and Quarantine Unit, International Potato Center (CIP), Av. La Molina 1895 La Molina, Lima 15023, Peru; (J.K.); (G.M.)
| | - Nikolaos Vakirlis
- Benaki Phytopathological Institute, Stefanou Delta 8, Kifissia, Attica, 14561 Athens, Greece; (N.V.); (D.B.); (C.V.)
| | - Despoina Beris
- Benaki Phytopathological Institute, Stefanou Delta 8, Kifissia, Attica, 14561 Athens, Greece; (N.V.); (D.B.); (C.V.)
| | - Christina Varveri
- Benaki Phytopathological Institute, Stefanou Delta 8, Kifissia, Attica, 14561 Athens, Greece; (N.V.); (D.B.); (C.V.)
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI)–Federal Research Centre for Cultivated Plants, Messeweg 11/12, 38104 Braunschweig, Germany;
- Correspondence:
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