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Davis RI, Jones LM, Pease B, Perkins SL, Vala HR, Kokoa P, Apa M, Dale CJ. Plant Virus and Virus-like Disease Threats to Australia's North Targeted by the Northern Australia Quarantine Strategy. PLANTS 2021; 10:plants10102175. [PMID: 34685987 PMCID: PMC8537380 DOI: 10.3390/plants10102175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 11/18/2022]
Abstract
The Northern Australia Quarantine Strategy (NAQS) is a biosecurity initiative operated by the Australian federal government’s Department of Agriculture, Water and the Environment (DAWE). It is unique worldwide because it deals specifically with the potential arrival via unregulated pathways of exotic threats from overseas in a vast and sparsely populated region. It aims to protect the nation’s animal- and plant-based production industries, as well as the environment, from incursions of organisms from countries that lie immediately to the north. These are diseases, pests, and weeds present in these countries that are currently either absent from, or under active containment in, Australia and may arrive by natural or human-assisted means. This review article focuses on the plant viruses and virus-like diseases that are most highly targeted by the NAQS program. It presents eight pathogen species/group entries in the NAQS A list of target pathogens, providing an overview of the historical and current situation, and collates some new data obtained from surveillance activities conducted in northern Australia and collaborative work overseas.
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Affiliation(s)
- Richard I. Davis
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
- Correspondence:
| | - Lynne M. Jones
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
| | - Bradley Pease
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
| | - Sandy L. Perkins
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
| | - Harshitsinh R. Vala
- Northern Australia Quarantine Strategy, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia; (L.M.J.); (B.P.); (S.L.P.); (H.R.V.)
| | - Pere Kokoa
- National Agriculture Quarantine and Inspection Authority (NAQIA), P.O. Box 741, Port Moresby 121, Papua New Guinea; (P.K.); (M.A.)
| | - Marilyn Apa
- National Agriculture Quarantine and Inspection Authority (NAQIA), P.O. Box 741, Port Moresby 121, Papua New Guinea; (P.K.); (M.A.)
| | - Christopher J. Dale
- International Plant Health Surveillance Program, Department of Agriculture Water and Environment, GPO Box 858, Canberra, ACT 2601, Australia;
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Gaafar YZA, Rabenstein F, Zia A, Gaafar ARZA, Ziebell H. Molecular characterisation of a new tenuivirus from Festuca sp. Virus Res 2021; 304:198509. [PMID: 34302922 DOI: 10.1016/j.virusres.2021.198509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/15/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
A novel virus with a quadruple genome of negative-sense, single-stranded RNA was identified by high-throughput sequencing (HTS) in a grass sample from Saxony-Anhalt, Germany, and tentatively called Festuca stripe-associated virus (FSaV). The genome of FSaV consists of four segments and a total of 16,535 nucleotides (nt) which encode seven open reading frames (ORF). FSaV shares highest nt identity (between 72.84% to 80.74%) to Iranian wheat stripe virus (IWSV) and rice hoja blanca virus (RHBV). Additionally, pairwise comparisons between the amino acid sequences of the ORFs on the genome of FSaV and the corresponding ones on the genomes of the members of the Tenuvirus genus showed that FSaV shared 83.17% and 90.85% (amino acid) aa identity to IWSV. Moreover, the non-coding intergenic regions (ncIR) shared only between 49.5% to 60.87% nt identity to the corresponding regions on the IWSV genome. Based on the ICTV species demarcation, the results suggest that FSaV may represent a new species of the genus Tenuivirus. Plastid sequence analysis of the HTS data showed that the original host is a member of the genus Festuca most likely the species Festuca pratensis.
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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, Braunschweig, Lower Saxony, Germany
| | - Frank Rabenstein
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Quedlinburg, Saxony-Anhalt, Germany
| | - Amjad Zia
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony, Germany
| | - Abdel-Rhman Z A Gaafar
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) - Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony, Germany.
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Bejerman N, Debat H, Dietzgen RG. The Plant Negative-Sense RNA Virosphere: Virus Discovery Through New Eyes. Front Microbiol 2020; 11:588427. [PMID: 33042103 PMCID: PMC7524893 DOI: 10.3389/fmicb.2020.588427] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
The use of high-throughput sequencing (HTS) for virus diagnostics, as well as the importance of this technology as a valuable tool for discovery of novel viruses has been extensively investigated. In this review, we consider the application of HTS approaches to uncover novel plant viruses with a focus on the negative-sense, single-stranded RNA virosphere. Plant viruses with negative-sense and ambisense RNA (NSR) genomes belong to several taxonomic families, including Rhabdoviridae, Aspiviridae, Fimoviridae, Tospoviridae, and Phenuiviridae. They include both emergent pathogens that infect a wide range of plant species, and potential endophytes which appear not to induce any visible symptoms. As a consequence of biased sampling based on a narrow focus on crops with disease symptoms, the number of NSR plant viruses identified so far represents only a fraction of this type of viruses present in the virosphere. Detection and molecular characterization of NSR viruses has often been challenging, but the widespread implementation of HTS has facilitated not only the identification but also the characterization of the genomic sequences of at least 70 NSR plant viruses in the last 7 years. Moreover, continuing advances in HTS technologies and bioinformatic pipelines, concomitant with a significant cost reduction has led to its use as a routine method of choice, supporting the foundations of a diverse array of novel applications such as quarantine analysis of traded plant materials and genetic resources, virus detection in insect vectors, analysis of virus communities in individual plants, and assessment of virus evolution through ecogenomics, among others. The insights from these advancements are shedding new light on the extensive diversity of NSR plant viruses and their complex evolution, and provide an essential framework for improved taxonomic classification of plant NSR viruses as part of the realm Riboviria. Thus, HTS-based methods for virus discovery, our ‘new eyes,’ are unraveling in real time the richness and magnitude of the plant RNA virosphere.
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Affiliation(s)
- Nicolás Bejerman
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
| | - Humberto Debat
- Instituto de Patología Vegetal - Centro de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria, Córdoba, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas, Unidad de Fitopatología y Modelización Agrícola, Buenos Aires, Argentina
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
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Braithwaite KS, Tom L, Kuniata LS. Planthopper Transmission of Ramu Stunt Virus, a Tenuivirus Causing the Sugarcane Disease Ramu Stunt, and its Distribution in Papua New Guinea. PLANT DISEASE 2019; 103:2527-2535. [PMID: 31432775 DOI: 10.1094/pdis-01-19-0058-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ramu stunt is a serious disease of sugarcane, currently only reported from Papua New Guinea. It is found in both commercial sugarcane grown on the Ramu Agri Industries Limited (RAIL) estate and in chewing canes (Saccharum officinarum L.) grown in village gardens. The vector of Ramu stunt disease is the island sugarcane planthopper, Eumetopina flavipes Muir. Here we report on the successful transmission of Ramu stunt using E. flavipes and verify that the disease is caused by Ramu stunt virus, a virus with homology to the genus Tenuivirus. Diagnostic reverse transcription PCR screening, with partial genome sequencing and viral protein characterization, was used for confirmation. Disease surveys were undertaken on the RAIL estate, along roadsides, and in village gardens in parts of Papua New Guinea. When the disease was identified, partial genome sequencing of the virus was performed to assess the extent of genome variability among isolates. The disease was less common than predicted from early surveys based on symptoms alone, and genotypic variation was associated with geographic location.
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Affiliation(s)
| | - Leka Tom
- Ramu Agri Industries Limited, Lae, Morobe Province, Papua New Guinea
| | - Lastus S Kuniata
- Ramu Agri Industries Limited, Lae, Morobe Province, Papua New Guinea
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Gaafar YZA, Richert-Pöggeler KR, Sieg-Müller A, Lüddecke P, Herz K, Hartrick J, Seide Y, Vetten HJ, Ziebell H. A divergent strain of melon chlorotic spot virus isolated from black medic (Medicago lupulina) in Austria. Virol J 2019; 16:89. [PMID: 31277670 PMCID: PMC6612211 DOI: 10.1186/s12985-019-1195-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 06/24/2019] [Indexed: 02/08/2023] Open
Abstract
A tenuivirus, referred to here as JKI 29327, was isolated from a black medic (Medicago lupulina) plant collected in Austria. The virus was mechanically transmitted to Nicotiana benthamiana, M. lupulina, M. sativa, Pisum sativum and Vicia faba. The complete genome was determined by high throughput sequencing. The genome of JKI 29327 consists of eight RNA segments closely related to those of melon chlorotic spot virus (MeCSV) isolate E11-018 from France. Since segments RNA 7 and 8 of JKI 29327 are shorter, its genome is slightly smaller (by 247 nts) than that of E11-018. Pairwise comparisons between the predicted virus proteins of JKI 29327 and their homologues in E11-018 showed aa identities ranging from 80.6 to 97.2%. Plants infected with E11-081 gave intermediate DAS-ELISA reactions with polyclonal antibodies to JKI 29327. Since JKI 29327 and E11-018 appear to be closely related both serologically and genetically, we propose to regard JKI 29327 as the black medic strain of MeCSV. To our knowledge, JKI 29327 represents the second tenuivirus identified from a dicotyledonous plant. Serological and molecular diagnostic methods were developed for future detection.
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Affiliation(s)
- Yahya Z. A. Gaafar
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Katja R. Richert-Pöggeler
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Angelika Sieg-Müller
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Petra Lüddecke
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Kerstin Herz
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Jonas Hartrick
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | - Yvonne Seide
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
| | | | - Heiko Ziebell
- Julius Kühn Institute, Institute for Epidemiology and Pathogen Diagnostics, Messeweg 11-12, 38104 Braunschweig, Germany
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Knierim D, Menzel W, Winter S. Immunocapture of virions with virus-specific antibodies prior to high-throughput sequencing effectively enriches for virus-specific sequences. PLoS One 2019; 14:e0216713. [PMID: 31071169 PMCID: PMC6542260 DOI: 10.1371/journal.pone.0216713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/26/2019] [Indexed: 12/21/2022] Open
Abstract
Virus discovery based on high-throughput sequencing relies on enrichment for virus sequences prior to library preparation to achieve a sufficient number of viral reads. In general, preparations of double-stranded RNA or total RNA preparations treated to remove rRNA are used for sequence enrichment. We used virus-specific antibodies to immunocapture virions from plant sap to conduct cDNA synthesis, followed by library preparation and HTS. For the four potato viruses PLRV, PVY, PVA and PYV, template preparation by virion immunocapture provided a simpler and less expensive method than the enrichment of total RNA by ribosomal depletion. Specific enrichment of viral sequences without an intermediate amplification step was achieved, and this high coverage of sequences across the viral genomes was important to identify rare sequence variations. Using this approach, the first complete genome sequence of a potato yellowing virus isolate (PYV, DSMZ PV-0706) was determined in this study. PYV can be confidently assigned as a distinct species in the genus Ilarvirus.
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Affiliation(s)
- Dennis Knierim
- Leibniz-Institute DSMZ—German Collection of Microorganisms
and Cell Cultures, Plant Virus Department, Braunschweig,
Germany
| | - Wulf Menzel
- Leibniz-Institute DSMZ—German Collection of Microorganisms
and Cell Cultures, Plant Virus Department, Braunschweig,
Germany
- * E-mail:
| | - Stephan Winter
- Leibniz-Institute DSMZ—German Collection of Microorganisms
and Cell Cultures, Plant Virus Department, Braunschweig,
Germany
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Lecoq H, Wipf-Scheibel C, Verdin E, Desbiez C. Characterization of the first tenuivirus naturally infecting dicotyledonous plants. Arch Virol 2018; 164:297-301. [DOI: 10.1007/s00705-018-4057-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 09/18/2018] [Indexed: 02/04/2023]
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Bratsch S, Lockhart B, Mollov D. Characterization of a New Nepovirus Causing a Leaf Mottling Disease in Petunia hybrida. PLANT DISEASE 2017; 101:1017-1021. [PMID: 30682926 DOI: 10.1094/pdis-12-16-1785-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Icosahedral virus-like particles were isolated from Petunia hybrida cuttings with interveinal chlorotic mottling. The virus was transmitted by mechanical inoculation from infected to healthy P. hybrida, and was found to contain a bipartite RNA genome of 7.6 and 3.8 kilobases. Full genomic sequence was obtained by high-throughput sequencing combined with RACE amplification of the 5'-termini of RNAs 1 and 2, and reverse-transcription PCR amplification of the 3'-termini with oligo-dT and sequence specific primers. Based on particle morphology, genome organization, and phylogenetic analyses, it was concluded that the new virus is a member of the genus Nepovirus, subgroup A. This new virus causing a leaf mottling disease of petunia was provisionally named Petunia chlorotic mottle virus (PCMoV).
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Affiliation(s)
- Sara Bratsch
- Department of Plant Pathology, University of Minnesota, St. Paul, MN
| | - Benham Lockhart
- Department of Plant Pathology, University of Minnesota, St. Paul, MN
| | - Dimitre Mollov
- USDA-ARS, National Germplasm Resources Laboratory, Beltsville, MD
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