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Silva JMF, Melo FL, Elena SF, Candresse T, Sabanadzovic S, Tzanetakis IE, Blouin AG, Villamor DEV, Mollov D, Constable F, Cao M, Saldarelli P, Cho WK, Nagata T. Virus classification based on in-depth sequence analyses and development of demarcation criteria using the Betaflexiviridae as a case study. J Gen Virol 2022; 103. [DOI: 10.1099/jgv.0.001806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Currently, many viruses are classified based on their genome organization and nucleotide/amino acid sequence identities of their capsid and replication-associated proteins. Although biological traits such as vector specificities and host range are also considered, this later information is scarce for the majority of recently identified viruses, characterized only from genomic sequences. Accordingly, genomic sequences and derived information are being frequently used as the major, if not only, criteria for virus classification and this calls for a full review of the process. Herein, we critically addressed current issues concerning classification of viruses in the family Betaflexiviridae in the era of high-throughput sequencing and propose an updated set of demarcation criteria based on a process involving pairwise identity analyses and phylogenetics. The proposed framework has been designed to solve the majority of current conundrums in taxonomy and to facilitate future virus classification. Finally, the analyses performed herein, alongside the proposed approaches, could be used as a blueprint for virus classification at-large.
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Affiliation(s)
- João Marcos Fagundes Silva
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, University of Brasília, Brasília 70910-900, Brazil
| | - Fernando Lucas Melo
- Departamento de Fitopatologia, Instituto de Biología Integrativa de Sistemas, University of Brasília, Brasília 70910-900, Brazil
| | - Santiago F. Elena
- The Santa Fe Institute, Santa Fe, NM 87501, USA
- Instituto de Biología Integrativa de Sistemas (I2 13 SysBio), CSIC-Universitat de València, Paterna 14 46980 València, Spain
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 BFP, 33140 Villenave d’Ornon, France
| | - Sead Sabanadzovic
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS 39762, USA
| | | | - Arnaud G. Blouin
- Virology-Phytoplasmology Laboratory, Agroscope, 1260 Nyon, Switzerland
| | | | - Dimitre Mollov
- USDA-ARS Horticultural Crops Disease and Pest Management Research Unit, Corvallis, OR, 97330, USA
| | - Fiona Constable
- Department of Jobs Precincts and Regions, Agriculture Victoria Research, Agribio, Bundoora, VIC 3083, Australia
| | - Mengji Cao
- National Citrus Engineering and Technology Research Center, Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, PR China
| | - Pasquale Saldarelli
- National Research Council of Italy (CNR), Institute for Sustainable Plant Protection (IPSP), Via Amendola 122/D, 70126 Bari, Italy
| | - Won Kyong Cho
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Seoburo 2066, Suwon 16419, Gyeonggi, Republic of Korea
| | - Tatsuya Nagata
- Departamento de Biologia Celular, Instituto de Ciências Biológicas, University of Brasília, Brasília 70910-900, Brazil
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Villamor DEV, Pillai SS, Eastwell KC. Systemic infection and symptom development of agro-inoculated cDNA clone of cherry rusty mottle-associated virus in sweet cherry (Prunus avium). Virus Res 2021; 296:198330. [PMID: 33556414 DOI: 10.1016/j.virusres.2021.198330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/16/2021] [Accepted: 01/24/2021] [Indexed: 01/25/2023]
Abstract
Cherry rusty mottle-associated virus (CRMaV), which belongs the genus Robigovirus of the family Betaflexiviridae, is strongly associated with cherry rusty mottle disease of sweet cherry, Prunus avium. Here, we report on the successful development of an Agrobacterium-based inoculation system for a cloned CRMaV cDNA construct. Agro-inoculation of virus-free cherry rootstock 'Krymsk6' [P. cerasus x (P. cerasus x P. maackii)] resulted in the development of chlorotic yellow mottle symptoms on systemic leaves beginning at 50 days post inoculation. The presence of CRMaV in 'Krymsk6' agro-inoculated plants was confirmed by RT-PCR and ELISA. Subsequently, CRMaV from agro-inoculated 'Krymsk6' was graft-transmissible onto virus-free sweet cherry rootstock P. avium 'Mazzard' as evidenced by the production of typical cherry rusty mottle symptoms beginning at 35 days post grafting, and further confirmed by western blotting and RT-PCR. These results showed conclusively that CRMaV is the causal agent of cherry rusty mottle disease in sweet cherry. The reverse genetic system presented in this study can be used as a tool to investigate the molecular biology of CRMaV and also a template for infectious clone development for other viruses in the genus Robigovirus.
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Affiliation(s)
- D E V Villamor
- Washington State University, Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Prosser, WA, 99350, United States.
| | - S S Pillai
- Washington State University, Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Prosser, WA, 99350, United States
| | - K C Eastwell
- Washington State University, Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Prosser, WA, 99350, United States
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Bragard C, Dehnen-Schmutz K, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, Van der Werf W, Vicent Civera A, Yuen J, Zappalà L, Candresse T, Chatzivassiliou E, Finelli F, Winter S, Bosco D, Chiumenti M, Di Serio F, Kaluski T, Minafra A, Rubino L. Pest categorisation of non-EU viruses and viroids of Prunus L. EFSA J 2019; 17:e05735. [PMID: 32626421 PMCID: PMC7009144 DOI: 10.2903/j.efsa.2019.5735] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Following a request from the EU Commission, the Panel on Plant Health addressed the pest categorisation of the viruses and viroids of Prunus L. determined as being either non‐EU or of undetermined standing in a previous EFSA opinion. These infectious agents belong to different genera and are heterogeneous in their biology. With the exclusion of Ilarvirus S1 and Ilarvirus S2, for which very limited information exists, the pest categorisation was completed for 26 viruses and 1 viroid having acknowledged identities and available detection methods. All these viruses are efficiently transmitted by vegetative plant propagation techniques, with plants for planting representing the major pathway for long‐distance dispersal and thus considered as the major pathway for entry. Depending on the virus, additional pathway(s) can also be Prunus seeds, pollen and/or vector(s). Most of the viruses categorised here are known to infect only one or few plant genera, but some of them have a wide host range, thus extending the possible entry pathways. Apple scar skin viroid, American plum line pattern virus, cherry mottle leaf virus, cherry rasp leaf virus, cherry rosette virus, cherry rusty mottle‐associated virus, cherry twisted leaf‐associated virus, peach enation virus, peach mosaic virus, peach rosette mosaic virus, tobacco ringspot virus and tomato ringspot virus meet all the criteria evaluated by EFSA to qualify as potential Union quarantine pests (QPs). With the exception of impact in the EU territory, on which the Panel was unable to conclude, apricot vein clearing virus, Asian prunus virus 1, Asian prunus virus 2, Asian prunus virus 3, Caucasus prunus virus, cherry virus B, Mume virus A, nectarine stem pitting‐associated virus, nectarine virus M, peach chlorotic mottle virus, peach leaf pitting‐associated virus, peach virus D, prunus virus F and prunus virus T satisfy all the other criteria to be considered as potential Union QPs. Prunus geminivirus A does not meet the criterion of having negative impact in the EU. For several viruses, especially those recently discovered, the categorisation is associated with high uncertainties mainly because of the absence of data on their biology, distribution and impact. Since this opinion addresses specifically the non‐EU viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non‐quarantine pests. This publication is linked to the following EFSA Journal articles: http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2019.5501/full, http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2019.5590/full, http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2019.5669/full, http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2019.5766/full
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Çağlayan K, Roumi V, Gazel M, Elçi E, Acioğlu M, Mavric Plesko I, Reynard JS, Maclot F, Massart S. Identification and Characterization of a Novel Robigovirus Species from Sweet Cherry in Turkey. Pathogens 2019; 8:pathogens8020057. [PMID: 31035571 PMCID: PMC6631170 DOI: 10.3390/pathogens8020057] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 04/09/2019] [Accepted: 04/16/2019] [Indexed: 11/16/2022] Open
Abstract
High throughput sequencing of total RNA isolated from symptomatic leaves of a sweet cherry tree (Prunus avium cv. 0900 Ziraat) from Turkey identified a new member of the genus Robigovirus designated cherry virus Turkey (CVTR). The presence of the virus was confirmed by electron microscopy and overlapping RT-PCR for sequencing its whole-genome. The virus has a ssRNA genome of 8464 nucleotides which encodes five open reading frames (ORFs) and comprises two non-coding regions, 5' UTR and 3' UTR of 97 and 296 nt, respectively. Compared to the five most closely related robigoviruses, RdRp, TGB1, TGB2, TGB3 and CP share amino acid identities ranging from 43-53%, 44-60%, 39-43%, 38-44% and 45-50%, respectively. Unlike the four cherry robigoviruses, CVTR lacks ORFs 2a and 5a. Its genome organization is therefore more similar to African oil palm ringspot virus (AOPRV). Using specific primers, the presence of CVTR was confirmed in 15 sweet cherries and two sour cherries out of 156 tested samples collected from three regions in Turkey. Among them, five samples were showing slight chlorotic symptoms on the leaves. It seems that CVTR infects cherry trees with or without eliciting obvious symptoms, but these data should be confirmed by bioassays in woody and possible herbaceous hosts in future studies.
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Affiliation(s)
- Kadriye Çağlayan
- Plant Protection Department, Agriculture Faculty, Mustafa Kemal University, 31034 Hatay, Turkey.
| | - Vahid Roumi
- Plant Protection Department, Faculty of Agriculture, University of Maragheh, 55181 Maragheh, Iran.
| | - Mona Gazel
- Plant Protection Department, Agriculture Faculty, Mustafa Kemal University, 31034 Hatay, Turkey.
| | - Eminur Elçi
- Plant Production and Technologies Department, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, 51240 Nigde, Turkey.
| | - Mehtap Acioğlu
- Plant Protection Department, Agriculture Faculty, Mustafa Kemal University, 31034 Hatay, Turkey.
| | - Irena Mavric Plesko
- Agricultural Institute of Slovenia, Hacquetova 17, SI- 1000 Ljubljana, Slovenia.
| | | | - Francois Maclot
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liege, Passage des Deportes, 2, 5030 Gembloux, Belgium.
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA-Gembloux Agro-Bio Tech, University of Liege, Passage des Deportes, 2, 5030 Gembloux, Belgium.
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Maliogka VI, Minafra A, Saldarelli P, Ruiz-García AB, Glasa M, Katis N, Olmos A. Recent Advances on Detection and Characterization of Fruit Tree Viruses Using High-Throughput Sequencing Technologies. Viruses 2018; 10:E436. [PMID: 30126105 PMCID: PMC6116224 DOI: 10.3390/v10080436] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 12/21/2022] Open
Abstract
Perennial crops, such as fruit trees, are infected by many viruses, which are transmitted through vegetative propagation and grafting of infected plant material. Some of these pathogens cause severe crop losses and often reduce the productive life of the orchards. Detection and characterization of these agents in fruit trees is challenging, however, during the last years, the wide application of high-throughput sequencing (HTS) technologies has significantly facilitated this task. In this review, we present recent advances in the discovery, detection, and characterization of fruit tree viruses and virus-like agents accomplished by HTS approaches. A high number of new viruses have been described in the last 5 years, some of them exhibiting novel genomic features that have led to the proposal of the creation of new genera, and the revision of the current virus taxonomy status. Interestingly, several of the newly identified viruses belong to virus genera previously unknown to infect fruit tree species (e.g., Fabavirus, Luteovirus) a fact that challenges our perspective of plant viruses in general. Finally, applied methodologies, including the use of different molecules as templates, as well as advantages and disadvantages and future directions of HTS in fruit tree virology are discussed.
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Affiliation(s)
- Varvara I Maliogka
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Angelantonio Minafra
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy.
| | - Pasquale Saldarelli
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Via G. Amendola 122/D, 70126 Bari, Italy.
| | - Ana B Ruiz-García
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain.
| | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava, Slovak Republic.
| | - Nikolaos Katis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Antonio Olmos
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Ctra. Moncada-Náquera km 4.5, 46113 Moncada, Valencia, Spain.
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Molecular Characterization of a Novel Species of Capillovirus from Japanese Apricot (Prunus mume). Viruses 2018; 10:v10040144. [PMID: 29570605 PMCID: PMC5923438 DOI: 10.3390/v10040144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/17/2018] [Accepted: 03/21/2018] [Indexed: 11/17/2022] Open
Abstract
With the increased use of high-throughput sequencing methods, new viruses infecting Prunus spp. are being discovered and characterized, especially in the family Betaflexiviridae. Double-stranded RNAs from symptomatic leaves of a Japanese apricot (Prunusmume) tree from Japan were purified and analyzed by Illumina sequencing. Blast comparisons of reconstructed contigs showed that the P. mume sample was infected by a putative novel virus with homologies to Cherry virus A (CVA) and to the newly described Currant virus A (CuVA), both members of genus Capillovirus. Completion of the genome showed the new agent to have a genomic organization typical of capilloviruses, with two overlapping open reading frames encoding a large replication-associated protein fused to the coat protein (CP), and a putative movement protein (MP). This virus shares only, respectively, 63.2% and 62.7% CP amino acid identity with the most closely related viruses, CVA and CuVA. Considering the species demarcation criteria in the family and phylogenetic analyses, this virus should be considered as representing a new viral species in the genus Capillovirus, for which the name of Mume virus A is proposed.
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Rott M, Xiang Y, Boyes I, Belton M, Saeed H, Kesanakurti P, Hayes S, Lawrence T, Birch C, Bhagwat B, Rast H. Application of Next Generation Sequencing for Diagnostic Testing of Tree Fruit Viruses and Viroids. PLANT DISEASE 2017; 101:1489-1499. [PMID: 30678581 DOI: 10.1094/pdis-03-17-0306-re] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Conventional detection of viruses and virus-like diseases of plants is accomplished using a combination of molecular, serological, and biological indexing. These are the primary tools used by plant virologists to monitor and ensure trees are free of known viral pathogens. The biological indexing assay, or bioassay, is considered to be the "gold standard" as it is the only method of the three that can detect new, uncharacterized, or poorly characterized viral disease agents. Unfortunately, this method is also the most labor intensive and can take up to three years to complete. Next generation sequencing (NGS) is a technology with rapidly expanding possibilities including potential applications for the detection of plant viruses. In this study, comparisons are made between tree fruit testing by conventional and NGS methods, to demonstrate the efficacy of NGS. A comparison of 178 infected trees, many infected with several viral pathogens, demonstrated that conventional and NGS were equally capable of detecting known viruses and viroids. Comparable results were obtained for 170 of 178 of the specimens. Of the remaining eight specimens, some discrepancies were observed between viruses detected by the two methods, representing less than 5% of the specimens. NGS was further demonstrated to be equal or superior for the detection of new or poorly characterized viruses when compared with a conventional bioassay. These results validated both the effectiveness of conventional virus testing methods and the use of NGS as an additional or alternative method for plant virus detection.
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Affiliation(s)
- M Rott
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - Y Xiang
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, V0H1Z0, Canada
| | - I Boyes
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - M Belton
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - H Saeed
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - P Kesanakurti
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - S Hayes
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - T Lawrence
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - C Birch
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
| | - B Bhagwat
- Summerland Research and Development Centre, Agriculture and Agri-Food Canada, Summerland, BC, V0H1Z0, Canada
| | - H Rast
- Centre for Plant Health, Sidney Laboratory, Canadian Food Inspection Agency, North Saanich, BC, V8L 1H3, Canada
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Villamor DEV, Pillai SS, Eastwell KC. High throughput sequencing reveals a novel fabavirus infecting sweet cherry. Arch Virol 2016; 162:811-816. [PMID: 27815695 DOI: 10.1007/s00705-016-3141-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 10/30/2016] [Indexed: 11/30/2022]
Abstract
The genus Fabavirus currently consists of five species represented by viruses that infect a wide range of hosts but none reported from temperate climate fruit trees. A virus with genomic features resembling fabaviruses (tentatively named Prunus virus F, PrVF) was revealed by high throughput sequencing of extracts from a sweet cherry tree (Prunus avium). PrVF was subsequently shown to be graft transmissible and further identified in three other non-symptomatic Prunus spp. from different geographical locations. Two genetic variants of RNA1 and RNA2 coexisted in the same samples. RNA1 consisted of 6,165 and 6,163 nucleotides, and RNA2 consisted of 3,622 and 3,468 nucleotides.
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Affiliation(s)
- D E V Villamor
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, 99350, USA.
| | - S S Pillai
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, 99350, USA
| | - K C Eastwell
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, 99350, USA
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Villamor DEV, Mekuria TA, Pillai SS, Eastwell KC. High-Throughput Sequencing Identifies Novel Viruses in Nectarine: Insights to the Etiology of Stem-Pitting Disease. PHYTOPATHOLOGY 2016; 106:519-527. [PMID: 26780433 DOI: 10.1094/phyto-07-15-0168-r] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recent studies have shown the superiority of high-throughput sequencing (HTS) technology over many standard protocols for pathogen detection. HTS was initiated on fruit tree accessions from disparate sources to improve and advance virus-testing procedures. A virus with genomic features resembling most closely that of the recently described Nectarine stem-pitting-associated virus, putative member of genus Luteovirus, was found in three nectarine trees (Prunus persica cv. nectarina), each exhibiting stem-pitting symptoms on the woody cylinder above the graft union. In these samples, HTS also revealed the presence of a coinfecting virus with genome characteristics typical of members of the genus Marafivirus. The same marafivirus- and luteovirus-like viruses were detected in nonsymptomatic nectarine and peach selections, indicating only a loose relationship between these two viruses with nectarine stem-pitting disease symptoms. Two selections infected with each of these viruses had previously tested free of known virus or virus-like agents using the current biological, serological, and molecular tests employed at the Clean Plant Center Northwest. Overall, this study presents the characterization by HTS of novel marafivirus- and luteovirus-like viruses of nectarine, and provides further insights into the etiology of nectarine stem-pitting disease. The discovery of these new viruses emphasizes the ability of HTS to reveal viruses that are not detected by existing protocols.
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Affiliation(s)
- D E V Villamor
- Department of Plant Pathology, Washington State University-Irrigated Agriculture Research and Extension Center, Prosser 99350
| | - T A Mekuria
- Department of Plant Pathology, Washington State University-Irrigated Agriculture Research and Extension Center, Prosser 99350
| | - S S Pillai
- Department of Plant Pathology, Washington State University-Irrigated Agriculture Research and Extension Center, Prosser 99350
| | - K C Eastwell
- Department of Plant Pathology, Washington State University-Irrigated Agriculture Research and Extension Center, Prosser 99350
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