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Saad N, Olmstead JW, Varsani A, Polston JE, Jones JB, Folimonova SY, Harmon PF. Discovery of Known and Novel Viruses in Wild and Cultivated Blueberry in Florida through Viral Metagenomic Approaches. Viruses 2021; 13:1165. [PMID: 34207047 PMCID: PMC8234961 DOI: 10.3390/v13061165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 11/18/2022] Open
Abstract
Southern highbush blueberry (interspecific hybrids of Vaccinium corymbosum L.) is cultivated near wild V. corymbosum as well as closely related species in Florida, USA. The expansion of blueberry cultivation into new areas in Florida and deployment of new cultivars containing viruses can potentially increase the diversity of viruses in wild and cultivated V. corymbosum. In this study, viral diversity in wild and cultivated blueberries (V. corymbosum) is described using a metagenomic approach. RNA viromes from V. corymbosum plants collected from six locations (two cultivated and four wild) in North Central Florida were generated by high throughput sequencing (HTS) and analyzed using a bioinformatic analysis pipeline. De novo assembled contigs obtained from viromes of both commercial and wild sites produced sequences with similarities to plant virus species from a diverse range of families (Amalgaviridae, Caulimoviridae, Endornaviridae, Ophioviridae, Phenuiviridae, and Virgaviridae). In addition, this study has enabled the identification of blueberry latent virus (BlLV) and blueberry mosaic associated ophiovirus (BlMaV) for the first time in Florida, as well as a tentative novel tepovirus (blueberry virus T) (BlVT) in blueberry. To the best of our knowledge, this is the first study that compares viral diversity in wild and cultivated blueberry using a metagenomic approach.
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Affiliation(s)
- Norsazilawati Saad
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (J.E.P.); (J.B.J.); (S.Y.F.)
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, Serdang 43400, Malaysia
| | - James W. Olmstead
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA;
| | - Arvind Varsani
- The Biodesign Center of Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and Medicine, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA;
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Jane E. Polston
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (J.E.P.); (J.B.J.); (S.Y.F.)
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (J.E.P.); (J.B.J.); (S.Y.F.)
| | - Svetlana Y. Folimonova
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (J.E.P.); (J.B.J.); (S.Y.F.)
| | - Philip F. Harmon
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA; (J.E.P.); (J.B.J.); (S.Y.F.)
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Thekke-Veetil T, Ho T, Postman JD, Martin RR, Tzanetakis IE. A Virus in American Blackcurrant ( Ribes americanum) with Distinct Genome Features Reshapes Classification in the Tymovirales. Viruses 2018; 10:v10080406. [PMID: 30081487 PMCID: PMC6115964 DOI: 10.3390/v10080406] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 07/16/2018] [Accepted: 07/26/2018] [Indexed: 12/15/2022] Open
Abstract
A novel virus with distinct genome features was discovered by high throughput sequencing in a symptomatic blackcurrant plant. The virus, tentatively named Ribes americanum virus A (RAVA), has distinct genome organization and molecular features bridging genera in the order Tymovirales. The genome consists of 7106 nucleotides excluding the poly(A) tail. Five open reading frames were identified, with the first encoding a putative viral replicase with methyl transferase (MTR), AlkB, helicase, and RNA dependent RNA polymerase (RdRp) domains. The genome organization downstream of the replicase resembles that of members of the order Tymovirales with an unconventional triple gene block (TGB) movement protein arrangement with none of the other four putative proteins exhibiting significant homology to viral proteins. Phylogenetic analysis using replicase conserved motifs loosely placed RAVA within the Betaflexiviridae. Data strongly suggest that RAVA is a novel virus that should be classified as a species in a new genus in the Betaflexiviridae or a new family within the order Tymovirales.
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Affiliation(s)
- Thanuja Thekke-Veetil
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
| | - Thien Ho
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
| | - Joseph D Postman
- National Clonal Germplasm Repository, United States Department of Agriculture, Corvallis, OR 97333, USA.
| | - Robert R Martin
- Horticultural Crops Research Unit, United States Department of Agriculture, Corvallis, OR 97331, USA.
| | - Ioannis E Tzanetakis
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
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Rutvisuttinunt W, Klungthong C, Thaisomboonsuk B, Chinnawirotpisan P, Ajariyakhajorn C, Manasatienkij W, Phonpakobsin T, Lon C, Saunders D, Wangchuk S, Shrestha SK, Velasco JMS, Alera MTP, Simasathien S, Buddhari D, Jarman RG, Macareo LR, Yoon IK, Fernandez S. Retrospective use of next-generation sequencing reveals the presence of Enteroviruses in acute influenza-like illness respiratory samples collected in South/South-East Asia during 2010-2013. J Clin Virol 2017; 94:91-99. [PMID: 28779659 PMCID: PMC7106496 DOI: 10.1016/j.jcv.2017.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 06/29/2017] [Accepted: 07/08/2017] [Indexed: 01/15/2023]
Abstract
Next-generation Sequencing (NGS) was adopted in routine respiratory pathogen surveillance from South/South East (S/SE) Asia during 2010–2013. From 12,865 respiratory collections from ILI patients, 324 CPE-positive from 4,478 viral isolations were negative by standard assays. The CPE-positive samples were pooled, screened using NGS and validated the presence of the pathogens identified from NGS. Herpes simplex virus type 1, parainfluenza, adenovirus, coronavirus, human metapneumovirus, mumps virus and enterovirus genus were detected. NGS on pooled samples can be applied to surveillance work, identifying medically important viruses which may have missed by conventional methods.
Background Emerging and re-emerging respiratory pathogens represent an increasing threat to public health. Etiological determination during outbreaks generally relies on clinical information, occasionally accompanied by traditional laboratory molecular or serological testing. Often, this limited testing leads to inconclusive findings. The Armed Forces Research Institute of Medical Sciences (AFRIMS) collected 12,865 nasopharyngeal specimens from acute influenza-like illness (ILI) patients in five countries in South/South East Asia during 2010–2013. Three hundred and twenty-four samples which were found to be negative for influenza virus after screening with real-time RT-PCR and cell-based culture techniques demonstrated the potential for viral infection with evident cytopathic effect (CPE) in several cell lines. Objective To assess whether whole genome next-generation sequencing (WG-NGS) together with conventional molecular assays can be used to reveal the etiology of influenza negative, but CPE positive specimens. Study design The supernatant of these CPE positive cell cultures were grouped in 32 pools containing 2–26 supernatants per pool. Three WG-NGS runs were performed on these supernatant pools. Sequence reads were used to identify positive pools containing viral pathogens. Individual samples in the positive pools were confirmed by qRT-PCR, RT-PCR, PCR and Sanger sequencing from the CPE culture and original clinical specimens. Results WG-NGS was an effective way to expand pathogen identification in surveillance studies. This enabled the identification of a viral agent in 71.3% (231/324) of unidentified surveillance samples, including common respiratory pathogens (100/324; 30.9%): enterovirus (16/100; 16.0%), coxsackievirus (31/100; 31.0%), echovirus (22/100; 22.0%), human rhinovirus (3/100; 3%), enterovirus genus (2/100; 2.0%), influenza A (9/100; 9.0%), influenza B, (5/100; 5.0%), human parainfluenza (4/100; 4.0%), human adenovirus (3/100; 3.0%), human coronavirus (1/100; 1.0%), human metapneumovirus (2/100; 2.0%), and mumps virus (2/100; 2.0%), in addition to the non-respiratory pathogen herpes simplex virus type 1 (HSV-1) (172/324; 53.1%) and HSV-1 co-infection with respiratory viruses (41/324; 12.7%).
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Affiliation(s)
- Wiriya Rutvisuttinunt
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand; Walter Reed/AFRIMS Research Unit Nepal, Kathmandu, Nepal.
| | - Chonticha Klungthong
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Butsaya Thaisomboonsuk
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Piyawan Chinnawirotpisan
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Chuanpis Ajariyakhajorn
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Wudtichai Manasatienkij
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Thipwipha Phonpakobsin
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Chanthap Lon
- Department of Immunology and Medicine, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - David Saunders
- Department of Immunology and Medicine, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Sonam Wangchuk
- Royal Centre for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Sanjaya K Shrestha
- Walter Reed/AFRIMS Research Unit Nepal, Kathmandu, Nepal; Center for International Health, University of Bergen, Norway
| | - John Mark S Velasco
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Maria Theresa P Alera
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | | | - Darunee Buddhari
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Richard G Jarman
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Louis R Macareo
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - In-Kyu Yoon
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand
| | - Stefan Fernandez
- Department of Virology, Armed Forces Research Institute of Medical Sciences, 315/6, Rajavithi Road, Rajathewi, Bangkok, Thailand.
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Ho T, Quito-Avila D, Keller KE, Postman JD, Martin RR, Tzanetakis IE. Evidence of sympatric speciation of elderberry carlaviruses. Virus Res 2016; 215:72-5. [PMID: 26851177 DOI: 10.1016/j.virusres.2016.01.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/14/2016] [Accepted: 01/22/2016] [Indexed: 10/22/2022]
Abstract
Five new carlaviruses infecting elderberry were characterized and tentatively named as elderberry virus A-E (ElVA-ElVE). Their genome organization is similar to that of other carlaviruses with size ranging from 8540 to 8628 nucleotides, excluding the polyadenylated tails. ElVA, ElVB and ElVD share a common ancestor as do ElVC and ElVE, indicating that speciation may be sympatric with all viruses having emerged in elderberry. Analyses of the carlavirus conserved domains indicate that the 2-oxoglutarate and Fe(II)-dependent oxygenase motifs are reliable indicators of virus phylogenetic classification with recombination playing a significant role in the evolution of the genus. A universal RT-PCR assay that detects all the elderberry carlaviruses and potentially other members of the genus has been developed. This tool can be used for research and regulatory purposes as elderberry cultivation is rapidly expanding to new areas where the viruses may be absent.
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Affiliation(s)
- Thien Ho
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA
| | - Diego Quito-Avila
- Centro de Investigaciones Biotecnologicas del Ecuador (CIBE), Escuela Superior Politecnica del Litoral (ESPOL), Guayaquil, Guayas EC090150, Ecuador
| | | | - Joseph D Postman
- National Clonal Germplasm Repository, USDA-ARS, Corvallis, OR 97333, USA
| | | | - Ioannis E Tzanetakis
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville, AR 72701, USA.
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