1
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Hodgetts J, Glover R, Cole J, Hall J, Boonham N. Genomics informed design of a suite of real-time PCR assays for the specific detection of each Xylella fastidiosa subspecies. J Appl Microbiol 2021; 131:855-872. [PMID: 33098196 DOI: 10.1111/jam.14903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 09/27/2020] [Accepted: 10/15/2020] [Indexed: 11/27/2022]
Abstract
AIMS Existing methods for the identification of the subspecies of Xylella fastidiosa are time-consuming which can lead to delays in diagnosis and the associated plant health response to outbreaks and interceptions. METHODS AND RESULTS Diagnostic markers were identified using a comparative genomics approach to allow fine differentiation of the very closely related subspecies. Five qPCR assays were designed to allow specific detection of X. fastidiosa subsp. fastidiosa, X. fastidiosa subsp. multiplex, X. fastidiosa subsp. pauca, X. fastidiosa subsp. morus and X. fastidiosa subsp. sandyi. All assays were validated according to the European and Mediterranean Plant Protection Organisation (EPPO) standard PM7/98(2). CONCLUSIONS All of the assays were shown to be specific to the target subspecies and all the assays could be used to detect femtogram quantities of X. fastidiosa DNA. SIGNIFICANCE AND IMPACT OF THE STUDY At present, diagnosing the subspecies of X. fastidiosa requires multiple conventional PCR assays (although only available for three of the five subspecies) or multi-locus sequence typing which takes several days. By comparison, the new assays provide a substantial reduction in the turnaround time for direct identification to the subspecies level in as little as 75 min.
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Affiliation(s)
- J Hodgetts
- Fera Science Ltd, The National Agri-Food Innovation Campus, York, UK
| | - R Glover
- Fera Science Ltd, The National Agri-Food Innovation Campus, York, UK
| | - J Cole
- Fera Science Ltd, The National Agri-Food Innovation Campus, York, UK
| | - J Hall
- Fera Science Ltd, The National Agri-Food Innovation Campus, York, UK
| | - N Boonham
- Fera Science Ltd, The National Agri-Food Innovation Campus, York, UK.,Institute for Agri-Food Research and Innovation, University of Newcastle, Newcastle upon Tyne, UK
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2
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Maxwell DJ, Partridge JC, Roberts NW, Boonham N, Foster GD. The effects of surface structure mutations in Arabidopsis thaliana on the polarization of reflections from virus-infected leaves. PLoS One 2017; 12:e0174014. [PMID: 28346494 PMCID: PMC5367784 DOI: 10.1371/journal.pone.0174014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 03/01/2017] [Indexed: 12/22/2022] Open
Abstract
The way in which light is polarized when reflected from leaves can be affected by infection with plant viruses. This has the potential to influence viral transmission by insect vectors due to altered visual attractiveness of infected plants. The optical and topological properties of cuticular waxes and trichomes are important determinants of how light is polarized upon reflection. Changes in expression of genes involved in the formation of surface structures have also been reported following viral infection. This paper investigates the role of altered surface structures in virus-induced changes to polarization reflection from leaves. The percentage polarization of reflections from Arabidopsis thaliana cer5, cer6 and cer8 wax synthesis mutants, and the gl1 leaf hair mutant, was compared to those from wild-type (WT) leaves. The cer5 mutant leaves were less polarizing than WT on the adaxial and abaxial surfaces; gl1 leaves were more polarizing than WT on the adaxial surfaces. The cer6 and cer8 mutations did not significantly affect polarization reflection. The impacts of Turnip vein clearing virus (TVCV) infection on the polarization of reflected light were significantly affected by cer5 mutation, with the reflections from cer5 mutants being higher than those from WT leaves, suggesting that changes in CER5 expression following infection could influence the polarization of the reflections. There was, however, no significant effect of the gl1 mutation on polarization following TVCV infection. The cer5 and gl1 mutations did not affect the changes in polarization following Cucumber mosaic virus (CMV) infection. The accumulation of TVCV and CMV did not differ significantly between mutant and WT leaves, suggesting that altered expression of surface structure genes does not significantly affect viral titres, raising the possibility that if such regulatory changes have any adaptive value it may possibly be through impacts on viral transmission.
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Affiliation(s)
- D. J. Maxwell
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - J. C. Partridge
- School of Animal Biology and Oceans Institute, University of Western Australia, Crawley, Western Australia, Australia
| | - N. W. Roberts
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - N. Boonham
- The Food and Environment Research Agency, Sand Hutton, York, United Kingdom
| | - G. D. Foster
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
- * E-mail:
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3
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Hodgetts J, Hall J, Karamura G, Grant M, Studholme DJ, Boonham N, Karamura E, Smith JJ. Rapid, specific, simple, in-field detection of Xanthomonas campestris pathovar musacearum by loop-mediated isothermal amplification. J Appl Microbiol 2016; 119:1651-8. [PMID: 26425811 DOI: 10.1111/jam.12959] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 09/17/2015] [Accepted: 09/21/2015] [Indexed: 11/27/2022]
Abstract
AIMS To develop and evaluate a loop-mediated isothermal amplification (LAMP) assay for Xanthomonas campestris pathovar musacearum (Xcm), the causal agent of banana Xanthomonas wilt, a major disease of banana in Africa. METHODS AND RESULTS LAMP primers were designed to the general secretion pathway protein D gene and tested against 17 isolates of Xcm encompassing the known genetic and geographic diversity of the bacterium and all isolates were detected. Seventeen other Xanthomonas isolates, including closely related Xanthomonas vasicola, other bacterial pathogens/endophytes of Musa and two healthy Musa varieties gave negative results with the LAMP assay. The assay showed good sensitivity, detecting as little as 51 fg of Xcm DNA, a greater level of sensitivity than that of an Xcm PCR assay. Amplification with the LAMP assay was very rapid, typically within 9 min from bacterial cultures. Symptomatic field samples of Musa from Uganda were tested and all produced amplification in less than 13 min. CONCLUSIONS The LAMP assay provides rapid, sensitive detection of the pathogen that is ideally suited for deployment in laboratories with basic facilities and in-field situations. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first LAMP assay for Xcm which provides a significant improvement compared to existing diagnostics.
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Affiliation(s)
- J Hodgetts
- Fera, National Agri-Food Innovation Campus, York, UK
| | - J Hall
- Fera, National Agri-Food Innovation Campus, York, UK
| | - G Karamura
- Fera, National Agri-Food Innovation Campus, York, UK.,Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, Devon, UK
| | - M Grant
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, Devon, UK
| | - D J Studholme
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, Devon, UK
| | - N Boonham
- Fera, National Agri-Food Innovation Campus, York, UK
| | - E Karamura
- Bioversity International/CRP-RTB, Nairobi, Kenya
| | - J J Smith
- Fera, National Agri-Food Innovation Campus, York, UK
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4
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Gandolfo DS, Mortimer H, Woodhall JW, Boonham N. Fourier transform infra-red spectroscopy using an attenuated total reflection probe to distinguish between Japanese larch, pine and citrus plants in healthy and diseased states. Spectrochim Acta A Mol Biomol Spectrosc 2016; 163:181-8. [PMID: 27054703 DOI: 10.1016/j.saa.2016.03.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 03/14/2016] [Accepted: 03/20/2016] [Indexed: 05/23/2023]
Abstract
FTIR spectroscopy coupled with an Attenuated Total Reflection (ATR) sampling probe has been demonstrated as a technique for detecting disease in plants. Spectral differences were detected in Japanese Larch (Larix kaempferi) infected with Phytophthora ramorum at 3403cm(-1) and 1730cm(-1), from pine (Pinus spp.) infected with Bursaphelenchus xylophilus at 1070cm(-1), 1425cm(-)1, 1621cm(-1) and 3403cm(-1) and from citrus (Citrus spp.) infected with 'Candidatus liberibacter' at 960cm(-1), 1087cm(-1), 1109cm(-1), 1154cm(-1), 1225cm(-1), 1385cm(-1), 1462cm(-1), 1707cm(-1), 2882cm(-1), 2982cm(-1) and 3650cm(-1). A spectral marker in healthy citrus has been identified as Pentanone but is absent from the diseased sample spectra. This agrees with recent work by Aksenov, 2014. Additionally, the spectral signature of Cutin was identified in the spectra of Pinus spp. and Citrus spp. and is consistent with work by Dubis, 1999 and Heredia-Guerrero, 2014.
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Affiliation(s)
- D S Gandolfo
- RAL Space, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, United Kingdom.
| | - H Mortimer
- RAL Space, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - J W Woodhall
- The Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, United Kingdom
| | - N Boonham
- The Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, United Kingdom
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5
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Hodgetts J, Karamura G, Johnson G, Hall J, Perkins K, Beed F, Nakato V, Grant M, Studholme DJ, Boonham N, Smith J. Development of a lateral flow device for in-field detection and evaluation of PCR-based diagnostic methods for Xanthomonas campestris pv. musacearum, the causal agent of banana xanthomonas wilt. Plant Pathol 2015; 64:559-567. [PMID: 32313307 PMCID: PMC7159137 DOI: 10.1111/ppa.12289] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Xanthomonas campestris pv. musacearum (Xcm) is the causal agent of banana xanthomonas wilt, a major threat to banana production in eastern and central Africa. The pathogen is present in very high levels within infected plants and can be transmitted by a broad range of mechanisms; therefore early specific detection is vital for effective disease management. In this study, a polyclonal antibody (pAb) was developed and deployed in a lateral flow device (LFD) format to allow rapid in-field detection of Xcm. Published Xcm PCR assays were also independently assessed: only two assays gave specific amplification of Xcm, whilst others cross-reacted with non-target Xanthomonas species. Pure cultures of Xcm were used to immunize a rabbit, the IgG antibodies purified from the serum and the resulting polyclonal antibodies tested using ELISA and LFD. Testing against a wide range of bacterial species showed the pAb detected all strains of Xcm, representing isolates from seven countries and the known genetic diversity of Xcm. The pAb also detected the closely related Xanthomonas axonopodis pv. vasculorum (Xav), primarily a sugarcane pathogen. Detection was successful in both naturally and experimentally infected banana plants, and the LFD limit of detection was 105 cells mL-1. Whilst the pAb is not fully specific for Xcm, Xav has never been found in banana. Therefore the LFD can be used as a first-line screening tool to detect Xcm in the field. Testing by LFD requires no equipment, can be performed by non-scientists and is cost-effective. Therefore this LFD provides a vital tool to aid in the management and control of Xcm.
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Affiliation(s)
- J Hodgetts
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
| | - G Karamura
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter Devon EX4 4QD UK
- National Agricultural Research Laboratories PO Box 7064 Kampala Uganda
| | - G Johnson
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
| | - J Hall
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
| | - K Perkins
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
| | - F Beed
- International Institute of Tropical Agriculture - Tanzania PO Box 34441 Dar es Salaam Tanzania
| | - V Nakato
- International Institute of Tropical Agriculture - Uganda PO Box 7878 Kampala Uganda
| | - M Grant
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter Devon EX4 4QD UK
| | - D J Studholme
- Biosciences College of Life and Environmental Sciences University of Exeter Exeter Devon EX4 4QD UK
| | - N Boonham
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
| | - J Smith
- The Food and Environment Research Agency Sand Hutton York YO41 1LZ UK
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6
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Kogovšek P, Hodgetts J, Hall J, Prezelj N, Nikolić P, Mehle N, Lenarčič R, Rotter A, Dickinson M, Boonham N, Dermastia M, Ravnikar M. LAMP assay and rapid sample preparation method for on-site detection of flavescence dorée phytoplasma in grapevine. Plant Pathol 2015; 64:286-296. [PMID: 26146413 PMCID: PMC4480326 DOI: 10.1111/ppa.12266] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/21/2014] [Indexed: 05/23/2023]
Abstract
In Europe the most devastating phytoplasma associated with grapevine yellows (GY) diseases is a quarantine pest, flavescence dorée (FDp), from the 16SrV taxonomic group. The on-site detection of FDp with an affordable device would contribute to faster and more efficient decisions on the control measures for FDp. Therefore, a real-time isothermal LAMP assay for detection of FDp was validated according to the EPPO standards and MIQE guidelines. The LAMP assay was shown to be specific and extremely sensitive, because it detected FDp in all leaf samples that were determined to be FDp infected using quantitative real-time PCR. The whole procedure of sample preparation and testing was designed and optimized for on-site detection and can be completed in one hour. The homogenization procedure of the grapevine samples (leaf vein, flower or berry) was optimized to allow direct testing of crude homogenates with the LAMP assay, without the need for DNA extraction, and was shown to be extremely sensitive.
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Affiliation(s)
- P Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
- Department of Biology, Biotechnical Faculty, University of LjubljanaVečna pot 111, 1000, Ljubljana, SIovenia
| | - J Hodgetts
- The Food and Environment Research AgencySand Hutton, York, YO41 1LZ, UK
| | - J Hall
- The Food and Environment Research AgencySand Hutton, York, YO41 1LZ, UK
| | - N Prezelj
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - P Nikolić
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - N Mehle
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - R Lenarčič
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - A Rotter
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - M Dickinson
- School of Biosciences, University of NottinghamSutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - N Boonham
- The Food and Environment Research AgencySand Hutton, York, YO41 1LZ, UK
| | - M Dermastia
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
| | - M Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of BiologyVečna pot 111, 1000, Ljubljana, SIovenia
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7
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Adams IP, Rai S, Deka M, Harju V, Hodges T, Hayward G, Skelton A, Fox A, Boonham N. Genome sequence of vanilla distortion mosaic virus infecting Coriandrum sativum. Arch Virol 2014; 159:3463-5. [PMID: 25252813 DOI: 10.1007/s00705-014-2215-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 08/26/2014] [Indexed: 10/24/2022]
Abstract
The 9573-nucleotide genome of a potyvirus was sequenced from a Coriandrum sativum plant from India with viral symptoms. On analysis, this virus was shown to have greater than 85 % nucleotide sequence identity to vanilla distortion mosaic virus (VDMV). Analysis of the putative coat protein sequence confirmed that this virus was in fact VDMV, with greater than 91 % amino acid sequence identity. The genome appears to encode a 3083-amino-acid polyprotein potentially cleaved into the 10 mature proteins expected in potyviruses. Phylogenetic analysis confirmed that VDMV is a distinct but ungrouped member of the genus Potyvirus.
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Affiliation(s)
- I P Adams
- The Crop Protection Centre, The Food and Environment Research Agency, Sand Hutton, York, YO41 1LZ, UK,
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8
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Richards RS, Adams IP, Kreuze JF, De Souza J, Cuellar W, Dullemans AM, Van Der Vlugt RAA, Glover R, Hany U, Dickinson M, Boonham N. The complete genome sequences of two isolates of potato black ringspot virus and their relationship to other isolates and nepoviruses. Arch Virol 2014; 159:811-5. [PMID: 24122155 DOI: 10.1007/s00705-013-1871-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 09/26/2013] [Indexed: 10/26/2022]
Abstract
The complete nucleotide sequences of RNA 1 and RNA 2 of the nepovirus potato black ringspot virus (PBRSV) from two different isolates were determined, as well as partial sequences from two additional isolates. RNA1 is 7,579-7,598 nucleotides long and contains one single open reading frame (ORF), which is translated into a large polyprotein with 2,325 amino acids and a molecular weight of 257 kDa. The complete sequence of RNA2 ranges from 3857 to 3918 nt between the different isolates. It encodes a polyprotein of 1079-1082 amino acids with a molecular weight of 120 kDa. Sequence comparison using the Pro-Pol region and CP showed that all four isolates formed two distinct groups, corresponding to potato and arracacha, that were closely related to each other and also to tobacco ringspot virus (TRSV). Comparing our data to those obtained with other nepoviruses, our results confirm that PBRSV belongs to a distinct species and is a member of subgroup A in the genus Nepovirus based on its RNA2 size, genome organization, and nucleotide sequence.
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9
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Adams I, Harju V, Hodges T, Hany U, Skelton A, Rai S, Deka M, Smith J, Fox A, Uzayisenga B, Ngaboyisonga C, Uwumukiza B, Rutikanga A, Rutherford M, Ricthis B, Phiri N, Boonham N. First report of maize lethal necrosis disease in Rwanda. ACTA ACUST UNITED AC 2014. [DOI: 10.5197/j.2044-0588.2014.029.022] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- I.P. Adams
- The Crop Protection CentreThe Food and Environment Research AgencySand HuttonYorkYO41 1LZUK
| | - V.A Harju
- The Crop Protection CentreThe Food and Environment Research AgencySand HuttonYorkYO41 1LZUK
| | - T. Hodges
- The Crop Protection CentreThe Food and Environment Research AgencySand HuttonYorkYO41 1LZUK
- University of YorkYorkYO10 5DDUK
| | - U. Hany
- The Crop Protection CentreThe Food and Environment Research AgencySand HuttonYorkYO41 1LZUK
| | - A. Skelton
- The Crop Protection CentreThe Food and Environment Research AgencySand HuttonYorkYO41 1LZUK
| | - S. Rai
- The Crop Protection CentreThe Food and Environment Research AgencySand HuttonYorkYO41 1LZUK
- University of YorkYorkYO10 5DDUK
| | - M.K. Deka
- The Crop Protection CentreThe Food and Environment Research AgencySand HuttonYorkYO41 1LZUK
- Department of EntomologyAssam Agricultural UniversityAssamIndia785013
| | - J. Smith
- The Crop Protection CentreThe Food and Environment Research AgencySand HuttonYorkYO41 1LZUK
| | - A. Fox
- The Crop Protection CentreThe Food and Environment Research AgencySand HuttonYorkYO41 1LZUK
| | | | | | - B. Uwumukiza
- Ministry of Agriculture and Animal ResourcesP.O. Box 621KigaliRwanda
| | - A. Rutikanga
- High Institute of Agriculture and Animal HusbandryP.O. Box 210MusanzeRwanda
| | | | | | - N. Phiri
- CAB International Africa Regional CentreNairobiKenya
| | - N. Boonham
- The Crop Protection CentreThe Food and Environment Research AgencySand HuttonYorkYO41 1LZUK
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10
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Hany U, Adams IP, Glover R, Bhat AI, Boonham N. The complete genome sequence of Piper yellow mottle virus (PYMoV). Arch Virol 2013; 159:385-8. [PMID: 24005374 DOI: 10.1007/s00705-013-1824-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/05/2013] [Indexed: 11/29/2022]
Abstract
This study reports the first complete genome sequence of Piper yellow mottle virus (PYMoV, KC808712) identified in black pepper. The genome is 7,622 nucleotides long, possessing four open reading frames (ORFs). ORF1, ORF2 and ORF4 of PYMoV are reported as hypothetical proteins of unknown function with a predicted molecular mass of 15.7, 17.1 and 17.9 kDa, respectively. ORF3 of PYMoV encodes a polyprotein of 218.6 kDa and consists of a viral movement protein (MP), trimeric dUTPase, zinc finger, retropepsin, RT-LTR, and RNAse H. Detailed PYMoV genome analysis confirmed that it is a member of the family Caulimoviridae, genus Badnavirus. Fragments of two additional novel sequences resembling those found in members of the family Caulimoviridae were also identified in the black pepper sample, and the viruses from which they were derived were tentatively named Piper DNA virus 1 and 2.
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Affiliation(s)
- U Hany
- Food and Environment Research Agency, Sand Hutton, York, UK,
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11
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Tomlinson JA, Ostoja-Starzewska S, Adams IP, Miano DW, Abidrabo P, Kinyua Z, Alicai T, Dickinson MJ, Peters D, Boonham N, Smith J. Loop-mediated isothermal amplification for rapid detection of the causal agents of cassava brown streak disease. J Virol Methods 2012; 191:148-54. [PMID: 22820076 DOI: 10.1016/j.jviromet.2012.07.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 07/05/2012] [Accepted: 07/11/2012] [Indexed: 11/30/2022]
Abstract
The causal agents of cassava brown streak disease have recently been identified as Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). Primers have been developed for rapid detection of these viruses by reverse transcription loop-mediated isothermal amplification (RT-LAMP). Performance of the RT-LAMP assays compared favourably with published RT-PCR and real-time RT-PCR methods. Furthermore, amplification by RT-LAMP is completed in 40 min and does not require thermal cycling equipment. Modification of the RT-LAMP reactions to use labelled primers allowed rapid detection of amplification products using lateral flow devices containing antibodies specific to the incorporated labels, avoiding the need for fluorescence detection or gel electrophoresis.
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Affiliation(s)
- J A Tomlinson
- The Food and Environment Research Agency, Sand Hutton, York YO41 1LZ, United Kingdom.
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12
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Harju V, Skelton A, Forde S, Bennett S, Glover R, Monger W, Adams I, Boonham N, Fox A. New virus detected on
Nasturtium officinale
(watercress). ACTA ACUST UNITED AC 2012. [DOI: 10.5197/j.2044-0588.2012.025.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- V. Harju
- The Food and Environment Research Agency, (Fera)Sand HuttonYorkYO41 1LZUK
| | - A. Skelton
- The Food and Environment Research Agency, (Fera)Sand HuttonYorkYO41 1LZUK
| | - S. Forde
- The Food and Environment Research Agency, (Fera)Sand HuttonYorkYO41 1LZUK
| | - S. Bennett
- The Food and Environment Research Agency, (Fera)Sand HuttonYorkYO41 1LZUK
| | - R. Glover
- The Food and Environment Research Agency, (Fera)Sand HuttonYorkYO41 1LZUK
| | - W. Monger
- The Food and Environment Research Agency, (Fera)Sand HuttonYorkYO41 1LZUK
| | - I. Adams
- The Food and Environment Research Agency, (Fera)Sand HuttonYorkYO41 1LZUK
| | - N. Boonham
- The Food and Environment Research Agency, (Fera)Sand HuttonYorkYO41 1LZUK
| | - A. Fox
- The Food and Environment Research Agency, (Fera)Sand HuttonYorkYO41 1LZUK
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13
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Kouassi N, Wendy M, Boonham N, Smith J. DEVELOPMENT OF A DIAGNOSTIC PROTOCOL FOR CUCUMBER MOSAIC VIRUS FOR SCREENING BANANA (MUSA SPP.) PLANTING MATERIAL IN IVORY COAST. ACTA ACUST UNITED AC 2010. [DOI: 10.17660/actahortic.2010.879.59] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Abstract
AIMS To develop a sensitive, rapid and simple method for detection of Botrytis cinerea based on loop-mediated isothermal amplification (LAMP) that would be suitable for use outside a conventional laboratory setting. METHODS AND RESULTS A LAMP assay was designed based on the intergenic spacer of the B. cinerea nuclear ribosomal DNA (rDNA). The resulting assay was characterized in terms of sensitivity and specificity using DNA extracted from cultures. The assay consistently amplified 65 pg B. cinerea DNA. No cross-reactivity was observed with a range of other fungal pathogens, with the exception of the closely related species Botrytis pelargonii. Use of a novel real-time LAMP platform (the OptiGene Genie I) allowed detection of B. cinerea in infected rose petals, with amplification occurring in <15 min. CONCLUSIONS The LAMP assay that was developed is suitable for rapid detection of B. cinerea in infected plant material. SIGNIFICANCE AND IMPACT OF THE STUDY The LAMP method combines the sensitivity and specificity of nucleic acid-based methods with simplified equipment and a reduced reaction time. These features make the method potentially suitable for on-site use, where the results of testing could help to inform decisions regarding the storage and processing of commodities affected by B. cinerea, such as cut flowers, fruit and vegetables.
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Affiliation(s)
- J A Tomlinson
- The Food and Environment Research Agency, Sand Hutton, York, UK.
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15
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Bonants P, Groenewald E, Rasplus JY, Maes M, de Vos P, Frey J, Boonham N, Nicolaisen M, Bertacini A, Robert V, Barker I, Kox L, Ravnikar M, Tomankova K, Caffier D, Li M, Armstrong K, Freitas-Astúa J, Stefani E, Cubero J, Mostert L. QBOL: a new EU project focusing on DNA barcoding of Quarantine organisms. ACTA ACUST UNITED AC 2010. [DOI: 10.1111/j.1365-2338.2009.02350.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Tomlinson JA, Dickinson M, Hobden E, Robinson S, Giltrap PM, Boonham N. A five-minute DNA extraction method for expedited detection of Phytophthora ramorum following prescreening using Phytophthora spp. lateral flow devices. J Microbiol Methods 2010; 81:116-20. [PMID: 20171248 DOI: 10.1016/j.mimet.2010.02.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2009] [Revised: 02/10/2010] [Accepted: 02/11/2010] [Indexed: 11/25/2022]
Abstract
In a direct comparison with established methods for Phytophthora ramorum detection (isolation followed by morphological identification, or conventional DNA extraction followed by TaqMan real-time PCR) a rapid, simplified detection method in which membranes of lateral flow devices (LFDs) are added directly to TaqMan real-time PCR reactions was used to test 202 plant samples collected by plant health inspectors in the field. P. ramorum prevalence within the 202 samples was approximately 40% according to routine testing by isolation or TaqMan real-time PCR. The diagnostic sensitivity and specificity of the rapid detection method were 96.3% and 91.2%, respectively. This method can be used in conjunction with Phytophthora spp. lateral flow devices to reduce the number of samples requiring testing using more laborious conventional methods. The effect of combining prescreening for Phytophthora spp. with P. ramorum-specific tests is discussed in terms of the positive and negative predictive values of species-specific detection when testing samples collected in different inspection scenarios.
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Affiliation(s)
- J A Tomlinson
- The Food and Environment Research Agency, Sand Hutton, York YO41 1LZ, United Kingdom.
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17
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Tomlinson JA, Dickinson MJ, Boonham N. Rapid detection of Phytophthora ramorum and P. kernoviae by two-minute DNA extraction followed by isothermal amplification and amplicon detection by generic lateral flow device. Phytopathology 2010; 100:143-9. [PMID: 20055648 DOI: 10.1094/phyto-100-2-0143] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
ABSTRACT A method for nucleic-acid-based detection of pathogens in plant material has been developed which comprises a simple and rapid method for extracting DNA on the nitrocellulose membranes of lateral-flow devices, loop-mediated isothermal amplification (LAMP) of target DNA using labeled primers, and detection of the generically labeled amplification products by a sandwich immunoassay in a lateral-flow-device format. Each of these steps can be performed without specialist equipment and is suitable for on-site use, and a result can be obtained in just over an hour. A LAMP assay for the detection of plant DNA (cytochrome oxidase gene) can be used in conjunction with pathogen-specific assays to confirm negative results. The use of this method is demonstrated for the detection of Phytophthora ramorum, the causal agent of sudden oak death and dieback/leaf blight in a range of tree, shrub, and herbaceous species, and the recently described pathogen P. kernoviae.
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Affiliation(s)
- J A Tomlinson
- The Food and Environmental Research Agency, Sand Hutton, York YO41 1LZ, United Kingdom.
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18
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Steel E, Barker I, Danks C, Coates D, Boonham N. A. tumefaciens-mediated transient expression as a tool for antigen production for cucurbit yellow stunting disorder virus. J Virol Methods 2010; 163:222-8. [PMID: 19819262 DOI: 10.1016/j.jviromet.2009.09.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Revised: 09/24/2009] [Accepted: 09/30/2009] [Indexed: 11/25/2022]
Abstract
The emerging importance of criniviruses, together with their limited characterisation, necessitates the development of simple tools to enable rapid detection and monitoring in case of an outbreak. While serological tools would be ideal, criniviruses are notoriously difficult to purify and traditional methods of antibody production, requiring purified virus particles, are extremely challenging. The development of a novel molecular strategy for in planta viral antigen preparation to bypass particle purification and allow antibody production are described. An A. tumefaciens-mediated transient expression system, coupled with a green fluorescent protein (GFP) purification method was employed to generate CYSDV coat protein (CP) in whole plant leaves. The CYSDV CP gene was ligated into a GFP construct, transformed into A. tumefaciens and agroinfiltrated into N. benthamiana. Expression levels of the recombinant protein were increased by co-infiltration with the viral gene-silencing suppressor P19 from TBSV. The recombinant protein, purified from plant leaves was used to immunise rats for the preparation of polyclonal antisera.
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Affiliation(s)
- E Steel
- The Food and Environment Research Agency Fera, Sand Hutton, York YO41 1LZ, UK.
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19
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Kogovšek P, Gow L, Pompe-Novak M, Gruden K, Foster G, Boonham N, Ravnikar M. Single-step RT real-time PCR for sensitive detection and discrimination of Potato virus Y isolates. J Virol Methods 2008; 149:1-11. [DOI: 10.1016/j.jviromet.2008.01.025] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/16/2008] [Accepted: 01/21/2008] [Indexed: 10/22/2022]
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20
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Gil-Salas FM, Morris J, Colyer A, Budge G, Boonham N, Cuadrado IM, Janssen D. Development of real-time RT-PCR assays for the detection of Cucumber vein yellowing virus (CVYV) and Cucurbit yellow stunting disorder virus (CYSDV) in the whitefly vector Bemisia tabaci. J Virol Methods 2007; 146:45-51. [PMID: 17624449 DOI: 10.1016/j.jviromet.2007.05.032] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 05/29/2007] [Accepted: 05/31/2007] [Indexed: 11/17/2022]
Abstract
Reverse transcription followed by real-time PCR assays based on TaqMan chemistry have been developed for the detection and quantification of Cucumber vein yellowing virus (CVYV) and Cucurbit yellow stunting disorder virus (CYSDV) in individual adults of the whitefly vector Bemisia tabaci. The method includes an internal control for the detection of a gene from B. tabaci to compensate for variations in extraction efficiency. The assays designed were used to estimate proportions of viruliferous whiteflies collected from commercial greenhouse-grown crops in Spain. In a significant number of whiteflies, both viruses were detected and their amounts were estimated. The assays could be used to assist risk assessment of CVYV and CYSDV which constitute limiting factors in cucurbit crops. They are also suited to investigating the epidemiology and plant-virus-vector relationships in these diseases.
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Affiliation(s)
- F M Gil-Salas
- Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (I.F.A.P.A., C.I.C.E.), Junta de Andalucía, 04745 La Mojonera, Almeria, Spain
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21
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Singh RP, Valkonen JPT, Gray SM, Boonham N, Jones RAC, Kerlan C, Schubert J. Discussion paper: The naming of Potato virus Y strains infecting potato. Arch Virol 2007; 153:1-13. [PMID: 17943395 DOI: 10.1007/s00705-007-1059-1] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2007] [Accepted: 08/27/2007] [Indexed: 11/30/2022]
Abstract
Potato virus Y (PVY) strain groups are based on host response and resistance gene interactions. The strain groups PVY(O), PVY(C) and PVY(N) are well established for the isolates infecting potato in the field. A switch in the emphasis from host response to nucleotide sequence differences in the virus genomes, detection of isolates recombining sequences of different strains, and the need to recognize isolates that cause necrotic symptoms in potato tubers have led to the assignment of new acronyms, especially to isolates of the PVY(N) strain group. This discussion paper proposes that any newly found isolates should be described within the context of the original strain groups based on the original methods of distinguishing strains (i.e., tobacco and potato assays involving use of 'differential' potato cultivars). Additionally, sequence characterization of the complete genomes of isolates is highly recommended. However, it is acceptable to amend the names of PVY isolates with additional, specific codes to show that the isolate differs at the molecular, serological or phenotypic level from the typical strains within a strain group. The new isolates should preferably not be named using geographical, cultivar, or place-association designations. Since many new variants of PVY are being discovered, any new static classification system will be meaningless for the time being. A more systematic investigation and characterization of PVY from potato at the biological and molecular levels should eventually result in a biologically meaningful genetic strain concept.
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Affiliation(s)
- R P Singh
- Potato Research Centre, Agriculture and Agri-Food Canada, New Brunswick, Canada.
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22
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Tomlinson JA, Barker I, Boonham N. Faster, simpler, more-specific methods for improved molecular detection of Phytophthora ramorum in the field. Appl Environ Microbiol 2007; 73:4040-7. [PMID: 17449689 PMCID: PMC1932743 DOI: 10.1128/aem.00161-07] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 04/13/2007] [Indexed: 01/12/2023] Open
Abstract
Phytophthora ramorum is the causal agent of sudden oak death. The pathogen also affects a wide range of tree, shrub, and herbaceous species in natural and landscaped environments as well as plants in the nursery industry. A TaqMan real-time PCR method for the detection of this pathogen in the field has been described previously; this paper describes the development of a number of assays based on this method which have various advantages for use in the field. A scorpion real-time PCR assay that is twice as fast as TaqMan was developed, allowing the detection of P. ramorum in less than 30 min. Also designed was a loop-mediated isothermal amplification (LAMP) assay, which allowed sensitive and specific detection of P. ramorum in 45 min using only a heated block. A positive reaction was identified by the detection of the LAMP product by color change visible to the naked eye.
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Affiliation(s)
- J A Tomlinson
- Central Science Laboratory, Sand Hutton, York YO41 1LZ, United Kingdom.
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23
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Ward L, Koenig R, Budge G, Garrido C, McGrath C, Stubbley H, Boonham N. Occurrence of two different types of RNA-5-containing beet necrotic yellow vein virus in the UK. Arch Virol 2006; 152:59-73. [PMID: 16941060 DOI: 10.1007/s00705-006-0832-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Accepted: 07/10/2006] [Indexed: 10/24/2022]
Abstract
Two types of RNA-5-containing beet necrotic yellow vein virus (BNYVV) have been detected in the UK at different sites in Norfolk. On the basis of nucleotide (nt) sequence comparisons, one virus source (UK-MH) was clearly identified as P type BNYVV, a virus type that had previously only been detected in two widely separated parts of the world, France and Kazakhstan. The other virus source (UK-FF) has a complex genome composition. The analysed portions of its RNAs 2 and 4 are closely related to the corresponding portions in the RNAs of the East Asian A type isolate S, whereas those of its RNAs 1 and 3 resemble P type RNA 1 from Kazakhstan and European A type RNA 3, respectively. Interestingly, the P25 encoded on its RNA 3 has an unique TYHG tetrad in the highly variable amino acid positions 67-70. RNA 5 of the UK-FF BNYVV source shares properties with P type RNA 5, but also with East Asian types of RNA 5. The possible origin and epidemiology of BNYVV types is discussed.
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Affiliation(s)
- L Ward
- Central Science Laboratory, Sand Hutton, York, UK
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24
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25
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Douglas AE, Price DRG, Minto LB, Jones E, Pescod KV, François CLMJ, Pritchard J, Boonham N. Sweet problems: insect traits defining the limits to dietary sugar utilisation by the pea aphid, Acyrthosiphon pisum. ACTA ACUST UNITED AC 2006; 209:1395-403. [PMID: 16574799 DOI: 10.1242/jeb.02148] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Plant phloem sap is an extreme diet for animals, partly because of its high and variable sugar content. The physiological and feeding traits of the pea aphid Acyrthosiphon pisum that define the upper and lower limits to the range of dietary sucrose concentrations utilised by this insect were determined principally using chemically defined diets containing 0.125-1.5 mol l(-1) sucrose. On the diets with 0.125 mol l(-1) and 1.5 mol l(-1) sucrose, the aphids died as larvae within 8 and 14 days of birth, respectively. On the other diets, 60-96% of aphids developed to adulthood, and the 0.5 mol l(-1) and 0.75 mol l(-1) diets supported the highest fecundity. The diet with 0.125 mol l(-1) sucrose was ingested at 36% of the rate of the 0.25 mol l(-1) sucrose diet, but >90% of ingested sucrose-carbon was assimilated on both diets. This suggests that the lower limit is dictated by the aphid feeding response, specifically, a requirement for a minimal concentration of sucrose for sustained feeding. The haemolymph osmotic pressure of aphids on diets with 0.125-1.5 mol l(-1) sucrose was up to 68% higher than on 0.125-1.0 mol l(-1) sucrose diets, but diet consumption and sucrose-carbon assimilation was not reduced on the very high sucrose diets relative to 1.0 mol l(-1) sucrose. This suggests that failure of the osmoregulatory capacity of the insects on high sucrose diets may define the upper limit to the range of dietary sucrose utilised by the aphids. The mean haemolymph osmotic pressure of aphids on plants with phloem sap containing 0.37-0.97 mol l(-1) sucrose was 1.61+/-0.063 MPa (mean +/- s.e.m.), not significantly different from that (1.47+/-0.059 MPa) on diets with 0.25-1.0 mol l(-1) sucrose. It is concluded that the osmoregulatory response of aphids to diets and plants are comparable, and, more generally, that the feeding and osmoregulatory capabilities of the aphids are compatible with the phloem sugar levels commonly encountered by aphids feeding on plants.
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Affiliation(s)
- A E Douglas
- Department of Biology (Area 2), University of York, UK.
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26
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López R, Asensio C, Guzman MM, Boonham N. Development of real-time and conventional RT-PCR assays for the detection of potato yellow vein virus (PYVV). J Virol Methods 2006; 136:24-9. [PMID: 16712962 DOI: 10.1016/j.jviromet.2006.03.026] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 03/22/2006] [Accepted: 03/27/2006] [Indexed: 11/30/2022]
Abstract
Potato yellow vein virus (PYVV) is considered a quarantine pathogen in the European and Mediterranean Plant Protection Organization (EPPO) area. This virus is widespread and damaging at its centre of origin in South America. Current detection methods are either time-consuming or difficult to interpret. This paper reports the development of a sensitive, high throughput, real-time reverse transcription (RT)-PCR assay, based on TaqMan chemistry, suitable for PYVV detection. In addition, a reliable conventional RT-PCR assay for PYVV detection is also presented. Although less sensitive (1000 times less sensitive in direct comparison), this method requires less sophisticated equipment and as such should be a useful alternative to the real-time technique in some testing laboratories. The two assays presented here could assist in the implementation of quarantine measures for PYVV identification and in routine indexing of PYVV for the production of virus-free seed potatoes in areas of South America where the virus is highly damaging.
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Affiliation(s)
- R López
- Central Science Laboratory, Sand Hutton, York YO41 1LZ, UK.
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27
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Chantawannakul P, Ward L, Boonham N, Brown M. A scientific note on the detection of honeybee viruses using real-time PCR (TaqMan) in Varroa mites collected from a Thai honeybee (Apis mellifera) apiary. J Invertebr Pathol 2006; 91:69-73. [PMID: 16376930 DOI: 10.1016/j.jip.2005.11.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 10/17/2005] [Accepted: 11/07/2005] [Indexed: 10/25/2022]
Abstract
Bee parasitic mite syndrome is a disease complex of colonies simultaneously infested with Varroa destructor mites and infected with viruses and accompanied by high mortality. By using real-time PCR (TaqMan), five out of seven bee viruses were detected in mite samples (V. destructor) collected from Thailand. Moreover, the results of this study provide an evidence for the co-existence of several bee viruses in a single mite. This is also the first report of bee viruses in mites from Thailand.
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Affiliation(s)
- P Chantawannakul
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand.
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28
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Cullen DW, Toth IK, Pitkin Y, Boonham N, Walsh K, Barker I, Lees AK. Use of quantitative molecular diagnostic assays to investigate fusarium dry rot in potato stocks and soil. Phytopathology 2005; 95:1462-1471. [PMID: 18943558 DOI: 10.1094/phyto-95-1462] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT Specific and sensitive quantitative diagnostics, based on real-time (TaqMan) polymerase chain reaction (PCR) and PCR enzyme-linked immunosorbent assay, were developed to detect dry-rot-causing Fusarium spp. (F. avenaceum, F. coeruleum, F. culmorum, and F. sulphureum). Each assay detected Fusarium spp. on potato seed stocks with equal efficiency. Four potato stocks, sampled over two seed generations from Scottish stores, were contaminated with F. avenaceum, F. sulphureum, F. culmorum, F. coeruleum or a combination of species, and there was a general trend towards increased Fusarium spp. contamination in the second generation of seed sampled. F. sulphureum and F. coeruleum caused significantly (P < 0.05) more disease in storage than the other species when disease-free tubers of potato cvs. Spunta and Morene were inoculated at a range of inoculum concentrations (0, 10(4), 10(5), and 10(6) conidia/ml). Increased DNA levels were correlated with increased disease severity between 8 and 12 weeks of storage. The threshold inoculum levels resulting in significant disease development on both cultivars were estimated to be 10(4) conidia/ml for F. sulphureum and 10(5) conidia/ml for F. coeruleum. To study the effect of soil infestation and harvest date on disease incidence, seed tubers of cvs. Morene and Spunta were planted in a field plot artificially infested with the four Fusarium spp. F. culmorum and F. sulphureum were detected in soil taken from these plots at harvest, and F. sulphureum DNA levels increased significantly (P < 0.05) at the final harvest. All four Fusarium spp. were detected in progeny tubers. There was a trend toward higher levels of F. culmorum detected in progeny tubers at the earliest harvest date, and higher levels of F. sulphureum at the final harvest. The use of diagnostic assays to detect fungal storage rot pathogens and implications for disease control strategies are discussed.
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29
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Tomlinson JA, Boonham N, Hughes KJD, Griffin RL, Barker I. On-site DNA extraction and real-time PCR for detection of Phytophthora ramorum in the field. Appl Environ Microbiol 2005; 71:6702-10. [PMID: 16269700 PMCID: PMC1287659 DOI: 10.1128/aem.71.11.6702-6710.2005] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2005] [Accepted: 06/23/2005] [Indexed: 11/20/2022] Open
Abstract
Phytophthora ramorum is a recently described pathogen causing oak mortality (sudden oak death) in forests in coastal areas of California and southern Oregon and dieback and leaf blight in a range of tree, shrub, and herbaceous species in the United States and Europe. Due to the threat posed by this organism, stringent quarantine regulations are in place, which restrict the movement of a number of hosts. Fast and accurate diagnostic tests are required in order to characterize the distribution of P. ramorum, prevent its introduction into pathogen-free areas, and minimize its spread within affected areas. However, sending samples to a laboratory for testing can cause a substantial delay between sampling and diagnosis. A rapid and simple DNA extraction method was developed for use at the point of sampling and used to extract DNAs from symptomatic foliage and stems in the field. A sensitive and specific single-round real-time PCR (TaqMan) assay for P. ramorum was performed using a portable real-time PCR platform (Cepheid SmartCycler II), and a cost-effective method for stabilizing PCR reagents was developed to allow their storage and transportation at room temperature. To our knowledge, this is the first description of a method for DNA extraction and molecular testing for a plant pathogen carried out entirely in the field, independent of any laboratory facilities.
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Affiliation(s)
- J A Tomlinson
- Central Science Laboratory, Sand Hutton, York YO41 1LZ, United Kingdom.
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Boonham N, Fisher T, Mumford RA. Investigating the specificity of real-time PCR assays using synthetic oligonucleotides. J Virol Methods 2005; 130:30-5. [PMID: 16051376 DOI: 10.1016/j.jviromet.2005.05.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Revised: 05/31/2005] [Accepted: 05/31/2005] [Indexed: 10/25/2022]
Abstract
Potato spindle tuber viroid (PSTVd) causes damaging diseases of solanaceous crops and is a quarantine pathogen in the European Union. Previously a one-tube real-time RT-PCR assay based on TaqMan chemistry was developed and shown to be ideally suited to PSTVd detection. However, since it was impossible to trace infected plant material for every published PSTVd sequence reported, in silico predictions were made about assay specificity based on the positions of nucleotide polymorphisms within the published viroid sequences and the regions of the primers and probe. The predictions could not be verified due to the absence of viroid material. This paper describes work investigating the detection of these sequence variants by designing synthetic oligonucleotides to sequences from the database and testing them with a real-time PCR assay. The results show that all PSTVd sequence variants are detected, and that the closely related Mexican papita viroid is also detected, although with a lower efficiency. The paper gives indications as to what effect nucleotide changes at different positions within primers and probes might do and should aid in the testing of future assays, although it is difficult to draw fixed rules about the possible effect changes may have.
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Affiliation(s)
- N Boonham
- Central Science Laboratory, Sand Hutton, York, UK.
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31
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Roenhorst JW, Jansen CCC, Kox LFF, de Haan EG, van den Bovenkamp GW, Boonham N, Fisher T, Mumford RA. Application of real-time RT-PCR for large-scale testing of potato for Potato spindle tuber pospiviroid. ACTA ACUST UNITED AC 2005. [DOI: 10.1111/j.1365-2338.2005.00798.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Harju VA, Skelton A, Clover GRG, Ratti C, Boonham N, Henry CM, Mumford RA. The use of real-time RT-PCR (TaqMan®) and post-ELISA virus release for the detection of Beet necrotic yellow vein virus types containing RNA 5 and its comparison with conventional RT-PCR. J Virol Methods 2005; 123:73-80. [PMID: 15582701 DOI: 10.1016/j.jviromet.2004.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Revised: 09/06/2004] [Accepted: 09/07/2004] [Indexed: 10/26/2022]
Abstract
Real-time RT-PCR (TaqMan) assays were developed for the specific detection of Beet necrotic yellow vein virus (BNYVV). The two assays designed were a broad-spectrum one that detected RNA 2 from all types and a second designed to detect types containing RNA 5. The assays were validated against a range of different isolates from Europe and the Far East. These real-time assays were compared to a conventional RT-PCR assay for the detection of RNA 5. Sensitivity comparisons showed that for the detection of RNA 5, TaqMan was 10,000 times more sensitive than the conventional RT-PCR assay. Further improvements were made to the test procedure by using post-ELISA virus release (VR), as an alternative to RNA extraction. This significantly increased the speed of processing samples and reduced the staff input required, allowing the TaqMan assay to be used routinely as part of an annual survey of UK field samples.
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Affiliation(s)
- V A Harju
- Central Science Laboratory (CSL), Sand Hutton, York YO41 1LZ, UK
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33
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Mumford R, Skelton A, Boonham N, Posthuma K, Kirby M, Adams A. THE IMPROVED DETECTION OF STRAWBERRY CRINKLE VIRUS USING REAL-TIME RT-PCR (TAQMAN®). ACTA ACUST UNITED AC 2004. [DOI: 10.17660/actahortic.2004.656.11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Boonham N, Pérez LG, Mendez MS, Peralta EL, Blockley A, Walsh K, Barker I, Mumford RA. Development of a real-time RT-PCR assay for the detection of potato spindle tuber viroid. J Virol Methods 2004; 116:139-46. [PMID: 14738980 DOI: 10.1016/j.jviromet.2003.11.005] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Potato spindle tuber viroid (PSTVd) is a quarantine pathogen in the European Union and causes damaging diseases of solanaceous crops. Under the EU Plant Health directive 2000/29/EC, countries must have the ability to detect and identify accurately and rapidly the introduction of harmful organisms in plants or plant products; furthermore, if the quarantine pathogen is found, be able to survey extensively for it. In this respect, PSTVd poses an interesting technical problem, since its RNA does not code for any proteins and thus any diagnostic method must be based on the detection of the RNA and be suitable for scaling up to testing large sample numbers. With this in mind a one-tube real-time RT-PCR assay based on TaqMan chemistry was developed. Investigations were carried out into various aspects of the assay relevant to the efficient amplification of targets that have a significant amount of secondary structure such as viroids. Thus comparisons were made of reverse transcription temperature, concentration and type of reverse transcriptase, RNA denaturation, sample purity and single versus two-tube reaction format. The assay developed was shown to be able to detect a wide range of isolates of PSTVd and in comparison with a chemi-luminescent hybridisation system was shown to be 1000-fold more sensitive. A further significant advantage of this assay format compared with hybridisation is that it is suitable for scaling up to large sample numbers using robotic liquid handling systems.
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Affiliation(s)
- N Boonham
- Central Science Laboratory, Sand Hutton, York YO41 1LZ, UK.
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Moravec T, Cerovská N, Boonham N. The detection of recombinant, tuber necrosing isolates of Potato virus Y (PVY(NTN)) using a three-primer PCR based in the coat protein gene. J Virol Methods 2003; 109:63-8. [PMID: 12668269 DOI: 10.1016/s0166-0934(03)00047-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A simple and reliable procedure for reverse transcription-polymerase chain reaction (RT-PCR) detection and strain differentiation of Potato virus Y (PVY) was developed. Three primers were designed within the coat protein (CP) and nuclear inclusion protein b (NIb) region, exploiting a single base polymorphism identified as being present in all the recombinant PVY(NTN) isolates published. Samples infected with PVY produce a single band of 569 bp, while isolates belonging to PVY(NTN) strain give an additional band of 334 bp. The technique was tested on a collection of well-characterised isolates of PVY from a range of strains and was found to detect all of the isolates reported as belonging to the PVY(NTN) strain. All of the isolates detected possess a recombination event within the coat protein. Further sequence analysis revealed that all the recombinant PVY(NTN) isolates reported thus far would be detected using this assay, whilst isolates thought to be PVY(NTN) that do not possess the coat protein recombination event would not be detected.
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Affiliation(s)
- T Moravec
- Institute of Experimental Botany, Czech Academy of Science, Na Karlovce 1, 16000 Prague, Czech Republic.
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Boonham N, Walsh K, Smith P, Madagan K, Graham I, Barker I. Detection of potato viruses using microarray technology: towards a generic method for plant viral disease diagnosis. J Virol Methods 2003; 108:181-7. [PMID: 12609685 DOI: 10.1016/s0166-0934(02)00284-7] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Currently, most diagnostic methodology is geared towards detection of a very specific target species and often a number of assays need to be run in parallel to reach a result. The generic methods that are available for virus testing tends to give identification to the genus level only. The method described in this paper addresses this problem by exploiting a technology that has potential to test for a large number of targets in a single assay. Using the array constructed, the method was able to detect several common potato viruses (PVY, PVX, PVA, PVS) in single and mixed infections. The method was shown to be able to discriminate sequences with less than 80% sequence identity but was able to detect sequence variants with greater than 90% sequence identity. Thus the method should be useful for discriminating at the species level, but able to cope well with the intrinsic variability found within the genomes of RNA viruses. The sensitivity of the assay was found to be comparable with ELISA. The paper illustrates a significant step forward in the development of diagnostic methodologies by presenting for the first time a method that could theoretically be used not just for viruses, but for all the plant pathogens and pests that a modern diagnostic laboratory would want to test for, in a single completely generic and highly parallel format.
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Affiliation(s)
- N Boonham
- Central Science Laboratory, Sand Hutton, YO41 1LZ, York, UK.
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Abstract
Yellow leaf syndrome (YLS) of sugarcane has been associated with Sugarcane yellow leaf virus (ScYLV) and has been reported from most sugarcane growing countries around the world. As sugarcane is vegetatively propagated, it is important to use effective and sensitive detection methods to screen new propagating material. Virus detection in symptomatic tissue is currently achieved using enzyme linked immunosorbent assay (ELISA), tissue blot immunoassay (TBIA) or a conventional RT-PCR based assay. This paper reports the development of an improved assay based on multiplex real-time fluorescent RT-PCR. The new assay is 100-fold more sensitive than conventional RT-PCR, and incorporates a novel 'RNA specific' internal positive control (based around the intron of the caffeic acid 3-o-methyltransferase gene) to guard against false negative results. The paper also describes the comparison of eight RNA extraction methods for sugarcane tissue giving a number of alternatives for different laboratory situations. The sensitivity of this assay has allowed the detection of ScYLV in many samples that were thought to be healthy following conventional testing (RT-PCR, ELISA or TBIA). The detection of ScYLV using this TaqMan assay can be applied to the production of ScYLV-free plants and prevents its spread through the propagation material.
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Boonham N, Smith P, Walsh K, Tame J, Morris J, Spence N, Bennison J, Barker I. The detection of Tomato spotted wilt virus (TSWV) in individual thrips using real time fluorescent RT-PCR (TaqMan). J Virol Methods 2002; 101:37-48. [PMID: 11849682 DOI: 10.1016/s0166-0934(01)00418-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tomato spotted wilt virus (TSWV) is an important virus, economically in the UK, causing damaging disease in ornamental and vegetable crops. The virus is vectored by several species of thrips, most importantly the western flower thrips (Frankliniella occidentalis Pergande [Thysanoptera: Thripidae]). The vector thrips themselves constitute a damaging pest and are difficult to control completely. Monitoring thrips numbers is an important part of the control of virus, but does not give information on how many of the thrips are viruliferous. Monitoring the presence of viruliferous thrips at an early stage of an epidemic may lead to improved disease control, since virus can be spread effectively whilst vector pressure is low and symptoms may take several weeks to appear on some hosts. This paper describes the development of a sensitive and robust, high-throughput method for the detection of TSWV in individual insects based on TaqMan chemistry. The method incorporates a novel RNA specific internal control to increase the reliability of the results. Results are also presented on comparisons of different extraction methods, including insects taken from sticky traps, for high-throughout testing. Implementation of a method such as this for the reliable detection of TSWV in individual thrips would aid the understanding of the progress of TSWV epidemics, and offer an early disease warning system for growers.
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Affiliation(s)
- N Boonham
- Central Science Laboratory, Sand Hutton, YO41 1LZ, York, UK.
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39
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Abstract
Most routine testing for plant viruses is currently carried out using monoclonal and polyclonal antibodies. Traditional methods of antibody production however can be time consuming and require the use of expensive cell culture facilities. Recombinant antibody technology however is starting to make an impact in this area, enabling the selection of antibody fragments in a few weeks compared with the many months associated with traditional methods and requires only basic microbiological facilities. Single chain Fv antibody fragments (scFv) have been selected from a synthetic phage-antibody library by affinity selection with purified Potato virus Y, ordinary strain (PVYO). The scFv selected was specific for PVY and detected 7 out of 9 isolates of PVYO whilst it did not detect 15 isolates from the closely related necrotic strains PVYN and PVYNTN. In ELISA the scFv could be used to detect virus at concentrations of 50 ng/ml in plant sap and was shown to have similar limits of detection as commercially available PVY monoclonal antibodies. These results highlight the potential of the technology for the selection of strain specific antibodies with an affinity and assay sensitivity similar to traditional monoclonal antibodies and their use in viral diagnostics.
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Affiliation(s)
- N Boonham
- Central Science Laboratory, Sand Hutton, York YO41 1LZ, UK.
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Walsh K, North J, Barker I, Boonham N. Detection of different strains of Potato virus Y and their mixed infections using competitive fluorescent RT-PCR. J Virol Methods 2001; 91:167-73. [PMID: 11164498 DOI: 10.1016/s0166-0934(00)00261-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A competitive fluorescent RT-PCR assay (CF RT-PCR) was developed for the rapid and reliable detection and discrimination of the two most common strains of Potato virus Y (PVY) found in potato (necrotic and ordinary). The assay incorporates two strain specific primers labelled with fluorescent labels, used in conjunction with a universal PVY primer. The strain specific primers compete for the same annealing site which further increases specificity. Discrimination is conferred by the fluorescent labels; green PCR products for PVY(O) and red for PVY(N), whilst mixed infections are detected as orange PCR products without the need for staining agarose gels. The assay can be scaled up for the processing of 96 samples simultaneously, with the detection of PCR products directly using a fluorescent microtitre plate reader. The assay successfully discriminated between 20 isolates of PVY tested, and could be used for the direct detection of PVY in potato tubers.
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Affiliation(s)
- K Walsh
- Central Science Laboratory MAFF, Sand Hutton, York, YO41 1LZ, UK.
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Weller SA, Elphinstone JG, Smith NC, Boonham N, Stead DE. Detection of Ralstonia solanacearum strains with a quantitative, multiplex, real-time, fluorogenic PCR (TaqMan) assay. Appl Environ Microbiol 2000; 66:2853-8. [PMID: 10877778 PMCID: PMC92083 DOI: 10.1128/aem.66.7.2853-2858.2000] [Citation(s) in RCA: 351] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/1999] [Accepted: 05/02/2000] [Indexed: 11/20/2022] Open
Abstract
A fluorogenic (TaqMan) PCR assay was developed to detect Ralstonia solanacearum strains. Two fluorogenic probes were utilized in a multiplex reaction; one broad-range probe (RS) detected all biovars of R. solanacearum, and a second more specific probe (B2) detected only biovar 2A. Amplification of the target was measured by the 5' nuclease activity of Taq DNA polymerase on each probe, resulting in emission of fluorescence. TaqMan PCR was performed with DNA extracted from 42 R. solanacearum and genetically or serologically related strains to demonstrate the specificity of the assay. In pure cultures, detection of R. solanacearum to >/=10(2) cells ml(-1) was achieved. Sensitivity decreased when TaqMan PCR was performed with inoculated potato tissue extracts, prepared by currently recommended extraction procedures. A third fluorogenic probe (COX), designed with the potato cytochrome oxidase gene sequence, was also developed for use as an internal PCR control and was shown to detect potato DNA in an RS-COX multiplex TaqMan PCR with infected potato tissue. The specificity and sensitivity of the assay, combined with high speed, robustness, reliability, and the possibility of automating the technique, offer potential advantages in routine indexing of potato tubers and other plant material for the presence of R. solanacearum.
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Affiliation(s)
- S A Weller
- Central Science Laboratory, MAFF, Sand Hutton, York, YO41 1LZ, United Kingdom.
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Mumford RA, Walsh K, Barker I, Boonham N. Detection of Potato mop top virus and Tobacco rattle virus Using a Multiplex Real-Time Fluorescent Reverse-Transcription Polymerase Chain Reaction Assay. Phytopathology 2000; 90:448-53. [PMID: 18944548 DOI: 10.1094/phyto.2000.90.5.448] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Tobacco rattle virus (TRV) and Potato mop top virus (PMTV) are important diseases of potato that are difficult to diagnose reliably by visual symptoms. Effective control strategies rely on accurate diagnosis. This paper describes the development of a multiplex assay for the detection of TRV and PMTV directly from potato tubers and leaves by polymerase chain reaction (PCR) combined with in-tube fluorescent product detection (TaqMan). This technology obviates any post-PCR manipulations and has many advantages including reducing contamination risks, eliminating the need for ethidium bromide staining, and removing the time and cost of gel running. The new assay also allows the replacement of the two separate tests (a TRV reverse-transcription-PCR and a PMTV enzyme-linked immuno-sorbent assay) currently used with a single-tube multiplex format. In addition to greatly simplifying the detection of these two viruses, the multiplex TaqMan assay was also shown to be more sensitive than either of the tests that it replaces, allowing 100- and 10,000-fold increases in sensitivity for TRV and PMTV detection, respectively. The test reliably detected over 40 different isolates of TRV and PMTV obtained from a wide range of different cultivars and geographical locations, including some samples in which existing tests failed to detect virus. The use of an assay of this kind in routine diagnosis helps to speed up and streamline the diagnostic laboratory; in addition, more reliable diagnosis should help in the control of this damaging disease.
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Uhde K, Kerschbaumer RJ, Koenig R, Hirschl S, Lemaire O, Boonham N, Roake W, Himmler G. Improved detection of Beet necrotic yellow vein virus in a DAS ELISA by means of antibody single chain fragments (scFv) which were selected to protease-stable epitopes from phage display libraries. Arch Virol 2000; 145:179-85. [PMID: 10664416 DOI: 10.1007/s007050050015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The detection of Beet necrotic yellow vein virus (BNYVV) in stored sugar beets by means of monoclonal antibodies or antibody single chain fragments (scFv) often poses problems, because the immunodominant C-terminal epitope of the viral coat protein is readily lost due to proteolysis. Clones which produce scFv specific for protease-stable BNYVV epitopes were selected from two naive phage display libraries. Fusion proteins of the scFv with a human IgG kappa chain (expressed from the newly designed vector pCL) or with alkaline phosphatase,respectively, allow the ELISA detection of BNYVV even in stored sugar beets with a sensitivity which was comparable or often higher than that achieved with polyclonal antibodies.
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Affiliation(s)
- K Uhde
- Biologische Bundesanstalt für Land -undForstwirtschaft, Institut für Pflanzenvirologie, Mikrobiologie undbiologische Sicherheit, Braunschweig, Germany
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Affiliation(s)
- N Boonham
- School of Biological Sciences, University of Birmingham, UK
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47
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Abstract
Single chain Fv antibody fragments have been selected from a synthetic phage-antibody library following three and four rounds of affinity selection with purified potato virus Y, common strain (PVY(O)). The selected fragments were highly specific for PVY and detected seven out of nine isolates of PVY(O) whilst failing to detect three isolates of PVY(N) and 12 isolates of PVY(NTN). Nucleotide sequence of the scFv genes showed the variable heavy fragments belonged to the human VH4 family, whilst the variable light fragments belonged to the Vlambda1 family. The fragments were used in ELISA to detect virus at concentrations of 50 ng/ml in plant sap and in comparisons with commercially available PVY monoclonal antibodies were shown to have similar limits of detection. This is the first report of the selection of a scFv specific for a member of the potyviridae, and its use in detecting and differentiating strains of PVY in infected plant sap. The results highlight the potential of the technology for the selection of strain specific antibodies with an avidity equivalent to traditional monoclonal antibodies raised against viral pathogens and their use for viral diagnosis.
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Affiliation(s)
- N Boonham
- Central Science Laboratory, Sand Hutton, York, UK.
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Abstract
Oat chlorotic stunt virus (OCSV) is a 35 nm icosahedral plant virus comprising of a single capsid protein with a Mr of 48.2 kDa and a 4.1 kb single stranded, positive sense genomic RNA. Northern blot analysis detected a single 3' terminal subgenomic RNA in extracts from infected plants, which was also found to be encapsidated. Virion RNA directs the synthesis of a 23 kDa polypeptide in a rabbit reticulocyte in vitro translation system. Primer extension analysis has been used to map the end of both the genomic and subgenomic RNA's, and has shown the genomic size to be 4115 nucleotides in length. The results have enabled a model for the genome expression to be proposed.
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Affiliation(s)
- N Boonham
- Central Science Laboratory, York, UK
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Boonham N, Henry CM, Wood KR. The nucleotide sequence and proposed genome organization of oat chlorotic stunt virus, a new soil-borne virus of cereals. J Gen Virol 1995; 76 ( Pt 8):2025-34. [PMID: 7636483 DOI: 10.1099/0022-1317-76-8-2025] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The complete genomic sequence of a new virus, first found infecting oats in Wales, UK, has been determined. The genome is a positive-sense ssRNA molecule, 4114 nucleotides in length, examination of which indicates the presence of four ORFs. The first ORF initiating at the 5' terminus (ORF1) encodes a protein with a predicted M(r) of 23476 (p23). ORF2 extends through the amber termination codon of ORF1 to give a protein with a predicted M(r) of 84355 (p84). The readthrough domain of p84 contains amino acid sequence similarities with a number of putative RNA-dependent RNA polymerases. ORF3 is in a different reading frame from ORF1/2 and encodes a protein with an M(r) of 48231 (p48), identified as the coat protein by direct peptide sequencing. ORF4 nests within ORF3 but is in a different frame from it and codes for a protein with a predicted M(r) of 8220 (p8). Comparisons of peptide sequence, particularly within the putative polymerase region and within the S domain of the coat protein, highlight similarities with members of both the tombusvirus and carmovirus groups. The coat protein region shows most similarity with members of the tombusvirus group, whilst the size and predicted strategy of the genome seem to be intermediate between that of the carmovirus and tombusvirus groups. These features highlight possible evolutionary links with each group whilst being distinct from both. We propose the name of oat chlorotic stunt for this new virus.
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Affiliation(s)
- N Boonham
- School of Biological Sciences, University of Birmingham, Edgbaston, UK
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