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Kidd SP, Burns D, Armson B, Beggs AD, Howson ELA, Williams A, Snell G, Wise EL, Goring A, Vincent-Mistiaen Z, Grippon S, Sawyer J, Cassar C, Cross D, Lewis T, Reid SM, Rivers S, James J, Skinner P, Banyard A, Davies K, Ptasinska A, Whalley C, Ferguson J, Bryer C, Poxon C, Bosworth A, Kidd M, Richter A, Burton J, Love H, Fouch S, Tillyer C, Sowood A, Patrick H, Moore N, Andreou M, Morant N, Houghton R, Parker J, Slater-Jefferies J, Brown I, Gretton C, Deans Z, Porter D, Cortes NJ, Douglas A, Hill SL, Godfrey KM, Fowler VL. Reverse-Transcription Loop-Mediated Isothermal Amplification Has High Accuracy for Detecting Severe Acute Respiratory Syndrome Coronavirus 2 in Saliva and Nasopharyngeal/Oropharyngeal Swabs from Asymptomatic and Symptomatic Individuals. J Mol Diagn 2022; 24:320-336. [PMID: 35121140 PMCID: PMC8806713 DOI: 10.1016/j.jmoldx.2021.12.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 09/13/2021] [Revised: 12/02/2021] [Accepted: 12/28/2021] [Indexed: 12/13/2022] Open
Abstract
Previous studies have described reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in nasopharyngeal/oropharyngeal swab and saliva samples. This multisite clinical evaluation describes the validation of an improved sample preparation method for extraction-free RT-LAMP and reports clinical performance of four RT-LAMP assay formats for SARS-CoV-2 detection. Direct RT-LAMP was performed on 559 swabs and 86,760 saliva samples and RNA RT-LAMP on extracted RNA from 12,619 swabs and 12,521 saliva samples from asymptomatic and symptomatic individuals across health care and community settings. For direct RT-LAMP, overall diagnostic sensitivity (DSe) was 70.35% (95% CI, 63.48%-76.60%) on swabs and 84.62% (95% CI, 79.50%-88.88%) on saliva, with diagnostic specificity of 100% (95% CI, 98.98%-100.00%) on swabs and 100% (95% CI, 99.72%-100.00%) on saliva, compared with quantitative RT-PCR (RT-qPCR); analyzing samples with RT-qPCR ORF1ab CT values of ≤25 and ≤33, DSe values were 100% (95% CI, 96.34%-100%) and 77.78% (95% CI, 70.99%-83.62%) for swabs, and 99.01% (95% CI, 94.61%-99.97%) and 87.61% (95% CI, 82.69%-91.54%) for saliva, respectively. For RNA RT-LAMP, overall DSe and diagnostic specificity were 96.06% (95% CI, 92.88%-98.12%) and 99.99% (95% CI, 99.95%-100%) for swabs, and 80.65% (95% CI, 73.54%-86.54%) and 99.99% (95% CI, 99.95%-100%) for saliva, respectively. These findings demonstrate that RT-LAMP is applicable to a variety of use cases, including frequent, interval-based direct RT-LAMP of saliva from asymptomatic individuals who may otherwise be missed using symptomatic testing alone.
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Affiliation(s)
- Stephen P Kidd
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Daniel Burns
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; School of Electronics and Computer Science, University of Southampton, Southampton, United Kingdom
| | - Bryony Armson
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom; vHive, School of Veterinary Medicine, University of Surrey, Guildford, United Kingdom
| | - Andrew D Beggs
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | | | - Anthony Williams
- University of Southampton and Division of Specialist Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Gemma Snell
- University of Southampton and Division of Specialist Medicine, University Hospital Southampton, Southampton, United Kingdom
| | - Emma L Wise
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Alice Goring
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | | | - Seden Grippon
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Jason Sawyer
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Claire Cassar
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - David Cross
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Thomas Lewis
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Scott M Reid
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Samantha Rivers
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Joe James
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Paul Skinner
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Ashley Banyard
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Kerrie Davies
- Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, United Kingdom
| | - Anetta Ptasinska
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Celina Whalley
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Jack Ferguson
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Claire Bryer
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Charlie Poxon
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Andrew Bosworth
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Michael Kidd
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom; Public Health West Midlands Laboratory, Birmingham, United Kingdom
| | - Alex Richter
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Jane Burton
- High Containment Microbiology, National Infection Service, Public Health England, Porton Down, United Kingdom
| | - Hannah Love
- High Containment Microbiology, National Infection Service, Public Health England, Porton Down, United Kingdom
| | - Sarah Fouch
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Claire Tillyer
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Amy Sowood
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Helen Patrick
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Nathan Moore
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | | | - Nick Morant
- GeneSys Biotech Limited, Camberley, Surrey, United Kingdom
| | - Rebecca Houghton
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom
| | - Joe Parker
- National Biofilms Innovation Centre, University of Southampton, Southampton, United Kingdom
| | | | - Ian Brown
- Animal and Plant Health Agency, Addlestone, Surrey, United Kingdom
| | - Cosima Gretton
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Zandra Deans
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Deborah Porter
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Nicholas J Cortes
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; Gibraltar Health Authority, Gibraltar, United Kingdom
| | - Angela Douglas
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Sue L Hill
- NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
| | - Keith M Godfrey
- National Institute for Health Research Southampton Biomedical Research Centre, University of Southampton and University Hospital, Southampton, United Kingdom; MRC Lifecourse Epidemiology Centre, University of Southampton, Southampton, United Kingdom.
| | - Veronica L Fowler
- Hampshire Hospitals National Health Service (NHS) Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, United Kingdom; NHS Test and Trace Programme, Department of Health and Social Care, London, United Kingdom
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2
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Howson ELA, Kidd SP, Armson B, Goring A, Sawyer J, Cassar C, Cross D, Lewis T, Hockey J, Rivers S, Cawthraw S, Banyard A, Anderson P, Rahou S, Andreou M, Morant N, Clark D, Walsh C, Laxman S, Houghton R, Slater-Jefferies J, Costello P, Brown I, Cortes N, Godfrey KM, Fowler VL. Preliminary optimisation of a simplified sample preparation method to permit direct detection of SARS-CoV-2 within saliva samples using reverse-transcription loop-mediated isothermal amplification (RT-LAMP). J Virol Methods 2021; 289:114048. [PMID: 33358911 PMCID: PMC7750029 DOI: 10.1016/j.jviromet.2020.114048] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/28/2020] [Accepted: 12/12/2020] [Indexed: 11/15/2022]
Abstract
We describe the optimisation of a simplified sample preparation method which permits rapid and direct detection of SARS-CoV-2 RNA within saliva, using reverse-transcription loop-mediated isothermal amplification (RT-LAMP). Treatment of saliva samples prior to RT-LAMP by dilution 1:1 in Mucolyse™, followed by dilution in 10 % (w/v) Chelex© 100 Resin and a 98 °C heat step for 2 min enabled detection of SARS-CoV-2 RNA in positive saliva samples. Using RT-LAMP, SARS-CoV-2 RNA was detected in as little as 05:43 min, with no amplification detected in 3097 real-time reverse transcription PCR (rRT-PCR) negative saliva samples from staff tested within a service evaluation study, or for other respiratory pathogens tested (n = 22). Saliva samples can be collected non-invasively, without the need for skilled staff and can be obtained from both healthcare and home settings. Critically, this approach overcomes the requirement for, and validation of, different swabs and the global bottleneck in obtaining access to extraction robots and reagents to enable molecular testing by rRT-PCR. Such testing opens the possibility of public health approaches for effective intervention during the COVID-19 pandemic through regular SARS-CoV-2 testing at a population scale, combined with isolation and contact tracing.
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Affiliation(s)
- Emma L A Howson
- GeneSys Biotech Limited, Camberley, Surrey, UK; The Pirbright Institute, Ash Road, Woking, Surrey, UK
| | - Stephen P Kidd
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK.
| | - Bryony Armson
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK; vHive, School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Alice Goring
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK
| | - Jason Sawyer
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Claire Cassar
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - David Cross
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Tom Lewis
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Jess Hockey
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | | | | | - Paul Anderson
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Sabah Rahou
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | | | - Nick Morant
- GeneSys Biotech Limited, Camberley, Surrey, UK
| | | | | | | | - Rebecca Houghton
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK
| | | | - Paula Costello
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK
| | - Ian Brown
- Animal and Plant Health Agency, Addlestone, Surrey, UK
| | - Nicholas Cortes
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK; Gibraltar Health Authority, Gibraltar, UK
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK; NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton, UK
| | - Veronica L Fowler
- Hampshire Hospitals NHS Foundation Trust, Department of Microbiology, Basingstoke and North Hants Hospital, Basingstoke, UK
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3
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Fowler VL, Armson B, Gonzales JL, Wise EL, Howson ELA, Vincent-Mistiaen Z, Fouch S, Maltby CJ, Grippon S, Munro S, Jones L, Holmes T, Tillyer C, Elwell J, Sowood A, de Peyer O, Dixon S, Hatcher T, Patrick H, Laxman S, Walsh C, Andreou M, Morant N, Clark D, Moore N, Houghton R, Cortes NJ, Kidd SP. A highly effective reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay for the rapid detection of SARS-CoV-2 infection. J Infect 2021; 82:117-125. [PMID: 33271166 PMCID: PMC7703389 DOI: 10.1016/j.jinf.2020.10.039] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/04/2020] [Accepted: 10/07/2020] [Indexed: 12/23/2022]
Abstract
The COVID-19 pandemic has illustrated the importance of simple, rapid and accurate diagnostic testing. This study describes the validation of a new rapid SARS-CoV-2 RT-LAMP assay for use on extracted RNA or directly from swab offering an alternative diagnostic pathway that does not rely on traditional reagents that are often in short supply during a pandemic. Analytical specificity (ASp) of this new RT-LAMP assay was 100% and analytical sensitivity (ASe) was between 1 × 101 and 1 × 102 copies per reaction when using a synthetic DNA target. The overall diagnostic sensitivity (DSe) and specificity (DSp) of RNA RT-LAMP was 97% and 99% respectively, relative to the standard of care rRT-PCR. When a CT cut-off of 33 was employed, above which increasingly evidence suggests there is a low risk of patients shedding infectious virus, the diagnostic sensitivity was 100%. The DSe and DSp of Direct RT-LAMP (that does not require RNA extraction) was 67% and 97%, respectively. When setting CT cut-offs of ≤33 and ≤25, the DSe increased to 75% and 100%, respectively, time from swab-to-result, CT < 25, was < 15 min. We propose that RNA RT-LAMP could replace rRT-PCR where there is a need for increased sample throughput and Direct RT-LAMP as a near-patient screening tool to rapidly identify highly contagious individuals within emergency departments and care homes during times of increased disease prevalence ensuring negative results still get laboratory confirmation.
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Affiliation(s)
- Veronica L Fowler
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; Eco Animal Health, The Grange, 100 The High Street, London, UK
| | - Bryony Armson
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; School of Veterinary Medicine, University of Surrey, Guildford, UK
| | - Jose L Gonzales
- Wageningen Bioveterinary Research (WBVR), PO Box 65, 8200 AB Lelystad, the Netherlands
| | - Emma L Wise
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Emma L A Howson
- GeneSys Biotech Limited, Camberley, Surrey, UK; The Pirbright Institute, Ash Road, Pirbright, Woking, UK
| | - Zoe Vincent-Mistiaen
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; Gibraltar Health Authority, Gibraltar, UK
| | - Sarah Fouch
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; School of Pharmacy and Biomedical Sciences, University of Portsmouth, UK
| | - Connor J Maltby
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Seden Grippon
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Simon Munro
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Lisa Jones
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Tom Holmes
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Claire Tillyer
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Joanne Elwell
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Amy Sowood
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Oliver de Peyer
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Sophie Dixon
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Thomas Hatcher
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Helen Patrick
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | | | | | | | - Nick Morant
- GeneSys Biotech Limited, Camberley, Surrey, UK
| | | | - Nathan Moore
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Rebecca Houghton
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK
| | - Nicholas J Cortes
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK; Gibraltar Health Authority, Gibraltar, UK
| | - Stephen P Kidd
- Hampshire Hospitals NHS Foundation Trust, Basingstoke & North Hampshire Hospital, Department of Microbiology, Basingstoke, UK.
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Blaser S, Heusser C, Diem H, Von Felten A, Gueuning M, Andreou M, Boonham N, Tomlinson J, Müller P, Utzinger J, Frey JE, Frey B, Bühlmann A. Dispersal of harmful fruit fly pests by international trade and a loop-mediated isothermal amplification assay to prevent their introduction. Geospat Health 2018; 13. [PMID: 30451481 DOI: 10.4081/gh.2018.726] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/19/2018] [Indexed: 06/09/2023]
Abstract
Global trade of plant products represents one of the major driving forces for the spread of invasive insect pests. This visualization illustrates the problem of unintended dispersal of economically harmful fruit fly pests using geospatial maps based on interception data from the Swiss import control process. Furthermore, it reports the development of a molecular diagnostic assay for rapid identification of these pests at points of entry such as sea- and airports as a prevention measure. The assay reliably differentiates between target and non-target species within one hour and has been successfully evaluated for on-site use at a Swiss point of entry.
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Affiliation(s)
- Simon Blaser
- Agroscope, Wädenswil; Swiss Tropical and Public Health Institute, Basel; University of Basel, Basel.
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Blaser S, Diem H, von Felten A, Gueuning M, Andreou M, Boonham N, Tomlinson J, Müller P, Utzinger J, Frey B, Frey JE, Bühlmann A. A Loop-mediated Isothermal Amplification (LAMP) Assay for Rapid Identification of Bemisia tabaci. J Vis Exp 2018. [PMID: 30417877 PMCID: PMC6235616 DOI: 10.3791/58502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The whitefly Bemisia tabaci (Gennadius) is an invasive pest of considerable importance, affecting the production of vegetable and ornamental crops in many countries around the world. Severe yield losses are caused by direct feeding, and even more importantly, also by the transmission of more than 100 harmful plant pathogenic viruses. As for other invasive pests, increased international trade facilitates the dispersal of B. tabaci to areas beyond its native range. Inspections of plant import products at points of entry such as seaports and airports are, therefore, seen as an important prevention measure. However, this last line of defense against pest invasions is only effective if rapid identification methods for suspicious insect specimens are readily available. Because the morphological differentiation between the regulated B. tabaci and close relatives without quarantine status is difficult for non-taxonomists, a rapid molecular identification assay based on the loop-mediated isothermal amplification (LAMP) technology has been developed. This publication reports the detailed protocol of the novel assay describing rapid DNA extraction, set-up of the LAMP reaction, as well as interpretation of its read-out, which allows identifying B. tabaci specimens within one hour. Compared to existing protocols for the detection of specific B. tabaci biotypes, the developed method targets the whole B. tabaci species complex in one assay. Moreover the assay is designed to be applied on-site by plant health inspectors with minimal laboratory training directly at points of entry. Thorough validation performed under laboratory and on-site conditions demonstrates that the reported LAMP assay is a rapid and reliable identification tool, improving the management of B. tabaci.
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Affiliation(s)
- Simon Blaser
- Department of Method Development and Analytics, Agroscope; Swiss Tropical and Public Health Institute; University of Basel;
| | - Hanspeter Diem
- Swiss Federal Plant Protection Service, Federal Office for Agriculture
| | | | | | | | - Neil Boonham
- Fera Science Limited; School of Natural and Environmental Sciences, Newcastle University
| | | | - Pie Müller
- Swiss Tropical and Public Health Institute; University of Basel
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute; University of Basel
| | - Beatrice Frey
- Department of Method Development and Analytics, Agroscope
| | - Jürg E Frey
- Department of Method Development and Analytics, Agroscope
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6
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Blaser S, Diem H, von Felten A, Gueuning M, Andreou M, Boonham N, Tomlinson J, Müller P, Utzinger J, Frey JE, Bühlmann A. From laboratory to point of entry: development and implementation of a loop-mediated isothermal amplification (LAMP)-based genetic identification system to prevent introduction of quarantine insect species. Pest Manag Sci 2018; 74:1504-1512. [PMID: 29363271 PMCID: PMC5969315 DOI: 10.1002/ps.4866] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [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: 10/06/2017] [Revised: 01/12/2018] [Accepted: 01/12/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Rapid genetic on-site identification methods at points of entry, such as seaports and airports, have the potential to become important tools to prevent the introduction and spread of economically harmful pest species that are unintentionally transported by the global trade of plant commodities. This paper reports the development and evaluation of a loop-mediated isothermal amplification (LAMP)-based identification system to prevent introduction of the three most frequently encountered regulated quarantine insect species groups at Swiss borders, Bemisia tabaci, Thrips palmi and several regulated fruit flies of the genera Bactrocera and Zeugodacus. RESULTS The LAMP primers were designed to target a fragment of the mitochondrial cytochrome c oxidase subunit I gene and were generated based on publicly available DNA sequences. Laboratory evaluations analysing 282 insect specimens suspected to be quarantine organisms revealed an overall test efficiency of 99%. Additional on-site evaluation at a point of entry using 37 specimens performed by plant health inspectors with minimal laboratory training resulted in an overall test efficiency of 95%. During both evaluation rounds, there were no false-positives and the observed false-negatives were attributable to human-induced manipulation errors. To overcome the possibility of accidental introduction of pests as a result of rare false-negative results, samples yielding negative results in the LAMP method were also subjected to DNA barcoding. CONCLUSION Our LAMP assays reliably differentiated between the tested regulated and non-regulated insect species within <1 h. Hence, LAMP assays represent suitable tools for rapid on-site identification of harmful pests, which might facilitate an accelerated import control process for plant commodities. © 2018 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Simon Blaser
- Agroscope, Department of Method Development and AnalyticsWädenswilSwitzerland
- Swiss Tropical and Public Health InstituteBaselSwitzerland
- University of BaselBaselSwitzerland
| | - Hanspeter Diem
- Federal Office for AgricultureSwiss Federal Plant Protection Service, Zurich AirportZurichSwitzerland
| | - Andreas von Felten
- Federal Office for AgricultureSwiss Federal Plant Protection ServiceBernSwitzerland
| | - Morgan Gueuning
- Agroscope, Department of Method Development and AnalyticsWädenswilSwitzerland
| | | | - Neil Boonham
- The Food and Environment Research AgencyYorkUK
- Newcastle UniversityNewcastle upon TyneUK
| | | | - Pie Müller
- Swiss Tropical and Public Health InstituteBaselSwitzerland
- University of BaselBaselSwitzerland
| | - Jürg Utzinger
- Swiss Tropical and Public Health InstituteBaselSwitzerland
- University of BaselBaselSwitzerland
| | - Jürg E Frey
- Agroscope, Department of Method Development and AnalyticsWädenswilSwitzerland
| | - Andreas Bühlmann
- Agroscope, Department of Plants and Plant ProductsWädenswilSwitzerland
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7
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Romero M, D'Agostino M, Arias AP, Robles S, Casado CF, Iturbe LO, Lerma OG, Andreou M, Cook N. An immunomagnetic separation/loop-mediated isothermal amplification method for rapid direct detection of thermotolerant Campylobacter
spp. during poultry production. J Appl Microbiol 2016; 120:469-77. [DOI: 10.1111/jam.13008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/06/2015] [Accepted: 11/13/2015] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - S. Robles
- Fera Science Ltd.; Sand Hutton York UK
| | | | | | | | | | - N. Cook
- Fera Science Ltd.; Sand Hutton York UK
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8
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Michalitsi M, Boultadaki A, Floros J, Rouchota M, Argyrou M, Valassi A, Baka I, Letsas B, Synefia S, Andreou M, Koutoulides B, Lyra M. Effective dose estimate and implementation of the size-specific dose estimate index in multiple myeloma patients examined by low dose MDCT Protocol. Phys Med 2014. [DOI: 10.1016/j.ejmp.2014.07.176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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Richardson JA, Morgan T, Andreou M, Brown T. Use of a large Stokes-shift fluorophore to increase the multiplexing capacity of a point-of-care DNA diagnostic device. Analyst 2013; 138:3626-8. [PMID: 23675581 DOI: 10.1039/c3an00593c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The intense demand for fluorescence-based point of care (POC) DNA diagnostics is driving developments to reduce the size of instrumentation, imposing limitations on the optical hardware that can be included. Here we describe a combination of instrumentation and fluorogenic probes to detect three fluorophores using two excitation and two detection channels.
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Affiliation(s)
- James A Richardson
- Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
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Bühlmann A, Pothier JF, Rezzonico F, Smits THM, Andreou M, Boonham N, Duffy B, Frey JE. Erwinia amylovora loop-mediated isothermal amplification (LAMP) assay for rapid pathogen detection and on-site diagnosis of fire blight. J Microbiol Methods 2012; 92:332-9. [PMID: 23275135 DOI: 10.1016/j.mimet.2012.12.017] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 12/17/2012] [Accepted: 12/20/2012] [Indexed: 11/16/2022]
Abstract
Several molecular methods have been developed for the detection of Erwinia amylovora, the causal agent of fire blight in pear and apple, but none are truly applicable for on-site use in the field. We developed a fast, reliable and field applicable detection method using a novel target on the E. amylovora chromosome that we identified by applying a comparative genomic pipeline. The target coding sequences (CDSs) are both uniquely specific for and all-inclusive of E. amylovora genotypes. This avoids potential false negatives that can occur with most commonly used methods based on amplification of plasmid gene targets, which can vary among strains. Loop-mediated isothermal AMPlification (LAMP) with OptiGene Genie II chemistry and instrumentation proved to be an exceptionally rapid (under 15 min) and robust method for detecting E. amylovora in orchards, as well as simple to use in the plant diagnostic laboratory. Comparative validation results using plant samples from inoculated greenhouse trials and from natural field infections (of regional and temporal diverse origin) showed that our LAMP had an equivalent or greater performance regarding sensitivity, specificity, speed and simplicity than real-time PCR (TaqMan), other LAMP assays, immunoassays and plating, demonstrating its utility for routine testing.
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Affiliation(s)
- Andreas Bühlmann
- Agroscope Changins-Wädenswil Research Station ACW, Plant Protection Division, CH-8820 Wädenswil, Switzerland
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Andreou M, Delipetrou P, Kadis C, Tsiamis G, Bourtzis K, Georghiou K. An integrated approach for the conservation of threatened plants: The case of Arabis kennedyae (Brassicaceae). Acta Oecologica 2011. [DOI: 10.1016/j.actao.2011.02.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Efstathopoulos EP, Pantos I, Andreou M, Gkatzis A, Carinou E, Koukorava C, Kelekis NL, Brountzos E. Occupational radiation doses to the extremities and the eyes in interventional radiology and cardiology procedures. Br J Radiol 2011; 84:70-7. [PMID: 21172967 DOI: 10.1259/bjr/83222759] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVES The aim of this study was to determine occupational dose levels in interventional radiology and cardiology procedures. METHODS The study covered a sample of 25 procedures and monitored occupational dose for all laboratory personnel. Each individual wore eight thermoluminescent dosemeters next to the eyes, wrists, fingers and legs during each procedure. Radiation protection shields used in each procedure were recorded. RESULTS The highest doses per procedure were recorded for interventionists at the left wrist (average 485 μSv, maximum 5239 μSv) and left finger (average 324 μSv, maximum 2877 μSv), whereas lower doses were recorded for the legs (average 124 μSv, maximum 1959 μSv) and the eyes (average 64 μSv, maximum 1129 μSv). Doses to the assisting nurses during the intervention were considerably lower; the highest doses were recorded at the wrists (average 26 μSv, maximum 41 μSv) and legs (average 18 μSv, maximum 22 μSv), whereas doses to the eyes were minimal (average 4 μSv, maximum 16 μSv). Occupational doses normalised to kerma area product (KAP) ranged from 11.9 to 117.3 μSv/1000 cGy cm² and KAP was poorly correlated to the interventionists' extremity doses. CONCLUSION Calculation of the dose burden for interventionists considering the actual number of procedures performed annually revealed that dose limits for the extremities and the lenses of the eyes were not exceeded. However, there are cases in which high doses have been recorded and this can lead to exceeding the dose limits when bad practices are followed and the radiation protection tools are not properly used.
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Affiliation(s)
- E P Efstathopoulos
- Second Department of Radiology, Medical School, University of Athens, Greece.
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