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

Stephen P Kidd; Daniel Burns; Bryony Armson; Andrew D Beggs; Emma L A Howson; Anthony Williams; Gemma Snell; Emma L Wise; Alice Goring; Zoe Vincent-Mistiaen; Seden Grippon; Jason Sawyer; Claire Cassar; David Cross; Thomas Lewis; Scott M Reid; Samantha Rivers; Joe James; Paul Skinner; Ashley Banyard; Kerrie Davies; Anetta Ptasinska; Celina Whalley; Jack Ferguson; Claire Bryer; Charlie Poxon; Andrew Bosworth; Michael Kidd; Alex Richter; Jane Burton; Hannah Love; Sarah Fouch; Claire Tillyer; Amy Sowood; Helen Patrick; Nathan Moore; Michael Andreou; Nick Morant; Rebecca Houghton; Joe Parker; Joanne Slater-Jefferies; Ian Brown; Cosima Gretton; Zandra Deans; Deborah Porter; Nicholas J Cortes; Angela Douglas; Sue L Hill; Keith M Godfrey; Veronica L Fowler

doi:10.1016/j.jmoldx.2021.12.007

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

Stephen P Kidd, Daniel Burns, Bryony Armson, Andrew D Beggs, Emma L A Howson, Anthony Williams, Gemma Snell, Emma L Wise, Alice Goring, Zoe Vincent-Mistiaen, Seden Grippon, Jason Sawyer, Claire Cassar, David Cross, Thomas Lewis, Scott M Reid, Samantha Rivers, Joe James, Paul Skinner, Ashley BanyardKerrie Davies, Anetta Ptasinska, Celina Whalley, Jack Ferguson, Claire Bryer, Charlie Poxon, Andrew Bosworth, Michael Kidd, Alex Richter, Jane Burton, Hannah Love, Sarah Fouch, Claire Tillyer, Amy Sowood, Helen Patrick, Nathan Moore, Michael Andreou, Nick Morant, Rebecca Houghton, Joe Parker, Joanne Slater-Jefferies, Ian Brown, Cosima Gretton, Zandra Deans, Deborah Porter, Nicholas J Cortes, Angela Douglas, Sue L Hill, Keith M Godfrey^*, Veronica L Fowler

^*Corresponding author for this work

Cancer and Genomic Sciences

Research output: Contribution to journal › Article › peer-review

60 Downloads (Pure)

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 C_T 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.

Original language	English
Pages (from-to)	320-336
Number of pages	17
Journal	Journal of Molecular Diagnostics
Volume	24
Issue number	4
Early online date	2 Feb 2022
DOIs	https://doi.org/10.1016/j.jmoldx.2021.12.007
Publication status	Published - Apr 2022

Bibliographical note

Funding Information:
OptiGene Ltd. supplied reagents free of charge for this study. Supported in part by a UK Department of Health and Social Care award to the University of Southampton grant reference number 2020/032 (feasibility study for city-wide testing using saliva 315 based LAMP testing). The views expressed are those of the authors and not necessarily those of the Department of Health and Social Care. K.M.G. is supported by the UK Medical Research Council MC_UU_12011/4, the National Institute for Health Research (NIHR) Senior Investigator NF-SI-0515-318 10042 and NIHR Southampton Biomedical Research Center IS-BRC-1215-20004, and the British Heart Foundation RG/15/17/3174. For part of this project, E.L.A.H. was on secondment at GeneSys Biotech Ltd, which was part supported by The Pirbright Institute Flexible Talent Mobility Account under Biotechnology and Biological Sciences Research Council grant BB/S507945/1. A.D.B. is currently supported by a Cancer Research UK Advanced Clinician Scientist award C31641/A23923, and his laboratory is supported by CRUK Center Birmingham C17422/A25154 and the Birmingham Experimental Cancer Medicine Center C11497/A25127. V.L.F., S.P.K., B.A., and Z.D. were on secondment to the Department of Health and Social Care for a period during this study. Animal and Plant Health Agency laboratory activities and expertise were supported by both the Safe and Certain project APHACSKL0085 and Defra project APHANSOM0416.Disclosures: M.A. is an employee of OptiSense Limited, and N.M. is an employee of GeneSys Biotech Limited; neither had any role in study design or data analysis. K.M.G. is part of an academic consortium that has received research funding from Abbott Nutrition, Nestec, BenevolentAI Bio Ltd, and Danone.

Funding Information:
OptiGene Ltd. supplied reagents free of charge for this study. Supported in part by a UK Department of Health and Social Care award to the University of Southampton grant reference number 2020/032 (feasibility study for city-wide testing using saliva 315 based LAMP testing). The views expressed are those of the authors and not necessarily those of the Department of Health and Social Care. K.M.G. is supported by the UK Medical Research Council MC_UU_12011/4 , the National Institute for Health Research (NIHR) Senior Investigator NF-SI-0515-318 10042 and NIHR Southampton Biomedical Research Center IS-BRC-1215-20004 , and the British Heart Foundation RG/15/17/3174 . For part of this project, E.L.A.H. was on secondment at GeneSys Biotech Ltd, which was part supported by The Pirbright Institute Flexible Talent Mobility Account under Biotechnology and Biological Sciences Research Council grant BB/S507945/1. A.D.B. is currently supported by a Cancer Research UK Advanced Clinician Scientist award C31641/A23923 , and his laboratory is supported by CRUK Center Birmingham C17422/A25154 and the Birmingham Experimental Cancer Medicine Center C11497/A25127 . V.L.F., S.P.K., B.A., and Z.D. were on secondment to the Department of Health and Social Care for a period during this study. Animal and Plant Health Agency laboratory activities and expertise were supported by both the Safe and Certain project APHACSKL0085 and Defra project APHANSOM0416 .

Publisher Copyright:
© 2022 Association for Molecular Pathology and American Society for Investigative Pathology

Keywords

COVID-19/diagnosis
COVID-19 Testing
Humans
Molecular Diagnostic Techniques/methods
Nucleic Acid Amplification Techniques/methods
RNA, Viral/analysis
SARS-CoV-2/genetics
Saliva
Sensitivity and Specificity

Access to Document

10.1016/j.jmoldx.2021.12.007Licence: Creative Commons: Attribution (CC BY)

KiddS2022ReverseFinal published version, 2.34 MBLicence: Creative Commons: Attribution (CC BY)

Fingerprint

Dive into the research topics of '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'. Together they form a unique fingerprint.

Cite this

Kidd, S. P., Burns, D., Armson, B., Beggs, A. D., Howson, E. L. A., Williams, A., Snell, G., Wise, E. L., Goring, A., Vincent-Mistiaen, Z., Grippon, S., Sawyer, J., Cassar, C., Cross, D., Lewis, T., Reid, S. M., Rivers, S., James, J., Skinner, P., ... Fowler, V. L. (2022). 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. Journal of Molecular Diagnostics, 24(4), 320-336. Advance online publication. https://doi.org/10.1016/j.jmoldx.2021.12.007

@article{678372fb13f54310af6d54455adf191d,

title = "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",

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.",

keywords = "COVID-19/diagnosis, COVID-19 Testing, Humans, Molecular Diagnostic Techniques/methods, Nucleic Acid Amplification Techniques/methods, RNA, Viral/analysis, SARS-CoV-2/genetics, Saliva, Sensitivity and Specificity",

author = "Kidd, {Stephen P} and Daniel Burns and Bryony Armson and Beggs, {Andrew D} and Howson, {Emma L A} and Anthony Williams and Gemma Snell and Wise, {Emma L} and Alice Goring and Zoe Vincent-Mistiaen and Seden Grippon and Jason Sawyer and Claire Cassar and David Cross and Thomas Lewis and Reid, {Scott M} and Samantha Rivers and Joe James and Paul Skinner and Ashley Banyard and Kerrie Davies and Anetta Ptasinska and Celina Whalley and Jack Ferguson and Claire Bryer and Charlie Poxon and Andrew Bosworth and Michael Kidd and Alex Richter and Jane Burton and Hannah Love and Sarah Fouch and Claire Tillyer and Amy Sowood and Helen Patrick and Nathan Moore and Michael Andreou and Nick Morant and Rebecca Houghton and Joe Parker and Joanne Slater-Jefferies and Ian Brown and Cosima Gretton and Zandra Deans and Deborah Porter and Cortes, {Nicholas J} and Angela Douglas and Hill, {Sue L} and Godfrey, {Keith M} and Fowler, {Veronica L}",

note = "Funding Information: OptiGene Ltd. supplied reagents free of charge for this study. Supported in part by a UK Department of Health and Social Care award to the University of Southampton grant reference number 2020/032 (feasibility study for city-wide testing using saliva 315 based LAMP testing). The views expressed are those of the authors and not necessarily those of the Department of Health and Social Care. K.M.G. is supported by the UK Medical Research Council MC_UU_12011/4, the National Institute for Health Research (NIHR) Senior Investigator NF-SI-0515-318 10042 and NIHR Southampton Biomedical Research Center IS-BRC-1215-20004, and the British Heart Foundation RG/15/17/3174. For part of this project, E.L.A.H. was on secondment at GeneSys Biotech Ltd, which was part supported by The Pirbright Institute Flexible Talent Mobility Account under Biotechnology and Biological Sciences Research Council grant BB/S507945/1. A.D.B. is currently supported by a Cancer Research UK Advanced Clinician Scientist award C31641/A23923, and his laboratory is supported by CRUK Center Birmingham C17422/A25154 and the Birmingham Experimental Cancer Medicine Center C11497/A25127. V.L.F., S.P.K., B.A., and Z.D. were on secondment to the Department of Health and Social Care for a period during this study. Animal and Plant Health Agency laboratory activities and expertise were supported by both the Safe and Certain project APHACSKL0085 and Defra project APHANSOM0416.Disclosures: M.A. is an employee of OptiSense Limited, and N.M. is an employee of GeneSys Biotech Limited; neither had any role in study design or data analysis. K.M.G. is part of an academic consortium that has received research funding from Abbott Nutrition, Nestec, BenevolentAI Bio Ltd, and Danone. Funding Information: OptiGene Ltd. supplied reagents free of charge for this study. Supported in part by a UK Department of Health and Social Care award to the University of Southampton grant reference number 2020/032 (feasibility study for city-wide testing using saliva 315 based LAMP testing). The views expressed are those of the authors and not necessarily those of the Department of Health and Social Care. K.M.G. is supported by the UK Medical Research Council MC_UU_12011/4 , the National Institute for Health Research (NIHR) Senior Investigator NF-SI-0515-318 10042 and NIHR Southampton Biomedical Research Center IS-BRC-1215-20004 , and the British Heart Foundation RG/15/17/3174 . For part of this project, E.L.A.H. was on secondment at GeneSys Biotech Ltd, which was part supported by The Pirbright Institute Flexible Talent Mobility Account under Biotechnology and Biological Sciences Research Council grant BB/S507945/1. A.D.B. is currently supported by a Cancer Research UK Advanced Clinician Scientist award C31641/A23923 , and his laboratory is supported by CRUK Center Birmingham C17422/A25154 and the Birmingham Experimental Cancer Medicine Center C11497/A25127 . V.L.F., S.P.K., B.A., and Z.D. were on secondment to the Department of Health and Social Care for a period during this study. Animal and Plant Health Agency laboratory activities and expertise were supported by both the Safe and Certain project APHACSKL0085 and Defra project APHANSOM0416 . Publisher Copyright: {\textcopyright} 2022 Association for Molecular Pathology and American Society for Investigative Pathology",

year = "2022",

month = apr,

doi = "10.1016/j.jmoldx.2021.12.007",

language = "English",

volume = "24",

pages = "320--336",

journal = "Journal of Molecular Diagnostics",

issn = "1525-1578",

publisher = "Association of Molecular Pathology",

number = "4",

}

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 2022, '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', Journal of Molecular Diagnostics, vol. 24, no. 4, pp. 320-336. https://doi.org/10.1016/j.jmoldx.2021.12.007

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. / Kidd, Stephen P; Burns, Daniel; Armson, Bryony et al.
In: Journal of Molecular Diagnostics, Vol. 24, No. 4, 04.2022, p. 320-336.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - 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

AU - Kidd, Stephen P

AU - Burns, Daniel

AU - Armson, Bryony

AU - Beggs, Andrew D

AU - Howson, Emma L A

AU - Williams, Anthony

AU - Snell, Gemma

AU - Wise, Emma L

AU - Goring, Alice

AU - Vincent-Mistiaen, Zoe

AU - Grippon, Seden

AU - Sawyer, Jason

AU - Cassar, Claire

AU - Cross, David

AU - Lewis, Thomas

AU - Reid, Scott M

AU - Rivers, Samantha

AU - James, Joe

AU - Skinner, Paul

AU - Banyard, Ashley

AU - Davies, Kerrie

AU - Ptasinska, Anetta

AU - Whalley, Celina

AU - Ferguson, Jack

AU - Bryer, Claire

AU - Poxon, Charlie

AU - Bosworth, Andrew

AU - Kidd, Michael

AU - Richter, Alex

AU - Burton, Jane

AU - Love, Hannah

AU - Fouch, Sarah

AU - Tillyer, Claire

AU - Sowood, Amy

AU - Patrick, Helen

AU - Moore, Nathan

AU - Andreou, Michael

AU - Morant, Nick

AU - Houghton, Rebecca

AU - Parker, Joe

AU - Slater-Jefferies, Joanne

AU - Brown, Ian

AU - Gretton, Cosima

AU - Deans, Zandra

AU - Porter, Deborah

AU - Cortes, Nicholas J

AU - Douglas, Angela

AU - Hill, Sue L

AU - Godfrey, Keith M

AU - Fowler, Veronica L

N1 - Funding Information: OptiGene Ltd. supplied reagents free of charge for this study. Supported in part by a UK Department of Health and Social Care award to the University of Southampton grant reference number 2020/032 (feasibility study for city-wide testing using saliva 315 based LAMP testing). The views expressed are those of the authors and not necessarily those of the Department of Health and Social Care. K.M.G. is supported by the UK Medical Research Council MC_UU_12011/4, the National Institute for Health Research (NIHR) Senior Investigator NF-SI-0515-318 10042 and NIHR Southampton Biomedical Research Center IS-BRC-1215-20004, and the British Heart Foundation RG/15/17/3174. For part of this project, E.L.A.H. was on secondment at GeneSys Biotech Ltd, which was part supported by The Pirbright Institute Flexible Talent Mobility Account under Biotechnology and Biological Sciences Research Council grant BB/S507945/1. A.D.B. is currently supported by a Cancer Research UK Advanced Clinician Scientist award C31641/A23923, and his laboratory is supported by CRUK Center Birmingham C17422/A25154 and the Birmingham Experimental Cancer Medicine Center C11497/A25127. V.L.F., S.P.K., B.A., and Z.D. were on secondment to the Department of Health and Social Care for a period during this study. Animal and Plant Health Agency laboratory activities and expertise were supported by both the Safe and Certain project APHACSKL0085 and Defra project APHANSOM0416.Disclosures: M.A. is an employee of OptiSense Limited, and N.M. is an employee of GeneSys Biotech Limited; neither had any role in study design or data analysis. K.M.G. is part of an academic consortium that has received research funding from Abbott Nutrition, Nestec, BenevolentAI Bio Ltd, and Danone. Funding Information: OptiGene Ltd. supplied reagents free of charge for this study. Supported in part by a UK Department of Health and Social Care award to the University of Southampton grant reference number 2020/032 (feasibility study for city-wide testing using saliva 315 based LAMP testing). The views expressed are those of the authors and not necessarily those of the Department of Health and Social Care. K.M.G. is supported by the UK Medical Research Council MC_UU_12011/4 , the National Institute for Health Research (NIHR) Senior Investigator NF-SI-0515-318 10042 and NIHR Southampton Biomedical Research Center IS-BRC-1215-20004 , and the British Heart Foundation RG/15/17/3174 . For part of this project, E.L.A.H. was on secondment at GeneSys Biotech Ltd, which was part supported by The Pirbright Institute Flexible Talent Mobility Account under Biotechnology and Biological Sciences Research Council grant BB/S507945/1. A.D.B. is currently supported by a Cancer Research UK Advanced Clinician Scientist award C31641/A23923 , and his laboratory is supported by CRUK Center Birmingham C17422/A25154 and the Birmingham Experimental Cancer Medicine Center C11497/A25127 . V.L.F., S.P.K., B.A., and Z.D. were on secondment to the Department of Health and Social Care for a period during this study. Animal and Plant Health Agency laboratory activities and expertise were supported by both the Safe and Certain project APHACSKL0085 and Defra project APHANSOM0416 . Publisher Copyright: © 2022 Association for Molecular Pathology and American Society for Investigative Pathology

PY - 2022/4

Y1 - 2022/4

N2 - 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.

AB - 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.

KW - COVID-19/diagnosis

KW - COVID-19 Testing

KW - Humans

KW - Molecular Diagnostic Techniques/methods

KW - Nucleic Acid Amplification Techniques/methods

KW - RNA, Viral/analysis

KW - SARS-CoV-2/genetics

KW - Saliva

KW - Sensitivity and Specificity

UR - http://www.scopus.com/inward/record.url?scp=85127186667&partnerID=8YFLogxK

U2 - 10.1016/j.jmoldx.2021.12.007

DO - 10.1016/j.jmoldx.2021.12.007

M3 - Article

C2 - 35121140

SN - 1525-1578

VL - 24

SP - 320

EP - 336

JO - Journal of Molecular Diagnostics

JF - Journal of Molecular Diagnostics

IS - 4

ER -

Kidd SP, Burns D, Armson B, Beggs AD, Howson ELA, Williams A et al. 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. Journal of Molecular Diagnostics. 2022 Apr;24(4):320-336. Epub 2022 Feb 2. doi: 10.1016/j.jmoldx.2021.12.007