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RT-LAMP has high accuracy for detecting SARS-CoV-2 in saliva and naso/oropharyngeal swabs from asymptomatic and symptomatic individuals
Stephen P Kidd; Dan Burns; Bryony Armson; Andrew D Beggs; Emma L. A Howson; Anthony P Williams; Gemma Snell; Emma L Wise; Alice Goring; Zoe Vincent-Mistiaen; Sedon Grippon; Jason Sawyer; Claire Cassar; David Cross; Tom Lewis; Scott M Reid; Samantha Rivers; Joe James; Paul Skinner; Kerry Davies; Anetta Ptasinska; Celina Whalley; Jack Ferguson; Claire Bryer; Charlie Poxen; Andrew Bosworth; Michael Kidd; Alex Richter; Jane Burton; Hannah Love; Sarah Fouch; Nathan Moore; Michael Andreou; Nick Morant; Rebecca Houghton; Joe Parker; Joanne Slater-Jefferies; Ian Brown; Zandra Deans; Cosima Gretton; Deborah Porter; Nicholas J Cortes; Angela Douglas; Sue L Hill; Keith M Godfrey; Veronica L Fowler.
Affiliation
  • Stephen P Kidd; Hampshire Hospitals NHS Foundation Trust
  • Dan Burns; School of Electronics and Computer Science, University of Southampton
  • Bryony Armson; vHive, School of Veterinary Medicine, University of Surrey
  • Andrew D Beggs; University of Birmingham
  • Emma L. A Howson; The Pirbright Institute
  • Anthony P Williams; Division of Specialist Medicine, University of Southampton
  • Gemma Snell; Division of Specialist Medicine, University Hospital Southampton
  • Emma L Wise; School of Biosciences and Medicine, University of Surrey
  • Alice Goring; Hampshire Hospitals NHS Foundation Trust
  • Zoe Vincent-Mistiaen; Gibraltar Health Authority
  • Sedon Grippon; Hampshire Hospitals NHS Foundation Trust
  • Jason Sawyer; Animal and Plant Health Agency
  • Claire Cassar; Animal and Plant Health Agency
  • David Cross; Animal and Plant Health Agency
  • Tom Lewis; Animal and Plant Health Agency
  • Scott M Reid; Animal and Plant Health Agency
  • Samantha Rivers; Animal and Plant Health Agency
  • Joe James; Animal and Plant Health Agency
  • Paul Skinner; Animal and Plant Health Agency
  • Kerry Davies; Leeds Teaching Hospitals NHS Trust
  • Anetta Ptasinska; University Hospitals Birmingham NHS Foundation Trust
  • Celina Whalley; University Hospitals Birmingham NHS Foundation Trust
  • Jack Ferguson; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
  • Claire Bryer; University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
  • Charlie Poxen; University Hospitals Birmingham NHS Foundation Trust
  • Andrew Bosworth; University Hospitals Birmingham NHS Foundation Trust
  • Michael Kidd; Public Health West Midlands Laboratory
  • Alex Richter; Institute of Immunology and Immunotherapy, University of Birmingham
  • Jane Burton; National Infection Service, Public Health England
  • Hannah Love; National Infection Service, Public Health England
  • Sarah Fouch; Hampshire Hospitals NHS Foundation Trust
  • Nathan Moore; Hampshire Hospitals NHS Foundation Trust
  • Michael Andreou; OptiSense Limited
  • Nick Morant; GeneSys Biotech Limited
  • Rebecca Houghton; Hampshire Hospitals NHS Foundation Trust
  • Joe Parker; National Biofilms Innovation Centre, University of Southampton
  • Joanne Slater-Jefferies; National Biofilms Innovation Centre, University of Southampton
  • Ian Brown; Animal and Plant Health Agency
  • Zandra Deans; NHS Test and Trace Programme, Department of Health and Social Care
  • Cosima Gretton; NHS Test and Trace Programme, Department of Health and Social Care
  • Deborah Porter; NHS Test and Trace Programme, Department of Health and Social Care
  • Nicholas J Cortes; Hampshire Hospitals NHS Foundation Trust & Gibraltar Health Authority
  • Angela Douglas; NHS Test and Trace Programme, Department of Health and Social Care
  • Sue L Hill; NHS Test and Trace Programme, Department of Health and Social Care
  • Keith M Godfrey; NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital
  • Veronica L Fowler; NHS Test and Trace Programme, Department of Health and Social Care
Preprint in English | medRxiv | ID: ppmedrxiv-21259398
ABSTRACT
Previous studies have described RT-LAMP methodology for the rapid detection of SARS-CoV-2 in nasopharyngeal (NP) and oropharyngeal (OP) swab and saliva samples. This study describes the validation of an improved sample preparation method for extraction free RT-LAMP and defines the clinical performance of four different RT-LAMP assay formats for detection of SARS-CoV-2 within a multisite clinical evaluation. 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 from asymptomatic and symptomatic individuals across healthcare and community settings. For Direct RT-LAMP, overall diagnostic sensitivity (DSe) of 70.35% (95% CI 63.48-76.60%) on swabs and 84.62% (79.50-88.88%) on saliva was observed, with diagnostic specificity (DSp) of 100% (98.98-100.00%) on swabs and 100% (99.72-100.00%) on saliva when compared to RT-qPCR; analysing samples with RT-qPCR ORF1ab CT values of [≤]25 and [≤]33, DSe of 100% (96.34-100%) and 77.78% (70.99-83.62%) for swabs were observed, and 99.01% (94.61-99.97%) and 87.61% (82.69-91.54%) for saliva, respectively. For RNA RT-LAMP, overall DSe and DSp were 96.06% (92.88-98.12%) and 99.99% (99.95-100%) for swabs, and 80.65% (73.54-86.54%) and 99.99% (99.95-100%) for saliva, respectively. These findings demonstrate that RT-LAMP is applicable to a variety of use-cases, including frequent, interval-based testing of saliva with Direct RT-LAMP from asymptomatic individuals that may otherwise be missed using symptomatic testing alone.
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Full text: Available Collection: Preprints Database: medRxiv Type of study: Diagnostic study / Experimental_studies / Prognostic study Language: English Year: 2021 Document type: Preprint
Fulltext
Add to My VHL
Print
XML
Search on Google
Full text: Available Collection: Preprints Database: medRxiv Type of study: Diagnostic study / Experimental_studies / Prognostic study Language: English Year: 2021 Document type: Preprint