Please use this identifier to cite or link to this item: https://ahro.austin.org.au/austinjspui/handle/1/24521
Title: Validation of a single-step, single-tube reverse transcription loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA.
Austin Authors: Lee, Jean Y H;Best, Nickala;McAuley, Julie;Porter, Jessica L;Seemann, Torsten;Schultz, Mark B;Sait, Michelle;Orlando, Nicole;Mercoulia, Karolina;Ballard, Susan A;Druce, Julian;Tran, Thomas;Catton, Mike G;Pryor, Melinda J;Cui, Huanhuan L;Luttick, Angela;McDonald, Sean;Greenhalgh, Arran;Kwong, Jason C ;Sherry, Norelle L ;Graham, Maryza;Hoang, Tuyet;Herisse, Marion;Pidot, Sacha J;Williamson, Deborah A;Howden, Benjamin P ;Monk, Ian R;Stinear, Timothy P
Affiliation: Department of Infectious Diseases, Monash Health, Clayton, Victoria, Australia
GenWorks Pty Ltd, Thebarton, South Australia, Australia
Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
Victorian Infectious Diseases Reference Laboratory, Melbourne Health at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
360Biolabs, Melbourne, Victoria, Australia
GenWorks Pty Ltd, Thebarton, South Australia, Australia
Infectious Diseases
Department of Microbiology, Monash Health, Clayton, Victoria, Australia
Melbourne Health, Melbourne, Victoria, Australia
Issue Date: Sep-2020
Date: 2020-07-31
Publication information: Journal of Medical Microbiology 2020; 69(6): 1169-1178
Abstract: Introduction. The SARS-CoV-2 pandemic of 2020 has resulted in unparalleled requirements for RNA extraction kits and enzymes required for virus detection, leading to global shortages. This has necessitated the exploration of alternative diagnostic options to alleviate supply chain issues.Aim. To establish and validate a reverse transcription loop-mediated isothermal amplification (RT- LAMP) assay for the detection of SARS-CoV-2 from nasopharyngeal swabs.Methodology. We used a commercial RT-LAMP mastermix from OptiGene in combination with a primer set designed to detect the CDC N1 region of the SARS-CoV-2 nucleocapsid (N) gene. A single-tube, single-step fluorescence assay was implemented whereby 1 µl of universal transport medium (UTM) directly from a nasopharyngeal swab could be used as template, bypassing the requirement for RNA purification. Amplification and detection could be conducted in any thermocycler capable of holding 65 °C for 30 min and measure fluorescence in the FAM channel at 1 min intervals.Results. Assay evaluation by assessment of 157 clinical specimens previously screened by E-gene RT-qPCR revealed assay sensitivity and specificity of 87 and 100%, respectively. Results were fast, with an average time-to-positive (Tp) for 93 clinical samples of 14 min (sd±7 min). Using dilutions of SARS-CoV-2 virus spiked into UTM, we also evaluated assay performance against FDA guidelines for implementation of emergency-use diagnostics and established a limit-of-detection of 54 Tissue Culture Infectious Dose 50 per ml (TCID50 ml-1), with satisfactory assay sensitivity and specificity. A comparison of 20 clinical specimens between four laboratories showed excellent interlaboratory concordance; performing equally well on three different, commonly used thermocyclers, pointing to the robustness of the assay.Conclusion. With a simplified workflow, The N1 gene Single Tube Optigene LAMP assay (N1-STOP-LAMP) is a powerful, scalable option for specific and rapid detection of SARS-CoV-2 and an additional resource in the diagnostic armamentarium against COVID-19.
URI: https://ahro.austin.org.au/austinjspui/handle/1/24521
DOI: 10.1099/jmm.0.001238
Journal: Journal of Medical Microbiology
PubMed URL: 32755529
Type: Journal Article
Subjects: RT-LAMP
SARS-CoV-2
nasopharyngeal swabs
universal transport media
COVID-19
Appears in Collections:Journal articles

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