Tags

Type your tag names separated by a space and hit enter

Validation of a single-step, single-tube reverse transcription loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA.
J Med Microbiol. 2020 Sep; 69(9):1169-1178.JM

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.

Authors+Show Affiliations

Department of Infectious Diseases, Monash Health, Clayton, Victoria, Australia. Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, 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.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. 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.Microbiological Diagnostic Unit Public Health Laboratory, 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.Microbiological Diagnostic Unit Public Health Laboratory, 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.Victorian Infectious Diseases Reference Laboratory, Melbourne Health 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.360Biolabs, Melbourne, Victoria, Australia.360Biolabs, Melbourne, Victoria, Australia.GenWorks Pty Ltd, Thebarton, South Australia, Australia.GenWorks Pty Ltd, Thebarton, South Australia, Australia.Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia. Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia. Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.Department of Microbiology, Monash Health, Clayton, Victoria, Australia.Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia. Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.Melbourne Health, Melbourne, Victoria, Australia. Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, 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. Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia. Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia.Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.

Pub Type(s)

Journal Article
Validation Study

Language

eng

PubMed ID

32755529

Citation

Lee, Jean Y H., et al. "Validation of a Single-step, Single-tube Reverse Transcription Loop-mediated Isothermal Amplification Assay for Rapid Detection of SARS-CoV-2 RNA." Journal of Medical Microbiology, vol. 69, no. 9, 2020, pp. 1169-1178.
Lee JYH, Best N, McAuley J, et al. Validation of a single-step, single-tube reverse transcription loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA. J Med Microbiol. 2020;69(9):1169-1178.
Lee, J. Y. H., Best, N., McAuley, J., Porter, J. L., Seemann, T., Schultz, M. B., Sait, M., Orlando, N., Mercoulia, K., Ballard, S. A., Druce, J., Tran, T., Catton, M. G., Pryor, M. J., Cui, H. L., Luttick, A., McDonald, S., Greenhalgh, A., Kwong, J. C., ... Stinear, T. P. (2020). Validation of a single-step, single-tube reverse transcription loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA. Journal of Medical Microbiology, 69(9), 1169-1178. https://doi.org/10.1099/jmm.0.001238
Lee JYH, et al. Validation of a Single-step, Single-tube Reverse Transcription Loop-mediated Isothermal Amplification Assay for Rapid Detection of SARS-CoV-2 RNA. J Med Microbiol. 2020;69(9):1169-1178. PubMed PMID: 32755529.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Validation of a single-step, single-tube reverse transcription loop-mediated isothermal amplification assay for rapid detection of SARS-CoV-2 RNA. AU - Lee,Jean Y H, AU - Best,Nickala, AU - McAuley,Julie, AU - Porter,Jessica L, AU - Seemann,Torsten, AU - Schultz,Mark B, AU - Sait,Michelle, AU - Orlando,Nicole, AU - Mercoulia,Karolina, AU - Ballard,Susan A, AU - Druce,Julian, AU - Tran,Thomas, AU - Catton,Mike G, AU - Pryor,Melinda J, AU - Cui,Huanhuan L, AU - Luttick,Angela, AU - McDonald,Sean, AU - Greenhalgh,Arran, AU - Kwong,Jason C, AU - Sherry,Norelle L, AU - Graham,Maryza, AU - Hoang,Tuyet, AU - Herisse,Marion, AU - Pidot,Sacha J, AU - Williamson,Deborah A, AU - Howden,Benjamin P, AU - Monk,Ian R, AU - Stinear,Timothy P, Y1 - 2020/07/31/ PY - 2020/8/7/pubmed PY - 2020/10/2/medline PY - 2020/8/7/entrez KW - RT-LAMP KW - SARS-CoV-2 KW - nasopharyngeal swabs KW - universal transport media SP - 1169 EP - 1178 JF - Journal of medical microbiology JO - J Med Microbiol VL - 69 IS - 9 N2 - 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. SN - 1473-5644 UR - https://www.unboundmedicine.com/medline/citation/32755529/Validation_of_a_single_step_single_tube_reverse_transcription_loop_mediated_isothermal_amplification_assay_for_rapid_detection_of_SARS_CoV_2_RNA_ DB - PRIME DP - Unbound Medicine ER -