Validation of a Single-step, Single-tube Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Rapid Detection of SARS-CoV-2 RNA

Lee, J. Y.; Best, N.; McAuley, J. L.; Porter, J.; Seemann, T.; Schultz, M. B.; Sait, M.; Orlando, N.; Mercoulia, K.; Ballard, S. A.; Druce, J.; Tran, T.; Catton, M.; Pryor, M. J.; Cui, H. L.; Luttick, A.; McDonald, S.; Greenhalgh, A.; Kwong, J. C.; Sherry, N. L.; Graham, M.; Hoang, T.; Herisse, M.; Pidot, S. J.; Williamson, D. A.; Howden, B. P.; Monk, I. R.; Stinear, T. P.

doi:10.1101/2020.04.28.067363

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bioRxiv · 10.1101/2020.04.28.067363

Validation of a Single-step, Single-tube Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Rapid Detection of SARS-CoV-2 RNA

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Abstract

2.IntroductionThe 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. AimTo establish and validate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of SARS-CoV-2 from nasopharyngeal swabs. MethodologyWe used a commercial RT-LAMP mastermix from OptiGene Ltd 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 as little as 1 L 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{degrees}C for 30 minutes and measure fluorescence in the FAM channel at one-minute intervals. ResultsAssay 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 minutes (SD {+/-}7 minutes). 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. ConclusionWith a simplified workflow, 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. 3. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

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Lee, J. Y., Best, N., McAuley, J. L., Porter, J., Seemann, T., Schultz, M. B., Sait, M., Orlando, N., Mercoulia, K., Ballard, S. A., Druce, J., Tran, T., Catton, M., Pryor, M. J., Cui, H. L., Luttick, A., McDonald, S., Greenhalgh, A., Kwong, J. C., Sherry, N. L., Graham, M., Hoang, T., Herisse, M., Pidot, S. J., Williamson, D. A., Howden, B. P., Monk, I. R., Stinear, T. P.. 2020-04-30. Validation of a Single-step, Single-tube Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Rapid Detection of SARS-CoV-2 RNA. https://doi.org/10.1101/2020.04.28.067363

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