Working Paper Article Version 1 This version is not peer-reviewed

Fast Detection of SARS-CoV-2 RNA Directly from Respiratory Samples Using a Loop-Mediated Isothermal Amplification (LAMP) Test

Version 1 : Received: 1 April 2021 / Approved: 5 April 2021 / Online: 5 April 2021 (12:21:19 CEST)

How to cite: Anastasiou, O.E.; Holtkamp, C.; Schäfer, M.; Schön, F.; Eis-Hübinger, A.M.; Krumbholz, A. Fast Detection of SARS-CoV-2 RNA Directly from Respiratory Samples Using a Loop-Mediated Isothermal Amplification (LAMP) Test. Preprints 2021, 2021040118 Anastasiou, O.E.; Holtkamp, C.; Schäfer, M.; Schön, F.; Eis-Hübinger, A.M.; Krumbholz, A. Fast Detection of SARS-CoV-2 RNA Directly from Respiratory Samples Using a Loop-Mediated Isothermal Amplification (LAMP) Test. Preprints 2021, 2021040118

Abstract

The availability of simple SARS-CoV-2 detection methods is crucial to contain the COVID-19 pandemic. This study examined whether a commercial LAMP assay can reliably detect SARS-CoV-2 genomes directly in respiratory samples without having to extract nucleic acids (NA) beforehand. Nasopharyngeal swabs (NPS, n = 220) were tested by real-time reverse transcription (RT)-PCR and with the LAMP assay. For RT-PCR, NA were investigated. For LAMP, NA from 26 NPS in viral transport medium (VTM) were tested. The other 194 NPS were analyzed directly without prior NA extraction [140 samples in VTM; 54 dry swab samples stirred in phosphate buffered saline]. Ten NPS were tested directly by LAMP using a sous-vide cooking unit. The isothermal assay demonstrated excellent specificity (100%) but moderate sensitivity (68.8%), with a positive predictive value of 1 and a negative predictive value of 0.65 for direct testing of NPS in VTM. The use of dry swabs, even without NA extraction, improved the analytical sensitivity; up to 6% of samples showed signs of inhibition. The LAMP could be performed successfully with a sous-vide cooking unit. This technique is very fast, requires little laboratory resources and can replace rapid antigen tests or verify reactive rapid tests on site.

Keywords

SARS-CoV-2; COVID-19; RT-PCR; nucleic acids; direct testing; loop-mediated isothermal amplification; LAMP

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