Use of the variplex™ SARS-CoV-2 RT-LAMP as a rapid molecular assay to complement RT-PCR for COVID-19 diagnosis
- PMID: 32891938
- PMCID: PMC7457909
- DOI: 10.1016/j.jcv.2020.104616
Use of the variplex™ SARS-CoV-2 RT-LAMP as a rapid molecular assay to complement RT-PCR for COVID-19 diagnosis
Abstract
Background: Molecular assays based on reverse transcription-loop-mediated isothermal amplification (RT-LAMP) may be useful for rapid diagnosis of the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) because of the easy performance and the option to bypass RNA extraction.
Objectives: This study was designed to evaluate the clinical performance of the CE-labeled variplexTM real time SARS-CoV-2 RT-LAMP assay in comparison to commercial RT-PCRs.
Study design: RNA extracted from pharyngeal swabs was tested by variplex™ RT-LAMP and Corman's LightMix™ E gene RT-PCR as reference. Samples of respiratory secretions from Coronavirus infection disease (COVID-19) and negative control patients were analyzed by variplex™ without RNA extraction and tested in parallel with the Allplex™ and VIASURE BD MAX RT-PCRs.
Results: Using isolated RNA variplex™ RT-LAMP showed a sensitivity of 75 % compared to LightMix E gene RT-PCR but contrary to the latter it produced no false-positive results. For the evaluation of samples from respiratory secretions concordance analysis showed only a moderate agreement between the variplex™ RT-LAMP conducted on unprocessed samples and Allplex™ and VIASURE RT-PCRs (Cohen's κ ranging from 0.52-0.56). Using the approach to define a sample as true-positive when at least two assays gave a positive result the clinical sensitivities were as follows: 76.3 % for variplex™, 84.2 % for Allplex™ and 68.4 % for VIASURE. However, when results of RT-PCR and RT-LAMP were combined diagnostic sensitivity was increased to 92-100 %.
Conclusion: The variplex RT-LAMP may serve as a rapid test to be combined with a RT-PCR assay to increase the diagnostic accuracy in patients with suspected COVID-19 infection.
Keywords: RT-LAMP; RT-PCR; Rapid diagnostics; SARS-CoV-2.
Copyright © 2020 Elsevier B.V. All rights reserved.
Conflict of interest statement
The authors report no declarations of interest.
Similar articles
-
Development and Clinical Application of a Rapid and Sensitive Loop-Mediated Isothermal Amplification Test for SARS-CoV-2 Infection.mSphere. 2020 Aug 26;5(4):e00808-20. doi: 10.1128/mSphere.00808-20. mSphere. 2020. PMID: 32848011 Free PMC article.
-
Colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) as a visual diagnostic platform for the detection of the emerging coronavirus SARS-CoV-2.Analyst. 2021 Jan 21;146(2):471-477. doi: 10.1039/d0an01775b. Epub 2020 Nov 9. Analyst. 2021. PMID: 33165486
-
Variplex™ test system fails to reliably detect SARS-CoV-2 directly from respiratory samples without RNA extraction.Eur J Clin Microbiol Infect Dis. 2020 Dec;39(12):2373-2377. doi: 10.1007/s10096-020-03983-9. Epub 2020 Jul 17. Eur J Clin Microbiol Infect Dis. 2020. PMID: 32681309 Free PMC article.
-
Laboratory-based molecular test alternatives to RT-PCR for the diagnosis of SARS-CoV-2 infection.Cochrane Database Syst Rev. 2024 Oct 14;10(10):CD015618. doi: 10.1002/14651858.CD015618. Cochrane Database Syst Rev. 2024. PMID: 39400904 Review.
-
A Recent Update on Advanced Molecular Diagnostic Techniques for COVID-19 Pandemic: An Overview.Front Immunol. 2021 Dec 14;12:732756. doi: 10.3389/fimmu.2021.732756. eCollection 2021. Front Immunol. 2021. PMID: 34970254 Free PMC article. Review.
Cited by
-
Developing a Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Seven Respiratory Viruses including SARS-CoV-2.Medicina (Kaunas). 2022 Sep 5;58(9):1224. doi: 10.3390/medicina58091224. Medicina (Kaunas). 2022. PMID: 36143901 Free PMC article.
-
Extraction Free RT-PCR Surveillance Testing and Reporting for SARS-CoV-2.COVID. 2023 Jul;3(7):1031-1041. doi: 10.3390/covid3070075. Epub 2023 Jul 21. COVID. 2023. PMID: 39381720 Free PMC article.
-
SaliVISION: a rapid saliva-based COVID-19 screening and diagnostic test with high sensitivity and specificity.Sci Rep. 2022 Apr 6;12(1):5729. doi: 10.1038/s41598-022-09718-4. Sci Rep. 2022. PMID: 35388102 Free PMC article.
-
RT-qPCR-based tests for SARS-CoV-2 detection in pooled saliva samples for massive population screening to monitor epidemics.Sci Rep. 2022 May 16;12(1):8082. doi: 10.1038/s41598-022-12179-4. Sci Rep. 2022. PMID: 35577836 Free PMC article.
-
Diagnostic tool or screening programme? Asymptomatic testing for SARS-CoV-2 needs clear goals and protocols.Lancet Reg Health Eur. 2021 Feb;1:100002. doi: 10.1016/j.lanepe.2020.100002. Epub 2020 Dec 15. Lancet Reg Health Eur. 2021. PMID: 34173617 Free PMC article. Review. No abstract available.
References
MeSH terms
LinkOut - more resources
Full Text Sources
Other Literature Sources
Medical
Miscellaneous