Use of the variplex™ SARS-CoV-2 RT-LAMP as a rapid molecular assay to complement RT-PCR for COVID-19 diagnosis

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 variplex (TM) 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 (TM) RT-LAMP and Corman's LightMix (TM) E gene RT-PCR as reference. Samples of respiratory secretions from Coronavirus infection disease (COVID19) and negative control patients were analyzed by variplex (TM) without RNA extraction and tested in parallel with the Allplex (TM) and VIASURE BD MAX RT-PCRs. Results: Using isolated RNA variplex (TM) RT-LAMP showed a sensitivity of 75 % compared to LightMix E gene RTPCR 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 (TM) RT-LAMP conducted on unprocessed samples and Allplex (TM) and VIASURE RT-PCRs (Cohen's kappa 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 (TM), 84.2 % for Allplex (TM) 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.