Rapid SARS-CoV-2 RT-LAMP assay setup using gene construct design approach

Background and Objective: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still an ongoing challenge in health system worldwide. Molecular detection methods including reverse transcription loop-mediated isothermal amplification (RT-LAMP) can help cutting off the transmission chain of the virus. In this study, prompt setting up of the RT-LAMP assays were investigated using gene construct design approach. Methods: RT-LAMP assays were initially setup and optimized using gene constructs as positive controls  which worked simultaneously for RT-LAMP and RT-PCR assays. Constructed genes included T7 promoter sequence and partial sequences of SARS-CoV-2 RdRp, N and E genes cloned into pUC57 multiple cloning site (MCS) via synthetic and subcloning procedures. These templates were then used for artificial RNA synthesis. Finally, the RT-LAMP assays parameters were optimized and applied on clinical RNA specimens. Results: As an initial rapid approach, RT-LAMP assays were successfully setup for SARS-CoV-2 diagnostic using in vitro RNA transcripts from gene constructs. The assays were then examined on clinical samples with reaction time of 35 and 40 min required for assay one and two respectively. The limit of detection was determined as 100 copies of target gene per reaction for each assay. Conclusion: Here, prompt setting up of RT-LAMP assays were carried out initially on designed gene constructs containing different SARS-CoV-2 target genes and simultaneous validation by RT-PCR. This approach could be used as an efficient solution where the clinical specimens may not initially be available, with feasibility for new target gene of interest to be inserted into MCS position.