Colorimetric tetra-combo loop-mediated isothermal amplification assay for efficient SARS-CoV-2 detection

Coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly and caused a pandemic in 2020. Both pharmaceutical approaches, such as vaccinations and non-pharmaceutical approaches such as social distancing through lockdown and international border restrictions had been implemented to control the outbreak and the transmission of SARS-CoV-2. However, the prolonged implementation of these measures negatively impacted the population and global economy, while the continuously emerging SARS-CoV-2 variants led to breakthrough infections among the vaccinated populations. Given the ongoing nature of COVID-19, an efficient detection method for SARS-CoV-2 that could enable mass screening and on-site screening is needed to manage the disease and prevent further outbreaks at large scale. Hence, we have developed a tetra-combo LAMP SARS-CoV-2 detection assay that targets four SARS-CoV-2 genes (RdRp, S, E and N), with an internal control (RNaseP). The LAMP assay was validated using 370 RNA samples extracted from nasopharyngeal and/or oropharyngeal swabs. The LAMP assay developed in this study has on-par performance as the qRT-PCR assay, which is the gold standard method for SARS-CoV-2 detection, with a shorter turnaround time (25 minutes). The LAMP assay possessed 98.13% sensitivity, 100% specificity, 100% positive predictive value (PPV), and 95.45% negative predictive value (NPV) for samples with Ct values <= 35.