Detection of SARS-CoV-2 RNA using RT-LAMP and molecular beacons

Abstract Background Rapid spread of SARS-CoV-2 has led to a global pandemic, resulting in the need for rapid assays allow diagnosis and prevention transmission. Reverse transcription-polymerase chain reaction (RT-PCR) provides gold standard assay RNA, but instrument costs are high supply chains potentially fragile, motivating interest additional methods. transcription loop-mediated isothermal amplification (RT-LAMP) an alternative that uses orthogonal often less expensive reagents without thermocyclers. The presence RNA is typically detected using dyes report bulk DNA; however, common artifact nonspecific DNA amplification, which complicates detection. Results Here we describe design testing molecular beacons, sequence-specific detection genomes with improved discrimination simple mixtures. To optimize beacons RT-LAMP, multiple locked nucleic acid monomers were incorporated elevate melting temperatures. We also show how different fluorescent labels can convenient multiplex several amplicons “single pot” reactions, including incorporation human LAMP-BEAC confirm sample integrity. Comparison RT-qPCR on clinical saliva samples showed good concordance between assays. facilitate implementation, developed custom polymerases inexpensive purification procedures, facilitates increasing sensitivity by volumes. Conclusions thus affordable suitable population screening; implementation allowed robust screening thousands per week.