FQ-LAMP Assay for Detection of CoV2 in Clinical Nasal Swabs v1

COVID-19 is a public health challenge requiring rapid testing for detecting infections and transmission. Nucleic acid amplification tests (NAAT) targeting SARS-CoV-2 (CoV2) are used to detect CoV2 in clinical samples.Real-time reverse transcription-quantitative PCR (RT-qPCR) is the standard NAAT for CoV2, although Reverse Transcription Loop-mediated isothermal amplification (RT-LAMP) is used in diagnostics. We show a sequence-specific RT-LAMP-based NAAT assay that is finished within 30 min using minimally processed clinical nasal swab samples and describe a fluorescent-quenched RT-LAMP assay (FQ-LAMP) using labeled primers and a quencher oligo. This assay can achieve rapid (30 min) and sensitive (1000 PFU/ml) fluorescent detection of CoV2 (WA1/2020), B.1.1.7 (Alpha), and variants of concern Delta (B.1.617.2) and Omicron (B.1.1.529) in nasal samples.