Abstract: Sequences for detection of SARS-CoV-2 are provided and include example, SEQ ID NOs:4-8. The sequences are useful for amplifying the SARS-CoV-2 nsp8 gene in a sample, using Reverse Transcriptional Loop-Mediated Isothermal Amplification (RT-LAMP) and it is preferably used in combination with a Cas enzyme/sgRNA pair and a reporter nucleic acid. The disclosed sequences can be use in methods of detecting SARS-CoV-2 nucleic acids in a sample. Generally, the specific gene sequence of SARS-CoV-2 RNA, herein nsp8, is amplified using RT-LAMP. The RT-LAMP products are scanned by the Cas12a-gRNA ribonucleoprotein (RNP) complex. The RNP binds to the specific complementary to gRNA, activating the transcleavage activity of Cas12a. The active Cas12a system cleaves a short ssDNA reporter that is labeled preferably, with a fluorophore and a quencher on either end. Cleavage of the reporter separates the quencher from the fluorophore, and fluorescence that is detectable with the naked eye is generated.

Abstract: Sequences for detection of SARS-CoV-2, probes and primers that target the target sequences, and methods of use thereof for the detection and diagnosis of SARS-CoV-2 are provided. Detection methods include, but are not limited to, microarray, differential display, RNase protection assay, northern blot, reverse transcriptase (RT) polymerase chain reaction (PCR), and combinations thereof. In preferred embodiments, the detection methods include RT-PCT, more preferably realtime or quantitative RT-PCR, most preferably wherein the RT-PCR includes target specific reverse transcription and/or target specific PCR. In some embodiments, the disclosed primers, probes, compositions, or methods are more sensitive, selective, or combination thereof for SARS-CoV-2 relative to one or more other human- and/or non-human pathogenic coronaviruses and/or respiratory pathogens.