OmiCrisp: A CRISPR SARS-CoV-2 test with Omicron detection

Abstract

AbstractWe have developed a CRISPR based assay that can detect the presence of SARS-CoV-2 in RNA extracted from human samples and also predict if it is an Omicron or non-Omicron variant of the virus. This is a nucleic acid amplification-based test (NAAT). The amplification and detection are carried out in two independent steps in this assay. Amplification is done using a standard one-step RT-PCR method. The detection is done using a method that utilizes the trans-cleavage activity of the Cas12a enzyme. We have evaluated the performance of OmiCrisp in more than 80 clinical samples and observed an agreement of 100% with the sequencing results, in labeling SARS-CoV-2 positive samples as Omicron or non-Omicron. OmiCrisp -like platform can be developed quickly and can potentially complement sequencing for quick and rapid tracking of the transmission of new pathogen variants.