OmiCrisp: A CRISPR SARS-CoV-2 Test with Omicron Detection

Author(s): Suruchi Sharma, Manasa Bagur Prakash, Reety Arora, Annes Siji, Bidipta Roy, Varsha Shridhar, Nimisha Gupta, Vijay Chandru, Vaijayanti Gupta

We have developed a CRISPR based assay that can detect the presence of SARS-CoV-2, in human as well as environmental samples, and predict if it is an Omicron or non-Omicron variant of the virus. This nucleic acid amplification-based test (NAAT) consists of two independent steps: a one-step multiplexed RT-PCR amplification using a standard kit, followed by CRISPR based detection that utilizes the trans-cleavage activity of the Cas12a enzyme. We have evaluated the performance of OmiCrisp in over 80 clinical samples and more than 160 sewage samples. We observed an agreement of >99% with the sequencing results in labeling SARS-CoV-2 positive samples as well as Omicron or non-Omicron call, in clinical cases. Similar accuracy was observed with qRT-PCR results in wastewater samples. Our OmiCrisp -like platforms can be developed quickly and can potentially complement sequencing for quick and rapid tracking of the transmission of emerging pathogenic variants.