Advancing Sewage Sample Surveillance with OmiCrisp: A CRISPR-Based Platform for Variant-Specific SARS-CoV-2 Detection

The detection and differentiation of SARS-CoV-2 variants are vital for disease management and timely patient isolation. Although qRT-PCR has been the standard method, our OmiCrisp assay has shown superior results in identifying Omicron and non-Omicron variants. The World Health Organization advises ongoing sewage surveillance to monitor community viral load, accounting for both symptomatic and asymptomatic individuals. In a previous study, our CRISPR-based assay achieved a 99% concordance with qRT-PCR in sewage samples. We expanded this research by analyzing 182 sewage samples from Bangalore during the JN.1 (BA.2.86.1.1) variant outbreak. Using the OmiCrisp assay, 153 samples (84.06%) tested positive, 16 (8.79%) were negative, and 13 (7.14%) were low positive. Results indicated a significant reduction in positivity rates by the end of the study. The OmiCrisp assay thus proves to be an accurate and effective tool for community-wide surveillance of SARS-CoV-2 variants.