Highly Sensitive Detection Method for HV69-70del in SARS-CoV-2 Alpha and Omicron Variants Based on CRISPR/Cas13a

• Main Authors: Dong, X. (Author), Han, Y. (Author), Hu, Q. (Author), Li, F. (Author), Li, H. (Author), Niu, M. (Author), Sun, Y. (Author), Xia, X. (Author), Yang, L. (Author), Zhang, Y. (Author)
• Format: Article
• Language: English
• Published: Frontiers Media S.A. 2022
• Subjects: Biomolecules; CRISPR/cas13a; CRISPR/Cas13a; Detection methods; Detection system; Diagnosis; Diagnostics tools; Diseases; Fluorescence; Highly sensitive detections; Lateral Flow; lateral flow strip; Lateral flow strip; nucleic acid detection; On-site detection; Polymerase chain reaction; RNA; SARS; SARS-CoV-2; Variant; variants
• Online Access: View Fulltext in Publisher

 As SARS-CoV-2 variants continue to evolve, identifying variants with adaptive diagnostic tool is critical to containing the ongoing COVID-19 pandemic. Herein, we establish a highly sensitive and portable on-site detection method for the HV69-70del which exist in SARS-CoV-2 Alpha and Omicron variants using a PCR-based CRISPR/Cas13a detection system (PCR-CRISPR). The specific crRNA (CRISPR RNA) targeting the HV69-70del is screened using the fluorescence-based CRISPR assay, and the sensitivity and specificity of this method are evaluated using diluted nucleic acids of SARS-CoV-2 variants and other pathogens. The results show that the PCR-CRISPR detection method can detect 1 copies/μL SARS-CoV-2 HV69-70del mutant RNA and identify 0.1% of mutant RNA in mixed samples, which is more sensitive than the RT-qPCR based commercial SARS-CoV-2 variants detection kits and sanger sequencing. And it has no cross reactivity with ten other pathogens nucleic acids. Additionally, by combined with our previously developed ERASE (Easy-Readout and Sensitive Enhanced) lateral flow strip suitable for CRISPR detection, we provide a novel diagnosis tool to identify SARS-CoV-2 variants in primary and resource-limited medical institutions without professional and expensive fluorescent detector. Copyright © 2022 Niu, Han, Dong, Yang, Li, Zhang, Hu, Xia, Li and Sun.