A CRISPR/Cas13a-powered catalytic hairpin assembly evanescent wave fluorescence biosensor for target amplification-free SARS-CoV-2 detection

The end of the coronavirus disease 2019 (COVID-19) pandemic still drives the development of rapid and accurate detection technology to prepare for diverse viral infections and emerging pandemics in the future. Herein, a CRISPR/Cas13a-powered catalytic hairpin assembly evanescent wave fluorescence biosensor (CAPABLE) was developed for amplification-free detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the ingenious design of trigger, the presence of SARS-CoV-2 activated the trans-cleavage activity of Cas13a, followed by the initiation of a catalytic hairpin assembly (CHA) system that exhibited excellent signal amplification efficiency. By integrating the biotin-avidin system, the detection sensitivity of the portable fluorescence platform was greatly improved. Quantitative SARS-CoV-2 detection was realized with a detection limit of 18.6 copies/μL within 50 min based on a fast extraction method. The proposed method exhibited a 100% positive detection rate for environmental water samples spiked with SARS-CoV-2 pseudovirus, which was consistent with standard RTqPCR results. Benefiting from amplification-free performance, the CAPABLE method holds great promise for rapid SARS-CoV-2 detection in field laboratories and primary facilities in resource-limited areas. With the inherent flexibility of the CRISPR/Cas system, the proposed method has the potential to be applied in the diagnosis of various infectious diseases.