Creating an ultra-sensitive detection platform for monkeypox virus DNA based on CRISPR technology

The recent major worldwide outbreak of monkeypox virus (MPXV) has highlighted the urgent need for accurate MPXV detection methods. Although quantitative PCR (qPCR) technique is currently the gold standard for MPXV diagnosis, the high costs associated with the technique and the need for complex instrumentation, limits its application in resource-poor settings. CRISPR technology has developed rapidly in recent years and provides an effective tool for point-of-care testing pathogen identification. Here, we exploited the cleavage properties of the Cas12a enzyme and Cas13a enzyme, to detect the MPXV specific genes, F3L gene and B6R gene, respectively. We developed two detection protocols: a 2-step method in which the CRISPR Dual System reaction and the multiplex recombinase polymerase amplification reaction were carried out in separate tubes and a single-tube method in which both reactions were carried out in one tube. Evaluation of the two methods showed that our protocol can detect the MPXV genome down to 10° copies/μL with good specificity and no cross-reactivity with other poxviruses pseudoviruses, and bacteria. Mock positive samples were used to assess clinical applicability, with the results showing satisfactory concordance with the qPCR method for parallel testing. In conclusion, our study provides a reliable molecular diagnostic strategy for detection of MPXV.