Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus

Background: The recent outbreak of infections by the 2019 novel coronavirus (2019-nCoV), the third zoonotic CoV has raised great public health concern. The demand for rapid and accurate diagnosis of this novel pathogen brought significant clinical and technological challenges. Currently, metagenomic next-generation sequencing (mNGS) and reverse-transcription PCR (RT-PCR) are the most widely used molecular diagnostics. Methods: 2019-nCoV infections were confirmed in 52 specimens by mNGS. Genomic information was analyzed and used for the design and development of an isothermal, CRISPR-based diagnostic for this novel virus. The diagnostic performance of CRISPR-nCoV was assessed and compared across three technology platforms (mNGS, RT-PCR and CRISPR). Results: 2019-nCoVs sequenced in our study were conserved with the Wuhan strain, and shared certain genetic similarity with SARS-CoV. A high degree of variation in the level of viral RNA was observed in clinical specimens. CRISPR-nCoV demonstrated a near single-copy sensitivity and great clinical sensitivity with a shorter turn-around time than RT-PCR. Conclusion: CRISPR-nCoV presents as a promising diagnostic option for the emerging pathogen.