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Wang Y, Xue T, Wang M, Ledesma-Amaro R, Lu Y, Hu X, Zhang T, Yang M, Li Y, Xiang J, Deng R, Ying B, Li W. CRISPR-Cas13a cascade-based viral RNA assay for detecting SARS-CoV-2 and its mutations in clinical samples. Sens Actuators B Chem 2022; 362:131765. [PMID: 35370361 PMCID: PMC8957482 DOI: 10.1016/j.snb.2022.131765] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 02/08/2023]
Abstract
SARS-CoV-2 is one of the greatest threats to global human health. Point-of-care diagnostic tools for SARS-CoV-2 could facilitate rapid therapeutic intervention and mitigate transmission. In this work, we report CRISPR-Cas13a cascade-based viral RNA (Cas13C) assay for label-free and isothermal determination of SARS-CoV-2 and its mutations in clinical samples. Cas13a/crRNA was utilized to directly recognize the target of SARS-CoV-2 RNA, and the recognition events sequentially initiate the transcription amplification to produce light-up RNA aptamers for output fluorescence signal. The recognition of viral RNA via Cas13a-guide RNA ensures a high specificity to distinguish SARS-CoV-2 from MERS-CoV and SARS-CoV, as well as viral mutations. A post transcription amplification strategy was triggered after CRISPR-Cas13a recognition contributes to an amplification cascade that achieves high sensitivity for detecting SARS-CoV-2 RNA, with a limit of detection of 0.216 fM. In addition, the Cas13C assay could be able to discriminate single-nucleotide mutation, which was proven with N501Y in SARS-Cov-2 variant. This method was validated by a 100% agreement with RT-qPCR results from 12 clinical throat swab specimens. The Cas13C assay has the potential to be used as a routine nucleic acid test of SARS-CoV-2 virus in resource-limited regions.
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Affiliation(s)
- Yuxi Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.,Targeted Tracer Research and development laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ting Xue
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering, Imperial College Centre for Synthetic Biology, Imperial College London, London, UK
| | - Ying Lu
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China.,State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xinyue Hu
- Targeted Tracer Research and development laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.,State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ting Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Ming Yang
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yalun Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jin Xiang
- Targeted Tracer Research and development laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu 610041, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.,Targeted Tracer Research and development laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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