Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform

He, Changsheng; Lin, Cailing; Mo, Guosheng; Xi, Binbin; Li, An′an; Huang, Dan; Wan, Yanbin; Chen, Feng; Liang, Yufeng; Zuo, Qingxia; Xu, Wanqing; Feng, Dongyan; Zhang, Guanting; Han, Lu; Ke, Changwen; Du, Hongli; Huang, Lizhen

doi:10.1016/j.bios.2021.113857

Cited by 38 publications

(24 citation statements)

References 55 publications

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“…CRISPR-based systems have a specific recognition mechanism enabled by the guide RNA (gRNA or crRNA) forming a complex with the Cas enzyme. As shown in Figure 3 a, the binding between crRNA and the target-activated CRISPR effector protein (Cas), at room temperature, enables cleavage activity on the target ( cis -cleavage) and subsequent non-specific activity on non-target ( trans -cleavage) [ 70 ]. For example, upon binding to ssDNA or ssRNA, the trans -cleavage mechanism can release a fluorescence reporter from the quenched fluorescence probe [ 9 , 12 , 20 , 70 , 71 , 72 , 73 , 74 , 75 , 76 ].…”

Section: Multiplex Viral Rna Detection and Amplification Methodsmentioning

confidence: 99%

Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19

et al. 2022

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The COVID-19 pandemic caused by SARS-CoV-2 has drawn attention to the need for fast and accurate diagnostic testing. Concerns from emerging SARS-CoV-2 variants and other circulating respiratory viral pathogens further underscore the importance of expanding diagnostic testing to multiplex detection, as single-plex diagnostic testing may fail to detect emerging variants and other viruses, while sequencing can be too slow and too expensive as a diagnostic tool. As a result, there have been significant advances in multiplex nucleic-acid-based virus diagnostic testing, creating a need for a timely review. This review first introduces frequent nucleic acid targets for multiplex virus diagnostic tests, then proceeds to a comprehensive and up-to-date overview of multiplex assays that incorporate various detection reactions and readout modalities. The performances, advantages, and disadvantages of these assays are discussed, followed by highlights of platforms that are amenable for point-of-care use. Finally, this review points out the remaining technical challenges and shares perspectives on future research and development. By examining the state of the art and synthesizing existing development in multiplex nucleic acid diagnostic tests, this review can provide a useful resource for facilitating future research and ultimately combating COVID-19.

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Section: Multiplex Viral Rna Detection and Amplification Methodsmentioning

confidence: 99%

Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19

et al. 2022

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“…Pathogenic bacterial infection can cause serious diseases such as respiratory infection, sepsis, and urinary inflammation, which has become one of the most serious public health problems in the world. − To reduce this threat, it is of significance to construct a universal platform for bacterial point-of-care testing (POCT) and elimination in that bacteria can contaminate air, water, and food and spread through human contact . Specifically, due to the SARS-CoV-2 pandemic, further significant attention is drawn to developing a simple and effective strategy for rapid detection and elimination of bacteria with low cost. − However, most of the developed strategies either focus on the sensitive detection of pathogenic bacteria without function of subsequent bacterial inactivation or focus on the high-efficiency inactivation of pathogenic bacteria without function of early warning. − The independent detection and sterilization delay the effective treatment.…”

Section: Introductionmentioning

confidence: 99%

Long-Lasting Chemiluminescence-Based POCT for Portable and Visual Pathogenic Detection and In Situ Inactivation

et al. 2022

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Bacterial infections seriously threaten human health and also bring huge financial burden. It is critical to construct multifunctional platforms for effectively inactivating bacteria right after point-of-care testing (POCT). Chemiluminescence (CL) bioassays are considered as powerful candidates for POCT as they are free from using an excitation light source, while the flash-type emission limits their further application. Herein, a CL system with long, persistent, and intensive intensity was constructed based on the peroxidase-like property of 4-mercaptophenylboronic acid (MPBA)-functionalized CuSe nanoprobes (CuSeNPs@MPBA), which improved the detection accuracy and sensitivity. By further integrating a smartphone as an analyzer, quantitative POCT of bacteria was realized with high sensitivity. The limit of detection was as low as 1.25 and 1.01 cfu mL–1 for Staphylococcus aureus and Escherichia coli detection, respectively. Specifically, bacteria can be eliminated with high efficiency due to excellent photothermal property of CuSeNPs@MPBA. The developed multifunctional platform also has advantages of simple operation with low cost, suggesting its high potential for use in food safety, environment monitoring, and clinical applications.

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“… 17 Even CRISPR-based systems, though effective, have a narrow range of target sites due to constraints imposed by the PAM region. 18 This method also requires an extra base pair mismatch in the CRISPR RNA sequence that can lead to genotyping errors. 19 As such, new POC diagnostics are needed to rapidly detect nucleic acid sequences with high sensitivity and single-base specificity.…”

Section: Introductionmentioning

confidence: 99%

“…Other approaches, such as S-gene target failure, TaqMan, and LAMP, suffer from limitations in their reliability, sensitivity, and specificity, making them suboptimal techniques for VOC genotyping . Even CRISPR-based systems, though effective, have a narrow range of target sites due to constraints imposed by the PAM region . This method also requires an extra base pair mismatch in the CRISPR RNA sequence that can lead to genotyping errors .…”

Section: Introductionmentioning

confidence: 99%

REVEALR-Based Genotyping of SARS-CoV-2 Variants of Concern in Clinical Samples

et al. 2022

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The SARS-CoV-2 virus has evolved into new strains that increase viral transmissibility and reduce vaccine protection. The rapid circulation of these more harmful strains across the globe has created a pressing need for alternative public health screening tools. REVEALR (RNA-encoded viral nucleic acid analytic reporter), a rapid and highly sensitive DNAzyme-based detection system, functions with perfect accuracy against patient-derived clinical samples. Here, we design REVEALR into a novel genotyping assay that detects single-base mismatches corresponding to each of the major SARS-CoV-2 strains found in the United States. Of 34 sequence-verified patient samples collected in early, mid, and late 2021 at the UCI Medical Center in Orange, California, REVEALR identified the correct variant [Wuhan-Hu-1, alpha (B.1.1.7), gamma (P.1), epsilon (B.1.427/9), delta (B.1.617.2), and omicron (B.1.1.529)] with 100% accuracy. The assay, which is programmable and amenable to multiplexing, offers an important new approach to personalized diagnostics.

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Rapid and accurate detection of SARS-CoV-2 mutations using a Cas12a-based sensing platform

Cited by 38 publications

References 55 publications

Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19

Emerging Multiplex Nucleic Acid Diagnostic Tests for Combating COVID-19

Long-Lasting Chemiluminescence-Based POCT for Portable and Visual Pathogenic Detection and In Situ Inactivation

REVEALR-Based Genotyping of SARS-CoV-2 Variants of Concern in Clinical Samples

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