17
views
0
recommends
+1 Recommend
1 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      A CRISPR/Cas12a-empowered surface plasmon resonance platform for rapid and specific diagnosis of the Omicron variant of SARS-CoV-2

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The outbreak of the COVID-19 pandemic was partially due to the challenge of identifying asymptomatic and presymptomatic carriers of the virus, and thus highlights a strong motivation for diagnostics with high sensitivity that can be rapidly deployed. On the other hand, several concerning SARS-CoV-2 variants, including Omicron, are required to be identified as soon as the samples are identified as ‘positive’. Unfortunately, a traditional PCR test does not allow their specific identification. Herein, for the first time, we have developed MOPCS (Methodologies of Photonic CRISPR Sensing), which combines an optical sensing technology-surface plasmon resonance (SPR) with the ‘gene scissors’ clustered regularly interspaced short palindromic repeat (CRISPR) technique to achieve both high sensitivity and specificity when it comes to measurement of viral variants. MOPCS is a low-cost, CRISPR/Cas12a-system-empowered SPR gene-detecting platform that can analyze viral RNA, without the need for amplification, within 38 min from sample input to results output, and achieve a limit of detection of 15 fM. MOPCS achieves a highly sensitive analysis of SARS-CoV-2, and mutations appear in variants B.1.617.2 (Delta), B.1.1.529 (Omicron) and BA.1 (a subtype of Omicron). This platform was also used to analyze some recently collected patient samples from a local outbreak in China, identified by the Centers for Disease Control and Prevention. This innovative CRISPR-empowered SPR platform will further contribute to the fast, sensitive and accurate detection of target nucleic acid sequences with single-base mutations.

          Abstract

          This paper presents an unprecedented SARS-CoV-2 variants gene detection platform MOPCS(Methodologies of Photonic CRISPR Sensing), which achieved high specificity and sensitivity at the same time by the innovative crossover of the unique sequence-specific recognizing ability of the CRISPR/Cas system and the superior sensitivity of the surface plasmon resonance sensing technique.

          Related collections

          Most cited references41

          • Record: found
          • Abstract: found
          • Article: not found

          Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization

          The SARS-CoV-2 B.1.617 lineage was identified in October 2020 in India1-5. Since then, it has become dominant in some regions of India and in the UK, and has spread to many other countries6. The lineage includes three main subtypes (B1.617.1, B.1.617.2 and B.1.617.3), which contain diverse mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein that may increase the immune evasion potential of these variants. B.1.617.2-also termed the Delta variant-is believed to spread faster than other variants. Here we isolated an infectious strain of the Delta variant from an individual with COVID-19 who had returned to France from India. We examined the sensitivity of this strain to monoclonal antibodies and to antibodies present in sera from individuals who had recovered from COVID-19 (hereafter referred to as convalescent individuals) or who had received a COVID-19 vaccine, and then compared this strain with other strains of SARS-CoV-2. The Delta variant was resistant to neutralization by some anti-NTD and anti-RBD monoclonal antibodies, including bamlanivimab, and these antibodies showed impaired binding to the spike protein. Sera collected from convalescent individuals up to 12 months after the onset of symptoms were fourfold less potent against the Delta variant relative to the Alpha variant (B.1.1.7). Sera from individuals who had received one dose of the Pfizer or the AstraZeneca vaccine had a barely discernible inhibitory effect on the Delta variant. Administration of two doses of the vaccine generated a neutralizing response in 95% of individuals, with titres three- to fivefold lower against the Delta variant than against the Alpha variant. Thus, the spread of the Delta variant is associated with an escape from antibodies that target non-RBD and RBD epitopes of the spike protein.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            CRISPR-Cas12–based detection of SARS-CoV-2

            An outbreak of betacoronavirus SARS-CoV-2 began in Wuhan, China in December 2019. COVID-19, the disease associated with infection, rapidly spread to produce a global pandemic. We report development of a rapid (<40 min), easy-to-implement and accurate CRISPR-Cas12-based lateral flow assay for detection of SARS-CoV-2 from respiratory swab RNA extracts. We validated our method using contrived reference samples and clinical samples from US patients, including 36 patients with COVID-19 infection and 42 patients with other viral respiratory infections. Our CRISPR-based DETECTR assay provides a visual and faster alternative to the US CDC SARS-CoV-2 real-time RT-PCR assay, with 95% positive predictive agreement and 100% negative predictive agreement.. SARS-CoV-2 in patient samples is detected in under an hour using a CRISPR-based lateral flow assay.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity

              CRISPR-Cas12a (Cpf1) proteins are RNA-guided enzymes that bind and cut DNA as components of bacterial adaptive immune systems. Like CRISPR-Cas9, Cas12a has been harnessed for genome editing based on its ability to generate targeted, double-stranded DNA (dsDNA) breaks. Here we show that RNA-guided DNA binding unleashes indiscriminate single-stranded DNA (ssDNA) cleavage activity by Cas12a that completely degrades ssDNA molecules. We find that target-activated, non-specific ssDNase cleavage is also a property of other type V CRISPR-Cas12 enzymes. By combining Cas12a ssDNase activation with isothermal amplification, we create a method termed DNA Endonuclease Targeted CRISPR Trans Reporter (DETECTR), which achieves attomolar sensitivity for DNA detection. DETECTR enables rapid and specific detection of human papillomavirus in patient samples, thereby providing a simple platform for molecular diagnostics.
                Bookmark

                Author and article information

                Contributors
                Journal
                Natl Sci Rev
                Natl Sci Rev
                nsr
                National Science Review
                Oxford University Press
                2095-5138
                2053-714X
                August 2022
                03 June 2022
                03 June 2022
                : 9
                : 8
                : nwac104
                Affiliations
                Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics; International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education; Shenzhen Institute of Translational Medicine; Department of Otolaryngology, Shenzhen Second People's Hospital; the First Affiliated Hospital; Institute of Microscale Optoelectronics, Shenzhen University , Shenzhen 518060, China
                Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics; International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education; Shenzhen Institute of Translational Medicine; Department of Otolaryngology, Shenzhen Second People's Hospital; the First Affiliated Hospital; Institute of Microscale Optoelectronics, Shenzhen University , Shenzhen 518060, China
                Shenzhen International Institute for Biomedical Research , Shenzhen 518116, China
                Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics; International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education; Shenzhen Institute of Translational Medicine; Department of Otolaryngology, Shenzhen Second People's Hospital; the First Affiliated Hospital; Institute of Microscale Optoelectronics, Shenzhen University , Shenzhen 518060, China
                Shenzhen International Institute for Biomedical Research , Shenzhen 518116, China
                Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics; International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education; Shenzhen Institute of Translational Medicine; Department of Otolaryngology, Shenzhen Second People's Hospital; the First Affiliated Hospital; Institute of Microscale Optoelectronics, Shenzhen University , Shenzhen 518060, China
                Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics; International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education; Shenzhen Institute of Translational Medicine; Department of Otolaryngology, Shenzhen Second People's Hospital; the First Affiliated Hospital; Institute of Microscale Optoelectronics, Shenzhen University , Shenzhen 518060, China
                Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics; International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education; Shenzhen Institute of Translational Medicine; Department of Otolaryngology, Shenzhen Second People's Hospital; the First Affiliated Hospital; Institute of Microscale Optoelectronics, Shenzhen University , Shenzhen 518060, China
                Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics; International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education; Shenzhen Institute of Translational Medicine; Department of Otolaryngology, Shenzhen Second People's Hospital; the First Affiliated Hospital; Institute of Microscale Optoelectronics, Shenzhen University , Shenzhen 518060, China
                Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics; International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education; Shenzhen Institute of Translational Medicine; Department of Otolaryngology, Shenzhen Second People's Hospital; the First Affiliated Hospital; Institute of Microscale Optoelectronics, Shenzhen University , Shenzhen 518060, China
                Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics; International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education; Shenzhen Institute of Translational Medicine; Department of Otolaryngology, Shenzhen Second People's Hospital; the First Affiliated Hospital; Institute of Microscale Optoelectronics, Shenzhen University , Shenzhen 518060, China
                Shenzhen Han's Tech Limited Company , Shenzhen 518000, China
                Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics; International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education; Shenzhen Institute of Translational Medicine; Department of Otolaryngology, Shenzhen Second People's Hospital; the First Affiliated Hospital; Institute of Microscale Optoelectronics, Shenzhen University , Shenzhen 518060, China
                Shenzhen Metasensing Tech Limited Company , Shenzhen 518000, China
                Department of Physics, Faculty of Science, King Abdulaziz University , Jeddah 21589, Saudi Arabia
                Department of Physics, Faculty of Science, King Abdulaziz University , Jeddah 21589, Saudi Arabia
                Research Center for Advanced Materials Science (RCAMS), King Khalid University , Abha 61413, Saudi Arabia
                Department of Chemistry, College of Science, King Khalid University , Abha 61413, Saudi Arabia
                Zhongmin (Shenzhen) Intelligent Ecology Co. Ltd , Shenzhen 518055, China
                Shenzhen International Institute for Biomedical Research , Shenzhen 518116, China
                Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University , Shenzhen 518060, China
                Department of Laboratory Medicine, Shenzhen Children's Hospital , Shenzhen 518038, China
                Optoelectronics Research Center, School of Science, Minzu University of China , Beijing 100081, China
                NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention , Beijing 102206, China
                Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences , Beijing 102206, China
                Institute of Pathogenic Organism, Shenzhen Center for Disease Control and Prevention , Shenzhen 518055, China
                Respiratory Department , Shenzhen Children's Hospital , Shenzhen 518038, China
                Institute of Pediatrics, Shenzhen Children's Hospital , Shenzhen 518038, China
                Shenzhen Engineering Laboratory of Phosphorene and Optoelectronics; International Collaborative Laboratory of 2D Materials for Optoelectronics Science and Technology of Ministry of Education; Shenzhen Institute of Translational Medicine; Department of Otolaryngology, Shenzhen Second People's Hospital; the First Affiliated Hospital; Institute of Microscale Optoelectronics, Shenzhen University , Shenzhen 518060, China
                Author notes
                Corresponding author. E-mail: heyaqing1019@ 123456126.com
                Corresponding author. E-mail: maxiaopeng@ 123456126.com
                Corresponding author. E-mail: zjxie@ 123456siitm.org.cn
                Corresponding author. E-mail: hzhang@ 123456szu.edu.cn

                Zhi Chen, Jingfeng Li are equally contributed to this work.

                Article
                nwac104
                10.1093/nsr/nwac104
                9385456
                35992231
                b13bdf8a-7f51-47b7-b3c9-dc228ff7d554
                © The Author(s) 2022. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 15 May 2022
                : 28 May 2022
                : 29 May 2022
                : 02 August 2022
                Page count
                Pages: 10
                Funding
                Funded by: Shanghai Key Discipline Construction Project, DOI 10.13039/501100012157;
                Award ID: SZXK032
                Funded by: Fund for Scientific and Technological Research, DOI 10.13039/501100006668;
                Award ID: 2019B1515120043
                Award ID: 2020A151501612
                Award ID: 2021A1515220109
                Award ID: 2022B1515020093
                Funded by: Shenzhen Science and Technology Innovation Commission, DOI 10.13039/501100010877;
                Award ID: JSGG20200225152648408
                Award ID: KCXFZ20201221173413038
                Funded by: Department of Education of Guangdong Province, DOI 10.13039/501100010226;
                Award ID: 2018KCXTD026
                Funded by: Beijing Science and Technology Plan Project, DOI 10.13039/501100012401;
                Award ID: JCYJ20200109105608771
                Categories
                Research Article
                Multidisciplinary
                AcademicSubjects/MED00010
                AcademicSubjects/SCI00010

                surface plasmon resonance,crispr,sars-cov-2,omicron variant

                Comments

                Comment on this article