iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2
Zahir Ali, Rashid Aman, Ahmed Mahas, Gundra Sivakrishna Rao, Muhammad Tehseen, Tin Marsic, Rahul Salunke, Amit K Subudhi, Sharif M Hala, Samir M Hamdan, Arnab Pain, Fadwa S Alofi, Afrah Alsomali, Anwar M Hashem, Asim Khogeer, Naif A M Almontashiri, Malak Abedalthagafi, Norhan Hassan, Magdy M Mahfouz, Zahir Ali, Rashid Aman, Ahmed Mahas, Gundra Sivakrishna Rao, Muhammad Tehseen, Tin Marsic, Rahul Salunke, Amit K Subudhi, Sharif M Hala, Samir M Hamdan, Arnab Pain, Fadwa S Alofi, Afrah Alsomali, Anwar M Hashem, Asim Khogeer, Naif A M Almontashiri, Malak Abedalthagafi, Norhan Hassan, Magdy M Mahfouz
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 affects all aspects of human life. Detection platforms that are efficient, rapid, accurate, specific, sensitive, and user friendly are urgently needed to manage and control the spread of SARS-CoV-2. RT-qPCR based methods are the gold standard for SARS-CoV-2 detection. However, these methods require trained personnel, sophisticated infrastructure, and a long turnaround time, thereby limiting their usefulness. Reverse transcription-loop-mediated isothermal amplification (RT-LAMP), a one-step nucleic acid amplification method conducted at a single temperature, has been used for colorimetric virus detection. CRISPR-Cas12 and CRISPR-Cas13 systems, which possess collateral activity against ssDNA and RNA, respectively, have also been harnessed for virus detection. Here, we built an efficient, rapid, specific, sensitive, user-friendly SARS-CoV-2 detection module that combines the robust virus amplification of RT-LAMP with the specific detection ability of SARS-CoV-2 by CRISPR-Cas12. Furthermore, we combined the RT-LAMP-CRISPR-Cas12 module with lateral flow cells to enable highly efficient point-of-care SARS-CoV-2 detection. Our iSCAN SARS-CoV-2 detection module, which exhibits the critical features of a robust molecular diagnostic device, should facilitate the effective management and control of COVID-19.
Keywords: Biosensors; COVID-19; CRISPR-Cas12; Diagnostics; Nucleic acid detection; RT-LAMP; SARS-CoV-2.
Copyright © 2020 The Authors. Published by Elsevier B.V. All rights reserved.
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References
- Zhou P. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020;579(7798):270–273.
- Zhu N. A novel coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med. 2020;382(8):727–733.
- Huang C. Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet. 2020;395(10223):497–506.
- Cui J., Li F., Shi Z.L. Origin and evolution of pathogenic coronaviruses. Nat. Rev. Microbiol. 2019;17(3):181–192.
- Cotten M. Full-genome deep sequencing and phylogenetic analysis of novel human betacoronavirus. Emerg. Infect Dis. 2013;19(5) p. 736-42B.
- Li Q. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. N. Engl. J. Med. 2020;382(13):1199–1207.
- Han Y., Yang H. The transmission and diagnosis of 2019 novel coronavirus infection disease (COVID-19): a Chinese perspective. J. Med. Virol. 2020
- Jones G. The French human Salmonella surveillance system: evaluation of timeliness of laboratory reporting and factors associated with delays, 2007 to 2011. Euro. Surveill. 2014;19(1)
- Isere E.E., Fatiregun A.A., Ajayi I.O. An overview of disease surveillance and notification system in Nigeria and the roles of clinicians in disease outbreak prevention and control. Niger. Med. J. 2015;56(3):161–168.
- Niemz A., Ferguson T.M., Boyle D.S. Point-of-care nucleic acid testing for infectious diseases. Trends Biotechnol. 2011;29(5):240–250.
- Dohla M. Rapid point-of-care testing for SARS-CoV-2 in a community screening setting shows low sensitivity. Public Health. 2020;182:170–172.
- Corman V.M. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro. Surveill. 2020;25(3)
- Morshed M.G. Molecular methods used in clinical laboratory: prospects and pitfalls. FEMS Immunol. Med. Microbiol. 2007;49(2):184–191.
- Nguyen T., Duong Bang D., Wolff A. 2019 novel coronavirus disease (COVID-19): paving the road for rapid detection and point-of-care diagnostics. Micromachines (Basel) 2020;11(3)
- Mabey D. Diagnostics for the developing world. Nat. Rev. Microbiol. 2004;2(3):231–240.
- Mori Y., Notomi T. Loop-mediated isothermal amplification (LAMP): a rapid, accurate, and cost-effective diagnostic method for infectious diseases. J. Infect. Chemother. 2009;15(2):62–69.
- Notomi T. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000;28(12):E63.
- Chou P.H. Real-time target-specific detection of loop-mediated isothermal amplification for white spot syndrome virus using fluorescence energy transfer-based probes. J. Virol. Methods. 2011;173(1):67–74.
- Nagai K. Diagnostic test accuracy of loop-mediated isothermal amplification assay for Mycobacterium tuberculosis: systematic review and meta-analysis. Sci. Rep. 2016;6:39090.
- Barrangou R., Marraffini L.A. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol. Cell. 2014;54(2):234–244.
- Sorek R., Lawrence C.M., Wiedenheft B. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu. Rev. Biochem. 2013;82:237–266.
- Mahas A., Aman R., Mahfouz M. CRISPR-Cas13d mediates robust RNA virus interference in plants. Genome Biol. 2019;20(1):263.
- Doudna J.A., Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346(6213):1258096.
- Mahas A., Neal Stewart C., Jr., Mahfouz M.M. Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation. Biotechnol. Adv. 2017
- Abudayyeh O.O. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science. 2016;353(6299):aaf5573.
- Chen J.S. CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity. Science. 2018;360(6387):436–439.
- Harrington L.B. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. Science. 2018;362(6416):839–842.
- Aman R., Mahas A., Mahfouz M. Nucleic acid detection using CRISPR/Cas biosensing technologies. ACS Synth. Biol. 2020
- Li Y. CRISPR/Cas systems towards next-generation biosensing. Trends Biotechnol. 2019;37(7):730–743.
- Li L. HOLMESv2: a CRISPR-Cas12b-Assisted platform for nucleic acid detection and DNA methylation quantitation. ACS Synth. Biol. 2019;8(10):2228–2237.
- Li S.Y. CRISPR-Cas12a-assisted nucleic acid detection. Cell Discov. 2018;4:20.
- Kellner M.J. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat. Protoc. 2019;14(10):2986–3012.
- Milligan J.N. Evolution of a thermophilic strand-displacing polymerase using high-temperature isothermal compartmentalized self-replication. Biochemistry. 2018;57(31):4607–4619.
- Ellefson J.W. Synthetic evolutionary origin of a proofreading reverse transcriptase. Science. 2016;352(6293):1590–1593.
- Zhang Y. Rapid molecular detection of SARS-CoV-2 (COVID-19) virus RNA using colorimetric LAMP. medRxiv. 2020
- Lu R. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. Lancet. 2020;395(10224):565–574.
- Kim D. The architecture of SARS-CoV-2 transcriptome. Cell. 2020
- Lu X. US CDC real-time reverse transcription PCR panel for detection of severe acute respiratory syndrome coronavirus 2. Emerg. Infect Dis. 2020;26(8)
- Teng F. Repurposing CRISPR-Cas12b for mammalian genome engineering. Cell Discov. 2018;4:63.
- Shmakov S. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol. Cell. 2015;60(3):385–397.
- Broughton J.P. CRISPR-Cas12-based detection of SARS-CoV-2. Nat. Biotechnol. 2020;38(7):870–874.
- Joung J. Point-of-care testing for COVID-19 using SHERLOCK diagnostics. medRxiv. 2020
- Bhadra S. Cellular reagents for diagnostics and synthetic biology. PLoS One. 2018;13(8):e0201681.
- Broughton J.P. CRISPR-Cas12-based detection of SARS-CoV-2. Nat. Biotechnol. 2020
- Wyllie A.L. Saliva is more sensitive for SARS-CoV-2 detection in COVID-19 patients than nasopharyngeal swabs. medRxiv. 2020
- Ma Y. Enhancement of polymerase activity of the large fragment in DNA polymerase I from Geobacillus stearothermophilus by site-directed mutagenesis at the active site. Biomed Res. Int. 2016;2016:2906484.
- Bhadra S., Maranhao A.C., Ellington A.D. A one-enzyme RT-qPCR assay for SARS-CoV-2, and procedures for reagent production. bioRxiv. 2020
- Wang Y. A one-pot toolbox based on Cas12a/crRNA enables rapid foodborne pathogen detection at Attomolar Level. ACS Sens. 2020
- Wang B. Cas12aVDet: a CRISPR/Cas12a-Based platform for rapid and visual nucleic acid detection. Anal. Chem. 2019;91(19):12156–12161.
Source: PubMed