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 Hamdan, Arnab Pain, Fadwa S Alofi, Afrah Alsomali, Anwar M Hashem, Asim Khogeer, Naif A M Almontashiri, Malak Abedalthagafi, Norhan Hassan, Magdy M. Mahfouz

Research output: Contribution to journalArticlepeer-review

205 Scopus citations


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.
Original languageEnglish (US)
Pages (from-to)198129
JournalVirus research
StatePublished - Aug 22 2020

Bibliographical note

KAUST Repository Item: Exported on 2020-12-08
Acknowledgements: We would like to thank members of the genome engineering and synthetic biology laboratory for insightful discussions and technical support. We thank Professor Andrew Ellington for providing the RTx and BstI clones. This work was supported, in part, by the Smart Health Initiative at KAUST and the IAF grant from the KAUST IED to MM. King Abdullah University of Science and Technology, SAUDI ARABIA. The samples were collected from patients providing verbal consent to the treating doctor after they read the patient consent form, or the doctor explained the content of consent form to the patient. Hence, as per the approved protocol, the doctors took samples only after receiving verbal consent from a concerned patient (due to infection hazard and no family member being available next to the patients due to infection control guidelines) and the treating doctor signed on the consent form on behalf of the patient before any sample collection took place. We have obtained the necessary ethical approval from the Saudi-MOH and the Mass Gathering directorate in Riyadh, Saudi Arabia, for the collection of the samples (Saudi MOH Approval #: H-02-K-076-0420-285, dated 13.04.2020; KAUST Approval #: 20IBEC14). We thank Sara Mfarrej and Fathia Ben Rached for their help during the handling of the clinical samples in KAUST.


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