iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2

• Published in: Virus research Vol. 288; p. 198129
• Main Authors: Ali, Zahir, Aman, Rashid, Mahas, Ahmed, Rao, Gundra Sivakrishna, Tehseen, Muhammad, Marsic, Tin, Salunke, Rahul, Subudhi, Amit K., Hala, Sharif M., Hamdan, Samir M., Pain, Arnab, Alofi, Fadwa S., Alsomali, Afrah, Hashem, Anwar M., Khogeer, Asim, Almontashiri, Naif A.M., Abedalthagafi, Malak, Hassan, Norhan, Mahfouz, Magdy M.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 15.10.2020; The Authors. Published by Elsevier B.V
• Subjects: Betacoronavirus - genetics; Biosensors; Clinical Laboratory Techniques - instrumentation; Clinical Laboratory Techniques - methods; colorimetry; Colorimetry - instrumentation; Colorimetry - methods; Coronavirus Infections - diagnosis; Coronavirus Infections - virology; COVID-19; COVID-19 infection; COVID-19 Testing; CRISPR-Cas Systems; CRISPR-Cas12; diagnostic techniques; Diagnostics; Endodeoxyribonucleases - chemistry; gene amplification; human resources; Humans; infrastructure; Molecular Diagnostic Techniques - instrumentation; Molecular Diagnostic Techniques - methods; Nucleic Acid Amplification Techniques - instrumentation; Nucleic Acid Amplification Techniques - methods; Nucleic acid detection; Pandemics; Pneumonia, Viral - diagnosis; Pneumonia, Viral - virology; Point-of-Care Systems; quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction; reverse transcription loop-mediated isothermal amplification; Rheology; RNA; RT-LAMP; SARS-CoV-2; Sensitivity and Specificity; Severe acute respiratory syndrome coronavirus 2; single-stranded DNA; temperature; viruses; COVID-19; RT-LAMP; CRISPR-Cas12; SARS-CoV-2; Diagnostics; Biosensors; Nucleic acid detection
• ISSN: 0168-1702; 1872-7492; 1872-7492
• DOI: 10.1016/j.virusres.2020.198129

•RT-LAMP coupled with CRISPR-Cas12 provides a sensitive and specific virus detection platform.•iSCAN sensitivity and specificity are comparable with RT-qPCR.•iSCAN is a 1 h detection module that can help in testing in low resource areas.•iSCAN can be developed as a one-pot assay.•iSCAN reagents can be produced locally and deployed for SARS-CoV2 detection. 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.