The current advances of CRISPR/Cas-based systems for the detection of COVID-19

Sasan Ghaffari, Hanif Kazerooni, Amir Salehi-Najafabadi

Abstract


The novel coronavirus disease 2019 (COVID-19) still poses a serious threat to every human on the planet nearly 1.5 years after its beginning. Unfortunately, the current diagnostic methods, although highly sensitive and specific, still suffer from many shortcomings. Faster and easy-to-operate diagnostic systems are undoubtedly sorely needed. The CRISPR/Cas platform has gained much attention in recent years in a wide range of biomedical sciences. Besides its treatment potential and drug and vaccine development, it can be used for disease diagnosis. Thus, the CRISPR/Cas-based system holds great promise for providing a rapid and easily deployable COVID-19 detection and is on par with the conventional diagnostic approaches in terms of sensitivity and specificity. In this review article, we discuss the latest advances of CRISPR/Cas technology as a fast and reliable severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection method.


Keywords


COVID-19; SARS-CoV-2; Diagnosis; CRISPR

References


Chan JF, Lau SK, To KK, Cheng VC, Woo PC, Yuen KY. Middle East respiratory syndrome coronavirus: another zoonotic betacoronavirus causing SARS-like disease. Clin Microbiol Rev. 2015; 28(2):465-522.

Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798):270-3.

Gordon DE, Jang GM, Bouhaddou M, Xu J, Obernier K, White KM, et al. A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature. 2020; 583(7816):459-68.

Tešija Kuna A, Hanžek M, Vukasović I, Nikolac Gabaj N, Vidranski V, Ćelap I, et al. Comparison of diagnostic accuracy for eight SARS-CoV-2 serological assays. Biochem Med (Zagreb). 2021; 31(1):010708.

Bustin SA, Nolan T. RT-qPCR Testing of SARS-CoV-2: A Primer. Int J Mol Sci. 2020; 21(8):3004.

Abbaszadeh-Goudarzi K, Nematollahi MH, Khanbabaei H, Nave HH, Mirzaei HR, Pourghadamyari H, et al. Targeted Delivery of CRISPR/Cas13 as a Promising Therapeutic Approach to Treat SARS-CoV-2. Curr Pharm Biotechnol. 2021; 22(9):1149-55.

Shen M, Zhou Y, Ye J, Abdullah Al-Maskri AA, Kang Y, Zeng S, et al. Recent advances and perspectives of nucleic acid detection for coronavirus. J Pharm Anal. 2020; 10(2):97-101.

Anantharajah A, Helaers R, Defour JP, Olive N, Kabera F, Croonen L, et al. How to choose the right real-time RT-PCR primer sets for the SARS-CoV-2 genome detection? J Virol Methods. 2021; 295:114197.

Jung Y, Park GS, Moon JH, Ku K, Beak SH, Lee CS, et al. Comparative Analysis of Primer-Probe Sets for RT-qPCR of COVID-19 Causative Virus (SARS-CoV-2). ACS Infect Dis. 2020; 6(9):2513-23.

Taylor SC, Laperriere G, Germain H. Droplet Digital PCR versus qPCR for gene expression analysis with low abundant targets: from variable nonsense to publication quality data. Sci Rep. 2017; 7(1):2409.

Mautner L, Baillie CK, Herold HM, Volkwein W, Guertler P, Eberle U, et al. Rapid point-of-care detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP). Virol J. 2020; 17(1):160.

Poljak M, Korva M, Knap Gašper N, Fujs Komloš K, Sagadin M, Uršič T, et al. Clinical Evaluation of the cobas SARS-CoV-2 Test and a Diagnostic Platform Switch during 48 Hours in the Midst of the COVID-19 Pandemic. J Clin Microbiol. 2020; 58(6):e00599-20.

Höhne M, Schreier E. Detection and characterization of norovirus outbreaks in Germany: application of a one-tube RT-PCR using a fluorogenic real-time detection system. J Med Virol. 2004; 72(2):312-9.

Dong L, Zhou J, Niu C, Wang Q, Pan Y, Sheng S, et al. Highly accurate and sensitive diagnostic detection of SARS-CoV-2 by digital PCR. Talanta. 2021; 224:121726.

Suo T, Liu X, Feng J, Guo M, Hu W, Guo D, et al. ddPCR: a more accurate tool for SARS-CoV-2 detection in low viral load specimens. Emerg Microbes Infect. 2020; 9(1):1259-68.

Qasem A, Shaw AM, Elkamel E, Naser SA. Coronavirus Disease 2019 (COVID-19) Diagnostic Tools: A Focus on Detection Technologies and Limitations. Curr Issues Mol Biol. 2021; 43(2):728-48.

Hou T, Zeng W, Yang M, Chen W, Ren L, Ai J, et al. Development and evaluation of a rapid CRISPR-based diagnostic for COVID-19. PLoS Pathog. 2020; 16(8):e1008705.

Tsou JH, Liu H, Stass SA, Jiang F. Rapid and Sensitive Detection of SARS-CoV-2 Using Clustered Regularly Interspaced Short Palindromic Repeats. Biomedicines. 2021; 9(3):239.

Ishino Y, Shinagawa H, Makino K, Amemura M, Nakata A. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. J Bacteriol. 1987; 169(12):5429-33.

Xu Y, Li Z. CRISPR-Cas systems: Overview, innovations and applications in human disease research and gene therapy. Comput Struct Biotechnol J. 2020; 18:2401-15.

Hu Y, Zhou Y, Zhang M, Ge W, Li Y, Yang L, et al. CRISPR/Cas9-Engineered Universal CD19/CD22 Dual-Targeted CAR-T Cell Therapy for Relapsed/Refractory B-cell Acute Lymphoblastic Leukemia. Clin Cancer Res. 2021; 27(10):2764-72.

Jayamohan H, Lambert CJ, Sant HJ, Jafek A, Patel D, Feng H, et al. SARS-CoV-2 pandemic: a review of molecular diagnostic tools including sample collection and commercial response with associated advantages and limitations. Anal Bioanal Chem. 2021; 413(1):49-71.

Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO, Metsky HC, Durbin AF, et al. Field-deployable viral diagnostics using CRISPR-Cas13. Science. 2018; 360(6387):444-8.

Broughton JP, Deng X, Yu G, Fasching CL, Servellita V, Singh J, et al. CRISPR-Cas12-based detection of SARS-CoV-2. Nat Biotechnol. 2020; 38(7):870-4.

Ding X, Yin K, Li Z, Lalla RV, Ballesteros E, Sfeir MM, et al. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nat Commun. 2020; 11(1):4711.

Wang X, Zhong M, Liu Y, Ma P, Dang L, Meng Q, et al. Rapid and sensitive detection of COVID-19 using CRISPR/Cas12a-based detection with naked eye readout, CRISPR/Cas12a-NER. Sci Bull (Beijing). 2020; 65(17):1436-9.

Huang Z, Tian D, Liu Y, Lin Z, Lyon CJ, Lai W, et al. Ultra-sensitive and high-throughput CRISPR-p owered COVID-19 diagnosis. Biosens Bioelectron. 2020; 164:112316.

Ali Z, Aman R, Mahas A, Rao GS, Tehseen M, Marsic T, et al. iSCAN: An RT-LAMP-coupled CRISPR-Cas12 module for rapid, sensitive detection of SARS-CoV-2. Virus Res. 2020; 288:198129.

Teng F, Guo L, Cui T, Wang XG, Xu K, Gao Q, et al. CDetection: CRISPR-Cas12b-based DNA detection with sub-attomolar sensitivity and single-base specificity. Genome Biol. 2019; 20(1):132.

Rahimi H, Salehiabar M, Barsbay M, Ghaffarlou M, Kavetskyy T, Sharafi A, et al. CRISPR Systems for COVID-19 Diagnosis. ACS Sens. 2021; 6(4):1430-45.

Brandsma E, Verhagen H, van de Laar TJW, Claas ECJ, Cornelissen M, van den Akker E. Rapid, Sensitive, and Specific Severe Acute Respiratory Syndrome Coronavirus 2 Detection: A Multicenter Comparison Between Standard Quantitative Reverse-Transcriptase Polymerase Chain Reaction and CRISPR-Based DETECTR. J Infect Dis. 2021; 223(2):206-13.

Ramachandran A, Huyke DA, Sharma E, Sahoo MK, Huang C, Banaei N, et al. Electric field-driven microfluidics for rapid CRISPR-based diagnostics and its application to detection of SARS-CoV-2. Proc Natl Acad Sci U S A. 2020; 117(47):29518-25.

Arizti-Sanz J, Freije CA, Stanton AC, Boehm CK, Petros BA, Siddiqui S, et al. Integrated sample inactivation, amplification, and Cas13-based detection of SARS-CoV-2. bioRxiv. 2020. [Preprint].

Rauch JN, Valois E, Solley SC, Braig F, Lach RS, Audouard M, et al. A Scalable, Easy-to-Deploy Protocol for Cas13-Based Detection of SARS-CoV-2 Genetic Material. J Clin Microbiol. 2021; 59(4):e02402-20.

Harvey WT, Carabelli AM, Jackson B, Gupta RK, Thomson EC, Harrison EM, et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021; 19(7):409-24.

Ooi KH, Liu MM, Tay JWD, Teo SY, Kaewsapsak P, Jin S, et al. An engineered CRISPR-Cas12a variant and DNA-RNA hybrid guides enable robust and rapid COVID-19 testing. Nat Commun. 2021; 12(1):1739.

Azhar M, Phutela R, Ansari AH, Sinha D, Sharma N, Kumar M, et al. Rapid, field-deployable nucleobase detection and identification using FnCas9. bioRxiv. 2020:2020.04.07.028167.

Acharya S, Mishra A, Paul D, Ansari AH, Azhar M, Kumar M, et al. Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing. Proc Natl Acad Sci U S A. 2019; 116(42):20959-68.

Yoshimi K, Takeshita K, Yamayoshi S, Shibumura S, Yamauchi Y, Yamamoto M, et al. Rapid and accurate detection of novel coronavirus SARS-CoV-2 using CRISPR-Cas3. medRxiv. 2020. [Preprint].




DOI: https://doi.org/10.52547/JCBioR.2.4.159

Refbacks

  • There are currently no refbacks.


Copyright (c) 2021 © The Author(s)

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.