CRISPR is a useful biological tool for detecting nucleic acid of SARS-CoV-2 in human clinical samples

Abstract

The recent pandemic of novel coronavirus disease (COVID-19) has spread globally and infected millions of people. The quick and specific detection of the nucleic acid of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) remains a challenge within healthcare providers. Currently, quantitative reverse transcription-polymerase chain reaction (RT-qPCR) is the widely used method to detect the SARS-CoV-2 from the human clinical samples. RT-qPCR is expensive equipment and needs skilled personnel as well as lengthy detection time. RT-qPCR limitation needed an alternative healthcare technique to overcome with a fast and cheaper detection method. By applying the principles of CRISPR technology, several promising detection methods giving hope to the healthcare community. CRISPR-based detection methods include SHERLOCK-Covid, STOP-Covid, AIOD-CRISPR, and DETECTR platform. These methods have comparative advantages and drawbacks. Among these methods, AIOD-CRISPR and DETECTR are reasonably better diagnostic methods than the others if we compare the time taken for the test, the cost associated with each test, and their capability of detecting SARS-CoV-2 in the clinical samples. It may expect that the promising CRISPR-based methods would facilitate point-of-care (POC) applications in the CRISPR-built next-generation novel coronavirus diagnostics.

Keywords: COVID-19; CRISPR; Diagnostics; Nucleic acid; SARS-CoV-2.

Graphical abstract

Fig. 1

Mechanism of CRISPR-based nucleotide detection. a Fluorescent tracking detection of nucleotide-based on specific binding and cutting activity of CRISPR/Cas9. Firstly, crRNA identifies the target nucleic acid for the spacer of the CRISPR Cas system. After identifying and detecting the sequence, specific Cas nucleases cut the target nucleic acid. After that, the vast amount of target fragments of nucleic acids was synthesized with the assistance of an isothermal amplification process. At last, fluorescent tracking finds out the target nucleotides in detection platforms. b Collateral cleavage based on CRISPR/Cas effectors. In the first instance, the vast amount of target nucleic acids synthesized with an isothermal amplification process, including LAMP, RPA, RT-LAMP. After that, crRNA identifies the target nucleic acid for the spacer of the CRISPR Cas system. After identifying and detecting the target sequence, specific Cas nucleases (Cas12a, AapCas12b, or Cas13) cut the target nucleic acid. Finally, the reporters cut by the activated Cas effectors to liberate visual fluorescent signals within detection platforms. c Cleavage of the reporter RNA and fluorescence generation do not occur without the Cas enzyme activation.