Harnessing CRISPR-Cas to Combat COVID-19: From Diagnostics to Therapeutics

Abstract

The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), remains a global threat with an ever-increasing death toll even after a year on. Hence, the rapid identification of infected individuals with diagnostic tests continues to be crucial in the on-going effort to combat the spread of COVID-19. Viral nucleic acid detection via real-time reverse transcription polymerase chain reaction (rRT-PCR) or sequencing is regarded as the gold standard for COVID-19 diagnosis, but these technically intricate molecular tests are limited to centralized laboratories due to the highly specialized instrument and skilled personnel requirements. Based on the current development in the field of diagnostics, the programmable clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated proteins (Cas) system appears to be a promising technology that can be further explored to create rapid, cost-effective, sensitive, and specific diagnostic tools for both laboratory and point-of-care (POC) testing. Other than diagnostics, the potential application of the CRISPR–Cas system as an antiviral agent has also been gaining attention. In this review, we highlight the recent advances in CRISPR–Cas-based nucleic acid detection strategies and the application of CRISPR–Cas as a potential antiviral agent in the context of COVID-19.

COVID-19 active case findings based on self-collected saliva samples with CRISPR-Cas12a detection

“…In combination with the isothermal amplification technique, several research groups have reported the advancement of diagnostic tool designs originating from the CRISPR-Cas system, and have developed various assays based on Cas12 and Cas13 to detect SARS-CoV-2. 2,5,6 Saliva samples were used as an attractive choice owing to their non-invasive, repeatable, and simple collection procedure. Moreover, during the first week of infection, it has been reported that more viral particles could be retrieved from saliva compared to NP swab samples.…”

“…4 Meanwhile, the use of the CRISPR (clustered regularly interspaced short palindromic repeats)-Cas system in molecular diagnostics has increased exponentially. 2,5,6 Several CRISPR/Cas-based assays have been developed because the system offers highly specific nucleic acid detection. In our previous studies, we reported the detection of SARS-CoV-2 RNA based on CRISPR-Cas12a.…”

In Silico Prediction and Selection of Target Sequences in the SARS-CoV-2 RNA Genome for an Antiviral Attack

“…Our research was focused on finding optimal target sequences in the SARS-CoV-2 RNA genome for a therapeutic attack, but this work may also have relevance for viral diagnostics based on the CRISPR-Cas technology, in particular, the interaction between the crRNA and the viral RNA genome [113][114][115]. It seems fair to extend our current finding of optimal therapeutic target sites to candidate target sequences for viral diagnostics.…”

Lateral Flow Immunoassays for SARS-CoV-2

“…Presently, a range of nucleic acid amplification tests (NAATs) have been granted emergency use authorization (EUA) status by the US Food and Drug Administration (FDA). These include non-isothermal- and isothermal-based amplification technologies with various amplicon detection methods being employed such as fluorometric, colorimetric, electrochemical, magnetic resonance, clustered regularly interspaced short palindromic repeats/Cas systems, matrix-assisted laser desorption ionization time-of-flight and sequencing [ 8 , 9 ]. However, the technical intricacies and sophisticated instrument requirements of FDA-EUA nucleic acid tests confine most of them to Clinical Laboratory Improvement Amendments (CLIA)-certified, high-complexity laboratories.…”