CRISPR detectives against SARS-CoV-2: a major setback against COVID-19 blowout

Abstract

The emergence of SARS-CoV-2 has brought the world to a standstill, and till date, effective treatments and diagnostics against this idiosyncratic pathogen are lacking. As compared to the standard WHO/CDC qPCR detection method, which consumes several hours for detection, CRISPR-based SHERLOCK, DETECTR, and FELUDA have emerged as rapid diagnostic tools for the detection of the RNA genome of SARS-CoV-2 within an hour with 100% accuracy, specificity, and sensitivity. These attributes of CRISPR-based detection technologies have taken themselves one step ahead of available detection systems and are emerging as an inevitable tool for quick detection of the virus. Further, the discovery of Cas13s nucleases and their orthologs has opened a new corridor for exploitation of Cas13s as an antiviral therapy against SARS-CoV-2 and other viral diseases. One such approach is Prophylactic Antiviral CRISPR in huMAN cells (PACMAN), which needs a long haul to bring into therapy. The approval of SHERLOCK as the first CRISPR-based SARS-CoV-2 test kit by the FDA, for emergency diagnosis of COVID-19 patients, has given positive hope to scientists that sooner human trials of CRISPR-based therapy will be ratified. In this review, we have extensively reviewed the present CRISPR-based approaches, challenges, and future prospects in the light of diagnostics and therapeutics against SARS-CoV-2. Key points • The discovery of Cas12 and Cas13 siblings allowed scientists to detect the viral genes. • Cas13d’s identification aided scientists in precisely cleaving the SARS-CoV-2 ssRNA. • CRISPR-Cas system acts as “molecular detector and antiviral proctor.”

Cas13d: A New Molecular Scissor for Transcriptome Engineering

“…Even though Cas9 stole all the limelight initially, it has limited therapeutic applications owing to its off-target effects. Further, the emergence of cas12 and Cas13 family nucleases, allowed the scientists to utilize CRISPR in several applications such as epigenetic modification, base editor, chromatin imaging, optogenetics, vesicle tracking, gene regulation, and the list is growing ( Gupta et al, 2021b ). Not only that the CRISPR Cas system has also been used in various biomedical applications to treat diseases such as HIV, Cancers, β-Thalassemia, sickle cell disease (SCD), cystic fibrosis, spinal muscular atrophy (SMA), Leber Congenital Amaurosis (LCA10), Hereditary transthyretin amyloidosis (hATTR), urinary tract infections (UTIs), etc., which are in preclinical and clinical trials ( Kotagama et al, 2019 ; Xu and Li 2020 ).…”

“…Finally, in 2020, Jennifer Doudna and Emmanuelle Charpentier won the Nobel Prize for introducing and utilizing the CRISPR Cas9 method to edit DNA 1 . Moreover, recently CRISPR tools have been approved by the FDA to be used in clinical diagnostic as a molecular detector against various viral diseases and even the most recent deadly virus SARS-CoV2 (COVID-19) ( Gupta et al, 2021b ). Both of these events have given immense hope to the CRISPR scientists that the CRISPR tool will be soon available in clinical practices to treat and control any diseases with ease but still, it is a long way to go.…”

“…Further, as discussed earlier that each type of V-subtypes has dissimilar Cas12 proteins which showed distinct targetable substrates i.e., it can target double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and even single-stranded RNA (ssRNA). Because of multi-substrate specificity CRISPR-Cas12 system has been used in a wide range of applications such as genome editing, transcriptional regulation, DNA and RNA base editing, detection of nucleic acid (DNA and RNA), detection of small molecules, and the list is growing ( Gupta et al, 2021b ; Li et al, 2021 ). However, the mismatch sensitivity, thermal stability, immunogenicity, and off-target effects are still the area of concern and need more in vitro and in vivo studies before they can be employed for any bio-medical or therapeutic application.…”

An Insight into Modern Targeted Genome-Editing Technologies with a Special Focus on CRISPR/Cas9 and its Applications

“…It is highly transmissible among humans and takes between 5 and 14 days upon infection to show symptoms. The most prevalent symptoms of the disease reported were muscle pain, fever, diarrhea, difficulty in breathing, dry cough, chest pain, elevated levels of cytokines in the bloodstream, and death in severe disease cases [ 76 ]. CRISPR/Cas technology has shown promise in providing methods for coronavirus detection and possible treatments (Table 3 ) [ 11 ].…”

The relevant information about the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using the five-question approach (when, where, what, why, and how) and its impact on the environment

“…This generates a gas signal, which is subsequently identified using a smartphone-specific application and camera (Silva et al 2021). The use of CRISPR systems in molecular diagnostics and detection has developed, and Rahimi et al (2021) and Gupta et al (2021) have extensively described several CRISPRbased diagnostic methods for identifying COVID-19.…”