Reprogrammed CRISPR Tool Could Target Emerging SARS-CoV-2 Variants

Science has come a long way in discovering the intriguing pathobiology of SARS-CoV-2, the deadly virus that led to the prevailing global pandemic. Although major advances have been made in preventing disease progression and combating severe infections, rapidly emerging COVID-19 variants pose new challenges.  

In a recent study published in Nature, a team of investigators from Melbourne, Australia, utilized genome-wide computational prediction and precise single nucleotide resolution screening to reprogram CRISPR-Cas13b to efficiently suppress replication of SARS-CoV-2 and overcome viral escape from host immunity and anti-viral therapeutics.

Reprogrammed CRISPR-Cas13 Tool

CRISPR-Cas13 is a type of adaptive immune mechanism found in bacteria and archaea. Substantial evidence points to the remarkable potential of certain Cas13 orthologs to silence endogenous and viral RNAs in mammalian cells. However, the underlying molecular mechanism by which Cas13 recognizes and suppresses SARS-CoV-2 replication in infected mammalian cells is elusive.

Interestingly, the study investigators have uncovered a novel role of the reprogrammed CRISPR-pspCas13b in efficiently suppressing SARS-CoV-2 replication, including the ancestral virus D614G and the alpha variant B.1.1.7, by targeting the Spike and Nucleocapsid transcripts precisely (>98% silencing efficiency). While the Spike glycoprotein facilitates viral invasion of host cells upon binding to the ACE2 surface receptor, the nucleocapsid protein is a highly conserved structural component indispensable for viral assembly.

By utilizing the Cas13b CRISPR RNAs (crRNAs) multiplexing approach, the authors have demonstrated that the simultaneous targeting of viral RNA regions alleviates the risk of target inaccessibility and mutation-driven evolution of viral escape of SARS-CoV-2, including B.1.1.7 variant, from host immunity and anti-viral therapeutics.

This appealing multiplexing strategy utilizes a cocktail of crRNAs to simultaneously target various conserved subunits of the virus by simultaneously achieving high silencing efficiency. Further, using comprehensive mutagenesis analysis of guide-target interaction, the authors demonstrated that single-nucleotide mismatches do not impede the potential of a single crRNA to simultaneously suppress ancestral and mutated SARS-CoV-2 strains in infected mammalian cells, including the Spike D614G mutant.

Additionally, the authors demonstrated that a single crRNA is tolerant to single nucleotide-mismatch and will likely remain catalytically active against future SARS-CoV-2 variants that arise due to de novo mutations.

Advantages of the Gene Editing Method

In conclusion, the findings from this study outline a promising future that could improve the lives and health of millions of people dealing with COVID-19.

“Unlike conventional therapeutics that typically requires years of modeling, design, and screening, the advantage of reprogrammed CRISPR-Cas13b lies in its design-flexibility, predictive efficacy, specificity, high silencing efficiency, and rapid deployment properties,” said Mohamed Fareh, a co-author of the study.

Strikingly, the exceptionally high resilience of single-nucleotide mismatch and the precise use of crRNA multiplexing can effectively suppress viral replication that would evade current treatment modalities involving antibody treatments. These striking characteristics are undoubtedly a remarkable indicator of the translation potential of this promising technology. If developed, it could prove to be a game-changer in defining the battle against SARS-CoV-2 and its variants.

Last but not least, CRISPR-Cas13b mediated suppression of viral replication is readily adaptable and expandable to other pathogenic viruses beyond SARS-CoV-2 and may therefore serve as a powerful tool for anti-viral therapeutics.

Related Article: Novel CRISPR Screen Unravels Disease-Related Genes in Neurons

Author

Isha Kapoor