Reprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance

Mohamed Fareh (), Wei Zhao, Wenxin Hu, Joshua M. L. Casan, Amit Kumar, Jori Symons, Jennifer M. Zerbato, Danielle Fong, Ilia Voskoboinik, Paul G. Ekert, Rajeev Rudraraju, Damian F. J. Purcell, Sharon R. Lewin () and Joseph A. Trapani
Additional contact information
Mohamed Fareh: Peter MacCallum Cancer Centre
Wei Zhao: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Wenxin Hu: Peter MacCallum Cancer Centre
Joshua M. L. Casan: Peter MacCallum Cancer Centre
Amit Kumar: Peter MacCallum Cancer Centre
Jori Symons: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Jennifer M. Zerbato: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Danielle Fong: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Ilia Voskoboinik: Peter MacCallum Cancer Centre
Paul G. Ekert: Peter MacCallum Cancer Centre
Rajeev Rudraraju: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Damian F. J. Purcell: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Sharon R. Lewin: The University of Melbourne at the Peter Doherty Institute for Infection and Immunity
Joseph A. Trapani: Peter MacCallum Cancer Centre

Nature Communications, 2021, vol. 12, issue 1, 1-16

Abstract: Abstract The recent dramatic appearance of variants of concern of SARS-coronavirus-2 (SARS-CoV-2) highlights the need for innovative approaches that simultaneously suppress viral replication and circumvent viral escape from host immunity and antiviral therapeutics. Here, we employ genome-wide computational prediction and single-nucleotide resolution screening to reprogram CRISPR-Cas13b against SARS-CoV-2 genomic and subgenomic RNAs. Reprogrammed Cas13b effectors targeting accessible regions of Spike and Nucleocapsid transcripts achieved >98% silencing efficiency in virus-free models. Further, optimized and multiplexed Cas13b CRISPR RNAs (crRNAs) suppress viral replication in mammalian cells infected with replication-competent SARS-CoV-2, including the recently emerging dominant variant of concern B.1.1.7. The comprehensive mutagenesis of guide-target interaction demonstrated that single-nucleotide mismatches does not impair the capacity of a potent single crRNA to simultaneously suppress ancestral and mutated SARS-CoV-2 strains in infected mammalian cells, including the Spike D614G mutant. The specificity, efficiency and rapid deployment properties of reprogrammed Cas13b described here provide a molecular blueprint for antiviral drug development to suppress and prevent a wide range of SARS-CoV-2 mutants, and is readily adaptable to other emerging pathogenic viruses.

Date: 2021
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DOI: 10.1038/s41467-021-24577-9

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