Journal article

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

Mohamed Fareh, Wei Zhao, Wenxin Hu, Joshua ML Casan, Amit Kumar, Jori Symons, Jennifer M Zerbato, Danielle Fong, Ilia Voskoboinik, Paul G Ekert, Rajeev Rudraraju, Damian FJ Purcell, Sharon R Lewin, Joseph A Trapani

NATURE COMMUNICATIONS | NATURE RESEARCH | Published : 2021

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 ..

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Grants

Awarded by Cancer Council Victoria Ventures grant


Funding Acknowledgements

We thank all lab members from the Trapani, Lewin, Voskoboinik, Subbarao, VIDRL, and Joo labs for facilitating experiments and discussions. We thank Dr. Georgia Deliyannis and Dr. David Jackson for providing the Calu-3 cells, and Dr. Julie McAuley for providing advices regarding Calu-3 cells infection. This work was supported by the National Health and Medical Research Council (NHMRC) of Australia through a program grant to J.A.T., and a program grant and practitioner fellowship to S.R.L. M.F. is supported by a Peter MacCallum Cancer centre strategic plan funding in partnership with the Childhood Cancer Institute Australia (CCIA). M.F., P.G.E., and J.A.T. are supported by a Cancer Council Victoria Ventures grant (ID 829606).