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Viruses
Volume 15
Issue 3
10.3390/v15030686
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Article

Efficient CRISPR-Cas13d-Based Antiviral Strategy to Combat SARS-CoV-2

by
Mouraya Hussein
1,
Zaria Andrade dos Ramos
1,
Monique A. Vink
1,
Pascal Kroon
1,
Zhenghao Yu
1,
Luis Enjuanes
2,
Sonia Zuñiga
2,
Ben Berkhout
1 and
Elena Herrera-Carrillo
1,*
1
Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
2
Department of Molecular and Cell Biology, National Center of Biotechnology (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
*
Author to whom correspondence should be addressed.
Viruses 2023, 15(3), 686; https://doi.org/10.3390/v15030686
Submission received: 17 January 2023 / Revised: 27 February 2023 / Accepted: 28 February 2023 / Published: 6 March 2023
(This article belongs to the Special Issue Advances in Antiviral Agents against SARS-CoV-2 and Its Variants)
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Abstract

The current SARS-CoV-2 pandemic forms a major global health burden. Although protective vaccines are available, concerns remain as new virus variants continue to appear. CRISPR-based gene-editing approaches offer an attractive therapeutic strategy as the CRISPR-RNA (crRNA) can be adjusted rapidly to accommodate a new viral genome sequence. This study aimed at using the RNA-targeting CRISPR-Cas13d system to attack highly conserved sequences in the viral RNA genome, thereby preparing for future zoonotic outbreaks of other coronaviruses. We designed 29 crRNAs targeting highly conserved sequences along the complete SARS-CoV-2 genome. Several crRNAs demonstrated efficient silencing of a reporter with the matching viral target sequence and efficient inhibition of a SARS-CoV-2 replicon. The crRNAs that suppress SARS-CoV-2 were also able to suppress SARS-CoV, thus demonstrating the breadth of this antiviral strategy. Strikingly, we observed that only crRNAs directed against the plus-genomic RNA demonstrated antiviral activity in the replicon assay, in contrast to those that bind the minus-genomic RNA, the replication intermediate. These results point to a major difference in the vulnerability and biology of the +RNA versus −RNA strands of the SARS-CoV-2 genome and provide important insights for the design of RNA-targeting antivirals.
Keywords: COVID-19; SARS-CoV-2 genome; CRISPR-Cas13d; RNA COVID-19; SARS-CoV-2 genome; CRISPR-Cas13d; RNA

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MDPI and ACS Style

Hussein, M.; Andrade dos Ramos, Z.; Vink, M.A.; Kroon, P.; Yu, Z.; Enjuanes, L.; Zuñiga, S.; Berkhout, B.; Herrera-Carrillo, E. Efficient CRISPR-Cas13d-Based Antiviral Strategy to Combat SARS-CoV-2. Viruses 2023, 15, 686. https://doi.org/10.3390/v15030686

AMA Style

Hussein M, Andrade dos Ramos Z, Vink MA, Kroon P, Yu Z, Enjuanes L, Zuñiga S, Berkhout B, Herrera-Carrillo E. Efficient CRISPR-Cas13d-Based Antiviral Strategy to Combat SARS-CoV-2. Viruses. 2023; 15(3):686. https://doi.org/10.3390/v15030686

Chicago/Turabian Style

Hussein, Mouraya, Zaria Andrade dos Ramos, Monique A. Vink, Pascal Kroon, Zhenghao Yu, Luis Enjuanes, Sonia Zuñiga, Ben Berkhout, and Elena Herrera-Carrillo. 2023. "Efficient CRISPR-Cas13d-Based Antiviral Strategy to Combat SARS-CoV-2" Viruses 15, no. 3: 686. https://doi.org/10.3390/v15030686

APA Style

Hussein, M., Andrade dos Ramos, Z., Vink, M. A., Kroon, P., Yu, Z., Enjuanes, L., Zuñiga, S., Berkhout, B., & Herrera-Carrillo, E. (2023). Efficient CRISPR-Cas13d-Based Antiviral Strategy to Combat SARS-CoV-2. Viruses, 15(3), 686. https://doi.org/10.3390/v15030686

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