Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro

Leiping Zeng; Yanxia Liu; Xammy Huu Nguyenla; Timothy R Abbott; Mengting Han; Yanyu Zhu; Augustine Chemparathy; Xueqiu Lin; Xinyi Chen; Haifeng Wang; Draven A Rane; Jordan M Spatz; Saket Jain; Arjun Rustagi; Benjamin Pinsky; Adrianna E Zepeda; Anastasia P Kadina; John A Walker 3rd; Kevin Holden; Nigel Temperton; Jennifer R Cochran; Annelise E Barron; Michael D Connolly; Catherine A Blish; David B Lewis; Sarah A Stanley; Marie F La Russa; Lei S Qi

doi:10.1038/s41467-022-30546-7

Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro

Nat Commun. 2022 May 19;13(1):2766. doi: 10.1038/s41467-022-30546-7.

Authors

Leiping Zeng^#¹, Yanxia Liu^#¹, Xammy Huu Nguyenla², Timothy R Abbott¹, Mengting Han¹, Yanyu Zhu¹, Augustine Chemparathy¹, Xueqiu Lin¹, Xinyi Chen¹, Haifeng Wang¹, Draven A Rane¹, Jordan M Spatz³, Saket Jain⁴, Arjun Rustagi⁵, Benjamin Pinsky^{5

6}, Adrianna E Zepeda⁷, Anastasia P Kadina⁷, John A Walker 3rd⁷, Kevin Holden⁷, Nigel Temperton⁸, Jennifer R Cochran¹, Annelise E Barron¹, Michael D Connolly⁹, Catherine A Blish^{5

10}, David B Lewis³, Sarah A Stanley¹¹, Marie F La Russa¹², Lei S Qi^{13

14

15}

Affiliations

¹ Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
² Department of Molecular and Cellular Biology, University of California, Berkeley, CA, 94720, USA.
³ Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA.
⁴ University of California San Francisco, San Francisco, CA, 94143, USA.
⁵ Department of Medicine, Stanford University, Stanford, CA, 94305, USA.
⁶ Department of Pathology, Stanford University, Stanford, CA, USA.
⁷ Synthego Corporation, Redwood City, CA, USA.
⁸ Viral Pseudotype Unit, Medway School of Pharmacy, Chatham, Kent ME4 4TB, UK.
⁹ Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
¹⁰ Chan Zuckerberg BioHub, San Francisco, CA, 94158, USA.
¹¹ Department of Molecular and Cellular Biology, University of California, Berkeley, CA, 94720, USA. sastanley@berkeley.edu.
¹² Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. mlarussa@stanford.edu.
¹³ Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA. stanley.qi@stanford.edu.
¹⁴ Chan Zuckerberg BioHub, San Francisco, CA, 94158, USA. stanley.qi@stanford.edu.
¹⁵ Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA. stanley.qi@stanford.edu.

^# Contributed equally.

Abstract

A major challenge in coronavirus vaccination and treatment is to counteract rapid viral evolution and mutations. Here we demonstrate that CRISPR-Cas13d offers a broad-spectrum antiviral (BSA) to inhibit many SARS-CoV-2 variants and diverse human coronavirus strains with >99% reduction of the viral titer. We show that Cas13d-mediated coronavirus inhibition is dependent on the crRNA cellular spatial colocalization with Cas13d and target viral RNA. Cas13d can significantly enhance the therapeutic effects of diverse small molecule drugs against coronaviruses for prophylaxis or treatment purposes, and the best combination reduced viral titer by over four orders of magnitude. Using lipid nanoparticle-mediated RNA delivery, we demonstrate that the Cas13d system can effectively treat infection from multiple variants of coronavirus, including Omicron SARS-CoV-2, in human primary airway epithelium air-liquid interface (ALI) cultures. Our study establishes CRISPR-Cas13 as a BSA which is highly complementary to existing vaccination and antiviral treatment strategies.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, N.I.H., Extramural

MeSH terms

Antiviral Agents / pharmacology
COVID-19 Drug Treatment*
Humans
Liposomes
Nanoparticles
SARS-CoV-2* / genetics

Broad-spectrum CRISPR-mediated inhibition of SARS-CoV-2 variants and endemic coronaviruses in vitro

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