A comprehensive analysis and resource to use CRISPR-Cas13 for broad-spectrum targeting of RNA viruses

Xueqiu Lin; Yanxia Liu; Augustine Chemparathy; Tara Pande; Marie La Russa; Lei S Qi

doi:10.1016/j.xcrm.2021.100245

A comprehensive analysis and resource to use CRISPR-Cas13 for broad-spectrum targeting of RNA viruses

Cell Rep Med. 2021 Apr 20;2(4):100245. doi: 10.1016/j.xcrm.2021.100245. Epub 2021 Mar 23.

Authors

Xueqiu Lin¹, Yanxia Liu¹, Augustine Chemparathy^{1

2}, Tara Pande³, Marie La Russa¹, Lei S Qi^{1

4

5}

Affiliations

¹ Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
² Department of Management Science and Engineering, Stanford University, Stanford, CA 94305, USA.
³ Los Altos High School, Los Altos, CA 94022, USA.
⁴ Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA.
⁵ ChEM-H, Stanford University, Stanford, CA 94305, USA.

Abstract

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) and variants has led to significant mortality. We recently reported that an RNA-targeting CRISPR-Cas13 system, called prophylactic antiviral CRISPR in human cells (PAC-MAN), offered an antiviral strategy against SARS-CoV-2 and influenza A virus. Here, we expand in silico analysis to use PAC-MAN to target a broad spectrum of human- or livestock-infectious RNA viruses with high specificity, coverage, and predicted efficiency. Our analysis reveals that a minimal set of 14 CRISPR RNAs (crRNAs) is able to target >90% of human-infectious viruses across 10 RNA virus families. We predict that a set of 5 experimentally validated crRNAs can target new SARS-CoV-2 variant sequences with zero mismatches. We also build an online resource (crispr-pacman.stanford.edu) to support community use of CRISPR-Cas13 for broad-spectrum RNA virus targeting. Our work provides a new bioinformatic resource for using CRISPR-Cas13 to target diverse RNA viruses to facilitate the development of CRISPR-based antivirals.

Keywords: COVID-19; CRISPR; Cas13; PAC-MAN; RNA virus; SARS-CoV-2; antiviral; infectious disease.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19 / pathology
COVID-19 / virology
CRISPR-Cas Systems / genetics*
Humans
RNA Virus Infections / pathology
RNA Virus Infections / virology
RNA Viruses / genetics*
RNA Viruses / isolation & purification
RNA, Guide, CRISPR-Cas Systems / metabolism*
RNA, Viral / metabolism
SARS-CoV-2 / genetics
SARS-CoV-2 / isolation & purification
Species Specificity

Substances

RNA, Guide, CRISPR-Cas Systems
RNA, Viral

Supplementary concepts

SARS-CoV-2 variants