Programmable Inhibition and Detection of RNA Viruses Using Cas13

Mol Cell. 2019 Dec 5;76(5):826-837.e11. doi: 10.1016/j.molcel.2019.09.013. Epub 2019 Oct 10.


The CRISPR effector Cas13 could be an effective antiviral for single-stranded RNA (ssRNA) viruses because it programmably cleaves RNAs complementary to its CRISPR RNA (crRNA). Here, we computationally identify thousands of potential Cas13 crRNA target sites in hundreds of ssRNA viral species that can potentially infect humans. We experimentally demonstrate Cas13's potent activity against three distinct ssRNA viruses: lymphocytic choriomeningitis virus (LCMV); influenza A virus (IAV); and vesicular stomatitis virus (VSV). Combining this antiviral activity with Cas13-based diagnostics, we develop Cas13-assisted restriction of viral expression and readout (CARVER), an end-to-end platform that uses Cas13 to detect and destroy viral RNA. We further screen hundreds of crRNAs along the LCMV genome to evaluate how conservation and target RNA nucleotide content influence Cas13's antiviral activity. Our results demonstrate that Cas13 can be harnessed to target a wide range of ssRNA viruses and CARVER's potential broad utility for rapid diagnostic and antiviral drug development.

Keywords: Arenavirus; CRISPR; Cas13; Cas13-based detection; RNA interference; RNA viruses; antiviral; crRNA design; influenza virus; multiplexing.

Publication types

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

MeSH terms

  • A549 Cells
  • Animals
  • CRISPR-Associated Proteins / genetics
  • CRISPR-Associated Proteins / metabolism*
  • CRISPR-Cas Systems*
  • Chlorocebus aethiops
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Dogs
  • Escherichia coli / enzymology
  • Escherichia coli / genetics
  • Gene Targeting / methods*
  • HEK293 Cells
  • Humans
  • Madin Darby Canine Kidney Cells
  • RNA Stability*
  • RNA Viruses / enzymology*
  • RNA Viruses / genetics
  • RNA, Viral / genetics
  • RNA, Viral / metabolism*
  • Vero Cells


  • CRISPR-Associated Proteins
  • RNA, Viral