Researchers harness Cas13 as an antiviral agent and diagnostic tool for RNA-based viruses
The need for new antiviral approaches is urgent. In the past 50 years, 90 clinically approved antiviral drugs have been produced, but they treat only nine diseases — and viral pathogens can rapidly evolve resistance to treatment. Only 16 viruses have FDA-approved vaccines.
To explore new antiviral strategies, the team focused on Cas13, which naturally targets viral RNA in bacteria. The enzyme can be programmed to target specific sequences of RNA with few limitations, is relatively easy to get into cells, and has been well-studied in mammalian cells by researchers including Broad Institute core member Feng Zhang.
The team first screened a suite of RNA-based viruses in search of viral RNA sequences that Cas13 could efficiently target. They primarily looked for pieces that are both least likely to mutate and most likely, when cut, to disable a virus.
“In theory, you could program Cas13 to attack virtually any part of a virus,” explained Myhrvold. “But there’s huge diversity within and among species, and much of the genome changes rapidly as a virus evolves. If you’re not careful, you could be going after a target that will ultimately have no effect.”
The researchers computationally identified thousands of sites, in hundreds of viral species, which could be effective targets for Cas13.
With a list of potential viral RNA targets in hand, the team could then program Cas13 to seek out and cut any of these nucleic acid sequences by engineering the enzyme’s guide RNA.
The researchers experimentally tested Cas13’s activity in human cells infected with one of three distinct RNA-based viruses: lymphocytic choriomeningitis virus (LCMV), influenza A virus (IAV), and vesicular stomatitis virus (VSV). They introduced the Cas13 gene and an engineered guide RNA into the cells, and 24 hours later, exposed the cells to the virus. After another 24 hours, the Cas13 enzymes had reduced the level of viral RNA in the cell cultures by up to 40-fold.
The team further explored Cas13’s effect on virus infectivity — in other words, how much of the remaining virus could actually continue to infect human cells. The data indicated that eight hours after viral exposure, Cas13 had reduced the infectivity of the flu virus by more than 300-fold.
To add a diagnostic component, the researchers also incorporated the Cas13-based nucleic acid detection technology SHERLOCK. The resulting CARVER system could rapidly measure the remaining levels of viral RNA in a sample.