CRISPR-based Dx could become a quick screen for Zika and other infections

Unlike traditional CRISPR-Cas9 gene editing systems, which target specific genes on DNA, the SHERLOCK diagnostic tool targets RNA, cutting it and any nearby, nontargeted RNA.

A Broad Institute-led team created a CRISPR-based diagnostic that can detect Zika virus at low concentrations in blood, urine or saliva. It could become a quick, cheap and accurate way to screen for infectious diseases at the point of care.

CRISPR-Cas9 systems use a guide RNA to target a DNA sequence and an enzyme to cut it, switching off the targeted gene. Researchers are studying CRISPR’s use in treating a number of conditions, including sickle cell disease, acute myeloid leukemia and retinitis pigmentosa.

Unlike CRISPR, the Broad's diagnostic tool, dubbed SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing), targets RNA rather than DNA, according to a statement. It uses the Cas13a enzyme, which, unlike DNA-targeting CRISPR enzymes, doesn’t stop at cutting its intended target. Instead, it also cuts RNA that happens to be nearby, which the scientists called “collateral cleavage.”

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In addition to rapidly detecting Zika virus at low concentrations, the system was able to distinguish between two different strains of the virus. The test could also differentiate between specific types of bacteria, spot antibiotic resistance genes and identify cancerous mutations in simulated cell-free DNA fragments, according to the statement. The research is published in Science.

Jennifer Doudna of CRISPR Therapeutics and her colleagues at UC Berkeley previously studied Cas13a for RNA detection, but it wasn’t sensitive enough. The Broad’s Feng Zhang, Jim Collins and their teams raised the levels of DNA or RNA in their samples using body heat and then performed a second amplification to convert the DNA to RNA, the Broad said in the statement. This improved the sensitivity of SHERLOCK by “a millionfold.”

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“This tool offers the sensitivity that could detect an extremely small amount of cancer DNA in a patient’s blood sample, for example, which would help researchers understand how cancer mutates over time,” Collins said. “For public health, it could help researchers monitor the frequency of antibiotic-resistant bacteria in a population. The scientific possibilities get very exciting very quickly.”

SHERLOCK can be packaged as a paper-based test that doesn’t need to be refrigerated, so it could be distributed and used quickly in resource-poor areas or during outbreaks.