When COVID first hit, waiting days for laboratory results from an ultrasensitive polymerase chain reaction (PCR) test was commonplace. Faster tests usable by anyone, anywhere, later became widely available but were far less accurate. New research paves the way for a diagnostic test that’s as quick and easy as a rapid COVID test and accurate as PCR technology.
Researchers had already adapted the gene-editing technology CRISPR to identify genetic material from pathogens such as the COVID-causing SARS-CoV-2 virus. But most such efforts involved boosting or “preamplifying” the amount of DNA or RNA to be measured—a step that requires special equipment and training.
A recent study in Nature Communications shows how CRISPR-based tests can detect SARS-CoV-2, as well as a dangerous bacterium and cancer mutations, at PCR-level sensitivity without requiring preamplification.
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CRISPR uses cutting enzymes attached to RNA molecules that match a targeted genetic sequence (in this case, one from the pathogen being tested for). The RNA “guides” the enzyme to this target and then activates the enzyme to cut the sequence. But some varieties of CRISPR enzyme don’t stop there; once activated, they go on to chop any nearby single-stranded DNA (ssDNA). Researchers can exploit this action by setting their test to trigger a flash of fluorescence when ssDNA is cut, confirming that CRISPR’s target pathogen was present.
But in that setup, each target DNA or RNA molecule activates only one cutting enzyme. To boost the signal, study senior author Ewa M. Goldys, a biomedical engineer at the University of New South Wales in Sydney, and her colleagues created tiny “nanocircles” of DNA with a short, single-stranded sequence that attaches to both ends of a target sequence. When in circular form, these strands do not trigger CRISPR enzymes. But after they’re cut, they unfold into linear DNA that CRISPR detects—activating yet more enzymes in a chain reaction. “This is easy to detect even if only a few molecules of the target are present,” Goldys says.
This strategy makes CRISPR-based tests a million times more sensitive. “Removing the preamplification step allows for an elegant, simple chemistry that can be more amenable to point-of-care systems,” says Massachusetts Institute of Technology biologist Jonathan Gootenberg, who co-developed an earlier CRISPR diagnostic system. The new approach could allow for cheap test-kit components, including lateral flow strips akin to those in current rapid COVID tests—each costing a few dollars to make.
The scientists’ nanocircle-based tests detected genetic material from SARS-CoV-2 and the ulcer-causing bacterium Helicobacter pylori, and they were also able to find tumor DNA circulating in mouse blood and in human plasma. Such tests can work within 15 minutes, whereas PCR typically takes an hour or more. “We believe we’ve created a technology that has a realistic chance to supersede PCR,” Goldys says.
The group is collaborating with commercial partners on viral diagnosis and parasite detection in water. The first product, though, is a box of general-use nanocircles that researchers can add to existing CRISPR tests to boost sensitivity. These circles come with their own guide RNA that targets the circles’ DNA once it unfolds.
The biggest hurdle will be simultaneously sensing multiple targets. Medical applications often require this capability (usually to check that tests function correctly), but Gootenberg says it will be difficult to implement. The researchers are investigating: “We don’t know how we’re going to meet [this challenge],” Goldys says, “but we’ll try.”