The new CRISPR-based diagnostic coronavirus can shorten the waiting time for tests.
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By Robert F. Service
Science‘O COVID-19 reporting is supported by the Pulitzer Center and the Heizing-Simmons Foundation.
Researchers have used the CRISPR gene-acquisition technique to come up with a test that can detect an epidemic coronavirus in just 5 minutes. Expensive lab equipment is not required to perform the diagnostics and potential doctors may be deployed in office fees, schools and office fee buildings.
“It looks like they have a really rock-solid test,” says Max Wilson, a nuclear biologist at the University of California, Santa Barbara. “It’s really gorgeous.”
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CRISPR diagnostics is one way that researchers are trying to speed up coronavirus testing. The new test is still CRISPR based diagnostic. In May, for example, two teams reported creating CRISPR-based coronavirus tests that can detect the virus in about an hour, faster than the 24 hours required for conventional coronavirus diagnostic tests.
CRISPR tests work by identifying the sequence of RNA – about 20 RNA bases long જે which is typical for SARS-Cavi-2. They do this by creating a “guide” RNA that complements the target RNA sequence and, thus, binds it to the solution. When the guide attaches to its target, the CRISPR tool’s CAS 13 “scissors” enzyme is turned on and cuts off any nearby single-strand RNA. This incision removes the fluorescent particles introduced separately in the test solution. When the sample is then hit by an explosion of laser light, the released fluorescent particles are released, indicating the presence of a virus.
In these early CRISPR tests, researchers needed to amplify any potential viral RNA before it could be run by diagnostics, in order to increase their barriers to signal detection. Added complexity, cost and time and put stress on rare chemical reagents.
Now, researchers led by Jennifer Doudna, who yesterday won a share of this year’s Nobel Prize in Chemistry for co-discovery of CRISPR, created a novel CRISPR diagnostic that does not amplify coronavirus RNA. Instead, Dowdna and her colleagues spent months testing hundreds of guided RNAs to find a number of guides that worked to increase test sensitivity.
In a new print, researchers say that with a single guide RNA, they can detect up to 100,000 viruses per microliter of solution. And if they add another guide RNA, they can detect up to 100 viruses per microliter.
It’s still not as good as a traditional coronavirus diagnostic setup that uses expensive lab-based machines to track a single virus per microliter, says UC San Francisco virologist Melanie Ott, who helped draw the project with Dowd. However, he says, the new setup was able to accurately identify batches of five positive clinical samples with absolute accuracy in just minutes per test, while it may take 1 day or more for results to return to standard testing.
Says Wilson: Another important advantage of the new test is to quantify the amount of virus in the sample. When standard coronavirus tests expand it to detect the genetic material of the virus, this changes the amount of genetic material present – and therefore eliminates any possibility of a certain amount of virus in the sample.
In contrast, TTTS and Doudna’s team found that the strength of a fluorescent signal is proportional to the amount of virus in their sample. This not only revealed whether a sample was positive, but also how much virus the patient had. That information can help doctors make treatment decisions for each patient’s condition, Wilson says.
Daudna and Tutt say they and their colleagues are now working to validate their test setup and find out how to commercialize it.
