New CRISPR-Based Test Diagnoses COVID-19 Infection in Less than an Hour

The new test – officially named the “SARS-CoV-2 DETECTR” – is easy to implement and to interpret, and requires no specialized equipment, which is likely to make the test more widely available than the current crop of COVID-19 test kits.

The new SARS-CoV-2 DETECTR assay is among the first to use CRISPR gene-targeting technology to test for the presence of the novel coronavirus. Since CRISPR can be modified to target any genetic sequence, the test kit’s developers “programmed” it to home in on two target regions in the genome of the novel coronavirus. One of these sequences is common to all “SARS-like” coronaviruses, while the other is unique to SARS-CoV-2, which causes COVID-19. Testing for the presence of both sequences ensures that the new DETECTR tool can distinguish between SARS-CoV-2 and closely related viruses.

Much like the diagnostic kits currently in use, the new test can detect the novel coronavirus in samples obtained from respiratory swabs. However, the new test is able to provide a diagnosis much more quickly. While the widely used tests based on polymerase chain reaction (PCR) techniques take about four hours to produce a result from a respiratory sample, the new DETECTR test takes only 45 minutes.

Another key advantage of the new DETECTR test is that it can be performed in virtually any lab, using off-the-shelf reagents and common equipment. This is in stark contrast to PCR-based tests, which require expensive, specialized equipment, limiting those tests to well-equipped diagnostic labs. Plus, the new DETECTR test is easy to interpret: much like a store-bought pregnancy test, dark lines that appear on test strips indicate the presence of viral genes.

The new test is also highly sensitive. It can detect the presence of as few as 10 coronaviruses in a micro liter of fluid taken from a patient – a volume many hundreds of times smaller than an average drop of water. Though slightly less sensitive than existing PCR-based tests, which can detect as few as 3.2 copies of the virus per micro liter, the difference is unlikely to have a noticeable impact in diagnosis, as infected patients typically have much higher viral loads. The new test has yet to receive formal approval for clinical use from the US Food and Drug Administration, although UCSF researchers are clinically validating the test in an effort to fast-track the approval process through Emergency Use Authorization.

“The introduction and availability of CRISPR technology will accelerate deployment of the next generation of tests to diagnose COVID-19 infection,” said Charles Chiu, MD, PhD, professor of laboratory medicine at UCSF and co-lead developer of the new test, which is described in a paper published April 16, 2020, in the journal Nature Biotechnology.

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