Coronavirus CRISPR test detects disease in less than 40 minutes

How the coronavirus pandemic has worsened, reliable, accurate and rapid tests to detect COVID-19 have become one of the most important measures to control the spread and bring back to life (something like) “normal”. A new test, using the incredibly powerful gene editing tool known as CRISPR, developed by researchers at the University of California, San Francisco and the biotech company Mammoth Biosciences, can determine if a patient is positive in 40 minutes.

The new method, published in the journal Nature Biotechnology on Thursday, is the first peer-reviewed publication showing CRISPR as a viable diagnostic tool for COVID-19. The CRISPR based system is known as “Detectr” and could reduce test times from around five hours to 40 minutes.

CRISPR is often described as “a pair of molecular scissors” because it can make precise cuts in DNA. To do this, it uses a guide and an enzyme that can be manipulated to search for specific DNA or RNA. It is like a ballistic missile for genetic sequences: click the coordinates and CRISPR sharpens it, ready to cut.

Playing now:
See this:

CRISPR explained with fried potatoes (and assorted snacks)

3:36

SARS-CoV-2, the coronavirus that causes COVID-19, is an RNA virus. By programming the CRISPR system to search for two genes in SARS-CoV-2, the research team showed that they could guide their system to recognize the coronavirus in patient samples. The results can be seen on a lateral flow strip, a device that displays a single line that marks a positive result, such as a pregnancy test.

In 40 CDC confirmed positive samples, Detectr was able to find 38 positives. Incorrectly identified 2 as negative, showing 95% according to current CDC protocol. In an analysis of 42 negative samples, Detectr did not mark any as false positive.

“The first results … look good and encouraging,” says Gaetan Burgio, a geneticist at the Australian National University in Canberra. “Overall, it has potential.”

The main advantage Detectr has over the current CDC method is speed. Both tests require the same sample of patients: a swab from the nose or throat. But the CDC uses real-time polymerase chain reaction (RT-PCR) to test for coronavirus, which requires a bulky machine and takes around four hours to run. Detectr can be run on a machine as large as a graphing calculator and uses a much faster method. However, it cannot perform as many concurrent tests as the CDC protocol.

“There are some drawbacks,” says Burgio. “The RT-PCR technique has the advantage of processing 386 samples [at] once, that is not the case with this CRISPR method.

“This is not the method of testing 3,000 tests in one day.”

The test also cannot achieve the same level of sensitivity observed in RT-PCR used by CDC, and there is still work to be done to determine its suitability for a larger implementation and FDA approval, Burgio notes.

One of the main concerns with COVID-19 is the proportion of people who can harbor the virus, but do not show symptoms of disease. Even if they feel good, they can spread the disease. Being able to capture this population in tests and screenings is invaluable in determining where another outbreak may occur, and a quick and accurate test like this can aid such an effort.

Progress in testing is also significant for the Detectr system. Mammoth Biosciences has been working on the development of the tool as a diagnostic device for a range of diseases. If another infectious disease arises, the guide used in Detectr could be changed to recognize the new disease, providing a system that can be reconfigured for emerging diseases in a matter of days.

Janice Chen, CTO of Mammoth Biosciences, says the company is working with UCSF to “expedite” the Detectr test for FDA approval through the “emergency use authorization process.”