Smartphone camera and CRISPR technology combine for rapid COVID-19 test

A novel rapid COVID-19 test has been proposed, promising to provide accurate results in less than 30 minutes using a simple hand-held device, a nasal swab and a smartphone camera. The breakthrough device can potentially be modified to detect many other viral diseases and was developed in collaboration with Jennifer Doudna, who recently won a Nobel Prize for co-discovering the revolutionary CRISPR gene editing technology.

The current gold-standard test for SARS-CoV-2 is polymerase chain reaction (PCR) testing. This test involves several steps involving the conversion of viral RNA into DNA, and then amplifying those DNA segments over several hours until they reach detectable levels. This entire process involves bulky lab equipment and can take hours.

This new innovation leverages CRISPR gene editing technology to essentially skip the RNA-to-DNA conversion process and directly detect the viral RNA in a given sample. The technology had previously been in development to detect HIV but early in 2020 the researchers shifted their focus to translate the technology into a rapid COVID-19 test.

“We knew the assay we were developing would be a logical fit to help the crisis by allowing rapid testing with minimal resources,” explains co-first author on the new study, Parinaz Fozouni. “Instead of the well-known CRISPR protein called Cas9, which recognizes and cleaves DNA, we used Cas13, which cleaves RNA.”

The technology uses the CRISPR Cas13 protein to identify and cleave SARS-CoV-2 RNA, and a second reporter molecule responds to the RNA cleaving by emitting a fluorescent signal. The sample is then slipped into a simple fluorescence detector that has an added lens, and a laser that magnifies the illumination. A smartphone camera placed on top can subsequently detect the emissions confirming the positive test result.

“What really makes this test unique is that it uses a one-step reaction to directly test the viral RNA, as opposed to the two-step process in traditional PCR tests,” says Melanie Ott, co-senior author on the new study. “The simpler chemistry, paired with the smartphone camera, cuts down detection time and doesn’t require complex lab equipment. It also allows the test to yield quantitative measurements rather than simply a positive or negative result.”

Because the test is not amplifying any trace of SARS-CoV-2, it offers clinicians the unique and vitally important ability to estimate the viral load of a given sample. This means doctors could not only monitor the progression of the disease in patients, but also estimate how infectious they may be.

“Monitoring the course of a patient’s infection could help health care professionals estimate the stage of infection and predict, in real time, how long is likely needed for recovery and how long the individual should quarantine,” suggests Daniel Fletcher, a bioengineer from UC Berkeley working on the project.

Describing the technology in the journal Cell, the researchers claim positive samples can be detected in less than five minutes, while samples with lower viral loads can take up to 30 minutes. However, the researchers say the system can be optimized for faster results.

More research will be needed before this system can be deployed in clinics, however, the researchers are hopeful a rapid point-of-care testing device could soon be available. And the general technology should be easily translated to allow for detection of a number of viral diseases, from HIV to the common cold.

Jennifer Doudna, who won a Nobel Prize earlier in 2020 for her work co-discovering the CRISPR gene-editing technology, has been working with colleagues for two years on this diagnostic technology. She suggests using CRISPR technology as a diagnostic tool could be a breakthrough in helping doctors quickly and accurately detect viral infections.

“One reason we’re excited about CRISPR-based diagnostics is the potential for quick, accurate results at the point of need,” adds Doudna. “This is especially helpful in places with limited access to testing, or when frequent, rapid testing is needed. It could eliminate a lot of the bottlenecks we’ve seen with COVID-19.”

The new study was published in the journal Cell.

Sources: Gladstone Institutes, UC Berkeley, Cell Press